--- /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 CLITKRELATIVEPOSITIONANALYZERFILTER_H
+#define CLITKRELATIVEPOSITIONANALYZERFILTER_H
+
+// clitk
+#include "clitkCommon.h"
+
+// itk
+#include <itkImageToImageFilter.h>
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ /*
+ TODO
+ */
+ //--------------------------------------------------------------------
+
+ template <class ImageType>
+ class ITK_EXPORT RelativePositionAnalyzerFilter:
+ public itk::ImageToImageFilter<ImageType, ImageType>
+ {
+
+ public:
+ /** Standard class typedefs. */
+ typedef itk::ImageToImageFilter<ImageType, ImageType> Superclass;
+ typedef RelativePositionAnalyzerFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ /** Method for creation through the object factory. */
+ itkNewMacro(Self);
+
+ /** Run-time type information (and related methods). */
+ itkTypeMacro(RelativePositionAnalyzerFilter, ImageToImageFilter);
+
+ /** Some convenient typedefs. */
+ typedef typename ImageType::ConstPointer ImageConstPointer;
+ typedef typename ImageType::Pointer ImagePointer;
+ typedef typename ImageType::RegionType RegionType;
+ typedef typename ImageType::PixelType PixelType;
+ typedef typename ImageType::SpacingType SpacingType;
+ typedef typename ImageType::SizeType SizeType;
+ typedef typename ImageType::IndexType IndexType;
+ typedef typename ImageType::PointType PointType;
+
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
+ typedef itk::Image<float, ImageDimension> FloatImageType;
+
+ /** Input : initial image and object */
+ void SetInputSupport(const ImageType * image);
+ void SetInputObject(const ImageType * image);
+ void SetInputTarget(const ImageType * image);
+
+ // Options
+ itkSetMacro(VerboseFlag, bool);
+ itkGetConstMacro(VerboseFlag, bool);
+ itkBooleanMacro(VerboseFlag);
+
+ itkGetConstMacro(BackgroundValue, PixelType);
+ itkSetMacro(BackgroundValue, PixelType);
+
+ itkGetConstMacro(ForegroundValue, PixelType);
+ itkSetMacro(ForegroundValue, PixelType);
+
+ // For debug
+ void PrintOptions();
+
+ protected:
+ RelativePositionAnalyzerFilter();
+ virtual ~RelativePositionAnalyzerFilter() {}
+
+ bool m_VerboseFlag;
+ PixelType m_BackgroundValue;
+ PixelType m_ForegroundValue;
+ ImagePointer m_Support;
+ ImagePointer m_Object;
+ ImagePointer m_Target;
+
+ virtual void GenerateData();
+
+ private:
+ RelativePositionAnalyzerFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkRelativePositionAnalyzerFilter.txx"
+#endif
+
+#endif
--- /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::RelativePositionAnalyzerFilter<ImageType>::
+RelativePositionAnalyzerFilter():
+itk::ImageToImageFilter<ImageType, ImageType>()
+{
+ this->SetNumberOfRequiredInputs(3); // support, object, target
+ VerboseFlagOff();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+SetInputSupport(const ImageType * image)
+{
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput(0, const_cast<ImageType *>(image));
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+SetInputObject(const ImageType * image)
+{
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput(1, const_cast<ImageType *>(image));
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+SetInputTarget(const ImageType * image)
+{
+ // Process object is not const-correct so the const casting is required.
+ this->SetNthInput(1, const_cast<ImageType *>(image));
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+PrintOptions()
+{
+ DD("TODO");
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::RelativePositionAnalyzerFilter<ImageType>::
+GenerateData()
+{
+ DD("Update");
+ // Get input pointer
+ m_Support = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+ m_Object = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
+ m_Target = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(2));
+ static const unsigned int dim = ImageType::ImageDimension;
+
+ /*
+ Prerequisite:
+ - target fully inside support ?
+ */
+
+ //for(int i=0; i<m_ListOfOrientation.size(); i++) {
+ //DD(i);
+
+ // Compute Fuzzy map
+
+ // Get minimal value in the target area
+
+ // Or -> analyze floating point values inside the target area (histo ?)
+
+ // Set threshold and compute new support
+
+ // Compute ratio of area before/after
+ // http://www.itk.org/Doxygen/html/classitk_1_1LabelStatisticsImageFilter.html#details
+ /*
+ typedef itk::LabelStatisticsImageFilter<ImageType, ImageType> StatisticsImageFilterType;
+ typename StatisticsImageFilterType::Pointer statisticsFilter = StatisticsImageFilterType::New();
+ statisticsFilter->SetInput(m_Input);
+ statisticsFilter->SetLabelInput(m_Input);
+ statisticsFilter->Update();
+ int n = labelStatisticsImageFilter->GetCount(GetForegroundValue());
+ DD(n);
+ statisticsFilter = StatisticsImageFilterType::New();
+ statisticsFilter->SetInput(m_Output);
+ statisticsFilter->SetLabelInput(m_Output);
+ statisticsFilter->Update();
+ int m = labelStatisticsImageFilter->GetCount(GetForegroundValue());
+ DD(m);
+ */
+
+ // Print results
+
+ //}
+
+
+ // Final Step -> set output TODO
+ // this->SetNthOutput(0, working_image);
+ // this->GraftOutput(working_image);
+}
+//--------------------------------------------------------------------
+
TARGET_LINK_LIBRARIES(clitkRelativePosition clitkCommon ${ITK_LIBRARIES})
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkRelativePosition)
+ WRAP_GGO(clitkRelativePositionAnalyzer_GGO_C clitkRelativePositionAnalyzer.ggo)
+ ADD_EXECUTABLE(clitkRelativePositionAnalyzer clitkRelativePositionAnalyzer.cxx ${clitkRelativePositionAnalyzer_GGO_C})
+ TARGET_LINK_LIBRARIES(clitkRelativePositionAnalyzer clitkCommon ${ITK_LIBRARIES})
+ SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkRelativePositionAnalyzer)
+
WRAP_GGO(clitkTransformLandmarks_GGO_C clitkTransformLandmarks.ggo)
ADD_EXECUTABLE(clitkTransformLandmarks clitkTransformLandmarks.cxx ${clitkTransformLandmarks_GGO_C})
TARGET_LINK_LIBRARIES(clitkTransformLandmarks clitkCommon ${ITK_LIBRARIES})
--- /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 "clitkRelativePositionAnalyzer_ggo.h"
+#include "clitkRelativePositionAnalyzerGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+ // Init command line
+ GGO(clitkRelativePositionAnalyzer, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::RelativePositionAnalyzerGenericFilter<args_info_clitkRelativePositionAnalyzer> 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_FAILURE;
+ }
+
+ return EXIT_SUCCESS;
+} // This is the end, my friend
+//--------------------------------------------------------------------
--- /dev/null
+#File clitkRelativePositionAnalyzer.ggo
+package "clitkRelativePositionAnalyzer"
+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 "support" i "Input mask support" string yes
+option "object" j "Input mask object" string yes
+option "target" t "Input mask target" string yes
+option "output" o "Output image " string yes
+
--- /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 CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H
+#define CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_H
+
+// clitk
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkRelativePositionAnalyzerFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+ template<class ArgsInfoType>
+ class ITK_EXPORT RelativePositionAnalyzerGenericFilter:
+ public ImageToImageGenericFilter<RelativePositionAnalyzerGenericFilter<ArgsInfoType> >
+ {
+ public:
+ //--------------------------------------------------------------------
+ RelativePositionAnalyzerGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ImageToImageGenericFilter<RelativePositionAnalyzerGenericFilter<ArgsInfoType> > Superclass;
+ typedef RelativePositionAnalyzerGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ itkNewMacro(Self);
+ itkTypeMacro(RelativePositionAnalyzerGenericFilter, 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:
+ RelativePositionAnalyzerGenericFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ };// end class
+ //--------------------------------------------------------------------
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkRelativePositionAnalyzerGenericFilter.txx"
+#endif
+
+#endif // #define CLITKRELATIVEPOSITIONANALYZERGENERICFILTER_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::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+RelativePositionAnalyzerGenericFilter():
+ ImageToImageGenericFilter<Self>("RelativePositionAnalyzer")
+{
+ // Default values
+ cmdline_parser_clitkRelativePositionAnalyzer_init(&mArgsInfo);
+ InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+InitializeImageType()
+{
+ ADD_IMAGE_TYPE(Dim, uchar);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+SetArgsInfo(const ArgsInfoType & a)
+{
+ mArgsInfo=a;
+ SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+ if (mArgsInfo.support_given) AddInputFilename(mArgsInfo.support_arg);
+ if (mArgsInfo.object_given) AddInputFilename(mArgsInfo.object_arg);
+ if (mArgsInfo.target_given) AddInputFilename(mArgsInfo.target_arg);
+ if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void clitk::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+
+}
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::RelativePositionAnalyzerGenericFilter<ArgsInfoType>::
+UpdateWithInputImageType()
+{
+ // Reading input
+ typename ImageType::Pointer support = this->template GetInput<ImageType>(0);
+ typename ImageType::Pointer object = this->template GetInput<ImageType>(1);
+ typename ImageType::Pointer target = this->template GetInput<ImageType>(2);
+
+ // Create filter
+ typedef clitk::RelativePositionAnalyzerFilter<ImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+
+ // Set global Options
+ filter->SetInputSupport(support);
+ filter->SetInputObject(object);
+ filter->SetInputTarget(target);
+ 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