--- /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
+===========================================================================**/
+
+/* =================================================
+ * @file clitkImageIntensityWindowingGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date 29 June 2029
+ *
+ * @brief ImageIntensityWindowing an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkImageIntensityWindowing_ggo.h"
+#include "clitkImageIntensityWindowingGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+ // Init command line
+ GGO(clitkImageIntensityWindowing, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::ImageIntensityWindowingGenericFilter<args_info_clitkImageIntensityWindowing> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
--- /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 CLITKImageIntensityWindowingGENERICFILTER_H
+#define CLITKImageIntensityWindowingGENERICFILTER_H
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+template<class args_info_type>
+class ITK_EXPORT ImageIntensityWindowingGenericFilter:
+ public ImageToImageGenericFilter<ImageIntensityWindowingGenericFilter<args_info_type> >
+{
+
+public:
+
+ //--------------------------------------------------------------------
+ ImageIntensityWindowingGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef ImageIntensityWindowingGenericFilter Self;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ //--------------------------------------------------------------------
+ // Method for creation through the object factory
+ // and Run-time type information (and related methods)
+ itkNewMacro(Self);
+ itkTypeMacro(ImageIntensityWindowingGenericFilter, LightObject);
+
+ //--------------------------------------------------------------------
+ void SetArgsInfo(const args_info_type & a);
+
+ //--------------------------------------------------------------------
+ // Main function called each time the filter is updated
+ template<class InputImageType>
+ void UpdateWithInputImageType();
+
+protected:
+ template<unsigned int Dim> void InitializeImageType();
+ args_info_type mArgsInfo;
+
+}; // end class
+//--------------------------------------------------------------------
+
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkImageIntensityWindowingGenericFilter.txx"
+#endif
+
+#endif // #define clitkImageIntensityWindowingGenericFilter_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
+===========================================================================**/
+#ifndef clitkImageIntensityWindowingGenericFilter_txx
+#define clitkImageIntensityWindowingGenericFilter_txx
+
+/* =================================================
+ * @file clitkImageIntensityWindowingGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date 29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkIntensityWindowingImageFilter.h"
+#include "itkLabelStatisticsImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+ImageIntensityWindowingGenericFilter<args_info_type>::ImageIntensityWindowingGenericFilter():
+ ImageToImageGenericFilter<Self>("ImageIntensityWindowing")
+{
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dim>
+void ImageIntensityWindowingGenericFilter<args_info_type>::InitializeImageType()
+{
+ ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void ImageIntensityWindowingGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
+{
+ mArgsInfo=a;
+ this->SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ this->SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ this->SetOutputFilename(mArgsInfo.output_arg);
+ }
+ if (mArgsInfo.mask_given) {
+ this->AddInputFilename(mArgsInfo.mask_arg);
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class InputImageType>
+void
+ImageIntensityWindowingGenericFilter<args_info_type>::UpdateWithInputImageType()
+{
+
+ // Main filter
+ typedef typename InputImageType::PixelType InputPixelType;
+ typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
+ typedef itk::Image<unsigned char, InputImageType::ImageDimension> MaskImageType;
+
+ // Reading input
+ typename OutputImageType::Pointer input = this->template GetInput<OutputImageType>(0);
+
+ typename MaskImageType::Pointer mask = NULL;
+ if(mArgsInfo.mask_given) {
+ mask = this->template GetInput<MaskImageType>(1);
+ }
+ else {
+ mask = MaskImageType::New();
+ mask->SetRegions(input->GetLargestPossibleRegion());
+ mask->SetOrigin(input->GetOrigin());
+ mask->SetSpacing(input->GetSpacing());
+ mask->Allocate();
+ mask->FillBuffer(1);
+ }
+ // Set mask iterator
+ typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
+ IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
+ //
+ typedef itk::LabelStatisticsImageFilter< OutputImageType, MaskImageType > LabelStatisticsImageFilterType;
+ typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
+ labelStatisticsImageFilter->SetLabelInput( mask );
+ labelStatisticsImageFilter->SetInput(input);
+ labelStatisticsImageFilter->Update();
+ float maxImg = labelStatisticsImageFilter->GetMaximum(1);
+ //std::cout << "maxImg: " << maxImg << std::endl;
+ // Filter
+ typedef itk::IntensityWindowingImageFilter <OutputImageType, OutputImageType> IntensityWindowingImageFilterType;
+ typename IntensityWindowingImageFilterType::Pointer filter = IntensityWindowingImageFilterType::New();
+ filter->SetInput(input);
+ filter->SetWindowMinimum(0.0);
+ filter->SetWindowMaximum(maxImg);
+ filter->SetOutputMinimum(0.0);
+ filter->SetOutputMaximum(1.0);
+ filter->Update();
+
+ // Set iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorType;
+ IteratorType it(filter->GetOutput(), filter->GetOutput()->GetLargestPossibleRegion());
+ //A little bit strange to do that but I think I need to do it.
+ // Create output image
+ typename OutputImageType::Pointer outputImage = OutputImageType::New();
+ outputImage->SetRegions(filter->GetOutput()->GetLargestPossibleRegion());
+ outputImage->SetOrigin(filter->GetOutput()->GetOrigin());
+ outputImage->SetSpacing(filter->GetOutput()->GetSpacing());
+ outputImage->Allocate();
+ outputImage->FillBuffer(-100.0);
+ // Set output iterator
+ typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
+ IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
+
+ it.GoToBegin();
+ ito.GoToBegin();
+ itm.GoToBegin();
+
+ while (!ito.IsAtEnd()) {
+ if(itm.Get() > 0) {
+ ito.Set(it.Get());
+ }
+ ++it;
+ ++ito;
+ ++itm;
+ }
+
+ // Write/Save results
+ this->template SetNextOutput<OutputImageType>(outputImage);
+}
+//--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkImageIntensityWindowingGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff