--- /dev/null
+/*=========================================================================
+ 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://www.centreleonberard.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
+ ===========================================================================**/
+
+//--------------------------------------------------------------------
+template <class ImageType>
+clitk::RelativePositionDataBaseBuilderFilter<ImageType>::
+RelativePositionDataBaseBuilderFilter():
+ clitk::FilterBase(),
+ clitk::FilterWithAnatomicalFeatureDatabaseManagement(),
+ itk::ImageToImageFilter<ImageType, ImageType>()
+{
+ this->SetNumberOfRequiredInputs(0); // support
+ VerboseFlagOff();
+ SetBackgroundValue(0);
+ SetForegroundValue(1);
+ SetNumberOfBins(100);
+ SetNumberOfAngles(4);
+ SetAreaLossTolerance(0.01);
+ m_ListOfAngles.clear();
+ // SetSupportSize(0);
+ // SetTargetSize(0);
+ // SetSizeWithThreshold(0);
+ // SetSizeWithReverseThreshold(0);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionDataBaseBuilderFilter<ImageType>::
+PrintOptions()
+{
+ DD("TODO");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionDataBaseBuilderFilter<ImageType>::
+GenerateOutputInformation()
+{
+ // ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+ // ImagePointer outputImage = this->GetOutput(0);
+ // outputImage->SetRegions(outputImage->GetLargestPossibleRegion());
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionDataBaseBuilderFilter<ImageType>::
+GenerateInputRequestedRegion()
+{
+ // Call default
+ // itk::ImageToImageFilter<ImageType, ImageType>::GenerateInputRequestedRegion();
+ // // Get input pointers and set requested region to common region
+ // ImagePointer input1 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+ // input1->SetRequestedRegion(input1->GetLargestPossibleRegion());
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionDataBaseBuilderFilter<ImageType>::
+GenerateData()
+{
+ // Load database of anatomical elements
+ static const unsigned int dim = ImageType::ImageDimension;
+ this->LoadAFDB();
+
+ // Get some information
+ std::string patient = this->GetAFDB()->GetTagValue("PatientID");
+
+ // Get input pointers
+ m_Support = this->GetAFDB()->template GetImage <ImageType>(GetSupportName());
+ m_Target = this->GetAFDB()->template GetImage <ImageType>(GetTargetName());
+
+ // Build the list of tested directions
+ m_ListOfAngles.clear();
+ for(uint i=0; i<GetNumberOfAngles(); i++) {
+ double a = i*360.0/GetNumberOfAngles();
+ if (a>180) a = 180-a;
+ m_ListOfAngles.push_back(clitk::deg2rad(a));
+ RelativePositionDirectionType r;
+ r.angle1 = clitk::deg2rad(a);
+ r.angle2 = 0;
+ r.notFlag = false;
+ m_ListOfDirections.push_back(r); // only one direction
+ }
+
+
+ // Perform the RelativePositionAnalyzerFilter for each objects
+ typedef typename clitk::RelativePositionAnalyzerFilter<ImageType> FilterType;
+ for (int i=0; i<GetNumberOfObjects(); i++) {
+ m_Object = this->GetAFDB()->template GetImage <ImageType>(GetObjectName(i));
+
+ for (int j=0; j<m_ListOfDirections.size(); j++) {
+ clitk::RelativePositionDirectionType direction = m_ListOfDirections[j];
+
+ // Create the filter
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetInputSupport(m_Support);
+ filter->SetInputTarget(m_Target);
+ filter->SetInputObject(m_Object); // FIXME do AndNot before + only compute supportSize once.
+ filter->SetNumberOfBins(GetNumberOfBins());
+ filter->SetAreaLossTolerance(GetAreaLossTolerance());
+ filter->SetDirection(direction);
+ filter->Update();
+
+ // Results
+ std::ostringstream s;
+ s << patient << " "
+ << GetSupportName() << " "
+ // << GetTargetName() << " " // No need
+ << GetObjectName(i) <<" ";
+ // Normal
+ // if (filter->GetInfo().sizeAfterThreshold != filter->GetInfo().sizeBeforeThreshold) {
+ std::ostringstream os;
+ os << s.str();
+ direction.notFlag = false;
+ direction.Print(os);
+ filter->GetInfo().Print(os);
+ std::cout << os.str() << std::endl;
+ // }
+ // Inverse
+ // if (filter->GetInfoReverse().sizeAfterThreshold != filter->GetInfoReverse().sizeBeforeThreshold) {
+ std::ostringstream oos;
+ oos << s.str();
+ direction.notFlag = true;
+ direction.Print(oos);
+ filter->GetInfoReverse().Print(oos);
+ std::cout << oos.str() << std::endl;
+ // }
+ } // end direction
+
+ } // end object
+}
+//--------------------------------------------------------------------
+
+
--- /dev/null
+/*=========================================================================
+ 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://www.centreleonberard.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 "clitkRelativePositionDataBaseBuilder_ggo.h"
+#include "clitkRelativePositionDataBaseBuilderGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+ // Init command line
+ GGO(clitkRelativePositionDataBaseBuilder, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::RelativePositionDataBaseBuilderGenericFilter<args_info_clitkRelativePositionDataBaseBuilder> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ // Set options
+ filter->SetArgsInfo(args_info);
+
+ // Add an input to determine the type of image
+ NewAFDB(afdb, args_info.afdb_arg);
+ std::string f = afdb->GetTagValue(args_info.supportName_arg);
+ f = std::string(args_info.afdb_path_arg)+"/"+f;
+ filter->AddInputFilename(f);
+
+ try {
+ filter->Update();
+ } catch(std::runtime_error e) {
+ std::cout << e.what() << std::endl;
+ return EXIT_FAILURE;
+ }
+
+ return EXIT_SUCCESS;
+} // This is the end, my friend
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkRelativePositionDataBaseBuilder.ggo
+package "clitkRelativePositionDataBaseBuilder"
+version "1.0"
+purpose "Analyze relative position of a target according to structures"
+
+section "General options"
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
+option "imagetypes" - "Display allowed image types" flag off
+
+section "Input/Output"
+option "afdb" a "Input Anatomical Feature DB" string yes
+option "afdb_path" - "Path to search image in afdb" string no
+
+option "supportName" i "Input mask support name in afdb" string yes
+option "targetName" t "Input mask target name in afdb" string yes
+option "objectName" j "Input mask object name in afdb" string yes multiple
+
+option "output" o "Output image " string yes
+
+section "Options for building the relative positions"
+option "bins" b "Number of histo bins for fuzzy map" int default="100" no
+option "nb" n "Number of angles to test" int default="4" no
+option "tol" - "Target area loss tolerance (|0-1])" double default="0.01" no
+
--- /dev/null
+/*=========================================================================
+ 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://www.centreleonberard.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 CLITKRelativePositionDataBaseBuilderGENERICFILTER_H
+#define CLITKRelativePositionDataBaseBuilderGENERICFILTER_H
+
+// clitk
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkRelativePositionDataBaseBuilderFilter.h"
+#include "clitkSliceBySliceRelativePositionFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+ template<class ArgsInfoType>
+ class ITK_EXPORT RelativePositionDataBaseBuilderGenericFilter:
+ public ImageToImageGenericFilter<RelativePositionDataBaseBuilderGenericFilter<ArgsInfoType> >
+ {
+ public:
+ //--------------------------------------------------------------------
+ RelativePositionDataBaseBuilderGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ImageToImageGenericFilter<RelativePositionDataBaseBuilderGenericFilter<ArgsInfoType> > Superclass;
+ typedef RelativePositionDataBaseBuilderGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ itkNewMacro(Self);
+ itkTypeMacro(RelativePositionDataBaseBuilderGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const ArgsInfoType & a);
+ 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:
+ RelativePositionDataBaseBuilderGenericFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ };// end class
+ //--------------------------------------------------------------------
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkRelativePositionDataBaseBuilderGenericFilter.txx"
+#endif
+
+#endif // #define CLITKRelativePositionDataBaseBuilderGENERICFILTER_H
--- /dev/null
+/*=========================================================================
+ 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://www.centreleonberard.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
+ ===========================================================================**/
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::RelativePositionDataBaseBuilderGenericFilter<ArgsInfoType>::
+RelativePositionDataBaseBuilderGenericFilter():
+ ImageToImageGenericFilter<Self>("RelativePositionDataBaseBuilder")
+{
+ // Default values
+ cmdline_parser_clitkRelativePositionDataBaseBuilder_init(&mArgsInfo);
+ InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::RelativePositionDataBaseBuilderGenericFilter<ArgsInfoType>::
+InitializeImageType()
+{
+ ADD_IMAGE_TYPE(Dim, uchar);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::RelativePositionDataBaseBuilderGenericFilter<ArgsInfoType>::
+SetArgsInfo(const ArgsInfoType & a)
+{
+ mArgsInfo=a;
+ SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void clitk::RelativePositionDataBaseBuilderGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+ f->SetAFDBFilename(mArgsInfo.afdb_arg);
+ f->SetAFDBPath(mArgsInfo.afdb_path_arg);
+ f->SetNumberOfBins(mArgsInfo.bins_arg);
+ f->SetNumberOfAngles(mArgsInfo.nb_arg);
+ f->SetAreaLossTolerance(mArgsInfo.tol_arg);
+ f->SetSupportName(mArgsInfo.supportName_arg);
+ f->SetTargetName(mArgsInfo.targetName_arg);
+ for(int i=0; i<mArgsInfo.objectName_given; i++)
+ f->AddObjectName(mArgsInfo.objectName_arg[i]);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::RelativePositionDataBaseBuilderGenericFilter<ArgsInfoType>::
+UpdateWithInputImageType()
+{
+ // Create filter
+ typedef clitk::RelativePositionDataBaseBuilderFilter<ImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+
+ // Set global Options
+ SetOptionsFromArgsInfoToFilter<FilterType>(filter);
+
+ // Go !
+ filter->Update();
+
+ // Write/Save results
+ // typename ImageType::Pointer output = filter->GetOutput();
+ //this->template SetNextOutput<ImageType>(output);
+
+}
+//--------------------------------------------------------------------
+
+
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff