manage anatomical features DB

diff --git a/segmentation/clitkAnatomicalFeatureDatabase.cxx b/segmentation/clitkAnatomicalFeatureDatabase.cxx
new file mode 100644 (file)
index 0000000..a132f58
--- /dev/null
+++ b/segmentation/clitkAnatomicalFeatureDatabase.cxx
@@ -0,0 +1,120 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to: 
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+  ======================================================================-====*/
+
+// clitk
+#include "clitkAnatomicalFeatureDatabase.h"
+
+// std
+#include <iterator>
+#include <sstream>
+
+//--------------------------------------------------------------------
+clitk::AnatomicalFeatureDatabase::AnatomicalFeatureDatabase() 
+{ 
+  SetFilename("noname.afdb"); 
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::AnatomicalFeatureDatabase::Write() 
+{
+  // open file
+  std::ofstream os;
+  openFileForWriting(os, GetFilename());
+  MapTagType::const_iterator iter = m_MapOfTag.begin();
+  while (iter != m_MapOfTag.end()) {
+    os << iter->first << " " << iter->second << std::endl;
+    iter++;
+  }
+  os.close();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::AnatomicalFeatureDatabase::Load() 
+{
+  // open file
+  std::ifstream is;
+  openFileForReading(is, GetFilename());
+  // load line by line string/string
+  while (!is.fail()) {
+    std::string tag;
+    is >> tag; DD(tag);
+    std::string value;
+    std::getline(is,value,'\n');
+    m_MapOfTag[tag] = value;
+  }
+}
+//--------------------------------------------------------------------
+
+   
+//--------------------------------------------------------------------
+void clitk::AnatomicalFeatureDatabase::SetPoint3D(std::string tag, PointType3D & p)
+{
+  ::itk::OStringStream value;
+  value << p[0] << " " << p[1] << " " << p[2];
+  m_MapOfTag[tag] = value.str();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::AnatomicalFeatureDatabase::GetPoint3D(std::string tag, PointType3D & p)
+{
+  if (m_MapOfTag.find(tag) == m_MapOfTag.end()) {
+    clitkExceptionMacro("Could not find the tag <" << tag << "> of type Point3D in the DB");
+  }
+  else {
+    std::string s = m_MapOfTag[tag];
+    
+    // construct a stream from the string
+    std::stringstream strstr(s);
+
+    // use stream iterators to copy the stream to the vector as
+    // whitespace separated strings
+    std::istream_iterator<std::string> it(strstr);
+    std::istream_iterator<std::string> end;
+    std::vector<std::string> results(it, end);
+
+    // parse the string into 3 doubles
+    for(int i=0; i<3; i++) {
+      DD(results[i]);
+      p[i] = atof(results[i].c_str());
+      DD(p[i]);
+    }
+
+    /*
+    // boost 
+    #include <boost/foreach.hpp>
+    #include <boost/tokenizer.hpp>
+    // parse the string into 3 doubles
+    boost::char_separator<char> sep(", ");
+    boost::tokenizer<boost::char_separator<char> > tokens(s, sep);
+    int i=0;
+    BOOST_FOREACH(std::string t, tokens) {
+      std::cout << t << "." << std::endl;
+      p[i] = atof(t.c_str());
+      i++;
+    }
+    */
+  }
+}
+//--------------------------------------------------------------------
+

diff --git a/segmentation/clitkAnatomicalFeatureDatabase.h b/segmentation/clitkAnatomicalFeatureDatabase.h
new file mode 100644 (file)
index 0000000..78f04e3
--- /dev/null
+++ b/segmentation/clitkAnatomicalFeatureDatabase.h
@@ -0,0 +1,61 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to: 
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+  ======================================================================-====*/
+
+#ifndef CLITKANATOMICALFEATUREDATABASE_H
+#define CLITKANATOMICALFEATUREDATABASE_H
+
+// clitk
+#include "clitkCommon.h"
+
+namespace clitk {
+  
+  //--------------------------------------------------------------------
+  /*
+    Class to store and retreive anatomical feature such as 3D
+    named landmarks points. 
+  */
+  class AnatomicalFeatureDatabase: public itk::Object
+  {
+  public:
+    AnatomicalFeatureDatabase();
+
+    // Set/Get filename 
+    itkSetMacro(Filename, std::string);
+    itkGetConstMacro(Filename, std::string);
+
+    // Read and write DB
+    void Write();
+    void Load();
+    
+    // Get landmarks
+    typedef itk::Point<double,3> PointType3D;
+    void SetPoint3D(std::string tag, PointType3D & p);
+    void GetPoint3D(std::string tag, PointType3D & p);
+    
+  protected:
+    std::string m_Filename;
+    typedef std::map<std::string, std::string> MapTagType;
+    MapTagType m_MapOfTag;
+
+  }; // end class
+  //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#endif // CLITKANATOMICALFEATUREDATABASE_H