gradient magnitude tool

diff --git a/make_new_tool.sh b/make_new_tool.sh
old mode 100644 (file)
new mode 100755 (executable)

diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 7ab7971afd2bc79d5311893f8a7963898cbf859f..339031f79ab818d1f9f8b744c8767c2e2f88e258 100644 (file)
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -304,6 +304,12 @@ IF (CLITK_BUILD_TOOLS)
   TARGET_LINK_LIBRARIES(clitkImageUncertainty clitkCommon ${ITK_LIBRARIES})
   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageUncertainty)
 
+  WRAP_GGO(clitkImageGradientMagnitude_GGO_C clitkImageGradientMagnitude.ggo)
+  ADD_EXECUTABLE(clitkImageGradientMagnitude clitkImageGradientMagnitude.cxx ${clitkImageGradientMagnitude_GGO_C})
+  TARGET_LINK_LIBRARIES(clitkImageGradientMagnitude clitkCommon )
+  SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageGradientMagnitude)
+
+
   #=========================================================
   option(CLITK_USE_ROOT "Build experimental tools using root" OFF)
   if (CLITK_USE_ROOT)

diff --git a/tools/clitkImageGradientMagnitude.cxx b/tools/clitkImageGradientMagnitude.cxx
new file mode 100644 (file)
index 0000000..7371bf0
--- /dev/null
+++ b/tools/clitkImageGradientMagnitude.cxx
@@ -0,0 +1,50 @@
+/*=========================================================================
+  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   clitkImageGradientMagnitudeGenericFilter.txx
+ * @author xxx <xxx@creatis.insa-lyon.fr>
+ * @date   29 June 2029
+ *
+ * @brief ImageGradientMagnitude an image
+ *
+ ===================================================*/
+
+// clitk
+#include "clitkImageGradientMagnitude_ggo.h"
+#include "clitkImageGradientMagnitudeGenericFilter.h"
+
+//--------------------------------------------------------------------
+int main(int argc, char * argv[])
+{
+
+  // Init command line
+  GGO(clitkImageGradientMagnitude, args_info);
+  CLITK_INIT;
+
+  // Filter
+  typedef clitk::ImageGradientMagnitudeGenericFilter<args_info_clitkImageGradientMagnitude> FilterType;
+  FilterType::Pointer filter = FilterType::New();
+
+  filter->SetArgsInfo(args_info);
+  filter->Update();
+
+  return EXIT_SUCCESS;
+}// end main
+
+//--------------------------------------------------------------------

diff --git a/tools/clitkImageGradientMagnitude.ggo b/tools/clitkImageGradientMagnitude.ggo
new file mode 100644 (file)
index 0000000..ae0d84f
--- /dev/null
+++ b/tools/clitkImageGradientMagnitude.ggo
@@ -0,0 +1,12 @@
+#File clitkImageGradientMagnitude.ggo
+package "clitkImageGradientMagnitude"
+version "1.0"
+purpose ""
+
+option "config"                -       "Config file"                     string        optional
+option "verbose"       v       "Verbose"                         flag          off
+
+option "imagetypes"    -       "Display allowed image types"     flag          off
+
+option "input"         i       "Input image filename"            string        required
+option "output"        o       "Output image filename"           string        required

diff --git a/tools/clitkImageGradientMagnitudeGenericFilter.h b/tools/clitkImageGradientMagnitudeGenericFilter.h
new file mode 100644 (file)
index 0000000..9d2b5f5
--- /dev/null
+++ b/tools/clitkImageGradientMagnitudeGenericFilter.h
@@ -0,0 +1,69 @@
+/*=========================================================================
+  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 CLITKImageGradientMagnitudeGENERICFILTER_H
+#define CLITKImageGradientMagnitudeGENERICFILTER_H
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk
+{
+
+template<class args_info_type>
+class ITK_EXPORT ImageGradientMagnitudeGenericFilter:
+        public ImageToImageGenericFilter<ImageGradientMagnitudeGenericFilter<args_info_type> >
+{
+
+public:
+
+    //--------------------------------------------------------------------
+    ImageGradientMagnitudeGenericFilter();
+
+    //--------------------------------------------------------------------
+    typedef ImageGradientMagnitudeGenericFilter         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(ImageGradientMagnitudeGenericFilter, 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 "clitkImageGradientMagnitudeGenericFilter.txx"
+#endif
+
+#endif // #define clitkImageGradientMagnitudeGenericFilter_h

diff --git a/tools/clitkImageGradientMagnitudeGenericFilter.txx b/tools/clitkImageGradientMagnitudeGenericFilter.txx
new file mode 100644 (file)
index 0000000..988aecb
--- /dev/null
+++ b/tools/clitkImageGradientMagnitudeGenericFilter.txx
@@ -0,0 +1,107 @@
+/*=========================================================================
+  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 clitkImageGradientMagnitudeGenericFilter_txx
+#define clitkImageGradientMagnitudeGenericFilter_txx
+
+/* =================================================
+ * @file   clitkImageGradientMagnitudeGenericFilter.txx
+ * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
+ * @date   29 june 2009
+ *
+ * @brief
+ *
+ ===================================================*/
+
+// itk include
+#include "itkGradientMagnitudeImageFilter.h"
+#include "itkMaskImageFilter.h"
+#include "itkMaskNegatedImageFilter.h"
+#include <clitkCommon.h>
+
+namespace clitk
+{
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+ImageGradientMagnitudeGenericFilter<args_info_type>::ImageGradientMagnitudeGenericFilter():
+  ImageToImageGenericFilter<Self>("ImageGradientMagnitude")
+{
+  InitializeImageType<2>();
+  InitializeImageType<3>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dim>
+void ImageGradientMagnitudeGenericFilter<args_info_type>::InitializeImageType()
+{
+  ADD_DEFAULT_IMAGE_TYPES(Dim);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class args_info_type>
+void ImageGradientMagnitudeGenericFilter<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);
+  }
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class args_info_type>
+template<class InputImageType>
+void
+ImageGradientMagnitudeGenericFilter<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<float, InputImageType::ImageDimension> OutputImageType;
+
+  // Filter
+  typedef itk::GradientMagnitudeImageFilter<InputImageType, OutputImageType> GradientMagnitudeImageFilterType;
+  typename GradientMagnitudeImageFilterType::Pointer gradientFilter=GradientMagnitudeImageFilterType::New();
+  gradientFilter->SetInput(input);
+  gradientFilter->Update();
+
+  typename OutputImageType::Pointer outputImage = gradientFilter->GetOutput();
+  this->template SetNextOutput<OutputImageType>(outputImage);
+}
+//--------------------------------------------------------------------
+
+
+}//end clitk
+
+#endif //#define clitkImageGradientMagnitudeGenericFilter_txx