MESSAGE(FATAL_ERROR
"Cannot build without ITK. Please set ITK_DIR.")
ENDIF(ITK_FOUND)
+
#=========================================================
IF(CLITK_BUILD_VV)
FIND_PACKAGE(VTK)
clitkVFResampleGenericFilter.cxx
clitkBinarizeImageGenericFilter.cxx
clitkBinarizeImage_ggo.c
- clitkMedianImageGenericFilter.cxx
+ clitkFooImage_ggo.c
+ clitkMedianImageGenericFilter.cxx
)
ADD_LIBRARY(clitkFilters STATIC ${clitkFilters_SRC})
option "fg" - "Foreground (FG) or 'inside' value" double no default="1"
option "bg" - "Background (BG) or 'ouside' value" double no default="0"
-option "mode" - "Use FG and/or BG values (if FG, the BG is replaced by the input image values)" values="FG","BG","both" default="both" no
+option "mode" - "Use FG and/or BG values (if FG, the BG is replaced by the input image values)" values="FG","BG","both" default="both" required
--- /dev/null
+#File clitkFooImage.ggo
+package "clitkFooImage"
+version "1.0"
+purpose ""
+
+option "config" - "Config file" string no
+option "verbose" v "Verbose" flag off
+
+option "imagetypes" - "Display allowed image types" flag off
+
+option "input" i "Input image filename" string yes
+option "output" o "Output image filename" string yes
+option "lower" l "Lower intensity (default=min), fg is greater than this value" double no
+option "upper" u "Upper intensity (default=max), fg is lower than this value" double no
+
+option "fg" - "Foreground (FG) or 'inside' value" double no default="1"
+ option "bg" - "Background (BG) or 'ouside' value" double no default="0"
+ option "mode" - "Use FG and/or BG values (if FG, the BG is replaced by the input image values)" values="FG","BG","both" default="both" 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://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 CLITKFooIMAGEGENERICFILTER_H
+#define CLITKFooIMAGEGENERICFILTER_H
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+template<class args_info_type>
+class ITK_EXPORT FooImageGenericFilter:
+ public ImageToImageGenericFilter<FooImageGenericFilter<args_info_type> >
+{
+
+public:
+
+ //--------------------------------------------------------------------
+ FooImageGenericFilter();
+
+ //--------------------------------------------------------------------
+ typedef FooImageGenericFilter 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(FooImageGenericFilter, 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 "clitkFooImageGenericFilter.txx"
+#endif
+
+#endif // #define clitkFooImageGenericFilter_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://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 clitkFooImageGenericFilter_txx
+#define clitkFooImageGenericFilter_txx
+
+/* =================================================
+ * @file clitkFooImageGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date 29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkBinaryThresholdImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+#include <tiff.h>
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+FooImageGenericFilter<args_info_type>::FooImageGenericFilter():
+ ImageToImageGenericFilter<Self>("FooImage") {
+ InitializeImageType<2>();
+ InitializeImageType<3>();
+ InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dim>
+void FooImageGenericFilter<args_info_type>::InitializeImageType() {
+ ADD_IMAGE_TYPE(Dim, char);
+ ADD_IMAGE_TYPE(Dim, uchar);
+ ADD_IMAGE_TYPE(Dim, short);
+ ADD_IMAGE_TYPE(Dim, ushort);
+ ADD_IMAGE_TYPE(Dim, int);
+ ADD_IMAGE_TYPE(Dim, uint16);
+ ADD_IMAGE_TYPE(Dim, float);
+ ADD_IMAGE_TYPE(Dim, double);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void FooImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
+ mArgsInfo=a;
+ SetIOVerbose(mArgsInfo.verbose_flag);
+ if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+
+ if (mArgsInfo.input_given) {
+ SetInputFilename(mArgsInfo.input_arg);
+ }
+ if (mArgsInfo.output_given) {
+ SetOutputFilename(mArgsInfo.output_arg);
+ }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class InputImageType>
+void
+FooImageGenericFilter<args_info_type>::UpdateWithInputImageType()
+{
+
+ // Reading input
+ typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
+
+ // Main filter
+ typedef typename InputImageType::PixelType PixelType;
+ typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
+
+ // Filter
+ typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
+ typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
+ thresholdFilter->SetInput(input);
+ thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
+
+ if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
+ if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
+
+ if (mArgsInfo.mode_arg == std::string("both")) {
+ thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
+ thresholdFilter->Update();
+
+ typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
+ this->template SetNextOutput<OutputImageType>(outputImage);
+ }
+ else {
+ typename InputImageType::Pointer outputImage;
+ thresholdFilter->SetOutsideValue(0);
+ if (mArgsInfo.mode_arg == std::string("BG")) {
+ typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
+ typename maskFilterType::Pointer maskFilter = maskFilterType::New();
+ maskFilter->SetInput1(input);
+ maskFilter->SetInput2(thresholdFilter->GetOutput());
+ maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
+ maskFilter->Update();
+ outputImage = maskFilter->GetOutput();
+ }
+ else {
+ typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
+ typename maskFilterType::Pointer maskFilter = maskFilterType::New();
+ maskFilter->SetInput1(input);
+ maskFilter->SetInput2(thresholdFilter->GetOutput());
+ maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
+ maskFilter->Update();
+ outputImage = maskFilter->GetOutput();
+ }
+ // Write/Save results
+ this->template SetNextOutput<InputImageType>(outputImage);
+ }
+}
+//--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkFooImageGenericFilter_txx
--- /dev/null
+#!/bin/bash
+
+if [ $# -ne 1 ]
+then
+ echo "Usage: `basename $0` ToolName"
+ exit 1
+fi
+
+find filters tools -name "clitkFooImage*" |
+while read i
+do
+ cp $i ${i/FooImage/$1}
+ sed -i "s/FooImage/$1/ig" ${i/FooImage/$1}
+done
+echo "Done!"
+echo "Don't forget to add your new tool to the various CMakeLists.txt files."
--- /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://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
+======================================================================-====*/
+
+/* =================================================
+ * @file clitkFooImageGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date 29 June 2029
+ *
+ * @brief FooImage an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkFooImage_ggo.h"
+#include "clitkFooImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[]) {
+
+ // Init command line
+ GGO(clitkFooImage, args_info);
+ CLITK_INIT;
+
+ // Filter
+ typedef clitk::FooImageGenericFilter<args_info_clitkFooImage> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+
+ filter->SetArgsInfo(args_info);
+ filter->Update();
+
+ return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------
#ITKIO
clitkCommon
clitkDicomRTStruct
- #clitkGGO
clitkFilters
${QT_QTCORE_LIBRARY}
${QT_QTGUI_LIBRARY}
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff