autocrop tool

diff --git a/filters/clitkAutoCrop.ggo b/filters/clitkAutoCrop.ggo
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+++ b/filters/clitkAutoCrop.ggo
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+#File clitkAutoCrop.ggo
+package "clitkAutoCrop"
+version "1.0"
+purpose "Crop a mask image"
+
+option "config"                -  "Config file"                  string        no
+option "imagetypes"     -  "Display allowed image types"  flag          off
+option "verbose"        v  "Verbose"                     flag          off
+option "verboseOption"  -  "Display options values"       flag          off
+option "verboseWarningOff" -  "Do not display warning"    flag          off
+
+section "I/O"
+
+option "input"         i       "Input image filename"            string        yes
+option "output"        o       "Output image filename"           string        yes
+
+option "BG"            -       "Background value in input."      double        default="0" no          

diff --git a/filters/clitkAutoCropGenericFilter.h b/filters/clitkAutoCropGenericFilter.h
new file mode 100644 (file)
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+++ b/filters/clitkAutoCropGenericFilter.h
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+/*=========================================================================
+  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 CLITKAUTOCROPGENERICFILTER_H
+#define CLITKAUTOCROPGENERICFILTER_H
+
+// clitk 
+#include "clitkIO.h"
+#include "clitkImageToImageGenericFilter.h"
+#include "clitkAutoCropFilter.h"
+
+//--------------------------------------------------------------------
+namespace clitk 
+{
+
+  template<class ArgsInfoType>
+  class ITK_EXPORT AutoCropGenericFilter:
+    public ImageToImageGenericFilter<AutoCropGenericFilter<ArgsInfoType> >
+  {
+  public:
+    //--------------------------------------------------------------------
+    AutoCropGenericFilter();
+  
+    //--------------------------------------------------------------------
+    typedef AutoCropGenericFilter   Self;
+    typedef ImageToImageGenericFilter<AutoCropGenericFilter<ArgsInfoType> > Superclass;
+    typedef itk::SmartPointer<Self>       Pointer;
+    typedef itk::SmartPointer<const Self> ConstPointer;
+   
+    //--------------------------------------------------------------------
+    itkNewMacro(Self);  
+    itkTypeMacro( AutoCropGenericFilter, LightObject );
+
+    //--------------------------------------------------------------------
+    void SetArgsInfo(const ArgsInfoType & a);
+
+    //--------------------------------------------------------------------
+    // Main function called each time the filter is updated
+    template<class ImageType>  
+    void UpdateWithInputImageType();
+
+  protected:
+    template<unsigned int Dim> void InitializeImageType();
+    ArgsInfoType mArgsInfo;
+
+  };// end class
+  //--------------------------------------------------------------------
+} // end namespace clitk
+
+#ifndef ITK_MANUAL_INSTANTIATION
+#include "clitkAutoCropGenericFilter.txx"
+#endif
+
+#endif // #define CLITKAUTOCROPGENERICFILTER_H

diff --git a/filters/clitkAutoCropGenericFilter.txx b/filters/clitkAutoCropGenericFilter.txx
new file mode 100644 (file)
index 0000000..fcc7384
--- /dev/null
+++ b/filters/clitkAutoCropGenericFilter.txx
@@ -0,0 +1,91 @@
+/*=========================================================================
+  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
+  ======================================================================-====*/
+
+#include "clitkImageCommon.h"
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+clitk::AutoCropGenericFilter<ArgsInfoType>::AutoCropGenericFilter():
+  ImageToImageGenericFilter<Self>("AutoCrop") 
+{
+  // Default values
+  cmdline_parser_clitkAutoCrop_init(&mArgsInfo);
+  //InitializeImageType<2>();
+  InitializeImageType<3>();
+  //InitializeImageType<4>();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<unsigned int Dim>
+void clitk::AutoCropGenericFilter<ArgsInfoType>::InitializeImageType() 
+{  
+  // ADD_DEFAULT_IMAGE_TYPES(Dim);
+  ADD_IMAGE_TYPE(Dim, uchar);
+  ADD_IMAGE_TYPE(Dim, ushort);
+  // ADD_IMAGE_TYPE(Dim, uint);
+ //  ADD_IMAGE_TYPE(Dim, ulong);
+  // ADD_IMAGE_TYPE(Dim, int);
+  // ADD_IMAGE_TYPE(Dim, float);
+}
+//--------------------------------------------------------------------
+  
+
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+void clitk::AutoCropGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a) 
+{
+  mArgsInfo=a;
+  SetIOVerbose(mArgsInfo.verbose_flag);
+  if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
+  if (mArgsInfo.input_given)   AddInputFilename(mArgsInfo.input_arg);
+  if (mArgsInfo.output_given)  AddOutputFilename(mArgsInfo.output_arg);
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//--------------------------------------------------------------------
+template<class ArgsInfoType>
+template<class ImageType>
+void clitk::AutoCropGenericFilter<ArgsInfoType>::UpdateWithInputImageType() 
+{ 
+  // Reading input
+  typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
+
+  // Create filter
+  typedef clitk::AutoCropFilter<ImageType> FilterType;
+  typename FilterType::Pointer filter = FilterType::New();
+    
+  // Set global Options 
+  filter->SetBackgroundValue(mArgsInfo.BG_arg);
+  filter->SetInput(input);
+
+  // Go !
+  filter->Update();
+
+  // Write/Save results
+  typename ImageType::Pointer output = filter->GetOutput();
+  this->template SetNextOutput<ImageType>(output); 
+}
+//--------------------------------------------------------------------
+
+