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@@ -10,73 +10,358 @@
 std::string Mthd::Aux::toString ( float n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( double n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( long double n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( char n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned char n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( short n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned short n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( long int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned long n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned long long n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<int> v ) {
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+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
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+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<float> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
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+        }
+    }
+    return _vector ;
+}
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+std::string Mthd::Aux::toString ( std::vector<double> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<long double> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<long int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<unsigned int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<unsigned long> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<unsigned long long> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::basic_string<char> > v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< int > > v ) {
+    std::ostringstream oss ;
+    std::string _vector_of_vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        std::string _vector = std::string ( "" ) ;
+        for ( long unsigned int j = 0 ; j < v.at ( j ).size ( ) ; j ++ ) {
+            oss << v.at ( i ).at ( j ) ;
+            _vector += oss.str ( ) ;
+            if ( i + 1 < v.size ( ) ) {
+                ///         ELEMENTS SPLIT TOKEN      ///
+                _vector += "," ;
+            }
+        }
+        if ( i + 1 < _vector_of_vector.size ( ) ) {
+            ///         VECTOR SPLIT TOKEN      ///
+            _vector_of_vector += _vector + "@@@@@" ;
+        }
+    }
+    return _vector_of_vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< float > > v ) {
+    std::ostringstream oss ;
+    std::string _vector_of_vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        std::string _vector = std::string ( "" ) ;
+        for ( long unsigned int j = 0 ; j < v.at ( j ).size ( ) ; j ++ ) {
+            oss << v.at ( i ).at ( j ) ;
+            _vector += oss.str ( ) ;
+            if ( i + 1 < v.size ( ) ) {
+                ///         ELEMENTS SPLIT TOKEN      ///
+                _vector += "," ;
+            }
+        }
+        if ( i + 1 < _vector_of_vector.size ( ) ) {
+            ///         VECTOR SPLIT TOKEN      ///
+            _vector_of_vector += _vector + "@@@@@" ;
+        }
+    }
+    return _vector_of_vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< double > > v ) {
+    std::ostringstream oss ;
+    std::string _vector_of_vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        std::string _vector = std::string ( "" ) ;
+        for ( long unsigned int j = 0 ; j < v.at ( j ).size ( ) ; j ++ ) {
+            oss << v.at ( i ).at ( j ) ;
+            _vector += oss.str ( ) ;
+            if ( i + 1 < v.size ( ) ) {
+                ///         ELEMENTS SPLIT TOKEN      ///
+                _vector += "," ;
+            }
+        }
+        if ( i + 1 < _vector_of_vector.size ( ) ) {
+            ///         VECTOR SPLIT TOKEN      ///
+            _vector_of_vector += _vector + "@@@@@" ;
+        }
+    }
+    return _vector_of_vector ;
+}
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+std::string Mthd::Aux::toString ( std::vector<std::vector< long int > > v ) {
+    std::ostringstream oss ;
+    std::string _vector_of_vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        std::string _vector = std::string ( "" ) ;
+        for ( long unsigned int j = 0 ; j < v.at ( j ).size ( ) ; j ++ ) {
+            oss << v.at ( i ).at ( j ) ;
+            _vector += oss.str ( ) ;
+            if ( i + 1 < v.size ( ) ) {
+                ///         ELEMENTS SPLIT TOKEN      ///
+                _vector += "," ;
+            }
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+        if ( i + 1 < _vector_of_vector.size ( ) ) {
+            ///         VECTOR SPLIT TOKEN      ///
+            _vector_of_vector += _vector + "@@@@@" ;
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+    return _vector_of_vector ;
+}
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+    std::ostringstream oss ;
+    std::string _vector_of_vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        std::string _vector = std::string ( "" ) ;
+        for ( long unsigned int j = 0 ; j < v.at ( j ).size ( ) ; j ++ ) {
+            oss << v.at ( i ).at ( j ) ;
+            _vector += oss.str ( ) ;
+            if ( i + 1 < v.size ( ) ) {
+                ///         ELEMENTS SPLIT TOKEN      ///
+                _vector += "," ;
+            }
+        }
+        if ( i + 1 < _vector_of_vector.size ( ) ) {
+            ///         VECTOR SPLIT TOKEN      ///
+            _vector_of_vector += _vector + "@@@@@" ;
+        }
+    }
+    return _vector_of_vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< unsigned int > > v ) {
+    std::ostringstream oss ;
+    std::string _vector_of_vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        std::string _vector = std::string ( "" ) ;
+        for ( long unsigned int j = 0 ; j < v.at ( j ).size ( ) ; j ++ ) {
+            oss << v.at ( i ).at ( j ) ;
+            _vector += oss.str ( ) ;
+            if ( i + 1 < v.size ( ) ) {
+                ///         ELEMENTS SPLIT TOKEN      ///
+                _vector += "," ;
+            }
+        }
+        if ( i + 1 < _vector_of_vector.size ( ) ) {
+            ///         VECTOR SPLIT TOKEN      ///
+            _vector_of_vector += _vector + "@@@@@" ;
+        }
+    }
+    return _vector_of_vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< unsigned long > > v ) {
+    std::ostringstream oss ;
+    std::string _vector_of_vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        std::string _vector = std::string ( "" ) ;
+        for ( long unsigned int j = 0 ; j < v.at ( j ).size ( ) ; j ++ ) {
+            oss << v.at ( i ).at ( j ) ;
+            _vector += oss.str ( ) ;
+            if ( i + 1 < v.size ( ) ) {
+                ///         ELEMENTS SPLIT TOKEN      ///
+                _vector += "," ;
+            }
+        }
+        if ( i + 1 < _vector_of_vector.size ( ) ) {
+            ///         VECTOR SPLIT TOKEN      ///
+            _vector_of_vector += _vector + "@@@@@" ;
+        }
+    }
+    return _vector_of_vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< unsigned long long > > v ) {
+    std::ostringstream oss ;
+    std::string _vector_of_vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        std::string _vector = std::string ( "" ) ;
+        for ( long unsigned int j = 0 ; j < v.at ( j ).size ( ) ; j ++ ) {
+            oss << v.at ( i ).at ( j ) ;
+            _vector += oss.str ( ) ;
+            if ( i + 1 < v.size ( ) ) {
+                ///         ELEMENTS SPLIT TOKEN      ///
+                _vector += "," ;
+            }
+        }
+        if ( i + 1 < _vector_of_vector.size ( ) ) {
+            ///         VECTOR SPLIT TOKEN      ///
+            _vector_of_vector += _vector + "@@@@@" ;
+        }
+    }
+    return _vector_of_vector ;
 }
 
 std::string Mthd::Aux::toString ( std::string n ) {
@@ -86,84 +371,188 @@ std::string Mthd::Aux::toString ( std::string n ) {
 char* Mthd::Aux::toCharArrray ( float n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( double n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( long double n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( char n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( unsigned char n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( short n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( unsigned short n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( long int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( unsigned int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( long unsigned int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( std::string n ) {
-    return const_cast < char* > ( n.data( ) ) ;
+    return const_cast < char* > ( n.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<float> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<double> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<long double> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<long int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<unsigned int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<unsigned long> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<unsigned long long> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
 }
 
 std::string Mthd::Aux::replace_str ( std::string input , std::string old_str , std::string new_str ) {
-    size_t found = input.find( old_str ) ;
+    size_t found = input.find ( old_str ) ;
     while ( found != std::string::npos ) {
-        input.replace( found , old_str.length( ) , new_str ) ;
-        found = input.find( old_str ) ;
+        input.replace ( found , old_str.length ( ) , new_str ) ;
+        found = input.find ( old_str ) ;
     }
     return input ;
 }
 
 bool Mthd::Aux::str_ends_with ( std::string total_str , std::string sub_str ) {
-    size_t found = total_str.find( sub_str ) ;
+    size_t found = total_str.find ( sub_str ) ;
     if ( found != std::string::npos ) {
         return true ;
     }

diff --git a/ModuleCall/CreationTool.h b/ModuleCall/CreationTool.h
index 27dcb8222bade35a5cfdae9151fca0470cbecc36..4fdbee9ae39460d5fdba7c42718126f73f87a013 100644 (file)
--- a/ModuleCall/CreationTool.h
+++ b/ModuleCall/CreationTool.h
@@ -11,6 +11,7 @@
 #include <string>
 #include <iostream>
 #include <sstream>
+#include <vector>
 
 namespace Mthd {
 
@@ -32,6 +33,26 @@ namespace Mthd {
         static std::string toString ( unsigned long n ) ;
         static std::string toString ( unsigned long long n ) ;
 
+        static std::string toString ( std::vector<int> v ) ;
+        static std::string toString ( std::vector<float> v ) ;
+        static std::string toString ( std::vector<double> v ) ;
+        static std::string toString ( std::vector<long int> v ) ;
+        static std::string toString ( std::vector<long double> v ) ;
+        static std::string toString ( std::vector<unsigned int> v ) ;
+        static std::string toString ( std::vector<unsigned long> v ) ;
+        static std::string toString ( std::vector<unsigned long long> v ) ;
+        static std::string toString ( std::vector<std::basic_string<char> > v ) ;
+
+        static std::string toString ( std::vector< std::vector< int > > v ) ;
+        static std::string toString ( std::vector< std::vector< float > > v ) ;
+        static std::string toString ( std::vector< std::vector< double > > v ) ;
+        static std::string toString ( std::vector< std::vector< long int > > v ) ;
+        static std::string toString ( std::vector< std::vector< long double > > v ) ;
+        static std::string toString ( std::vector< std::vector< unsigned int > > v ) ;
+        static std::string toString ( std::vector< std::vector< unsigned long > > v ) ;
+        static std::string toString ( std::vector< std::vector< unsigned long long > > v ) ;
+
+
         static std::string toString ( std::string n ) ;
 
         static char* toCharArrray ( float n ) ;
@@ -49,10 +70,19 @@ namespace Mthd {
         static char* toCharArrray ( unsigned int n ) ;
         static char* toCharArrray ( long unsigned int n ) ;
 
+        static char* toCharArrray ( std::vector<int> v ) ;
+        static char* toCharArrray ( std::vector<float> v ) ;
+        static char* toCharArrray ( std::vector<double> v ) ;
+        static char* toCharArrray ( std::vector<long int> v ) ;
+        static char* toCharArrray ( std::vector<long double> v ) ;
+        static char* toCharArrray ( std::vector<unsigned int> v ) ;
+        static char* toCharArrray ( std::vector<unsigned long> v ) ;
+        static char* toCharArrray ( std::vector<unsigned long long> v ) ;
+
         static char* toCharArrray ( std::string n ) ;
 
         static bool str_ends_with ( std::string total_str , std::string sub_str ) ;
-        static std::string replace_str ( std::string input , std::string old_str , std::string new_str ) ;      
+        static std::string replace_str ( std::string input , std::string old_str , std::string new_str ) ;
 
     } ;
 

diff --git a/ModuleCall/GenSrc/bbSlicerACPCTransform.cxx b/ModuleCall/GenSrc/bbSlicerACPCTransform.cxx
new file mode 100644 (file)
index 0000000..d458ed8
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerACPCTransform.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerACPCTransform.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ACPCTransform )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ACPCTransform, bbtk::AtomicBlackBox );
+
+    void ACPCTransform::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRealignLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--acpc"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputACPC( ) ) ) ,"@@@@@"," --acpc ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--midline"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMidline( ) ) ) ,"@@@@@"," --midline ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdebugSwitch( ) ) ) ,"@@@@@"," -d ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ACPCTransform::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ACPCTransform::bbUserSetDefaultValues ( ) {
+    }
+
+    void ACPCTransform::bbUserInitializeProcessing ( ) {
+    }
+
+    void ACPCTransform::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerACPCTransform.h b/ModuleCall/GenSrc/bbSlicerACPCTransform.h
new file mode 100644 (file)
index 0000000..f5da823
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerACPCTransform.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerACPCTransform_h_INCLUDED__
+#define __bbSlicerACPCTransform_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ACPCTransform
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ACPCTransform , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( ACPC , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( Midline , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( debugSwitch , bool );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ACPCTransform , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ACPCTransform" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH" ) ;
+    BBTK_DESCRIPTION ( "pCalculate a transformation from two lists of fiducial points./ppACPC line is two fiducial points, one at the anterior commissure and one at the posterior commissure. The resulting transform will bring the line connecting them to horizontal to the AP axis./ppThe midline is a series of points defining the division between the hemispheres of the brain the mid sagittal plane. The resulting transform will put the output volume with the mid sagittal plane lined up with the AS plane./ppUse the Filtering module bResample Scalar/Vector/DWI Volume/b to apply the transformation to a volume./p" ) ;
+    BBTK_CATEGORY ( "Registration.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ACPCTransform , ACPC , "ACPC" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ACPCTransform , Midline , "Midline" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ACPCTransform , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(ACPCTransform , debugSwitch , "debugSwitch" , bool, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ACPCTransform ) ;
+}
+
+#endif // __bbSlicerACPCTransform_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerAddImages.cxx b/ModuleCall/GenSrc/bbSlicerAddImages.cxx
new file mode 100644 (file)
index 0000000..ec5f7a5
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerAddImages.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerAddImages.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, AddImages )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( AddImages, bbtk::AtomicBlackBox );
+
+    void AddImages::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libAddLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--order"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputorder( ) ) ) ,"@@@@@"," --order ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void AddImages::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void AddImages::bbUserSetDefaultValues ( ) {
+    }
+
+    void AddImages::bbUserInitializeProcessing ( ) {
+    }
+
+    void AddImages::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerAddImages.h b/ModuleCall/GenSrc/bbSlicerAddImages.h
new file mode 100644 (file)
index 0000000..6cd6801
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerAddImages.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerAddImages_h_INCLUDED__
+#define __bbSlicerAddImages_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT AddImages
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( AddImages , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume1 , std::string );
+BBTK_DECLARE_INPUT ( inputVolume2 , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( order , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( AddImages , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "AddImages" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Adds two images. Although all image types are supported on input, only signed types are produced. The two images do not have to have the same dimensions." ) ;
+    BBTK_CATEGORY ( "Filtering.Arithmetic" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(AddImages , inputVolume1 , "inputVolume1" , std::string, "");
+BBTK_INPUT(AddImages , inputVolume2 , "inputVolume2" , std::string, "");
+BBTK_INPUT(AddImages , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(AddImages , order , "order" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( AddImages ) ;
+}
+
+#endif // __bbSlicerAddImages_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerBSplinetodeformationfield.cxx b/ModuleCall/GenSrc/bbSlicerBSplinetodeformationfield.cxx
new file mode 100644 (file)
index 0000000..9ed73da
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerBSplinetodeformationfield.cxx
@@ -0,0 +1,57 @@
+#include "bbSlicerBSplinetodeformationfield.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, BSplinetodeformationfield )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( BSplinetodeformationfield, bbtk::AtomicBlackBox );
+
+    void BSplinetodeformationfield::Process ( ) {
+
+        // GENERATED
+
+int _argc =3;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBSplineToDeformationFieldLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--tfm"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputTransformName( ) ) ) ,"@@@@@"," --tfm ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--refImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreferenceImageName( ) ) ) ,"@@@@@"," --refImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--defImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdeformationFieldName( ) ) ) ,"@@@@@"," --defImage ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void BSplinetodeformationfield::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void BSplinetodeformationfield::bbUserSetDefaultValues ( ) {
+    }
+
+    void BSplinetodeformationfield::bbUserInitializeProcessing ( ) {
+    }
+
+    void BSplinetodeformationfield::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerBSplinetodeformationfield.h b/ModuleCall/GenSrc/bbSlicerBSplinetodeformationfield.h
new file mode 100644 (file)
index 0000000..4815d58
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerBSplinetodeformationfield.h
@@ -0,0 +1,62 @@
+#ifndef __bbSlicerBSplinetodeformationfield_h_INCLUDED__
+#define __bbSlicerBSplinetodeformationfield_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT BSplinetodeformationfield
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( BSplinetodeformationfield , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputTransformName , std::string );
+BBTK_DECLARE_INPUT ( referenceImageName , std::string );
+BBTK_DECLARE_INPUT ( deformationFieldName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( BSplinetodeformationfield , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "BSplinetodeformationfield" ) ;
+    BBTK_AUTHOR ( "Andrey Fedorov, BWH" ) ;
+    BBTK_DESCRIPTION ( "Create a dense deformation field from a bspline+bulk transform." ) ;
+    BBTK_CATEGORY ( "Legacy.Converters" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(BSplinetodeformationfield , inputTransformName , "inputTransformName" , std::string, "");
+BBTK_INPUT(BSplinetodeformationfield , referenceImageName , "referenceImageName" , std::string, "");
+BBTK_INPUT(BSplinetodeformationfield , deformationFieldName , "deformationFieldName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( BSplinetodeformationfield ) ;
+}
+
+#endif // __bbSlicerBSplinetodeformationfield_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCastImage.cxx b/ModuleCall/GenSrc/bbSlicerCastImage.cxx
new file mode 100644 (file)
index 0000000..8715b97
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCastImage.cxx
@@ -0,0 +1,57 @@
+#include "bbSlicerCastImage.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, CastImage )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( CastImage, bbtk::AtomicBlackBox );
+
+    void CastImage::Process ( ) {
+
+        // GENERATED
+
+int _argc =3;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libCastLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputType( ) ) ) ,"@@@@@"," -t ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void CastImage::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void CastImage::bbUserSetDefaultValues ( ) {
+    }
+
+    void CastImage::bbUserInitializeProcessing ( ) {
+    }
+
+    void CastImage::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCastImage.h b/ModuleCall/GenSrc/bbSlicerCastImage.h
new file mode 100644 (file)
index 0000000..ba1237a
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCastImage.h
@@ -0,0 +1,62 @@
+#ifndef __bbSlicerCastImage_h_INCLUDED__
+#define __bbSlicerCastImage_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT CastImage
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( CastImage , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( OutputVolume , std::string );
+BBTK_DECLARE_INPUT ( Type , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( CastImage , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "CastImage" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH" ) ;
+    BBTK_DESCRIPTION ( "Cast a volume to a given data type.Use at your own risk when casting an input volume into a lower precision type!Allows casting to the same type as the input volume." ) ;
+    BBTK_CATEGORY ( "Filtering.Arithmetic" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(CastImage , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(CastImage , OutputVolume , "OutputVolume" , std::string, "");
+BBTK_INPUT(CastImage , Type , "Type" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( CastImage ) ;
+}
+
+#endif // __bbSlicerCastImage_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCheckerBoardFilter.cxx b/ModuleCall/GenSrc/bbSlicerCheckerBoardFilter.cxx
new file mode 100644 (file)
index 0000000..3201891
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCheckerBoardFilter.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerCheckerBoardFilter.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, CheckerBoardFilter )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( CheckerBoardFilter, bbtk::AtomicBlackBox );
+
+    void CheckerBoardFilter::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libCheckerBoardLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--checkerPattern"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcheckerPattern( ) ) ) ,"@@@@@"," --checkerPattern ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void CheckerBoardFilter::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void CheckerBoardFilter::bbUserSetDefaultValues ( ) {
+    }
+
+    void CheckerBoardFilter::bbUserInitializeProcessing ( ) {
+    }
+
+    void CheckerBoardFilter::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCheckerBoardFilter.h b/ModuleCall/GenSrc/bbSlicerCheckerBoardFilter.h
new file mode 100644 (file)
index 0000000..7bd4a22
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCheckerBoardFilter.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerCheckerBoardFilter_h_INCLUDED__
+#define __bbSlicerCheckerBoardFilter_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT CheckerBoardFilter
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( CheckerBoardFilter , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( checkerPattern , std::vector<int> );
+BBTK_DECLARE_INPUT ( inputVolume1 , std::string );
+BBTK_DECLARE_INPUT ( inputVolume2 , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( CheckerBoardFilter , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "CheckerBoardFilter" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Create a checkerboard volume of two volumes. The output volume will show the two inputs alternating according to the user supplied checkerPattern. This filter is often used to compare the results of image registration. Note that the second input is resampled to the same origin, spacing and direction before it is composed with the first input. The scalar type of the output volume will be the same as the input image scalar type." ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(CheckerBoardFilter , checkerPattern , "checkerPattern" , std::vector<int>, "");
+BBTK_INPUT(CheckerBoardFilter , inputVolume1 , "inputVolume1" , std::string, "");
+BBTK_INPUT(CheckerBoardFilter , inputVolume2 , "inputVolume2" , std::string, "");
+BBTK_INPUT(CheckerBoardFilter , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( CheckerBoardFilter ) ;
+}
+
+#endif // __bbSlicerCheckerBoardFilter_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCommandLineModuleTest.cxx b/ModuleCall/GenSrc/bbSlicerCommandLineModuleTest.cxx
new file mode 100644 (file)
index 0000000..4b63cfb
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCommandLineModuleTest.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerCommandLineModuleTest.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, CommandLineModuleTest )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( CommandLineModuleTest, bbtk::AtomicBlackBox );
+
+    void CommandLineModuleTest::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libCLIModule4TestLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputvalue1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputValue1( ) ) ) ,"@@@@@"," --inputvalue1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputvalue2"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputValue2( ) ) ) ,"@@@@@"," --inputvalue2 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--operationtype"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOperationType( ) ) ) ,"@@@@@"," --operationtype ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputFile( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void CommandLineModuleTest::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void CommandLineModuleTest::bbUserSetDefaultValues ( ) {
+    }
+
+    void CommandLineModuleTest::bbUserInitializeProcessing ( ) {
+    }
+
+    void CommandLineModuleTest::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCommandLineModuleTest.h b/ModuleCall/GenSrc/bbSlicerCommandLineModuleTest.h
new file mode 100644 (file)
index 0000000..d8c2809
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCommandLineModuleTest.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerCommandLineModuleTest_h_INCLUDED__
+#define __bbSlicerCommandLineModuleTest_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT CommandLineModuleTest
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( CommandLineModuleTest , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputValue1 , int );
+BBTK_DECLARE_INPUT ( InputValue2 , int );
+BBTK_DECLARE_INPUT ( OperationType , std::string );
+BBTK_DECLARE_INPUT ( OutputFile , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( CommandLineModuleTest , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "CommandLineModuleTest" ) ;
+    BBTK_AUTHOR ( "Jean-Christophe Fillion-Robin" ) ;
+    BBTK_DESCRIPTION ( "Command line module used to test the automatic UI generator." ) ;
+    BBTK_CATEGORY ( "Testing" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(CommandLineModuleTest , InputValue1 , "InputValue1" , int, "");
+BBTK_INPUT(CommandLineModuleTest , InputValue2 , "InputValue2" , int, "");
+BBTK_INPUT(CommandLineModuleTest , OperationType , "OperationType" , std::string, "");
+BBTK_INPUT(CommandLineModuleTest , OutputFile , "OutputFile" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( CommandLineModuleTest ) ;
+}
+
+#endif // __bbSlicerCommandLineModuleTest_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCreateaDICOMSeries.cxx b/ModuleCall/GenSrc/bbSlicerCreateaDICOMSeries.cxx
new file mode 100644 (file)
index 0000000..a51004b
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCreateaDICOMSeries.cxx
@@ -0,0 +1,74 @@
+#include "bbSlicerCreateaDICOMSeries.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, CreateaDICOMSeries )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( CreateaDICOMSeries, bbtk::AtomicBlackBox );
+
+    void CreateaDICOMSeries::Process ( ) {
+
+        // GENERATED
+
+int _argc =20;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libImageReadDicomWriteLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--patientName"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpatientName( ) ) ) ,"@@@@@"," --patientName ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--patientID"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpatientID( ) ) ) ,"@@@@@"," --patientID ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--patientComments"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpatientComments( ) ) ) ,"@@@@@"," --patientComments ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyID"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstudyID( ) ) ) ,"@@@@@"," --studyID ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyDate"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstudyDate( ) ) ) ,"@@@@@"," --studyDate ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyComments"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstudyComments( ) ) ) ,"@@@@@"," --studyComments ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyDescription"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstudyDescription( ) ) ) ,"@@@@@"," --studyDescription ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--modality"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmodality( ) ) ) ,"@@@@@"," --modality ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--manufacturer"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmanufacturer( ) ) ) ,"@@@@@"," --manufacturer ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--model"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmodel( ) ) ) ,"@@@@@"," --model ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seriesNumber"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseriesNumber( ) ) ) ,"@@@@@"," --seriesNumber ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seriesDescription"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseriesDescription( ) ) ) ,"@@@@@"," --seriesDescription ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rescaleIntercept"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrescaleIntercept( ) ) ) ,"@@@@@"," --rescaleIntercept ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rescaleSlope"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrescaleSlope( ) ) ) ,"@@@@@"," --rescaleSlope ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dicomDirectory"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdicomDirectory( ) ) ) ,"@@@@@"," --dicomDirectory ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dicomPrefix"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdicomPrefix( ) ) ) ,"@@@@@"," --dicomPrefix ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dicomNumberFormat"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdicomNumberFormat( ) ) ) ,"@@@@@"," --dicomNumberFormat ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--reverseImages"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreverseImages( ) ) ) ,"@@@@@"," --reverseImages ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useCompression"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseCompression( ) ) ) ,"@@@@@"," --useCompression ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void CreateaDICOMSeries::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void CreateaDICOMSeries::bbUserSetDefaultValues ( ) {
+    }
+
+    void CreateaDICOMSeries::bbUserInitializeProcessing ( ) {
+    }
+
+    void CreateaDICOMSeries::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCreateaDICOMSeries.h b/ModuleCall/GenSrc/bbSlicerCreateaDICOMSeries.h
new file mode 100644 (file)
index 0000000..a7f3d19
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCreateaDICOMSeries.h
@@ -0,0 +1,96 @@
+#ifndef __bbSlicerCreateaDICOMSeries_h_INCLUDED__
+#define __bbSlicerCreateaDICOMSeries_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT CreateaDICOMSeries
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( CreateaDICOMSeries , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( patientName , std::string );
+BBTK_DECLARE_INPUT ( patientID , std::string );
+BBTK_DECLARE_INPUT ( patientComments , std::string );
+BBTK_DECLARE_INPUT ( studyID , std::string );
+BBTK_DECLARE_INPUT ( studyDate , std::string );
+BBTK_DECLARE_INPUT ( studyComments , std::string );
+BBTK_DECLARE_INPUT ( studyDescription , std::string );
+BBTK_DECLARE_INPUT ( modality , std::string );
+BBTK_DECLARE_INPUT ( manufacturer , std::string );
+BBTK_DECLARE_INPUT ( model , std::string );
+BBTK_DECLARE_INPUT ( seriesNumber , std::string );
+BBTK_DECLARE_INPUT ( seriesDescription , std::string );
+BBTK_DECLARE_INPUT ( rescaleIntercept , double );
+BBTK_DECLARE_INPUT ( rescaleSlope , double );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( dicomDirectory , std::string );
+BBTK_DECLARE_INPUT ( dicomPrefix , std::string );
+BBTK_DECLARE_INPUT ( dicomNumberFormat , std::string );
+BBTK_DECLARE_INPUT ( reverseImages , bool );
+BBTK_DECLARE_INPUT ( useCompression , bool );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( CreateaDICOMSeries , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "CreateaDICOMSeries" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Create a DICOM Series from a Slicer volume. User can specify values for selected DICOM tags in the UI. Given the number of tags DICOM series have, it is impossible to expose all tags in UI. So only important tags can be set by the user." ) ;
+    BBTK_CATEGORY ( "Converters" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(CreateaDICOMSeries , patientName , "patientName" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , patientID , "patientID" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , patientComments , "patientComments" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , studyID , "studyID" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , studyDate , "studyDate" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , studyComments , "studyComments" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , studyDescription , "studyDescription" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , modality , "modality" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , manufacturer , "manufacturer" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , model , "model" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , seriesNumber , "seriesNumber" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , seriesDescription , "seriesDescription" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , rescaleIntercept , "rescaleIntercept" , double, "");
+BBTK_INPUT(CreateaDICOMSeries , rescaleSlope , "rescaleSlope" , double, "");
+BBTK_INPUT(CreateaDICOMSeries , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , dicomDirectory , "dicomDirectory" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , dicomPrefix , "dicomPrefix" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , dicomNumberFormat , "dicomNumberFormat" , std::string, "");
+BBTK_INPUT(CreateaDICOMSeries , reverseImages , "reverseImages" , bool, "");
+BBTK_INPUT(CreateaDICOMSeries , useCompression , "useCompression" , bool, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( CreateaDICOMSeries ) ;
+}
+
+#endif // __bbSlicerCreateaDICOMSeries_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCurvatureAnisotropicDiffusion.cxx b/ModuleCall/GenSrc/bbSlicerCurvatureAnisotropicDiffusion.cxx
new file mode 100644 (file)
index 0000000..a356744
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCurvatureAnisotropicDiffusion.cxx
@@ -0,0 +1,59 @@
+#include "bbSlicerCurvatureAnisotropicDiffusion.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, CurvatureAnisotropicDiffusion )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( CurvatureAnisotropicDiffusion, bbtk::AtomicBlackBox );
+
+    void CurvatureAnisotropicDiffusion::Process ( ) {
+
+        // GENERATED
+
+int _argc =5;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libCurvatureAnisotropicDiffusionLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--conductance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputconductance( ) ) ) ,"@@@@@"," --conductance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --iterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--timeStep"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtimeStep( ) ) ) ,"@@@@@"," --timeStep ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void CurvatureAnisotropicDiffusion::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void CurvatureAnisotropicDiffusion::bbUserSetDefaultValues ( ) {
+    }
+
+    void CurvatureAnisotropicDiffusion::bbUserInitializeProcessing ( ) {
+    }
+
+    void CurvatureAnisotropicDiffusion::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerCurvatureAnisotropicDiffusion.h b/ModuleCall/GenSrc/bbSlicerCurvatureAnisotropicDiffusion.h
new file mode 100644 (file)
index 0000000..fc17218
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerCurvatureAnisotropicDiffusion.h
@@ -0,0 +1,66 @@
+#ifndef __bbSlicerCurvatureAnisotropicDiffusion_h_INCLUDED__
+#define __bbSlicerCurvatureAnisotropicDiffusion_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT CurvatureAnisotropicDiffusion
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( CurvatureAnisotropicDiffusion , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( conductance , double );
+BBTK_DECLARE_INPUT ( numberOfIterations , int );
+BBTK_DECLARE_INPUT ( timeStep , double );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( CurvatureAnisotropicDiffusion , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "CurvatureAnisotropicDiffusion" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Performs anisotropic diffusion on an image using a modified curvature diffusion equation MCDE.MCDE does not exhibit the edge enhancing properties of classic anisotropic diffusion, which can under certain conditions undergo a 'negative' diffusion, which enhances the contrast of edges.  Equations of the form of MCDE always undergo positive diffusion, with the conductance term only varying the strength of that diffusion.  Qualitatively, MCDE compares well with other non-linear diffusion techniques.  It is less sensitive to contrast than classic Perona-Malik style diffusion, and preserves finer detailed structures in images.  There is a potential speed trade-off for using this function in place of Gradient Anisotropic Diffusion.  Each iteration of the solution takes roughly twice as long.  Fewer iterations, however, may be required to reach an acceptable solution." ) ;
+    BBTK_CATEGORY ( "Filtering.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(CurvatureAnisotropicDiffusion , conductance , "conductance" , double, "");
+BBTK_INPUT(CurvatureAnisotropicDiffusion , numberOfIterations , "numberOfIterations" , int, "");
+BBTK_INPUT(CurvatureAnisotropicDiffusion , timeStep , "timeStep" , double, "");
+BBTK_INPUT(CurvatureAnisotropicDiffusion , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(CurvatureAnisotropicDiffusion , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( CurvatureAnisotropicDiffusion ) ;
+}
+
+#endif // __bbSlicerCurvatureAnisotropicDiffusion_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerDemonRegistrationBRAINS.cxx b/ModuleCall/GenSrc/bbSlicerDemonRegistrationBRAINS.cxx
new file mode 100644 (file)
index 0000000..bef5a5e
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerDemonRegistrationBRAINS.cxx
@@ -0,0 +1,94 @@
+#include "bbSlicerDemonRegistrationBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, DemonRegistrationBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( DemonRegistrationBRAINS, bbtk::AtomicBlackBox );
+
+    void DemonRegistrationBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =40;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBRAINSDemonWarpLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-m"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingVolume( ) ) ) ,"@@@@@"," -m ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedVolume( ) ) ) ,"@@@@@"," -f ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputPixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputPixelType( ) ) ) ,"@@@@@"," --inputPixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-o"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," -o ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-O"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDisplacementFieldVolume( ) ) ) ,"@@@@@"," -O ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputPixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputPixelType( ) ) ) ,"@@@@@"," --outputPixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolationMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationMode( ) ) ) ,"@@@@@"," --interpolationMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--registrationFilterType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputregistrationFilterType( ) ) ) ,"@@@@@"," --registrationFilterType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothDisplacementFieldSigma( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-n"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfPyramidLevels( ) ) ) ,"@@@@@"," -n ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumFixedPyramid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumFixedPyramid( ) ) ) ,"@@@@@"," --minimumFixedPyramid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumMovingPyramid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumMovingPyramid( ) ) ) ,"@@@@@"," --minimumMovingPyramid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputarrayOfPyramidLevelIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputhistogramMatch( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfHistogramBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfHistogramBins( ) ) ) ,"@@@@@"," --numberOfHistogramBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfMatchPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfMatchPoints( ) ) ) ,"@@@@@"," --numberOfMatchPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--medianFilterSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmedianFilterSize( ) ) ) ,"@@@@@"," --medianFilterSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeWithDisplacementField"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeWithDisplacementField( ) ) ) ,"@@@@@"," --initializeWithDisplacementField ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeWithTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeWithTransform( ) ) ) ,"@@@@@"," --initializeWithTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maskProcessingMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaskProcessingMode( ) ) ) ,"@@@@@"," --maskProcessingMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedBinaryVolume( ) ) ) ,"@@@@@"," --fixedBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingBinaryVolume( ) ) ) ,"@@@@@"," --movingBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--lowerThresholdForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlowerThresholdForBOBF( ) ) ) ,"@@@@@"," --lowerThresholdForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--upperThresholdForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputupperThresholdForBOBF( ) ) ) ,"@@@@@"," --upperThresholdForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--backgroundFillValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbackgroundFillValue( ) ) ) ,"@@@@@"," --backgroundFillValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seedForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseedForBOBF( ) ) ) ,"@@@@@"," --seedForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--neighborhoodForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputneighborhoodForBOBF( ) ) ) ,"@@@@@"," --neighborhoodForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputDisplacementFieldPrefix"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDisplacementFieldPrefix( ) ) ) ,"@@@@@"," --outputDisplacementFieldPrefix ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputCheckerboardVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputCheckerboardVolume( ) ) ) ,"@@@@@"," --outputCheckerboardVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--checkerboardPatternSubdivisions"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcheckerboardPatternSubdivisions( ) ) ) ,"@@@@@"," --checkerboardPatternSubdivisions ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputNormalized"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputNormalized( ) ) ) ,"@@@@@"," --outputNormalized ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDebug( ) ) ) ,"@@@@@"," -v ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgradientType( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothingUp( ) ) ) ,"@@@@@"," -g ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxStepLength( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-a"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputturnOffDiffeomorph( ) ) ) ,"@@@@@"," -a ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-G"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputUseDebugImageViewer( ) ) ) ,"@@@@@"," -G ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-p"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPromptAfterImageSend( ) ) ) ,"@@@@@"," -p ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfBCHApproximationTerms"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfBCHApproximationTerms( ) ) ) ,"@@@@@"," --numberOfBCHApproximationTerms ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void DemonRegistrationBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void DemonRegistrationBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void DemonRegistrationBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void DemonRegistrationBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerDemonRegistrationBRAINS.h b/ModuleCall/GenSrc/bbSlicerDemonRegistrationBRAINS.h
new file mode 100644 (file)
index 0000000..8482ead
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerDemonRegistrationBRAINS.h
@@ -0,0 +1,136 @@
+#ifndef __bbSlicerDemonRegistrationBRAINS_h_INCLUDED__
+#define __bbSlicerDemonRegistrationBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT DemonRegistrationBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( DemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( movingVolume , std::string );
+BBTK_DECLARE_INPUT ( fixedVolume , std::string );
+BBTK_DECLARE_INPUT ( inputPixelType , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldVolume , std::string );
+BBTK_DECLARE_INPUT ( outputPixelType , std::string );
+BBTK_DECLARE_INPUT ( interpolationMode , std::string );
+BBTK_DECLARE_INPUT ( registrationFilterType , std::string );
+BBTK_DECLARE_INPUT ( smoothDisplacementFieldSigma , double );
+BBTK_DECLARE_INPUT ( numberOfPyramidLevels , int );
+BBTK_DECLARE_INPUT ( minimumFixedPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( minimumMovingPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( arrayOfPyramidLevelIterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( histogramMatch , bool );
+BBTK_DECLARE_INPUT ( numberOfHistogramBins , int );
+BBTK_DECLARE_INPUT ( numberOfMatchPoints , int );
+BBTK_DECLARE_INPUT ( medianFilterSize , std::vector<int> );
+BBTK_DECLARE_INPUT ( initializeWithDisplacementField , std::string );
+BBTK_DECLARE_INPUT ( initializeWithTransform , std::string );
+BBTK_DECLARE_INPUT ( maskProcessingMode , std::string );
+BBTK_DECLARE_INPUT ( fixedBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( movingBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( lowerThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( upperThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( backgroundFillValue , int );
+BBTK_DECLARE_INPUT ( seedForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( neighborhoodForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldPrefix , std::string );
+BBTK_DECLARE_INPUT ( outputCheckerboardVolume , std::string );
+BBTK_DECLARE_INPUT ( checkerboardPatternSubdivisions , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputNormalized , bool );
+BBTK_DECLARE_INPUT ( outputDebug , bool );
+BBTK_DECLARE_INPUT ( gradientType , int );
+BBTK_DECLARE_INPUT ( smoothingUp , double );
+BBTK_DECLARE_INPUT ( maxStepLength , double );
+BBTK_DECLARE_INPUT ( turnOffDiffeomorph , bool );
+BBTK_DECLARE_INPUT ( UseDebugImageViewer , bool );
+BBTK_DECLARE_INPUT ( PromptAfterImageSend , bool );
+BBTK_DECLARE_INPUT ( numberOfBCHApproximationTerms , int );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( DemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "DemonRegistrationBRAINS" ) ;
+    BBTK_AUTHOR ( "This tool was developed by Hans J. Johnson and Greg Harris." ) ;
+    BBTK_DESCRIPTION ( "This program finds a deformation field to warp a moving image onto a fixed image.  The images must be of the same signal kind, and contain an image of the same kind of object.  This program uses the Thirion Demons warp software in ITK, the Insight Toolkit.  Additional information is available at: http://www.nitrc.org/projects/brainsdemonwarp." ) ;
+    BBTK_CATEGORY ( "Registration.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(DemonRegistrationBRAINS , movingVolume , "movingVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , fixedVolume , "fixedVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , inputPixelType , "inputPixelType" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputDisplacementFieldVolume , "outputDisplacementFieldVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputPixelType , "outputPixelType" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , interpolationMode , "interpolationMode" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , registrationFilterType , "registrationFilterType" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , smoothDisplacementFieldSigma , "smoothDisplacementFieldSigma" , double, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfPyramidLevels , "numberOfPyramidLevels" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , minimumFixedPyramid , "minimumFixedPyramid" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , minimumMovingPyramid , "minimumMovingPyramid" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , arrayOfPyramidLevelIterations , "arrayOfPyramidLevelIterations" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , histogramMatch , "histogramMatch" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfHistogramBins , "numberOfHistogramBins" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfMatchPoints , "numberOfMatchPoints" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , medianFilterSize , "medianFilterSize" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , initializeWithDisplacementField , "initializeWithDisplacementField" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , initializeWithTransform , "initializeWithTransform" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , maskProcessingMode , "maskProcessingMode" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , fixedBinaryVolume , "fixedBinaryVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , movingBinaryVolume , "movingBinaryVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , lowerThresholdForBOBF , "lowerThresholdForBOBF" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , upperThresholdForBOBF , "upperThresholdForBOBF" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , backgroundFillValue , "backgroundFillValue" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , seedForBOBF , "seedForBOBF" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , neighborhoodForBOBF , "neighborhoodForBOBF" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputDisplacementFieldPrefix , "outputDisplacementFieldPrefix" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputCheckerboardVolume , "outputCheckerboardVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , checkerboardPatternSubdivisions , "checkerboardPatternSubdivisions" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputNormalized , "outputNormalized" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputDebug , "outputDebug" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , gradientType , "gradientType" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , smoothingUp , "smoothingUp" , double, "");
+BBTK_INPUT(DemonRegistrationBRAINS , maxStepLength , "maxStepLength" , double, "");
+BBTK_INPUT(DemonRegistrationBRAINS , turnOffDiffeomorph , "turnOffDiffeomorph" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , UseDebugImageViewer , "UseDebugImageViewer" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , PromptAfterImageSend , "PromptAfterImageSend" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfBCHApproximationTerms , "numberOfBCHApproximationTerms" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( DemonRegistrationBRAINS ) ;
+}
+
+#endif // __bbSlicerDemonRegistrationBRAINS_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerDicomtoNrrdConverter.cxx b/ModuleCall/GenSrc/bbSlicerDicomtoNrrdConverter.cxx
new file mode 100644 (file)
index 0000000..49caf5c
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerDicomtoNrrdConverter.cxx
@@ -0,0 +1,61 @@
+#include "bbSlicerDicomtoNrrdConverter.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, DicomtoNrrdConverter )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( DicomtoNrrdConverter, bbtk::AtomicBlackBox );
+
+    void DicomtoNrrdConverter::Process ( ) {
+
+        // GENERATED
+
+int _argc =7;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libDicomToNrrdConverterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputDicomDirectory"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputDicomDirectory( ) ) ) ,"@@@@@"," --inputDicomDirectory ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputDirectory"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDirectory( ) ) ) ,"@@@@@"," --outputDirectory ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," --outputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--smallGradientThreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmallGradientThreshold( ) ) ) ,"@@@@@"," --smallGradientThreshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--writeProtocolGradientsFile"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputwriteProtocolGradientsFile( ) ) ) ,"@@@@@"," --writeProtocolGradientsFile ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useIdentityMeaseurementFrame"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseIdentityMeaseurementFrame( ) ) ) ,"@@@@@"," --useIdentityMeaseurementFrame ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useBMatrixGradientDirections"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseBMatrixGradientDirections( ) ) ) ,"@@@@@"," --useBMatrixGradientDirections ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void DicomtoNrrdConverter::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void DicomtoNrrdConverter::bbUserSetDefaultValues ( ) {
+    }
+
+    void DicomtoNrrdConverter::bbUserInitializeProcessing ( ) {
+    }
+
+    void DicomtoNrrdConverter::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerDicomtoNrrdConverter.h b/ModuleCall/GenSrc/bbSlicerDicomtoNrrdConverter.h
new file mode 100644 (file)
index 0000000..808c738
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerDicomtoNrrdConverter.h
@@ -0,0 +1,70 @@
+#ifndef __bbSlicerDicomtoNrrdConverter_h_INCLUDED__
+#define __bbSlicerDicomtoNrrdConverter_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT DicomtoNrrdConverter
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( DicomtoNrrdConverter , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputDicomDirectory , std::string );
+BBTK_DECLARE_INPUT ( outputDirectory , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( smallGradientThreshold , double );
+BBTK_DECLARE_INPUT ( writeProtocolGradientsFile , bool );
+BBTK_DECLARE_INPUT ( useIdentityMeaseurementFrame , bool );
+BBTK_DECLARE_INPUT ( useBMatrixGradientDirections , bool );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( DicomtoNrrdConverter , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "DicomtoNrrdConverter" ) ;
+    BBTK_AUTHOR ( "Xiaodong Tao" ) ;
+    BBTK_DESCRIPTION ( "Converts diffusion weighted MR images in dicom series into Nrrd format for analysis in Slicer. This program has been tested on only a limited subset of DTI dicom formats available from Siemens, GE, and Phillips scanners. Work in progress to support dicom multi-frame data. The program parses dicom header to extract necessary information about measurement frame, diffusion weighting directions, b-values, etc, and write out a nrrd image. For non-diffusion weighted dicom images, it loads in an entire dicom series and writes out a single dicom volume in a .nhdr/.raw pair." ) ;
+    BBTK_CATEGORY ( "Converters" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(DicomtoNrrdConverter , inputDicomDirectory , "inputDicomDirectory" , std::string, "");
+BBTK_INPUT(DicomtoNrrdConverter , outputDirectory , "outputDirectory" , std::string, "");
+BBTK_INPUT(DicomtoNrrdConverter , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(DicomtoNrrdConverter , smallGradientThreshold , "smallGradientThreshold" , double, "");
+BBTK_INPUT(DicomtoNrrdConverter , writeProtocolGradientsFile , "writeProtocolGradientsFile" , bool, "");
+BBTK_INPUT(DicomtoNrrdConverter , useIdentityMeaseurementFrame , "useIdentityMeaseurementFrame" , bool, "");
+BBTK_INPUT(DicomtoNrrdConverter , useBMatrixGradientDirections , "useBMatrixGradientDirections" , bool, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( DicomtoNrrdConverter ) ;
+}
+
+#endif // __bbSlicerDicomtoNrrdConverter_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerExecutionModelTour.cxx b/ModuleCall/GenSrc/bbSlicerExecutionModelTour.cxx
new file mode 100644 (file)
index 0000000..659a398
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerExecutionModelTour.cxx
@@ -0,0 +1,82 @@
+#include "bbSlicerExecutionModelTour.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ExecutionModelTour )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ExecutionModelTour, bbtk::AtomicBlackBox );
+
+    void ExecutionModelTour::Process ( ) {
+
+        // GENERATED
+
+int _argc =28;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libExecutionModelTourLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputintegerVariable( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdoubleVariable( ) ) ) ,"@@@@@"," -d ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfloatVector( ) ) ) ,"@@@@@"," -f ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--string_vector"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstringVector( ) ) ) ,"@@@@@"," --string_vector ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstringChoice( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--boolean1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputboolean1( ) ) ) ,"@@@@@"," --boolean1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--boolean2"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputboolean2( ) ) ) ,"@@@@@"," --boolean2 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--boolean3"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputboolean3( ) ) ) ,"@@@@@"," --boolean3 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--file1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfile1( ) ) ) ,"@@@@@"," --file1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--files"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfiles( ) ) ) ,"@@@@@"," --files ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--directory1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdirectory1( ) ) ) ,"@@@@@"," --directory1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--image1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputimage1( ) ) ) ,"@@@@@"," --image1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--image2"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputimage2( ) ) ) ,"@@@@@"," --image2 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transform1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransform1( ) ) ) ,"@@@@@"," --transform1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transform2"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransform2( ) ) ) ,"@@@@@"," --transform2 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seed"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseed( ) ) ) ,"@@@@@"," --seed ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputarg0( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputarg1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--region"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputregions( ) ) ) ,"@@@@@"," --region ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputFA"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputFA( ) ) ) ,"@@@@@"," --inputFA ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputFA"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputFA( ) ) ) ,"@@@@@"," --outputFA ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputanintegerreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputabooleanreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputafloatreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputadoublereturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputastringreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputanintegervectorreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputastringchoicereturn( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ExecutionModelTour::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ExecutionModelTour::bbUserSetDefaultValues ( ) {
+    }
+
+    void ExecutionModelTour::bbUserInitializeProcessing ( ) {
+    }
+
+    void ExecutionModelTour::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerExecutionModelTour.h b/ModuleCall/GenSrc/bbSlicerExecutionModelTour.h
new file mode 100644 (file)
index 0000000..b867459
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerExecutionModelTour.h
@@ -0,0 +1,112 @@
+#ifndef __bbSlicerExecutionModelTour_h_INCLUDED__
+#define __bbSlicerExecutionModelTour_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ExecutionModelTour
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ExecutionModelTour , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( integerVariable , int );
+BBTK_DECLARE_INPUT ( doubleVariable , double );
+BBTK_DECLARE_INPUT ( floatVector , std::vector<float> );
+BBTK_DECLARE_INPUT ( stringVector , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( stringChoice , std::string );
+BBTK_DECLARE_INPUT ( boolean1 , bool );
+BBTK_DECLARE_INPUT ( boolean2 , bool );
+BBTK_DECLARE_INPUT ( boolean3 , bool );
+BBTK_DECLARE_INPUT ( file1 , std::string );
+BBTK_DECLARE_INPUT ( files , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( directory1 , std::string );
+BBTK_DECLARE_INPUT ( image1 , std::string );
+BBTK_DECLARE_INPUT ( image2 , std::string );
+BBTK_DECLARE_INPUT ( transform1 , std::string );
+BBTK_DECLARE_INPUT ( transform2 , std::string );
+BBTK_DECLARE_INPUT ( seed , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( arg0 , std::string );
+BBTK_DECLARE_INPUT ( arg1 , std::string );
+BBTK_DECLARE_INPUT ( regions , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( inputFA , std::string );
+BBTK_DECLARE_INPUT ( outputFA , std::string );
+BBTK_DECLARE_INPUT ( anintegerreturn , int );
+BBTK_DECLARE_INPUT ( abooleanreturn , bool );
+BBTK_DECLARE_INPUT ( afloatreturn , float );
+BBTK_DECLARE_INPUT ( adoublereturn , double );
+BBTK_DECLARE_INPUT ( astringreturn , std::string );
+BBTK_DECLARE_INPUT ( anintegervectorreturn , std::vector<int> );
+BBTK_DECLARE_INPUT ( astringchoicereturn , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ExecutionModelTour , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ExecutionModelTour" ) ;
+    BBTK_AUTHOR ( "Daniel Blezek, Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Shows one of each type of parameter." ) ;
+    BBTK_CATEGORY ( "Developer Tools" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ExecutionModelTour , integerVariable , "integerVariable" , int, "");
+BBTK_INPUT(ExecutionModelTour , doubleVariable , "doubleVariable" , double, "");
+BBTK_INPUT(ExecutionModelTour , floatVector , "floatVector" , std::vector<float>, "");
+BBTK_INPUT(ExecutionModelTour , stringVector , "stringVector" , std::vector<std::string>, "");
+BBTK_INPUT(ExecutionModelTour , stringChoice , "stringChoice" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , boolean1 , "boolean1" , bool, "");
+BBTK_INPUT(ExecutionModelTour , boolean2 , "boolean2" , bool, "");
+BBTK_INPUT(ExecutionModelTour , boolean3 , "boolean3" , bool, "");
+BBTK_INPUT(ExecutionModelTour , file1 , "file1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , files , "files" , std::vector<std::string>, "");
+BBTK_INPUT(ExecutionModelTour , directory1 , "directory1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , image1 , "image1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , image2 , "image2" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , transform1 , "transform1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , transform2 , "transform2" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , seed , "seed" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ExecutionModelTour , arg0 , "arg0" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , arg1 , "arg1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , regions , "regions" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ExecutionModelTour , inputFA , "inputFA" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , outputFA , "outputFA" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , anintegerreturn , "anintegerreturn" , int, "");
+BBTK_INPUT(ExecutionModelTour , abooleanreturn , "abooleanreturn" , bool, "");
+BBTK_INPUT(ExecutionModelTour , afloatreturn , "afloatreturn" , float, "");
+BBTK_INPUT(ExecutionModelTour , adoublereturn , "adoublereturn" , double, "");
+BBTK_INPUT(ExecutionModelTour , astringreturn , "astringreturn" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , anintegervectorreturn , "anintegervectorreturn" , std::vector<int>, "");
+BBTK_INPUT(ExecutionModelTour , astringchoicereturn , "astringchoicereturn" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ExecutionModelTour ) ;
+}
+
+#endif // __bbSlicerExecutionModelTour_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerExpertAutomatedRegistration.cxx b/ModuleCall/GenSrc/bbSlicerExpertAutomatedRegistration.cxx
new file mode 100644 (file)
index 0000000..61ea18d
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerExpertAutomatedRegistration.cxx
@@ -0,0 +1,82 @@
+#include "bbSlicerExpertAutomatedRegistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ExpertAutomatedRegistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ExpertAutomatedRegistration, bbtk::AtomicBlackBox );
+
+    void ExpertAutomatedRegistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =28;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRegisterImagesModule.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImage( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingImage( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputresampledImage( ) ) ) ,"@@@@@"," --resampledImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--loadTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputloadTransform( ) ) ) ,"@@@@@"," --loadTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--saveTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsaveTransform( ) ) ) ,"@@@@@"," --saveTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialization"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitialization( ) ) ) ,"@@@@@"," --initialization ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--registration"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputregistration( ) ) ) ,"@@@@@"," --registration ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--metric"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmetric( ) ) ) ,"@@@@@"," --metric ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--expectedOffset"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedOffset( ) ) ) ,"@@@@@"," --expectedOffset ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--expectedRotation"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedRotation( ) ) ) ,"@@@@@"," --expectedRotation ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--expectedScale"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedScale( ) ) ) ,"@@@@@"," --expectedScale ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--expectedSkew"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedSkew( ) ) ) ,"@@@@@"," --expectedSkew ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--verbosityLevel"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputverbosityLevel( ) ) ) ,"@@@@@"," --verbosityLevel ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--sampleFromOverlap"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsampleFromOverlap( ) ) ) ,"@@@@@"," --sampleFromOverlap ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedImageMask"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImageMask( ) ) ) ,"@@@@@"," --fixedImageMask ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--randomNumberSeed"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrandomNumberSeed( ) ) ) ,"@@@@@"," --randomNumberSeed ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimizeMemory"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimizeMemory( ) ) ) ,"@@@@@"," --minimizeMemory ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolation"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolation( ) ) ) ,"@@@@@"," --interpolation ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedLandmarks"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedLandmarks( ) ) ) ,"@@@@@"," --fixedLandmarks ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingLandmarks"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingLandmarks( ) ) ) ,"@@@@@"," --movingLandmarks ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rigidMaxIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrigidMaxIterations( ) ) ) ,"@@@@@"," --rigidMaxIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rigidSamplingRatio"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrigidSamplingRatio( ) ) ) ,"@@@@@"," --rigidSamplingRatio ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--affineMaxIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputaffineMaxIterations( ) ) ) ,"@@@@@"," --affineMaxIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--affineSamplingRatio"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputaffineSamplingRatio( ) ) ) ,"@@@@@"," --affineSamplingRatio ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--bsplineMaxIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbsplineMaxIterations( ) ) ) ,"@@@@@"," --bsplineMaxIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--bsplineSamplingRatio"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbsplineSamplingRatio( ) ) ) ,"@@@@@"," --bsplineSamplingRatio ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--controlPointSpacing"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcontrolPointSpacing( ) ) ) ,"@@@@@"," --controlPointSpacing ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ExpertAutomatedRegistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ExpertAutomatedRegistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void ExpertAutomatedRegistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void ExpertAutomatedRegistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerExpertAutomatedRegistration.h b/ModuleCall/GenSrc/bbSlicerExpertAutomatedRegistration.h
new file mode 100644 (file)
index 0000000..5c0312d
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerExpertAutomatedRegistration.h
@@ -0,0 +1,112 @@
+#ifndef __bbSlicerExpertAutomatedRegistration_h_INCLUDED__
+#define __bbSlicerExpertAutomatedRegistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ExpertAutomatedRegistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ExpertAutomatedRegistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( fixedImage , std::string );
+BBTK_DECLARE_INPUT ( movingImage , std::string );
+BBTK_DECLARE_INPUT ( resampledImage , std::string );
+BBTK_DECLARE_INPUT ( loadTransform , std::string );
+BBTK_DECLARE_INPUT ( saveTransform , std::string );
+BBTK_DECLARE_INPUT ( initialization , std::string );
+BBTK_DECLARE_INPUT ( registration , std::string );
+BBTK_DECLARE_INPUT ( metric , std::string );
+BBTK_DECLARE_INPUT ( expectedOffset , float );
+BBTK_DECLARE_INPUT ( expectedRotation , float );
+BBTK_DECLARE_INPUT ( expectedScale , float );
+BBTK_DECLARE_INPUT ( expectedSkew , float );
+BBTK_DECLARE_INPUT ( verbosityLevel , std::string );
+BBTK_DECLARE_INPUT ( sampleFromOverlap , bool );
+BBTK_DECLARE_INPUT ( fixedImageMask , std::string );
+BBTK_DECLARE_INPUT ( randomNumberSeed , int );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+BBTK_DECLARE_INPUT ( minimizeMemory , bool );
+BBTK_DECLARE_INPUT ( interpolation , std::string );
+BBTK_DECLARE_INPUT ( fixedLandmarks , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( movingLandmarks , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( rigidMaxIterations , int );
+BBTK_DECLARE_INPUT ( rigidSamplingRatio , float );
+BBTK_DECLARE_INPUT ( affineMaxIterations , int );
+BBTK_DECLARE_INPUT ( affineSamplingRatio , float );
+BBTK_DECLARE_INPUT ( bsplineMaxIterations , int );
+BBTK_DECLARE_INPUT ( bsplineSamplingRatio , float );
+BBTK_DECLARE_INPUT ( controlPointSpacing , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ExpertAutomatedRegistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ExpertAutomatedRegistration" ) ;
+    BBTK_AUTHOR ( "Stephen R Aylward, Casey B Goodlett" ) ;
+    BBTK_DESCRIPTION ( "Provides rigid, affine, and BSpline registration methods via a simple GUI" ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ExpertAutomatedRegistration , fixedImage , "fixedImage" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , movingImage , "movingImage" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , resampledImage , "resampledImage" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , loadTransform , "loadTransform" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , saveTransform , "saveTransform" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , initialization , "initialization" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , registration , "registration" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , metric , "metric" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , expectedOffset , "expectedOffset" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , expectedRotation , "expectedRotation" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , expectedScale , "expectedScale" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , expectedSkew , "expectedSkew" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , verbosityLevel , "verbosityLevel" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , sampleFromOverlap , "sampleFromOverlap" , bool, "");
+BBTK_INPUT(ExpertAutomatedRegistration , fixedImageMask , "fixedImageMask" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , randomNumberSeed , "randomNumberSeed" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , numberOfThreads , "numberOfThreads" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , minimizeMemory , "minimizeMemory" , bool, "");
+BBTK_INPUT(ExpertAutomatedRegistration , interpolation , "interpolation" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , fixedLandmarks , "fixedLandmarks" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ExpertAutomatedRegistration , movingLandmarks , "movingLandmarks" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ExpertAutomatedRegistration , rigidMaxIterations , "rigidMaxIterations" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , rigidSamplingRatio , "rigidSamplingRatio" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , affineMaxIterations , "affineMaxIterations" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , affineSamplingRatio , "affineSamplingRatio" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , bsplineMaxIterations , "bsplineMaxIterations" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , bsplineSamplingRatio , "bsplineSamplingRatio" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , controlPointSpacing , "controlPointSpacing" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ExpertAutomatedRegistration ) ;
+}
+
+#endif // __bbSlicerExpertAutomatedRegistration_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerExtractSkeleton.cxx b/ModuleCall/GenSrc/bbSlicerExtractSkeleton.cxx
new file mode 100644 (file)
index 0000000..ca15465
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerExtractSkeleton.cxx
@@ -0,0 +1,60 @@
+#include "bbSlicerExtractSkeleton.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ExtractSkeleton )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ExtractSkeleton, bbtk::AtomicBlackBox );
+
+    void ExtractSkeleton::Process ( ) {
+
+        // GENERATED
+
+int _argc =6;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libExtractSkeletonLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--type"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSkeletonType( ) ) ) ,"@@@@@"," --type ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dontPrune"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputDontPruneBranches( ) ) ) ,"@@@@@"," --dontPrune ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputNumberOfPoints( ) ) ) ,"@@@@@"," --numPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--pointsFile"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputPointsFileName( ) ) ) ,"@@@@@"," --pointsFile ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ExtractSkeleton::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ExtractSkeleton::bbUserSetDefaultValues ( ) {
+    }
+
+    void ExtractSkeleton::bbUserInitializeProcessing ( ) {
+    }
+
+    void ExtractSkeleton::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerExtractSkeleton.h b/ModuleCall/GenSrc/bbSlicerExtractSkeleton.h
new file mode 100644 (file)
index 0000000..3b47fb2
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerExtractSkeleton.h
@@ -0,0 +1,68 @@
+#ifndef __bbSlicerExtractSkeleton_h_INCLUDED__
+#define __bbSlicerExtractSkeleton_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ExtractSkeleton
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ExtractSkeleton , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputImageFileName , std::string );
+BBTK_DECLARE_INPUT ( OutputImageFileName , std::string );
+BBTK_DECLARE_INPUT ( SkeletonType , std::string );
+BBTK_DECLARE_INPUT ( DontPruneBranches , bool );
+BBTK_DECLARE_INPUT ( NumberOfPoints , int );
+BBTK_DECLARE_INPUT ( OutputPointsFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ExtractSkeleton , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ExtractSkeleton" ) ;
+    BBTK_AUTHOR ( "Pierre Seroul, Martin Styner, Guido Gerig, and Stephen Aylward" ) ;
+    BBTK_DESCRIPTION ( "Extract the skeleton of a binary object.  The skeleton can be limited to being a 1D curve or allowed to be a full 2D manifold.  The branches of the skeleton can be pruned so that only the maximal center skeleton is returned." ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ExtractSkeleton , InputImageFileName , "InputImageFileName" , std::string, "");
+BBTK_INPUT(ExtractSkeleton , OutputImageFileName , "OutputImageFileName" , std::string, "");
+BBTK_INPUT(ExtractSkeleton , SkeletonType , "SkeletonType" , std::string, "");
+BBTK_INPUT(ExtractSkeleton , DontPruneBranches , "DontPruneBranches" , bool, "");
+BBTK_INPUT(ExtractSkeleton , NumberOfPoints , "NumberOfPoints" , int, "");
+BBTK_INPUT(ExtractSkeleton , OutputPointsFileName , "OutputPointsFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ExtractSkeleton ) ;
+}
+
+#endif // __bbSlicerExtractSkeleton_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerFastAffineregistration.cxx b/ModuleCall/GenSrc/bbSlicerFastAffineregistration.cxx
new file mode 100644 (file)
index 0000000..b2b8a79
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerFastAffineregistration.cxx
@@ -0,0 +1,65 @@
+#include "bbSlicerFastAffineregistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, FastAffineregistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( FastAffineregistration, bbtk::AtomicBlackBox );
+
+    void FastAffineregistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =11;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libAffineRegistrationLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageSmoothingFactor( ) ) ) ,"@@@@@"," --fixedsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageSmoothingFactor( ) ) ) ,"@@@@@"," --movingsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputHistogramBins( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSpatialSamples( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputTranslationScale( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInitialTransform( ) ) ) ,"@@@@@"," --initialtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledmovingfilename"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputResampledImageFileName( ) ) ) ,"@@@@@"," --resampledmovingfilename ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void FastAffineregistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void FastAffineregistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void FastAffineregistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void FastAffineregistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerFastAffineregistration.h b/ModuleCall/GenSrc/bbSlicerFastAffineregistration.h
new file mode 100644 (file)
index 0000000..ae6c4a6
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerFastAffineregistration.h
@@ -0,0 +1,78 @@
+#ifndef __bbSlicerFastAffineregistration_h_INCLUDED__
+#define __bbSlicerFastAffineregistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT FastAffineregistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( FastAffineregistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( FixedImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( MovingImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( HistogramBins , int );
+BBTK_DECLARE_INPUT ( SpatialSamples , int );
+BBTK_DECLARE_INPUT ( Iterations , int );
+BBTK_DECLARE_INPUT ( TranslationScale , double );
+BBTK_DECLARE_INPUT ( InitialTransform , std::string );
+BBTK_DECLARE_INPUT ( FixedImageFileName , std::string );
+BBTK_DECLARE_INPUT ( MovingImageFileName , std::string );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( ResampledImageFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( FastAffineregistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "FastAffineregistration" ) ;
+    BBTK_AUTHOR ( "Daniel Blezek" ) ;
+    BBTK_DESCRIPTION ( "Registers two images together using an affine transform and mutual information. This module is often used to align images of different subjects or images of the same subject from different modalities.This module can smooth images prior to registration to mitigate noise and improve convergence. Many of the registration parameters require a working knowledge of the algorithm although the default parameters are sufficient for many registration tasks." ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(FastAffineregistration , FixedImageSmoothingFactor , "FixedImageSmoothingFactor" , int, "");
+BBTK_INPUT(FastAffineregistration , MovingImageSmoothingFactor , "MovingImageSmoothingFactor" , int, "");
+BBTK_INPUT(FastAffineregistration , HistogramBins , "HistogramBins" , int, "");
+BBTK_INPUT(FastAffineregistration , SpatialSamples , "SpatialSamples" , int, "");
+BBTK_INPUT(FastAffineregistration , Iterations , "Iterations" , int, "");
+BBTK_INPUT(FastAffineregistration , TranslationScale , "TranslationScale" , double, "");
+BBTK_INPUT(FastAffineregistration , InitialTransform , "InitialTransform" , std::string, "");
+BBTK_INPUT(FastAffineregistration , FixedImageFileName , "FixedImageFileName" , std::string, "");
+BBTK_INPUT(FastAffineregistration , MovingImageFileName , "MovingImageFileName" , std::string, "");
+BBTK_INPUT(FastAffineregistration , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(FastAffineregistration , ResampledImageFileName , "ResampledImageFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( FastAffineregistration ) ;
+}
+
+#endif // __bbSlicerFastAffineregistration_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerFastNonrigidBSplineregistration.cxx b/ModuleCall/GenSrc/bbSlicerFastNonrigidBSplineregistration.cxx
new file mode 100644 (file)
index 0000000..cb3326a
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerFastNonrigidBSplineregistration.cxx
@@ -0,0 +1,67 @@
+#include "bbSlicerFastNonrigidBSplineregistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, FastNonrigidBSplineregistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( FastNonrigidBSplineregistration, bbtk::AtomicBlackBox );
+
+    void FastNonrigidBSplineregistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =13;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBSplineDeformableRegistrationLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgridSize( ) ) ) ,"@@@@@"," -g ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputHistogramBins( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSpatialSamples( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--constrain"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputConstrainDeformation( ) ) ) ,"@@@@@"," --constrain ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-m"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMaximumDeformation( ) ) ) ,"@@@@@"," -m ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputDefaultPixelValue( ) ) ) ,"@@@@@"," -d ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInitialTransform( ) ) ) ,"@@@@@"," --initialtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputwarp"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputWarp( ) ) ) ,"@@@@@"," --outputwarp ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledmovingfilename"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputResampledImageFileName( ) ) ) ,"@@@@@"," --resampledmovingfilename ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void FastNonrigidBSplineregistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void FastNonrigidBSplineregistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void FastNonrigidBSplineregistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void FastNonrigidBSplineregistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerFastNonrigidBSplineregistration.h b/ModuleCall/GenSrc/bbSlicerFastNonrigidBSplineregistration.h
new file mode 100644 (file)
index 0000000..dbb3cf3
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerFastNonrigidBSplineregistration.h
@@ -0,0 +1,82 @@
+#ifndef __bbSlicerFastNonrigidBSplineregistration_h_INCLUDED__
+#define __bbSlicerFastNonrigidBSplineregistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT FastNonrigidBSplineregistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( FastNonrigidBSplineregistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( Iterations , int );
+BBTK_DECLARE_INPUT ( gridSize , int );
+BBTK_DECLARE_INPUT ( HistogramBins , int );
+BBTK_DECLARE_INPUT ( SpatialSamples , int );
+BBTK_DECLARE_INPUT ( ConstrainDeformation , bool );
+BBTK_DECLARE_INPUT ( MaximumDeformation , float );
+BBTK_DECLARE_INPUT ( DefaultPixelValue , int );
+BBTK_DECLARE_INPUT ( InitialTransform , std::string );
+BBTK_DECLARE_INPUT ( FixedImageFileName , std::string );
+BBTK_DECLARE_INPUT ( MovingImageFileName , std::string );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( OutputWarp , std::string );
+BBTK_DECLARE_INPUT ( ResampledImageFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( FastNonrigidBSplineregistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "FastNonrigidBSplineregistration" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Registers two images together using BSpline transform and mutual information." ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(FastNonrigidBSplineregistration , Iterations , "Iterations" , int, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , gridSize , "gridSize" , int, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , HistogramBins , "HistogramBins" , int, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , SpatialSamples , "SpatialSamples" , int, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , ConstrainDeformation , "ConstrainDeformation" , bool, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , MaximumDeformation , "MaximumDeformation" , float, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , DefaultPixelValue , "DefaultPixelValue" , int, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , InitialTransform , "InitialTransform" , std::string, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , FixedImageFileName , "FixedImageFileName" , std::string, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , MovingImageFileName , "MovingImageFileName" , std::string, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , OutputWarp , "OutputWarp" , std::string, "");
+BBTK_INPUT(FastNonrigidBSplineregistration , ResampledImageFileName , "ResampledImageFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( FastNonrigidBSplineregistration ) ;
+}
+
+#endif // __bbSlicerFastNonrigidBSplineregistration_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerFastRigidregistration.cxx b/ModuleCall/GenSrc/bbSlicerFastRigidregistration.cxx
new file mode 100644 (file)
index 0000000..ef25e18
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerFastRigidregistration.cxx
@@ -0,0 +1,67 @@
+#include "bbSlicerFastRigidregistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, FastRigidregistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( FastRigidregistration, bbtk::AtomicBlackBox );
+
+    void FastRigidregistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =13;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRigidRegistrationLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageSmoothingFactor( ) ) ) ,"@@@@@"," --fixedsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageSmoothingFactor( ) ) ) ,"@@@@@"," --movingsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--testingmode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputTestingMode( ) ) ) ,"@@@@@"," --testingmode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputHistogramBins( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSpatialSamples( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLearningRate( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputTranslationScale( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInitialTransform( ) ) ) ,"@@@@@"," --initialtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledmovingfilename"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputResampledImageFileName( ) ) ) ,"@@@@@"," --resampledmovingfilename ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void FastRigidregistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void FastRigidregistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void FastRigidregistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void FastRigidregistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerFastRigidregistration.h b/ModuleCall/GenSrc/bbSlicerFastRigidregistration.h
new file mode 100644 (file)
index 0000000..9628e70
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerFastRigidregistration.h
@@ -0,0 +1,82 @@
+#ifndef __bbSlicerFastRigidregistration_h_INCLUDED__
+#define __bbSlicerFastRigidregistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT FastRigidregistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( FastRigidregistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( FixedImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( MovingImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( TestingMode , bool );
+BBTK_DECLARE_INPUT ( HistogramBins , int );
+BBTK_DECLARE_INPUT ( SpatialSamples , int );
+BBTK_DECLARE_INPUT ( Iterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( LearningRate , std::vector<double> );
+BBTK_DECLARE_INPUT ( TranslationScale , double );
+BBTK_DECLARE_INPUT ( InitialTransform , std::string );
+BBTK_DECLARE_INPUT ( FixedImageFileName , std::string );
+BBTK_DECLARE_INPUT ( MovingImageFileName , std::string );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( ResampledImageFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( FastRigidregistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "FastRigidregistration" ) ;
+    BBTK_AUTHOR ( "Daniel Blezek" ) ;
+    BBTK_DESCRIPTION ( "Registers two images together using a rigid transform and mutual information.This module was originally distributed as 'Linear registration' but has been renamed to eliminate confusion with the 'Affine registration' module.This module is often used to align images of different subjects or images of the same subject from different modalities.This module can smooth images prior to registration to mitigate noise and improve convergence. Many of the registration parameters require a working knowledge of the algorithm although the default parameters are sufficient for many registration tasks." ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(FastRigidregistration , FixedImageSmoothingFactor , "FixedImageSmoothingFactor" , int, "");
+BBTK_INPUT(FastRigidregistration , MovingImageSmoothingFactor , "MovingImageSmoothingFactor" , int, "");
+BBTK_INPUT(FastRigidregistration , TestingMode , "TestingMode" , bool, "");
+BBTK_INPUT(FastRigidregistration , HistogramBins , "HistogramBins" , int, "");
+BBTK_INPUT(FastRigidregistration , SpatialSamples , "SpatialSamples" , int, "");
+BBTK_INPUT(FastRigidregistration , Iterations , "Iterations" , std::vector<int>, "");
+BBTK_INPUT(FastRigidregistration , LearningRate , "LearningRate" , std::vector<double>, "");
+BBTK_INPUT(FastRigidregistration , TranslationScale , "TranslationScale" , double, "");
+BBTK_INPUT(FastRigidregistration , InitialTransform , "InitialTransform" , std::string, "");
+BBTK_INPUT(FastRigidregistration , FixedImageFileName , "FixedImageFileName" , std::string, "");
+BBTK_INPUT(FastRigidregistration , MovingImageFileName , "MovingImageFileName" , std::string, "");
+BBTK_INPUT(FastRigidregistration , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(FastRigidregistration , ResampledImageFileName , "ResampledImageFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( FastRigidregistration ) ;
+}
+
+#endif // __bbSlicerFastRigidregistration_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerFiducialRegistration.cxx b/ModuleCall/GenSrc/bbSlicerFiducialRegistration.cxx
new file mode 100644 (file)
index 0000000..0d6bca8
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerFiducialRegistration.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerFiducialRegistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, FiducialRegistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( FiducialRegistration, bbtk::AtomicBlackBox );
+
+    void FiducialRegistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libTransformFromFiducialsModule.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedLandmarks"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedLandmarks( ) ) ) ,"@@@@@"," --fixedLandmarks ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingLandmarks"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingLandmarks( ) ) ) ,"@@@@@"," --movingLandmarks ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--saveTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsaveTransform( ) ) ) ,"@@@@@"," --saveTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transformType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformType( ) ) ) ,"@@@@@"," --transformType ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void FiducialRegistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void FiducialRegistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void FiducialRegistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void FiducialRegistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerFiducialRegistration.h b/ModuleCall/GenSrc/bbSlicerFiducialRegistration.h
new file mode 100644 (file)
index 0000000..46870b4
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerFiducialRegistration.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerFiducialRegistration_h_INCLUDED__
+#define __bbSlicerFiducialRegistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT FiducialRegistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( FiducialRegistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( fixedLandmarks , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( movingLandmarks , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( saveTransform , std::string );
+BBTK_DECLARE_INPUT ( transformType , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( FiducialRegistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "FiducialRegistration" ) ;
+    BBTK_AUTHOR ( "Casey B Goodlett" ) ;
+    BBTK_DESCRIPTION ( "Computes a rigid, similarity or affine transform from a matched list of fiducials" ) ;
+    BBTK_CATEGORY ( "Registration.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(FiducialRegistration , fixedLandmarks , "fixedLandmarks" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(FiducialRegistration , movingLandmarks , "movingLandmarks" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(FiducialRegistration , saveTransform , "saveTransform" , std::string, "");
+BBTK_INPUT(FiducialRegistration , transformType , "transformType" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( FiducialRegistration ) ;
+}
+
+#endif // __bbSlicerFiducialRegistration_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerForegroundmaskingBRAINS.cxx b/ModuleCall/GenSrc/bbSlicerForegroundmaskingBRAINS.cxx
new file mode 100644 (file)
index 0000000..5ba6b77
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerForegroundmaskingBRAINS.cxx
@@ -0,0 +1,63 @@
+#include "bbSlicerForegroundmaskingBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ForegroundmaskingBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ForegroundmaskingBRAINS, bbtk::AtomicBlackBox );
+
+    void ForegroundmaskingBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =9;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBRAINSROIAutoLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@"," --inputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputROIMaskVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputROIMaskVolume( ) ) ) ,"@@@@@"," --outputROIMaskVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputClippedVolumeROI"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputClippedVolumeROI( ) ) ) ,"@@@@@"," --outputClippedVolumeROI ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--otsuPercentileThreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputotsuPercentileThreshold( ) ) ) ,"@@@@@"," --otsuPercentileThreshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--thresholdCorrectionFactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputthresholdCorrectionFactor( ) ) ) ,"@@@@@"," --thresholdCorrectionFactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--closingSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputclosingSize( ) ) ) ,"@@@@@"," --closingSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ROIAutoDilateSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputROIAutoDilateSize( ) ) ) ,"@@@@@"," --ROIAutoDilateSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolumePixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolumePixelType( ) ) ) ,"@@@@@"," --outputVolumePixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ForegroundmaskingBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ForegroundmaskingBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void ForegroundmaskingBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void ForegroundmaskingBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerForegroundmaskingBRAINS.h b/ModuleCall/GenSrc/bbSlicerForegroundmaskingBRAINS.h
new file mode 100644 (file)
index 0000000..ae8f25e
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerForegroundmaskingBRAINS.h
@@ -0,0 +1,74 @@
+#ifndef __bbSlicerForegroundmaskingBRAINS_h_INCLUDED__
+#define __bbSlicerForegroundmaskingBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ForegroundmaskingBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ForegroundmaskingBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputROIMaskVolume , std::string );
+BBTK_DECLARE_INPUT ( outputClippedVolumeROI , std::string );
+BBTK_DECLARE_INPUT ( otsuPercentileThreshold , double );
+BBTK_DECLARE_INPUT ( thresholdCorrectionFactor , double );
+BBTK_DECLARE_INPUT ( closingSize , double );
+BBTK_DECLARE_INPUT ( ROIAutoDilateSize , double );
+BBTK_DECLARE_INPUT ( outputVolumePixelType , std::string );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ForegroundmaskingBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ForegroundmaskingBRAINS" ) ;
+    BBTK_AUTHOR ( "Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu" ) ;
+    BBTK_DESCRIPTION ( "This tool uses a combination of otsu thresholding and a closing operations to identify the most prominant foreground region in an image." ) ;
+    BBTK_CATEGORY ( "Segmentation.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ForegroundmaskingBRAINS , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , outputROIMaskVolume , "outputROIMaskVolume" , std::string, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , outputClippedVolumeROI , "outputClippedVolumeROI" , std::string, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , otsuPercentileThreshold , "otsuPercentileThreshold" , double, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , thresholdCorrectionFactor , "thresholdCorrectionFactor" , double, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , closingSize , "closingSize" , double, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , ROIAutoDilateSize , "ROIAutoDilateSize" , double, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , outputVolumePixelType , "outputVolumePixelType" , std::string, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ForegroundmaskingBRAINS ) ;
+}
+
+#endif // __bbSlicerForegroundmaskingBRAINS_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGaussianBlur.cxx b/ModuleCall/GenSrc/bbSlicerGaussianBlur.cxx
new file mode 100644 (file)
index 0000000..71d5e09
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGaussianBlur.cxx
@@ -0,0 +1,57 @@
+#include "bbSlicerGaussianBlur.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, GaussianBlur )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( GaussianBlur, bbtk::AtomicBlackBox );
+
+    void GaussianBlur::Process ( ) {
+
+        // GENERATED
+
+int _argc =3;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libGaussianBlurImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsigma( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void GaussianBlur::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void GaussianBlur::bbUserSetDefaultValues ( ) {
+    }
+
+    void GaussianBlur::bbUserInitializeProcessing ( ) {
+    }
+
+    void GaussianBlur::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGaussianBlur.h b/ModuleCall/GenSrc/bbSlicerGaussianBlur.h
new file mode 100644 (file)
index 0000000..98aa7bf
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGaussianBlur.h
@@ -0,0 +1,62 @@
+#ifndef __bbSlicerGaussianBlur_h_INCLUDED__
+#define __bbSlicerGaussianBlur_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT GaussianBlur
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( GaussianBlur , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( sigma , double );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( GaussianBlur , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "GaussianBlur" ) ;
+    BBTK_AUTHOR ( "Julien Jomier and Stephen Aylward" ) ;
+    BBTK_DESCRIPTION ( "Apply a gaussian blurr to an image" ) ;
+    BBTK_CATEGORY ( "Filtering.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(GaussianBlur , sigma , "sigma" , double, "");
+BBTK_INPUT(GaussianBlur , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(GaussianBlur , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( GaussianBlur ) ;
+}
+
+#endif // __bbSlicerGaussianBlur_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGeneralRegistrationBRAINS.cxx b/ModuleCall/GenSrc/bbSlicerGeneralRegistrationBRAINS.cxx
new file mode 100644 (file)
index 0000000..43a0846
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGeneralRegistrationBRAINS.cxx
@@ -0,0 +1,114 @@
+#include "bbSlicerGeneralRegistrationBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, GeneralRegistrationBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( GeneralRegistrationBRAINS, bbtk::AtomicBlackBox );
+
+    void GeneralRegistrationBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =60;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBRAINSFitLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedVolume( ) ) ) ,"@@@@@"," --fixedVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingVolume( ) ) ) ,"@@@@@"," --movingVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--bsplineTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbsplineTransform( ) ) ) ,"@@@@@"," --bsplineTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--linearTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlinearTransform( ) ) ) ,"@@@@@"," --linearTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," --outputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitialTransform( ) ) ) ,"@@@@@"," --initialTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeTransformMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeTransformMode( ) ) ) ,"@@@@@"," --initializeTransformMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useRigid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseRigid( ) ) ) ,"@@@@@"," --useRigid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useScaleVersor3D"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseScaleVersor3D( ) ) ) ,"@@@@@"," --useScaleVersor3D ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useScaleSkewVersor3D"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseScaleSkewVersor3D( ) ) ) ,"@@@@@"," --useScaleSkewVersor3D ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useAffine"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseAffine( ) ) ) ,"@@@@@"," --useAffine ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useBSpline"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseBSpline( ) ) ) ,"@@@@@"," --useBSpline ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfSamples"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfSamples( ) ) ) ,"@@@@@"," --numberOfSamples ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--splineGridSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsplineGridSize( ) ) ) ,"@@@@@"," --splineGridSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --numberOfIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maskProcessingMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaskProcessingMode( ) ) ) ,"@@@@@"," --maskProcessingMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedBinaryVolume( ) ) ) ,"@@@@@"," --fixedBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingBinaryVolume( ) ) ) ,"@@@@@"," --movingBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputFixedVolumeROI"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputFixedVolumeROI( ) ) ) ,"@@@@@"," --outputFixedVolumeROI ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputMovingVolumeROI"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputMovingVolumeROI( ) ) ) ,"@@@@@"," --outputMovingVolumeROI ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolumePixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolumePixelType( ) ) ) ,"@@@@@"," --outputVolumePixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--backgroundFillValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbackgroundFillValue( ) ) ) ,"@@@@@"," --backgroundFillValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maskInferiorCutOffFromCenter"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaskInferiorCutOffFromCenter( ) ) ) ,"@@@@@"," --maskInferiorCutOffFromCenter ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--scaleOutputValues"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputscaleOutputValues( ) ) ) ,"@@@@@"," --scaleOutputValues ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolationMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationMode( ) ) ) ,"@@@@@"," --interpolationMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumStepLength"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumStepLength( ) ) ) ,"@@@@@"," --minimumStepLength ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--translationScale"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtranslationScale( ) ) ) ,"@@@@@"," --translationScale ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--reproportionScale"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreproportionScale( ) ) ) ,"@@@@@"," --reproportionScale ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--skewScale"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputskewScale( ) ) ) ,"@@@@@"," --skewScale ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxBSplineDisplacement"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxBSplineDisplacement( ) ) ) ,"@@@@@"," --maxBSplineDisplacement ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputhistogramMatch( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfHistogramBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfHistogramBins( ) ) ) ,"@@@@@"," --numberOfHistogramBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfMatchPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfMatchPoints( ) ) ) ,"@@@@@"," --numberOfMatchPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--strippedOutputTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstrippedOutputTransform( ) ) ) ,"@@@@@"," --strippedOutputTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transformType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformType( ) ) ) ,"@@@@@"," --transformType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputTransform( ) ) ) ,"@@@@@"," --outputTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedVolumeTimeIndex"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedVolumeTimeIndex( ) ) ) ,"@@@@@"," --fixedVolumeTimeIndex ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingVolumeTimeIndex"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingVolumeTimeIndex( ) ) ) ,"@@@@@"," --movingVolumeTimeIndex ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--medianFilterSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmedianFilterSize( ) ) ) ,"@@@@@"," --medianFilterSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--removeIntensityOutliers"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputremoveIntensityOutliers( ) ) ) ,"@@@@@"," --removeIntensityOutliers ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useCachingOfBSplineWeightsMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseCachingOfBSplineWeightsMode( ) ) ) ,"@@@@@"," --useCachingOfBSplineWeightsMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useExplicitPDFDerivativesMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseExplicitPDFDerivativesMode( ) ) ) ,"@@@@@"," --useExplicitPDFDerivativesMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ROIAutoDilateSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputROIAutoDilateSize( ) ) ) ,"@@@@@"," --ROIAutoDilateSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ROIAutoClosingSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputROIAutoClosingSize( ) ) ) ,"@@@@@"," --ROIAutoClosingSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--relaxationFactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrelaxationFactor( ) ) ) ,"@@@@@"," --relaxationFactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maximumStepLength"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaximumStepLength( ) ) ) ,"@@@@@"," --maximumStepLength ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--failureExitCode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfailureExitCode( ) ) ) ,"@@@@@"," --failureExitCode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--writeTransformOnFailure"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputwriteTransformOnFailure( ) ) ) ,"@@@@@"," --writeTransformOnFailure ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--forceMINumberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputforceMINumberOfThreads( ) ) ) ,"@@@@@"," --forceMINumberOfThreads ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--debugLevel"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdebugLevel( ) ) ) ,"@@@@@"," --debugLevel ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--costFunctionConvergenceFactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcostFunctionConvergenceFactor( ) ) ) ,"@@@@@"," --costFunctionConvergenceFactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--projectedGradientTolerance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputprojectedGradientTolerance( ) ) ) ,"@@@@@"," --projectedGradientTolerance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-G"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputUseDebugImageViewer( ) ) ) ,"@@@@@"," -G ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-p"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPromptAfterImageSend( ) ) ) ,"@@@@@"," -p ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseMomentsAlign( ) ) ) ,"@@@@@"," --NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseGeometryAlign( ) ) ) ,"@@@@@"," --NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseCenterOfHeadAlign( ) ) ) ,"@@@@@"," --NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--permitParameterVariation"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpermitParameterVariation( ) ) ) ,"@@@@@"," --permitParameterVariation ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--costMetric"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcostMetric( ) ) ) ,"@@@@@"," --costMetric ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void GeneralRegistrationBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void GeneralRegistrationBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void GeneralRegistrationBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void GeneralRegistrationBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGeneralRegistrationBRAINS.h b/ModuleCall/GenSrc/bbSlicerGeneralRegistrationBRAINS.h
new file mode 100644 (file)
index 0000000..6bdf64a
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGeneralRegistrationBRAINS.h
@@ -0,0 +1,176 @@
+#ifndef __bbSlicerGeneralRegistrationBRAINS_h_INCLUDED__
+#define __bbSlicerGeneralRegistrationBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT GeneralRegistrationBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( GeneralRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( fixedVolume , std::string );
+BBTK_DECLARE_INPUT ( movingVolume , std::string );
+BBTK_DECLARE_INPUT ( bsplineTransform , std::string );
+BBTK_DECLARE_INPUT ( linearTransform , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( initialTransform , std::string );
+BBTK_DECLARE_INPUT ( initializeTransformMode , std::string );
+BBTK_DECLARE_INPUT ( useRigid , bool );
+BBTK_DECLARE_INPUT ( useScaleVersor3D , bool );
+BBTK_DECLARE_INPUT ( useScaleSkewVersor3D , bool );
+BBTK_DECLARE_INPUT ( useAffine , bool );
+BBTK_DECLARE_INPUT ( useBSpline , bool );
+BBTK_DECLARE_INPUT ( numberOfSamples , int );
+BBTK_DECLARE_INPUT ( splineGridSize , std::vector<int> );
+BBTK_DECLARE_INPUT ( numberOfIterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( maskProcessingMode , std::string );
+BBTK_DECLARE_INPUT ( fixedBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( movingBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( outputFixedVolumeROI , std::string );
+BBTK_DECLARE_INPUT ( outputMovingVolumeROI , std::string );
+BBTK_DECLARE_INPUT ( outputVolumePixelType , std::string );
+BBTK_DECLARE_INPUT ( backgroundFillValue , double );
+BBTK_DECLARE_INPUT ( maskInferiorCutOffFromCenter , double );
+BBTK_DECLARE_INPUT ( scaleOutputValues , bool );
+BBTK_DECLARE_INPUT ( interpolationMode , std::string );
+BBTK_DECLARE_INPUT ( minimumStepLength , std::vector<double> );
+BBTK_DECLARE_INPUT ( translationScale , double );
+BBTK_DECLARE_INPUT ( reproportionScale , double );
+BBTK_DECLARE_INPUT ( skewScale , double );
+BBTK_DECLARE_INPUT ( maxBSplineDisplacement , double );
+BBTK_DECLARE_INPUT ( histogramMatch , bool );
+BBTK_DECLARE_INPUT ( numberOfHistogramBins , int );
+BBTK_DECLARE_INPUT ( numberOfMatchPoints , int );
+BBTK_DECLARE_INPUT ( strippedOutputTransform , std::string );
+BBTK_DECLARE_INPUT ( transformType , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( outputTransform , std::string );
+BBTK_DECLARE_INPUT ( fixedVolumeTimeIndex , int );
+BBTK_DECLARE_INPUT ( movingVolumeTimeIndex , int );
+BBTK_DECLARE_INPUT ( medianFilterSize , std::vector<int> );
+BBTK_DECLARE_INPUT ( removeIntensityOutliers , double );
+BBTK_DECLARE_INPUT ( useCachingOfBSplineWeightsMode , std::string );
+BBTK_DECLARE_INPUT ( useExplicitPDFDerivativesMode , std::string );
+BBTK_DECLARE_INPUT ( ROIAutoDilateSize , double );
+BBTK_DECLARE_INPUT ( ROIAutoClosingSize , double );
+BBTK_DECLARE_INPUT ( relaxationFactor , double );
+BBTK_DECLARE_INPUT ( maximumStepLength , double );
+BBTK_DECLARE_INPUT ( failureExitCode , int );
+BBTK_DECLARE_INPUT ( writeTransformOnFailure , bool );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+BBTK_DECLARE_INPUT ( forceMINumberOfThreads , int );
+BBTK_DECLARE_INPUT ( debugLevel , int );
+BBTK_DECLARE_INPUT ( costFunctionConvergenceFactor , double );
+BBTK_DECLARE_INPUT ( projectedGradientTolerance , double );
+BBTK_DECLARE_INPUT ( UseDebugImageViewer , bool );
+BBTK_DECLARE_INPUT ( PromptAfterImageSend , bool );
+BBTK_DECLARE_INPUT ( useMomentsAlign , bool );
+BBTK_DECLARE_INPUT ( useGeometryAlign , bool );
+BBTK_DECLARE_INPUT ( useCenterOfHeadAlign , bool );
+BBTK_DECLARE_INPUT ( permitParameterVariation , std::vector<int> );
+BBTK_DECLARE_INPUT ( costMetric , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( GeneralRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "GeneralRegistrationBRAINS" ) ;
+    BBTK_AUTHOR ( "Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu" ) ;
+    BBTK_DESCRIPTION ( "Register a three-dimensional volume to a reference volume Mattes Mutual Information by default. Described in BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit, Johnson H.J., Harris G., Williams K., The Insight Journal, 2007. http://hdl.handle.net/1926/1291" ) ;
+    BBTK_CATEGORY ( "Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(GeneralRegistrationBRAINS , fixedVolume , "fixedVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , movingVolume , "movingVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , bsplineTransform , "bsplineTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , linearTransform , "linearTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , initialTransform , "initialTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , initializeTransformMode , "initializeTransformMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useRigid , "useRigid" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useScaleVersor3D , "useScaleVersor3D" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useScaleSkewVersor3D , "useScaleSkewVersor3D" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useAffine , "useAffine" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useBSpline , "useBSpline" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfSamples , "numberOfSamples" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , splineGridSize , "splineGridSize" , std::vector<int>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfIterations , "numberOfIterations" , std::vector<int>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , maskProcessingMode , "maskProcessingMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , fixedBinaryVolume , "fixedBinaryVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , movingBinaryVolume , "movingBinaryVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputFixedVolumeROI , "outputFixedVolumeROI" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputMovingVolumeROI , "outputMovingVolumeROI" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputVolumePixelType , "outputVolumePixelType" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , backgroundFillValue , "backgroundFillValue" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , maskInferiorCutOffFromCenter , "maskInferiorCutOffFromCenter" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , scaleOutputValues , "scaleOutputValues" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , interpolationMode , "interpolationMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , minimumStepLength , "minimumStepLength" , std::vector<double>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , translationScale , "translationScale" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , reproportionScale , "reproportionScale" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , skewScale , "skewScale" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , maxBSplineDisplacement , "maxBSplineDisplacement" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , histogramMatch , "histogramMatch" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfHistogramBins , "numberOfHistogramBins" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfMatchPoints , "numberOfMatchPoints" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , strippedOutputTransform , "strippedOutputTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , transformType , "transformType" , std::vector<std::string>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputTransform , "outputTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , fixedVolumeTimeIndex , "fixedVolumeTimeIndex" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , movingVolumeTimeIndex , "movingVolumeTimeIndex" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , medianFilterSize , "medianFilterSize" , std::vector<int>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , removeIntensityOutliers , "removeIntensityOutliers" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useCachingOfBSplineWeightsMode , "useCachingOfBSplineWeightsMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useExplicitPDFDerivativesMode , "useExplicitPDFDerivativesMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , ROIAutoDilateSize , "ROIAutoDilateSize" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , ROIAutoClosingSize , "ROIAutoClosingSize" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , relaxationFactor , "relaxationFactor" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , maximumStepLength , "maximumStepLength" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , failureExitCode , "failureExitCode" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , writeTransformOnFailure , "writeTransformOnFailure" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , forceMINumberOfThreads , "forceMINumberOfThreads" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , debugLevel , "debugLevel" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , costFunctionConvergenceFactor , "costFunctionConvergenceFactor" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , projectedGradientTolerance , "projectedGradientTolerance" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , UseDebugImageViewer , "UseDebugImageViewer" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , PromptAfterImageSend , "PromptAfterImageSend" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useMomentsAlign , "useMomentsAlign" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useGeometryAlign , "useGeometryAlign" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useCenterOfHeadAlign , "useCenterOfHeadAlign" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , permitParameterVariation , "permitParameterVariation" , std::vector<int>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , costMetric , "costMetric" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( GeneralRegistrationBRAINS ) ;
+}
+
+#endif // __bbSlicerGeneralRegistrationBRAINS_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGradientAnisotropicDiffusion.cxx b/ModuleCall/GenSrc/bbSlicerGradientAnisotropicDiffusion.cxx
new file mode 100644 (file)
index 0000000..ef5ab1b
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGradientAnisotropicDiffusion.cxx
@@ -0,0 +1,59 @@
+#include "bbSlicerGradientAnisotropicDiffusion.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, GradientAnisotropicDiffusion )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( GradientAnisotropicDiffusion, bbtk::AtomicBlackBox );
+
+    void GradientAnisotropicDiffusion::Process ( ) {
+
+        // GENERATED
+
+int _argc =5;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libGradientAnisotropicDiffusionLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--conductance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputconductance( ) ) ) ,"@@@@@"," --conductance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --iterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--timeStep"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtimeStep( ) ) ) ,"@@@@@"," --timeStep ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void GradientAnisotropicDiffusion::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void GradientAnisotropicDiffusion::bbUserSetDefaultValues ( ) {
+    }
+
+    void GradientAnisotropicDiffusion::bbUserInitializeProcessing ( ) {
+    }
+
+    void GradientAnisotropicDiffusion::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGradientAnisotropicDiffusion.h b/ModuleCall/GenSrc/bbSlicerGradientAnisotropicDiffusion.h
new file mode 100644 (file)
index 0000000..eb9e3ad
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGradientAnisotropicDiffusion.h
@@ -0,0 +1,66 @@
+#ifndef __bbSlicerGradientAnisotropicDiffusion_h_INCLUDED__
+#define __bbSlicerGradientAnisotropicDiffusion_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT GradientAnisotropicDiffusion
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( GradientAnisotropicDiffusion , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( conductance , double );
+BBTK_DECLARE_INPUT ( numberOfIterations , int );
+BBTK_DECLARE_INPUT ( timeStep , double );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( GradientAnisotropicDiffusion , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "GradientAnisotropicDiffusion" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Runs gradient anisotropic diffusion on a volume.Anisotropic diffusion methods reduce noise or unwanted detail in images while preserving specific image features, like edges.  For many applications, there is an assumption that light-dark transitions edges are interesting.  Standard isotropic diffusion methods move and blur light-dark boundaries.  Anisotropic diffusion methods are formulated to specifically preserve edges. The conductance term for this implementation is a function of the gradient magnitude of the image at each point, reducing the strength of diffusion at edges. The numerical implementation of this equation is similar to that described in the Perona-Malik paper, but uses a more robust technique for gradient magnitude estimation and has been generalized to N-dimensions." ) ;
+    BBTK_CATEGORY ( "Filtering.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(GradientAnisotropicDiffusion , conductance , "conductance" , double, "");
+BBTK_INPUT(GradientAnisotropicDiffusion , numberOfIterations , "numberOfIterations" , int, "");
+BBTK_INPUT(GradientAnisotropicDiffusion , timeStep , "timeStep" , double, "");
+BBTK_INPUT(GradientAnisotropicDiffusion , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(GradientAnisotropicDiffusion , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( GradientAnisotropicDiffusion ) ;
+}
+
+#endif // __bbSlicerGradientAnisotropicDiffusion_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGrayscaleFillHole.cxx b/ModuleCall/GenSrc/bbSlicerGrayscaleFillHole.cxx
new file mode 100644 (file)
index 0000000..3300e5d
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGrayscaleFillHole.cxx
@@ -0,0 +1,56 @@
+#include "bbSlicerGrayscaleFillHole.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, GrayscaleFillHole )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( GrayscaleFillHole, bbtk::AtomicBlackBox );
+
+    void GrayscaleFillHole::Process ( ) {
+
+        // GENERATED
+
+int _argc =2;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libGrayscaleFillHoleImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void GrayscaleFillHole::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void GrayscaleFillHole::bbUserSetDefaultValues ( ) {
+    }
+
+    void GrayscaleFillHole::bbUserInitializeProcessing ( ) {
+    }
+
+    void GrayscaleFillHole::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGrayscaleFillHole.h b/ModuleCall/GenSrc/bbSlicerGrayscaleFillHole.h
new file mode 100644 (file)
index 0000000..695d7e2
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGrayscaleFillHole.h
@@ -0,0 +1,60 @@
+#ifndef __bbSlicerGrayscaleFillHole_h_INCLUDED__
+#define __bbSlicerGrayscaleFillHole_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT GrayscaleFillHole
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( GrayscaleFillHole , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( GrayscaleFillHole , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "GrayscaleFillHole" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "GrayscaleFillholeImageFilter fills holes in a grayscale image.  Holes are local minima in the grayscale topography that are not connected to boundaries of the image. Gray level values adjacent to a hole are extrapolated across the hole.This filter is used to smooth over local minima without affecting the values of local maxima.  If you take the difference between the output of this filter and the original image and perhaps threshold the difference above a small value, you'll obtain a map of the local minima.This filter uses the itkGrayscaleGeodesicErodeImageFilter.  It provides its own input as the 'mask' input to the geodesic erosion.  The 'marker' image for the geodesic erosion is constructed such that boundary pixels match the boundary pixels of the input image and the interior pixels are set to the maximum pixel value in the input image. Geodesic morphology and the Fillhole algorithm is described in Chapter 6 of Pierre Soille's book 'Morphological Image Analysis: Principles and Applications', Second Edition, Springer, 2003.  A companion filter, Grayscale Grind Peak, removes peaks in grayscale images." ) ;
+    BBTK_CATEGORY ( "Filtering.Morphology" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(GrayscaleFillHole , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(GrayscaleFillHole , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( GrayscaleFillHole ) ;
+}
+
+#endif // __bbSlicerGrayscaleFillHole_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGrayscaleGrindPeak.cxx b/ModuleCall/GenSrc/bbSlicerGrayscaleGrindPeak.cxx
new file mode 100644 (file)
index 0000000..aae444b
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGrayscaleGrindPeak.cxx
@@ -0,0 +1,56 @@
+#include "bbSlicerGrayscaleGrindPeak.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, GrayscaleGrindPeak )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( GrayscaleGrindPeak, bbtk::AtomicBlackBox );
+
+    void GrayscaleGrindPeak::Process ( ) {
+
+        // GENERATED
+
+int _argc =2;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libGrayscaleGrindPeakImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void GrayscaleGrindPeak::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void GrayscaleGrindPeak::bbUserSetDefaultValues ( ) {
+    }
+
+    void GrayscaleGrindPeak::bbUserInitializeProcessing ( ) {
+    }
+
+    void GrayscaleGrindPeak::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerGrayscaleGrindPeak.h b/ModuleCall/GenSrc/bbSlicerGrayscaleGrindPeak.h
new file mode 100644 (file)
index 0000000..0b43992
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerGrayscaleGrindPeak.h
@@ -0,0 +1,60 @@
+#ifndef __bbSlicerGrayscaleGrindPeak_h_INCLUDED__
+#define __bbSlicerGrayscaleGrindPeak_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT GrayscaleGrindPeak
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( GrayscaleGrindPeak , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( GrayscaleGrindPeak , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "GrayscaleGrindPeak" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "GrayscaleGrindPeakImageFilter removes peaks in a grayscale image. Peaks are local maxima in the grayscale topography that are not connected to boundaries of the image. Gray level values adjacent to a peak are extrapolated through the peak.This filter is used to smooth over local maxima without affecting the values of local minima.  If you take the difference between the output of this filter and the original image and perhaps threshold the difference above a small value, you'll obtain a map of the local maxima.This filter uses the GrayscaleGeodesicDilateImageFilter.  It provides its own input as the 'mask' input to the geodesic erosion.  The 'marker' image for the geodesic erosion is constructed such that boundary pixels match the boundary pixels of the input image and the interior pixels are set to the minimum pixel value in the input image.This filter is the dual to the GrayscaleFillholeImageFilter which implements the Fillhole algorithm.  Since it is a dual, it is somewhat superfluous but is provided as a convenience.Geodesic morphology and the Fillhole algorithm is described in Chapter 6 of Pierre Soille's book 'Morphological Image Analysis: Principles and Applications', Second Edition, Springer, 2003.A companion filter, Grayscale Fill Hole, fills holes in grayscale images." ) ;
+    BBTK_CATEGORY ( "Filtering.Morphology" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(GrayscaleGrindPeak , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(GrayscaleGrindPeak , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( GrayscaleGrindPeak ) ;
+}
+
+#endif // __bbSlicerGrayscaleGrindPeak_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerHistogramMatching.cxx b/ModuleCall/GenSrc/bbSlicerHistogramMatching.cxx
new file mode 100644 (file)
index 0000000..b78a83f
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerHistogramMatching.cxx
@@ -0,0 +1,60 @@
+#include "bbSlicerHistogramMatching.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, HistogramMatching )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( HistogramMatching, bbtk::AtomicBlackBox );
+
+    void HistogramMatching::Process ( ) {
+
+        // GENERATED
+
+int _argc =6;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libHistogramMatchingLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfHistogramLevels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfHistogramLevels( ) ) ) ,"@@@@@"," --numberOfHistogramLevels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfMatchPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfMatchPoints( ) ) ) ,"@@@@@"," --numberOfMatchPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--threshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputthresholdAtMeanIntensity( ) ) ) ,"@@@@@"," --threshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreferenceVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void HistogramMatching::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void HistogramMatching::bbUserSetDefaultValues ( ) {
+    }
+
+    void HistogramMatching::bbUserInitializeProcessing ( ) {
+    }
+
+    void HistogramMatching::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerHistogramMatching.h b/ModuleCall/GenSrc/bbSlicerHistogramMatching.h
new file mode 100644 (file)
index 0000000..efdcef4
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerHistogramMatching.h
@@ -0,0 +1,68 @@
+#ifndef __bbSlicerHistogramMatching_h_INCLUDED__
+#define __bbSlicerHistogramMatching_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT HistogramMatching
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( HistogramMatching , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( numberOfHistogramLevels , int );
+BBTK_DECLARE_INPUT ( numberOfMatchPoints , int );
+BBTK_DECLARE_INPUT ( thresholdAtMeanIntensity , bool );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( referenceVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( HistogramMatching , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "HistogramMatching" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Normalizes the grayscale values of a source image based on the grayscale values of a reference image.  This filter uses a histogram matching technique where the histograms of the two images are matched only at a specified number of quantile values.The filter was orginally designed to normalize MR images of the sameMR protocol and same body part. The algorithm works best if background pixels are excluded from both the source and reference histograms.  A simple background exclusion method is to exclude all pixels whose grayscale values are smaller than the mean grayscale value. ThresholdAtMeanIntensity switches on this simple background exclusion method.Number of match points governs the number of quantile values to be matched.The filter assumes that both the source and reference are of the same type and that the input and output image type have the same number of dimension and have scalar pixel types." ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(HistogramMatching , numberOfHistogramLevels , "numberOfHistogramLevels" , int, "");
+BBTK_INPUT(HistogramMatching , numberOfMatchPoints , "numberOfMatchPoints" , int, "");
+BBTK_INPUT(HistogramMatching , thresholdAtMeanIntensity , "thresholdAtMeanIntensity" , bool, "");
+BBTK_INPUT(HistogramMatching , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(HistogramMatching , referenceVolume , "referenceVolume" , std::string, "");
+BBTK_INPUT(HistogramMatching , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( HistogramMatching ) ;
+}
+
+#endif // __bbSlicerHistogramMatching_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerImageLabelCombine.cxx b/ModuleCall/GenSrc/bbSlicerImageLabelCombine.cxx
new file mode 100644 (file)
index 0000000..686720d
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerImageLabelCombine.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerImageLabelCombine.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ImageLabelCombine )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ImageLabelCombine, bbtk::AtomicBlackBox );
+
+    void ImageLabelCombine::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libImageLabelCombineLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputLabelMap_A( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputLabelMap_B( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputLabelMap( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFirstOverwrites( ) ) ) ,"@@@@@"," -f ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ImageLabelCombine::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ImageLabelCombine::bbUserSetDefaultValues ( ) {
+    }
+
+    void ImageLabelCombine::bbUserInitializeProcessing ( ) {
+    }
+
+    void ImageLabelCombine::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerImageLabelCombine.h b/ModuleCall/GenSrc/bbSlicerImageLabelCombine.h
new file mode 100644 (file)
index 0000000..6404950
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerImageLabelCombine.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerImageLabelCombine_h_INCLUDED__
+#define __bbSlicerImageLabelCombine_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ImageLabelCombine
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ImageLabelCombine , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputLabelMap_A , std::string );
+BBTK_DECLARE_INPUT ( InputLabelMap_B , std::string );
+BBTK_DECLARE_INPUT ( OutputLabelMap , std::string );
+BBTK_DECLARE_INPUT ( FirstOverwrites , bool );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ImageLabelCombine , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ImageLabelCombine" ) ;
+    BBTK_AUTHOR ( "Alex Yarmarkovich" ) ;
+    BBTK_DESCRIPTION ( "Combine two label maps into one" ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ImageLabelCombine , InputLabelMap_A , "InputLabelMap_A" , std::string, "");
+BBTK_INPUT(ImageLabelCombine , InputLabelMap_B , "InputLabelMap_B" , std::string, "");
+BBTK_INPUT(ImageLabelCombine , OutputLabelMap , "OutputLabelMap" , std::string, "");
+BBTK_INPUT(ImageLabelCombine , FirstOverwrites , "FirstOverwrites" , bool, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ImageLabelCombine ) ;
+}
+
+#endif // __bbSlicerImageLabelCombine_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerJointRicianLMMSEImageFilter.cxx b/ModuleCall/GenSrc/bbSlicerJointRicianLMMSEImageFilter.cxx
new file mode 100644 (file)
index 0000000..374606d
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerJointRicianLMMSEImageFilter.cxx
@@ -0,0 +1,59 @@
+#include "bbSlicerJointRicianLMMSEImageFilter.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, JointRicianLMMSEImageFilter )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( JointRicianLMMSEImageFilter, bbtk::AtomicBlackBox );
+
+    void JointRicianLMMSEImageFilter::Process ( ) {
+
+        // GENERATED
+
+int _argc =5;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libjointLMMSELib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--re"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusEstimation( ) ) ) ,"@@@@@"," --re ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rf"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusFiltering( ) ) ) ,"@@@@@"," --rf ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ng"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiNumNeighbors( ) ) ) ,"@@@@@"," --ng ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void JointRicianLMMSEImageFilter::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void JointRicianLMMSEImageFilter::bbUserSetDefaultValues ( ) {
+    }
+
+    void JointRicianLMMSEImageFilter::bbUserInitializeProcessing ( ) {
+    }
+
+    void JointRicianLMMSEImageFilter::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerJointRicianLMMSEImageFilter.h b/ModuleCall/GenSrc/bbSlicerJointRicianLMMSEImageFilter.h
new file mode 100644 (file)
index 0000000..ace562e
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerJointRicianLMMSEImageFilter.h
@@ -0,0 +1,66 @@
+#ifndef __bbSlicerJointRicianLMMSEImageFilter_h_INCLUDED__
+#define __bbSlicerJointRicianLMMSEImageFilter_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT JointRicianLMMSEImageFilter
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( JointRicianLMMSEImageFilter , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( iRadiusEstimation , std::vector<int> );
+BBTK_DECLARE_INPUT ( iRadiusFiltering , std::vector<int> );
+BBTK_DECLARE_INPUT ( iNumNeighbors , int );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( JointRicianLMMSEImageFilter , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "JointRicianLMMSEImageFilter" ) ;
+    BBTK_AUTHOR ( "Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid SPAIN. Partially founded by grant number TEC2007-67073/TCM from the Comision Interministerial de Ciencia y Tecnologia Spain." ) ;
+    BBTK_DESCRIPTION ( "This module reduces Rician noise or unwanted detail on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. The N closest gradient directions to the direction being processed are filtered together to improve the results: the noise-free signal is seen as an n-diemensional vector which has to be estimated with the LMMSE method from a set of corrupted measurements. To that end, the covariance matrix of the noise-free vector and the cross covariance between this signal and the noise have to be estimated, which is done taking into account the image formation process.The noise parameter is automatically estimated from a rough segmentation of the background of the image. In this area the signal is simply 0, so that Rician statistics reduce to Rayleigh and the noise power can be easily estimated from the mode of the histogram.A complete description of the algorithm may be found in:Antonio Tristan-Vega and Santiago Aja-Fernandez, DWI filtering using joint information for DTI and HARDI, Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010." ) ;
+    BBTK_CATEGORY ( "Diffusion.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(JointRicianLMMSEImageFilter , iRadiusEstimation , "iRadiusEstimation" , std::vector<int>, "");
+BBTK_INPUT(JointRicianLMMSEImageFilter , iRadiusFiltering , "iRadiusFiltering" , std::vector<int>, "");
+BBTK_INPUT(JointRicianLMMSEImageFilter , iNumNeighbors , "iNumNeighbors" , int, "");
+BBTK_INPUT(JointRicianLMMSEImageFilter , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(JointRicianLMMSEImageFilter , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( JointRicianLMMSEImageFilter ) ;
+}
+
+#endif // __bbSlicerJointRicianLMMSEImageFilter_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerLabelMapSmoothing.cxx b/ModuleCall/GenSrc/bbSlicerLabelMapSmoothing.cxx
new file mode 100644 (file)
index 0000000..3bd0ff5
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerLabelMapSmoothing.cxx
@@ -0,0 +1,60 @@
+#include "bbSlicerLabelMapSmoothing.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, LabelMapSmoothing )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( LabelMapSmoothing, bbtk::AtomicBlackBox );
+
+    void LabelMapSmoothing::Process ( ) {
+
+        // GENERATED
+
+int _argc =6;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libLabelMapSmoothingLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--labelToSmooth"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlabelToSmooth( ) ) ) ,"@@@@@"," --labelToSmooth ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --numberOfIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxRMSError"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxRMSError( ) ) ) ,"@@@@@"," --maxRMSError ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--gaussianSigma"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgaussianSigma( ) ) ) ,"@@@@@"," --gaussianSigma ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void LabelMapSmoothing::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void LabelMapSmoothing::bbUserSetDefaultValues ( ) {
+    }
+
+    void LabelMapSmoothing::bbUserInitializeProcessing ( ) {
+    }
+
+    void LabelMapSmoothing::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerLabelMapSmoothing.h b/ModuleCall/GenSrc/bbSlicerLabelMapSmoothing.h
new file mode 100644 (file)
index 0000000..38f5675
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerLabelMapSmoothing.h
@@ -0,0 +1,68 @@
+#ifndef __bbSlicerLabelMapSmoothing_h_INCLUDED__
+#define __bbSlicerLabelMapSmoothing_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT LabelMapSmoothing
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( LabelMapSmoothing , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( labelToSmooth , int );
+BBTK_DECLARE_INPUT ( numberOfIterations , int );
+BBTK_DECLARE_INPUT ( maxRMSError , float );
+BBTK_DECLARE_INPUT ( gaussianSigma , float );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( LabelMapSmoothing , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "LabelMapSmoothing" ) ;
+    BBTK_AUTHOR ( "Dirk Padfield, Josh Cates, Ross Whitaker" ) ;
+    BBTK_DESCRIPTION ( "This filter smoothes a binary label map.  With a label map as input, this filter runs an anti-alising algorithm followed by a Gaussian smoothing algorithm.  The output is a smoothed label map." ) ;
+    BBTK_CATEGORY ( "Surface Models" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(LabelMapSmoothing , labelToSmooth , "labelToSmooth" , int, "");
+BBTK_INPUT(LabelMapSmoothing , numberOfIterations , "numberOfIterations" , int, "");
+BBTK_INPUT(LabelMapSmoothing , maxRMSError , "maxRMSError" , float, "");
+BBTK_INPUT(LabelMapSmoothing , gaussianSigma , "gaussianSigma" , float, "");
+BBTK_INPUT(LabelMapSmoothing , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(LabelMapSmoothing , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( LabelMapSmoothing ) ;
+}
+
+#endif // __bbSlicerLabelMapSmoothing_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerLinearregistration.cxx b/ModuleCall/GenSrc/bbSlicerLinearregistration.cxx
new file mode 100644 (file)
index 0000000..98f4d66
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerLinearregistration.cxx
@@ -0,0 +1,66 @@
+#include "bbSlicerLinearregistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, Linearregistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( Linearregistration, bbtk::AtomicBlackBox );
+
+    void Linearregistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =12;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libLinearRegistrationLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageSmoothingFactor( ) ) ) ,"@@@@@"," --fixedsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageSmoothingFactor( ) ) ) ,"@@@@@"," --movingsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputHistogramBins( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSpatialSamples( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLearningRate( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputTranslationScale( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInitialTransform( ) ) ) ,"@@@@@"," --initialtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledmovingfilename"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputResampledImageFileName( ) ) ) ,"@@@@@"," --resampledmovingfilename ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void Linearregistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void Linearregistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void Linearregistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void Linearregistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerLinearregistration.h b/ModuleCall/GenSrc/bbSlicerLinearregistration.h
new file mode 100644 (file)
index 0000000..3f1013c
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerLinearregistration.h
@@ -0,0 +1,80 @@
+#ifndef __bbSlicerLinearregistration_h_INCLUDED__
+#define __bbSlicerLinearregistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT Linearregistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( Linearregistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( FixedImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( MovingImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( HistogramBins , int );
+BBTK_DECLARE_INPUT ( SpatialSamples , int );
+BBTK_DECLARE_INPUT ( Iterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( LearningRate , std::vector<double> );
+BBTK_DECLARE_INPUT ( TranslationScale , double );
+BBTK_DECLARE_INPUT ( InitialTransform , std::string );
+BBTK_DECLARE_INPUT ( FixedImageFileName , std::string );
+BBTK_DECLARE_INPUT ( MovingImageFileName , std::string );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( ResampledImageFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( Linearregistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "Linearregistration" ) ;
+    BBTK_AUTHOR ( "Daniel Blezek" ) ;
+    BBTK_DESCRIPTION ( "Registers two images together using a rigid transform and mutual information." ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(Linearregistration , FixedImageSmoothingFactor , "FixedImageSmoothingFactor" , int, "");
+BBTK_INPUT(Linearregistration , MovingImageSmoothingFactor , "MovingImageSmoothingFactor" , int, "");
+BBTK_INPUT(Linearregistration , HistogramBins , "HistogramBins" , int, "");
+BBTK_INPUT(Linearregistration , SpatialSamples , "SpatialSamples" , int, "");
+BBTK_INPUT(Linearregistration , Iterations , "Iterations" , std::vector<int>, "");
+BBTK_INPUT(Linearregistration , LearningRate , "LearningRate" , std::vector<double>, "");
+BBTK_INPUT(Linearregistration , TranslationScale , "TranslationScale" , double, "");
+BBTK_INPUT(Linearregistration , InitialTransform , "InitialTransform" , std::string, "");
+BBTK_INPUT(Linearregistration , FixedImageFileName , "FixedImageFileName" , std::string, "");
+BBTK_INPUT(Linearregistration , MovingImageFileName , "MovingImageFileName" , std::string, "");
+BBTK_INPUT(Linearregistration , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(Linearregistration , ResampledImageFileName , "ResampledImageFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( Linearregistration ) ;
+}
+
+#endif // __bbSlicerLinearregistration_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMRIBiasFieldCorrection.cxx b/ModuleCall/GenSrc/bbSlicerMRIBiasFieldCorrection.cxx
new file mode 100644 (file)
index 0000000..61d0ffe
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMRIBiasFieldCorrection.cxx
@@ -0,0 +1,64 @@
+#include "bbSlicerMRIBiasFieldCorrection.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, MRIBiasFieldCorrection )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( MRIBiasFieldCorrection, bbtk::AtomicBlackBox );
+
+    void MRIBiasFieldCorrection::Process ( ) {
+
+        // GENERATED
+
+int _argc =10;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMRIBiasFieldCorrectionLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputImage( ) ) ) ,"@@@@@"," --inputImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputMask"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputMask( ) ) ) ,"@@@@@"," --inputMask ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputImage( ) ) ) ,"@@@@@"," --outputImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--algorithmType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputAlgorithmType( ) ) ) ,"@@@@@"," --algorithmType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--shrinkFactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputShrinkFactor( ) ) ) ,"@@@@@"," --shrinkFactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maximumNumberOfIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMaximumNumberOfIterations( ) ) ) ,"@@@@@"," --maximumNumberOfIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfFittingLevels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputNumberOfFittingLevels( ) ) ) ,"@@@@@"," --numberOfFittingLevels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--wienerFilterNoise"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputWienerFilterNoise( ) ) ) ,"@@@@@"," --wienerFilterNoise ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fullWidthAtHalfMaximum"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFullWidthAtHalfMaximum( ) ) ) ,"@@@@@"," --fullWidthAtHalfMaximum ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--convergenceThreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputConvergenceThreshold( ) ) ) ,"@@@@@"," --convergenceThreshold ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void MRIBiasFieldCorrection::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void MRIBiasFieldCorrection::bbUserSetDefaultValues ( ) {
+    }
+
+    void MRIBiasFieldCorrection::bbUserInitializeProcessing ( ) {
+    }
+
+    void MRIBiasFieldCorrection::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMRIBiasFieldCorrection.h b/ModuleCall/GenSrc/bbSlicerMRIBiasFieldCorrection.h
new file mode 100644 (file)
index 0000000..10533e1
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMRIBiasFieldCorrection.h
@@ -0,0 +1,76 @@
+#ifndef __bbSlicerMRIBiasFieldCorrection_h_INCLUDED__
+#define __bbSlicerMRIBiasFieldCorrection_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT MRIBiasFieldCorrection
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( MRIBiasFieldCorrection , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputImage , std::string );
+BBTK_DECLARE_INPUT ( InputMask , std::string );
+BBTK_DECLARE_INPUT ( OutputImage , std::string );
+BBTK_DECLARE_INPUT ( AlgorithmType , std::string );
+BBTK_DECLARE_INPUT ( ShrinkFactor , int );
+BBTK_DECLARE_INPUT ( MaximumNumberOfIterations , int );
+BBTK_DECLARE_INPUT ( NumberOfFittingLevels , int );
+BBTK_DECLARE_INPUT ( WienerFilterNoise , double );
+BBTK_DECLARE_INPUT ( FullWidthAtHalfMaximum , double );
+BBTK_DECLARE_INPUT ( ConvergenceThreshold , double );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MRIBiasFieldCorrection , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "MRIBiasFieldCorrection" ) ;
+    BBTK_AUTHOR ( "Sylvain Jaume MIT" ) ;
+    BBTK_DESCRIPTION ( "Corrects 3D MRI images corrupted by MRI gain field effect.  This module removes the slow-varying intensity variation from a 3D image.  The output image has a higher contrast locally and the visualization and reading of the image are improved.  This is an important pre-processinbg step for image operations requiring intensity perfect images, such as the Expectation Maximization segmentation see EMSegment module. The N3 and N4 methods are described in N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction, Tustison N., Gee J., Insight Journal, 2009. http://hdl.handle.net/10380/3053 The Slicer code was contributed by Sylvain Jaume MIT for NA-MIC http://na-mic.org." ) ;
+    BBTK_CATEGORY ( "Legacy.Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(MRIBiasFieldCorrection , InputImage , "InputImage" , std::string, "");
+BBTK_INPUT(MRIBiasFieldCorrection , InputMask , "InputMask" , std::string, "");
+BBTK_INPUT(MRIBiasFieldCorrection , OutputImage , "OutputImage" , std::string, "");
+BBTK_INPUT(MRIBiasFieldCorrection , AlgorithmType , "AlgorithmType" , std::string, "");
+BBTK_INPUT(MRIBiasFieldCorrection , ShrinkFactor , "ShrinkFactor" , int, "");
+BBTK_INPUT(MRIBiasFieldCorrection , MaximumNumberOfIterations , "MaximumNumberOfIterations" , int, "");
+BBTK_INPUT(MRIBiasFieldCorrection , NumberOfFittingLevels , "NumberOfFittingLevels" , int, "");
+BBTK_INPUT(MRIBiasFieldCorrection , WienerFilterNoise , "WienerFilterNoise" , double, "");
+BBTK_INPUT(MRIBiasFieldCorrection , FullWidthAtHalfMaximum , "FullWidthAtHalfMaximum" , double, "");
+BBTK_INPUT(MRIBiasFieldCorrection , ConvergenceThreshold , "ConvergenceThreshold" , double, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( MRIBiasFieldCorrection ) ;
+}
+
+#endif // __bbSlicerMRIBiasFieldCorrection_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMaskImage.cxx b/ModuleCall/GenSrc/bbSlicerMaskImage.cxx
new file mode 100644 (file)
index 0000000..1df060b
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMaskImage.cxx
@@ -0,0 +1,59 @@
+#include "bbSlicerMaskImage.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, MaskImage )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( MaskImage, bbtk::AtomicBlackBox );
+
+    void MaskImage::Process ( ) {
+
+        // GENERATED
+
+int _argc =5;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMaskLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMaskVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLabel( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-r"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputReplace( ) ) ) ,"@@@@@"," -r ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void MaskImage::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void MaskImage::bbUserSetDefaultValues ( ) {
+    }
+
+    void MaskImage::bbUserInitializeProcessing ( ) {
+    }
+
+    void MaskImage::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMaskImage.h b/ModuleCall/GenSrc/bbSlicerMaskImage.h
new file mode 100644 (file)
index 0000000..73f9b29
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMaskImage.h
@@ -0,0 +1,66 @@
+#ifndef __bbSlicerMaskImage_h_INCLUDED__
+#define __bbSlicerMaskImage_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT MaskImage
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( MaskImage , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( MaskVolume , std::string );
+BBTK_DECLARE_INPUT ( OutputVolume , std::string );
+BBTK_DECLARE_INPUT ( Label , int );
+BBTK_DECLARE_INPUT ( Replace , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MaskImage , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "MaskImage" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH" ) ;
+    BBTK_DESCRIPTION ( "Masks two images. The output image is set to 0 everywhere except where the chosen label from the mask volume is present, at which point it will retain it's original values. Although all image types are supported on input, only signed types are produced. The two images do not have to have the same dimensions." ) ;
+    BBTK_CATEGORY ( "Filtering.Arithmetic" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(MaskImage , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(MaskImage , MaskVolume , "MaskVolume" , std::string, "");
+BBTK_INPUT(MaskImage , OutputVolume , "OutputVolume" , std::string, "");
+BBTK_INPUT(MaskImage , Label , "Label" , int, "");
+BBTK_INPUT(MaskImage , Replace , "Replace" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( MaskImage ) ;
+}
+
+#endif // __bbSlicerMaskImage_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMedianFilter.cxx b/ModuleCall/GenSrc/bbSlicerMedianFilter.cxx
new file mode 100644 (file)
index 0000000..80f8a20
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMedianFilter.cxx
@@ -0,0 +1,57 @@
+#include "bbSlicerMedianFilter.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, MedianFilter )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( MedianFilter, bbtk::AtomicBlackBox );
+
+    void MedianFilter::Process ( ) {
+
+        // GENERATED
+
+int _argc =3;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMedianImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--neighborhood"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputneighborhood( ) ) ) ,"@@@@@"," --neighborhood ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void MedianFilter::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void MedianFilter::bbUserSetDefaultValues ( ) {
+    }
+
+    void MedianFilter::bbUserInitializeProcessing ( ) {
+    }
+
+    void MedianFilter::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMedianFilter.h b/ModuleCall/GenSrc/bbSlicerMedianFilter.h
new file mode 100644 (file)
index 0000000..3518df1
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMedianFilter.h
@@ -0,0 +1,62 @@
+#ifndef __bbSlicerMedianFilter_h_INCLUDED__
+#define __bbSlicerMedianFilter_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT MedianFilter
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( MedianFilter , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( neighborhood , std::vector<int> );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MedianFilter , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "MedianFilter" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "The MedianImageFilter is commonly used as a robust approach for noise reduction. This filter is particularly efficient against 'salt-and-pepper' noise. In other words, it is robust to the presence of gray-level outliers. MedianImageFilter computes the value of each output pixel as the statistical median of the neighborhood of values around the corresponding input pixel." ) ;
+    BBTK_CATEGORY ( "Filtering.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(MedianFilter , neighborhood , "neighborhood" , std::vector<int>, "");
+BBTK_INPUT(MedianFilter , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(MedianFilter , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( MedianFilter ) ;
+}
+
+#endif // __bbSlicerMedianFilter_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMergeModels.cxx b/ModuleCall/GenSrc/bbSlicerMergeModels.cxx
new file mode 100644 (file)
index 0000000..94312c1
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMergeModels.cxx
@@ -0,0 +1,57 @@
+#include "bbSlicerMergeModels.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, MergeModels )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( MergeModels, bbtk::AtomicBlackBox );
+
+    void MergeModels::Process ( ) {
+
+        // GENERATED
+
+int _argc =3;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMergeModelsLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModel1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModel2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModelOutput( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void MergeModels::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void MergeModels::bbUserSetDefaultValues ( ) {
+    }
+
+    void MergeModels::bbUserInitializeProcessing ( ) {
+    }
+
+    void MergeModels::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMergeModels.h b/ModuleCall/GenSrc/bbSlicerMergeModels.h
new file mode 100644 (file)
index 0000000..085777e
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMergeModels.h
@@ -0,0 +1,62 @@
+#ifndef __bbSlicerMergeModels_h_INCLUDED__
+#define __bbSlicerMergeModels_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT MergeModels
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( MergeModels , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( Model1 , std::string );
+BBTK_DECLARE_INPUT ( Model2 , std::string );
+BBTK_DECLARE_INPUT ( ModelOutput , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MergeModels , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "MergeModels" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin BWH Ron Kikinis, BWH, Daniel Haehn" ) ;
+    BBTK_DESCRIPTION ( "Merge the polydata from two input models and output a new model with the added polydata. Uses the vtkAppendPolyData filter. Works on .vtp and .vtk surface files." ) ;
+    BBTK_CATEGORY ( "Surface Models" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(MergeModels , Model1 , "Model1" , std::string, "");
+BBTK_INPUT(MergeModels , Model2 , "Model2" , std::string, "");
+BBTK_INPUT(MergeModels , ModelOutput , "ModelOutput" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( MergeModels ) ;
+}
+
+#endif // __bbSlicerMergeModels_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMeshContourSegmentation.cxx b/ModuleCall/GenSrc/bbSlicerMeshContourSegmentation.cxx
new file mode 100644 (file)
index 0000000..bdb8ba9
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMeshContourSegmentation.cxx
@@ -0,0 +1,64 @@
+#include "bbSlicerMeshContourSegmentation.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, MeshContourSegmentation )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( MeshContourSegmentation, bbtk::AtomicBlackBox );
+
+    void MeshContourSegmentation::Process ( ) {
+
+        // GENERATED
+
+int _argc =10;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libSparseFieldLevelSetContourLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputScene"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputSurface( ) ) ) ,"@@@@@"," --inputScene ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-c"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputContourSeedPts( ) ) ) ,"@@@@@"," -c ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputModel"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputModel( ) ) ) ,"@@@@@"," --outputModel ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--evolve_its"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputevolve_its( ) ) ) ,"@@@@@"," --evolve_its ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--mesh_smooth_its"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmesh_smooth_its( ) ) ) ,"@@@@@"," --mesh_smooth_its ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--H_smooth_its"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputH_smooth_its( ) ) ) ,"@@@@@"," --H_smooth_its ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--adj_levels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputadj_levels( ) ) ) ,"@@@@@"," --adj_levels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--showLS"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputshowLS( ) ) ) ,"@@@@@"," --showLS ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rightHandMesh"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrightHandMesh( ) ) ) ,"@@@@@"," --rightHandMesh ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--is_test"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputis_test( ) ) ) ,"@@@@@"," --is_test ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void MeshContourSegmentation::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void MeshContourSegmentation::bbUserSetDefaultValues ( ) {
+    }
+
+    void MeshContourSegmentation::bbUserInitializeProcessing ( ) {
+    }
+
+    void MeshContourSegmentation::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMeshContourSegmentation.h b/ModuleCall/GenSrc/bbSlicerMeshContourSegmentation.h
new file mode 100644 (file)
index 0000000..0f9cdf4
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMeshContourSegmentation.h
@@ -0,0 +1,76 @@
+#ifndef __bbSlicerMeshContourSegmentation_h_INCLUDED__
+#define __bbSlicerMeshContourSegmentation_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT MeshContourSegmentation
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( MeshContourSegmentation , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputSurface , std::string );
+BBTK_DECLARE_INPUT ( ContourSeedPts , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( OutputModel , std::string );
+BBTK_DECLARE_INPUT ( evolve_its , int );
+BBTK_DECLARE_INPUT ( mesh_smooth_its , int );
+BBTK_DECLARE_INPUT ( H_smooth_its , int );
+BBTK_DECLARE_INPUT ( adj_levels , int );
+BBTK_DECLARE_INPUT ( showLS , bool );
+BBTK_DECLARE_INPUT ( rightHandMesh , bool );
+BBTK_DECLARE_INPUT ( is_test , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MeshContourSegmentation , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "MeshContourSegmentation" ) ;
+    BBTK_AUTHOR ( "Peter Karasev, pkarasev@gatech.edu, Allen Tannenbaum, tannenba@ece.gatech.edu" ) ;
+    BBTK_DESCRIPTION ( "Sparse-Field Levelset Mesh Segmentation. Given some initial points in polydata will construct a contour and evolve it to high mean-curvature areas, returning the interior region indices.Once the output surface has been loaded into Slicer, go to the Models module, Model Display pane, and set the Scalar Visibility Flag, select the LevelSetValue as the active scalar array, and pick the FreeSurfer RedGreen Scalar Color Map. The InitialCurvature and SmoothedCurvature may appear if the path finding failed.  An example calling convention from the commandline for this module:--inputScene C:/.../bin/Release/LSVTKOut1.vtk' -c '1.5,1.5,0' -c '-1.5,1.5,0' -c '-1.5,-1.5,0' -c '1.5,-1.5,0' --outputFilename 'tempOut.vtk'This gives it an initial geometry in the vtk file, four seed points in x,y,z coordinates, and where to write the output.The resulting output contains a colormap that defines interior/exterior of the surface as determined by evolving the curve into high mean curvature areas." ) ;
+    BBTK_CATEGORY ( "Segmentation.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(MeshContourSegmentation , InputSurface , "InputSurface" , std::string, "");
+BBTK_INPUT(MeshContourSegmentation , ContourSeedPts , "ContourSeedPts" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(MeshContourSegmentation , OutputModel , "OutputModel" , std::string, "");
+BBTK_INPUT(MeshContourSegmentation , evolve_its , "evolve_its" , int, "");
+BBTK_INPUT(MeshContourSegmentation , mesh_smooth_its , "mesh_smooth_its" , int, "");
+BBTK_INPUT(MeshContourSegmentation , H_smooth_its , "H_smooth_its" , int, "");
+BBTK_INPUT(MeshContourSegmentation , adj_levels , "adj_levels" , int, "");
+BBTK_INPUT(MeshContourSegmentation , showLS , "showLS" , bool, "");
+BBTK_INPUT(MeshContourSegmentation , rightHandMesh , "rightHandMesh" , bool, "");
+BBTK_INPUT(MeshContourSegmentation , is_test , "is_test" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( MeshContourSegmentation ) ;
+}
+
+#endif // __bbSlicerMeshContourSegmentation_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerModelMaker.cxx b/ModuleCall/GenSrc/bbSlicerModelMaker.cxx
new file mode 100644 (file)
index 0000000..2f7737c
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerModelMaker.cxx
@@ -0,0 +1,72 @@
+#include "bbSlicerModelMaker.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ModelMaker )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ModelMaker, bbtk::AtomicBlackBox );
+
+    void ModelMaker::Process ( ) {
+
+        // GENERATED
+
+int _argc =18;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libModelMakerLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--color"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputColorTable( ) ) ) ,"@@@@@"," --color ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--modelSceneFile"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModelSceneFile( ) ) ) ,"@@@@@"," --modelSceneFile ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-n"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputName( ) ) ) ,"@@@@@"," -n ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--generateAll"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputGenerateAll( ) ) ) ,"@@@@@"," --generateAll ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLabels( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputStartLabel( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputEndLabel( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--skipUnNamed"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSkipUnNamed( ) ) ) ,"@@@@@"," --skipUnNamed ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-j"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputJointSmoothing( ) ) ) ,"@@@@@"," -j ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--smooth"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSmooth( ) ) ) ,"@@@@@"," --smooth ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--filtertype"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFilterType( ) ) ) ,"@@@@@"," --filtertype ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--decimate"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputDecimate( ) ) ) ,"@@@@@"," --decimate ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--splitnormals"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSplitNormals( ) ) ) ,"@@@@@"," --splitnormals ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--pointnormals"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPointNormals( ) ) ) ,"@@@@@"," --pointnormals ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--pad"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPad( ) ) ) ,"@@@@@"," --pad ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--saveIntermediateModels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSaveIntermediateModels( ) ) ) ,"@@@@@"," --saveIntermediateModels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdebug( ) ) ) ,"@@@@@"," -d ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ModelMaker::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ModelMaker::bbUserSetDefaultValues ( ) {
+    }
+
+    void ModelMaker::bbUserInitializeProcessing ( ) {
+    }
+
+    void ModelMaker::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerModelMaker.h b/ModuleCall/GenSrc/bbSlicerModelMaker.h
new file mode 100644 (file)
index 0000000..05045b3
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerModelMaker.h
@@ -0,0 +1,92 @@
+#ifndef __bbSlicerModelMaker_h_INCLUDED__
+#define __bbSlicerModelMaker_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ModelMaker
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ModelMaker , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( ColorTable , std::string );
+BBTK_DECLARE_INPUT ( ModelSceneFile , std::string );
+BBTK_DECLARE_INPUT ( Name , std::string );
+BBTK_DECLARE_INPUT ( GenerateAll , bool );
+BBTK_DECLARE_INPUT ( Labels , std::vector<int> );
+BBTK_DECLARE_INPUT ( StartLabel , int );
+BBTK_DECLARE_INPUT ( EndLabel , int );
+BBTK_DECLARE_INPUT ( SkipUnNamed , bool );
+BBTK_DECLARE_INPUT ( JointSmoothing , bool );
+BBTK_DECLARE_INPUT ( Smooth , int );
+BBTK_DECLARE_INPUT ( FilterType , std::string );
+BBTK_DECLARE_INPUT ( Decimate , float );
+BBTK_DECLARE_INPUT ( SplitNormals , bool );
+BBTK_DECLARE_INPUT ( PointNormals , bool );
+BBTK_DECLARE_INPUT ( Pad , bool );
+BBTK_DECLARE_INPUT ( SaveIntermediateModels , bool );
+BBTK_DECLARE_INPUT ( debug , bool );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ModelMaker , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ModelMaker" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH, Bill Lorensen GE" ) ;
+    BBTK_DESCRIPTION ( "Create 3D surface models from segmented data. pModels are imported into Slicer under a model hierarchy node in a MRML scene. The model colors are set by the color table associated with the input volume these colours will only be visible if you load the model scene file. /ppbCreate Multiple:/b/pp If you specify a list of Labels, it will over ride any start/end label settings. /pp If you click iGenerate All/i it will over ride the list of lables and any start/end label settings. /ppbModel Maker Settings:/b/pp You can set the number of smoothing iterations, target reduction in number of polygons decimal percentage. Use 0 and 1 if you wish no smoothing nor decimation. brYou can set the flags to split normals or generate point normals in this pane as well. brYou can save a copy of the models after intermediate steps marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation; these models are not saved in the mrml file, turn off deleting temporary files first in the python window: brislicer.modules.modelmaker.cliModuleLogic.DeleteTemporaryFilesOff/i/p" ) ;
+    BBTK_CATEGORY ( "Surface Models" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ModelMaker , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(ModelMaker , ColorTable , "ColorTable" , std::string, "");
+BBTK_INPUT(ModelMaker , ModelSceneFile , "ModelSceneFile" , std::string, "");
+BBTK_INPUT(ModelMaker , Name , "Name" , std::string, "");
+BBTK_INPUT(ModelMaker , GenerateAll , "GenerateAll" , bool, "");
+BBTK_INPUT(ModelMaker , Labels , "Labels" , std::vector<int>, "");
+BBTK_INPUT(ModelMaker , StartLabel , "StartLabel" , int, "");
+BBTK_INPUT(ModelMaker , EndLabel , "EndLabel" , int, "");
+BBTK_INPUT(ModelMaker , SkipUnNamed , "SkipUnNamed" , bool, "");
+BBTK_INPUT(ModelMaker , JointSmoothing , "JointSmoothing" , bool, "");
+BBTK_INPUT(ModelMaker , Smooth , "Smooth" , int, "");
+BBTK_INPUT(ModelMaker , FilterType , "FilterType" , std::string, "");
+BBTK_INPUT(ModelMaker , Decimate , "Decimate" , float, "");
+BBTK_INPUT(ModelMaker , SplitNormals , "SplitNormals" , bool, "");
+BBTK_INPUT(ModelMaker , PointNormals , "PointNormals" , bool, "");
+BBTK_INPUT(ModelMaker , Pad , "Pad" , bool, "");
+BBTK_INPUT(ModelMaker , SaveIntermediateModels , "SaveIntermediateModels" , bool, "");
+BBTK_INPUT(ModelMaker , debug , "debug" , bool, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ModelMaker ) ;
+}
+
+#endif // __bbSlicerModelMaker_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMultiplemodelsexample.cxx b/ModuleCall/GenSrc/bbSlicerMultiplemodelsexample.cxx
new file mode 100644 (file)
index 0000000..4eb9c42
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMultiplemodelsexample.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerMultiplemodelsexample.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, Multiplemodelsexample )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( Multiplemodelsexample, bbtk::AtomicBlackBox );
+
+    void Multiplemodelsexample::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMultipleModelsExampleLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--color"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputColorTable( ) ) ) ,"@@@@@"," --color ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfModels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputNumberOfModels( ) ) ) ,"@@@@@"," --numberOfModels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--models"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModels( ) ) ) ,"@@@@@"," --models ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void Multiplemodelsexample::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void Multiplemodelsexample::bbUserSetDefaultValues ( ) {
+    }
+
+    void Multiplemodelsexample::bbUserInitializeProcessing ( ) {
+    }
+
+    void Multiplemodelsexample::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMultiplemodelsexample.h b/ModuleCall/GenSrc/bbSlicerMultiplemodelsexample.h
new file mode 100644 (file)
index 0000000..5b663ce
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMultiplemodelsexample.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerMultiplemodelsexample_h_INCLUDED__
+#define __bbSlicerMultiplemodelsexample_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT Multiplemodelsexample
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( Multiplemodelsexample , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( ColorTable , std::string );
+BBTK_DECLARE_INPUT ( NumberOfModels , int );
+BBTK_DECLARE_INPUT ( Models , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( Multiplemodelsexample , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "Multiplemodelsexample" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin" ) ;
+    BBTK_DESCRIPTION ( "Create 3D surface models from segmented data.This example exports colors and imports a set of models automatically.If specify a list of Labels, it will over ride any start/end label settings." ) ;
+    BBTK_CATEGORY ( "Developer Tools" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(Multiplemodelsexample , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(Multiplemodelsexample , ColorTable , "ColorTable" , std::string, "");
+BBTK_INPUT(Multiplemodelsexample , NumberOfModels , "NumberOfModels" , int, "");
+BBTK_INPUT(Multiplemodelsexample , Models , "Models" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( Multiplemodelsexample ) ;
+}
+
+#endif // __bbSlicerMultiplemodelsexample_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMultiplyImages.cxx b/ModuleCall/GenSrc/bbSlicerMultiplyImages.cxx
new file mode 100644 (file)
index 0000000..2e2414d
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMultiplyImages.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerMultiplyImages.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, MultiplyImages )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( MultiplyImages, bbtk::AtomicBlackBox );
+
+    void MultiplyImages::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMultiplyLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--order"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputorder( ) ) ) ,"@@@@@"," --order ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void MultiplyImages::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void MultiplyImages::bbUserSetDefaultValues ( ) {
+    }
+
+    void MultiplyImages::bbUserInitializeProcessing ( ) {
+    }
+
+    void MultiplyImages::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerMultiplyImages.h b/ModuleCall/GenSrc/bbSlicerMultiplyImages.h
new file mode 100644 (file)
index 0000000..4b41b7e
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerMultiplyImages.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerMultiplyImages_h_INCLUDED__
+#define __bbSlicerMultiplyImages_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT MultiplyImages
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( MultiplyImages , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume1 , std::string );
+BBTK_DECLARE_INPUT ( inputVolume2 , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( order , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MultiplyImages , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "MultiplyImages" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Multiplies two images. Although all image types are supported on input, only signed types are produced. The two images do not have to have the same dimensions." ) ;
+    BBTK_CATEGORY ( "Filtering.Arithmetic" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(MultiplyImages , inputVolume1 , "inputVolume1" , std::string, "");
+BBTK_INPUT(MultiplyImages , inputVolume2 , "inputVolume2" , std::string, "");
+BBTK_INPUT(MultiplyImages , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(MultiplyImages , order , "order" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( MultiplyImages ) ;
+}
+
+#endif // __bbSlicerMultiplyImages_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerN4ITKMRIBiascorrection.cxx b/ModuleCall/GenSrc/bbSlicerN4ITKMRIBiascorrection.cxx
new file mode 100644 (file)
index 0000000..5cf847e
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerN4ITKMRIBiascorrection.cxx
@@ -0,0 +1,66 @@
+#include "bbSlicerN4ITKMRIBiascorrection.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, N4ITKMRIBiascorrection )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( N4ITKMRIBiascorrection, bbtk::AtomicBlackBox );
+
+    void N4ITKMRIBiascorrection::Process ( ) {
+
+        // GENERATED
+
+int _argc =12;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libN4ITKBiasFieldCorrectionLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputimage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputImageName( ) ) ) ,"@@@@@"," --inputimage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maskimage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaskImageName( ) ) ) ,"@@@@@"," --maskimage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputimage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputImageName( ) ) ) ,"@@@@@"," --outputimage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputbiasfield"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputBiasFieldName( ) ) ) ,"@@@@@"," --outputbiasfield ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --iterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--convergencethreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputconvergenceThreshold( ) ) ) ,"@@@@@"," --convergencethreshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--meshresolution"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitialMeshResolution( ) ) ) ,"@@@@@"," --meshresolution ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--splinedistance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsplineDistance( ) ) ) ,"@@@@@"," --splinedistance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--shrinkfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputshrinkFactor( ) ) ) ,"@@@@@"," --shrinkfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--bsplineorder"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbsplineOrder( ) ) ) ,"@@@@@"," --bsplineorder ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--weightimage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputweightImageName( ) ) ) ,"@@@@@"," --weightimage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--histogramsharpening"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputhistogramSharpening( ) ) ) ,"@@@@@"," --histogramsharpening ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void N4ITKMRIBiascorrection::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void N4ITKMRIBiascorrection::bbUserSetDefaultValues ( ) {
+    }
+
+    void N4ITKMRIBiascorrection::bbUserInitializeProcessing ( ) {
+    }
+
+    void N4ITKMRIBiascorrection::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerN4ITKMRIBiascorrection.h b/ModuleCall/GenSrc/bbSlicerN4ITKMRIBiascorrection.h
new file mode 100644 (file)
index 0000000..288c385
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerN4ITKMRIBiascorrection.h
@@ -0,0 +1,80 @@
+#ifndef __bbSlicerN4ITKMRIBiascorrection_h_INCLUDED__
+#define __bbSlicerN4ITKMRIBiascorrection_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT N4ITKMRIBiascorrection
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( N4ITKMRIBiascorrection , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputImageName , std::string );
+BBTK_DECLARE_INPUT ( maskImageName , std::string );
+BBTK_DECLARE_INPUT ( outputImageName , std::string );
+BBTK_DECLARE_INPUT ( outputBiasFieldName , std::string );
+BBTK_DECLARE_INPUT ( numberOfIterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( convergenceThreshold , float );
+BBTK_DECLARE_INPUT ( initialMeshResolution , std::vector<float> );
+BBTK_DECLARE_INPUT ( splineDistance , float );
+BBTK_DECLARE_INPUT ( shrinkFactor , int );
+BBTK_DECLARE_INPUT ( bsplineOrder , int );
+BBTK_DECLARE_INPUT ( weightImageName , std::string );
+BBTK_DECLARE_INPUT ( histogramSharpening , std::vector<float> );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( N4ITKMRIBiascorrection , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "N4ITKMRIBiascorrection" ) ;
+    BBTK_AUTHOR ( "Nick Tustison algorithm and ITK implementation, Andrey Fedorov Slicer wrapping, Ron Kikinis PI" ) ;
+    BBTK_DESCRIPTION ( "Performs MRI bias correction using N4 algorithm. This module is based on the ITK filters contributed in the following publication:  Tustison N, Gee J 'N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction', The Insight Journal 2009 January-June, http://hdl.handle.net/10380/3053" ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(N4ITKMRIBiascorrection , inputImageName , "inputImageName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , maskImageName , "maskImageName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , outputImageName , "outputImageName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , outputBiasFieldName , "outputBiasFieldName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , numberOfIterations , "numberOfIterations" , std::vector<int>, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , convergenceThreshold , "convergenceThreshold" , float, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , initialMeshResolution , "initialMeshResolution" , std::vector<float>, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , splineDistance , "splineDistance" , float, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , shrinkFactor , "shrinkFactor" , int, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , bsplineOrder , "bsplineOrder" , int, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , weightImageName , "weightImageName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , histogramSharpening , "histogramSharpening" , std::vector<float>, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( N4ITKMRIBiascorrection ) ;
+}
+
+#endif // __bbSlicerN4ITKMRIBiascorrection_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerOrientImages.cxx b/ModuleCall/GenSrc/bbSlicerOrientImages.cxx
new file mode 100644 (file)
index 0000000..defb112
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerOrientImages.cxx
@@ -0,0 +1,57 @@
+#include "bbSlicerOrientImages.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, OrientImages )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( OrientImages, bbtk::AtomicBlackBox );
+
+    void OrientImages::Process ( ) {
+
+        // GENERATED
+
+int _argc =3;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libOrientImageLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-o"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputorientation( ) ) ) ,"@@@@@"," -o ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void OrientImages::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void OrientImages::bbUserSetDefaultValues ( ) {
+    }
+
+    void OrientImages::bbUserInitializeProcessing ( ) {
+    }
+
+    void OrientImages::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerOrientImages.h b/ModuleCall/GenSrc/bbSlicerOrientImages.h
new file mode 100644 (file)
index 0000000..4c6becd
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerOrientImages.h
@@ -0,0 +1,62 @@
+#ifndef __bbSlicerOrientImages_h_INCLUDED__
+#define __bbSlicerOrientImages_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT OrientImages
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( OrientImages , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume1 , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( orientation , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( OrientImages , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "OrientImages" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Orients an output volume. Rearranges the slices in a volume according to the selected orientation. The slices are not interpolated. They are just reordered and/or permuted. The resulting volume will cover the original volume. NOTE: since Slicer takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume, To see the difference, save the volume and display it with a system that either ignores the orientation of the image e.g. Paraview or displays individual images." ) ;
+    BBTK_CATEGORY ( "Converters" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(OrientImages , inputVolume1 , "inputVolume1" , std::string, "");
+BBTK_INPUT(OrientImages , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(OrientImages , orientation , "orientation" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( OrientImages ) ;
+}
+
+#endif // __bbSlicerOrientImages_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerOtsuThreshold.cxx b/ModuleCall/GenSrc/bbSlicerOtsuThreshold.cxx
new file mode 100644 (file)
index 0000000..1dfb42b
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerOtsuThreshold.cxx
@@ -0,0 +1,59 @@
+#include "bbSlicerOtsuThreshold.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, OtsuThreshold )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( OtsuThreshold, bbtk::AtomicBlackBox );
+
+    void OtsuThreshold::Process ( ) {
+
+        // GENERATED
+
+int _argc =5;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libOtsuThresholdImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--insideValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinsideValue( ) ) ) ,"@@@@@"," --insideValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outsideValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutsideValue( ) ) ) ,"@@@@@"," --outsideValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfBins( ) ) ) ,"@@@@@"," --numberOfBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void OtsuThreshold::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void OtsuThreshold::bbUserSetDefaultValues ( ) {
+    }
+
+    void OtsuThreshold::bbUserInitializeProcessing ( ) {
+    }
+
+    void OtsuThreshold::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerOtsuThreshold.h b/ModuleCall/GenSrc/bbSlicerOtsuThreshold.h
new file mode 100644 (file)
index 0000000..d179f2d
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerOtsuThreshold.h
@@ -0,0 +1,66 @@
+#ifndef __bbSlicerOtsuThreshold_h_INCLUDED__
+#define __bbSlicerOtsuThreshold_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT OtsuThreshold
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( OtsuThreshold , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( insideValue , int );
+BBTK_DECLARE_INPUT ( outsideValue , int );
+BBTK_DECLARE_INPUT ( numberOfBins , int );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( OtsuThreshold , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "OtsuThreshold" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "This filter creates a binary thresholded image that separates an image into foreground and background components. The filter calculates the optimum threshold separating those two classes so that their combined spread intra-class variance is minimal see http://en.wikipedia.org/wiki/Otsu%27s_method.  Then the filter applies that threshold to the input image using the itkBinaryThresholdImageFilter. The numberOfHistogram bins can be set for the Otsu Calculator. The insideValue and outsideValue can be set for the BinaryThresholdImageFilter.  The filter produces a labeled volume.The original reference is: N.Otsu, ‘‘A threshold selection method from gray level histograms,’’ IEEE Trans.Syst.ManCybern.SMC-9,62–66 1979." ) ;
+    BBTK_CATEGORY ( "Legacy.Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(OtsuThreshold , insideValue , "insideValue" , int, "");
+BBTK_INPUT(OtsuThreshold , outsideValue , "outsideValue" , int, "");
+BBTK_INPUT(OtsuThreshold , numberOfBins , "numberOfBins" , int, "");
+BBTK_INPUT(OtsuThreshold , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(OtsuThreshold , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( OtsuThreshold ) ;
+}
+
+#endif // __bbSlicerOtsuThreshold_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerOtsuThresholdSegmentation.cxx b/ModuleCall/GenSrc/bbSlicerOtsuThresholdSegmentation.cxx
new file mode 100644 (file)
index 0000000..7be627b
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerOtsuThresholdSegmentation.cxx
@@ -0,0 +1,60 @@
+#include "bbSlicerOtsuThresholdSegmentation.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, OtsuThresholdSegmentation )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( OtsuThresholdSegmentation, bbtk::AtomicBlackBox );
+
+    void OtsuThresholdSegmentation::Process ( ) {
+
+        // GENERATED
+
+int _argc =6;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libOtsuThresholdSegmentationLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--brightObjects"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbrightObjects( ) ) ) ,"@@@@@"," --brightObjects ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfBins( ) ) ) ,"@@@@@"," --numberOfBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--faceConnected"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfaceConnected( ) ) ) ,"@@@@@"," --faceConnected ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumObjectSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumObjectSize( ) ) ) ,"@@@@@"," --minimumObjectSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void OtsuThresholdSegmentation::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void OtsuThresholdSegmentation::bbUserSetDefaultValues ( ) {
+    }
+
+    void OtsuThresholdSegmentation::bbUserInitializeProcessing ( ) {
+    }
+
+    void OtsuThresholdSegmentation::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerOtsuThresholdSegmentation.h b/ModuleCall/GenSrc/bbSlicerOtsuThresholdSegmentation.h
new file mode 100644 (file)
index 0000000..f96db1b
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerOtsuThresholdSegmentation.h
@@ -0,0 +1,68 @@
+#ifndef __bbSlicerOtsuThresholdSegmentation_h_INCLUDED__
+#define __bbSlicerOtsuThresholdSegmentation_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT OtsuThresholdSegmentation
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( OtsuThresholdSegmentation , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( brightObjects , bool );
+BBTK_DECLARE_INPUT ( numberOfBins , int );
+BBTK_DECLARE_INPUT ( faceConnected , bool );
+BBTK_DECLARE_INPUT ( minimumObjectSize , int );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( OtsuThresholdSegmentation , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "OtsuThresholdSegmentation" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "This filter creates a labeled image from a grayscale image. First, it calculates an optimal threshold that separates the image into foreground and background. This threshold separates those two classes so that their intra-class variance is minimal see http://en.wikipedia.org/wiki/Otsu%27s_method. Then the filter runs a connected component algorithm to generate unique labels for each connected region of the foreground. Finally, the resulting image is relabeled to provide consecutive numbering." ) ;
+    BBTK_CATEGORY ( "Legacy.Segmentation" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(OtsuThresholdSegmentation , brightObjects , "brightObjects" , bool, "");
+BBTK_INPUT(OtsuThresholdSegmentation , numberOfBins , "numberOfBins" , int, "");
+BBTK_INPUT(OtsuThresholdSegmentation , faceConnected , "faceConnected" , bool, "");
+BBTK_INPUT(OtsuThresholdSegmentation , minimumObjectSize , "minimumObjectSize" , int, "");
+BBTK_INPUT(OtsuThresholdSegmentation , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(OtsuThresholdSegmentation , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( OtsuThresholdSegmentation ) ;
+}
+
+#endif // __bbSlicerOtsuThresholdSegmentation_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerPolyDataToLabelMap.cxx b/ModuleCall/GenSrc/bbSlicerPolyDataToLabelMap.cxx
new file mode 100644 (file)
index 0000000..bc2f2aa
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerPolyDataToLabelMap.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerPolyDataToLabelMap.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, PolyDataToLabelMap )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( PolyDataToLabelMap, bbtk::AtomicBlackBox );
+
+    void PolyDataToLabelMap::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libPolyDataToLabelmapLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--distance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsampleDistance( ) ) ) ,"@@@@@"," --distance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsurface( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void PolyDataToLabelMap::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void PolyDataToLabelMap::bbUserSetDefaultValues ( ) {
+    }
+
+    void PolyDataToLabelMap::bbUserInitializeProcessing ( ) {
+    }
+
+    void PolyDataToLabelMap::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerPolyDataToLabelMap.h b/ModuleCall/GenSrc/bbSlicerPolyDataToLabelMap.h
new file mode 100644 (file)
index 0000000..b35d201
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerPolyDataToLabelMap.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerPolyDataToLabelMap_h_INCLUDED__
+#define __bbSlicerPolyDataToLabelMap_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT PolyDataToLabelMap
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( PolyDataToLabelMap , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( sampleDistance , float );
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( surface , std::string );
+BBTK_DECLARE_INPUT ( OutputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( PolyDataToLabelMap , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "PolyDataToLabelMap" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin BWH, Xiaodong Tao, GE" ) ;
+    BBTK_DESCRIPTION ( "Intersects an input model with an reference volume and produces an output label map." ) ;
+    BBTK_CATEGORY ( "Surface Models" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(PolyDataToLabelMap , sampleDistance , "sampleDistance" , float, "");
+BBTK_INPUT(PolyDataToLabelMap , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(PolyDataToLabelMap , surface , "surface" , std::string, "");
+BBTK_INPUT(PolyDataToLabelMap , OutputVolume , "OutputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( PolyDataToLabelMap ) ;
+}
+
+#endif // __bbSlicerPolyDataToLabelMap_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerResampleDTIVolume.cxx b/ModuleCall/GenSrc/bbSlicerResampleDTIVolume.cxx
new file mode 100644 (file)
index 0000000..1584f25
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerResampleDTIVolume.cxx
@@ -0,0 +1,80 @@
+#include "bbSlicerResampleDTIVolume.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ResampleDTIVolume )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ResampleDTIVolume, bbtk::AtomicBlackBox );
+
+    void ResampleDTIVolume::Process ( ) {
+
+        // GENERATED
+
+int _argc =26;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libResampleDTILib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-R"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreferenceVolume( ) ) ) ,"@@@@@"," -R ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformationFile( ) ) ) ,"@@@@@"," -f ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-H"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdeffield( ) ) ) ,"@@@@@"," -H ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--hfieldtype"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtypeOfField( ) ) ) ,"@@@@@"," --hfieldtype ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationType( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--correction"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcorrection( ) ) ) ,"@@@@@"," --correction ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-T"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputppd( ) ) ) ,"@@@@@"," -T ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transform_order"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformsOrder( ) ) ) ,"@@@@@"," --transform_order ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--notbulk"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnotbulk( ) ) ) ,"@@@@@"," --notbulk ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--spaceChange"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputspace( ) ) ) ,"@@@@@"," --spaceChange ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-r"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrotationPoint( ) ) ) ,"@@@@@"," -r ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-c"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcenteredTransform( ) ) ) ,"@@@@@"," -c ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--image_center"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputimageCenter( ) ) ) ,"@@@@@"," --image_center ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinverseITKTransformation( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputImageSpacing( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-z"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputImageSize( ) ) ) ,"@@@@@"," -z ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-O"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputImageOrigin( ) ) ) ,"@@@@@"," -O ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdirectionMatrix( ) ) ) ,"@@@@@"," -d ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-n"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThread( ) ) ) ,"@@@@@"," -n ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-p"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdefaultPixelValue( ) ) ) ,"@@@@@"," -p ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-W"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputwindowFunction( ) ) ) ,"@@@@@"," -W ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-o"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsplineOrder( ) ) ) ,"@@@@@"," -o ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-m"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformMatrix( ) ) ) ,"@@@@@"," -m ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformType( ) ) ) ,"@@@@@"," -t ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ResampleDTIVolume::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ResampleDTIVolume::bbUserSetDefaultValues ( ) {
+    }
+
+    void ResampleDTIVolume::bbUserInitializeProcessing ( ) {
+    }
+
+    void ResampleDTIVolume::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerResampleDTIVolume.h b/ModuleCall/GenSrc/bbSlicerResampleDTIVolume.h
new file mode 100644 (file)
index 0000000..0c7f48f
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerResampleDTIVolume.h
@@ -0,0 +1,108 @@
+#ifndef __bbSlicerResampleDTIVolume_h_INCLUDED__
+#define __bbSlicerResampleDTIVolume_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ResampleDTIVolume
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ResampleDTIVolume , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( referenceVolume , std::string );
+BBTK_DECLARE_INPUT ( transformationFile , std::string );
+BBTK_DECLARE_INPUT ( deffield , std::string );
+BBTK_DECLARE_INPUT ( typeOfField , std::string );
+BBTK_DECLARE_INPUT ( interpolationType , std::string );
+BBTK_DECLARE_INPUT ( correction , std::string );
+BBTK_DECLARE_INPUT ( ppd , std::string );
+BBTK_DECLARE_INPUT ( transformsOrder , std::string );
+BBTK_DECLARE_INPUT ( notbulk , bool );
+BBTK_DECLARE_INPUT ( space , bool );
+BBTK_DECLARE_INPUT ( rotationPoint , std::vector<float> );
+BBTK_DECLARE_INPUT ( centeredTransform , bool );
+BBTK_DECLARE_INPUT ( imageCenter , std::string );
+BBTK_DECLARE_INPUT ( inverseITKTransformation , bool );
+BBTK_DECLARE_INPUT ( outputImageSpacing , std::vector<double> );
+BBTK_DECLARE_INPUT ( outputImageSize , std::vector<double> );
+BBTK_DECLARE_INPUT ( outputImageOrigin , std::vector<float> );
+BBTK_DECLARE_INPUT ( directionMatrix , std::vector<double> );
+BBTK_DECLARE_INPUT ( numberOfThread , int );
+BBTK_DECLARE_INPUT ( defaultPixelValue , double );
+BBTK_DECLARE_INPUT ( windowFunction , std::string );
+BBTK_DECLARE_INPUT ( splineOrder , int );
+BBTK_DECLARE_INPUT ( transformMatrix , std::vector<double> );
+BBTK_DECLARE_INPUT ( transformType , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ResampleDTIVolume , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ResampleDTIVolume" ) ;
+    BBTK_AUTHOR ( "Francois Budin" ) ;
+    BBTK_DESCRIPTION ( "Resampling an image is a very important task in image analysis. It is especially important in the frame of image registration. This module implements DT image resampling through the use of itk Transforms. The resampling is controlled by the Output Spacing. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions." ) ;
+    BBTK_CATEGORY ( "Diffusion.Utilities" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ResampleDTIVolume , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , referenceVolume , "referenceVolume" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , transformationFile , "transformationFile" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , deffield , "deffield" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , typeOfField , "typeOfField" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , interpolationType , "interpolationType" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , correction , "correction" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , ppd , "ppd" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , transformsOrder , "transformsOrder" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , notbulk , "notbulk" , bool, "");
+BBTK_INPUT(ResampleDTIVolume , space , "space" , bool, "");
+BBTK_INPUT(ResampleDTIVolume , rotationPoint , "rotationPoint" , std::vector<float>, "");
+BBTK_INPUT(ResampleDTIVolume , centeredTransform , "centeredTransform" , bool, "");
+BBTK_INPUT(ResampleDTIVolume , imageCenter , "imageCenter" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , inverseITKTransformation , "inverseITKTransformation" , bool, "");
+BBTK_INPUT(ResampleDTIVolume , outputImageSpacing , "outputImageSpacing" , std::vector<double>, "");
+BBTK_INPUT(ResampleDTIVolume , outputImageSize , "outputImageSize" , std::vector<double>, "");
+BBTK_INPUT(ResampleDTIVolume , outputImageOrigin , "outputImageOrigin" , std::vector<float>, "");
+BBTK_INPUT(ResampleDTIVolume , directionMatrix , "directionMatrix" , std::vector<double>, "");
+BBTK_INPUT(ResampleDTIVolume , numberOfThread , "numberOfThread" , int, "");
+BBTK_INPUT(ResampleDTIVolume , defaultPixelValue , "defaultPixelValue" , double, "");
+BBTK_INPUT(ResampleDTIVolume , windowFunction , "windowFunction" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , splineOrder , "splineOrder" , int, "");
+BBTK_INPUT(ResampleDTIVolume , transformMatrix , "transformMatrix" , std::vector<double>, "");
+BBTK_INPUT(ResampleDTIVolume , transformType , "transformType" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ResampleDTIVolume ) ;
+}
+
+#endif // __bbSlicerResampleDTIVolume_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerResampleImageBRAINS.cxx b/ModuleCall/GenSrc/bbSlicerResampleImageBRAINS.cxx
new file mode 100644 (file)
index 0000000..40b2238
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerResampleImageBRAINS.cxx
@@ -0,0 +1,65 @@
+#include "bbSlicerResampleImageBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ResampleImageBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ResampleImageBRAINS, bbtk::AtomicBlackBox );
+
+    void ResampleImageBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =11;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBRAINSResampleLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@"," --inputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--referenceVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreferenceVolume( ) ) ) ,"@@@@@"," --referenceVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," --outputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--pixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpixelType( ) ) ) ,"@@@@@"," --pixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--deformationVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdeformationVolume( ) ) ) ,"@@@@@"," --deformationVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--warpTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputwarpTransform( ) ) ) ,"@@@@@"," --warpTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolationMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationMode( ) ) ) ,"@@@@@"," --interpolationMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inverseTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinverseTransform( ) ) ) ,"@@@@@"," --inverseTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--defaultValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdefaultValue( ) ) ) ,"@@@@@"," --defaultValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--gridSpacing"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgridSpacing( ) ) ) ,"@@@@@"," --gridSpacing ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ResampleImageBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ResampleImageBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void ResampleImageBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void ResampleImageBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerResampleImageBRAINS.h b/ModuleCall/GenSrc/bbSlicerResampleImageBRAINS.h
new file mode 100644 (file)
index 0000000..536d0a8
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerResampleImageBRAINS.h
@@ -0,0 +1,78 @@
+#ifndef __bbSlicerResampleImageBRAINS_h_INCLUDED__
+#define __bbSlicerResampleImageBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ResampleImageBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ResampleImageBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( referenceVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( pixelType , std::string );
+BBTK_DECLARE_INPUT ( deformationVolume , std::string );
+BBTK_DECLARE_INPUT ( warpTransform , std::string );
+BBTK_DECLARE_INPUT ( interpolationMode , std::string );
+BBTK_DECLARE_INPUT ( inverseTransform , bool );
+BBTK_DECLARE_INPUT ( defaultValue , float );
+BBTK_DECLARE_INPUT ( gridSpacing , std::vector<int> );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ResampleImageBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ResampleImageBRAINS" ) ;
+    BBTK_AUTHOR ( "This tool was developed by Vincent Magnotta, Greg Harris, and Hans Johnson." ) ;
+    BBTK_DESCRIPTION ( "This program resamples an image image using a deformation field or a transform BSpline, Affine, Rigid, etc.." ) ;
+    BBTK_CATEGORY ( "Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ResampleImageBRAINS , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , referenceVolume , "referenceVolume" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , pixelType , "pixelType" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , deformationVolume , "deformationVolume" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , warpTransform , "warpTransform" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , interpolationMode , "interpolationMode" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , inverseTransform , "inverseTransform" , bool, "");
+BBTK_INPUT(ResampleImageBRAINS , defaultValue , "defaultValue" , float, "");
+BBTK_INPUT(ResampleImageBRAINS , gridSpacing , "gridSpacing" , std::vector<int>, "");
+BBTK_INPUT(ResampleImageBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ResampleImageBRAINS ) ;
+}
+
+#endif // __bbSlicerResampleImageBRAINS_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerResampleScalarVolume.cxx b/ModuleCall/GenSrc/bbSlicerResampleScalarVolume.cxx
new file mode 100644 (file)
index 0000000..69a8256
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerResampleScalarVolume.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerResampleScalarVolume.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ResampleScalarVolume )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ResampleScalarVolume, bbtk::AtomicBlackBox );
+
+    void ResampleScalarVolume::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libResampleVolumeLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputPixelSpacing( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationType( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ResampleScalarVolume::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ResampleScalarVolume::bbUserSetDefaultValues ( ) {
+    }
+
+    void ResampleScalarVolume::bbUserInitializeProcessing ( ) {
+    }
+
+    void ResampleScalarVolume::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerResampleScalarVolume.h b/ModuleCall/GenSrc/bbSlicerResampleScalarVolume.h
new file mode 100644 (file)
index 0000000..a7ba623
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerResampleScalarVolume.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerResampleScalarVolume_h_INCLUDED__
+#define __bbSlicerResampleScalarVolume_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ResampleScalarVolume
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ResampleScalarVolume , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( outputPixelSpacing , std::vector<float> );
+BBTK_DECLARE_INPUT ( interpolationType , std::string );
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( OutputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ResampleScalarVolume , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ResampleScalarVolume" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Resampling an image is an important task in image analysis. It is especially important in the frame of image registration. This module implements image resampling through the use of itk Transforms. This module uses an Identity Transform. The resampling is controlled by the Output Spacing. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions. Several interpolators are available: linear, nearest neighbor, bspline and five flavors of sinc. The sinc interpolators, although more precise, are much slower than the linear and nearest neighbor interpolator. To resample label volumnes, nearest neighbor interpolation should be used exclusively." ) ;
+    BBTK_CATEGORY ( "Legacy.Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ResampleScalarVolume , outputPixelSpacing , "outputPixelSpacing" , std::vector<float>, "");
+BBTK_INPUT(ResampleScalarVolume , interpolationType , "interpolationType" , std::string, "");
+BBTK_INPUT(ResampleScalarVolume , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(ResampleScalarVolume , OutputVolume , "OutputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ResampleScalarVolume ) ;
+}
+
+#endif // __bbSlicerResampleScalarVolume_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerRicianLMMSEImageFilter.cxx b/ModuleCall/GenSrc/bbSlicerRicianLMMSEImageFilter.cxx
new file mode 100644 (file)
index 0000000..0635dd4
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerRicianLMMSEImageFilter.cxx
@@ -0,0 +1,65 @@
+#include "bbSlicerRicianLMMSEImageFilter.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, RicianLMMSEImageFilter )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( RicianLMMSEImageFilter, bbtk::AtomicBlackBox );
+
+    void RicianLMMSEImageFilter::Process ( ) {
+
+        // GENERATED
+
+int _argc =11;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libdwiNoiseFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iter"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiIterations( ) ) ) ,"@@@@@"," --iter ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--re"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusEstimation( ) ) ) ,"@@@@@"," --re ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rf"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusFiltering( ) ) ) ,"@@@@@"," --rf ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--mnvf"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiMinimumNumberOfUsedVoxelsF( ) ) ) ,"@@@@@"," --mnvf ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--mnve"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiMinimumNumberOfUsedVoxelsE( ) ) ) ,"@@@@@"," --mnve ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minnstd"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdMinSTD( ) ) ) ,"@@@@@"," --minnstd ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxnstd"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdMaxSTD( ) ) ) ,"@@@@@"," --maxnstd ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--hrf"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdResFact( ) ) ) ,"@@@@@"," --hrf ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--uav"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbUseAbsoluteValue( ) ) ) ,"@@@@@"," --uav ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void RicianLMMSEImageFilter::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void RicianLMMSEImageFilter::bbUserSetDefaultValues ( ) {
+    }
+
+    void RicianLMMSEImageFilter::bbUserInitializeProcessing ( ) {
+    }
+
+    void RicianLMMSEImageFilter::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerRicianLMMSEImageFilter.h b/ModuleCall/GenSrc/bbSlicerRicianLMMSEImageFilter.h
new file mode 100644 (file)
index 0000000..b734698
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerRicianLMMSEImageFilter.h
@@ -0,0 +1,78 @@
+#ifndef __bbSlicerRicianLMMSEImageFilter_h_INCLUDED__
+#define __bbSlicerRicianLMMSEImageFilter_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT RicianLMMSEImageFilter
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( RicianLMMSEImageFilter , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( iIterations , int );
+BBTK_DECLARE_INPUT ( iRadiusEstimation , std::vector<int> );
+BBTK_DECLARE_INPUT ( iRadiusFiltering , std::vector<int> );
+BBTK_DECLARE_INPUT ( iMinimumNumberOfUsedVoxelsF , int );
+BBTK_DECLARE_INPUT ( iMinimumNumberOfUsedVoxelsE , int );
+BBTK_DECLARE_INPUT ( dMinSTD , int );
+BBTK_DECLARE_INPUT ( dMaxSTD , int );
+BBTK_DECLARE_INPUT ( dResFact , double );
+BBTK_DECLARE_INPUT ( bUseAbsoluteValue , bool );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( RicianLMMSEImageFilter , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "RicianLMMSEImageFilter" ) ;
+    BBTK_AUTHOR ( "Antonio Tristan Vega, Santiago Aja Fernandez and Marc Niethammer. Partially founded by grant number TEC2007-67073/TCM from the Comision Interministerial de Ciencia y Tecnologia Spain." ) ;
+    BBTK_DESCRIPTION ( "This module reduces noise or unwanted detail on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. Images corresponding to each gradient direction, including baseline, are processed individually. The noise parameter is automatically estimated noise estimation improved but slower.Note that this is a general purpose filter for MRi images. The module jointLMMSE has been specifically designed for DWI volumes and shows a better performance, so its use is recommended instead.A complete description of the algorithm in this module can be found in:S. Aja-Fernandez, M. Niethammer, M. Kubicki, M. Shenton, and C.-F. Westin. Restoration of DWI data using a Rician LMMSE estimator. IEEE Transactions on Medical Imaging, 2710: pp. 1389-1403, Oct. 2008." ) ;
+    BBTK_CATEGORY ( "Diffusion.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(RicianLMMSEImageFilter , iIterations , "iIterations" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , iRadiusEstimation , "iRadiusEstimation" , std::vector<int>, "");
+BBTK_INPUT(RicianLMMSEImageFilter , iRadiusFiltering , "iRadiusFiltering" , std::vector<int>, "");
+BBTK_INPUT(RicianLMMSEImageFilter , iMinimumNumberOfUsedVoxelsF , "iMinimumNumberOfUsedVoxelsF" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , iMinimumNumberOfUsedVoxelsE , "iMinimumNumberOfUsedVoxelsE" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , dMinSTD , "dMinSTD" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , dMaxSTD , "dMaxSTD" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , dResFact , "dResFact" , double, "");
+BBTK_INPUT(RicianLMMSEImageFilter , bUseAbsoluteValue , "bUseAbsoluteValue" , bool, "");
+BBTK_INPUT(RicianLMMSEImageFilter , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(RicianLMMSEImageFilter , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( RicianLMMSEImageFilter ) ;
+}
+
+#endif // __bbSlicerRicianLMMSEImageFilter_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerRobustMultiresolutionAffineRegistration.cxx b/ModuleCall/GenSrc/bbSlicerRobustMultiresolutionAffineRegistration.cxx
new file mode 100644 (file)
index 0000000..eec8b2d
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerRobustMultiresolutionAffineRegistration.cxx
@@ -0,0 +1,65 @@
+#include "bbSlicerRobustMultiresolutionAffineRegistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, RobustMultiresolutionAffineRegistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( RobustMultiresolutionAffineRegistration, bbtk::AtomicBlackBox );
+
+    void RobustMultiresolutionAffineRegistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =11;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRegisterImagesMultiResModule.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImage( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingImage( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputresampledImage( ) ) ) ,"@@@@@"," --resampledImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--saveTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputTransform( ) ) ) ,"@@@@@"," --saveTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedImageMask"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImageMask( ) ) ) ,"@@@@@"," --fixedImageMask ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedImageROI"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImageROI( ) ) ) ,"@@@@@"," --fixedImageROI ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumIterations( ) ) ) ,"@@@@@"," --numIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numLineIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumLineIterations( ) ) ) ,"@@@@@"," --numLineIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--stepSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstepSize( ) ) ) ,"@@@@@"," --stepSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--stepTolerance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstepTolerance( ) ) ) ,"@@@@@"," --stepTolerance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--metricTolerance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmetricTolerance( ) ) ) ,"@@@@@"," --metricTolerance ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void RobustMultiresolutionAffineRegistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void RobustMultiresolutionAffineRegistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void RobustMultiresolutionAffineRegistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void RobustMultiresolutionAffineRegistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerRobustMultiresolutionAffineRegistration.h b/ModuleCall/GenSrc/bbSlicerRobustMultiresolutionAffineRegistration.h
new file mode 100644 (file)
index 0000000..e71228a
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerRobustMultiresolutionAffineRegistration.h
@@ -0,0 +1,78 @@
+#ifndef __bbSlicerRobustMultiresolutionAffineRegistration_h_INCLUDED__
+#define __bbSlicerRobustMultiresolutionAffineRegistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT RobustMultiresolutionAffineRegistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( RobustMultiresolutionAffineRegistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( fixedImage , std::string );
+BBTK_DECLARE_INPUT ( movingImage , std::string );
+BBTK_DECLARE_INPUT ( resampledImage , std::string );
+BBTK_DECLARE_INPUT ( outputTransform , std::string );
+BBTK_DECLARE_INPUT ( fixedImageMask , std::string );
+BBTK_DECLARE_INPUT ( fixedImageROI , std::vector<float> );
+BBTK_DECLARE_INPUT ( numIterations , int );
+BBTK_DECLARE_INPUT ( numLineIterations , int );
+BBTK_DECLARE_INPUT ( stepSize , float );
+BBTK_DECLARE_INPUT ( stepTolerance , float );
+BBTK_DECLARE_INPUT ( metricTolerance , float );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( RobustMultiresolutionAffineRegistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "RobustMultiresolutionAffineRegistration" ) ;
+    BBTK_AUTHOR ( "Casey B Goodlett" ) ;
+    BBTK_DESCRIPTION ( "Provides affine registration using multiple resolution levels and decomposed affine transforms." ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , fixedImage , "fixedImage" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , movingImage , "movingImage" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , resampledImage , "resampledImage" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , outputTransform , "outputTransform" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , fixedImageMask , "fixedImageMask" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , fixedImageROI , "fixedImageROI" , std::vector<float>, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , numIterations , "numIterations" , int, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , numLineIterations , "numLineIterations" , int, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , stepSize , "stepSize" , float, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , stepTolerance , "stepTolerance" , float, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , metricTolerance , "metricTolerance" , float, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( RobustMultiresolutionAffineRegistration ) ;
+}
+
+#endif // __bbSlicerRobustMultiresolutionAffineRegistration_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerRobustStatisticsSegmentation.cxx b/ModuleCall/GenSrc/bbSlicerRobustStatisticsSegmentation.cxx
new file mode 100644 (file)
index 0000000..8d0ea03
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerRobustStatisticsSegmentation.cxx
@@ -0,0 +1,62 @@
+#include "bbSlicerRobustStatisticsSegmentation.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, RobustStatisticsSegmentation )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( RobustStatisticsSegmentation, bbtk::AtomicBlackBox );
+
+    void RobustStatisticsSegmentation::Process ( ) {
+
+        // GENERATED
+
+int _argc =8;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRobustStatSegmenterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedVolume( ) ) ) ,"@@@@@"," -v ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--intensityHomogeneity"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputintensityHomogeneity( ) ) ) ,"@@@@@"," --intensityHomogeneity ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-c"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcurvatureWeight( ) ) ) ,"@@@@@"," -c ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--labelValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlabelValue( ) ) ) ,"@@@@@"," --labelValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxRunningTime"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxRunningTime( ) ) ) ,"@@@@@"," --maxRunningTime ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoriginalImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlabelImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsegmentedImageFileName( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void RobustStatisticsSegmentation::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void RobustStatisticsSegmentation::bbUserSetDefaultValues ( ) {
+    }
+
+    void RobustStatisticsSegmentation::bbUserInitializeProcessing ( ) {
+    }
+
+    void RobustStatisticsSegmentation::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerRobustStatisticsSegmentation.h b/ModuleCall/GenSrc/bbSlicerRobustStatisticsSegmentation.h
new file mode 100644 (file)
index 0000000..404a527
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerRobustStatisticsSegmentation.h
@@ -0,0 +1,72 @@
+#ifndef __bbSlicerRobustStatisticsSegmentation_h_INCLUDED__
+#define __bbSlicerRobustStatisticsSegmentation_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT RobustStatisticsSegmentation
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( RobustStatisticsSegmentation , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( expectedVolume , double );
+BBTK_DECLARE_INPUT ( intensityHomogeneity , double );
+BBTK_DECLARE_INPUT ( curvatureWeight , double );
+BBTK_DECLARE_INPUT ( labelValue , int );
+BBTK_DECLARE_INPUT ( maxRunningTime , double );
+BBTK_DECLARE_INPUT ( originalImageFileName , std::string );
+BBTK_DECLARE_INPUT ( labelImageFileName , std::string );
+BBTK_DECLARE_INPUT ( segmentedImageFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( RobustStatisticsSegmentation , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "RobustStatisticsSegmentation" ) ;
+    BBTK_AUTHOR ( "Yi Gao, Allen Tannenbaum, Ron Kikinis" ) ;
+    BBTK_DESCRIPTION ( "Active contour segmentation using robust statistic." ) ;
+    BBTK_CATEGORY ( "Segmentation.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(RobustStatisticsSegmentation , expectedVolume , "expectedVolume" , double, "");
+BBTK_INPUT(RobustStatisticsSegmentation , intensityHomogeneity , "intensityHomogeneity" , double, "");
+BBTK_INPUT(RobustStatisticsSegmentation , curvatureWeight , "curvatureWeight" , double, "");
+BBTK_INPUT(RobustStatisticsSegmentation , labelValue , "labelValue" , int, "");
+BBTK_INPUT(RobustStatisticsSegmentation , maxRunningTime , "maxRunningTime" , double, "");
+BBTK_INPUT(RobustStatisticsSegmentation , originalImageFileName , "originalImageFileName" , std::string, "");
+BBTK_INPUT(RobustStatisticsSegmentation , labelImageFileName , "labelImageFileName" , std::string, "");
+BBTK_INPUT(RobustStatisticsSegmentation , segmentedImageFileName , "segmentedImageFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( RobustStatisticsSegmentation ) ;
+}
+
+#endif // __bbSlicerRobustStatisticsSegmentation_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerSimpleIOTest.cxx b/ModuleCall/GenSrc/bbSlicerSimpleIOTest.cxx
new file mode 100644 (file)
index 0000000..ff6badd
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerSimpleIOTest.cxx
@@ -0,0 +1,56 @@
+#include "bbSlicerSimpleIOTest.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, SimpleIOTest )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( SimpleIOTest, bbtk::AtomicBlackBox );
+
+    void SimpleIOTest::Process ( ) {
+
+        // GENERATED
+
+int _argc =2;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libDiffusionTensorTestLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void SimpleIOTest::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void SimpleIOTest::bbUserSetDefaultValues ( ) {
+    }
+
+    void SimpleIOTest::bbUserInitializeProcessing ( ) {
+    }
+
+    void SimpleIOTest::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerSimpleIOTest.h b/ModuleCall/GenSrc/bbSlicerSimpleIOTest.h
new file mode 100644 (file)
index 0000000..d0d353a
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerSimpleIOTest.h
@@ -0,0 +1,60 @@
+#ifndef __bbSlicerSimpleIOTest_h_INCLUDED__
+#define __bbSlicerSimpleIOTest_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT SimpleIOTest
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( SimpleIOTest , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( SimpleIOTest , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "SimpleIOTest" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Simple test of tensor IO" ) ;
+    BBTK_CATEGORY ( "Legacy.Work in Progress.Diffusion Tensor.Test" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(SimpleIOTest , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(SimpleIOTest , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( SimpleIOTest ) ;
+}
+
+#endif // __bbSlicerSimpleIOTest_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerSimpleregiongrowing.cxx b/ModuleCall/GenSrc/bbSlicerSimpleregiongrowing.cxx
new file mode 100644 (file)
index 0000000..0c272a2
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerSimpleregiongrowing.cxx
@@ -0,0 +1,63 @@
+#include "bbSlicerSimpleregiongrowing.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, Simpleregiongrowing )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( Simpleregiongrowing, bbtk::AtomicBlackBox );
+
+    void Simpleregiongrowing::Process ( ) {
+
+        // GENERATED
+
+int _argc =9;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libConfidenceConnectedLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--smoothingIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothingIterations( ) ) ) ,"@@@@@"," --smoothingIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--timestep"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtimestep( ) ) ) ,"@@@@@"," --timestep ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiterations( ) ) ) ,"@@@@@"," --iterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--multiplier"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmultiplier( ) ) ) ,"@@@@@"," --multiplier ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--neighborhood"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputneighborhood( ) ) ) ,"@@@@@"," --neighborhood ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--labelvalue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlabelvalue( ) ) ) ,"@@@@@"," --labelvalue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seed"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseed( ) ) ) ,"@@@@@"," --seed ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void Simpleregiongrowing::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void Simpleregiongrowing::bbUserSetDefaultValues ( ) {
+    }
+
+    void Simpleregiongrowing::bbUserInitializeProcessing ( ) {
+    }
+
+    void Simpleregiongrowing::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerSimpleregiongrowing.h b/ModuleCall/GenSrc/bbSlicerSimpleregiongrowing.h
new file mode 100644 (file)
index 0000000..ba02e16
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerSimpleregiongrowing.h
@@ -0,0 +1,74 @@
+#ifndef __bbSlicerSimpleregiongrowing_h_INCLUDED__
+#define __bbSlicerSimpleregiongrowing_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT Simpleregiongrowing
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( Simpleregiongrowing , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( smoothingIterations , int );
+BBTK_DECLARE_INPUT ( timestep , double );
+BBTK_DECLARE_INPUT ( iterations , int );
+BBTK_DECLARE_INPUT ( multiplier , double );
+BBTK_DECLARE_INPUT ( neighborhood , int );
+BBTK_DECLARE_INPUT ( labelvalue , int );
+BBTK_DECLARE_INPUT ( seed , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( Simpleregiongrowing , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "Simpleregiongrowing" ) ;
+    BBTK_AUTHOR ( "Jim Miller" ) ;
+    BBTK_DESCRIPTION ( "A simple region growing segmentation algorithm based on intensity statistics. To create a list of fiducials Seeds for this algorithm, click on the tool bar icon of an arrow pointing to a starburst fiducial to enter the 'place a new object mode' and then use the fiducials module. This module uses the Slicer Command Line Interface CLI and the ITK filters CurvatureFlowImageFilter and ConfidenceConnectedImageFilter." ) ;
+    BBTK_CATEGORY ( "Segmentation" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(Simpleregiongrowing , smoothingIterations , "smoothingIterations" , int, "");
+BBTK_INPUT(Simpleregiongrowing , timestep , "timestep" , double, "");
+BBTK_INPUT(Simpleregiongrowing , iterations , "iterations" , int, "");
+BBTK_INPUT(Simpleregiongrowing , multiplier , "multiplier" , double, "");
+BBTK_INPUT(Simpleregiongrowing , neighborhood , "neighborhood" , int, "");
+BBTK_INPUT(Simpleregiongrowing , labelvalue , "labelvalue" , int, "");
+BBTK_INPUT(Simpleregiongrowing , seed , "seed" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(Simpleregiongrowing , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(Simpleregiongrowing , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( Simpleregiongrowing ) ;
+}
+
+#endif // __bbSlicerSimpleregiongrowing_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerSubtractImages.cxx b/ModuleCall/GenSrc/bbSlicerSubtractImages.cxx
new file mode 100644 (file)
index 0000000..8373771
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerSubtractImages.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerSubtractImages.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, SubtractImages )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( SubtractImages, bbtk::AtomicBlackBox );
+
+    void SubtractImages::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libSubtractLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--order"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputorder( ) ) ) ,"@@@@@"," --order ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void SubtractImages::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void SubtractImages::bbUserSetDefaultValues ( ) {
+    }
+
+    void SubtractImages::bbUserInitializeProcessing ( ) {
+    }
+
+    void SubtractImages::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerSubtractImages.h b/ModuleCall/GenSrc/bbSlicerSubtractImages.h
new file mode 100644 (file)
index 0000000..2a53b19
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerSubtractImages.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerSubtractImages_h_INCLUDED__
+#define __bbSlicerSubtractImages_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT SubtractImages
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( SubtractImages , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume1 , std::string );
+BBTK_DECLARE_INPUT ( inputVolume2 , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( order , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( SubtractImages , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "SubtractImages" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Subtracts two images. Although all image types are supported on input, only sugned types are produced. The two images do not have to have the same dimensions." ) ;
+    BBTK_CATEGORY ( "Filtering.Arithmetic" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(SubtractImages , inputVolume1 , "inputVolume1" , std::string, "");
+BBTK_INPUT(SubtractImages , inputVolume2 , "inputVolume2" , std::string, "");
+BBTK_INPUT(SubtractImages , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(SubtractImages , order , "order" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( SubtractImages ) ;
+}
+
+#endif // __bbSlicerSubtractImages_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerTestGridTransformregistration.cxx b/ModuleCall/GenSrc/bbSlicerTestGridTransformregistration.cxx
new file mode 100644 (file)
index 0000000..2878e28
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerTestGridTransformregistration.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerTestGridTransformregistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, TestGridTransformregistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( TestGridTransformregistration, bbtk::AtomicBlackBox );
+
+    void TestGridTransformregistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libTestGridTransformRegistrationLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgridSize( ) ) ) ,"@@@@@"," -g ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void TestGridTransformregistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void TestGridTransformregistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void TestGridTransformregistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void TestGridTransformregistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerTestGridTransformregistration.h b/ModuleCall/GenSrc/bbSlicerTestGridTransformregistration.h
new file mode 100644 (file)
index 0000000..e7e7d54
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerTestGridTransformregistration.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerTestGridTransformregistration_h_INCLUDED__
+#define __bbSlicerTestGridTransformregistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT TestGridTransformregistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( TestGridTransformregistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( gridSize , int );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( FixedImageFileName , std::string );
+BBTK_DECLARE_INPUT ( MovingImageFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( TestGridTransformregistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "TestGridTransformregistration" ) ;
+    BBTK_AUTHOR ( "Yinglin Lee" ) ;
+    BBTK_DESCRIPTION ( "Generates a GridTransform to test the communication facilities" ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(TestGridTransformregistration , gridSize , "gridSize" , int, "");
+BBTK_INPUT(TestGridTransformregistration , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(TestGridTransformregistration , FixedImageFileName , "FixedImageFileName" , std::string, "");
+BBTK_INPUT(TestGridTransformregistration , MovingImageFileName , "MovingImageFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( TestGridTransformregistration ) ;
+}
+
+#endif // __bbSlicerTestGridTransformregistration_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerThresholdImage.cxx b/ModuleCall/GenSrc/bbSlicerThresholdImage.cxx
new file mode 100644 (file)
index 0000000..2525df8
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerThresholdImage.cxx
@@ -0,0 +1,61 @@
+#include "bbSlicerThresholdImage.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ThresholdImage )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ThresholdImage, bbtk::AtomicBlackBox );
+
+    void ThresholdImage::Process ( ) {
+
+        // GENERATED
+
+int _argc =7;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libThresholdLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputThresholdValue( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLower( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-u"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputUpper( ) ) ) ,"@@@@@"," -u ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutsideValue( ) ) ) ,"@@@@@"," -v ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--thresholdtype"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputThresholdType( ) ) ) ,"@@@@@"," --thresholdtype ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ThresholdImage::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ThresholdImage::bbUserSetDefaultValues ( ) {
+    }
+
+    void ThresholdImage::bbUserInitializeProcessing ( ) {
+    }
+
+    void ThresholdImage::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerThresholdImage.h b/ModuleCall/GenSrc/bbSlicerThresholdImage.h
new file mode 100644 (file)
index 0000000..8170aa5
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerThresholdImage.h
@@ -0,0 +1,70 @@
+#ifndef __bbSlicerThresholdImage_h_INCLUDED__
+#define __bbSlicerThresholdImage_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ThresholdImage
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ThresholdImage , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( OutputVolume , std::string );
+BBTK_DECLARE_INPUT ( ThresholdValue , int );
+BBTK_DECLARE_INPUT ( Lower , int );
+BBTK_DECLARE_INPUT ( Upper , int );
+BBTK_DECLARE_INPUT ( OutsideValue , int );
+BBTK_DECLARE_INPUT ( ThresholdType , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ThresholdImage , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ThresholdImage" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH" ) ;
+    BBTK_DESCRIPTION ( "pThreshold an image./ppSet image values to a user-specified outside value if they are below, above, or between simple threshold values./ppThresholdAbove: The values greater than or equal to the threshold value are set to OutsideValue./ppThresholdBelow: The values less than or equal to the threshold value are set to OutsideValue./ppThresholdOutside: The values outside the range Lower-Upper are set to OutsideValue./ppAlthough all image types are supported on input, only signed types are produced./pp" ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ThresholdImage , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(ThresholdImage , OutputVolume , "OutputVolume" , std::string, "");
+BBTK_INPUT(ThresholdImage , ThresholdValue , "ThresholdValue" , int, "");
+BBTK_INPUT(ThresholdImage , Lower , "Lower" , int, "");
+BBTK_INPUT(ThresholdImage , Upper , "Upper" , int, "");
+BBTK_INPUT(ThresholdImage , OutsideValue , "OutsideValue" , int, "");
+BBTK_INPUT(ThresholdImage , ThresholdType , "ThresholdType" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ThresholdImage ) ;
+}
+
+#endif // __bbSlicerThresholdImage_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerUnbiasedNonLocalMeansfilterforDWI.cxx b/ModuleCall/GenSrc/bbSlicerUnbiasedNonLocalMeansfilterforDWI.cxx
new file mode 100644 (file)
index 0000000..0aefec5
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerUnbiasedNonLocalMeansfilterforDWI.cxx
@@ -0,0 +1,61 @@
+#include "bbSlicerUnbiasedNonLocalMeansfilterforDWI.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, UnbiasedNonLocalMeansfilterforDWI )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( UnbiasedNonLocalMeansfilterforDWI, bbtk::AtomicBlackBox );
+
+    void UnbiasedNonLocalMeansfilterforDWI::Process ( ) {
+
+        // GENERATED
+
+int _argc =7;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libdwiUNLMLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rs"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusSearch( ) ) ) ,"@@@@@"," --rs ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rc"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusComp( ) ) ) ,"@@@@@"," --rc ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--hp"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiH( ) ) ) ,"@@@@@"," --hp ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ng"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiNumNeighbors( ) ) ) ,"@@@@@"," --ng ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--re"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusEstimation( ) ) ) ,"@@@@@"," --re ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void UnbiasedNonLocalMeansfilterforDWI::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void UnbiasedNonLocalMeansfilterforDWI::bbUserSetDefaultValues ( ) {
+    }
+
+    void UnbiasedNonLocalMeansfilterforDWI::bbUserInitializeProcessing ( ) {
+    }
+
+    void UnbiasedNonLocalMeansfilterforDWI::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerUnbiasedNonLocalMeansfilterforDWI.h b/ModuleCall/GenSrc/bbSlicerUnbiasedNonLocalMeansfilterforDWI.h
new file mode 100644 (file)
index 0000000..29ca6a8
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerUnbiasedNonLocalMeansfilterforDWI.h
@@ -0,0 +1,70 @@
+#ifndef __bbSlicerUnbiasedNonLocalMeansfilterforDWI_h_INCLUDED__
+#define __bbSlicerUnbiasedNonLocalMeansfilterforDWI_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT UnbiasedNonLocalMeansfilterforDWI
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( UnbiasedNonLocalMeansfilterforDWI , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( iRadiusSearch , std::vector<int> );
+BBTK_DECLARE_INPUT ( iRadiusComp , std::vector<int> );
+BBTK_DECLARE_INPUT ( iH , float );
+BBTK_DECLARE_INPUT ( iNumNeighbors , int );
+BBTK_DECLARE_INPUT ( iRadiusEstimation , std::vector<int> );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( UnbiasedNonLocalMeansfilterforDWI , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "UnbiasedNonLocalMeansfilterforDWI" ) ;
+    BBTK_AUTHOR ( "Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid SPAIN. Partially founded by grant number TEC2007-67073/TCM from the Comision Interministerial de Ciencia y Tecnologia Spain." ) ;
+    BBTK_DESCRIPTION ( "This module reduces noise or unwanted detail on a set of diffusion weighted images. For this, it filters the images using a Unbiased Non Local Means for Rician noise algorithm. It exploits not only the spatial redundancy, but the redundancy in similar gradient directions as well; it takes into account the N closest gradient directions to the direction being processed a maximum of 5 gradient directions is allowed to keep a reasonable computational load, since we do not use neither similarity maps nor block-wise implementation.The noise parameter is automatically estimated in the same way as in the jointLMMSE module.A complete description of the algorithm may be found in:Antonio Tristan-Vega and Santiago Aja-Fernandez, DWI filtering using joint information for DTI and HARDI, Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.Please, note that the execution of this filter is extremely slow, son only very conservative parameters block size and search size as small as possible should be used. Even so, its execution may take several hours. The advantage of this filter over joint LMMSE is its better preservation of edges and fine structures." ) ;
+    BBTK_CATEGORY ( "Legacy.Diffusion.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iRadiusSearch , "iRadiusSearch" , std::vector<int>, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iRadiusComp , "iRadiusComp" , std::vector<int>, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iH , "iH" , float, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iNumNeighbors , "iNumNeighbors" , int, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iRadiusEstimation , "iRadiusEstimation" , std::vector<int>, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( UnbiasedNonLocalMeansfilterforDWI ) ;
+}
+
+#endif // __bbSlicerUnbiasedNonLocalMeansfilterforDWI_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerVectorDemonRegistrationBRAINS.cxx b/ModuleCall/GenSrc/bbSlicerVectorDemonRegistrationBRAINS.cxx
new file mode 100644 (file)
index 0000000..83c45ee
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerVectorDemonRegistrationBRAINS.cxx
@@ -0,0 +1,95 @@
+#include "bbSlicerVectorDemonRegistrationBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, VectorDemonRegistrationBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( VectorDemonRegistrationBRAINS, bbtk::AtomicBlackBox );
+
+    void VectorDemonRegistrationBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =41;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libVBRAINSDemonWarpLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-m"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingVolume( ) ) ) ,"@@@@@"," -m ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedVolume( ) ) ) ,"@@@@@"," -f ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputPixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputPixelType( ) ) ) ,"@@@@@"," --inputPixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-o"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," -o ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-O"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDisplacementFieldVolume( ) ) ) ,"@@@@@"," -O ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputPixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputPixelType( ) ) ) ,"@@@@@"," --outputPixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolationMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationMode( ) ) ) ,"@@@@@"," --interpolationMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--registrationFilterType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputregistrationFilterType( ) ) ) ,"@@@@@"," --registrationFilterType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothDisplacementFieldSigma( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-n"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfPyramidLevels( ) ) ) ,"@@@@@"," -n ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumFixedPyramid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumFixedPyramid( ) ) ) ,"@@@@@"," --minimumFixedPyramid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumMovingPyramid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumMovingPyramid( ) ) ) ,"@@@@@"," --minimumMovingPyramid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputarrayOfPyramidLevelIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputhistogramMatch( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfHistogramBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfHistogramBins( ) ) ) ,"@@@@@"," --numberOfHistogramBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfMatchPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfMatchPoints( ) ) ) ,"@@@@@"," --numberOfMatchPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--medianFilterSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmedianFilterSize( ) ) ) ,"@@@@@"," --medianFilterSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeWithDisplacementField"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeWithDisplacementField( ) ) ) ,"@@@@@"," --initializeWithDisplacementField ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeWithTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeWithTransform( ) ) ) ,"@@@@@"," --initializeWithTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--makeBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmakeBOBF( ) ) ) ,"@@@@@"," --makeBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedBinaryVolume( ) ) ) ,"@@@@@"," --fixedBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingBinaryVolume( ) ) ) ,"@@@@@"," --movingBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--lowerThresholdForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlowerThresholdForBOBF( ) ) ) ,"@@@@@"," --lowerThresholdForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--upperThresholdForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputupperThresholdForBOBF( ) ) ) ,"@@@@@"," --upperThresholdForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--backgroundFillValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbackgroundFillValue( ) ) ) ,"@@@@@"," --backgroundFillValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seedForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseedForBOBF( ) ) ) ,"@@@@@"," --seedForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--neighborhoodForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputneighborhoodForBOBF( ) ) ) ,"@@@@@"," --neighborhoodForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputDisplacementFieldPrefix"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDisplacementFieldPrefix( ) ) ) ,"@@@@@"," --outputDisplacementFieldPrefix ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputCheckerboardVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputCheckerboardVolume( ) ) ) ,"@@@@@"," --outputCheckerboardVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--checkerboardPatternSubdivisions"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcheckerboardPatternSubdivisions( ) ) ) ,"@@@@@"," --checkerboardPatternSubdivisions ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputNormalized"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputNormalized( ) ) ) ,"@@@@@"," --outputNormalized ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDebug( ) ) ) ,"@@@@@"," -v ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-w"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputweightFactors( ) ) ) ,"@@@@@"," -w ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgradientType( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothingUp( ) ) ) ,"@@@@@"," -g ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxStepLength( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-a"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputturnOffDiffeomorph( ) ) ) ,"@@@@@"," -a ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-G"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputUseDebugImageViewer( ) ) ) ,"@@@@@"," -G ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-p"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPromptAfterImageSend( ) ) ) ,"@@@@@"," -p ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfBCHApproximationTerms"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfBCHApproximationTerms( ) ) ) ,"@@@@@"," --numberOfBCHApproximationTerms ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void VectorDemonRegistrationBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void VectorDemonRegistrationBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void VectorDemonRegistrationBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void VectorDemonRegistrationBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerVectorDemonRegistrationBRAINS.h b/ModuleCall/GenSrc/bbSlicerVectorDemonRegistrationBRAINS.h
new file mode 100644 (file)
index 0000000..0a2bb9b
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerVectorDemonRegistrationBRAINS.h
@@ -0,0 +1,138 @@
+#ifndef __bbSlicerVectorDemonRegistrationBRAINS_h_INCLUDED__
+#define __bbSlicerVectorDemonRegistrationBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT VectorDemonRegistrationBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( VectorDemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( movingVolume , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( fixedVolume , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( inputPixelType , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldVolume , std::string );
+BBTK_DECLARE_INPUT ( outputPixelType , std::string );
+BBTK_DECLARE_INPUT ( interpolationMode , std::string );
+BBTK_DECLARE_INPUT ( registrationFilterType , std::string );
+BBTK_DECLARE_INPUT ( smoothDisplacementFieldSigma , double );
+BBTK_DECLARE_INPUT ( numberOfPyramidLevels , int );
+BBTK_DECLARE_INPUT ( minimumFixedPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( minimumMovingPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( arrayOfPyramidLevelIterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( histogramMatch , bool );
+BBTK_DECLARE_INPUT ( numberOfHistogramBins , int );
+BBTK_DECLARE_INPUT ( numberOfMatchPoints , int );
+BBTK_DECLARE_INPUT ( medianFilterSize , std::vector<int> );
+BBTK_DECLARE_INPUT ( initializeWithDisplacementField , std::string );
+BBTK_DECLARE_INPUT ( initializeWithTransform , std::string );
+BBTK_DECLARE_INPUT ( makeBOBF , bool );
+BBTK_DECLARE_INPUT ( fixedBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( movingBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( lowerThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( upperThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( backgroundFillValue , int );
+BBTK_DECLARE_INPUT ( seedForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( neighborhoodForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldPrefix , std::string );
+BBTK_DECLARE_INPUT ( outputCheckerboardVolume , std::string );
+BBTK_DECLARE_INPUT ( checkerboardPatternSubdivisions , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputNormalized , bool );
+BBTK_DECLARE_INPUT ( outputDebug , bool );
+BBTK_DECLARE_INPUT ( weightFactors , std::vector<float> );
+BBTK_DECLARE_INPUT ( gradientType , int );
+BBTK_DECLARE_INPUT ( smoothingUp , double );
+BBTK_DECLARE_INPUT ( maxStepLength , double );
+BBTK_DECLARE_INPUT ( turnOffDiffeomorph , bool );
+BBTK_DECLARE_INPUT ( UseDebugImageViewer , bool );
+BBTK_DECLARE_INPUT ( PromptAfterImageSend , bool );
+BBTK_DECLARE_INPUT ( numberOfBCHApproximationTerms , int );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( VectorDemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "VectorDemonRegistrationBRAINS" ) ;
+    BBTK_AUTHOR ( "This tool was developed by Hans J. Johnson and Greg Harris." ) ;
+    BBTK_DESCRIPTION ( "This program finds a deformation field to warp a moving image onto a fixed image.  The images must be of the same signal kind, and contain an image of the same kind of object.  This program uses the Thirion Demons warp software in ITK, the Insight Toolkit.  Additional information is available at: http://www.nitrc.org/projects/brainsdemonwarp." ) ;
+    BBTK_CATEGORY ( "Registration.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(VectorDemonRegistrationBRAINS , movingVolume , "movingVolume" , std::vector<std::string>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , fixedVolume , "fixedVolume" , std::vector<std::string>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , inputPixelType , "inputPixelType" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputDisplacementFieldVolume , "outputDisplacementFieldVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputPixelType , "outputPixelType" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , interpolationMode , "interpolationMode" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , registrationFilterType , "registrationFilterType" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , smoothDisplacementFieldSigma , "smoothDisplacementFieldSigma" , double, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfPyramidLevels , "numberOfPyramidLevels" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , minimumFixedPyramid , "minimumFixedPyramid" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , minimumMovingPyramid , "minimumMovingPyramid" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , arrayOfPyramidLevelIterations , "arrayOfPyramidLevelIterations" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , histogramMatch , "histogramMatch" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfHistogramBins , "numberOfHistogramBins" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfMatchPoints , "numberOfMatchPoints" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , medianFilterSize , "medianFilterSize" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , initializeWithDisplacementField , "initializeWithDisplacementField" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , initializeWithTransform , "initializeWithTransform" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , makeBOBF , "makeBOBF" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , fixedBinaryVolume , "fixedBinaryVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , movingBinaryVolume , "movingBinaryVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , lowerThresholdForBOBF , "lowerThresholdForBOBF" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , upperThresholdForBOBF , "upperThresholdForBOBF" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , backgroundFillValue , "backgroundFillValue" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , seedForBOBF , "seedForBOBF" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , neighborhoodForBOBF , "neighborhoodForBOBF" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputDisplacementFieldPrefix , "outputDisplacementFieldPrefix" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputCheckerboardVolume , "outputCheckerboardVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , checkerboardPatternSubdivisions , "checkerboardPatternSubdivisions" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputNormalized , "outputNormalized" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputDebug , "outputDebug" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , weightFactors , "weightFactors" , std::vector<float>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , gradientType , "gradientType" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , smoothingUp , "smoothingUp" , double, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , maxStepLength , "maxStepLength" , double, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , turnOffDiffeomorph , "turnOffDiffeomorph" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , UseDebugImageViewer , "UseDebugImageViewer" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , PromptAfterImageSend , "PromptAfterImageSend" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfBCHApproximationTerms , "numberOfBCHApproximationTerms" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( VectorDemonRegistrationBRAINS ) ;
+}
+
+#endif // __bbSlicerVectorDemonRegistrationBRAINS_h_INCLUDED__
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerVotingBinaryHoleFilling.cxx b/ModuleCall/GenSrc/bbSlicerVotingBinaryHoleFilling.cxx
new file mode 100644 (file)
index 0000000..d3fe3b1
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerVotingBinaryHoleFilling.cxx
@@ -0,0 +1,60 @@
+#include "bbSlicerVotingBinaryHoleFilling.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, VotingBinaryHoleFilling )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( VotingBinaryHoleFilling, bbtk::AtomicBlackBox );
+
+    void VotingBinaryHoleFilling::Process ( ) {
+
+        // GENERATED
+
+int _argc =6;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libVotingBinaryHoleFillingImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--radius"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputradius( ) ) ) ,"@@@@@"," --radius ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--majorityThreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmajorityThreshold( ) ) ) ,"@@@@@"," --majorityThreshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--background"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbackground( ) ) ) ,"@@@@@"," --background ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--foreground"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputforeground( ) ) ) ,"@@@@@"," --foreground ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void VotingBinaryHoleFilling::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void VotingBinaryHoleFilling::bbUserSetDefaultValues ( ) {
+    }
+
+    void VotingBinaryHoleFilling::bbUserInitializeProcessing ( ) {
+    }
+
+    void VotingBinaryHoleFilling::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/ModuleCall/GenSrc/bbSlicerVotingBinaryHoleFilling.h b/ModuleCall/GenSrc/bbSlicerVotingBinaryHoleFilling.h
new file mode 100644 (file)
index 0000000..d03fa19
--- /dev/null
+++ b/ModuleCall/GenSrc/bbSlicerVotingBinaryHoleFilling.h
@@ -0,0 +1,68 @@
+#ifndef __bbSlicerVotingBinaryHoleFilling_h_INCLUDED__
+#define __bbSlicerVotingBinaryHoleFilling_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT VotingBinaryHoleFilling
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( VotingBinaryHoleFilling , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( radius , std::vector<int> );
+BBTK_DECLARE_INPUT ( majorityThreshold , int );
+BBTK_DECLARE_INPUT ( background , int );
+BBTK_DECLARE_INPUT ( foreground , int );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( VotingBinaryHoleFilling , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "VotingBinaryHoleFilling" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Applies a voting operation in order to fill-in cavities. This can be used for smoothing contours and for filling holes in binary images. This technique is used frequently when segmenting complete organs that may have ducts or vasculature that may not have been included in the initial segmentation, e.g. lungs, kidneys, liver." ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(VotingBinaryHoleFilling , radius , "radius" , std::vector<int>, "");
+BBTK_INPUT(VotingBinaryHoleFilling , majorityThreshold , "majorityThreshold" , int, "");
+BBTK_INPUT(VotingBinaryHoleFilling , background , "background" , int, "");
+BBTK_INPUT(VotingBinaryHoleFilling , foreground , "foreground" , int, "");
+BBTK_INPUT(VotingBinaryHoleFilling , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(VotingBinaryHoleFilling , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( VotingBinaryHoleFilling ) ;
+}
+
+#endif // __bbSlicerVotingBinaryHoleFilling_h_INCLUDED__
+
+

diff --git a/ModuleCall/build/Debug/GNU-Linux-x86/main.o b/ModuleCall/build/Debug/GNU-Linux-x86/main.o
new file mode 100644 (file)
index 0000000..090ee18
Binary files /dev/null and b/ModuleCall/build/Debug/GNU-Linux-x86/main.o differ

diff --git a/ModuleCall/build/Debug/GNU-Linux-x86/main.o.d b/ModuleCall/build/Debug/GNU-Linux-x86/main.o.d
new file mode 100644 (file)
index 0000000..fd85132
--- /dev/null
+++ b/ModuleCall/build/Debug/GNU-Linux-x86/main.o.d
@@ -0,0 +1 @@
+build/Debug/GNU-Linux-x86/main.o: main.cpp

diff --git a/ModuleCall/build/Release/GNU-Linux-x86/main.o b/ModuleCall/build/Release/GNU-Linux-x86/main.o
new file mode 100644 (file)
index 0000000..d5d61cf
Binary files /dev/null and b/ModuleCall/build/Release/GNU-Linux-x86/main.o differ

diff --git a/ModuleCall/build/Release/GNU-Linux-x86/main.o.d b/ModuleCall/build/Release/GNU-Linux-x86/main.o.d
new file mode 100644 (file)
index 0000000..b5964ab
--- /dev/null
+++ b/ModuleCall/build/Release/GNU-Linux-x86/main.o.d
@@ -0,0 +1 @@
+build/Release/GNU-Linux-x86/main.o: main.cpp

diff --git a/ModuleCall/dist/Debug/GNU-Linux-x86/modulecall b/ModuleCall/dist/Debug/GNU-Linux-x86/modulecall
new file mode 100755 (executable)
index 0000000..00bee6d
Binary files /dev/null and b/ModuleCall/dist/Debug/GNU-Linux-x86/modulecall differ

diff --git a/ModuleCall/dist/Release/GNU-Linux-x86/modulecall b/ModuleCall/dist/Release/GNU-Linux-x86/modulecall
new file mode 100755 (executable)
index 0000000..00bee6d
Binary files /dev/null and b/ModuleCall/dist/Release/GNU-Linux-x86/modulecall differ

diff --git a/ModuleCall/interoperating_Baby b/ModuleCall/interoperating_Baby
index 232b6113a3d152501608a6682828cbd269870691..60bfdce2bfdea97fb6e958ee58d2909bdc517d74 100755 (executable)
Binary files a/ModuleCall/interoperating_Baby and b/ModuleCall/interoperating_Baby differ

diff --git a/ModuleCall/main.cpp b/ModuleCall/main.cpp
index afb754449fac9786369d44ff34a22954addf4bb1..70764132b90a178a46423df6b85bbecc26845b5e 100644 (file)
--- a/ModuleCall/main.cpp
+++ b/ModuleCall/main.cpp
@@ -32,23 +32,23 @@
 
 char* getModuleDescription ( const std::string lib ) {
 
-    void* handle = dlopen( lib.c_str( ) , RTLD_NOW | RTLD_LOCAL ) ;
+    void* handle = dlopen ( lib.c_str ( ) , RTLD_NOW | RTLD_LOCAL ) ;
     if ( ! handle ) {
-        std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n' ;
+        std::cerr << "CAN'T OPEN LIBRARY: " << dlerror ( ) << '\n' ;
         return NULL ;
     }
     typedef char* ( *method_t )( void ) ;
     // RESET ERRORS
-    dlerror( ) ;
-    method_t myMethod = ( method_t ) dlsym( handle , "GetXMLModuleDescription" ) ;
-    const char *dlsym_error = dlerror( ) ;
+    dlerror ( ) ;
+    method_t myMethod = ( method_t ) dlsym ( handle , "GetXMLModuleDescription" ) ;
+    const char *dlsym_error = dlerror ( ) ;
     if ( dlsym_error ) {
         std::cerr << "CAN'T LOAD SYMBOL 'GetXMLModuleDescription: " << dlsym_error << '\n' ;
-        dlclose( handle ) ;
+        dlclose ( handle ) ;
         return NULL ;
     }
     // CALLING METHOD
-    char* descrption = myMethod( ) ;
+    char* descrption = myMethod ( ) ;
     // CLOSING LIB
 
     //dlclose( handle ) ;
@@ -58,123 +58,178 @@ char* getModuleDescription ( const std::string lib ) {
 }
 
 void execute ( const std::string lib , int _argc , char * _argv[] ) {
-    void* handle = dlopen( lib.c_str( ) , RTLD_NOW | RTLD_LOCAL ) ;
+    void* handle = dlopen ( lib.c_str ( ) , RTLD_NOW | RTLD_LOCAL ) ;
     if ( ! handle ) {
-        std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n' ;
+        std::cerr << "CAN'T OPEN LIBRARY: " << dlerror ( ) << '\n' ;
         return ;
     }
     typedef int (*method_t )( int argc , char * argv[] ) ;
     // RESET ERRORS
-    dlerror( ) ;
-    method_t myMethod = ( method_t ) dlsym( handle , "ModuleEntryPoint" ) ;
-    const char *dlsym_error = dlerror( ) ;
+    dlerror ( ) ;
+    method_t myMethod = ( method_t ) dlsym ( handle , "ModuleEntryPoint" ) ;
+    const char *dlsym_error = dlerror ( ) ;
     if ( dlsym_error ) {
         std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint' " << dlsym_error << '\n' ;
-        dlclose( handle ) ;
+        dlclose ( handle ) ;
         return ;
     }
     // CALLING METHOD
-    myMethod( _argc , _argv ) ;
+    myMethod ( _argc , _argv ) ;
     // CLOSING LIB
-    dlclose( handle ) ;
+    dlclose ( handle ) ;
 }
 
 ///     FILE RELATED     ///
 
 void saveFile ( const std::string content , const std::string file_name ) {
     std::ofstream myfile ;
-    myfile.open( file_name.c_str( ) ) ;
+    myfile.open ( file_name.c_str ( ) ) ;
     myfile << content ;
-    myfile.close( ) ;
+    myfile.close ( ) ;
 }
 
 std::string loadFile ( const std::string filename ) {
-    std::string line = std::string( "" ) ;
-    std::string content = std::string( "" ) ;
+    std::string line = std::string ( "" ) ;
+    std::string content = std::string ( "" ) ;
 
     std::ifstream infile ;
-    infile.open( filename.c_str( ) ) ;
-    while ( ! infile.eof( ) ) {
-        getline( infile , line ) ;
+    infile.open ( filename.c_str ( ) ) ;
+    while ( ! infile.eof ( ) ) {
+        getline ( infile , line ) ;
         content += line + "\n" ;
-        line.clear( ) ;
+        line.clear ( ) ;
     }
-    infile.close( ) ;
+    infile.close ( ) ;
     return content ;
 
 }
 
 std::string loadDummyBody ( ) {
-    return loadFile( "bbSlicerDummy.dummy_cxx" ) ;
+    return loadFile ( "bbSlicerDummy.dummy_cxx" ) ;
 }
 
 std::string loadDummyHeader ( ) {
-    return loadFile( "bbSlicerDummy.dummy_h" ) ;
+    return loadFile ( "bbSlicerDummy.dummy_h" ) ;
 }
 
 ///     BBTK BOX CREATION       /// 
 
 std::string updateBoxDescription ( const ModuleDescription* module , std::string _header ) {
-    _header = Mthd::Aux::replace_str( _header , "_NNNNN_" , Mthd::Aux::replace_str( module->GetTitle( ) , " " , "" ) ) ;
-    _header = Mthd::Aux::replace_str( _header , "_AAAAA_" , module->GetContributor( ) ) ;
-    _header = Mthd::Aux::replace_str( _header , "_DDDDD_" , module->GetDescription( ) ) ;
-    _header = Mthd::Aux::replace_str( _header , "_CCCCC_" , module->GetCategory( ) ) ;
+
+    std::string tmp_str = std::string ( "" ) ;
+    tmp_str = module->GetTitle ( ) ;
+
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , " " , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , "<" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , ">" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , "(" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , ")" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , "\n" , "" ) ;
+    _header = Mthd::Aux::replace_str ( _header , "_NNNNN_" , tmp_str ) ;
+
+    tmp_str.clear ( ) ;
+    tmp_str = module->GetContributor ( ) ;
+
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , "<" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , ">" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , "(" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , ")" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , "\n" , "" ) ;
+    _header = Mthd::Aux::replace_str ( _header , "_AAAAA_" , tmp_str ) ;
+
+    tmp_str.clear ( ) ;
+    tmp_str = module->GetDescription ( ) ;
+
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , "<" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , ">" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , "(" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , ")" , "" ) ;
+    tmp_str = Mthd::Aux::replace_str ( tmp_str , "\n" , "" ) ;
+    _header = Mthd::Aux::replace_str ( _header , "_DDDDD_" , tmp_str ) ;
+
+
+    _header = Mthd::Aux::replace_str ( _header , "_CCCCC_" , module->GetCategory ( ) ) ;
     return _header ;
 }
 
 std::string updateBoxName ( const ModuleDescription* module , std::string content ) {
-    std::string _new_box_name = Mthd::Aux::replace_str( module->GetTitle( ) , " " , "" ) ;
-    content = Mthd::Aux::replace_str( content , "Dummy" , _new_box_name ) ;
+    std::string _new_box_name = module->GetTitle ( ) ;
+    _new_box_name = Mthd::Aux::replace_str ( _new_box_name , " " , "" ) ;
+    _new_box_name = Mthd::Aux::replace_str ( _new_box_name , "<" , "" ) ;
+    _new_box_name = Mthd::Aux::replace_str ( _new_box_name , ">" , "" ) ;
+    _new_box_name = Mthd::Aux::replace_str ( _new_box_name , "(" , "" ) ;
+    _new_box_name = Mthd::Aux::replace_str ( _new_box_name , ")" , "" ) ;
+    _new_box_name = Mthd::Aux::replace_str ( _new_box_name , "\n" , "" ) ;
+    content = Mthd::Aux::replace_str ( content , "Dummy" , _new_box_name ) ;
     return content ;
 }
 
 std::string getHeaderFileName ( const ModuleDescription* module ) {
-    std::string name = Mthd::Aux::replace_str( module->GetTitle( ) , " " , "" ) ;
+    std::string name = Mthd::Aux::replace_str ( module->GetTitle ( ) , " " , "" ) ;
+    name = Mthd::Aux::replace_str ( name , "<" , "" ) ;
+    name = Mthd::Aux::replace_str ( name , ">" , "" ) ;
+    name = Mthd::Aux::replace_str ( name , "(" , "" ) ;
+    name = Mthd::Aux::replace_str ( name , ")" , "" ) ;
+    name = Mthd::Aux::replace_str ( name , "\n" , "" ) ;
     return "bbSlicer" + name + ".h" ;
 }
 
 std::string getBodyFileName ( const ModuleDescription* module ) {
-    std::string name = Mthd::Aux::replace_str( module->GetTitle( ) , " " , "" ) ;
-
+    std::string name = module->GetTitle ( ) ;
+    name = Mthd::Aux::replace_str ( name , " " , "" ) ;
+    name = Mthd::Aux::replace_str ( name , "<" , "" ) ;
+    name = Mthd::Aux::replace_str ( name , ">" , "" ) ;
+    name = Mthd::Aux::replace_str ( name , "(" , "" ) ;
+    name = Mthd::Aux::replace_str ( name , ")" , "" ) ;
+    name = Mthd::Aux::replace_str ( name , "\n" , "" ) ;
     return "bbSlicer" + name + ".cxx" ;
 }
 
 std::string updateBoxInputs ( const ModuleDescription* module , std::string content ) {
 
-    std::string _cxx_inputs = std::string( "\n" ) ;
-    std::string _cxx_inputs_end = std::string( "\n" ) ;
-    std::string _box_name = Mthd::Aux::replace_str( module->GetTitle( ) , " " , "" ) ;
+    std::string _cxx_inputs = std::string ( "\n" ) ;
+    std::string _cxx_inputs_end = std::string ( "\n" ) ;
+
+    std::string _box_name = module->GetTitle ( ) ;
+    _box_name = Mthd::Aux::replace_str ( _box_name , " " , "" ) ;
+    _box_name = Mthd::Aux::replace_str ( _box_name , "<" , "" ) ;
+    _box_name = Mthd::Aux::replace_str ( _box_name , ">" , "" ) ;
+    _box_name = Mthd::Aux::replace_str ( _box_name , "(" , "" ) ;
+    _box_name = Mthd::Aux::replace_str ( _box_name , ")" , "" ) ;
+    _box_name = Mthd::Aux::replace_str ( _box_name , "\n" , "" ) ;
+
+    for ( unsigned long int i = 0 ; i < module->GetParameterGroups ( ).size ( ) ; i ++ ) {
+        ModuleParameterGroup pGroup = module->GetParameterGroups ( ).at ( i ) ;
+        for ( unsigned long int j = 0 ; j < pGroup.GetParameters ( ).size ( ) ; j ++ ) {
+
+            ModuleParameter mPara = pGroup.GetParameters ( ).at ( j ) ;
 
-    for ( unsigned long int i = 0 ; i < module->GetParameterGroups( ).size( ) ; i ++ ) {
-        ModuleParameterGroup pGroup = module->GetParameterGroups( ).at( i ) ;
-        for ( unsigned long int j = 0 ; j < pGroup.GetParameters( ).size( ) ; j ++ ) {
-            ModuleParameter mPara = pGroup.GetParameters( ).at( j ) ;
             _cxx_inputs +=
                     "BBTK_DECLARE_INPUT ( " +
-                    mPara.GetName( ) + " , " +
-                    mPara.GetCPPType( ) + " );\n" ;
+                    mPara.GetName ( ) + " , " +
+                    mPara.GetCPPType ( ) + " );\n" ;
 
             _cxx_inputs_end +=
                     "BBTK_INPUT(" +
                     _box_name + " , " +
-                    mPara.GetName( ) + " , " +
-                    "\"" + mPara.GetName( ) + "\"" + " , " +
-                    mPara.GetCPPType( ) + ", \"\");\n" ;
+                    mPara.GetName ( ) + " , " +
+                    "\"" + mPara.GetName ( ) + "\"" + " , " +
+                    mPara.GetCPPType ( ) + ", \"\");\n" ;
         }
     }
-    content = Mthd::Aux::replace_str( content , "_11111_" , _cxx_inputs ) ;
-    content = Mthd::Aux::replace_str( content , "_22222_" , _cxx_inputs_end ) ;
+    content = Mthd::Aux::replace_str ( content , "_11111_" , _cxx_inputs ) ;
+    content = Mthd::Aux::replace_str ( content , "_22222_" , _cxx_inputs_end ) ;
 
     return content ;
 }
 
 const int getNumberOfArguments ( const ModuleDescription* module ) {
     int number = 0 ;
-    for ( unsigned long int i = 0 ; i < module->GetParameterGroups( ).size( ) ; i ++ ) {
-        ModuleParameterGroup pGroup = module->GetParameterGroups( ).at( i ) ;
-        for ( unsigned long int j = 0 ; j < pGroup.GetParameters( ).size( ) ; j ++ ) {
+    for ( unsigned long int i = 0 ; i < module->GetParameterGroups ( ).size ( ) ; i ++ ) {
+        ModuleParameterGroup pGroup = module->GetParameterGroups ( ).at ( i ) ;
+        for ( unsigned long int j = 0 ; j < pGroup.GetParameters ( ).size ( ) ; j ++ ) {
 
-            ModuleParameter mPara = pGroup.GetParameters( ).at( j ) ;
+            ModuleParameter mPara = pGroup.GetParameters ( ).at ( j ) ;
             number ++ ;
         }
     }
@@ -183,56 +238,58 @@ const int getNumberOfArguments ( const ModuleDescription* module ) {
 
 std::string updateProcessMethod ( const ModuleDescription* module , std::string content , std::string lib ) {
     int number = 0 ;
-    std::string arg_list = std::string( "" ) ;
-    for ( unsigned long int i = 0 ; i < module->GetParameterGroups( ).size( ) ; i ++ ) {
-        ModuleParameterGroup pGroup = module->GetParameterGroups( ).at( i ) ;
-        for ( unsigned long int j = 0 ; j < pGroup.GetParameters( ).size( ) ; j ++ ) {
-
-            ModuleParameter mPara = pGroup.GetParameters( ).at( j ) ;
+    std::string arg_list = std::string ( "" ) ;
+    for ( unsigned long int i = 0 ; i < module->GetParameterGroups ( ).size ( ) ; i ++ ) {
+        ModuleParameterGroup pGroup = module->GetParameterGroups ( ).at ( i ) ;
+        for ( unsigned long int j = 0 ; j < pGroup.GetParameters ( ).size ( ) ; j ++ ) {
 
+            std::string flag = std::string ( "\"\"" ) ;
+            ModuleParameter mPara = pGroup.GetParameters ( ).at ( j ) ;
             arg_list += "Mthd::Aux::toCharArrray( " ;
-            if ( mPara.GetFlag( ) != "" ) {
+            if ( mPara.GetFlag ( ) != "" ) {
                 arg_list += "Mthd::Aux::toString( \"" ;
-                arg_list += "-" + mPara.GetFlag( ) + "\" " ;
+                arg_list += "-" + mPara.GetFlag ( ) + "\" " ;
                 arg_list += " ) + " ;
+                flag = "\" -" + mPara.GetFlag ( ) +" \"" ;
 
-            } else if ( mPara.GetLongFlag( ) != "" ) {
+            } else if ( mPara.GetLongFlag ( ) != "" ) {
                 arg_list += "Mthd::Aux::toString( \"" ;
-                arg_list += "--" + mPara.GetLongFlag( ) + "\" " ;
+                arg_list += "--" + mPara.GetLongFlag ( ) + "\" " ;
                 arg_list += " ) + " ;
+                flag = "\" --" + mPara.GetLongFlag ( ) +" \"" ;
             }
 
-            arg_list += "Mthd::Aux::toString( bbGetInput" + mPara.GetName( ) + "( ) )" ;
-            arg_list += " ),\n" ;
+            arg_list += "Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInput" + mPara.GetName ( ) + "( ) )" ;
+            arg_list += " ) ,\"@@@@@\"," + flag + ") ),\n" ;
             number ++ ;
         }
 
     }
     arg_list += "_EEENNNDDD_" ;
-    arg_list = Mthd::Aux::replace_str( arg_list , ",\n_EEENNNDDD_" , "" ) ;
-    std::string _argc = "\nint _argc =" + Mthd::Aux::toString( number ) + ";\n" ;
+    arg_list = Mthd::Aux::replace_str ( arg_list , ",\n_EEENNNDDD_" , "" ) ;
+    std::string _argc = "\nint _argc =" + Mthd::Aux::toString ( number ) + ";\n" ;
     std::string _slib = "std::string lib = \"" + lib + "\";\n" ;
     std::string _argv = "char * _argv[ ] = { " + arg_list + " };\n" ;
-    return Mthd::Aux::replace_str( content , "_33333_" , _argc + _slib + _argv ) ;
+    return Mthd::Aux::replace_str ( content , "_33333_" , _argc + _slib + _argv ) ;
 }
 
 std::vector < std::string > getFilesByExtention ( std::string dir , std::string ext ) {
     std::vector < std::string > files ;
-    files.clear( ) ;
+    files.clear ( ) ;
     DIR *dp ;
     struct dirent *dirp ;
-    if ( ( dp = opendir( dir.c_str( ) ) ) == NULL ) {
+    if ( ( dp = opendir ( dir.c_str ( ) ) ) == NULL ) {
         std::cout << "ERROR OPENING " << dir << std::endl ;
         return files ;
     }
 
-    while ( ( dirp = readdir( dp ) ) != NULL ) {
-        std::string file = std::string( dirp->d_name ) ;
-        if ( Mthd::Aux::str_ends_with( file , ext ) ) {
-            files.push_back( file ) ;
+    while ( ( dirp = readdir ( dp ) ) != NULL ) {
+        std::string file = std::string ( dirp->d_name ) ;
+        if ( Mthd::Aux::str_ends_with ( file , ext ) ) {
+            files.push_back ( file ) ;
         }
     }
-    closedir( dp ) ;
+    closedir ( dp ) ;
     return files ;
 }
 
@@ -242,53 +299,53 @@ int main ( int argc , char* argv[] ) {
     //    char * _argv[] = { "-s 20" , "/home/riveros/Desktop/Experiments/RA1.mhd" , "/home/riveros/Desktop/Experiments/RA1-OUT-MAIN.mhd" } ;
     //    execute( gblib , _argc , _argv ) ;
 
-    const std::string dummy_body_str = loadDummyBody( ) ;
-    const std::string dummy_header_str = loadDummyHeader( ) ;
+    const std::string dummy_body_str = loadDummyBody ( ) ;
+    const std::string dummy_header_str = loadDummyHeader ( ) ;
 
     const std::string directory = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/" ;
-    const std::vector < std::string > files = getFilesByExtention( directory , ".so" ) ;
+    const std::vector < std::string > files = getFilesByExtention ( directory , ".so" ) ;
 
-    for ( unsigned int i = 0 ; i < files.size( ) ; i ++ ) {
+    for ( unsigned int i = 0 ; i < files.size ( ) ; i ++ ) {
 
-        std::string gblib = directory + files.at( i ) ;
-        std::cout << "/// " << files.at( i ) << " ///" << std::endl ;
+        std::string gblib = directory + files.at ( i ) ;
+        std::cout << "/// " << files.at ( i ) << " ///" << std::endl ;
 
         ///     MODULE INFORMATION      ///
-        std::string des = getModuleDescription( gblib ) ;
+        std::string des = getModuleDescription ( gblib ) ;
         std::cout << "  getModuleDescription( gblib )...OK" << std::endl ;
 
         ModuleDescription module ;
         ModuleDescriptionParser parser ;
 
-        parser.Parse( des , module ) ;
+        parser.Parse ( des , module ) ;
         std::cout << "  parser.Parse( des , module )...OK" << std::endl ;
 
         ///     LOADING DUMMY FILES     ///
-        std::string _body = std::string( dummy_body_str ) ;
+        std::string _body = std::string ( dummy_body_str ) ;
         std::cout << "  loadDummyBody( )...OK" << std::endl ;
-        std::string _header = std::string( dummy_header_str ) ;
+        std::string _header = std::string ( dummy_header_str ) ;
         std::cout << "  loadDummyHeader( )...OK" << std::endl ;
 
         ///     SETTING HEADER FILE     ///
-        _header = updateBoxName( &module , _header ) ;
+        _header = updateBoxName ( &module , _header ) ;
         std::cout << "  updateBoxName( &module , _header )...OK" << std::endl ;
-        _header = updateBoxDescription( &module , _header ) ;
+        _header = updateBoxDescription ( &module , _header ) ;
         std::cout << "  updateBoxDescription( &module , _header )...OK" << std::endl ;
-        _header = updateBoxInputs( &module , _header ) ;
+        _header = updateBoxInputs ( &module , _header ) ;
         std::cout << "  updateBoxInputs( &module , _header )...OK" << std::endl ;
-        saveFile( _header , getHeaderFileName( &module ) ) ;
+        saveFile ( _header , "./GenSrc/" + getHeaderFileName ( &module ) ) ;
 
         ///     SETTING BODY FILE       ///
-        _body = updateBoxName( &module , _body ) ;
+        _body = updateBoxName ( &module , _body ) ;
         std::cout << "  updateBoxName( &module , _body )...OK" << std::endl ;
-        _body = updateProcessMethod( &module , _body , gblib ) ;
+        _body = updateProcessMethod ( &module , _body , gblib ) ;
         std::cout << "  updateProcessMethod( &module , _body , gblib )...OK" << std::endl ;
-        saveFile( _body , getBodyFileName( &module ) ) ;
+        saveFile ( _body , "./GenSrc/" + getBodyFileName ( &module ) ) ;
 
-        std::cout << "/// EO " << files.at( i ) << " ///" << std::endl << std::endl ;
+        std::cout << "/// EO " << files.at ( i ) << " ///" << std::endl << std::endl ;
 
-        gblib.clear( ) ;
-        des.clear( ) ;
+        gblib.clear ( ) ;
+        des.clear ( ) ;
         //while ( getchar( ) != '\n' ) ;
 
     }

diff --git a/ModuleCall/nbproject/Makefile-Debug.mk b/ModuleCall/nbproject/Makefile-Debug.mk
new file mode 100644 (file)
index 0000000..403ae0c
--- /dev/null
+++ b/ModuleCall/nbproject/Makefile-Debug.mk
@@ -0,0 +1,89 @@
+#
+# Generated Makefile - do not edit!
+#
+# Edit the Makefile in the project folder instead (../Makefile). Each target
+# has a -pre and a -post target defined where you can add customized code.
+#
+# This makefile implements configuration specific macros and targets.
+
+
+# Environment
+MKDIR=mkdir
+CP=cp
+GREP=grep
+NM=nm
+CCADMIN=CCadmin
+RANLIB=ranlib
+CC=gcc
+CCC=g++
+CXX=g++
+FC=gfortran
+AS=as
+
+# Macros
+CND_PLATFORM=GNU-Linux-x86
+CND_CONF=Debug
+CND_DISTDIR=dist
+CND_BUILDDIR=build
+
+# Include project Makefile
+include Makefile
+
+# Object Directory
+OBJECTDIR=${CND_BUILDDIR}/${CND_CONF}/${CND_PLATFORM}
+
+# Object Files
+OBJECTFILES= \
+       ${OBJECTDIR}/main.o \
+       ${OBJECTDIR}/CreationTool.o
+
+
+# C Compiler Flags
+CFLAGS=
+
+# CC Compiler Flags
+CCFLAGS=-ldl
+CXXFLAGS=-ldl
+
+# Fortran Compiler Flags
+FFLAGS=
+
+# Assembler Flags
+ASFLAGS=
+
+# Link Libraries and Options
+LDLIBSOPTIONS=
+
+# Build Targets
+.build-conf: ${BUILD_SUBPROJECTS}
+       "${MAKE}"  -f nbproject/Makefile-${CND_CONF}.mk ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall
+
+${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall: ${OBJECTFILES}
+       ${MKDIR} -p ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}
+       ${LINK.cc} -o ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall ${OBJECTFILES} ${LDLIBSOPTIONS} 
+
+${OBJECTDIR}/main.o: nbproject/Makefile-${CND_CONF}.mk main.cpp 
+       ${MKDIR} -p ${OBJECTDIR}
+       ${RM} $@.d
+       $(COMPILE.cc) -g -MMD -MP -MF $@.d -o ${OBJECTDIR}/main.o main.cpp
+
+${OBJECTDIR}/CreationTool.o: nbproject/Makefile-${CND_CONF}.mk CreationTool.cxx 
+       ${MKDIR} -p ${OBJECTDIR}
+       ${RM} $@.d
+       $(COMPILE.cc) -g -MMD -MP -MF $@.d -o ${OBJECTDIR}/CreationTool.o CreationTool.cxx
+
+# Subprojects
+.build-subprojects:
+
+# Clean Targets
+.clean-conf: ${CLEAN_SUBPROJECTS}
+       ${RM} -r ${CND_BUILDDIR}/${CND_CONF}
+       ${RM} ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall
+
+# Subprojects
+.clean-subprojects:
+
+# Enable dependency checking
+.dep.inc: .depcheck-impl
+
+include .dep.inc

diff --git a/ModuleCall/nbproject/Makefile-Release.mk b/ModuleCall/nbproject/Makefile-Release.mk
new file mode 100644 (file)
index 0000000..3e0453a
--- /dev/null
+++ b/ModuleCall/nbproject/Makefile-Release.mk
@@ -0,0 +1,89 @@
+#
+# Generated Makefile - do not edit!
+#
+# Edit the Makefile in the project folder instead (../Makefile). Each target
+# has a -pre and a -post target defined where you can add customized code.
+#
+# This makefile implements configuration specific macros and targets.
+
+
+# Environment
+MKDIR=mkdir
+CP=cp
+GREP=grep
+NM=nm
+CCADMIN=CCadmin
+RANLIB=ranlib
+CC=gcc
+CCC=g++
+CXX=g++
+FC=gfortran
+AS=as
+
+# Macros
+CND_PLATFORM=GNU-Linux-x86
+CND_CONF=Release
+CND_DISTDIR=dist
+CND_BUILDDIR=build
+
+# Include project Makefile
+include Makefile
+
+# Object Directory
+OBJECTDIR=${CND_BUILDDIR}/${CND_CONF}/${CND_PLATFORM}
+
+# Object Files
+OBJECTFILES= \
+       ${OBJECTDIR}/main.o \
+       ${OBJECTDIR}/CreationTool.o
+
+
+# C Compiler Flags
+CFLAGS=
+
+# CC Compiler Flags
+CCFLAGS=-ldl -w
+CXXFLAGS=-ldl -w
+
+# Fortran Compiler Flags
+FFLAGS=
+
+# Assembler Flags
+ASFLAGS=
+
+# Link Libraries and Options
+LDLIBSOPTIONS=
+
+# Build Targets
+.build-conf: ${BUILD_SUBPROJECTS}
+       "${MAKE}"  -f nbproject/Makefile-${CND_CONF}.mk ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall
+
+${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall: ${OBJECTFILES}
+       ${MKDIR} -p ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}
+       ${LINK.cc} -o ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall ${OBJECTFILES} ${LDLIBSOPTIONS} 
+
+${OBJECTDIR}/main.o: nbproject/Makefile-${CND_CONF}.mk main.cpp 
+       ${MKDIR} -p ${OBJECTDIR}
+       ${RM} $@.d
+       $(COMPILE.cc) -O2 -MMD -MP -MF $@.d -o ${OBJECTDIR}/main.o main.cpp
+
+${OBJECTDIR}/CreationTool.o: nbproject/Makefile-${CND_CONF}.mk CreationTool.cxx 
+       ${MKDIR} -p ${OBJECTDIR}
+       ${RM} $@.d
+       $(COMPILE.cc) -O2 -MMD -MP -MF $@.d -o ${OBJECTDIR}/CreationTool.o CreationTool.cxx
+
+# Subprojects
+.build-subprojects:
+
+# Clean Targets
+.clean-conf: ${CLEAN_SUBPROJECTS}
+       ${RM} -r ${CND_BUILDDIR}/${CND_CONF}
+       ${RM} ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall
+
+# Subprojects
+.clean-subprojects:
+
+# Enable dependency checking
+.dep.inc: .depcheck-impl
+
+include .dep.inc

diff --git a/ModuleCall/nbproject/Makefile-impl.mk b/ModuleCall/nbproject/Makefile-impl.mk
new file mode 100644 (file)
index 0000000..5b21938
--- /dev/null
+++ b/ModuleCall/nbproject/Makefile-impl.mk
@@ -0,0 +1,133 @@
+# 
+# Generated Makefile - do not edit! 
+# 
+# Edit the Makefile in the project folder instead (../Makefile). Each target
+# has a pre- and a post- target defined where you can add customization code.
+#
+# This makefile implements macros and targets common to all configurations.
+#
+# NOCDDL
+
+
+# Building and Cleaning subprojects are done by default, but can be controlled with the SUB
+# macro. If SUB=no, subprojects will not be built or cleaned. The following macro
+# statements set BUILD_SUB-CONF and CLEAN_SUB-CONF to .build-reqprojects-conf
+# and .clean-reqprojects-conf unless SUB has the value 'no'
+SUB_no=NO
+SUBPROJECTS=${SUB_${SUB}}
+BUILD_SUBPROJECTS_=.build-subprojects
+BUILD_SUBPROJECTS_NO=
+BUILD_SUBPROJECTS=${BUILD_SUBPROJECTS_${SUBPROJECTS}}
+CLEAN_SUBPROJECTS_=.clean-subprojects
+CLEAN_SUBPROJECTS_NO=
+CLEAN_SUBPROJECTS=${CLEAN_SUBPROJECTS_${SUBPROJECTS}}
+
+
+# Project Name
+PROJECTNAME=ModuleCall
+
+# Active Configuration
+DEFAULTCONF=Debug
+CONF=${DEFAULTCONF}
+
+# All Configurations
+ALLCONFS=Debug Release 
+
+
+# build
+.build-impl: .build-pre .validate-impl .depcheck-impl
+       @#echo "=> Running $@... Configuration=$(CONF)"
+       "${MAKE}" -f nbproject/Makefile-${CONF}.mk QMAKE=${QMAKE} SUBPROJECTS=${SUBPROJECTS} .build-conf
+
+
+# clean
+.clean-impl: .clean-pre .validate-impl .depcheck-impl
+       @#echo "=> Running $@... Configuration=$(CONF)"
+       "${MAKE}" -f nbproject/Makefile-${CONF}.mk QMAKE=${QMAKE} SUBPROJECTS=${SUBPROJECTS} .clean-conf
+
+
+# clobber 
+.clobber-impl: .clobber-pre .depcheck-impl
+       @#echo "=> Running $@..."
+       for CONF in ${ALLCONFS}; \
+       do \
+           "${MAKE}" -f nbproject/Makefile-$${CONF}.mk QMAKE=${QMAKE} SUBPROJECTS=${SUBPROJECTS} .clean-conf; \
+       done
+
+# all 
+.all-impl: .all-pre .depcheck-impl
+       @#echo "=> Running $@..."
+       for CONF in ${ALLCONFS}; \
+       do \
+           "${MAKE}" -f nbproject/Makefile-$${CONF}.mk QMAKE=${QMAKE} SUBPROJECTS=${SUBPROJECTS} .build-conf; \
+       done
+
+# build tests
+.build-tests-impl: .build-impl .build-tests-pre
+       @#echo "=> Running $@... Configuration=$(CONF)"
+       "${MAKE}" -f nbproject/Makefile-${CONF}.mk SUBPROJECTS=${SUBPROJECTS} .build-tests-conf
+
+# run tests
+.test-impl: .build-tests-impl .test-pre
+       @#echo "=> Running $@... Configuration=$(CONF)"
+       "${MAKE}" -f nbproject/Makefile-${CONF}.mk SUBPROJECTS=${SUBPROJECTS} .test-conf
+
+# dependency checking support
+.depcheck-impl:
+       @echo "# This code depends on make tool being used" >.dep.inc
+       @if [ -n "${MAKE_VERSION}" ]; then \
+           echo "DEPFILES=\$$(wildcard \$$(addsuffix .d, \$${OBJECTFILES}))" >>.dep.inc; \
+           echo "ifneq (\$${DEPFILES},)" >>.dep.inc; \
+           echo "include \$${DEPFILES}" >>.dep.inc; \
+           echo "endif" >>.dep.inc; \
+       else \
+           echo ".KEEP_STATE:" >>.dep.inc; \
+           echo ".KEEP_STATE_FILE:.make.state.\$${CONF}" >>.dep.inc; \
+       fi
+
+# configuration validation
+.validate-impl:
+       @if [ ! -f nbproject/Makefile-${CONF}.mk ]; \
+       then \
+           echo ""; \
+           echo "Error: can not find the makefile for configuration '${CONF}' in project ${PROJECTNAME}"; \
+           echo "See 'make help' for details."; \
+           echo "Current directory: " `pwd`; \
+           echo ""; \
+       fi
+       @if [ ! -f nbproject/Makefile-${CONF}.mk ]; \
+       then \
+           exit 1; \
+       fi
+
+
+# help
+.help-impl: .help-pre
+       @echo "This makefile supports the following configurations:"
+       @echo "    ${ALLCONFS}"
+       @echo ""
+       @echo "and the following targets:"
+       @echo "    build  (default target)"
+       @echo "    clean"
+       @echo "    clobber"
+       @echo "    all"
+       @echo "    help"
+       @echo ""
+       @echo "Makefile Usage:"
+       @echo "    make [CONF=<CONFIGURATION>] [SUB=no] build"
+       @echo "    make [CONF=<CONFIGURATION>] [SUB=no] clean"
+       @echo "    make [SUB=no] clobber"
+       @echo "    make [SUB=no] all"
+       @echo "    make help"
+       @echo ""
+       @echo "Target 'build' will build a specific configuration and, unless 'SUB=no',"
+       @echo "    also build subprojects."
+       @echo "Target 'clean' will clean a specific configuration and, unless 'SUB=no',"
+       @echo "    also clean subprojects."
+       @echo "Target 'clobber' will remove all built files from all configurations and,"
+       @echo "    unless 'SUB=no', also from subprojects."
+       @echo "Target 'all' will will build all configurations and, unless 'SUB=no',"
+       @echo "    also build subprojects."
+       @echo "Target 'help' prints this message."
+       @echo ""
+

diff --git a/ModuleCall/nbproject/Makefile-variables.mk b/ModuleCall/nbproject/Makefile-variables.mk
new file mode 100644 (file)
index 0000000..4cf87ff
--- /dev/null
+++ b/ModuleCall/nbproject/Makefile-variables.mk
@@ -0,0 +1,35 @@
+#
+# Generated - do not edit!
+#
+# NOCDDL
+#
+CND_BASEDIR=`pwd`
+CND_BUILDDIR=build
+CND_DISTDIR=dist
+# Debug configuration
+CND_PLATFORM_Debug=GNU-Linux-x86
+CND_ARTIFACT_DIR_Debug=dist/Debug/GNU-Linux-x86
+CND_ARTIFACT_NAME_Debug=modulecall
+CND_ARTIFACT_PATH_Debug=dist/Debug/GNU-Linux-x86/modulecall
+CND_PACKAGE_DIR_Debug=dist/Debug/GNU-Linux-x86/package
+CND_PACKAGE_NAME_Debug=modulecall.tar
+CND_PACKAGE_PATH_Debug=dist/Debug/GNU-Linux-x86/package/modulecall.tar
+# Release configuration
+CND_PLATFORM_Release=GNU-Linux-x86
+CND_ARTIFACT_DIR_Release=dist/Release/GNU-Linux-x86
+CND_ARTIFACT_NAME_Release=modulecall
+CND_ARTIFACT_PATH_Release=dist/Release/GNU-Linux-x86/modulecall
+CND_PACKAGE_DIR_Release=dist/Release/GNU-Linux-x86/package
+CND_PACKAGE_NAME_Release=modulecall.tar
+CND_PACKAGE_PATH_Release=dist/Release/GNU-Linux-x86/package/modulecall.tar
+#
+# include compiler specific variables
+#
+# dmake command
+ROOT:sh = test -f nbproject/private/Makefile-variables.mk || \
+       (mkdir -p nbproject/private && touch nbproject/private/Makefile-variables.mk)
+#
+# gmake command
+.PHONY: $(shell test -f nbproject/private/Makefile-variables.mk || (mkdir -p nbproject/private && touch nbproject/private/Makefile-variables.mk))
+#
+include nbproject/private/Makefile-variables.mk

diff --git a/ModuleCall/nbproject/Package-Debug.bash b/ModuleCall/nbproject/Package-Debug.bash
new file mode 100644 (file)
index 0000000..4ed3e78
--- /dev/null
+++ b/ModuleCall/nbproject/Package-Debug.bash
@@ -0,0 +1,75 @@
+#!/bin/bash -x
+
+#
+# Generated - do not edit!
+#
+
+# Macros
+TOP=`pwd`
+CND_PLATFORM=GNU-Linux-x86
+CND_CONF=Debug
+CND_DISTDIR=dist
+CND_BUILDDIR=build
+NBTMPDIR=${CND_BUILDDIR}/${CND_CONF}/${CND_PLATFORM}/tmp-packaging
+TMPDIRNAME=tmp-packaging
+OUTPUT_PATH=${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall
+OUTPUT_BASENAME=modulecall
+PACKAGE_TOP_DIR=modulecall/
+
+# Functions
+function checkReturnCode
+{
+    rc=$?
+    if [ $rc != 0 ]
+    then
+        exit $rc
+    fi
+}
+function makeDirectory
+# $1 directory path
+# $2 permission (optional)
+{
+    mkdir -p "$1"
+    checkReturnCode
+    if [ "$2" != "" ]
+    then
+      chmod $2 "$1"
+      checkReturnCode
+    fi
+}
+function copyFileToTmpDir
+# $1 from-file path
+# $2 to-file path
+# $3 permission
+{
+    cp "$1" "$2"
+    checkReturnCode
+    if [ "$3" != "" ]
+    then
+        chmod $3 "$2"
+        checkReturnCode
+    fi
+}
+
+# Setup
+cd "${TOP}"
+mkdir -p ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/package
+rm -rf ${NBTMPDIR}
+mkdir -p ${NBTMPDIR}
+
+# Copy files and create directories and links
+cd "${TOP}"
+makeDirectory "${NBTMPDIR}/modulecall/bin"
+copyFileToTmpDir "${OUTPUT_PATH}" "${NBTMPDIR}/${PACKAGE_TOP_DIR}bin/${OUTPUT_BASENAME}" 0755
+
+
+# Generate tar file
+cd "${TOP}"
+rm -f ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/package/modulecall.tar
+cd ${NBTMPDIR}
+tar -vcf ../../../../${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/package/modulecall.tar *
+checkReturnCode
+
+# Cleanup
+cd "${TOP}"
+rm -rf ${NBTMPDIR}

diff --git a/ModuleCall/nbproject/Package-Release.bash b/ModuleCall/nbproject/Package-Release.bash
new file mode 100644 (file)
index 0000000..1708a01
--- /dev/null
+++ b/ModuleCall/nbproject/Package-Release.bash
@@ -0,0 +1,75 @@
+#!/bin/bash -x
+
+#
+# Generated - do not edit!
+#
+
+# Macros
+TOP=`pwd`
+CND_PLATFORM=GNU-Linux-x86
+CND_CONF=Release
+CND_DISTDIR=dist
+CND_BUILDDIR=build
+NBTMPDIR=${CND_BUILDDIR}/${CND_CONF}/${CND_PLATFORM}/tmp-packaging
+TMPDIRNAME=tmp-packaging
+OUTPUT_PATH=${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/modulecall
+OUTPUT_BASENAME=modulecall
+PACKAGE_TOP_DIR=modulecall/
+
+# Functions
+function checkReturnCode
+{
+    rc=$?
+    if [ $rc != 0 ]
+    then
+        exit $rc
+    fi
+}
+function makeDirectory
+# $1 directory path
+# $2 permission (optional)
+{
+    mkdir -p "$1"
+    checkReturnCode
+    if [ "$2" != "" ]
+    then
+      chmod $2 "$1"
+      checkReturnCode
+    fi
+}
+function copyFileToTmpDir
+# $1 from-file path
+# $2 to-file path
+# $3 permission
+{
+    cp "$1" "$2"
+    checkReturnCode
+    if [ "$3" != "" ]
+    then
+        chmod $3 "$2"
+        checkReturnCode
+    fi
+}
+
+# Setup
+cd "${TOP}"
+mkdir -p ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/package
+rm -rf ${NBTMPDIR}
+mkdir -p ${NBTMPDIR}
+
+# Copy files and create directories and links
+cd "${TOP}"
+makeDirectory "${NBTMPDIR}/modulecall/bin"
+copyFileToTmpDir "${OUTPUT_PATH}" "${NBTMPDIR}/${PACKAGE_TOP_DIR}bin/${OUTPUT_BASENAME}" 0755
+
+
+# Generate tar file
+cd "${TOP}"
+rm -f ${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/package/modulecall.tar
+cd ${NBTMPDIR}
+tar -vcf ../../../../${CND_DISTDIR}/${CND_CONF}/${CND_PLATFORM}/package/modulecall.tar *
+checkReturnCode
+
+# Cleanup
+cd "${TOP}"
+rm -rf ${NBTMPDIR}

diff --git a/ModuleCall/nbproject/configurations.xml b/ModuleCall/nbproject/configurations.xml
new file mode 100644 (file)
index 0000000..f83998e
--- /dev/null
+++ b/ModuleCall/nbproject/configurations.xml
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configurationDescriptor version="80">
+  <logicalFolder name="root" displayName="root" projectFiles="true" kind="ROOT">
+    <logicalFolder name="HeaderFiles"
+                   displayName="Header Files"
+                   projectFiles="true">
+    </logicalFolder>
+    <logicalFolder name="ResourceFiles"
+                   displayName="Resource Files"
+                   projectFiles="true">
+    </logicalFolder>
+    <logicalFolder name="SourceFiles"
+                   displayName="Source Files"
+                   projectFiles="true">
+      <itemPath>CreationTool.cxx</itemPath>
+      <itemPath>CreationTool.h</itemPath>
+      <itemPath>main.cpp</itemPath>
+    </logicalFolder>
+    <logicalFolder name="TestFiles"
+                   displayName="Test Files"
+                   projectFiles="false"
+                   kind="TEST_LOGICAL_FOLDER">
+    </logicalFolder>
+    <logicalFolder name="ExternalFiles"
+                   displayName="Important Files"
+                   projectFiles="false"
+                   kind="IMPORTANT_FILES_FOLDER">
+      <itemPath>Makefile</itemPath>
+    </logicalFolder>
+  </logicalFolder>
+  <projectmakefile>Makefile</projectmakefile>
+  <confs>
+    <conf name="Debug" type="1">
+      <toolsSet>
+        <remote-sources-mode>LOCAL_SOURCES</remote-sources-mode>
+        <compilerSet>default</compilerSet>
+      </toolsSet>
+      <compileType>
+        <ccTool>
+          <commandLine>-ldl</commandLine>
+        </ccTool>
+      </compileType>
+    </conf>
+    <conf name="Release" type="1">
+      <toolsSet>
+        <remote-sources-mode>LOCAL_SOURCES</remote-sources-mode>
+        <compilerSet>default</compilerSet>
+      </toolsSet>
+      <compileType>
+        <cTool>
+          <developmentMode>5</developmentMode>
+        </cTool>
+        <ccTool>
+          <developmentMode>5</developmentMode>
+          <commandLine>-ldl -w</commandLine>
+        </ccTool>
+        <fortranCompilerTool>
+          <developmentMode>5</developmentMode>
+        </fortranCompilerTool>
+        <asmTool>
+          <developmentMode>5</developmentMode>
+        </asmTool>
+      </compileType>
+    </conf>
+  </confs>
+</configurationDescriptor>

diff --git a/ModuleCall/nbproject/private/Makefile-variables.mk b/ModuleCall/nbproject/private/Makefile-variables.mk
new file mode 100644 (file)
index 0000000..a64183e
--- /dev/null
+++ b/ModuleCall/nbproject/private/Makefile-variables.mk
@@ -0,0 +1,7 @@
+#
+# Generated - do not edit!
+#
+# NOCDDL
+#
+# Debug configuration
+# Release configuration

diff --git a/ModuleCall/nbproject/private/configurations.xml b/ModuleCall/nbproject/private/configurations.xml
new file mode 100644 (file)
index 0000000..10e0756
--- /dev/null
+++ b/ModuleCall/nbproject/private/configurations.xml
@@ -0,0 +1,72 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<configurationDescriptor version="80">
+  <projectmakefile>Makefile</projectmakefile>
+  <confs>
+    <conf name="Debug" type="1">
+      <toolsSet>
+        <developmentServer>localhost</developmentServer>
+        <platform>2</platform>
+      </toolsSet>
+      <dbx_gdbdebugger version="1">
+        <gdb_pathmaps>
+        </gdb_pathmaps>
+        <gdb_interceptlist>
+          <gdbinterceptoptions gdb_all="false" gdb_unhandled="true" gdb_unexpected="true"/>
+        </gdb_interceptlist>
+        <gdb_options>
+          <DebugOptions>
+          </DebugOptions>
+        </gdb_options>
+        <gdb_buildfirst gdb_buildfirst_overriden="false" gdb_buildfirst_old="false"/>
+      </dbx_gdbdebugger>
+      <nativedebugger version="1">
+        <engine>gdb</engine>
+      </nativedebugger>
+      <runprofile version="9">
+        <runcommandpicklist>
+          <runcommandpicklistitem>"${OUTPUT_PATH}"</runcommandpicklistitem>
+        </runcommandpicklist>
+        <runcommand>"${OUTPUT_PATH}"</runcommand>
+        <rundir></rundir>
+        <buildfirst>true</buildfirst>
+        <terminal-type>0</terminal-type>
+        <remove-instrumentation>0</remove-instrumentation>
+        <environment>
+        </environment>
+      </runprofile>
+    </conf>
+    <conf name="Release" type="1">
+      <toolsSet>
+        <developmentServer>localhost</developmentServer>
+        <platform>2</platform>
+      </toolsSet>
+      <dbx_gdbdebugger version="1">
+        <gdb_pathmaps>
+        </gdb_pathmaps>
+        <gdb_interceptlist>
+          <gdbinterceptoptions gdb_all="false" gdb_unhandled="true" gdb_unexpected="true"/>
+        </gdb_interceptlist>
+        <gdb_options>
+          <DebugOptions>
+          </DebugOptions>
+        </gdb_options>
+        <gdb_buildfirst gdb_buildfirst_overriden="false" gdb_buildfirst_old="false"/>
+      </dbx_gdbdebugger>
+      <nativedebugger version="1">
+        <engine>gdb</engine>
+      </nativedebugger>
+      <runprofile version="9">
+        <runcommandpicklist>
+          <runcommandpicklistitem>"${OUTPUT_PATH}"</runcommandpicklistitem>
+        </runcommandpicklist>
+        <runcommand>"${OUTPUT_PATH}"</runcommand>
+        <rundir></rundir>
+        <buildfirst>true</buildfirst>
+        <terminal-type>0</terminal-type>
+        <remove-instrumentation>0</remove-instrumentation>
+        <environment>
+        </environment>
+      </runprofile>
+    </conf>
+  </confs>
+</configurationDescriptor>

diff --git a/ModuleCall/nbproject/private/private.xml b/ModuleCall/nbproject/private/private.xml
new file mode 100644 (file)
index 0000000..c15bbcb
--- /dev/null
+++ b/ModuleCall/nbproject/private/private.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project-private xmlns="http://www.netbeans.org/ns/project-private/1">
+    <data xmlns="http://www.netbeans.org/ns/make-project-private/1">
+        <activeConfTypeElem>1</activeConfTypeElem>
+        <activeConfIndexElem>1</activeConfIndexElem>
+    </data>
+    <editor-bookmarks xmlns="http://www.netbeans.org/ns/editor-bookmarks/1"/>
+</project-private>

diff --git a/ModuleCall/nbproject/project.xml b/ModuleCall/nbproject/project.xml
new file mode 100644 (file)
index 0000000..949b38c
--- /dev/null
+++ b/ModuleCall/nbproject/project.xml
@@ -0,0 +1,25 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://www.netbeans.org/ns/project/1">
+    <type>org.netbeans.modules.cnd.makeproject</type>
+    <configuration>
+        <data xmlns="http://www.netbeans.org/ns/make-project/1">
+            <name>ModuleCall</name>
+            <c-extensions/>
+            <cpp-extensions>cpp,cxx</cpp-extensions>
+            <header-extensions>h</header-extensions>
+            <sourceEncoding>UTF-8</sourceEncoding>
+            <make-dep-projects/>
+            <sourceRootList/>
+            <confList>
+                <confElem>
+                    <name>Debug</name>
+                    <type>1</type>
+                </confElem>
+                <confElem>
+                    <name>Release</name>
+                    <type>1</type>
+                </confElem>
+            </confList>
+        </data>
+    </configuration>
+</project>

diff --git a/bbtk_Slicer_PKG/src/CreationTool.cxx b/bbtk_Slicer_PKG/src/CreationTool.cxx
index b3c7095aefde5de275e3c81a2ed125c7f8b8b97c..872fc7c03de8d3b31783962abd862b0a4d9dbf8d 100644 (file)
--- a/bbtk_Slicer_PKG/src/CreationTool.cxx
+++ b/bbtk_Slicer_PKG/src/CreationTool.cxx
@@ -10,73 +10,222 @@
 std::string Mthd::Aux::toString ( float n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( double n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( long double n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( char n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned char n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( short n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned short n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( long int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned long n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
 }
 
 std::string Mthd::Aux::toString ( unsigned long long n ) {
     std::ostringstream oss ;
     oss << n ;
-    return oss.str( ) ;
+    return oss.str ( ) ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<float> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<double> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<long double> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<long int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<unsigned int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<unsigned long> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<unsigned long long> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::basic_string<char> > v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return _vector ;
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< int > > v ) {
+    return "Not implemented";
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< float > > v ) {
+    return "Not implemented";
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< double > > v ) {
+    return "Not implemented";
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< long int > > v ) {
+    return "Not implemented";
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< long double > > v ) {
+    return "Not implemented";
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< unsigned int > > v ) {
+    return "Not implemented";
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< unsigned long > > v ) {
+    return "Not implemented";
+}
+
+std::string Mthd::Aux::toString ( std::vector<std::vector< unsigned long long > > v ) {
+    return "Not implemented";
 }
 
 std::string Mthd::Aux::toString ( std::string n ) {
@@ -86,84 +235,188 @@ std::string Mthd::Aux::toString ( std::string n ) {
 char* Mthd::Aux::toCharArrray ( float n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( double n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( long double n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( char n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( unsigned char n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( short n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( unsigned short n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( long int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( unsigned int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( long unsigned int n ) {
     std::ostringstream oss ;
     oss << n ;
-    return const_cast < char* > ( oss.str( ).data( ) ) ;
+    return const_cast < char* > ( oss.str ( ).data ( ) ) ;
 }
 
 char* Mthd::Aux::toCharArrray ( std::string n ) {
-    return const_cast < char* > ( n.data( ) ) ;
+    return const_cast < char* > ( n.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<float> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<double> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<long double> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<long int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<unsigned int> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<unsigned long> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
+}
+
+char* Mthd::Aux::toCharArrray ( std::vector<unsigned long long> v ) {
+    std::ostringstream oss ;
+    std::string _vector = std::string ( "" ) ;
+    for ( long unsigned int i = 0 ; i < v.size ( ) ; i ++ ) {
+        oss << v.at ( i ) ;
+        _vector += oss.str ( ) ;
+        if ( i + 1 < v.size ( ) ) {
+            _vector += "," ;
+        }
+    }
+    return const_cast < char* > ( _vector.data ( ) ) ;
 }
 
 std::string Mthd::Aux::replace_str ( std::string input , std::string old_str , std::string new_str ) {
-    size_t found = input.find( old_str ) ;
+    size_t found = input.find ( old_str ) ;
     while ( found != std::string::npos ) {
-        input.replace( found , old_str.length( ) , new_str ) ;
-        found = input.find( old_str ) ;
+        input.replace ( found , old_str.length ( ) , new_str ) ;
+        found = input.find ( old_str ) ;
     }
     return input ;
 }
 
 bool Mthd::Aux::str_ends_with ( std::string total_str , std::string sub_str ) {
-    size_t found = total_str.find( sub_str ) ;
+    size_t found = total_str.find ( sub_str ) ;
     if ( found != std::string::npos ) {
         return true ;
     }

diff --git a/bbtk_Slicer_PKG/src/CreationTool.h b/bbtk_Slicer_PKG/src/CreationTool.h
index 27dcb8222bade35a5cfdae9151fca0470cbecc36..4fdbee9ae39460d5fdba7c42718126f73f87a013 100644 (file)
--- a/bbtk_Slicer_PKG/src/CreationTool.h
+++ b/bbtk_Slicer_PKG/src/CreationTool.h
@@ -11,6 +11,7 @@
 #include <string>
 #include <iostream>
 #include <sstream>
+#include <vector>
 
 namespace Mthd {
 
@@ -32,6 +33,26 @@ namespace Mthd {
         static std::string toString ( unsigned long n ) ;
         static std::string toString ( unsigned long long n ) ;
 
+        static std::string toString ( std::vector<int> v ) ;
+        static std::string toString ( std::vector<float> v ) ;
+        static std::string toString ( std::vector<double> v ) ;
+        static std::string toString ( std::vector<long int> v ) ;
+        static std::string toString ( std::vector<long double> v ) ;
+        static std::string toString ( std::vector<unsigned int> v ) ;
+        static std::string toString ( std::vector<unsigned long> v ) ;
+        static std::string toString ( std::vector<unsigned long long> v ) ;
+        static std::string toString ( std::vector<std::basic_string<char> > v ) ;
+
+        static std::string toString ( std::vector< std::vector< int > > v ) ;
+        static std::string toString ( std::vector< std::vector< float > > v ) ;
+        static std::string toString ( std::vector< std::vector< double > > v ) ;
+        static std::string toString ( std::vector< std::vector< long int > > v ) ;
+        static std::string toString ( std::vector< std::vector< long double > > v ) ;
+        static std::string toString ( std::vector< std::vector< unsigned int > > v ) ;
+        static std::string toString ( std::vector< std::vector< unsigned long > > v ) ;
+        static std::string toString ( std::vector< std::vector< unsigned long long > > v ) ;
+
+
         static std::string toString ( std::string n ) ;
 
         static char* toCharArrray ( float n ) ;
@@ -49,10 +70,19 @@ namespace Mthd {
         static char* toCharArrray ( unsigned int n ) ;
         static char* toCharArrray ( long unsigned int n ) ;
 
+        static char* toCharArrray ( std::vector<int> v ) ;
+        static char* toCharArrray ( std::vector<float> v ) ;
+        static char* toCharArrray ( std::vector<double> v ) ;
+        static char* toCharArrray ( std::vector<long int> v ) ;
+        static char* toCharArrray ( std::vector<long double> v ) ;
+        static char* toCharArrray ( std::vector<unsigned int> v ) ;
+        static char* toCharArrray ( std::vector<unsigned long> v ) ;
+        static char* toCharArrray ( std::vector<unsigned long long> v ) ;
+
         static char* toCharArrray ( std::string n ) ;
 
         static bool str_ends_with ( std::string total_str , std::string sub_str ) ;
-        static std::string replace_str ( std::string input , std::string old_str , std::string new_str ) ;      
+        static std::string replace_str ( std::string input , std::string old_str , std::string new_str ) ;
 
     } ;
 

diff --git a/bbtk_Slicer_PKG/src/bbSlicerACPCTransform.cxx b/bbtk_Slicer_PKG/src/bbSlicerACPCTransform.cxx
new file mode 100644 (file)
index 0000000..d458ed8
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerACPCTransform.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerACPCTransform.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ACPCTransform )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ACPCTransform, bbtk::AtomicBlackBox );
+
+    void ACPCTransform::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRealignLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--acpc"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputACPC( ) ) ) ,"@@@@@"," --acpc ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--midline"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMidline( ) ) ) ,"@@@@@"," --midline ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdebugSwitch( ) ) ) ,"@@@@@"," -d ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ACPCTransform::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ACPCTransform::bbUserSetDefaultValues ( ) {
+    }
+
+    void ACPCTransform::bbUserInitializeProcessing ( ) {
+    }
+
+    void ACPCTransform::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerACPCTransform.h b/bbtk_Slicer_PKG/src/bbSlicerACPCTransform.h
new file mode 100644 (file)
index 0000000..f5da823
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerACPCTransform.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerACPCTransform_h_INCLUDED__
+#define __bbSlicerACPCTransform_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ACPCTransform
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ACPCTransform , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( ACPC , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( Midline , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( debugSwitch , bool );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ACPCTransform , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ACPCTransform" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH" ) ;
+    BBTK_DESCRIPTION ( "pCalculate a transformation from two lists of fiducial points./ppACPC line is two fiducial points, one at the anterior commissure and one at the posterior commissure. The resulting transform will bring the line connecting them to horizontal to the AP axis./ppThe midline is a series of points defining the division between the hemispheres of the brain the mid sagittal plane. The resulting transform will put the output volume with the mid sagittal plane lined up with the AS plane./ppUse the Filtering module bResample Scalar/Vector/DWI Volume/b to apply the transformation to a volume./p" ) ;
+    BBTK_CATEGORY ( "Registration.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ACPCTransform , ACPC , "ACPC" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ACPCTransform , Midline , "Midline" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ACPCTransform , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(ACPCTransform , debugSwitch , "debugSwitch" , bool, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ACPCTransform ) ;
+}
+
+#endif // __bbSlicerACPCTransform_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerAddImages.cxx b/bbtk_Slicer_PKG/src/bbSlicerAddImages.cxx
index d66e444c7a55ded2dffce3c6e06766c623dffb1c..ec5f7a5eba147ab5320a43bf8669f149ec7c3113 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerAddImages.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerAddImages.cxx
@@ -11,10 +11,10 @@ namespace bbSlicer {
 
 int _argc =4;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libAddLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--order"  ) + Mthd::Aux::toString( bbGetInputorder( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--order"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputorder( ) ) ) ,"@@@@@"," --order ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerBSplinetodeformationfield.cxx b/bbtk_Slicer_PKG/src/bbSlicerBSplinetodeformationfield.cxx
index 263332950bf9bafd8e3022c7333ec24c46cd077b..9ed73dafd5caefc5a1e2e3a8470b5a36c22f9f74 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerBSplinetodeformationfield.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerBSplinetodeformationfield.cxx
@@ -11,9 +11,9 @@ namespace bbSlicer {
 
 int _argc =3;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBSplineToDeformationFieldLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--tfm"  ) + Mthd::Aux::toString( bbGetInputinputTransformName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--refImage"  ) + Mthd::Aux::toString( bbGetInputreferenceImageName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--defImage"  ) + Mthd::Aux::toString( bbGetInputdeformationFieldName( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--tfm"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputTransformName( ) ) ) ,"@@@@@"," --tfm ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--refImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreferenceImageName( ) ) ) ,"@@@@@"," --refImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--defImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdeformationFieldName( ) ) ) ,"@@@@@"," --defImage ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerCastImage.cxx b/bbtk_Slicer_PKG/src/bbSlicerCastImage.cxx
new file mode 100644 (file)
index 0000000..8715b97
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerCastImage.cxx
@@ -0,0 +1,57 @@
+#include "bbSlicerCastImage.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, CastImage )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( CastImage, bbtk::AtomicBlackBox );
+
+    void CastImage::Process ( ) {
+
+        // GENERATED
+
+int _argc =3;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libCastLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputType( ) ) ) ,"@@@@@"," -t ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void CastImage::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void CastImage::bbUserSetDefaultValues ( ) {
+    }
+
+    void CastImage::bbUserInitializeProcessing ( ) {
+    }
+
+    void CastImage::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerCastImage.h b/bbtk_Slicer_PKG/src/bbSlicerCastImage.h
new file mode 100644 (file)
index 0000000..ba1237a
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerCastImage.h
@@ -0,0 +1,62 @@
+#ifndef __bbSlicerCastImage_h_INCLUDED__
+#define __bbSlicerCastImage_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT CastImage
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( CastImage , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( OutputVolume , std::string );
+BBTK_DECLARE_INPUT ( Type , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( CastImage , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "CastImage" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH" ) ;
+    BBTK_DESCRIPTION ( "Cast a volume to a given data type.Use at your own risk when casting an input volume into a lower precision type!Allows casting to the same type as the input volume." ) ;
+    BBTK_CATEGORY ( "Filtering.Arithmetic" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(CastImage , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(CastImage , OutputVolume , "OutputVolume" , std::string, "");
+BBTK_INPUT(CastImage , Type , "Type" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( CastImage ) ;
+}
+
+#endif // __bbSlicerCastImage_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerCheckerBoardFilter.cxx b/bbtk_Slicer_PKG/src/bbSlicerCheckerBoardFilter.cxx
new file mode 100644 (file)
index 0000000..3201891
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerCheckerBoardFilter.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerCheckerBoardFilter.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, CheckerBoardFilter )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( CheckerBoardFilter, bbtk::AtomicBlackBox );
+
+    void CheckerBoardFilter::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libCheckerBoardLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--checkerPattern"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcheckerPattern( ) ) ) ,"@@@@@"," --checkerPattern ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void CheckerBoardFilter::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void CheckerBoardFilter::bbUserSetDefaultValues ( ) {
+    }
+
+    void CheckerBoardFilter::bbUserInitializeProcessing ( ) {
+    }
+
+    void CheckerBoardFilter::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerCheckerBoardFilter.h b/bbtk_Slicer_PKG/src/bbSlicerCheckerBoardFilter.h
new file mode 100644 (file)
index 0000000..7bd4a22
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerCheckerBoardFilter.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerCheckerBoardFilter_h_INCLUDED__
+#define __bbSlicerCheckerBoardFilter_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT CheckerBoardFilter
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( CheckerBoardFilter , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( checkerPattern , std::vector<int> );
+BBTK_DECLARE_INPUT ( inputVolume1 , std::string );
+BBTK_DECLARE_INPUT ( inputVolume2 , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( CheckerBoardFilter , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "CheckerBoardFilter" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Create a checkerboard volume of two volumes. The output volume will show the two inputs alternating according to the user supplied checkerPattern. This filter is often used to compare the results of image registration. Note that the second input is resampled to the same origin, spacing and direction before it is composed with the first input. The scalar type of the output volume will be the same as the input image scalar type." ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(CheckerBoardFilter , checkerPattern , "checkerPattern" , std::vector<int>, "");
+BBTK_INPUT(CheckerBoardFilter , inputVolume1 , "inputVolume1" , std::string, "");
+BBTK_INPUT(CheckerBoardFilter , inputVolume2 , "inputVolume2" , std::string, "");
+BBTK_INPUT(CheckerBoardFilter , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( CheckerBoardFilter ) ;
+}
+
+#endif // __bbSlicerCheckerBoardFilter_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerCommandLineModuleTest.cxx b/bbtk_Slicer_PKG/src/bbSlicerCommandLineModuleTest.cxx
index ba3a3581dc2a96685041d4e3c53a13dd11193c88..4b63cfb3ef2942bf5a4a019ec8cb8778dab9c112 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerCommandLineModuleTest.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerCommandLineModuleTest.cxx
@@ -11,10 +11,10 @@ namespace bbSlicer {
 
 int _argc =4;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libCLIModule4TestLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputvalue1"  ) + Mthd::Aux::toString( bbGetInputInputValue1( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputvalue2"  ) + Mthd::Aux::toString( bbGetInputInputValue2( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--operationtype"  ) + Mthd::Aux::toString( bbGetInputOperationType( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputOutputFile( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputvalue1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputValue1( ) ) ) ,"@@@@@"," --inputvalue1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputvalue2"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputValue2( ) ) ) ,"@@@@@"," --inputvalue2 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--operationtype"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOperationType( ) ) ) ,"@@@@@"," --operationtype ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputFile( ) ) ) ,"@@@@@","") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerCreateaDICOMSeries.cxx b/bbtk_Slicer_PKG/src/bbSlicerCreateaDICOMSeries.cxx
index 1fe0e73025f30e2f6b7a0c2e4e74e2fc12696035..a51004b47b1509c593d2405fbbb0b52f9688aaa7 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerCreateaDICOMSeries.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerCreateaDICOMSeries.cxx
@@ -11,26 +11,26 @@ namespace bbSlicer {
 
 int _argc =20;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libImageReadDicomWriteLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--patientName"  ) + Mthd::Aux::toString( bbGetInputpatientName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--patientID"  ) + Mthd::Aux::toString( bbGetInputpatientID( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--patientComments"  ) + Mthd::Aux::toString( bbGetInputpatientComments( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyID"  ) + Mthd::Aux::toString( bbGetInputstudyID( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyDate"  ) + Mthd::Aux::toString( bbGetInputstudyDate( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyComments"  ) + Mthd::Aux::toString( bbGetInputstudyComments( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyDescription"  ) + Mthd::Aux::toString( bbGetInputstudyDescription( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--modality"  ) + Mthd::Aux::toString( bbGetInputmodality( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--manufacturer"  ) + Mthd::Aux::toString( bbGetInputmanufacturer( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--model"  ) + Mthd::Aux::toString( bbGetInputmodel( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seriesNumber"  ) + Mthd::Aux::toString( bbGetInputseriesNumber( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seriesDescription"  ) + Mthd::Aux::toString( bbGetInputseriesDescription( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rescaleIntercept"  ) + Mthd::Aux::toString( bbGetInputrescaleIntercept( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rescaleSlope"  ) + Mthd::Aux::toString( bbGetInputrescaleSlope( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dicomDirectory"  ) + Mthd::Aux::toString( bbGetInputdicomDirectory( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dicomPrefix"  ) + Mthd::Aux::toString( bbGetInputdicomPrefix( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dicomNumberFormat"  ) + Mthd::Aux::toString( bbGetInputdicomNumberFormat( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--reverseImages"  ) + Mthd::Aux::toString( bbGetInputreverseImages( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useCompression"  ) + Mthd::Aux::toString( bbGetInputuseCompression( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--patientName"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpatientName( ) ) ) ,"@@@@@"," --patientName ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--patientID"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpatientID( ) ) ) ,"@@@@@"," --patientID ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--patientComments"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpatientComments( ) ) ) ,"@@@@@"," --patientComments ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyID"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstudyID( ) ) ) ,"@@@@@"," --studyID ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyDate"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstudyDate( ) ) ) ,"@@@@@"," --studyDate ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyComments"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstudyComments( ) ) ) ,"@@@@@"," --studyComments ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--studyDescription"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstudyDescription( ) ) ) ,"@@@@@"," --studyDescription ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--modality"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmodality( ) ) ) ,"@@@@@"," --modality ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--manufacturer"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmanufacturer( ) ) ) ,"@@@@@"," --manufacturer ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--model"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmodel( ) ) ) ,"@@@@@"," --model ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seriesNumber"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseriesNumber( ) ) ) ,"@@@@@"," --seriesNumber ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seriesDescription"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseriesDescription( ) ) ) ,"@@@@@"," --seriesDescription ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rescaleIntercept"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrescaleIntercept( ) ) ) ,"@@@@@"," --rescaleIntercept ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rescaleSlope"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrescaleSlope( ) ) ) ,"@@@@@"," --rescaleSlope ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dicomDirectory"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdicomDirectory( ) ) ) ,"@@@@@"," --dicomDirectory ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dicomPrefix"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdicomPrefix( ) ) ) ,"@@@@@"," --dicomPrefix ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dicomNumberFormat"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdicomNumberFormat( ) ) ) ,"@@@@@"," --dicomNumberFormat ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--reverseImages"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreverseImages( ) ) ) ,"@@@@@"," --reverseImages ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useCompression"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseCompression( ) ) ) ,"@@@@@"," --useCompression ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerCurvatureAnisotropicDiffusion.cxx b/bbtk_Slicer_PKG/src/bbSlicerCurvatureAnisotropicDiffusion.cxx
new file mode 100644 (file)
index 0000000..a356744
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerCurvatureAnisotropicDiffusion.cxx
@@ -0,0 +1,59 @@
+#include "bbSlicerCurvatureAnisotropicDiffusion.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, CurvatureAnisotropicDiffusion )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( CurvatureAnisotropicDiffusion, bbtk::AtomicBlackBox );
+
+    void CurvatureAnisotropicDiffusion::Process ( ) {
+
+        // GENERATED
+
+int _argc =5;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libCurvatureAnisotropicDiffusionLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--conductance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputconductance( ) ) ) ,"@@@@@"," --conductance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --iterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--timeStep"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtimeStep( ) ) ) ,"@@@@@"," --timeStep ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void CurvatureAnisotropicDiffusion::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void CurvatureAnisotropicDiffusion::bbUserSetDefaultValues ( ) {
+    }
+
+    void CurvatureAnisotropicDiffusion::bbUserInitializeProcessing ( ) {
+    }
+
+    void CurvatureAnisotropicDiffusion::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerCurvatureAnisotropicDiffusion.h b/bbtk_Slicer_PKG/src/bbSlicerCurvatureAnisotropicDiffusion.h
new file mode 100644 (file)
index 0000000..fc17218
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerCurvatureAnisotropicDiffusion.h
@@ -0,0 +1,66 @@
+#ifndef __bbSlicerCurvatureAnisotropicDiffusion_h_INCLUDED__
+#define __bbSlicerCurvatureAnisotropicDiffusion_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT CurvatureAnisotropicDiffusion
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( CurvatureAnisotropicDiffusion , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( conductance , double );
+BBTK_DECLARE_INPUT ( numberOfIterations , int );
+BBTK_DECLARE_INPUT ( timeStep , double );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( CurvatureAnisotropicDiffusion , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "CurvatureAnisotropicDiffusion" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Performs anisotropic diffusion on an image using a modified curvature diffusion equation MCDE.MCDE does not exhibit the edge enhancing properties of classic anisotropic diffusion, which can under certain conditions undergo a 'negative' diffusion, which enhances the contrast of edges.  Equations of the form of MCDE always undergo positive diffusion, with the conductance term only varying the strength of that diffusion.  Qualitatively, MCDE compares well with other non-linear diffusion techniques.  It is less sensitive to contrast than classic Perona-Malik style diffusion, and preserves finer detailed structures in images.  There is a potential speed trade-off for using this function in place of Gradient Anisotropic Diffusion.  Each iteration of the solution takes roughly twice as long.  Fewer iterations, however, may be required to reach an acceptable solution." ) ;
+    BBTK_CATEGORY ( "Filtering.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(CurvatureAnisotropicDiffusion , conductance , "conductance" , double, "");
+BBTK_INPUT(CurvatureAnisotropicDiffusion , numberOfIterations , "numberOfIterations" , int, "");
+BBTK_INPUT(CurvatureAnisotropicDiffusion , timeStep , "timeStep" , double, "");
+BBTK_INPUT(CurvatureAnisotropicDiffusion , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(CurvatureAnisotropicDiffusion , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( CurvatureAnisotropicDiffusion ) ;
+}
+
+#endif // __bbSlicerCurvatureAnisotropicDiffusion_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerDemonRegistrationBRAINS.cxx b/bbtk_Slicer_PKG/src/bbSlicerDemonRegistrationBRAINS.cxx
new file mode 100644 (file)
index 0000000..bef5a5e
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerDemonRegistrationBRAINS.cxx
@@ -0,0 +1,94 @@
+#include "bbSlicerDemonRegistrationBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, DemonRegistrationBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( DemonRegistrationBRAINS, bbtk::AtomicBlackBox );
+
+    void DemonRegistrationBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =40;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBRAINSDemonWarpLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-m"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingVolume( ) ) ) ,"@@@@@"," -m ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedVolume( ) ) ) ,"@@@@@"," -f ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputPixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputPixelType( ) ) ) ,"@@@@@"," --inputPixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-o"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," -o ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-O"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDisplacementFieldVolume( ) ) ) ,"@@@@@"," -O ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputPixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputPixelType( ) ) ) ,"@@@@@"," --outputPixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolationMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationMode( ) ) ) ,"@@@@@"," --interpolationMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--registrationFilterType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputregistrationFilterType( ) ) ) ,"@@@@@"," --registrationFilterType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothDisplacementFieldSigma( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-n"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfPyramidLevels( ) ) ) ,"@@@@@"," -n ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumFixedPyramid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumFixedPyramid( ) ) ) ,"@@@@@"," --minimumFixedPyramid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumMovingPyramid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumMovingPyramid( ) ) ) ,"@@@@@"," --minimumMovingPyramid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputarrayOfPyramidLevelIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputhistogramMatch( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfHistogramBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfHistogramBins( ) ) ) ,"@@@@@"," --numberOfHistogramBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfMatchPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfMatchPoints( ) ) ) ,"@@@@@"," --numberOfMatchPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--medianFilterSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmedianFilterSize( ) ) ) ,"@@@@@"," --medianFilterSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeWithDisplacementField"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeWithDisplacementField( ) ) ) ,"@@@@@"," --initializeWithDisplacementField ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeWithTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeWithTransform( ) ) ) ,"@@@@@"," --initializeWithTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maskProcessingMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaskProcessingMode( ) ) ) ,"@@@@@"," --maskProcessingMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedBinaryVolume( ) ) ) ,"@@@@@"," --fixedBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingBinaryVolume( ) ) ) ,"@@@@@"," --movingBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--lowerThresholdForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlowerThresholdForBOBF( ) ) ) ,"@@@@@"," --lowerThresholdForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--upperThresholdForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputupperThresholdForBOBF( ) ) ) ,"@@@@@"," --upperThresholdForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--backgroundFillValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbackgroundFillValue( ) ) ) ,"@@@@@"," --backgroundFillValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seedForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseedForBOBF( ) ) ) ,"@@@@@"," --seedForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--neighborhoodForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputneighborhoodForBOBF( ) ) ) ,"@@@@@"," --neighborhoodForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputDisplacementFieldPrefix"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDisplacementFieldPrefix( ) ) ) ,"@@@@@"," --outputDisplacementFieldPrefix ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputCheckerboardVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputCheckerboardVolume( ) ) ) ,"@@@@@"," --outputCheckerboardVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--checkerboardPatternSubdivisions"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcheckerboardPatternSubdivisions( ) ) ) ,"@@@@@"," --checkerboardPatternSubdivisions ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputNormalized"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputNormalized( ) ) ) ,"@@@@@"," --outputNormalized ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDebug( ) ) ) ,"@@@@@"," -v ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgradientType( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothingUp( ) ) ) ,"@@@@@"," -g ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxStepLength( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-a"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputturnOffDiffeomorph( ) ) ) ,"@@@@@"," -a ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-G"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputUseDebugImageViewer( ) ) ) ,"@@@@@"," -G ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-p"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPromptAfterImageSend( ) ) ) ,"@@@@@"," -p ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfBCHApproximationTerms"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfBCHApproximationTerms( ) ) ) ,"@@@@@"," --numberOfBCHApproximationTerms ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void DemonRegistrationBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void DemonRegistrationBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void DemonRegistrationBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void DemonRegistrationBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerDemonRegistrationBRAINS.h b/bbtk_Slicer_PKG/src/bbSlicerDemonRegistrationBRAINS.h
new file mode 100644 (file)
index 0000000..8482ead
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerDemonRegistrationBRAINS.h
@@ -0,0 +1,136 @@
+#ifndef __bbSlicerDemonRegistrationBRAINS_h_INCLUDED__
+#define __bbSlicerDemonRegistrationBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT DemonRegistrationBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( DemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( movingVolume , std::string );
+BBTK_DECLARE_INPUT ( fixedVolume , std::string );
+BBTK_DECLARE_INPUT ( inputPixelType , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldVolume , std::string );
+BBTK_DECLARE_INPUT ( outputPixelType , std::string );
+BBTK_DECLARE_INPUT ( interpolationMode , std::string );
+BBTK_DECLARE_INPUT ( registrationFilterType , std::string );
+BBTK_DECLARE_INPUT ( smoothDisplacementFieldSigma , double );
+BBTK_DECLARE_INPUT ( numberOfPyramidLevels , int );
+BBTK_DECLARE_INPUT ( minimumFixedPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( minimumMovingPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( arrayOfPyramidLevelIterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( histogramMatch , bool );
+BBTK_DECLARE_INPUT ( numberOfHistogramBins , int );
+BBTK_DECLARE_INPUT ( numberOfMatchPoints , int );
+BBTK_DECLARE_INPUT ( medianFilterSize , std::vector<int> );
+BBTK_DECLARE_INPUT ( initializeWithDisplacementField , std::string );
+BBTK_DECLARE_INPUT ( initializeWithTransform , std::string );
+BBTK_DECLARE_INPUT ( maskProcessingMode , std::string );
+BBTK_DECLARE_INPUT ( fixedBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( movingBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( lowerThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( upperThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( backgroundFillValue , int );
+BBTK_DECLARE_INPUT ( seedForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( neighborhoodForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldPrefix , std::string );
+BBTK_DECLARE_INPUT ( outputCheckerboardVolume , std::string );
+BBTK_DECLARE_INPUT ( checkerboardPatternSubdivisions , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputNormalized , bool );
+BBTK_DECLARE_INPUT ( outputDebug , bool );
+BBTK_DECLARE_INPUT ( gradientType , int );
+BBTK_DECLARE_INPUT ( smoothingUp , double );
+BBTK_DECLARE_INPUT ( maxStepLength , double );
+BBTK_DECLARE_INPUT ( turnOffDiffeomorph , bool );
+BBTK_DECLARE_INPUT ( UseDebugImageViewer , bool );
+BBTK_DECLARE_INPUT ( PromptAfterImageSend , bool );
+BBTK_DECLARE_INPUT ( numberOfBCHApproximationTerms , int );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( DemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "DemonRegistrationBRAINS" ) ;
+    BBTK_AUTHOR ( "This tool was developed by Hans J. Johnson and Greg Harris." ) ;
+    BBTK_DESCRIPTION ( "This program finds a deformation field to warp a moving image onto a fixed image.  The images must be of the same signal kind, and contain an image of the same kind of object.  This program uses the Thirion Demons warp software in ITK, the Insight Toolkit.  Additional information is available at: http://www.nitrc.org/projects/brainsdemonwarp." ) ;
+    BBTK_CATEGORY ( "Registration.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(DemonRegistrationBRAINS , movingVolume , "movingVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , fixedVolume , "fixedVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , inputPixelType , "inputPixelType" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputDisplacementFieldVolume , "outputDisplacementFieldVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputPixelType , "outputPixelType" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , interpolationMode , "interpolationMode" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , registrationFilterType , "registrationFilterType" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , smoothDisplacementFieldSigma , "smoothDisplacementFieldSigma" , double, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfPyramidLevels , "numberOfPyramidLevels" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , minimumFixedPyramid , "minimumFixedPyramid" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , minimumMovingPyramid , "minimumMovingPyramid" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , arrayOfPyramidLevelIterations , "arrayOfPyramidLevelIterations" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , histogramMatch , "histogramMatch" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfHistogramBins , "numberOfHistogramBins" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfMatchPoints , "numberOfMatchPoints" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , medianFilterSize , "medianFilterSize" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , initializeWithDisplacementField , "initializeWithDisplacementField" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , initializeWithTransform , "initializeWithTransform" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , maskProcessingMode , "maskProcessingMode" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , fixedBinaryVolume , "fixedBinaryVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , movingBinaryVolume , "movingBinaryVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , lowerThresholdForBOBF , "lowerThresholdForBOBF" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , upperThresholdForBOBF , "upperThresholdForBOBF" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , backgroundFillValue , "backgroundFillValue" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , seedForBOBF , "seedForBOBF" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , neighborhoodForBOBF , "neighborhoodForBOBF" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputDisplacementFieldPrefix , "outputDisplacementFieldPrefix" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputCheckerboardVolume , "outputCheckerboardVolume" , std::string, "");
+BBTK_INPUT(DemonRegistrationBRAINS , checkerboardPatternSubdivisions , "checkerboardPatternSubdivisions" , std::vector<int>, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputNormalized , "outputNormalized" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , outputDebug , "outputDebug" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , gradientType , "gradientType" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , smoothingUp , "smoothingUp" , double, "");
+BBTK_INPUT(DemonRegistrationBRAINS , maxStepLength , "maxStepLength" , double, "");
+BBTK_INPUT(DemonRegistrationBRAINS , turnOffDiffeomorph , "turnOffDiffeomorph" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , UseDebugImageViewer , "UseDebugImageViewer" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , PromptAfterImageSend , "PromptAfterImageSend" , bool, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfBCHApproximationTerms , "numberOfBCHApproximationTerms" , int, "");
+BBTK_INPUT(DemonRegistrationBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( DemonRegistrationBRAINS ) ;
+}
+
+#endif // __bbSlicerDemonRegistrationBRAINS_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerDicomtoNrrdConverter.cxx b/bbtk_Slicer_PKG/src/bbSlicerDicomtoNrrdConverter.cxx
index 87e2029f97db92c48e95ab949bbc88f3e20fc179..49caf5cd28dcd8d8b764fcd873504f6c1b687bc5 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerDicomtoNrrdConverter.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerDicomtoNrrdConverter.cxx
@@ -11,13 +11,13 @@ namespace bbSlicer {
 
 int _argc =7;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libDicomToNrrdConverterLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputDicomDirectory"  ) + Mthd::Aux::toString( bbGetInputinputDicomDirectory( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputDirectory"  ) + Mthd::Aux::toString( bbGetInputoutputDirectory( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolume"  ) + Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--smallGradientThreshold"  ) + Mthd::Aux::toString( bbGetInputsmallGradientThreshold( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--writeProtocolGradientsFile"  ) + Mthd::Aux::toString( bbGetInputwriteProtocolGradientsFile( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useIdentityMeaseurementFrame"  ) + Mthd::Aux::toString( bbGetInputuseIdentityMeaseurementFrame( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useBMatrixGradientDirections"  ) + Mthd::Aux::toString( bbGetInputuseBMatrixGradientDirections( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputDicomDirectory"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputDicomDirectory( ) ) ) ,"@@@@@"," --inputDicomDirectory ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputDirectory"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDirectory( ) ) ) ,"@@@@@"," --outputDirectory ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," --outputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--smallGradientThreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmallGradientThreshold( ) ) ) ,"@@@@@"," --smallGradientThreshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--writeProtocolGradientsFile"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputwriteProtocolGradientsFile( ) ) ) ,"@@@@@"," --writeProtocolGradientsFile ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useIdentityMeaseurementFrame"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseIdentityMeaseurementFrame( ) ) ) ,"@@@@@"," --useIdentityMeaseurementFrame ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useBMatrixGradientDirections"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseBMatrixGradientDirections( ) ) ) ,"@@@@@"," --useBMatrixGradientDirections ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerExecutionModelTour.cxx b/bbtk_Slicer_PKG/src/bbSlicerExecutionModelTour.cxx
new file mode 100644 (file)
index 0000000..659a398
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerExecutionModelTour.cxx
@@ -0,0 +1,82 @@
+#include "bbSlicerExecutionModelTour.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ExecutionModelTour )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ExecutionModelTour, bbtk::AtomicBlackBox );
+
+    void ExecutionModelTour::Process ( ) {
+
+        // GENERATED
+
+int _argc =28;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libExecutionModelTourLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputintegerVariable( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdoubleVariable( ) ) ) ,"@@@@@"," -d ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfloatVector( ) ) ) ,"@@@@@"," -f ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--string_vector"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstringVector( ) ) ) ,"@@@@@"," --string_vector ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstringChoice( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--boolean1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputboolean1( ) ) ) ,"@@@@@"," --boolean1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--boolean2"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputboolean2( ) ) ) ,"@@@@@"," --boolean2 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--boolean3"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputboolean3( ) ) ) ,"@@@@@"," --boolean3 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--file1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfile1( ) ) ) ,"@@@@@"," --file1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--files"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfiles( ) ) ) ,"@@@@@"," --files ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--directory1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdirectory1( ) ) ) ,"@@@@@"," --directory1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--image1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputimage1( ) ) ) ,"@@@@@"," --image1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--image2"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputimage2( ) ) ) ,"@@@@@"," --image2 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transform1"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransform1( ) ) ) ,"@@@@@"," --transform1 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transform2"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransform2( ) ) ) ,"@@@@@"," --transform2 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seed"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseed( ) ) ) ,"@@@@@"," --seed ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputarg0( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputarg1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--region"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputregions( ) ) ) ,"@@@@@"," --region ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputFA"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputFA( ) ) ) ,"@@@@@"," --inputFA ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputFA"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputFA( ) ) ) ,"@@@@@"," --outputFA ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputanintegerreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputabooleanreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputafloatreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputadoublereturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputastringreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputanintegervectorreturn( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputastringchoicereturn( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ExecutionModelTour::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ExecutionModelTour::bbUserSetDefaultValues ( ) {
+    }
+
+    void ExecutionModelTour::bbUserInitializeProcessing ( ) {
+    }
+
+    void ExecutionModelTour::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerExecutionModelTour.h b/bbtk_Slicer_PKG/src/bbSlicerExecutionModelTour.h
new file mode 100644 (file)
index 0000000..b867459
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerExecutionModelTour.h
@@ -0,0 +1,112 @@
+#ifndef __bbSlicerExecutionModelTour_h_INCLUDED__
+#define __bbSlicerExecutionModelTour_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ExecutionModelTour
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ExecutionModelTour , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( integerVariable , int );
+BBTK_DECLARE_INPUT ( doubleVariable , double );
+BBTK_DECLARE_INPUT ( floatVector , std::vector<float> );
+BBTK_DECLARE_INPUT ( stringVector , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( stringChoice , std::string );
+BBTK_DECLARE_INPUT ( boolean1 , bool );
+BBTK_DECLARE_INPUT ( boolean2 , bool );
+BBTK_DECLARE_INPUT ( boolean3 , bool );
+BBTK_DECLARE_INPUT ( file1 , std::string );
+BBTK_DECLARE_INPUT ( files , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( directory1 , std::string );
+BBTK_DECLARE_INPUT ( image1 , std::string );
+BBTK_DECLARE_INPUT ( image2 , std::string );
+BBTK_DECLARE_INPUT ( transform1 , std::string );
+BBTK_DECLARE_INPUT ( transform2 , std::string );
+BBTK_DECLARE_INPUT ( seed , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( arg0 , std::string );
+BBTK_DECLARE_INPUT ( arg1 , std::string );
+BBTK_DECLARE_INPUT ( regions , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( inputFA , std::string );
+BBTK_DECLARE_INPUT ( outputFA , std::string );
+BBTK_DECLARE_INPUT ( anintegerreturn , int );
+BBTK_DECLARE_INPUT ( abooleanreturn , bool );
+BBTK_DECLARE_INPUT ( afloatreturn , float );
+BBTK_DECLARE_INPUT ( adoublereturn , double );
+BBTK_DECLARE_INPUT ( astringreturn , std::string );
+BBTK_DECLARE_INPUT ( anintegervectorreturn , std::vector<int> );
+BBTK_DECLARE_INPUT ( astringchoicereturn , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ExecutionModelTour , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ExecutionModelTour" ) ;
+    BBTK_AUTHOR ( "Daniel Blezek, Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Shows one of each type of parameter." ) ;
+    BBTK_CATEGORY ( "Developer Tools" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ExecutionModelTour , integerVariable , "integerVariable" , int, "");
+BBTK_INPUT(ExecutionModelTour , doubleVariable , "doubleVariable" , double, "");
+BBTK_INPUT(ExecutionModelTour , floatVector , "floatVector" , std::vector<float>, "");
+BBTK_INPUT(ExecutionModelTour , stringVector , "stringVector" , std::vector<std::string>, "");
+BBTK_INPUT(ExecutionModelTour , stringChoice , "stringChoice" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , boolean1 , "boolean1" , bool, "");
+BBTK_INPUT(ExecutionModelTour , boolean2 , "boolean2" , bool, "");
+BBTK_INPUT(ExecutionModelTour , boolean3 , "boolean3" , bool, "");
+BBTK_INPUT(ExecutionModelTour , file1 , "file1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , files , "files" , std::vector<std::string>, "");
+BBTK_INPUT(ExecutionModelTour , directory1 , "directory1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , image1 , "image1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , image2 , "image2" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , transform1 , "transform1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , transform2 , "transform2" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , seed , "seed" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ExecutionModelTour , arg0 , "arg0" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , arg1 , "arg1" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , regions , "regions" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ExecutionModelTour , inputFA , "inputFA" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , outputFA , "outputFA" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , anintegerreturn , "anintegerreturn" , int, "");
+BBTK_INPUT(ExecutionModelTour , abooleanreturn , "abooleanreturn" , bool, "");
+BBTK_INPUT(ExecutionModelTour , afloatreturn , "afloatreturn" , float, "");
+BBTK_INPUT(ExecutionModelTour , adoublereturn , "adoublereturn" , double, "");
+BBTK_INPUT(ExecutionModelTour , astringreturn , "astringreturn" , std::string, "");
+BBTK_INPUT(ExecutionModelTour , anintegervectorreturn , "anintegervectorreturn" , std::vector<int>, "");
+BBTK_INPUT(ExecutionModelTour , astringchoicereturn , "astringchoicereturn" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ExecutionModelTour ) ;
+}
+
+#endif // __bbSlicerExecutionModelTour_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerExpertAutomatedRegistration.cxx b/bbtk_Slicer_PKG/src/bbSlicerExpertAutomatedRegistration.cxx
new file mode 100644 (file)
index 0000000..61ea18d
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerExpertAutomatedRegistration.cxx
@@ -0,0 +1,82 @@
+#include "bbSlicerExpertAutomatedRegistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ExpertAutomatedRegistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ExpertAutomatedRegistration, bbtk::AtomicBlackBox );
+
+    void ExpertAutomatedRegistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =28;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRegisterImagesModule.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImage( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingImage( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputresampledImage( ) ) ) ,"@@@@@"," --resampledImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--loadTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputloadTransform( ) ) ) ,"@@@@@"," --loadTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--saveTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsaveTransform( ) ) ) ,"@@@@@"," --saveTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialization"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitialization( ) ) ) ,"@@@@@"," --initialization ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--registration"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputregistration( ) ) ) ,"@@@@@"," --registration ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--metric"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmetric( ) ) ) ,"@@@@@"," --metric ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--expectedOffset"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedOffset( ) ) ) ,"@@@@@"," --expectedOffset ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--expectedRotation"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedRotation( ) ) ) ,"@@@@@"," --expectedRotation ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--expectedScale"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedScale( ) ) ) ,"@@@@@"," --expectedScale ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--expectedSkew"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedSkew( ) ) ) ,"@@@@@"," --expectedSkew ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--verbosityLevel"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputverbosityLevel( ) ) ) ,"@@@@@"," --verbosityLevel ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--sampleFromOverlap"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsampleFromOverlap( ) ) ) ,"@@@@@"," --sampleFromOverlap ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedImageMask"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImageMask( ) ) ) ,"@@@@@"," --fixedImageMask ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--randomNumberSeed"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrandomNumberSeed( ) ) ) ,"@@@@@"," --randomNumberSeed ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimizeMemory"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimizeMemory( ) ) ) ,"@@@@@"," --minimizeMemory ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolation"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolation( ) ) ) ,"@@@@@"," --interpolation ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedLandmarks"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedLandmarks( ) ) ) ,"@@@@@"," --fixedLandmarks ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingLandmarks"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingLandmarks( ) ) ) ,"@@@@@"," --movingLandmarks ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rigidMaxIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrigidMaxIterations( ) ) ) ,"@@@@@"," --rigidMaxIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rigidSamplingRatio"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrigidSamplingRatio( ) ) ) ,"@@@@@"," --rigidSamplingRatio ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--affineMaxIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputaffineMaxIterations( ) ) ) ,"@@@@@"," --affineMaxIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--affineSamplingRatio"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputaffineSamplingRatio( ) ) ) ,"@@@@@"," --affineSamplingRatio ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--bsplineMaxIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbsplineMaxIterations( ) ) ) ,"@@@@@"," --bsplineMaxIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--bsplineSamplingRatio"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbsplineSamplingRatio( ) ) ) ,"@@@@@"," --bsplineSamplingRatio ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--controlPointSpacing"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcontrolPointSpacing( ) ) ) ,"@@@@@"," --controlPointSpacing ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ExpertAutomatedRegistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ExpertAutomatedRegistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void ExpertAutomatedRegistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void ExpertAutomatedRegistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerExpertAutomatedRegistration.h b/bbtk_Slicer_PKG/src/bbSlicerExpertAutomatedRegistration.h
new file mode 100644 (file)
index 0000000..5c0312d
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerExpertAutomatedRegistration.h
@@ -0,0 +1,112 @@
+#ifndef __bbSlicerExpertAutomatedRegistration_h_INCLUDED__
+#define __bbSlicerExpertAutomatedRegistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ExpertAutomatedRegistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ExpertAutomatedRegistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( fixedImage , std::string );
+BBTK_DECLARE_INPUT ( movingImage , std::string );
+BBTK_DECLARE_INPUT ( resampledImage , std::string );
+BBTK_DECLARE_INPUT ( loadTransform , std::string );
+BBTK_DECLARE_INPUT ( saveTransform , std::string );
+BBTK_DECLARE_INPUT ( initialization , std::string );
+BBTK_DECLARE_INPUT ( registration , std::string );
+BBTK_DECLARE_INPUT ( metric , std::string );
+BBTK_DECLARE_INPUT ( expectedOffset , float );
+BBTK_DECLARE_INPUT ( expectedRotation , float );
+BBTK_DECLARE_INPUT ( expectedScale , float );
+BBTK_DECLARE_INPUT ( expectedSkew , float );
+BBTK_DECLARE_INPUT ( verbosityLevel , std::string );
+BBTK_DECLARE_INPUT ( sampleFromOverlap , bool );
+BBTK_DECLARE_INPUT ( fixedImageMask , std::string );
+BBTK_DECLARE_INPUT ( randomNumberSeed , int );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+BBTK_DECLARE_INPUT ( minimizeMemory , bool );
+BBTK_DECLARE_INPUT ( interpolation , std::string );
+BBTK_DECLARE_INPUT ( fixedLandmarks , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( movingLandmarks , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( rigidMaxIterations , int );
+BBTK_DECLARE_INPUT ( rigidSamplingRatio , float );
+BBTK_DECLARE_INPUT ( affineMaxIterations , int );
+BBTK_DECLARE_INPUT ( affineSamplingRatio , float );
+BBTK_DECLARE_INPUT ( bsplineMaxIterations , int );
+BBTK_DECLARE_INPUT ( bsplineSamplingRatio , float );
+BBTK_DECLARE_INPUT ( controlPointSpacing , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ExpertAutomatedRegistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ExpertAutomatedRegistration" ) ;
+    BBTK_AUTHOR ( "Stephen R Aylward, Casey B Goodlett" ) ;
+    BBTK_DESCRIPTION ( "Provides rigid, affine, and BSpline registration methods via a simple GUI" ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ExpertAutomatedRegistration , fixedImage , "fixedImage" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , movingImage , "movingImage" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , resampledImage , "resampledImage" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , loadTransform , "loadTransform" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , saveTransform , "saveTransform" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , initialization , "initialization" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , registration , "registration" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , metric , "metric" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , expectedOffset , "expectedOffset" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , expectedRotation , "expectedRotation" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , expectedScale , "expectedScale" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , expectedSkew , "expectedSkew" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , verbosityLevel , "verbosityLevel" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , sampleFromOverlap , "sampleFromOverlap" , bool, "");
+BBTK_INPUT(ExpertAutomatedRegistration , fixedImageMask , "fixedImageMask" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , randomNumberSeed , "randomNumberSeed" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , numberOfThreads , "numberOfThreads" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , minimizeMemory , "minimizeMemory" , bool, "");
+BBTK_INPUT(ExpertAutomatedRegistration , interpolation , "interpolation" , std::string, "");
+BBTK_INPUT(ExpertAutomatedRegistration , fixedLandmarks , "fixedLandmarks" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ExpertAutomatedRegistration , movingLandmarks , "movingLandmarks" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(ExpertAutomatedRegistration , rigidMaxIterations , "rigidMaxIterations" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , rigidSamplingRatio , "rigidSamplingRatio" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , affineMaxIterations , "affineMaxIterations" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , affineSamplingRatio , "affineSamplingRatio" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , bsplineMaxIterations , "bsplineMaxIterations" , int, "");
+BBTK_INPUT(ExpertAutomatedRegistration , bsplineSamplingRatio , "bsplineSamplingRatio" , float, "");
+BBTK_INPUT(ExpertAutomatedRegistration , controlPointSpacing , "controlPointSpacing" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ExpertAutomatedRegistration ) ;
+}
+
+#endif // __bbSlicerExpertAutomatedRegistration_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerExtractSkeleton.cxx b/bbtk_Slicer_PKG/src/bbSlicerExtractSkeleton.cxx
index 5afd4d6d8cb0c6c4bb3648afb83981b2d6b211a5..ca154652c66b114241e9056ae6ab93f1dd2fd8c9 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerExtractSkeleton.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerExtractSkeleton.cxx
@@ -11,12 +11,12 @@ namespace bbSlicer {
 
 int _argc =6;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libExtractSkeletonLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputInputImageFileName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputOutputImageFileName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--type"  ) + Mthd::Aux::toString( bbGetInputSkeletonType( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dontPrune"  ) + Mthd::Aux::toString( bbGetInputDontPruneBranches( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numPoints"  ) + Mthd::Aux::toString( bbGetInputNumberOfPoints( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--pointsFile"  ) + Mthd::Aux::toString( bbGetInputOutputPointsFileName( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--type"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSkeletonType( ) ) ) ,"@@@@@"," --type ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--dontPrune"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputDontPruneBranches( ) ) ) ,"@@@@@"," --dontPrune ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputNumberOfPoints( ) ) ) ,"@@@@@"," --numPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--pointsFile"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputPointsFileName( ) ) ) ,"@@@@@"," --pointsFile ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerFastAffineregistration.cxx b/bbtk_Slicer_PKG/src/bbSlicerFastAffineregistration.cxx
new file mode 100644 (file)
index 0000000..b2b8a79
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerFastAffineregistration.cxx
@@ -0,0 +1,65 @@
+#include "bbSlicerFastAffineregistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, FastAffineregistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( FastAffineregistration, bbtk::AtomicBlackBox );
+
+    void FastAffineregistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =11;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libAffineRegistrationLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageSmoothingFactor( ) ) ) ,"@@@@@"," --fixedsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageSmoothingFactor( ) ) ) ,"@@@@@"," --movingsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputHistogramBins( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSpatialSamples( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputTranslationScale( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInitialTransform( ) ) ) ,"@@@@@"," --initialtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledmovingfilename"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputResampledImageFileName( ) ) ) ,"@@@@@"," --resampledmovingfilename ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void FastAffineregistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void FastAffineregistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void FastAffineregistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void FastAffineregistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerFastAffineregistration.h b/bbtk_Slicer_PKG/src/bbSlicerFastAffineregistration.h
new file mode 100644 (file)
index 0000000..ae6c4a6
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerFastAffineregistration.h
@@ -0,0 +1,78 @@
+#ifndef __bbSlicerFastAffineregistration_h_INCLUDED__
+#define __bbSlicerFastAffineregistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT FastAffineregistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( FastAffineregistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( FixedImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( MovingImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( HistogramBins , int );
+BBTK_DECLARE_INPUT ( SpatialSamples , int );
+BBTK_DECLARE_INPUT ( Iterations , int );
+BBTK_DECLARE_INPUT ( TranslationScale , double );
+BBTK_DECLARE_INPUT ( InitialTransform , std::string );
+BBTK_DECLARE_INPUT ( FixedImageFileName , std::string );
+BBTK_DECLARE_INPUT ( MovingImageFileName , std::string );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( ResampledImageFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( FastAffineregistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "FastAffineregistration" ) ;
+    BBTK_AUTHOR ( "Daniel Blezek" ) ;
+    BBTK_DESCRIPTION ( "Registers two images together using an affine transform and mutual information. This module is often used to align images of different subjects or images of the same subject from different modalities.This module can smooth images prior to registration to mitigate noise and improve convergence. Many of the registration parameters require a working knowledge of the algorithm although the default parameters are sufficient for many registration tasks." ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(FastAffineregistration , FixedImageSmoothingFactor , "FixedImageSmoothingFactor" , int, "");
+BBTK_INPUT(FastAffineregistration , MovingImageSmoothingFactor , "MovingImageSmoothingFactor" , int, "");
+BBTK_INPUT(FastAffineregistration , HistogramBins , "HistogramBins" , int, "");
+BBTK_INPUT(FastAffineregistration , SpatialSamples , "SpatialSamples" , int, "");
+BBTK_INPUT(FastAffineregistration , Iterations , "Iterations" , int, "");
+BBTK_INPUT(FastAffineregistration , TranslationScale , "TranslationScale" , double, "");
+BBTK_INPUT(FastAffineregistration , InitialTransform , "InitialTransform" , std::string, "");
+BBTK_INPUT(FastAffineregistration , FixedImageFileName , "FixedImageFileName" , std::string, "");
+BBTK_INPUT(FastAffineregistration , MovingImageFileName , "MovingImageFileName" , std::string, "");
+BBTK_INPUT(FastAffineregistration , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(FastAffineregistration , ResampledImageFileName , "ResampledImageFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( FastAffineregistration ) ;
+}
+
+#endif // __bbSlicerFastAffineregistration_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerFastNonrigidBSplineregistration.cxx b/bbtk_Slicer_PKG/src/bbSlicerFastNonrigidBSplineregistration.cxx
index a4f41cbf22071dbfbb388764adf13c2181e16715..cb3326a8784247c3d663063757d0d24ccc1985e2 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerFastNonrigidBSplineregistration.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerFastNonrigidBSplineregistration.cxx
@@ -11,19 +11,19 @@ namespace bbSlicer {
 
 int _argc =13;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBSplineDeformableRegistrationLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::toString( bbGetInputIterations( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::toString( bbGetInputgridSize( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::toString( bbGetInputHistogramBins( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::toString( bbGetInputSpatialSamples( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--constrain"  ) + Mthd::Aux::toString( bbGetInputConstrainDeformation( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-m"  ) + Mthd::Aux::toString( bbGetInputMaximumDeformation( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::toString( bbGetInputDefaultPixelValue( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialtransform"  ) + Mthd::Aux::toString( bbGetInputInitialTransform( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputwarp"  ) + Mthd::Aux::toString( bbGetInputOutputWarp( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledmovingfilename"  ) + Mthd::Aux::toString( bbGetInputResampledImageFileName( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgridSize( ) ) ) ,"@@@@@"," -g ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputHistogramBins( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSpatialSamples( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--constrain"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputConstrainDeformation( ) ) ) ,"@@@@@"," --constrain ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-m"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMaximumDeformation( ) ) ) ,"@@@@@"," -m ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputDefaultPixelValue( ) ) ) ,"@@@@@"," -d ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInitialTransform( ) ) ) ,"@@@@@"," --initialtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputwarp"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputWarp( ) ) ) ,"@@@@@"," --outputwarp ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledmovingfilename"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputResampledImageFileName( ) ) ) ,"@@@@@"," --resampledmovingfilename ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerFastRigidregistration.cxx b/bbtk_Slicer_PKG/src/bbSlicerFastRigidregistration.cxx
new file mode 100644 (file)
index 0000000..ef25e18
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerFastRigidregistration.cxx
@@ -0,0 +1,67 @@
+#include "bbSlicerFastRigidregistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, FastRigidregistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( FastRigidregistration, bbtk::AtomicBlackBox );
+
+    void FastRigidregistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =13;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRigidRegistrationLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageSmoothingFactor( ) ) ) ,"@@@@@"," --fixedsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageSmoothingFactor( ) ) ) ,"@@@@@"," --movingsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--testingmode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputTestingMode( ) ) ) ,"@@@@@"," --testingmode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputHistogramBins( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSpatialSamples( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLearningRate( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputTranslationScale( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInitialTransform( ) ) ) ,"@@@@@"," --initialtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledmovingfilename"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputResampledImageFileName( ) ) ) ,"@@@@@"," --resampledmovingfilename ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void FastRigidregistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void FastRigidregistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void FastRigidregistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void FastRigidregistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerFastRigidregistration.h b/bbtk_Slicer_PKG/src/bbSlicerFastRigidregistration.h
new file mode 100644 (file)
index 0000000..9628e70
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerFastRigidregistration.h
@@ -0,0 +1,82 @@
+#ifndef __bbSlicerFastRigidregistration_h_INCLUDED__
+#define __bbSlicerFastRigidregistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT FastRigidregistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( FastRigidregistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( FixedImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( MovingImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( TestingMode , bool );
+BBTK_DECLARE_INPUT ( HistogramBins , int );
+BBTK_DECLARE_INPUT ( SpatialSamples , int );
+BBTK_DECLARE_INPUT ( Iterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( LearningRate , std::vector<double> );
+BBTK_DECLARE_INPUT ( TranslationScale , double );
+BBTK_DECLARE_INPUT ( InitialTransform , std::string );
+BBTK_DECLARE_INPUT ( FixedImageFileName , std::string );
+BBTK_DECLARE_INPUT ( MovingImageFileName , std::string );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( ResampledImageFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( FastRigidregistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "FastRigidregistration" ) ;
+    BBTK_AUTHOR ( "Daniel Blezek" ) ;
+    BBTK_DESCRIPTION ( "Registers two images together using a rigid transform and mutual information.This module was originally distributed as 'Linear registration' but has been renamed to eliminate confusion with the 'Affine registration' module.This module is often used to align images of different subjects or images of the same subject from different modalities.This module can smooth images prior to registration to mitigate noise and improve convergence. Many of the registration parameters require a working knowledge of the algorithm although the default parameters are sufficient for many registration tasks." ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(FastRigidregistration , FixedImageSmoothingFactor , "FixedImageSmoothingFactor" , int, "");
+BBTK_INPUT(FastRigidregistration , MovingImageSmoothingFactor , "MovingImageSmoothingFactor" , int, "");
+BBTK_INPUT(FastRigidregistration , TestingMode , "TestingMode" , bool, "");
+BBTK_INPUT(FastRigidregistration , HistogramBins , "HistogramBins" , int, "");
+BBTK_INPUT(FastRigidregistration , SpatialSamples , "SpatialSamples" , int, "");
+BBTK_INPUT(FastRigidregistration , Iterations , "Iterations" , std::vector<int>, "");
+BBTK_INPUT(FastRigidregistration , LearningRate , "LearningRate" , std::vector<double>, "");
+BBTK_INPUT(FastRigidregistration , TranslationScale , "TranslationScale" , double, "");
+BBTK_INPUT(FastRigidregistration , InitialTransform , "InitialTransform" , std::string, "");
+BBTK_INPUT(FastRigidregistration , FixedImageFileName , "FixedImageFileName" , std::string, "");
+BBTK_INPUT(FastRigidregistration , MovingImageFileName , "MovingImageFileName" , std::string, "");
+BBTK_INPUT(FastRigidregistration , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(FastRigidregistration , ResampledImageFileName , "ResampledImageFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( FastRigidregistration ) ;
+}
+
+#endif // __bbSlicerFastRigidregistration_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerFiducialRegistration.cxx b/bbtk_Slicer_PKG/src/bbSlicerFiducialRegistration.cxx
new file mode 100644 (file)
index 0000000..0d6bca8
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerFiducialRegistration.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerFiducialRegistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, FiducialRegistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( FiducialRegistration, bbtk::AtomicBlackBox );
+
+    void FiducialRegistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libTransformFromFiducialsModule.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedLandmarks"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedLandmarks( ) ) ) ,"@@@@@"," --fixedLandmarks ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingLandmarks"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingLandmarks( ) ) ) ,"@@@@@"," --movingLandmarks ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--saveTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsaveTransform( ) ) ) ,"@@@@@"," --saveTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transformType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformType( ) ) ) ,"@@@@@"," --transformType ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void FiducialRegistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void FiducialRegistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void FiducialRegistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void FiducialRegistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerFiducialRegistration.h b/bbtk_Slicer_PKG/src/bbSlicerFiducialRegistration.h
new file mode 100644 (file)
index 0000000..46870b4
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerFiducialRegistration.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerFiducialRegistration_h_INCLUDED__
+#define __bbSlicerFiducialRegistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT FiducialRegistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( FiducialRegistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( fixedLandmarks , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( movingLandmarks , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( saveTransform , std::string );
+BBTK_DECLARE_INPUT ( transformType , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( FiducialRegistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "FiducialRegistration" ) ;
+    BBTK_AUTHOR ( "Casey B Goodlett" ) ;
+    BBTK_DESCRIPTION ( "Computes a rigid, similarity or affine transform from a matched list of fiducials" ) ;
+    BBTK_CATEGORY ( "Registration.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(FiducialRegistration , fixedLandmarks , "fixedLandmarks" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(FiducialRegistration , movingLandmarks , "movingLandmarks" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(FiducialRegistration , saveTransform , "saveTransform" , std::string, "");
+BBTK_INPUT(FiducialRegistration , transformType , "transformType" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( FiducialRegistration ) ;
+}
+
+#endif // __bbSlicerFiducialRegistration_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerForegroundmaskingBRAINS.cxx b/bbtk_Slicer_PKG/src/bbSlicerForegroundmaskingBRAINS.cxx
new file mode 100644 (file)
index 0000000..5ba6b77
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerForegroundmaskingBRAINS.cxx
@@ -0,0 +1,63 @@
+#include "bbSlicerForegroundmaskingBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ForegroundmaskingBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ForegroundmaskingBRAINS, bbtk::AtomicBlackBox );
+
+    void ForegroundmaskingBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =9;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBRAINSROIAutoLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@"," --inputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputROIMaskVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputROIMaskVolume( ) ) ) ,"@@@@@"," --outputROIMaskVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputClippedVolumeROI"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputClippedVolumeROI( ) ) ) ,"@@@@@"," --outputClippedVolumeROI ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--otsuPercentileThreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputotsuPercentileThreshold( ) ) ) ,"@@@@@"," --otsuPercentileThreshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--thresholdCorrectionFactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputthresholdCorrectionFactor( ) ) ) ,"@@@@@"," --thresholdCorrectionFactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--closingSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputclosingSize( ) ) ) ,"@@@@@"," --closingSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ROIAutoDilateSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputROIAutoDilateSize( ) ) ) ,"@@@@@"," --ROIAutoDilateSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolumePixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolumePixelType( ) ) ) ,"@@@@@"," --outputVolumePixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ForegroundmaskingBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ForegroundmaskingBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void ForegroundmaskingBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void ForegroundmaskingBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerForegroundmaskingBRAINS.h b/bbtk_Slicer_PKG/src/bbSlicerForegroundmaskingBRAINS.h
new file mode 100644 (file)
index 0000000..ae8f25e
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerForegroundmaskingBRAINS.h
@@ -0,0 +1,74 @@
+#ifndef __bbSlicerForegroundmaskingBRAINS_h_INCLUDED__
+#define __bbSlicerForegroundmaskingBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ForegroundmaskingBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ForegroundmaskingBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputROIMaskVolume , std::string );
+BBTK_DECLARE_INPUT ( outputClippedVolumeROI , std::string );
+BBTK_DECLARE_INPUT ( otsuPercentileThreshold , double );
+BBTK_DECLARE_INPUT ( thresholdCorrectionFactor , double );
+BBTK_DECLARE_INPUT ( closingSize , double );
+BBTK_DECLARE_INPUT ( ROIAutoDilateSize , double );
+BBTK_DECLARE_INPUT ( outputVolumePixelType , std::string );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ForegroundmaskingBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ForegroundmaskingBRAINS" ) ;
+    BBTK_AUTHOR ( "Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu" ) ;
+    BBTK_DESCRIPTION ( "This tool uses a combination of otsu thresholding and a closing operations to identify the most prominant foreground region in an image." ) ;
+    BBTK_CATEGORY ( "Segmentation.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ForegroundmaskingBRAINS , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , outputROIMaskVolume , "outputROIMaskVolume" , std::string, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , outputClippedVolumeROI , "outputClippedVolumeROI" , std::string, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , otsuPercentileThreshold , "otsuPercentileThreshold" , double, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , thresholdCorrectionFactor , "thresholdCorrectionFactor" , double, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , closingSize , "closingSize" , double, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , ROIAutoDilateSize , "ROIAutoDilateSize" , double, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , outputVolumePixelType , "outputVolumePixelType" , std::string, "");
+BBTK_INPUT(ForegroundmaskingBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ForegroundmaskingBRAINS ) ;
+}
+
+#endif // __bbSlicerForegroundmaskingBRAINS_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerGaussianBlur.cxx b/bbtk_Slicer_PKG/src/bbSlicerGaussianBlur.cxx
index bb99921b0f9ec18f2fc2170804a3430917a01c32..71d5e09bdd072c8df180149ce94f0179127722f5 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerGaussianBlur.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerGaussianBlur.cxx
@@ -11,9 +11,9 @@ namespace bbSlicer {
 
 int _argc =3;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libGaussianBlurImageFilterLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::toString( bbGetInputsigma( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsigma( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerGeneralRegistrationBRAINS.cxx b/bbtk_Slicer_PKG/src/bbSlicerGeneralRegistrationBRAINS.cxx
new file mode 100644 (file)
index 0000000..43a0846
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerGeneralRegistrationBRAINS.cxx
@@ -0,0 +1,114 @@
+#include "bbSlicerGeneralRegistrationBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, GeneralRegistrationBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( GeneralRegistrationBRAINS, bbtk::AtomicBlackBox );
+
+    void GeneralRegistrationBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =60;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBRAINSFitLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedVolume( ) ) ) ,"@@@@@"," --fixedVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingVolume( ) ) ) ,"@@@@@"," --movingVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--bsplineTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbsplineTransform( ) ) ) ,"@@@@@"," --bsplineTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--linearTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlinearTransform( ) ) ) ,"@@@@@"," --linearTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," --outputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitialTransform( ) ) ) ,"@@@@@"," --initialTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeTransformMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeTransformMode( ) ) ) ,"@@@@@"," --initializeTransformMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useRigid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseRigid( ) ) ) ,"@@@@@"," --useRigid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useScaleVersor3D"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseScaleVersor3D( ) ) ) ,"@@@@@"," --useScaleVersor3D ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useScaleSkewVersor3D"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseScaleSkewVersor3D( ) ) ) ,"@@@@@"," --useScaleSkewVersor3D ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useAffine"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseAffine( ) ) ) ,"@@@@@"," --useAffine ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useBSpline"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseBSpline( ) ) ) ,"@@@@@"," --useBSpline ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfSamples"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfSamples( ) ) ) ,"@@@@@"," --numberOfSamples ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--splineGridSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsplineGridSize( ) ) ) ,"@@@@@"," --splineGridSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --numberOfIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maskProcessingMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaskProcessingMode( ) ) ) ,"@@@@@"," --maskProcessingMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedBinaryVolume( ) ) ) ,"@@@@@"," --fixedBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingBinaryVolume( ) ) ) ,"@@@@@"," --movingBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputFixedVolumeROI"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputFixedVolumeROI( ) ) ) ,"@@@@@"," --outputFixedVolumeROI ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputMovingVolumeROI"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputMovingVolumeROI( ) ) ) ,"@@@@@"," --outputMovingVolumeROI ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolumePixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolumePixelType( ) ) ) ,"@@@@@"," --outputVolumePixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--backgroundFillValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbackgroundFillValue( ) ) ) ,"@@@@@"," --backgroundFillValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maskInferiorCutOffFromCenter"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaskInferiorCutOffFromCenter( ) ) ) ,"@@@@@"," --maskInferiorCutOffFromCenter ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--scaleOutputValues"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputscaleOutputValues( ) ) ) ,"@@@@@"," --scaleOutputValues ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolationMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationMode( ) ) ) ,"@@@@@"," --interpolationMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumStepLength"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumStepLength( ) ) ) ,"@@@@@"," --minimumStepLength ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--translationScale"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtranslationScale( ) ) ) ,"@@@@@"," --translationScale ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--reproportionScale"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreproportionScale( ) ) ) ,"@@@@@"," --reproportionScale ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--skewScale"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputskewScale( ) ) ) ,"@@@@@"," --skewScale ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxBSplineDisplacement"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxBSplineDisplacement( ) ) ) ,"@@@@@"," --maxBSplineDisplacement ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputhistogramMatch( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfHistogramBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfHistogramBins( ) ) ) ,"@@@@@"," --numberOfHistogramBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfMatchPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfMatchPoints( ) ) ) ,"@@@@@"," --numberOfMatchPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--strippedOutputTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstrippedOutputTransform( ) ) ) ,"@@@@@"," --strippedOutputTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transformType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformType( ) ) ) ,"@@@@@"," --transformType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputTransform( ) ) ) ,"@@@@@"," --outputTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedVolumeTimeIndex"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedVolumeTimeIndex( ) ) ) ,"@@@@@"," --fixedVolumeTimeIndex ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingVolumeTimeIndex"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingVolumeTimeIndex( ) ) ) ,"@@@@@"," --movingVolumeTimeIndex ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--medianFilterSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmedianFilterSize( ) ) ) ,"@@@@@"," --medianFilterSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--removeIntensityOutliers"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputremoveIntensityOutliers( ) ) ) ,"@@@@@"," --removeIntensityOutliers ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useCachingOfBSplineWeightsMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseCachingOfBSplineWeightsMode( ) ) ) ,"@@@@@"," --useCachingOfBSplineWeightsMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--useExplicitPDFDerivativesMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseExplicitPDFDerivativesMode( ) ) ) ,"@@@@@"," --useExplicitPDFDerivativesMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ROIAutoDilateSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputROIAutoDilateSize( ) ) ) ,"@@@@@"," --ROIAutoDilateSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ROIAutoClosingSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputROIAutoClosingSize( ) ) ) ,"@@@@@"," --ROIAutoClosingSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--relaxationFactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrelaxationFactor( ) ) ) ,"@@@@@"," --relaxationFactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maximumStepLength"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaximumStepLength( ) ) ) ,"@@@@@"," --maximumStepLength ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--failureExitCode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfailureExitCode( ) ) ) ,"@@@@@"," --failureExitCode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--writeTransformOnFailure"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputwriteTransformOnFailure( ) ) ) ,"@@@@@"," --writeTransformOnFailure ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--forceMINumberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputforceMINumberOfThreads( ) ) ) ,"@@@@@"," --forceMINumberOfThreads ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--debugLevel"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdebugLevel( ) ) ) ,"@@@@@"," --debugLevel ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--costFunctionConvergenceFactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcostFunctionConvergenceFactor( ) ) ) ,"@@@@@"," --costFunctionConvergenceFactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--projectedGradientTolerance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputprojectedGradientTolerance( ) ) ) ,"@@@@@"," --projectedGradientTolerance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-G"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputUseDebugImageViewer( ) ) ) ,"@@@@@"," -G ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-p"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPromptAfterImageSend( ) ) ) ,"@@@@@"," -p ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseMomentsAlign( ) ) ) ,"@@@@@"," --NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseGeometryAlign( ) ) ) ,"@@@@@"," --NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputuseCenterOfHeadAlign( ) ) ) ,"@@@@@"," --NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02 ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--permitParameterVariation"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpermitParameterVariation( ) ) ) ,"@@@@@"," --permitParameterVariation ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--costMetric"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcostMetric( ) ) ) ,"@@@@@"," --costMetric ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void GeneralRegistrationBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void GeneralRegistrationBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void GeneralRegistrationBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void GeneralRegistrationBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerGeneralRegistrationBRAINS.h b/bbtk_Slicer_PKG/src/bbSlicerGeneralRegistrationBRAINS.h
new file mode 100644 (file)
index 0000000..6bdf64a
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerGeneralRegistrationBRAINS.h
@@ -0,0 +1,176 @@
+#ifndef __bbSlicerGeneralRegistrationBRAINS_h_INCLUDED__
+#define __bbSlicerGeneralRegistrationBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT GeneralRegistrationBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( GeneralRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( fixedVolume , std::string );
+BBTK_DECLARE_INPUT ( movingVolume , std::string );
+BBTK_DECLARE_INPUT ( bsplineTransform , std::string );
+BBTK_DECLARE_INPUT ( linearTransform , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( initialTransform , std::string );
+BBTK_DECLARE_INPUT ( initializeTransformMode , std::string );
+BBTK_DECLARE_INPUT ( useRigid , bool );
+BBTK_DECLARE_INPUT ( useScaleVersor3D , bool );
+BBTK_DECLARE_INPUT ( useScaleSkewVersor3D , bool );
+BBTK_DECLARE_INPUT ( useAffine , bool );
+BBTK_DECLARE_INPUT ( useBSpline , bool );
+BBTK_DECLARE_INPUT ( numberOfSamples , int );
+BBTK_DECLARE_INPUT ( splineGridSize , std::vector<int> );
+BBTK_DECLARE_INPUT ( numberOfIterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( maskProcessingMode , std::string );
+BBTK_DECLARE_INPUT ( fixedBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( movingBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( outputFixedVolumeROI , std::string );
+BBTK_DECLARE_INPUT ( outputMovingVolumeROI , std::string );
+BBTK_DECLARE_INPUT ( outputVolumePixelType , std::string );
+BBTK_DECLARE_INPUT ( backgroundFillValue , double );
+BBTK_DECLARE_INPUT ( maskInferiorCutOffFromCenter , double );
+BBTK_DECLARE_INPUT ( scaleOutputValues , bool );
+BBTK_DECLARE_INPUT ( interpolationMode , std::string );
+BBTK_DECLARE_INPUT ( minimumStepLength , std::vector<double> );
+BBTK_DECLARE_INPUT ( translationScale , double );
+BBTK_DECLARE_INPUT ( reproportionScale , double );
+BBTK_DECLARE_INPUT ( skewScale , double );
+BBTK_DECLARE_INPUT ( maxBSplineDisplacement , double );
+BBTK_DECLARE_INPUT ( histogramMatch , bool );
+BBTK_DECLARE_INPUT ( numberOfHistogramBins , int );
+BBTK_DECLARE_INPUT ( numberOfMatchPoints , int );
+BBTK_DECLARE_INPUT ( strippedOutputTransform , std::string );
+BBTK_DECLARE_INPUT ( transformType , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( outputTransform , std::string );
+BBTK_DECLARE_INPUT ( fixedVolumeTimeIndex , int );
+BBTK_DECLARE_INPUT ( movingVolumeTimeIndex , int );
+BBTK_DECLARE_INPUT ( medianFilterSize , std::vector<int> );
+BBTK_DECLARE_INPUT ( removeIntensityOutliers , double );
+BBTK_DECLARE_INPUT ( useCachingOfBSplineWeightsMode , std::string );
+BBTK_DECLARE_INPUT ( useExplicitPDFDerivativesMode , std::string );
+BBTK_DECLARE_INPUT ( ROIAutoDilateSize , double );
+BBTK_DECLARE_INPUT ( ROIAutoClosingSize , double );
+BBTK_DECLARE_INPUT ( relaxationFactor , double );
+BBTK_DECLARE_INPUT ( maximumStepLength , double );
+BBTK_DECLARE_INPUT ( failureExitCode , int );
+BBTK_DECLARE_INPUT ( writeTransformOnFailure , bool );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+BBTK_DECLARE_INPUT ( forceMINumberOfThreads , int );
+BBTK_DECLARE_INPUT ( debugLevel , int );
+BBTK_DECLARE_INPUT ( costFunctionConvergenceFactor , double );
+BBTK_DECLARE_INPUT ( projectedGradientTolerance , double );
+BBTK_DECLARE_INPUT ( UseDebugImageViewer , bool );
+BBTK_DECLARE_INPUT ( PromptAfterImageSend , bool );
+BBTK_DECLARE_INPUT ( useMomentsAlign , bool );
+BBTK_DECLARE_INPUT ( useGeometryAlign , bool );
+BBTK_DECLARE_INPUT ( useCenterOfHeadAlign , bool );
+BBTK_DECLARE_INPUT ( permitParameterVariation , std::vector<int> );
+BBTK_DECLARE_INPUT ( costMetric , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( GeneralRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "GeneralRegistrationBRAINS" ) ;
+    BBTK_AUTHOR ( "Hans J. Johnson, hans-johnson -at- uiowa.edu, http://wwww.psychiatry.uiowa.edu" ) ;
+    BBTK_DESCRIPTION ( "Register a three-dimensional volume to a reference volume Mattes Mutual Information by default. Described in BRAINSFit: Mutual Information Registrations of Whole-Brain 3D Images, Using the Insight Toolkit, Johnson H.J., Harris G., Williams K., The Insight Journal, 2007. http://hdl.handle.net/1926/1291" ) ;
+    BBTK_CATEGORY ( "Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(GeneralRegistrationBRAINS , fixedVolume , "fixedVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , movingVolume , "movingVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , bsplineTransform , "bsplineTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , linearTransform , "linearTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , initialTransform , "initialTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , initializeTransformMode , "initializeTransformMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useRigid , "useRigid" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useScaleVersor3D , "useScaleVersor3D" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useScaleSkewVersor3D , "useScaleSkewVersor3D" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useAffine , "useAffine" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useBSpline , "useBSpline" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfSamples , "numberOfSamples" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , splineGridSize , "splineGridSize" , std::vector<int>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfIterations , "numberOfIterations" , std::vector<int>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , maskProcessingMode , "maskProcessingMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , fixedBinaryVolume , "fixedBinaryVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , movingBinaryVolume , "movingBinaryVolume" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputFixedVolumeROI , "outputFixedVolumeROI" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputMovingVolumeROI , "outputMovingVolumeROI" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputVolumePixelType , "outputVolumePixelType" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , backgroundFillValue , "backgroundFillValue" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , maskInferiorCutOffFromCenter , "maskInferiorCutOffFromCenter" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , scaleOutputValues , "scaleOutputValues" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , interpolationMode , "interpolationMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , minimumStepLength , "minimumStepLength" , std::vector<double>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , translationScale , "translationScale" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , reproportionScale , "reproportionScale" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , skewScale , "skewScale" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , maxBSplineDisplacement , "maxBSplineDisplacement" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , histogramMatch , "histogramMatch" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfHistogramBins , "numberOfHistogramBins" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfMatchPoints , "numberOfMatchPoints" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , strippedOutputTransform , "strippedOutputTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , transformType , "transformType" , std::vector<std::string>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , outputTransform , "outputTransform" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , fixedVolumeTimeIndex , "fixedVolumeTimeIndex" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , movingVolumeTimeIndex , "movingVolumeTimeIndex" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , medianFilterSize , "medianFilterSize" , std::vector<int>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , removeIntensityOutliers , "removeIntensityOutliers" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useCachingOfBSplineWeightsMode , "useCachingOfBSplineWeightsMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useExplicitPDFDerivativesMode , "useExplicitPDFDerivativesMode" , std::string, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , ROIAutoDilateSize , "ROIAutoDilateSize" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , ROIAutoClosingSize , "ROIAutoClosingSize" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , relaxationFactor , "relaxationFactor" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , maximumStepLength , "maximumStepLength" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , failureExitCode , "failureExitCode" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , writeTransformOnFailure , "writeTransformOnFailure" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , forceMINumberOfThreads , "forceMINumberOfThreads" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , debugLevel , "debugLevel" , int, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , costFunctionConvergenceFactor , "costFunctionConvergenceFactor" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , projectedGradientTolerance , "projectedGradientTolerance" , double, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , UseDebugImageViewer , "UseDebugImageViewer" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , PromptAfterImageSend , "PromptAfterImageSend" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useMomentsAlign , "useMomentsAlign" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useGeometryAlign , "useGeometryAlign" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , useCenterOfHeadAlign , "useCenterOfHeadAlign" , bool, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , permitParameterVariation , "permitParameterVariation" , std::vector<int>, "");
+BBTK_INPUT(GeneralRegistrationBRAINS , costMetric , "costMetric" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( GeneralRegistrationBRAINS ) ;
+}
+
+#endif // __bbSlicerGeneralRegistrationBRAINS_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerGradientAnisotropicDiffusion.cxx b/bbtk_Slicer_PKG/src/bbSlicerGradientAnisotropicDiffusion.cxx
new file mode 100644 (file)
index 0000000..ef5ab1b
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerGradientAnisotropicDiffusion.cxx
@@ -0,0 +1,59 @@
+#include "bbSlicerGradientAnisotropicDiffusion.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, GradientAnisotropicDiffusion )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( GradientAnisotropicDiffusion, bbtk::AtomicBlackBox );
+
+    void GradientAnisotropicDiffusion::Process ( ) {
+
+        // GENERATED
+
+int _argc =5;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libGradientAnisotropicDiffusionLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--conductance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputconductance( ) ) ) ,"@@@@@"," --conductance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --iterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--timeStep"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtimeStep( ) ) ) ,"@@@@@"," --timeStep ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void GradientAnisotropicDiffusion::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void GradientAnisotropicDiffusion::bbUserSetDefaultValues ( ) {
+    }
+
+    void GradientAnisotropicDiffusion::bbUserInitializeProcessing ( ) {
+    }
+
+    void GradientAnisotropicDiffusion::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerGradientAnisotropicDiffusion.h b/bbtk_Slicer_PKG/src/bbSlicerGradientAnisotropicDiffusion.h
new file mode 100644 (file)
index 0000000..eb9e3ad
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerGradientAnisotropicDiffusion.h
@@ -0,0 +1,66 @@
+#ifndef __bbSlicerGradientAnisotropicDiffusion_h_INCLUDED__
+#define __bbSlicerGradientAnisotropicDiffusion_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT GradientAnisotropicDiffusion
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( GradientAnisotropicDiffusion , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( conductance , double );
+BBTK_DECLARE_INPUT ( numberOfIterations , int );
+BBTK_DECLARE_INPUT ( timeStep , double );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( GradientAnisotropicDiffusion , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "GradientAnisotropicDiffusion" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Runs gradient anisotropic diffusion on a volume.Anisotropic diffusion methods reduce noise or unwanted detail in images while preserving specific image features, like edges.  For many applications, there is an assumption that light-dark transitions edges are interesting.  Standard isotropic diffusion methods move and blur light-dark boundaries.  Anisotropic diffusion methods are formulated to specifically preserve edges. The conductance term for this implementation is a function of the gradient magnitude of the image at each point, reducing the strength of diffusion at edges. The numerical implementation of this equation is similar to that described in the Perona-Malik paper, but uses a more robust technique for gradient magnitude estimation and has been generalized to N-dimensions." ) ;
+    BBTK_CATEGORY ( "Filtering.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(GradientAnisotropicDiffusion , conductance , "conductance" , double, "");
+BBTK_INPUT(GradientAnisotropicDiffusion , numberOfIterations , "numberOfIterations" , int, "");
+BBTK_INPUT(GradientAnisotropicDiffusion , timeStep , "timeStep" , double, "");
+BBTK_INPUT(GradientAnisotropicDiffusion , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(GradientAnisotropicDiffusion , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( GradientAnisotropicDiffusion ) ;
+}
+
+#endif // __bbSlicerGradientAnisotropicDiffusion_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerGrayscaleFillHole.cxx b/bbtk_Slicer_PKG/src/bbSlicerGrayscaleFillHole.cxx
new file mode 100644 (file)
index 0000000..3300e5d
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerGrayscaleFillHole.cxx
@@ -0,0 +1,56 @@
+#include "bbSlicerGrayscaleFillHole.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, GrayscaleFillHole )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( GrayscaleFillHole, bbtk::AtomicBlackBox );
+
+    void GrayscaleFillHole::Process ( ) {
+
+        // GENERATED
+
+int _argc =2;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libGrayscaleFillHoleImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void GrayscaleFillHole::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void GrayscaleFillHole::bbUserSetDefaultValues ( ) {
+    }
+
+    void GrayscaleFillHole::bbUserInitializeProcessing ( ) {
+    }
+
+    void GrayscaleFillHole::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerGrayscaleFillHole.h b/bbtk_Slicer_PKG/src/bbSlicerGrayscaleFillHole.h
new file mode 100644 (file)
index 0000000..695d7e2
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerGrayscaleFillHole.h
@@ -0,0 +1,60 @@
+#ifndef __bbSlicerGrayscaleFillHole_h_INCLUDED__
+#define __bbSlicerGrayscaleFillHole_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT GrayscaleFillHole
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( GrayscaleFillHole , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( GrayscaleFillHole , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "GrayscaleFillHole" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "GrayscaleFillholeImageFilter fills holes in a grayscale image.  Holes are local minima in the grayscale topography that are not connected to boundaries of the image. Gray level values adjacent to a hole are extrapolated across the hole.This filter is used to smooth over local minima without affecting the values of local maxima.  If you take the difference between the output of this filter and the original image and perhaps threshold the difference above a small value, you'll obtain a map of the local minima.This filter uses the itkGrayscaleGeodesicErodeImageFilter.  It provides its own input as the 'mask' input to the geodesic erosion.  The 'marker' image for the geodesic erosion is constructed such that boundary pixels match the boundary pixels of the input image and the interior pixels are set to the maximum pixel value in the input image. Geodesic morphology and the Fillhole algorithm is described in Chapter 6 of Pierre Soille's book 'Morphological Image Analysis: Principles and Applications', Second Edition, Springer, 2003.  A companion filter, Grayscale Grind Peak, removes peaks in grayscale images." ) ;
+    BBTK_CATEGORY ( "Filtering.Morphology" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(GrayscaleFillHole , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(GrayscaleFillHole , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( GrayscaleFillHole ) ;
+}
+
+#endif // __bbSlicerGrayscaleFillHole_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerGrayscaleGrindPeak.cxx b/bbtk_Slicer_PKG/src/bbSlicerGrayscaleGrindPeak.cxx
new file mode 100644 (file)
index 0000000..aae444b
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerGrayscaleGrindPeak.cxx
@@ -0,0 +1,56 @@
+#include "bbSlicerGrayscaleGrindPeak.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, GrayscaleGrindPeak )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( GrayscaleGrindPeak, bbtk::AtomicBlackBox );
+
+    void GrayscaleGrindPeak::Process ( ) {
+
+        // GENERATED
+
+int _argc =2;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libGrayscaleGrindPeakImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void GrayscaleGrindPeak::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void GrayscaleGrindPeak::bbUserSetDefaultValues ( ) {
+    }
+
+    void GrayscaleGrindPeak::bbUserInitializeProcessing ( ) {
+    }
+
+    void GrayscaleGrindPeak::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerGrayscaleGrindPeak.h b/bbtk_Slicer_PKG/src/bbSlicerGrayscaleGrindPeak.h
new file mode 100644 (file)
index 0000000..0b43992
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerGrayscaleGrindPeak.h
@@ -0,0 +1,60 @@
+#ifndef __bbSlicerGrayscaleGrindPeak_h_INCLUDED__
+#define __bbSlicerGrayscaleGrindPeak_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT GrayscaleGrindPeak
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( GrayscaleGrindPeak , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( GrayscaleGrindPeak , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "GrayscaleGrindPeak" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "GrayscaleGrindPeakImageFilter removes peaks in a grayscale image. Peaks are local maxima in the grayscale topography that are not connected to boundaries of the image. Gray level values adjacent to a peak are extrapolated through the peak.This filter is used to smooth over local maxima without affecting the values of local minima.  If you take the difference between the output of this filter and the original image and perhaps threshold the difference above a small value, you'll obtain a map of the local maxima.This filter uses the GrayscaleGeodesicDilateImageFilter.  It provides its own input as the 'mask' input to the geodesic erosion.  The 'marker' image for the geodesic erosion is constructed such that boundary pixels match the boundary pixels of the input image and the interior pixels are set to the minimum pixel value in the input image.This filter is the dual to the GrayscaleFillholeImageFilter which implements the Fillhole algorithm.  Since it is a dual, it is somewhat superfluous but is provided as a convenience.Geodesic morphology and the Fillhole algorithm is described in Chapter 6 of Pierre Soille's book 'Morphological Image Analysis: Principles and Applications', Second Edition, Springer, 2003.A companion filter, Grayscale Fill Hole, fills holes in grayscale images." ) ;
+    BBTK_CATEGORY ( "Filtering.Morphology" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(GrayscaleGrindPeak , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(GrayscaleGrindPeak , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( GrayscaleGrindPeak ) ;
+}
+
+#endif // __bbSlicerGrayscaleGrindPeak_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerHistogramMatching.cxx b/bbtk_Slicer_PKG/src/bbSlicerHistogramMatching.cxx
new file mode 100644 (file)
index 0000000..b78a83f
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerHistogramMatching.cxx
@@ -0,0 +1,60 @@
+#include "bbSlicerHistogramMatching.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, HistogramMatching )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( HistogramMatching, bbtk::AtomicBlackBox );
+
+    void HistogramMatching::Process ( ) {
+
+        // GENERATED
+
+int _argc =6;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libHistogramMatchingLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfHistogramLevels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfHistogramLevels( ) ) ) ,"@@@@@"," --numberOfHistogramLevels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfMatchPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfMatchPoints( ) ) ) ,"@@@@@"," --numberOfMatchPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--threshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputthresholdAtMeanIntensity( ) ) ) ,"@@@@@"," --threshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreferenceVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void HistogramMatching::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void HistogramMatching::bbUserSetDefaultValues ( ) {
+    }
+
+    void HistogramMatching::bbUserInitializeProcessing ( ) {
+    }
+
+    void HistogramMatching::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerHistogramMatching.h b/bbtk_Slicer_PKG/src/bbSlicerHistogramMatching.h
new file mode 100644 (file)
index 0000000..efdcef4
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerHistogramMatching.h
@@ -0,0 +1,68 @@
+#ifndef __bbSlicerHistogramMatching_h_INCLUDED__
+#define __bbSlicerHistogramMatching_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT HistogramMatching
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( HistogramMatching , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( numberOfHistogramLevels , int );
+BBTK_DECLARE_INPUT ( numberOfMatchPoints , int );
+BBTK_DECLARE_INPUT ( thresholdAtMeanIntensity , bool );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( referenceVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( HistogramMatching , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "HistogramMatching" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Normalizes the grayscale values of a source image based on the grayscale values of a reference image.  This filter uses a histogram matching technique where the histograms of the two images are matched only at a specified number of quantile values.The filter was orginally designed to normalize MR images of the sameMR protocol and same body part. The algorithm works best if background pixels are excluded from both the source and reference histograms.  A simple background exclusion method is to exclude all pixels whose grayscale values are smaller than the mean grayscale value. ThresholdAtMeanIntensity switches on this simple background exclusion method.Number of match points governs the number of quantile values to be matched.The filter assumes that both the source and reference are of the same type and that the input and output image type have the same number of dimension and have scalar pixel types." ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(HistogramMatching , numberOfHistogramLevels , "numberOfHistogramLevels" , int, "");
+BBTK_INPUT(HistogramMatching , numberOfMatchPoints , "numberOfMatchPoints" , int, "");
+BBTK_INPUT(HistogramMatching , thresholdAtMeanIntensity , "thresholdAtMeanIntensity" , bool, "");
+BBTK_INPUT(HistogramMatching , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(HistogramMatching , referenceVolume , "referenceVolume" , std::string, "");
+BBTK_INPUT(HistogramMatching , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( HistogramMatching ) ;
+}
+
+#endif // __bbSlicerHistogramMatching_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerImageLabelCombine.cxx b/bbtk_Slicer_PKG/src/bbSlicerImageLabelCombine.cxx
index cf71b1ead60f6e680951edfc4383bec86bcda76e..686720dd740044590e560fce62bb0c48586c801e 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerImageLabelCombine.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerImageLabelCombine.cxx
@@ -11,10 +11,10 @@ namespace bbSlicer {
 
 int _argc =4;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libImageLabelCombineLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputInputLabelMap_A( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputInputLabelMap_B( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputOutputLabelMap( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::toString( bbGetInputFirstOverwrites( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputLabelMap_A( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputLabelMap_B( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputLabelMap( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFirstOverwrites( ) ) ) ,"@@@@@"," -f ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerJointRicianLMMSEImageFilter.cxx b/bbtk_Slicer_PKG/src/bbSlicerJointRicianLMMSEImageFilter.cxx
new file mode 100644 (file)
index 0000000..374606d
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerJointRicianLMMSEImageFilter.cxx
@@ -0,0 +1,59 @@
+#include "bbSlicerJointRicianLMMSEImageFilter.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, JointRicianLMMSEImageFilter )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( JointRicianLMMSEImageFilter, bbtk::AtomicBlackBox );
+
+    void JointRicianLMMSEImageFilter::Process ( ) {
+
+        // GENERATED
+
+int _argc =5;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libjointLMMSELib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--re"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusEstimation( ) ) ) ,"@@@@@"," --re ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rf"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusFiltering( ) ) ) ,"@@@@@"," --rf ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ng"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiNumNeighbors( ) ) ) ,"@@@@@"," --ng ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void JointRicianLMMSEImageFilter::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void JointRicianLMMSEImageFilter::bbUserSetDefaultValues ( ) {
+    }
+
+    void JointRicianLMMSEImageFilter::bbUserInitializeProcessing ( ) {
+    }
+
+    void JointRicianLMMSEImageFilter::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerJointRicianLMMSEImageFilter.h b/bbtk_Slicer_PKG/src/bbSlicerJointRicianLMMSEImageFilter.h
new file mode 100644 (file)
index 0000000..ace562e
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerJointRicianLMMSEImageFilter.h
@@ -0,0 +1,66 @@
+#ifndef __bbSlicerJointRicianLMMSEImageFilter_h_INCLUDED__
+#define __bbSlicerJointRicianLMMSEImageFilter_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT JointRicianLMMSEImageFilter
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( JointRicianLMMSEImageFilter , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( iRadiusEstimation , std::vector<int> );
+BBTK_DECLARE_INPUT ( iRadiusFiltering , std::vector<int> );
+BBTK_DECLARE_INPUT ( iNumNeighbors , int );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( JointRicianLMMSEImageFilter , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "JointRicianLMMSEImageFilter" ) ;
+    BBTK_AUTHOR ( "Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid SPAIN. Partially founded by grant number TEC2007-67073/TCM from the Comision Interministerial de Ciencia y Tecnologia Spain." ) ;
+    BBTK_DESCRIPTION ( "This module reduces Rician noise or unwanted detail on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. The N closest gradient directions to the direction being processed are filtered together to improve the results: the noise-free signal is seen as an n-diemensional vector which has to be estimated with the LMMSE method from a set of corrupted measurements. To that end, the covariance matrix of the noise-free vector and the cross covariance between this signal and the noise have to be estimated, which is done taking into account the image formation process.The noise parameter is automatically estimated from a rough segmentation of the background of the image. In this area the signal is simply 0, so that Rician statistics reduce to Rayleigh and the noise power can be easily estimated from the mode of the histogram.A complete description of the algorithm may be found in:Antonio Tristan-Vega and Santiago Aja-Fernandez, DWI filtering using joint information for DTI and HARDI, Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010." ) ;
+    BBTK_CATEGORY ( "Diffusion.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(JointRicianLMMSEImageFilter , iRadiusEstimation , "iRadiusEstimation" , std::vector<int>, "");
+BBTK_INPUT(JointRicianLMMSEImageFilter , iRadiusFiltering , "iRadiusFiltering" , std::vector<int>, "");
+BBTK_INPUT(JointRicianLMMSEImageFilter , iNumNeighbors , "iNumNeighbors" , int, "");
+BBTK_INPUT(JointRicianLMMSEImageFilter , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(JointRicianLMMSEImageFilter , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( JointRicianLMMSEImageFilter ) ;
+}
+
+#endif // __bbSlicerJointRicianLMMSEImageFilter_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerLabelMapSmoothing.cxx b/bbtk_Slicer_PKG/src/bbSlicerLabelMapSmoothing.cxx
index 8d6febce9a9949c884a3ea34081d1870f4d533b5..3bd0ff50528591372651879661cc909493a3abdb 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerLabelMapSmoothing.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerLabelMapSmoothing.cxx
@@ -11,12 +11,12 @@ namespace bbSlicer {
 
 int _argc =6;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libLabelMapSmoothingLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--labelToSmooth"  ) + Mthd::Aux::toString( bbGetInputlabelToSmooth( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfIterations"  ) + Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxRMSError"  ) + Mthd::Aux::toString( bbGetInputmaxRMSError( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--gaussianSigma"  ) + Mthd::Aux::toString( bbGetInputgaussianSigma( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--labelToSmooth"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlabelToSmooth( ) ) ) ,"@@@@@"," --labelToSmooth ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --numberOfIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxRMSError"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxRMSError( ) ) ) ,"@@@@@"," --maxRMSError ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--gaussianSigma"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgaussianSigma( ) ) ) ,"@@@@@"," --gaussianSigma ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerLinearregistration.cxx b/bbtk_Slicer_PKG/src/bbSlicerLinearregistration.cxx
new file mode 100644 (file)
index 0000000..98f4d66
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerLinearregistration.cxx
@@ -0,0 +1,66 @@
+#include "bbSlicerLinearregistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, Linearregistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( Linearregistration, bbtk::AtomicBlackBox );
+
+    void Linearregistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =12;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libLinearRegistrationLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageSmoothingFactor( ) ) ) ,"@@@@@"," --fixedsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingsmoothingfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageSmoothingFactor( ) ) ) ,"@@@@@"," --movingsmoothingfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputHistogramBins( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSpatialSamples( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLearningRate( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputTranslationScale( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initialtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInitialTransform( ) ) ) ,"@@@@@"," --initialtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledmovingfilename"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputResampledImageFileName( ) ) ) ,"@@@@@"," --resampledmovingfilename ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void Linearregistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void Linearregistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void Linearregistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void Linearregistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerLinearregistration.h b/bbtk_Slicer_PKG/src/bbSlicerLinearregistration.h
new file mode 100644 (file)
index 0000000..3f1013c
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerLinearregistration.h
@@ -0,0 +1,80 @@
+#ifndef __bbSlicerLinearregistration_h_INCLUDED__
+#define __bbSlicerLinearregistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT Linearregistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( Linearregistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( FixedImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( MovingImageSmoothingFactor , int );
+BBTK_DECLARE_INPUT ( HistogramBins , int );
+BBTK_DECLARE_INPUT ( SpatialSamples , int );
+BBTK_DECLARE_INPUT ( Iterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( LearningRate , std::vector<double> );
+BBTK_DECLARE_INPUT ( TranslationScale , double );
+BBTK_DECLARE_INPUT ( InitialTransform , std::string );
+BBTK_DECLARE_INPUT ( FixedImageFileName , std::string );
+BBTK_DECLARE_INPUT ( MovingImageFileName , std::string );
+BBTK_DECLARE_INPUT ( OutputTransform , std::string );
+BBTK_DECLARE_INPUT ( ResampledImageFileName , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( Linearregistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "Linearregistration" ) ;
+    BBTK_AUTHOR ( "Daniel Blezek" ) ;
+    BBTK_DESCRIPTION ( "Registers two images together using a rigid transform and mutual information." ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(Linearregistration , FixedImageSmoothingFactor , "FixedImageSmoothingFactor" , int, "");
+BBTK_INPUT(Linearregistration , MovingImageSmoothingFactor , "MovingImageSmoothingFactor" , int, "");
+BBTK_INPUT(Linearregistration , HistogramBins , "HistogramBins" , int, "");
+BBTK_INPUT(Linearregistration , SpatialSamples , "SpatialSamples" , int, "");
+BBTK_INPUT(Linearregistration , Iterations , "Iterations" , std::vector<int>, "");
+BBTK_INPUT(Linearregistration , LearningRate , "LearningRate" , std::vector<double>, "");
+BBTK_INPUT(Linearregistration , TranslationScale , "TranslationScale" , double, "");
+BBTK_INPUT(Linearregistration , InitialTransform , "InitialTransform" , std::string, "");
+BBTK_INPUT(Linearregistration , FixedImageFileName , "FixedImageFileName" , std::string, "");
+BBTK_INPUT(Linearregistration , MovingImageFileName , "MovingImageFileName" , std::string, "");
+BBTK_INPUT(Linearregistration , OutputTransform , "OutputTransform" , std::string, "");
+BBTK_INPUT(Linearregistration , ResampledImageFileName , "ResampledImageFileName" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( Linearregistration ) ;
+}
+
+#endif // __bbSlicerLinearregistration_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMRIBiasFieldCorrection.cxx b/bbtk_Slicer_PKG/src/bbSlicerMRIBiasFieldCorrection.cxx
index 946408f6d6f6154cf69f162afd48ea99501f36e8..61d0ffea2c9435f2b921399243f866aac050e61c 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerMRIBiasFieldCorrection.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerMRIBiasFieldCorrection.cxx
@@ -11,16 +11,16 @@ namespace bbSlicer {
 
 int _argc =10;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMRIBiasFieldCorrectionLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputImage"  ) + Mthd::Aux::toString( bbGetInputInputImage( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputMask"  ) + Mthd::Aux::toString( bbGetInputInputMask( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputImage"  ) + Mthd::Aux::toString( bbGetInputOutputImage( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--algorithmType"  ) + Mthd::Aux::toString( bbGetInputAlgorithmType( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--shrinkFactor"  ) + Mthd::Aux::toString( bbGetInputShrinkFactor( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maximumNumberOfIterations"  ) + Mthd::Aux::toString( bbGetInputMaximumNumberOfIterations( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfFittingLevels"  ) + Mthd::Aux::toString( bbGetInputNumberOfFittingLevels( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--wienerFilterNoise"  ) + Mthd::Aux::toString( bbGetInputWienerFilterNoise( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fullWidthAtHalfMaximum"  ) + Mthd::Aux::toString( bbGetInputFullWidthAtHalfMaximum( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--convergenceThreshold"  ) + Mthd::Aux::toString( bbGetInputConvergenceThreshold( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputImage( ) ) ) ,"@@@@@"," --inputImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputMask"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputMask( ) ) ) ,"@@@@@"," --inputMask ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputImage( ) ) ) ,"@@@@@"," --outputImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--algorithmType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputAlgorithmType( ) ) ) ,"@@@@@"," --algorithmType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--shrinkFactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputShrinkFactor( ) ) ) ,"@@@@@"," --shrinkFactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maximumNumberOfIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMaximumNumberOfIterations( ) ) ) ,"@@@@@"," --maximumNumberOfIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfFittingLevels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputNumberOfFittingLevels( ) ) ) ,"@@@@@"," --numberOfFittingLevels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--wienerFilterNoise"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputWienerFilterNoise( ) ) ) ,"@@@@@"," --wienerFilterNoise ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fullWidthAtHalfMaximum"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFullWidthAtHalfMaximum( ) ) ) ,"@@@@@"," --fullWidthAtHalfMaximum ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--convergenceThreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputConvergenceThreshold( ) ) ) ,"@@@@@"," --convergenceThreshold ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMRIBiasFieldCorrection.h b/bbtk_Slicer_PKG/src/bbSlicerMRIBiasFieldCorrection.h
index 7b491ff3ffade0d2d0130eedf89d7722945d752a..10533e1c1e2f82ff87180cd718cf300174712f3f 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerMRIBiasFieldCorrection.h
+++ b/bbtk_Slicer_PKG/src/bbSlicerMRIBiasFieldCorrection.h
@@ -49,8 +49,8 @@ BBTK_DECLARE_INPUT ( ConvergenceThreshold , double );
 
     BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MRIBiasFieldCorrection , bbtk::AtomicBlackBox ) ;
     BBTK_NAME ( "MRIBiasFieldCorrection" ) ;
-    BBTK_AUTHOR ( "Sylvain Jaume (MIT)" ) ;
-    BBTK_DESCRIPTION ( "Corrects 3D MRI images corrupted by MRI gain field effect.  This module removes the slow-varying intensity variation from a 3D image.  The output image has a higher contrast locally and the visualization and reading of the image are improved.  This is an important pre-processinbg step for image operations requiring intensity perfect images, such as the Expectation Maximization segmentation (see EMSegment module). The N3 and N4 methods are described in N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction, Tustison N., Gee J., Insight Journal, 2009. http://hdl.handle.net/10380/3053 The Slicer code was contributed by Sylvain Jaume (MIT) for NA-MIC (http://na-mic.org)." ) ;
+    BBTK_AUTHOR ( "Sylvain Jaume MIT" ) ;
+    BBTK_DESCRIPTION ( "Corrects 3D MRI images corrupted by MRI gain field effect.  This module removes the slow-varying intensity variation from a 3D image.  The output image has a higher contrast locally and the visualization and reading of the image are improved.  This is an important pre-processinbg step for image operations requiring intensity perfect images, such as the Expectation Maximization segmentation see EMSegment module. The N3 and N4 methods are described in N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction, Tustison N., Gee J., Insight Journal, 2009. http://hdl.handle.net/10380/3053 The Slicer code was contributed by Sylvain Jaume MIT for NA-MIC http://na-mic.org." ) ;
     BBTK_CATEGORY ( "Legacy.Filtering" ) ;
 
     // GENERATED DESCRPTION

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMaskImage.cxx b/bbtk_Slicer_PKG/src/bbSlicerMaskImage.cxx
index e657ec1a7d6adb6b1d518d5f995c35f86198fbbd..1df060b248bc3a7b4b56b00d0c1f77e286c6e498 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerMaskImage.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerMaskImage.cxx
@@ -11,11 +11,11 @@ namespace bbSlicer {
 
 int _argc =5;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMaskLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputMaskVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::toString( bbGetInputLabel( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-r"  ) + Mthd::Aux::toString( bbGetInputReplace( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMaskVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLabel( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-r"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputReplace( ) ) ) ,"@@@@@"," -r ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMaskImage.h b/bbtk_Slicer_PKG/src/bbSlicerMaskImage.h
index 1dbe285fe64d180bc49eddef492afcc4fc50f0ee..73f9b29a3bd5b96d020b88a8478ae1cc2f6537f7 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerMaskImage.h
+++ b/bbtk_Slicer_PKG/src/bbSlicerMaskImage.h
@@ -44,7 +44,7 @@ BBTK_DECLARE_INPUT ( Replace , int );
 
     BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MaskImage , bbtk::AtomicBlackBox ) ;
     BBTK_NAME ( "MaskImage" ) ;
-    BBTK_AUTHOR ( "Nicole Aucoin, BWH (Ron Kikinis, BWH)" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH" ) ;
     BBTK_DESCRIPTION ( "Masks two images. The output image is set to 0 everywhere except where the chosen label from the mask volume is present, at which point it will retain it's original values. Although all image types are supported on input, only signed types are produced. The two images do not have to have the same dimensions." ) ;
     BBTK_CATEGORY ( "Filtering.Arithmetic" ) ;
 

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMedianFilter.cxx b/bbtk_Slicer_PKG/src/bbSlicerMedianFilter.cxx
new file mode 100644 (file)
index 0000000..80f8a20
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerMedianFilter.cxx
@@ -0,0 +1,57 @@
+#include "bbSlicerMedianFilter.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, MedianFilter )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( MedianFilter, bbtk::AtomicBlackBox );
+
+    void MedianFilter::Process ( ) {
+
+        // GENERATED
+
+int _argc =3;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMedianImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--neighborhood"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputneighborhood( ) ) ) ,"@@@@@"," --neighborhood ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void MedianFilter::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void MedianFilter::bbUserSetDefaultValues ( ) {
+    }
+
+    void MedianFilter::bbUserInitializeProcessing ( ) {
+    }
+
+    void MedianFilter::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMedianFilter.h b/bbtk_Slicer_PKG/src/bbSlicerMedianFilter.h
new file mode 100644 (file)
index 0000000..3518df1
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerMedianFilter.h
@@ -0,0 +1,62 @@
+#ifndef __bbSlicerMedianFilter_h_INCLUDED__
+#define __bbSlicerMedianFilter_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT MedianFilter
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( MedianFilter , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( neighborhood , std::vector<int> );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MedianFilter , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "MedianFilter" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "The MedianImageFilter is commonly used as a robust approach for noise reduction. This filter is particularly efficient against 'salt-and-pepper' noise. In other words, it is robust to the presence of gray-level outliers. MedianImageFilter computes the value of each output pixel as the statistical median of the neighborhood of values around the corresponding input pixel." ) ;
+    BBTK_CATEGORY ( "Filtering.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(MedianFilter , neighborhood , "neighborhood" , std::vector<int>, "");
+BBTK_INPUT(MedianFilter , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(MedianFilter , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( MedianFilter ) ;
+}
+
+#endif // __bbSlicerMedianFilter_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMergeModels.cxx b/bbtk_Slicer_PKG/src/bbSlicerMergeModels.cxx
index fec4de36301487e95114e374e3957baa3fcdbf54..94312c1f24564d462932d93727b14497d03c90e0 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerMergeModels.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerMergeModels.cxx
@@ -11,9 +11,9 @@ namespace bbSlicer {
 
 int _argc =3;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMergeModelsLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputModel1( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputModel2( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputModelOutput( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModel1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModel2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModelOutput( ) ) ) ,"@@@@@","") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMergeModels.h b/bbtk_Slicer_PKG/src/bbSlicerMergeModels.h
index 2ff5f2de4ca2e9901575b8dce9d1a16d83f228ff..085777efe865089295a16530f290932afa1653a1 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerMergeModels.h
+++ b/bbtk_Slicer_PKG/src/bbSlicerMergeModels.h
@@ -42,7 +42,7 @@ BBTK_DECLARE_INPUT ( ModelOutput , std::string );
 
     BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MergeModels , bbtk::AtomicBlackBox ) ;
     BBTK_NAME ( "MergeModels" ) ;
-    BBTK_AUTHOR ( "Nicole Aucoin BWH (Ron Kikinis, BWH), Daniel Haehn" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin BWH Ron Kikinis, BWH, Daniel Haehn" ) ;
     BBTK_DESCRIPTION ( "Merge the polydata from two input models and output a new model with the added polydata. Uses the vtkAppendPolyData filter. Works on .vtp and .vtk surface files." ) ;
     BBTK_CATEGORY ( "Surface Models" ) ;
 

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMeshContourSegmentation.cxx b/bbtk_Slicer_PKG/src/bbSlicerMeshContourSegmentation.cxx
new file mode 100644 (file)
index 0000000..bdb8ba9
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerMeshContourSegmentation.cxx
@@ -0,0 +1,64 @@
+#include "bbSlicerMeshContourSegmentation.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, MeshContourSegmentation )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( MeshContourSegmentation, bbtk::AtomicBlackBox );
+
+    void MeshContourSegmentation::Process ( ) {
+
+        // GENERATED
+
+int _argc =10;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libSparseFieldLevelSetContourLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputScene"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputSurface( ) ) ) ,"@@@@@"," --inputScene ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-c"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputContourSeedPts( ) ) ) ,"@@@@@"," -c ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputModel"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputModel( ) ) ) ,"@@@@@"," --outputModel ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--evolve_its"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputevolve_its( ) ) ) ,"@@@@@"," --evolve_its ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--mesh_smooth_its"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmesh_smooth_its( ) ) ) ,"@@@@@"," --mesh_smooth_its ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--H_smooth_its"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputH_smooth_its( ) ) ) ,"@@@@@"," --H_smooth_its ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--adj_levels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputadj_levels( ) ) ) ,"@@@@@"," --adj_levels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--showLS"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputshowLS( ) ) ) ,"@@@@@"," --showLS ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rightHandMesh"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrightHandMesh( ) ) ) ,"@@@@@"," --rightHandMesh ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--is_test"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputis_test( ) ) ) ,"@@@@@"," --is_test ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void MeshContourSegmentation::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void MeshContourSegmentation::bbUserSetDefaultValues ( ) {
+    }
+
+    void MeshContourSegmentation::bbUserInitializeProcessing ( ) {
+    }
+
+    void MeshContourSegmentation::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMeshContourSegmentation.h b/bbtk_Slicer_PKG/src/bbSlicerMeshContourSegmentation.h
new file mode 100644 (file)
index 0000000..0f9cdf4
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerMeshContourSegmentation.h
@@ -0,0 +1,76 @@
+#ifndef __bbSlicerMeshContourSegmentation_h_INCLUDED__
+#define __bbSlicerMeshContourSegmentation_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT MeshContourSegmentation
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( MeshContourSegmentation , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputSurface , std::string );
+BBTK_DECLARE_INPUT ( ContourSeedPts , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( OutputModel , std::string );
+BBTK_DECLARE_INPUT ( evolve_its , int );
+BBTK_DECLARE_INPUT ( mesh_smooth_its , int );
+BBTK_DECLARE_INPUT ( H_smooth_its , int );
+BBTK_DECLARE_INPUT ( adj_levels , int );
+BBTK_DECLARE_INPUT ( showLS , bool );
+BBTK_DECLARE_INPUT ( rightHandMesh , bool );
+BBTK_DECLARE_INPUT ( is_test , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( MeshContourSegmentation , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "MeshContourSegmentation" ) ;
+    BBTK_AUTHOR ( "Peter Karasev, pkarasev@gatech.edu, Allen Tannenbaum, tannenba@ece.gatech.edu" ) ;
+    BBTK_DESCRIPTION ( "Sparse-Field Levelset Mesh Segmentation. Given some initial points in polydata will construct a contour and evolve it to high mean-curvature areas, returning the interior region indices.Once the output surface has been loaded into Slicer, go to the Models module, Model Display pane, and set the Scalar Visibility Flag, select the LevelSetValue as the active scalar array, and pick the FreeSurfer RedGreen Scalar Color Map. The InitialCurvature and SmoothedCurvature may appear if the path finding failed.  An example calling convention from the commandline for this module:--inputScene C:/.../bin/Release/LSVTKOut1.vtk' -c '1.5,1.5,0' -c '-1.5,1.5,0' -c '-1.5,-1.5,0' -c '1.5,-1.5,0' --outputFilename 'tempOut.vtk'This gives it an initial geometry in the vtk file, four seed points in x,y,z coordinates, and where to write the output.The resulting output contains a colormap that defines interior/exterior of the surface as determined by evolving the curve into high mean curvature areas." ) ;
+    BBTK_CATEGORY ( "Segmentation.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(MeshContourSegmentation , InputSurface , "InputSurface" , std::string, "");
+BBTK_INPUT(MeshContourSegmentation , ContourSeedPts , "ContourSeedPts" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(MeshContourSegmentation , OutputModel , "OutputModel" , std::string, "");
+BBTK_INPUT(MeshContourSegmentation , evolve_its , "evolve_its" , int, "");
+BBTK_INPUT(MeshContourSegmentation , mesh_smooth_its , "mesh_smooth_its" , int, "");
+BBTK_INPUT(MeshContourSegmentation , H_smooth_its , "H_smooth_its" , int, "");
+BBTK_INPUT(MeshContourSegmentation , adj_levels , "adj_levels" , int, "");
+BBTK_INPUT(MeshContourSegmentation , showLS , "showLS" , bool, "");
+BBTK_INPUT(MeshContourSegmentation , rightHandMesh , "rightHandMesh" , bool, "");
+BBTK_INPUT(MeshContourSegmentation , is_test , "is_test" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( MeshContourSegmentation ) ;
+}
+
+#endif // __bbSlicerMeshContourSegmentation_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerModelMaker.cxx b/bbtk_Slicer_PKG/src/bbSlicerModelMaker.cxx
new file mode 100644 (file)
index 0000000..2f7737c
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerModelMaker.cxx
@@ -0,0 +1,72 @@
+#include "bbSlicerModelMaker.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ModelMaker )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ModelMaker, bbtk::AtomicBlackBox );
+
+    void ModelMaker::Process ( ) {
+
+        // GENERATED
+
+int _argc =18;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libModelMakerLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--color"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputColorTable( ) ) ) ,"@@@@@"," --color ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--modelSceneFile"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModelSceneFile( ) ) ) ,"@@@@@"," --modelSceneFile ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-n"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputName( ) ) ) ,"@@@@@"," -n ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--generateAll"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputGenerateAll( ) ) ) ,"@@@@@"," --generateAll ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLabels( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputStartLabel( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputEndLabel( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--skipUnNamed"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSkipUnNamed( ) ) ) ,"@@@@@"," --skipUnNamed ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-j"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputJointSmoothing( ) ) ) ,"@@@@@"," -j ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--smooth"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSmooth( ) ) ) ,"@@@@@"," --smooth ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--filtertype"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFilterType( ) ) ) ,"@@@@@"," --filtertype ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--decimate"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputDecimate( ) ) ) ,"@@@@@"," --decimate ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--splitnormals"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSplitNormals( ) ) ) ,"@@@@@"," --splitnormals ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--pointnormals"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPointNormals( ) ) ) ,"@@@@@"," --pointnormals ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--pad"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPad( ) ) ) ,"@@@@@"," --pad ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--saveIntermediateModels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputSaveIntermediateModels( ) ) ) ,"@@@@@"," --saveIntermediateModels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdebug( ) ) ) ,"@@@@@"," -d ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ModelMaker::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ModelMaker::bbUserSetDefaultValues ( ) {
+    }
+
+    void ModelMaker::bbUserInitializeProcessing ( ) {
+    }
+
+    void ModelMaker::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerModelMaker.h b/bbtk_Slicer_PKG/src/bbSlicerModelMaker.h
new file mode 100644 (file)
index 0000000..05045b3
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerModelMaker.h
@@ -0,0 +1,92 @@
+#ifndef __bbSlicerModelMaker_h_INCLUDED__
+#define __bbSlicerModelMaker_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ModelMaker
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ModelMaker , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( ColorTable , std::string );
+BBTK_DECLARE_INPUT ( ModelSceneFile , std::string );
+BBTK_DECLARE_INPUT ( Name , std::string );
+BBTK_DECLARE_INPUT ( GenerateAll , bool );
+BBTK_DECLARE_INPUT ( Labels , std::vector<int> );
+BBTK_DECLARE_INPUT ( StartLabel , int );
+BBTK_DECLARE_INPUT ( EndLabel , int );
+BBTK_DECLARE_INPUT ( SkipUnNamed , bool );
+BBTK_DECLARE_INPUT ( JointSmoothing , bool );
+BBTK_DECLARE_INPUT ( Smooth , int );
+BBTK_DECLARE_INPUT ( FilterType , std::string );
+BBTK_DECLARE_INPUT ( Decimate , float );
+BBTK_DECLARE_INPUT ( SplitNormals , bool );
+BBTK_DECLARE_INPUT ( PointNormals , bool );
+BBTK_DECLARE_INPUT ( Pad , bool );
+BBTK_DECLARE_INPUT ( SaveIntermediateModels , bool );
+BBTK_DECLARE_INPUT ( debug , bool );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ModelMaker , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ModelMaker" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH, Bill Lorensen GE" ) ;
+    BBTK_DESCRIPTION ( "Create 3D surface models from segmented data. pModels are imported into Slicer under a model hierarchy node in a MRML scene. The model colors are set by the color table associated with the input volume these colours will only be visible if you load the model scene file. /ppbCreate Multiple:/b/pp If you specify a list of Labels, it will over ride any start/end label settings. /pp If you click iGenerate All/i it will over ride the list of lables and any start/end label settings. /ppbModel Maker Settings:/b/pp You can set the number of smoothing iterations, target reduction in number of polygons decimal percentage. Use 0 and 1 if you wish no smoothing nor decimation. brYou can set the flags to split normals or generate point normals in this pane as well. brYou can save a copy of the models after intermediate steps marching cubes, smoothing, and decimation if not joint smoothing, otherwise just after decimation; these models are not saved in the mrml file, turn off deleting temporary files first in the python window: brislicer.modules.modelmaker.cliModuleLogic.DeleteTemporaryFilesOff/i/p" ) ;
+    BBTK_CATEGORY ( "Surface Models" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ModelMaker , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(ModelMaker , ColorTable , "ColorTable" , std::string, "");
+BBTK_INPUT(ModelMaker , ModelSceneFile , "ModelSceneFile" , std::string, "");
+BBTK_INPUT(ModelMaker , Name , "Name" , std::string, "");
+BBTK_INPUT(ModelMaker , GenerateAll , "GenerateAll" , bool, "");
+BBTK_INPUT(ModelMaker , Labels , "Labels" , std::vector<int>, "");
+BBTK_INPUT(ModelMaker , StartLabel , "StartLabel" , int, "");
+BBTK_INPUT(ModelMaker , EndLabel , "EndLabel" , int, "");
+BBTK_INPUT(ModelMaker , SkipUnNamed , "SkipUnNamed" , bool, "");
+BBTK_INPUT(ModelMaker , JointSmoothing , "JointSmoothing" , bool, "");
+BBTK_INPUT(ModelMaker , Smooth , "Smooth" , int, "");
+BBTK_INPUT(ModelMaker , FilterType , "FilterType" , std::string, "");
+BBTK_INPUT(ModelMaker , Decimate , "Decimate" , float, "");
+BBTK_INPUT(ModelMaker , SplitNormals , "SplitNormals" , bool, "");
+BBTK_INPUT(ModelMaker , PointNormals , "PointNormals" , bool, "");
+BBTK_INPUT(ModelMaker , Pad , "Pad" , bool, "");
+BBTK_INPUT(ModelMaker , SaveIntermediateModels , "SaveIntermediateModels" , bool, "");
+BBTK_INPUT(ModelMaker , debug , "debug" , bool, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ModelMaker ) ;
+}
+
+#endif // __bbSlicerModelMaker_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMultiplemodelsexample.cxx b/bbtk_Slicer_PKG/src/bbSlicerMultiplemodelsexample.cxx
new file mode 100644 (file)
index 0000000..4eb9c42
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerMultiplemodelsexample.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerMultiplemodelsexample.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, Multiplemodelsexample )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( Multiplemodelsexample, bbtk::AtomicBlackBox );
+
+    void Multiplemodelsexample::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMultipleModelsExampleLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--color"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputColorTable( ) ) ) ,"@@@@@"," --color ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfModels"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputNumberOfModels( ) ) ) ,"@@@@@"," --numberOfModels ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--models"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputModels( ) ) ) ,"@@@@@"," --models ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void Multiplemodelsexample::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void Multiplemodelsexample::bbUserSetDefaultValues ( ) {
+    }
+
+    void Multiplemodelsexample::bbUserInitializeProcessing ( ) {
+    }
+
+    void Multiplemodelsexample::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMultiplemodelsexample.h b/bbtk_Slicer_PKG/src/bbSlicerMultiplemodelsexample.h
new file mode 100644 (file)
index 0000000..5b663ce
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerMultiplemodelsexample.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerMultiplemodelsexample_h_INCLUDED__
+#define __bbSlicerMultiplemodelsexample_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT Multiplemodelsexample
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( Multiplemodelsexample , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( ColorTable , std::string );
+BBTK_DECLARE_INPUT ( NumberOfModels , int );
+BBTK_DECLARE_INPUT ( Models , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( Multiplemodelsexample , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "Multiplemodelsexample" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin" ) ;
+    BBTK_DESCRIPTION ( "Create 3D surface models from segmented data.This example exports colors and imports a set of models automatically.If specify a list of Labels, it will over ride any start/end label settings." ) ;
+    BBTK_CATEGORY ( "Developer Tools" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(Multiplemodelsexample , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(Multiplemodelsexample , ColorTable , "ColorTable" , std::string, "");
+BBTK_INPUT(Multiplemodelsexample , NumberOfModels , "NumberOfModels" , int, "");
+BBTK_INPUT(Multiplemodelsexample , Models , "Models" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( Multiplemodelsexample ) ;
+}
+
+#endif // __bbSlicerMultiplemodelsexample_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerMultiplyImages.cxx b/bbtk_Slicer_PKG/src/bbSlicerMultiplyImages.cxx
index d7afe4c56780c001104c4295ade09a2e785e5c19..2e2414def868787048d6e193a56a75a5e550f10e 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerMultiplyImages.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerMultiplyImages.cxx
@@ -11,10 +11,10 @@ namespace bbSlicer {
 
 int _argc =4;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libMultiplyLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--order"  ) + Mthd::Aux::toString( bbGetInputorder( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--order"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputorder( ) ) ) ,"@@@@@"," --order ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerN4ITKMRIBiascorrection.cxx b/bbtk_Slicer_PKG/src/bbSlicerN4ITKMRIBiascorrection.cxx
new file mode 100644 (file)
index 0000000..5cf847e
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerN4ITKMRIBiascorrection.cxx
@@ -0,0 +1,66 @@
+#include "bbSlicerN4ITKMRIBiascorrection.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, N4ITKMRIBiascorrection )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( N4ITKMRIBiascorrection, bbtk::AtomicBlackBox );
+
+    void N4ITKMRIBiascorrection::Process ( ) {
+
+        // GENERATED
+
+int _argc =12;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libN4ITKBiasFieldCorrectionLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputimage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputImageName( ) ) ) ,"@@@@@"," --inputimage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maskimage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaskImageName( ) ) ) ,"@@@@@"," --maskimage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputimage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputImageName( ) ) ) ,"@@@@@"," --outputimage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputbiasfield"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputBiasFieldName( ) ) ) ,"@@@@@"," --outputbiasfield ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfIterations( ) ) ) ,"@@@@@"," --iterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--convergencethreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputconvergenceThreshold( ) ) ) ,"@@@@@"," --convergencethreshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--meshresolution"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitialMeshResolution( ) ) ) ,"@@@@@"," --meshresolution ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--splinedistance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsplineDistance( ) ) ) ,"@@@@@"," --splinedistance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--shrinkfactor"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputshrinkFactor( ) ) ) ,"@@@@@"," --shrinkfactor ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--bsplineorder"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbsplineOrder( ) ) ) ,"@@@@@"," --bsplineorder ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--weightimage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputweightImageName( ) ) ) ,"@@@@@"," --weightimage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--histogramsharpening"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputhistogramSharpening( ) ) ) ,"@@@@@"," --histogramsharpening ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void N4ITKMRIBiascorrection::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void N4ITKMRIBiascorrection::bbUserSetDefaultValues ( ) {
+    }
+
+    void N4ITKMRIBiascorrection::bbUserInitializeProcessing ( ) {
+    }
+
+    void N4ITKMRIBiascorrection::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerN4ITKMRIBiascorrection.h b/bbtk_Slicer_PKG/src/bbSlicerN4ITKMRIBiascorrection.h
new file mode 100644 (file)
index 0000000..288c385
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerN4ITKMRIBiascorrection.h
@@ -0,0 +1,80 @@
+#ifndef __bbSlicerN4ITKMRIBiascorrection_h_INCLUDED__
+#define __bbSlicerN4ITKMRIBiascorrection_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT N4ITKMRIBiascorrection
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( N4ITKMRIBiascorrection , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputImageName , std::string );
+BBTK_DECLARE_INPUT ( maskImageName , std::string );
+BBTK_DECLARE_INPUT ( outputImageName , std::string );
+BBTK_DECLARE_INPUT ( outputBiasFieldName , std::string );
+BBTK_DECLARE_INPUT ( numberOfIterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( convergenceThreshold , float );
+BBTK_DECLARE_INPUT ( initialMeshResolution , std::vector<float> );
+BBTK_DECLARE_INPUT ( splineDistance , float );
+BBTK_DECLARE_INPUT ( shrinkFactor , int );
+BBTK_DECLARE_INPUT ( bsplineOrder , int );
+BBTK_DECLARE_INPUT ( weightImageName , std::string );
+BBTK_DECLARE_INPUT ( histogramSharpening , std::vector<float> );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( N4ITKMRIBiascorrection , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "N4ITKMRIBiascorrection" ) ;
+    BBTK_AUTHOR ( "Nick Tustison algorithm and ITK implementation, Andrey Fedorov Slicer wrapping, Ron Kikinis PI" ) ;
+    BBTK_DESCRIPTION ( "Performs MRI bias correction using N4 algorithm. This module is based on the ITK filters contributed in the following publication:  Tustison N, Gee J 'N4ITK: Nick's N3 ITK Implementation For MRI Bias Field Correction', The Insight Journal 2009 January-June, http://hdl.handle.net/10380/3053" ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(N4ITKMRIBiascorrection , inputImageName , "inputImageName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , maskImageName , "maskImageName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , outputImageName , "outputImageName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , outputBiasFieldName , "outputBiasFieldName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , numberOfIterations , "numberOfIterations" , std::vector<int>, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , convergenceThreshold , "convergenceThreshold" , float, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , initialMeshResolution , "initialMeshResolution" , std::vector<float>, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , splineDistance , "splineDistance" , float, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , shrinkFactor , "shrinkFactor" , int, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , bsplineOrder , "bsplineOrder" , int, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , weightImageName , "weightImageName" , std::string, "");
+BBTK_INPUT(N4ITKMRIBiascorrection , histogramSharpening , "histogramSharpening" , std::vector<float>, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( N4ITKMRIBiascorrection ) ;
+}
+
+#endif // __bbSlicerN4ITKMRIBiascorrection_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerOrientImages.cxx b/bbtk_Slicer_PKG/src/bbSlicerOrientImages.cxx
index ad000d52cf6b7f7815c032dc8c726385fb03078e..defb112068e14ed315a2b1d76ed86fcf885e9593 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerOrientImages.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerOrientImages.cxx
@@ -11,9 +11,9 @@ namespace bbSlicer {
 
 int _argc =3;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libOrientImageLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-o"  ) + Mthd::Aux::toString( bbGetInputorientation( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-o"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputorientation( ) ) ) ,"@@@@@"," -o ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerOrientImages.h b/bbtk_Slicer_PKG/src/bbSlicerOrientImages.h
index aa56ba3f4cfb698e9d1fb9952d4e09f7b9f8c7eb..4c6becdae61100900f834df9d68a7c2e846c36fc 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerOrientImages.h
+++ b/bbtk_Slicer_PKG/src/bbSlicerOrientImages.h
@@ -43,7 +43,7 @@ BBTK_DECLARE_INPUT ( orientation , std::string );
     BBTK_BEGIN_DESCRIBE_BLACK_BOX ( OrientImages , bbtk::AtomicBlackBox ) ;
     BBTK_NAME ( "OrientImages" ) ;
     BBTK_AUTHOR ( "Bill Lorensen" ) ;
-    BBTK_DESCRIPTION ( "Orients an output volume. Rearranges the slices in a volume according to the selected orientation. The slices are not interpolated. They are just reordered and/or permuted. The resulting volume will cover the original volume. NOTE: since Slicer takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume, To see the difference, save the volume and display it with a system that either ignores the orientation of the image (e.g. Paraview) or displays individual images." ) ;
+    BBTK_DESCRIPTION ( "Orients an output volume. Rearranges the slices in a volume according to the selected orientation. The slices are not interpolated. They are just reordered and/or permuted. The resulting volume will cover the original volume. NOTE: since Slicer takes into account the orientation of a volume, the re-oriented volume will not show any difference from the original volume, To see the difference, save the volume and display it with a system that either ignores the orientation of the image e.g. Paraview or displays individual images." ) ;
     BBTK_CATEGORY ( "Converters" ) ;
 
     // GENERATED DESCRPTION

diff --git a/bbtk_Slicer_PKG/src/bbSlicerOtsuThreshold.cxx b/bbtk_Slicer_PKG/src/bbSlicerOtsuThreshold.cxx
new file mode 100644 (file)
index 0000000..1dfb42b
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerOtsuThreshold.cxx
@@ -0,0 +1,59 @@
+#include "bbSlicerOtsuThreshold.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, OtsuThreshold )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( OtsuThreshold, bbtk::AtomicBlackBox );
+
+    void OtsuThreshold::Process ( ) {
+
+        // GENERATED
+
+int _argc =5;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libOtsuThresholdImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--insideValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinsideValue( ) ) ) ,"@@@@@"," --insideValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outsideValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutsideValue( ) ) ) ,"@@@@@"," --outsideValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfBins( ) ) ) ,"@@@@@"," --numberOfBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void OtsuThreshold::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void OtsuThreshold::bbUserSetDefaultValues ( ) {
+    }
+
+    void OtsuThreshold::bbUserInitializeProcessing ( ) {
+    }
+
+    void OtsuThreshold::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerOtsuThreshold.h b/bbtk_Slicer_PKG/src/bbSlicerOtsuThreshold.h
new file mode 100644 (file)
index 0000000..d179f2d
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerOtsuThreshold.h
@@ -0,0 +1,66 @@
+#ifndef __bbSlicerOtsuThreshold_h_INCLUDED__
+#define __bbSlicerOtsuThreshold_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT OtsuThreshold
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( OtsuThreshold , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( insideValue , int );
+BBTK_DECLARE_INPUT ( outsideValue , int );
+BBTK_DECLARE_INPUT ( numberOfBins , int );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( OtsuThreshold , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "OtsuThreshold" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "This filter creates a binary thresholded image that separates an image into foreground and background components. The filter calculates the optimum threshold separating those two classes so that their combined spread intra-class variance is minimal see http://en.wikipedia.org/wiki/Otsu%27s_method.  Then the filter applies that threshold to the input image using the itkBinaryThresholdImageFilter. The numberOfHistogram bins can be set for the Otsu Calculator. The insideValue and outsideValue can be set for the BinaryThresholdImageFilter.  The filter produces a labeled volume.The original reference is: N.Otsu, ‘‘A threshold selection method from gray level histograms,’’ IEEE Trans.Syst.ManCybern.SMC-9,62–66 1979." ) ;
+    BBTK_CATEGORY ( "Legacy.Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(OtsuThreshold , insideValue , "insideValue" , int, "");
+BBTK_INPUT(OtsuThreshold , outsideValue , "outsideValue" , int, "");
+BBTK_INPUT(OtsuThreshold , numberOfBins , "numberOfBins" , int, "");
+BBTK_INPUT(OtsuThreshold , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(OtsuThreshold , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( OtsuThreshold ) ;
+}
+
+#endif // __bbSlicerOtsuThreshold_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerOtsuThresholdSegmentation.cxx b/bbtk_Slicer_PKG/src/bbSlicerOtsuThresholdSegmentation.cxx
index 7b0ad99543b1db377b161b3c7b33ba3cbddaafd5..7be627b6175dd133a06787d0750846a9c2e659f1 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerOtsuThresholdSegmentation.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerOtsuThresholdSegmentation.cxx
@@ -11,12 +11,12 @@ namespace bbSlicer {
 
 int _argc =6;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libOtsuThresholdSegmentationLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--brightObjects"  ) + Mthd::Aux::toString( bbGetInputbrightObjects( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfBins"  ) + Mthd::Aux::toString( bbGetInputnumberOfBins( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--faceConnected"  ) + Mthd::Aux::toString( bbGetInputfaceConnected( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumObjectSize"  ) + Mthd::Aux::toString( bbGetInputminimumObjectSize( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--brightObjects"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbrightObjects( ) ) ) ,"@@@@@"," --brightObjects ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfBins( ) ) ) ,"@@@@@"," --numberOfBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--faceConnected"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfaceConnected( ) ) ) ,"@@@@@"," --faceConnected ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumObjectSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumObjectSize( ) ) ) ,"@@@@@"," --minimumObjectSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerOtsuThresholdSegmentation.h b/bbtk_Slicer_PKG/src/bbSlicerOtsuThresholdSegmentation.h
index f05b8f9e258f733ef762be4706fb47e0bfcbaf1f..f96db1bd8f28d1a302dff4dc8d8bdce4a8b63147 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerOtsuThresholdSegmentation.h
+++ b/bbtk_Slicer_PKG/src/bbSlicerOtsuThresholdSegmentation.h
@@ -46,7 +46,7 @@ BBTK_DECLARE_INPUT ( outputVolume , std::string );
     BBTK_BEGIN_DESCRIBE_BLACK_BOX ( OtsuThresholdSegmentation , bbtk::AtomicBlackBox ) ;
     BBTK_NAME ( "OtsuThresholdSegmentation" ) ;
     BBTK_AUTHOR ( "Bill Lorensen" ) ;
-    BBTK_DESCRIPTION ( "This filter creates a labeled image from a grayscale image. First, it calculates an optimal threshold that separates the image into foreground and background. This threshold separates those two classes so that their intra-class variance is minimal (see http://en.wikipedia.org/wiki/Otsu%27s_method). Then the filter runs a connected component algorithm to generate unique labels for each connected region of the foreground. Finally, the resulting image is relabeled to provide consecutive numbering." ) ;
+    BBTK_DESCRIPTION ( "This filter creates a labeled image from a grayscale image. First, it calculates an optimal threshold that separates the image into foreground and background. This threshold separates those two classes so that their intra-class variance is minimal see http://en.wikipedia.org/wiki/Otsu%27s_method. Then the filter runs a connected component algorithm to generate unique labels for each connected region of the foreground. Finally, the resulting image is relabeled to provide consecutive numbering." ) ;
     BBTK_CATEGORY ( "Legacy.Segmentation" ) ;
 
     // GENERATED DESCRPTION

diff --git a/bbtk_Slicer_PKG/src/bbSlicerPolyDataToLabelMap.cxx b/bbtk_Slicer_PKG/src/bbSlicerPolyDataToLabelMap.cxx
index c5d57d75a2c9c0d2b7556d708bfe809ed2c40611..bc2f2aaaa6032f4762d01af3ccfd4adc46497550 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerPolyDataToLabelMap.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerPolyDataToLabelMap.cxx
@@ -11,10 +11,10 @@ namespace bbSlicer {
 
 int _argc =4;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libPolyDataToLabelmapLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--distance"  ) + Mthd::Aux::toString( bbGetInputsampleDistance( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputsurface( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--distance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsampleDistance( ) ) ) ,"@@@@@"," --distance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsurface( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerResampleDTIVolume.cxx b/bbtk_Slicer_PKG/src/bbSlicerResampleDTIVolume.cxx
new file mode 100644 (file)
index 0000000..1584f25
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerResampleDTIVolume.cxx
@@ -0,0 +1,80 @@
+#include "bbSlicerResampleDTIVolume.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ResampleDTIVolume )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ResampleDTIVolume, bbtk::AtomicBlackBox );
+
+    void ResampleDTIVolume::Process ( ) {
+
+        // GENERATED
+
+int _argc =26;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libResampleDTILib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-R"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreferenceVolume( ) ) ) ,"@@@@@"," -R ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformationFile( ) ) ) ,"@@@@@"," -f ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-H"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdeffield( ) ) ) ,"@@@@@"," -H ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--hfieldtype"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtypeOfField( ) ) ) ,"@@@@@"," --hfieldtype ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationType( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--correction"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcorrection( ) ) ) ,"@@@@@"," --correction ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-T"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputppd( ) ) ) ,"@@@@@"," -T ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--transform_order"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformsOrder( ) ) ) ,"@@@@@"," --transform_order ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--notbulk"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnotbulk( ) ) ) ,"@@@@@"," --notbulk ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--spaceChange"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputspace( ) ) ) ,"@@@@@"," --spaceChange ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-r"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputrotationPoint( ) ) ) ,"@@@@@"," -r ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-c"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcenteredTransform( ) ) ) ,"@@@@@"," -c ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--image_center"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputimageCenter( ) ) ) ,"@@@@@"," --image_center ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-b"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinverseITKTransformation( ) ) ) ,"@@@@@"," -b ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputImageSpacing( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-z"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputImageSize( ) ) ) ,"@@@@@"," -z ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-O"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputImageOrigin( ) ) ) ,"@@@@@"," -O ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-d"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdirectionMatrix( ) ) ) ,"@@@@@"," -d ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-n"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThread( ) ) ) ,"@@@@@"," -n ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-p"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdefaultPixelValue( ) ) ) ,"@@@@@"," -p ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-W"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputwindowFunction( ) ) ) ,"@@@@@"," -W ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-o"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsplineOrder( ) ) ) ,"@@@@@"," -o ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-m"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformMatrix( ) ) ) ,"@@@@@"," -m ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtransformType( ) ) ) ,"@@@@@"," -t ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ResampleDTIVolume::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ResampleDTIVolume::bbUserSetDefaultValues ( ) {
+    }
+
+    void ResampleDTIVolume::bbUserInitializeProcessing ( ) {
+    }
+
+    void ResampleDTIVolume::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerResampleDTIVolume.h b/bbtk_Slicer_PKG/src/bbSlicerResampleDTIVolume.h
new file mode 100644 (file)
index 0000000..0c7f48f
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerResampleDTIVolume.h
@@ -0,0 +1,108 @@
+#ifndef __bbSlicerResampleDTIVolume_h_INCLUDED__
+#define __bbSlicerResampleDTIVolume_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ResampleDTIVolume
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ResampleDTIVolume , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( referenceVolume , std::string );
+BBTK_DECLARE_INPUT ( transformationFile , std::string );
+BBTK_DECLARE_INPUT ( deffield , std::string );
+BBTK_DECLARE_INPUT ( typeOfField , std::string );
+BBTK_DECLARE_INPUT ( interpolationType , std::string );
+BBTK_DECLARE_INPUT ( correction , std::string );
+BBTK_DECLARE_INPUT ( ppd , std::string );
+BBTK_DECLARE_INPUT ( transformsOrder , std::string );
+BBTK_DECLARE_INPUT ( notbulk , bool );
+BBTK_DECLARE_INPUT ( space , bool );
+BBTK_DECLARE_INPUT ( rotationPoint , std::vector<float> );
+BBTK_DECLARE_INPUT ( centeredTransform , bool );
+BBTK_DECLARE_INPUT ( imageCenter , std::string );
+BBTK_DECLARE_INPUT ( inverseITKTransformation , bool );
+BBTK_DECLARE_INPUT ( outputImageSpacing , std::vector<double> );
+BBTK_DECLARE_INPUT ( outputImageSize , std::vector<double> );
+BBTK_DECLARE_INPUT ( outputImageOrigin , std::vector<float> );
+BBTK_DECLARE_INPUT ( directionMatrix , std::vector<double> );
+BBTK_DECLARE_INPUT ( numberOfThread , int );
+BBTK_DECLARE_INPUT ( defaultPixelValue , double );
+BBTK_DECLARE_INPUT ( windowFunction , std::string );
+BBTK_DECLARE_INPUT ( splineOrder , int );
+BBTK_DECLARE_INPUT ( transformMatrix , std::vector<double> );
+BBTK_DECLARE_INPUT ( transformType , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ResampleDTIVolume , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ResampleDTIVolume" ) ;
+    BBTK_AUTHOR ( "Francois Budin" ) ;
+    BBTK_DESCRIPTION ( "Resampling an image is a very important task in image analysis. It is especially important in the frame of image registration. This module implements DT image resampling through the use of itk Transforms. The resampling is controlled by the Output Spacing. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions." ) ;
+    BBTK_CATEGORY ( "Diffusion.Utilities" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ResampleDTIVolume , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , referenceVolume , "referenceVolume" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , transformationFile , "transformationFile" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , deffield , "deffield" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , typeOfField , "typeOfField" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , interpolationType , "interpolationType" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , correction , "correction" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , ppd , "ppd" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , transformsOrder , "transformsOrder" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , notbulk , "notbulk" , bool, "");
+BBTK_INPUT(ResampleDTIVolume , space , "space" , bool, "");
+BBTK_INPUT(ResampleDTIVolume , rotationPoint , "rotationPoint" , std::vector<float>, "");
+BBTK_INPUT(ResampleDTIVolume , centeredTransform , "centeredTransform" , bool, "");
+BBTK_INPUT(ResampleDTIVolume , imageCenter , "imageCenter" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , inverseITKTransformation , "inverseITKTransformation" , bool, "");
+BBTK_INPUT(ResampleDTIVolume , outputImageSpacing , "outputImageSpacing" , std::vector<double>, "");
+BBTK_INPUT(ResampleDTIVolume , outputImageSize , "outputImageSize" , std::vector<double>, "");
+BBTK_INPUT(ResampleDTIVolume , outputImageOrigin , "outputImageOrigin" , std::vector<float>, "");
+BBTK_INPUT(ResampleDTIVolume , directionMatrix , "directionMatrix" , std::vector<double>, "");
+BBTK_INPUT(ResampleDTIVolume , numberOfThread , "numberOfThread" , int, "");
+BBTK_INPUT(ResampleDTIVolume , defaultPixelValue , "defaultPixelValue" , double, "");
+BBTK_INPUT(ResampleDTIVolume , windowFunction , "windowFunction" , std::string, "");
+BBTK_INPUT(ResampleDTIVolume , splineOrder , "splineOrder" , int, "");
+BBTK_INPUT(ResampleDTIVolume , transformMatrix , "transformMatrix" , std::vector<double>, "");
+BBTK_INPUT(ResampleDTIVolume , transformType , "transformType" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ResampleDTIVolume ) ;
+}
+
+#endif // __bbSlicerResampleDTIVolume_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerResampleImageBRAINS.cxx b/bbtk_Slicer_PKG/src/bbSlicerResampleImageBRAINS.cxx
new file mode 100644 (file)
index 0000000..40b2238
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerResampleImageBRAINS.cxx
@@ -0,0 +1,65 @@
+#include "bbSlicerResampleImageBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ResampleImageBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ResampleImageBRAINS, bbtk::AtomicBlackBox );
+
+    void ResampleImageBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =11;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libBRAINSResampleLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@"," --inputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--referenceVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputreferenceVolume( ) ) ) ,"@@@@@"," --referenceVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," --outputVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--pixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputpixelType( ) ) ) ,"@@@@@"," --pixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--deformationVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdeformationVolume( ) ) ) ,"@@@@@"," --deformationVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--warpTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputwarpTransform( ) ) ) ,"@@@@@"," --warpTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolationMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationMode( ) ) ) ,"@@@@@"," --interpolationMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inverseTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinverseTransform( ) ) ) ,"@@@@@"," --inverseTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--defaultValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdefaultValue( ) ) ) ,"@@@@@"," --defaultValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--gridSpacing"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgridSpacing( ) ) ) ,"@@@@@"," --gridSpacing ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ResampleImageBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ResampleImageBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void ResampleImageBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void ResampleImageBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerResampleImageBRAINS.h b/bbtk_Slicer_PKG/src/bbSlicerResampleImageBRAINS.h
new file mode 100644 (file)
index 0000000..536d0a8
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerResampleImageBRAINS.h
@@ -0,0 +1,78 @@
+#ifndef __bbSlicerResampleImageBRAINS_h_INCLUDED__
+#define __bbSlicerResampleImageBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ResampleImageBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ResampleImageBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( referenceVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( pixelType , std::string );
+BBTK_DECLARE_INPUT ( deformationVolume , std::string );
+BBTK_DECLARE_INPUT ( warpTransform , std::string );
+BBTK_DECLARE_INPUT ( interpolationMode , std::string );
+BBTK_DECLARE_INPUT ( inverseTransform , bool );
+BBTK_DECLARE_INPUT ( defaultValue , float );
+BBTK_DECLARE_INPUT ( gridSpacing , std::vector<int> );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ResampleImageBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ResampleImageBRAINS" ) ;
+    BBTK_AUTHOR ( "This tool was developed by Vincent Magnotta, Greg Harris, and Hans Johnson." ) ;
+    BBTK_DESCRIPTION ( "This program resamples an image image using a deformation field or a transform BSpline, Affine, Rigid, etc.." ) ;
+    BBTK_CATEGORY ( "Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ResampleImageBRAINS , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , referenceVolume , "referenceVolume" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , pixelType , "pixelType" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , deformationVolume , "deformationVolume" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , warpTransform , "warpTransform" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , interpolationMode , "interpolationMode" , std::string, "");
+BBTK_INPUT(ResampleImageBRAINS , inverseTransform , "inverseTransform" , bool, "");
+BBTK_INPUT(ResampleImageBRAINS , defaultValue , "defaultValue" , float, "");
+BBTK_INPUT(ResampleImageBRAINS , gridSpacing , "gridSpacing" , std::vector<int>, "");
+BBTK_INPUT(ResampleImageBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ResampleImageBRAINS ) ;
+}
+
+#endif // __bbSlicerResampleImageBRAINS_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerResampleScalarVolume.cxx b/bbtk_Slicer_PKG/src/bbSlicerResampleScalarVolume.cxx
new file mode 100644 (file)
index 0000000..69a8256
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerResampleScalarVolume.cxx
@@ -0,0 +1,58 @@
+#include "bbSlicerResampleScalarVolume.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, ResampleScalarVolume )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( ResampleScalarVolume, bbtk::AtomicBlackBox );
+
+    void ResampleScalarVolume::Process ( ) {
+
+        // GENERATED
+
+int _argc =4;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libResampleVolumeLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputPixelSpacing( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationType( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void ResampleScalarVolume::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void ResampleScalarVolume::bbUserSetDefaultValues ( ) {
+    }
+
+    void ResampleScalarVolume::bbUserInitializeProcessing ( ) {
+    }
+
+    void ResampleScalarVolume::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerResampleScalarVolume.h b/bbtk_Slicer_PKG/src/bbSlicerResampleScalarVolume.h
new file mode 100644 (file)
index 0000000..a7ba623
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerResampleScalarVolume.h
@@ -0,0 +1,64 @@
+#ifndef __bbSlicerResampleScalarVolume_h_INCLUDED__
+#define __bbSlicerResampleScalarVolume_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT ResampleScalarVolume
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( ResampleScalarVolume , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( outputPixelSpacing , std::vector<float> );
+BBTK_DECLARE_INPUT ( interpolationType , std::string );
+BBTK_DECLARE_INPUT ( InputVolume , std::string );
+BBTK_DECLARE_INPUT ( OutputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ResampleScalarVolume , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "ResampleScalarVolume" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Resampling an image is an important task in image analysis. It is especially important in the frame of image registration. This module implements image resampling through the use of itk Transforms. This module uses an Identity Transform. The resampling is controlled by the Output Spacing. 'Resampling' is performed in space coordinates, not pixel/grid coordinates. It is quite important to ensure that image spacing is properly set on the images involved. The interpolator is required since the mapping from one space to the other will often require evaluation of the intensity of the image at non-grid positions. Several interpolators are available: linear, nearest neighbor, bspline and five flavors of sinc. The sinc interpolators, although more precise, are much slower than the linear and nearest neighbor interpolator. To resample label volumnes, nearest neighbor interpolation should be used exclusively." ) ;
+    BBTK_CATEGORY ( "Legacy.Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(ResampleScalarVolume , outputPixelSpacing , "outputPixelSpacing" , std::vector<float>, "");
+BBTK_INPUT(ResampleScalarVolume , interpolationType , "interpolationType" , std::string, "");
+BBTK_INPUT(ResampleScalarVolume , InputVolume , "InputVolume" , std::string, "");
+BBTK_INPUT(ResampleScalarVolume , OutputVolume , "OutputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( ResampleScalarVolume ) ;
+}
+
+#endif // __bbSlicerResampleScalarVolume_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerRicianLMMSEImageFilter.cxx b/bbtk_Slicer_PKG/src/bbSlicerRicianLMMSEImageFilter.cxx
new file mode 100644 (file)
index 0000000..0635dd4
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerRicianLMMSEImageFilter.cxx
@@ -0,0 +1,65 @@
+#include "bbSlicerRicianLMMSEImageFilter.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, RicianLMMSEImageFilter )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( RicianLMMSEImageFilter, bbtk::AtomicBlackBox );
+
+    void RicianLMMSEImageFilter::Process ( ) {
+
+        // GENERATED
+
+int _argc =11;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libdwiNoiseFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iter"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiIterations( ) ) ) ,"@@@@@"," --iter ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--re"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusEstimation( ) ) ) ,"@@@@@"," --re ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rf"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusFiltering( ) ) ) ,"@@@@@"," --rf ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--mnvf"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiMinimumNumberOfUsedVoxelsF( ) ) ) ,"@@@@@"," --mnvf ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--mnve"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiMinimumNumberOfUsedVoxelsE( ) ) ) ,"@@@@@"," --mnve ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minnstd"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdMinSTD( ) ) ) ,"@@@@@"," --minnstd ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxnstd"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdMaxSTD( ) ) ) ,"@@@@@"," --maxnstd ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--hrf"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputdResFact( ) ) ) ,"@@@@@"," --hrf ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--uav"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbUseAbsoluteValue( ) ) ) ,"@@@@@"," --uav ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void RicianLMMSEImageFilter::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void RicianLMMSEImageFilter::bbUserSetDefaultValues ( ) {
+    }
+
+    void RicianLMMSEImageFilter::bbUserInitializeProcessing ( ) {
+    }
+
+    void RicianLMMSEImageFilter::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerRicianLMMSEImageFilter.h b/bbtk_Slicer_PKG/src/bbSlicerRicianLMMSEImageFilter.h
new file mode 100644 (file)
index 0000000..b734698
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerRicianLMMSEImageFilter.h
@@ -0,0 +1,78 @@
+#ifndef __bbSlicerRicianLMMSEImageFilter_h_INCLUDED__
+#define __bbSlicerRicianLMMSEImageFilter_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT RicianLMMSEImageFilter
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( RicianLMMSEImageFilter , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( iIterations , int );
+BBTK_DECLARE_INPUT ( iRadiusEstimation , std::vector<int> );
+BBTK_DECLARE_INPUT ( iRadiusFiltering , std::vector<int> );
+BBTK_DECLARE_INPUT ( iMinimumNumberOfUsedVoxelsF , int );
+BBTK_DECLARE_INPUT ( iMinimumNumberOfUsedVoxelsE , int );
+BBTK_DECLARE_INPUT ( dMinSTD , int );
+BBTK_DECLARE_INPUT ( dMaxSTD , int );
+BBTK_DECLARE_INPUT ( dResFact , double );
+BBTK_DECLARE_INPUT ( bUseAbsoluteValue , bool );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( RicianLMMSEImageFilter , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "RicianLMMSEImageFilter" ) ;
+    BBTK_AUTHOR ( "Antonio Tristan Vega, Santiago Aja Fernandez and Marc Niethammer. Partially founded by grant number TEC2007-67073/TCM from the Comision Interministerial de Ciencia y Tecnologia Spain." ) ;
+    BBTK_DESCRIPTION ( "This module reduces noise or unwanted detail on a set of diffusion weighted images. For this, it filters the image in the mean squared error sense using a Rician noise model. Images corresponding to each gradient direction, including baseline, are processed individually. The noise parameter is automatically estimated noise estimation improved but slower.Note that this is a general purpose filter for MRi images. The module jointLMMSE has been specifically designed for DWI volumes and shows a better performance, so its use is recommended instead.A complete description of the algorithm in this module can be found in:S. Aja-Fernandez, M. Niethammer, M. Kubicki, M. Shenton, and C.-F. Westin. Restoration of DWI data using a Rician LMMSE estimator. IEEE Transactions on Medical Imaging, 2710: pp. 1389-1403, Oct. 2008." ) ;
+    BBTK_CATEGORY ( "Diffusion.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(RicianLMMSEImageFilter , iIterations , "iIterations" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , iRadiusEstimation , "iRadiusEstimation" , std::vector<int>, "");
+BBTK_INPUT(RicianLMMSEImageFilter , iRadiusFiltering , "iRadiusFiltering" , std::vector<int>, "");
+BBTK_INPUT(RicianLMMSEImageFilter , iMinimumNumberOfUsedVoxelsF , "iMinimumNumberOfUsedVoxelsF" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , iMinimumNumberOfUsedVoxelsE , "iMinimumNumberOfUsedVoxelsE" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , dMinSTD , "dMinSTD" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , dMaxSTD , "dMaxSTD" , int, "");
+BBTK_INPUT(RicianLMMSEImageFilter , dResFact , "dResFact" , double, "");
+BBTK_INPUT(RicianLMMSEImageFilter , bUseAbsoluteValue , "bUseAbsoluteValue" , bool, "");
+BBTK_INPUT(RicianLMMSEImageFilter , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(RicianLMMSEImageFilter , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( RicianLMMSEImageFilter ) ;
+}
+
+#endif // __bbSlicerRicianLMMSEImageFilter_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerRobustMultiresolutionAffineRegistration.cxx b/bbtk_Slicer_PKG/src/bbSlicerRobustMultiresolutionAffineRegistration.cxx
new file mode 100644 (file)
index 0000000..eec8b2d
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerRobustMultiresolutionAffineRegistration.cxx
@@ -0,0 +1,65 @@
+#include "bbSlicerRobustMultiresolutionAffineRegistration.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, RobustMultiresolutionAffineRegistration )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( RobustMultiresolutionAffineRegistration, bbtk::AtomicBlackBox );
+
+    void RobustMultiresolutionAffineRegistration::Process ( ) {
+
+        // GENERATED
+
+int _argc =11;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRegisterImagesMultiResModule.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImage( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingImage( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--resampledImage"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputresampledImage( ) ) ) ,"@@@@@"," --resampledImage ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--saveTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputTransform( ) ) ) ,"@@@@@"," --saveTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedImageMask"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImageMask( ) ) ) ,"@@@@@"," --fixedImageMask ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedImageROI"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedImageROI( ) ) ) ,"@@@@@"," --fixedImageROI ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumIterations( ) ) ) ,"@@@@@"," --numIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numLineIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumLineIterations( ) ) ) ,"@@@@@"," --numLineIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--stepSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstepSize( ) ) ) ,"@@@@@"," --stepSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--stepTolerance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputstepTolerance( ) ) ) ,"@@@@@"," --stepTolerance ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--metricTolerance"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmetricTolerance( ) ) ) ,"@@@@@"," --metricTolerance ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void RobustMultiresolutionAffineRegistration::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void RobustMultiresolutionAffineRegistration::bbUserSetDefaultValues ( ) {
+    }
+
+    void RobustMultiresolutionAffineRegistration::bbUserInitializeProcessing ( ) {
+    }
+
+    void RobustMultiresolutionAffineRegistration::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerRobustMultiresolutionAffineRegistration.h b/bbtk_Slicer_PKG/src/bbSlicerRobustMultiresolutionAffineRegistration.h
new file mode 100644 (file)
index 0000000..e71228a
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerRobustMultiresolutionAffineRegistration.h
@@ -0,0 +1,78 @@
+#ifndef __bbSlicerRobustMultiresolutionAffineRegistration_h_INCLUDED__
+#define __bbSlicerRobustMultiresolutionAffineRegistration_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT RobustMultiresolutionAffineRegistration
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( RobustMultiresolutionAffineRegistration , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( fixedImage , std::string );
+BBTK_DECLARE_INPUT ( movingImage , std::string );
+BBTK_DECLARE_INPUT ( resampledImage , std::string );
+BBTK_DECLARE_INPUT ( outputTransform , std::string );
+BBTK_DECLARE_INPUT ( fixedImageMask , std::string );
+BBTK_DECLARE_INPUT ( fixedImageROI , std::vector<float> );
+BBTK_DECLARE_INPUT ( numIterations , int );
+BBTK_DECLARE_INPUT ( numLineIterations , int );
+BBTK_DECLARE_INPUT ( stepSize , float );
+BBTK_DECLARE_INPUT ( stepTolerance , float );
+BBTK_DECLARE_INPUT ( metricTolerance , float );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( RobustMultiresolutionAffineRegistration , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "RobustMultiresolutionAffineRegistration" ) ;
+    BBTK_AUTHOR ( "Casey B Goodlett" ) ;
+    BBTK_DESCRIPTION ( "Provides affine registration using multiple resolution levels and decomposed affine transforms." ) ;
+    BBTK_CATEGORY ( "Legacy.Registration" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , fixedImage , "fixedImage" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , movingImage , "movingImage" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , resampledImage , "resampledImage" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , outputTransform , "outputTransform" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , fixedImageMask , "fixedImageMask" , std::string, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , fixedImageROI , "fixedImageROI" , std::vector<float>, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , numIterations , "numIterations" , int, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , numLineIterations , "numLineIterations" , int, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , stepSize , "stepSize" , float, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , stepTolerance , "stepTolerance" , float, "");
+BBTK_INPUT(RobustMultiresolutionAffineRegistration , metricTolerance , "metricTolerance" , float, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( RobustMultiresolutionAffineRegistration ) ;
+}
+
+#endif // __bbSlicerRobustMultiresolutionAffineRegistration_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerRobustStatisticsSegmentation.cxx b/bbtk_Slicer_PKG/src/bbSlicerRobustStatisticsSegmentation.cxx
index 9c4da331561e369dfaefcc0c99ea55aea53a8f75..8d0ea03e5d66a173c0b02d2eb2a08e69af7ffc05 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerRobustStatisticsSegmentation.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerRobustStatisticsSegmentation.cxx
@@ -11,14 +11,14 @@ namespace bbSlicer {
 
 int _argc =8;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libRobustStatSegmenterLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::toString( bbGetInputexpectedVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--intensityHomogeneity"  ) + Mthd::Aux::toString( bbGetInputintensityHomogeneity( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-c"  ) + Mthd::Aux::toString( bbGetInputcurvatureWeight( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--labelValue"  ) + Mthd::Aux::toString( bbGetInputlabelValue( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxRunningTime"  ) + Mthd::Aux::toString( bbGetInputmaxRunningTime( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputoriginalImageFileName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputlabelImageFileName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputsegmentedImageFileName( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputexpectedVolume( ) ) ) ,"@@@@@"," -v ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--intensityHomogeneity"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputintensityHomogeneity( ) ) ) ,"@@@@@"," --intensityHomogeneity ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-c"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcurvatureWeight( ) ) ) ,"@@@@@"," -c ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--labelValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlabelValue( ) ) ) ,"@@@@@"," --labelValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--maxRunningTime"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxRunningTime( ) ) ) ,"@@@@@"," --maxRunningTime ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoriginalImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlabelImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsegmentedImageFileName( ) ) ) ,"@@@@@","") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerSimpleIOTest.cxx b/bbtk_Slicer_PKG/src/bbSlicerSimpleIOTest.cxx
index 11b5ec4f3c17a5226f990b5f6f53de273e9c554a..ff6badd98ba44731bb1d3197b32c359caa40818d 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerSimpleIOTest.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerSimpleIOTest.cxx
@@ -11,8 +11,8 @@ namespace bbSlicer {
 
 int _argc =2;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libDiffusionTensorTestLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerSimpleregiongrowing.cxx b/bbtk_Slicer_PKG/src/bbSlicerSimpleregiongrowing.cxx
new file mode 100644 (file)
index 0000000..0c272a2
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerSimpleregiongrowing.cxx
@@ -0,0 +1,63 @@
+#include "bbSlicerSimpleregiongrowing.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, Simpleregiongrowing )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( Simpleregiongrowing, bbtk::AtomicBlackBox );
+
+    void Simpleregiongrowing::Process ( ) {
+
+        // GENERATED
+
+int _argc =9;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libConfidenceConnectedLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--smoothingIterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothingIterations( ) ) ) ,"@@@@@"," --smoothingIterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--timestep"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputtimestep( ) ) ) ,"@@@@@"," --timestep ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--iterations"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiterations( ) ) ) ,"@@@@@"," --iterations ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--multiplier"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmultiplier( ) ) ) ,"@@@@@"," --multiplier ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--neighborhood"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputneighborhood( ) ) ) ,"@@@@@"," --neighborhood ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--labelvalue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlabelvalue( ) ) ) ,"@@@@@"," --labelvalue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seed"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseed( ) ) ) ,"@@@@@"," --seed ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void Simpleregiongrowing::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void Simpleregiongrowing::bbUserSetDefaultValues ( ) {
+    }
+
+    void Simpleregiongrowing::bbUserInitializeProcessing ( ) {
+    }
+
+    void Simpleregiongrowing::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerSimpleregiongrowing.h b/bbtk_Slicer_PKG/src/bbSlicerSimpleregiongrowing.h
new file mode 100644 (file)
index 0000000..ba02e16
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerSimpleregiongrowing.h
@@ -0,0 +1,74 @@
+#ifndef __bbSlicerSimpleregiongrowing_h_INCLUDED__
+#define __bbSlicerSimpleregiongrowing_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT Simpleregiongrowing
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( Simpleregiongrowing , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( smoothingIterations , int );
+BBTK_DECLARE_INPUT ( timestep , double );
+BBTK_DECLARE_INPUT ( iterations , int );
+BBTK_DECLARE_INPUT ( multiplier , double );
+BBTK_DECLARE_INPUT ( neighborhood , int );
+BBTK_DECLARE_INPUT ( labelvalue , int );
+BBTK_DECLARE_INPUT ( seed , std::vector<std::vector<float> > );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( Simpleregiongrowing , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "Simpleregiongrowing" ) ;
+    BBTK_AUTHOR ( "Jim Miller" ) ;
+    BBTK_DESCRIPTION ( "A simple region growing segmentation algorithm based on intensity statistics. To create a list of fiducials Seeds for this algorithm, click on the tool bar icon of an arrow pointing to a starburst fiducial to enter the 'place a new object mode' and then use the fiducials module. This module uses the Slicer Command Line Interface CLI and the ITK filters CurvatureFlowImageFilter and ConfidenceConnectedImageFilter." ) ;
+    BBTK_CATEGORY ( "Segmentation" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(Simpleregiongrowing , smoothingIterations , "smoothingIterations" , int, "");
+BBTK_INPUT(Simpleregiongrowing , timestep , "timestep" , double, "");
+BBTK_INPUT(Simpleregiongrowing , iterations , "iterations" , int, "");
+BBTK_INPUT(Simpleregiongrowing , multiplier , "multiplier" , double, "");
+BBTK_INPUT(Simpleregiongrowing , neighborhood , "neighborhood" , int, "");
+BBTK_INPUT(Simpleregiongrowing , labelvalue , "labelvalue" , int, "");
+BBTK_INPUT(Simpleregiongrowing , seed , "seed" , std::vector<std::vector<float> >, "");
+BBTK_INPUT(Simpleregiongrowing , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(Simpleregiongrowing , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( Simpleregiongrowing ) ;
+}
+
+#endif // __bbSlicerSimpleregiongrowing_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerSubtractImages.cxx b/bbtk_Slicer_PKG/src/bbSlicerSubtractImages.cxx
index 61efd452a6c6fdbda83ba5184f0d38dc223f8e8d..8373771b063bb4bcf0dbefb18d450014e38a0f72 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerSubtractImages.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerSubtractImages.cxx
@@ -11,10 +11,10 @@ namespace bbSlicer {
 
 int _argc =4;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libSubtractLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--order"  ) + Mthd::Aux::toString( bbGetInputorder( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume1( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume2( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--order"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputorder( ) ) ) ,"@@@@@"," --order ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerTestGridTransformregistration.cxx b/bbtk_Slicer_PKG/src/bbSlicerTestGridTransformregistration.cxx
index b9a81fe9d5b64450a9c51cb327d3cb0bb62b2b7f..2878e28cf7993f7558b1581f522a0b5eac65c592 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerTestGridTransformregistration.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerTestGridTransformregistration.cxx
@@ -11,10 +11,10 @@ namespace bbSlicer {
 
 int _argc =4;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libTestGridTransformRegistrationLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::toString( bbGetInputgridSize( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgridSize( ) ) ) ,"@@@@@"," -g ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputtransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputTransform( ) ) ) ,"@@@@@"," --outputtransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputFixedImageFileName( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputMovingImageFileName( ) ) ) ,"@@@@@","") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerThresholdImage.cxx b/bbtk_Slicer_PKG/src/bbSlicerThresholdImage.cxx
index 611ce07de068f62944fa7f223ab2390b4d9dbc64..2525df878c0ebe1bf69abb4d077fe5d72dacc626 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerThresholdImage.cxx
+++ b/bbtk_Slicer_PKG/src/bbSlicerThresholdImage.cxx
@@ -11,13 +11,13 @@ namespace bbSlicer {
 
 int _argc =7;
 std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libThresholdLib.so";
-char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::toString( bbGetInputThresholdValue( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::toString( bbGetInputLower( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-u"  ) + Mthd::Aux::toString( bbGetInputUpper( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::toString( bbGetInputOutsideValue( ) ) ),
-Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--thresholdtype"  ) + Mthd::Aux::toString( bbGetInputThresholdType( ) ) ) };
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputInputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputThresholdValue( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputLower( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-u"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputUpper( ) ) ) ,"@@@@@"," -u ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputOutsideValue( ) ) ) ,"@@@@@"," -v ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--thresholdtype"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputThresholdType( ) ) ) ,"@@@@@"," --thresholdtype ") ) };
 
         // EO GENERATED
         this->execute( lib, _argc, _argv );

diff --git a/bbtk_Slicer_PKG/src/bbSlicerThresholdImage.h b/bbtk_Slicer_PKG/src/bbSlicerThresholdImage.h
index 622007f68c2f45a1f94a80a8fe0aa8c5cc37e4d9..8170aa509b83fb605dedf06f394a833a6084268e 100644 (file)
--- a/bbtk_Slicer_PKG/src/bbSlicerThresholdImage.h
+++ b/bbtk_Slicer_PKG/src/bbSlicerThresholdImage.h
@@ -46,8 +46,8 @@ BBTK_DECLARE_INPUT ( ThresholdType , std::string );
 
     BBTK_BEGIN_DESCRIBE_BLACK_BOX ( ThresholdImage , bbtk::AtomicBlackBox ) ;
     BBTK_NAME ( "ThresholdImage" ) ;
-    BBTK_AUTHOR ( "Nicole Aucoin, BWH (Ron Kikinis, BWH)" ) ;
-    BBTK_DESCRIPTION ( "<p>Threshold an image.</p><p>Set image values to a user-specified outside value if they are below, above, or between simple threshold values.</p><p>ThresholdAbove: The values greater than or equal to the threshold value are set to OutsideValue.</p><p>ThresholdBelow: The values less than or equal to the threshold value are set to OutsideValue.</p><p>ThresholdOutside: The values outside the range Lower-Upper are set to OutsideValue.</p><p>Although all image types are supported on input, only signed types are produced.</p><p>" ) ;
+    BBTK_AUTHOR ( "Nicole Aucoin, BWH Ron Kikinis, BWH" ) ;
+    BBTK_DESCRIPTION ( "pThreshold an image./ppSet image values to a user-specified outside value if they are below, above, or between simple threshold values./ppThresholdAbove: The values greater than or equal to the threshold value are set to OutsideValue./ppThresholdBelow: The values less than or equal to the threshold value are set to OutsideValue./ppThresholdOutside: The values outside the range Lower-Upper are set to OutsideValue./ppAlthough all image types are supported on input, only signed types are produced./pp" ) ;
     BBTK_CATEGORY ( "Filtering" ) ;
 
     // GENERATED DESCRPTION

diff --git a/bbtk_Slicer_PKG/src/bbSlicerUnbiasedNonLocalMeansfilterforDWI.cxx b/bbtk_Slicer_PKG/src/bbSlicerUnbiasedNonLocalMeansfilterforDWI.cxx
new file mode 100644 (file)
index 0000000..0aefec5
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerUnbiasedNonLocalMeansfilterforDWI.cxx
@@ -0,0 +1,61 @@
+#include "bbSlicerUnbiasedNonLocalMeansfilterforDWI.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, UnbiasedNonLocalMeansfilterforDWI )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( UnbiasedNonLocalMeansfilterforDWI, bbtk::AtomicBlackBox );
+
+    void UnbiasedNonLocalMeansfilterforDWI::Process ( ) {
+
+        // GENERATED
+
+int _argc =7;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libdwiUNLMLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rs"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusSearch( ) ) ) ,"@@@@@"," --rs ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--rc"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusComp( ) ) ) ,"@@@@@"," --rc ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--hp"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiH( ) ) ) ,"@@@@@"," --hp ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--ng"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiNumNeighbors( ) ) ) ,"@@@@@"," --ng ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--re"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputiRadiusEstimation( ) ) ) ,"@@@@@"," --re ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void UnbiasedNonLocalMeansfilterforDWI::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void UnbiasedNonLocalMeansfilterforDWI::bbUserSetDefaultValues ( ) {
+    }
+
+    void UnbiasedNonLocalMeansfilterforDWI::bbUserInitializeProcessing ( ) {
+    }
+
+    void UnbiasedNonLocalMeansfilterforDWI::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerUnbiasedNonLocalMeansfilterforDWI.h b/bbtk_Slicer_PKG/src/bbSlicerUnbiasedNonLocalMeansfilterforDWI.h
new file mode 100644 (file)
index 0000000..29ca6a8
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerUnbiasedNonLocalMeansfilterforDWI.h
@@ -0,0 +1,70 @@
+#ifndef __bbSlicerUnbiasedNonLocalMeansfilterforDWI_h_INCLUDED__
+#define __bbSlicerUnbiasedNonLocalMeansfilterforDWI_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT UnbiasedNonLocalMeansfilterforDWI
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( UnbiasedNonLocalMeansfilterforDWI , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( iRadiusSearch , std::vector<int> );
+BBTK_DECLARE_INPUT ( iRadiusComp , std::vector<int> );
+BBTK_DECLARE_INPUT ( iH , float );
+BBTK_DECLARE_INPUT ( iNumNeighbors , int );
+BBTK_DECLARE_INPUT ( iRadiusEstimation , std::vector<int> );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( UnbiasedNonLocalMeansfilterforDWI , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "UnbiasedNonLocalMeansfilterforDWI" ) ;
+    BBTK_AUTHOR ( "Antonio Tristan Vega, Santiago Aja Fernandez. University of Valladolid SPAIN. Partially founded by grant number TEC2007-67073/TCM from the Comision Interministerial de Ciencia y Tecnologia Spain." ) ;
+    BBTK_DESCRIPTION ( "This module reduces noise or unwanted detail on a set of diffusion weighted images. For this, it filters the images using a Unbiased Non Local Means for Rician noise algorithm. It exploits not only the spatial redundancy, but the redundancy in similar gradient directions as well; it takes into account the N closest gradient directions to the direction being processed a maximum of 5 gradient directions is allowed to keep a reasonable computational load, since we do not use neither similarity maps nor block-wise implementation.The noise parameter is automatically estimated in the same way as in the jointLMMSE module.A complete description of the algorithm may be found in:Antonio Tristan-Vega and Santiago Aja-Fernandez, DWI filtering using joint information for DTI and HARDI, Medical Image Analysis, Volume 14, Issue 2, Pages 205-218. 2010.Please, note that the execution of this filter is extremely slow, son only very conservative parameters block size and search size as small as possible should be used. Even so, its execution may take several hours. The advantage of this filter over joint LMMSE is its better preservation of edges and fine structures." ) ;
+    BBTK_CATEGORY ( "Legacy.Diffusion.Denoising" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iRadiusSearch , "iRadiusSearch" , std::vector<int>, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iRadiusComp , "iRadiusComp" , std::vector<int>, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iH , "iH" , float, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iNumNeighbors , "iNumNeighbors" , int, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , iRadiusEstimation , "iRadiusEstimation" , std::vector<int>, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(UnbiasedNonLocalMeansfilterforDWI , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( UnbiasedNonLocalMeansfilterforDWI ) ;
+}
+
+#endif // __bbSlicerUnbiasedNonLocalMeansfilterforDWI_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerVectorDemonRegistrationBRAINS.cxx b/bbtk_Slicer_PKG/src/bbSlicerVectorDemonRegistrationBRAINS.cxx
new file mode 100644 (file)
index 0000000..83c45ee
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerVectorDemonRegistrationBRAINS.cxx
@@ -0,0 +1,95 @@
+#include "bbSlicerVectorDemonRegistrationBRAINS.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, VectorDemonRegistrationBRAINS )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( VectorDemonRegistrationBRAINS, bbtk::AtomicBlackBox );
+
+    void VectorDemonRegistrationBRAINS::Process ( ) {
+
+        // GENERATED
+
+int _argc =41;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libVBRAINSDemonWarpLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-m"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingVolume( ) ) ) ,"@@@@@"," -m ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-f"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedVolume( ) ) ) ,"@@@@@"," -f ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--inputPixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputPixelType( ) ) ) ,"@@@@@"," --inputPixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-o"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@"," -o ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-O"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDisplacementFieldVolume( ) ) ) ,"@@@@@"," -O ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputPixelType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputPixelType( ) ) ) ,"@@@@@"," --outputPixelType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--interpolationMode"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinterpolationMode( ) ) ) ,"@@@@@"," --interpolationMode ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--registrationFilterType"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputregistrationFilterType( ) ) ) ,"@@@@@"," --registrationFilterType ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-s"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothDisplacementFieldSigma( ) ) ) ,"@@@@@"," -s ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-n"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfPyramidLevels( ) ) ) ,"@@@@@"," -n ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumFixedPyramid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumFixedPyramid( ) ) ) ,"@@@@@"," --minimumFixedPyramid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--minimumMovingPyramid"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputminimumMovingPyramid( ) ) ) ,"@@@@@"," --minimumMovingPyramid ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-i"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputarrayOfPyramidLevelIterations( ) ) ) ,"@@@@@"," -i ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-e"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputhistogramMatch( ) ) ) ,"@@@@@"," -e ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfHistogramBins"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfHistogramBins( ) ) ) ,"@@@@@"," --numberOfHistogramBins ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfMatchPoints"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfMatchPoints( ) ) ) ,"@@@@@"," --numberOfMatchPoints ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--medianFilterSize"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmedianFilterSize( ) ) ) ,"@@@@@"," --medianFilterSize ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeWithDisplacementField"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeWithDisplacementField( ) ) ) ,"@@@@@"," --initializeWithDisplacementField ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--initializeWithTransform"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinitializeWithTransform( ) ) ) ,"@@@@@"," --initializeWithTransform ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--makeBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmakeBOBF( ) ) ) ,"@@@@@"," --makeBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--fixedBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputfixedBinaryVolume( ) ) ) ,"@@@@@"," --fixedBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--movingBinaryVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmovingBinaryVolume( ) ) ) ,"@@@@@"," --movingBinaryVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--lowerThresholdForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputlowerThresholdForBOBF( ) ) ) ,"@@@@@"," --lowerThresholdForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--upperThresholdForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputupperThresholdForBOBF( ) ) ) ,"@@@@@"," --upperThresholdForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--backgroundFillValue"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbackgroundFillValue( ) ) ) ,"@@@@@"," --backgroundFillValue ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--seedForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputseedForBOBF( ) ) ) ,"@@@@@"," --seedForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--neighborhoodForBOBF"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputneighborhoodForBOBF( ) ) ) ,"@@@@@"," --neighborhoodForBOBF ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputDisplacementFieldPrefix"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDisplacementFieldPrefix( ) ) ) ,"@@@@@"," --outputDisplacementFieldPrefix ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputCheckerboardVolume"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputCheckerboardVolume( ) ) ) ,"@@@@@"," --outputCheckerboardVolume ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--checkerboardPatternSubdivisions"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputcheckerboardPatternSubdivisions( ) ) ) ,"@@@@@"," --checkerboardPatternSubdivisions ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--outputNormalized"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputNormalized( ) ) ) ,"@@@@@"," --outputNormalized ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-v"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputDebug( ) ) ) ,"@@@@@"," -v ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-w"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputweightFactors( ) ) ) ,"@@@@@"," -w ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-t"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputgradientType( ) ) ) ,"@@@@@"," -t ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-g"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputsmoothingUp( ) ) ) ,"@@@@@"," -g ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-l"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmaxStepLength( ) ) ) ,"@@@@@"," -l ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-a"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputturnOffDiffeomorph( ) ) ) ,"@@@@@"," -a ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-G"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputUseDebugImageViewer( ) ) ) ,"@@@@@"," -G ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "-p"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputPromptAfterImageSend( ) ) ) ,"@@@@@"," -p ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfBCHApproximationTerms"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfBCHApproximationTerms( ) ) ) ,"@@@@@"," --numberOfBCHApproximationTerms ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--numberOfThreads"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputnumberOfThreads( ) ) ) ,"@@@@@"," --numberOfThreads ") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void VectorDemonRegistrationBRAINS::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void VectorDemonRegistrationBRAINS::bbUserSetDefaultValues ( ) {
+    }
+
+    void VectorDemonRegistrationBRAINS::bbUserInitializeProcessing ( ) {
+    }
+
+    void VectorDemonRegistrationBRAINS::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerVectorDemonRegistrationBRAINS.h b/bbtk_Slicer_PKG/src/bbSlicerVectorDemonRegistrationBRAINS.h
new file mode 100644 (file)
index 0000000..0a2bb9b
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerVectorDemonRegistrationBRAINS.h
@@ -0,0 +1,138 @@
+#ifndef __bbSlicerVectorDemonRegistrationBRAINS_h_INCLUDED__
+#define __bbSlicerVectorDemonRegistrationBRAINS_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT VectorDemonRegistrationBRAINS
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( VectorDemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( movingVolume , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( fixedVolume , std::vector<std::string> );
+BBTK_DECLARE_INPUT ( inputPixelType , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldVolume , std::string );
+BBTK_DECLARE_INPUT ( outputPixelType , std::string );
+BBTK_DECLARE_INPUT ( interpolationMode , std::string );
+BBTK_DECLARE_INPUT ( registrationFilterType , std::string );
+BBTK_DECLARE_INPUT ( smoothDisplacementFieldSigma , double );
+BBTK_DECLARE_INPUT ( numberOfPyramidLevels , int );
+BBTK_DECLARE_INPUT ( minimumFixedPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( minimumMovingPyramid , std::vector<int> );
+BBTK_DECLARE_INPUT ( arrayOfPyramidLevelIterations , std::vector<int> );
+BBTK_DECLARE_INPUT ( histogramMatch , bool );
+BBTK_DECLARE_INPUT ( numberOfHistogramBins , int );
+BBTK_DECLARE_INPUT ( numberOfMatchPoints , int );
+BBTK_DECLARE_INPUT ( medianFilterSize , std::vector<int> );
+BBTK_DECLARE_INPUT ( initializeWithDisplacementField , std::string );
+BBTK_DECLARE_INPUT ( initializeWithTransform , std::string );
+BBTK_DECLARE_INPUT ( makeBOBF , bool );
+BBTK_DECLARE_INPUT ( fixedBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( movingBinaryVolume , std::string );
+BBTK_DECLARE_INPUT ( lowerThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( upperThresholdForBOBF , int );
+BBTK_DECLARE_INPUT ( backgroundFillValue , int );
+BBTK_DECLARE_INPUT ( seedForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( neighborhoodForBOBF , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputDisplacementFieldPrefix , std::string );
+BBTK_DECLARE_INPUT ( outputCheckerboardVolume , std::string );
+BBTK_DECLARE_INPUT ( checkerboardPatternSubdivisions , std::vector<int> );
+BBTK_DECLARE_INPUT ( outputNormalized , bool );
+BBTK_DECLARE_INPUT ( outputDebug , bool );
+BBTK_DECLARE_INPUT ( weightFactors , std::vector<float> );
+BBTK_DECLARE_INPUT ( gradientType , int );
+BBTK_DECLARE_INPUT ( smoothingUp , double );
+BBTK_DECLARE_INPUT ( maxStepLength , double );
+BBTK_DECLARE_INPUT ( turnOffDiffeomorph , bool );
+BBTK_DECLARE_INPUT ( UseDebugImageViewer , bool );
+BBTK_DECLARE_INPUT ( PromptAfterImageSend , bool );
+BBTK_DECLARE_INPUT ( numberOfBCHApproximationTerms , int );
+BBTK_DECLARE_INPUT ( numberOfThreads , int );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( VectorDemonRegistrationBRAINS , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "VectorDemonRegistrationBRAINS" ) ;
+    BBTK_AUTHOR ( "This tool was developed by Hans J. Johnson and Greg Harris." ) ;
+    BBTK_DESCRIPTION ( "This program finds a deformation field to warp a moving image onto a fixed image.  The images must be of the same signal kind, and contain an image of the same kind of object.  This program uses the Thirion Demons warp software in ITK, the Insight Toolkit.  Additional information is available at: http://www.nitrc.org/projects/brainsdemonwarp." ) ;
+    BBTK_CATEGORY ( "Registration.Specialized" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(VectorDemonRegistrationBRAINS , movingVolume , "movingVolume" , std::vector<std::string>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , fixedVolume , "fixedVolume" , std::vector<std::string>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , inputPixelType , "inputPixelType" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputVolume , "outputVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputDisplacementFieldVolume , "outputDisplacementFieldVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputPixelType , "outputPixelType" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , interpolationMode , "interpolationMode" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , registrationFilterType , "registrationFilterType" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , smoothDisplacementFieldSigma , "smoothDisplacementFieldSigma" , double, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfPyramidLevels , "numberOfPyramidLevels" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , minimumFixedPyramid , "minimumFixedPyramid" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , minimumMovingPyramid , "minimumMovingPyramid" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , arrayOfPyramidLevelIterations , "arrayOfPyramidLevelIterations" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , histogramMatch , "histogramMatch" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfHistogramBins , "numberOfHistogramBins" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfMatchPoints , "numberOfMatchPoints" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , medianFilterSize , "medianFilterSize" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , initializeWithDisplacementField , "initializeWithDisplacementField" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , initializeWithTransform , "initializeWithTransform" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , makeBOBF , "makeBOBF" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , fixedBinaryVolume , "fixedBinaryVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , movingBinaryVolume , "movingBinaryVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , lowerThresholdForBOBF , "lowerThresholdForBOBF" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , upperThresholdForBOBF , "upperThresholdForBOBF" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , backgroundFillValue , "backgroundFillValue" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , seedForBOBF , "seedForBOBF" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , neighborhoodForBOBF , "neighborhoodForBOBF" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputDisplacementFieldPrefix , "outputDisplacementFieldPrefix" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputCheckerboardVolume , "outputCheckerboardVolume" , std::string, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , checkerboardPatternSubdivisions , "checkerboardPatternSubdivisions" , std::vector<int>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputNormalized , "outputNormalized" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , outputDebug , "outputDebug" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , weightFactors , "weightFactors" , std::vector<float>, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , gradientType , "gradientType" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , smoothingUp , "smoothingUp" , double, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , maxStepLength , "maxStepLength" , double, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , turnOffDiffeomorph , "turnOffDiffeomorph" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , UseDebugImageViewer , "UseDebugImageViewer" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , PromptAfterImageSend , "PromptAfterImageSend" , bool, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfBCHApproximationTerms , "numberOfBCHApproximationTerms" , int, "");
+BBTK_INPUT(VectorDemonRegistrationBRAINS , numberOfThreads , "numberOfThreads" , int, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( VectorDemonRegistrationBRAINS ) ;
+}
+
+#endif // __bbSlicerVectorDemonRegistrationBRAINS_h_INCLUDED__
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerVotingBinaryHoleFilling.cxx b/bbtk_Slicer_PKG/src/bbSlicerVotingBinaryHoleFilling.cxx
new file mode 100644 (file)
index 0000000..d3fe3b1
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerVotingBinaryHoleFilling.cxx
@@ -0,0 +1,60 @@
+#include "bbSlicerVotingBinaryHoleFilling.h"
+#include "bbSlicerPackage.h"
+
+namespace bbSlicer {
+    BBTK_ADD_BLACK_BOX_TO_PACKAGE ( Slicer, VotingBinaryHoleFilling )
+    BBTK_BLACK_BOX_IMPLEMENTATION ( VotingBinaryHoleFilling, bbtk::AtomicBlackBox );
+
+    void VotingBinaryHoleFilling::Process ( ) {
+
+        // GENERATED
+
+int _argc =6;
+std::string lib = "/home/riveros/.slicer/Slicer4-bin/Slicer-build/lib/Slicer-4.0/cli-modules/libVotingBinaryHoleFillingImageFilterLib.so";
+char * _argv[ ] = { Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--radius"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputradius( ) ) ) ,"@@@@@"," --radius ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--majorityThreshold"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputmajorityThreshold( ) ) ) ,"@@@@@"," --majorityThreshold ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--background"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputbackground( ) ) ) ,"@@@@@"," --background ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::toString( "--foreground"  ) + Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputforeground( ) ) ) ,"@@@@@"," --foreground ") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputinputVolume( ) ) ) ,"@@@@@","") ),
+Mthd::Aux::toCharArrray( Mthd::Aux::replace_str ( ( Mthd::Aux::toString( bbGetInputoutputVolume( ) ) ) ,"@@@@@","") ) };
+
+        // EO GENERATED
+        this->execute( lib, _argc, _argv );
+
+    }
+
+    void VotingBinaryHoleFilling::execute ( std::string lib, int _argc, char * _argv[] ) {
+        void* handle = dlopen( lib.c_str( ), RTLD_NOW | RTLD_GLOBAL );
+        if ( ! handle ) {
+            std::cerr << "CAN'T OPEN LIBRARY: " << dlerror( ) << '\n';
+            return;
+        }
+        typedef int (*method_t )( int argc, char * argv[] );
+        // RESET ERROR
+        dlerror( );
+        // PROTOTYPE
+        method_t myMethod = ( method_t ) dlsym( handle, "ModuleEntryPoint" );
+        const char *dlsym_error = dlerror( );
+        if ( dlsym_error ) {
+            std::cerr << "CAN'T LOAD SYMBOL 'ModuleEntryPoint':" << dlsym_error << '\n';
+            dlclose( handle );
+            return;
+        }
+        // METHOD CALL
+        myMethod( _argc, _argv );
+        // CLOSING LIB
+        dlclose( handle );
+    }
+
+    void VotingBinaryHoleFilling::bbUserSetDefaultValues ( ) {
+    }
+
+    void VotingBinaryHoleFilling::bbUserInitializeProcessing ( ) {
+    }
+
+    void VotingBinaryHoleFilling::bbUserFinalizeProcessing ( ) {
+    }
+}
+// EO namespace bbSlicer
+
+

diff --git a/bbtk_Slicer_PKG/src/bbSlicerVotingBinaryHoleFilling.h b/bbtk_Slicer_PKG/src/bbSlicerVotingBinaryHoleFilling.h
new file mode 100644 (file)
index 0000000..d03fa19
--- /dev/null
+++ b/bbtk_Slicer_PKG/src/bbSlicerVotingBinaryHoleFilling.h
@@ -0,0 +1,68 @@
+#ifndef __bbSlicerVotingBinaryHoleFilling_h_INCLUDED__
+#define __bbSlicerVotingBinaryHoleFilling_h_INCLUDED__
+
+#include "bbSlicer_EXPORT.h"
+#include "bbtkAtomicBlackBox.h"
+
+#include <vector>
+#include <cstdlib>
+#include <dlfcn.h>
+#include <sstream>
+#include <fstream>
+#include <iostream>
+
+#include <ModuleDescriptionUtilities.h>
+#include <ModuleDescriptionParser.h>
+#include <ModuleParameterGroup.h>
+#include <ModuleDescription.h>
+#include <ModuleParameter.h>
+
+#include "CreationTool.h"
+
+namespace bbSlicer {
+
+    class bbSlicer_EXPORT VotingBinaryHoleFilling
+    :
+    public bbtk::AtomicBlackBox {
+        BBTK_BLACK_BOX_INTERFACE ( VotingBinaryHoleFilling , bbtk::AtomicBlackBox ) ;
+
+        // GENERATED ARGS        
+        
+BBTK_DECLARE_INPUT ( radius , std::vector<int> );
+BBTK_DECLARE_INPUT ( majorityThreshold , int );
+BBTK_DECLARE_INPUT ( background , int );
+BBTK_DECLARE_INPUT ( foreground , int );
+BBTK_DECLARE_INPUT ( inputVolume , std::string );
+BBTK_DECLARE_INPUT ( outputVolume , std::string );
+
+        // EO GENERATED ARGS
+
+        BBTK_PROCESS ( Process ) ;
+        void Process ( ) ;
+    private:
+        void execute ( std::string lib , int _argc , char * _argv[] ) ;
+    } ;
+
+    BBTK_BEGIN_DESCRIBE_BLACK_BOX ( VotingBinaryHoleFilling , bbtk::AtomicBlackBox ) ;
+    BBTK_NAME ( "VotingBinaryHoleFilling" ) ;
+    BBTK_AUTHOR ( "Bill Lorensen" ) ;
+    BBTK_DESCRIPTION ( "Applies a voting operation in order to fill-in cavities. This can be used for smoothing contours and for filling holes in binary images. This technique is used frequently when segmenting complete organs that may have ducts or vasculature that may not have been included in the initial segmentation, e.g. lungs, kidneys, liver." ) ;
+    BBTK_CATEGORY ( "Filtering" ) ;
+
+    // GENERATED DESCRPTION
+    
+BBTK_INPUT(VotingBinaryHoleFilling , radius , "radius" , std::vector<int>, "");
+BBTK_INPUT(VotingBinaryHoleFilling , majorityThreshold , "majorityThreshold" , int, "");
+BBTK_INPUT(VotingBinaryHoleFilling , background , "background" , int, "");
+BBTK_INPUT(VotingBinaryHoleFilling , foreground , "foreground" , int, "");
+BBTK_INPUT(VotingBinaryHoleFilling , inputVolume , "inputVolume" , std::string, "");
+BBTK_INPUT(VotingBinaryHoleFilling , outputVolume , "outputVolume" , std::string, "");
+
+    // EO GENERATED DESCRIPTION
+
+    BBTK_END_DESCRIBE_BLACK_BOX ( VotingBinaryHoleFilling ) ;
+}
+
+#endif // __bbSlicerVotingBinaryHoleFilling_h_INCLUDED__
+
+