--- /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 CLITKLABELIMAGEOVERLAPMEASUREFILTER_H
+#define CLITKRELATIVEPOSITIONANALYZERFILTER_H
+
+// clitk
+#include "clitkFilterBase.h"
+#include "clitkCropLikeImageFilter.h"
+#include "clitkSegmentationUtils.h"
+// #include "itkLabelOverlapMeasuresImageFilter.h"
+
+// itk
+#include <itkImageToImageFilter.h>
+#include <itkLabelStatisticsImageFilter.h>
+
+namespace clitk {
+
+ //--------------------------------------------------------------------
+ /*
+ Analyze the relative position of a Target (mask image) according
+ to some Object, in a given Support. Indicate the main important
+ position of this Target according the Object.
+ */
+ //--------------------------------------------------------------------
+
+ template <class ImageType>
+ class LabelImageOverlapMeasureFilter:
+ public virtual FilterBase,
+ public itk::ImageToImageFilter<ImageType, ImageType>
+ {
+
+ public:
+ /** Standard class typedefs. */
+ typedef itk::ImageToImageFilter<ImageType, ImageType> Superclass;
+ typedef LabelImageOverlapMeasureFilter<ImageType> 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(LabelImageOverlapMeasureFilter, 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);
+ FILTERBASE_INIT;
+
+ // Options
+ itkGetConstMacro(BackgroundValue, PixelType);
+ itkSetMacro(BackgroundValue, PixelType);
+
+ itkGetConstMacro(Label1, PixelType);
+ itkSetMacro(Label1, PixelType);
+
+ itkGetConstMacro(Label2, PixelType);
+ itkSetMacro(Label2, PixelType);
+
+ // I dont want to verify inputs information
+ virtual void VerifyInputInformation() { }
+
+ protected:
+ LabelImageOverlapMeasureFilter();
+ virtual ~LabelImageOverlapMeasureFilter() {}
+
+ PixelType m_BackgroundValue;
+ PixelType m_Label1;
+ PixelType m_Label2;
+ ImagePointer m_Input1;
+ ImagePointer m_Input2;
+
+ virtual void GenerateOutputInformation();
+ virtual void GenerateInputRequestedRegion();
+ virtual void GenerateData();
+
+ private:
+ LabelImageOverlapMeasureFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ }; // end class
+ //--------------------------------------------------------------------
+
+} // end namespace clitk
+//--------------------------------------------------------------------
+
+#include "clitkLabelImageOverlapMeasureFilter.txx"
+
+#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::LabelImageOverlapMeasureFilter<ImageType>::
+LabelImageOverlapMeasureFilter():
+ clitk::FilterBase(),
+ itk::ImageToImageFilter<ImageType, ImageType>()
+{
+ this->SetNumberOfRequiredInputs(2);
+ SetLabel1(1);
+ SetLabel2(1);
+ SetBackgroundValue(0);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::LabelImageOverlapMeasureFilter<ImageType>::
+GenerateOutputInformation()
+{
+ // DD("GenerateOutputInformation");
+ //ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+ // ImagePointer outputImage = this->GetOutput(0);
+ // outputImage->SetRegions(outputImage->GetLargestPossibleRegion());
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::LabelImageOverlapMeasureFilter<ImageType>::
+GenerateInputRequestedRegion()
+{
+ // DD("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));
+ ImagePointer input2 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
+ input1->SetRequestedRegion(input1->GetLargestPossibleRegion());
+ input2->SetRequestedRegion(input2->GetLargestPossibleRegion());
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::LabelImageOverlapMeasureFilter<ImageType>::
+GenerateData()
+{
+ // DD("GenerateData");
+
+ // Get input pointer
+ m_Input1 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
+ m_Input2 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
+ static const unsigned int dim = ImageType::ImageDimension;
+
+ // Compute union of bounding boxes
+ typedef itk::BoundingBox<unsigned long, dim> BBType;
+ typename BBType::Pointer bb1 = BBType::New();
+ ComputeBBFromImageRegion<ImageType>(m_Input1, m_Input1->GetLargestPossibleRegion(), bb1);
+ typename BBType::Pointer bb2 = BBType::New();
+ ComputeBBFromImageRegion<ImageType>(m_Input2, m_Input2->GetLargestPossibleRegion(), bb2);
+ typename BBType::Pointer bbo = BBType::New();
+ ComputeBBUnion<dim>(bbo, bb1, bb2);
+
+ // Resize like the union
+ ImagePointer input1 = clitk::ResizeImageLike<ImageType>(m_Input1, bbo, GetBackgroundValue());
+ ImagePointer input2 = clitk::ResizeImageLike<ImageType>(m_Input2, bbo, GetBackgroundValue());
+
+ // Compute overlap image
+ ImagePointer image_union = clitk::Clone<ImageType>(input1);
+ ImagePointer image_intersection = clitk::Clone<ImageType>(input1);
+ clitk::Or<ImageType>(image_union, input2, GetBackgroundValue());
+ clitk::And<ImageType>(image_intersection, input2, GetBackgroundValue());
+
+ writeImage<ImageType>(image_union, "union.mha");
+ writeImage<ImageType>(image_intersection, "intersection.mha");
+
+ // Compute size
+ typedef itk::LabelStatisticsImageFilter<ImageType, ImageType> StatFilterType;
+ typename StatFilterType::Pointer statFilter = StatFilterType::New();
+ statFilter->SetInput(image_union);
+ statFilter->SetLabelInput(image_union);
+ statFilter->Update();
+ int u = statFilter->GetCount(GetLabel1());
+
+ statFilter->SetInput(image_intersection);
+ statFilter->SetLabelInput(image_intersection);
+ statFilter->Update();
+ int inter = statFilter->GetCount(GetLabel1());
+
+ statFilter->SetInput(m_Input1);
+ statFilter->SetLabelInput(m_Input1);
+ statFilter->Update();
+ int in1 = statFilter->GetCount(GetLabel1());
+
+ statFilter->SetInput(m_Input2);
+ statFilter->SetLabelInput(m_Input2);
+ statFilter->Update();
+ int in2 = statFilter->GetCount(GetLabel1());
+
+ std::cout << in1 << " " << in2 << " " << inter << " " << u << " " << (double)inter/(double)u << std::endl;
+}
+//--------------------------------------------------------------------
+
--- /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 "clitkIO.h"
+#include "clitkLabelImageOverlapMeasure_ggo.h"
+#include "clitkLabelImageOverlapMeasureGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+ // Init command line
+ GGO(clitkLabelImageOverlapMeasure, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::LabelImageOverlapMeasureGenericFilter<args_info_clitkLabelImageOverlapMeasure> 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 clitkLabelImageOverlapMeasure.ggo
+package "clitkLabelImageOverlapMeasure"
+version "1.0"
+purpose "Compute Dice and other coefficients between label images"
+
+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"
+option "input1" i "Input mask 1" string yes
+option "input2" j "Input mask 2" string yes
+
+option "label1" l "Label in input1" int no default="1"
+option "label2" m "Label in input2" int no default="1"
+option "BG" b "Background value" int no default="0"
+
+
+
+
--- /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 CLITKLABELIMAGEOVERLAPMEASUREGENERICFILTER_H
+#define CLITKLABELIMAGEOVERLAPMEASUREGENERICFILTER_H
+
+// clitk
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkLabelImageOverlapMeasureFilter.h"
+#include "clitkBoundingBoxUtils.h"
+#include "clitkCropLikeImageFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+ template<class ArgsInfoType>
+ class ITK_EXPORT LabelImageOverlapMeasureGenericFilter:
+ public ImageToImageGenericFilter<LabelImageOverlapMeasureGenericFilter<ArgsInfoType> >
+ {
+ public:
+ //--------------------------------------------------------------------
+ LabelImageOverlapMeasureGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ImageToImageGenericFilter<LabelImageOverlapMeasureGenericFilter<ArgsInfoType> > Superclass;
+ typedef LabelImageOverlapMeasureGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ itkNewMacro(Self);
+ itkTypeMacro(LabelImageOverlapMeasureGenericFilter, 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:
+ LabelImageOverlapMeasureGenericFilter(const Self&); //purposely not implemented
+ void operator=(const Self&); //purposely not implemented
+
+ };// end class
+ //--------------------------------------------------------------------
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkLabelImageOverlapMeasureGenericFilter.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::LabelImageOverlapMeasureGenericFilter<ArgsInfoType>::
+LabelImageOverlapMeasureGenericFilter():
+ ImageToImageGenericFilter<Self>("LabelImageOverlapMeasure")
+{
+ // Default values
+ cmdline_parser_clitkLabelImageOverlapMeasure_init(&mArgsInfo);
+ //InitializeImageType<2>();
+ InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::LabelImageOverlapMeasureGenericFilter<ArgsInfoType>::
+InitializeImageType()
+{
+ ADD_IMAGE_TYPE(Dim, uchar);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::LabelImageOverlapMeasureGenericFilter<ArgsInfoType>::
+SetArgsInfo(const ArgsInfoType & a)
+{
+ mArgsInfo=a;
+ SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+ if (mArgsInfo.input1_given) AddInputFilename(mArgsInfo.input1_arg);
+ if (mArgsInfo.input2_given) AddInputFilename(mArgsInfo.input2_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class FilterType>
+void clitk::LabelImageOverlapMeasureGenericFilter<ArgsInfoType>::
+SetOptionsFromArgsInfoToFilter(FilterType * f)
+{
+ f->SetLabel1(mArgsInfo.label1_arg);
+ f->SetLabel2(mArgsInfo.label2_arg);
+}
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::LabelImageOverlapMeasureGenericFilter<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::LabelImageOverlapMeasureFilter<ImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+
+ // Set global Options
+ filter->SetInput(0, input1);
+ filter->SetInput(1, input2);
+ 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