Add clitkBool to perform boolean operation

diff --git a/segmentation/clitkBool.cxx b/segmentation/clitkBool.cxx
new file mode 100644 (file)
index 0000000..dbb313c
--- /dev/null
+++ b/segmentation/clitkBool.cxx
@@ -0,0 +1,45 @@
+/*=========================================================================
+  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 "clitkBool_ggo.h"
+#include "clitkBooleanOperatorLabelImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+  // Init command line
+  GGO(clitkBool, args_info);
+  CLITK_INIT;
+
+  // Filter
+  typedef clitk::BooleanOperatorLabelImageGenericFilter<args_info_clitkBool> FilterType;
+  FilterType::Pointer filter = FilterType::New();
+
+  filter->SetArgsInfo(args_info);
+  
+  try {
+    filter->Update();
+  } catch(std::runtime_error e) {
+    std::cout << e.what() << std::endl;
+  }
+
+  return EXIT_SUCCESS;
+} // This is the end, my friend
+//--------------------------------------------------------------------

diff --git a/segmentation/clitkBool.ggo b/segmentation/clitkBool.ggo
new file mode 100644 (file)
index 0000000..ede9646
--- /dev/null
+++ b/segmentation/clitkBool.ggo
@@ -0,0 +1,14 @@
+#File clitkExtractMediastinalVessels.ggo
+package "clitkExtractMediastinalVessels"
+version "1.0"
+purpose "Extract MediastinalVessels"
+
+option "config"                -  "Config file"                  string        no
+option "imagetypes"     -  "Display allowed image types"  flag          off
+option "verbose"        v  "Verbose"                     flag          off
+
+option "input"         i       "Input mask 1"               string     yes
+option "input2"        j       "Input mask 2"               string     yes
+option "output"        o       "Output filename"            string     yes
+
+option "type"          t       "Bool type : "               int default="1" no

diff --git a/segmentation/clitkBooleanOperatorLabelImageGenericFilter.h b/segmentation/clitkBooleanOperatorLabelImageGenericFilter.h
new file mode 100644 (file)
index 0000000..acd69ff
--- /dev/null
+++ b/segmentation/clitkBooleanOperatorLabelImageGenericFilter.h
@@ -0,0 +1,80 @@
+/*=========================================================================
+  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 CLITKBOOLEANOPERATORLABELIMAGEGENERICFILTER_H
+#define CLITKBOOLEANOPERATORLABELIMAGEGENERICFILTER_H
+
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkBooleanOperatorLabelImageFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk 
+{
+  
+  template<class ArgsInfoType>
+  class ITK_EXPORT BooleanOperatorLabelImageGenericFilter: 
+    public ImageToImageGenericFilter<BooleanOperatorLabelImageGenericFilter<ArgsInfoType> >
+  {
+    
+  public:
+    //--------------------------------------------------------------------
+    BooleanOperatorLabelImageGenericFilter();
+
+    //--------------------------------------------------------------------
+    typedef ImageToImageGenericFilter<BooleanOperatorLabelImageGenericFilter<ArgsInfoType> > Superclass;
+    typedef BooleanOperatorLabelImageGenericFilter Self;
+    typedef itk::SmartPointer<Self>           Pointer;
+    typedef itk::SmartPointer<const Self>     ConstPointer;
+
+    //--------------------------------------------------------------------
+    itkNewMacro(Self);  
+    itkTypeMacro(BooleanOperatorLabelImageGenericFilter, LightObject);
+
+    //--------------------------------------------------------------------
+    // Options for the GenericFilter
+    void SetArgsInfo(const ArgsInfoType & a);
+
+    //--------------------------------------------------------------------
+    // Options for the Filter
+    template<class FilterType> 
+    void SetOptionsFromArgsInfoToFilter(FilterType * f) ;
+
+    //--------------------------------------------------------------------
+    // Main function called each time the filter is updated
+    template<class ImageType>  
+    void UpdateWithInputImageType();
+
+  protected:
+    template<unsigned int Dim> void InitializeImageType();
+    ArgsInfoType mArgsInfo;
+    
+  private:
+    BooleanOperatorLabelImageGenericFilter(const Self&); //purposely not implemented
+    void operator=(const Self&); //purposely not implemented
+    
+  }; // end class
+  //--------------------------------------------------------------------
+    
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkBooleanOperatorLabelImageGenericFilter.txx"
+#endif
+
+#endif // #define CLITKBOOLEANOPERATORLABELIMAGEGENERICFILTER_H

diff --git a/segmentation/clitkBooleanOperatorLabelImageGenericFilter.txx b/segmentation/clitkBooleanOperatorLabelImageGenericFilter.txx
new file mode 100644 (file)
index 0000000..0c07b67
--- /dev/null
+++ b/segmentation/clitkBooleanOperatorLabelImageGenericFilter.txx
@@ -0,0 +1,104 @@
+/*=========================================================================
+  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 CLITKBOOLEANOPERATORLABELIMAGEGENERICFILTER_TXX
+#define CLITKBOOLEANOPERATORLABELIMAGEGENERICFILTER_TXX
+
+#include "clitkImageCommon.h"
+  
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::BooleanOperatorLabelImageGenericFilter<ArgsInfoType>::BooleanOperatorLabelImageGenericFilter():
+  ImageToImageGenericFilter<Self>("BooleanOperatorLabelImage") 
+{
+  // Default values
+  cmdline_parser_clitkBool_init(&mArgsInfo);
+  InitializeImageType<3>(); // Only for 3D images
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::BooleanOperatorLabelImageGenericFilter<ArgsInfoType>::InitializeImageType() 
+{  
+  ADD_IMAGE_TYPE(Dim, uchar); // Can add float later
+}
+//--------------------------------------------------------------------
+  
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::BooleanOperatorLabelImageGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a) 
+{
+  mArgsInfo=a;
+  SetIOVerbose(mArgsInfo.verbose_flag);
+  if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+  if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg);
+  if (mArgsInfo.input2_given) AddInputFilename(mArgsInfo.input2_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void 
+clitk::BooleanOperatorLabelImageGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+  // Operation type
+  f->SetOperationType(typename FilterType::OperationTypeEnumeration(mArgsInfo.type_arg));
+ 
+  // Output filename
+  this->AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::BooleanOperatorLabelImageGenericFilter<ArgsInfoType>::UpdateWithInputImageType() 
+{ 
+  // Reading input
+  typename ImageType::Pointer input1 = this->template GetInput<ImageType>(0);
+  typename ImageType::Pointer input2 = this->template GetInput<ImageType>(1);
+
+  // Create filter
+  typedef clitk::BooleanOperatorLabelImageFilter<ImageType> FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+    
+  // Set global Options 
+  filter->SetInput1(input1);
+  filter->SetInput2(input2);
+  SetOptionsFromArgsInfoToFilter<FilterType>(filter);
+
+  // Go !
+  filter->Update();
+
+  // Write/Save results
+  typename ImageType::Pointer output = filter->GetOutput();
+  this->template SetNextOutput<ImageType>(output); 
+}
+//--------------------------------------------------------------------
+
+#endif //#define CLITKBOOLEANOPERATORLABELIMAGEGENERICFILTER_TXX