From fe84550383bbefaf777d2a27abb86502f1e12745 Mon Sep 17 00:00:00 2001
From: =?utf8?q?Beno=C3=AEt=20Presles?= <benoit.presles@creatis.insa-lyon.fr>
Date: Mon, 2 Jun 2014 16:44:21 +0200
Subject: [PATCH] Agata - why did you delete these tools ?

---
 tools/CMakeLists.txt                            |  9 +++++++++
 tools/clitkBlurImage.ggo                        |  2 +-
 tools/clitkBlurImageGenericFilter.txx           | 17 +++++++++++++----
 tools/clitkImageGradientMagnitude.ggo           |  2 +-
 ...clitkImageGradientMagnitudeGenericFilter.txx |  1 +
 tools/clitkImageLaplacian.ggo                   |  2 +-
 tools/clitkImageLaplacianGenericFilter.txx      |  1 +
 7 files changed, 27 insertions(+), 7 deletions(-)

diff --git a/tools/CMakeLists.txt b/tools/CMakeLists.txt
index 0b12205..08c4a25 100644
--- a/tools/CMakeLists.txt
+++ b/tools/CMakeLists.txt
@@ -305,6 +305,11 @@ IF (CLITK_BUILD_TOOLS)
   TARGET_LINK_LIBRARIES(clitkImageUncertainty clitkCommon ${ITK_LIBRARIES})
   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageUncertainty)
 
+  WRAP_GGO(clitkNormalizeImageFilter_GGO_C clitkNormalizeImageFilter.ggo)
+  ADD_EXECUTABLE(clitkNormalizeImageFilter clitkNormalizeImageFilter.cxx ${clitkNormalizeImageFilter_GGO_C})
+  TARGET_LINK_LIBRARIES(clitkNormalizeImageFilter clitkCommon )
+  SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkNormalizeImageFilter)
+
   WRAP_GGO(clitkImageGradientMagnitude_GGO_C clitkImageGradientMagnitude.ggo)
   ADD_EXECUTABLE(clitkImageGradientMagnitude clitkImageGradientMagnitude.cxx ${clitkImageGradientMagnitude_GGO_C})
   TARGET_LINK_LIBRARIES(clitkImageGradientMagnitude clitkCommon )
@@ -320,6 +325,10 @@ IF (CLITK_BUILD_TOOLS)
   TARGET_LINK_LIBRARIES(clitkImageIntensityWindowing clitkCommon )
   SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkImageIntensityWindowing)
 
+  WRAP_GGO(clitkBlurImage_GGO_C clitkBlurImage.ggo)
+  ADD_EXECUTABLE(clitkBlurImage clitkBlurImage.cxx ${clitkBlurImage_GGO_C})
+  TARGET_LINK_LIBRARIES(clitkBlurImage clitkCommon )
+  SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkBlurImage)
 
   #=========================================================
   option(CLITK_USE_ROOT "Build experimental tools using root" OFF)
diff --git a/tools/clitkBlurImage.ggo b/tools/clitkBlurImage.ggo
index a97becd..cbcd40c 100644
--- a/tools/clitkBlurImage.ggo
+++ b/tools/clitkBlurImage.ggo
@@ -11,4 +11,4 @@ option "imagetypes" 	-   	"Display allowed image types"	  flag		off
 option "input"		i	"Input image filename"		  string  	required
 option "output"    	o   	"Output image filename"		  string 	required
 
-option "variance"       -   	"value of the gaussian variance (multiple values=number of image dimension)"    double  required    multiple
+option "variance"       -   	"value of the gaussian variance (multiple values=number of image dimension) - default=1.0" double  optional  multiple
diff --git a/tools/clitkBlurImageGenericFilter.txx b/tools/clitkBlurImageGenericFilter.txx
index 6868320..307ddb6 100644
--- a/tools/clitkBlurImageGenericFilter.txx
+++ b/tools/clitkBlurImageGenericFilter.txx
@@ -86,15 +86,22 @@ BlurImageGenericFilter<args_info_type>::UpdateWithInputImageType()
 
   //std::cout<<"mArgsInfo.variance_given"<<mArgsInfo.variance_given<<std::endl;
 
-  if (mArgsInfo.variance_given != dim) {
-    std::cerr << "The number of variance parameters must be equal to the image dimension." << std::endl;
-    return;
-  }
 
+  //if (mArgsInfo.variance_given != dim) {
+  //  std::cerr << "The number of variance parameters must be equal to the image dimension." << std::endl;
+  //  return;
+  //}
+
+  if (mArgsInfo.variance_given && mArgsInfo.variance_given == dim) {
   for (unsigned int i = 0; i < dim; i++) {
     //std::cout<<"mArgsInfo.variance_arg[i]"<<mArgsInfo.variance_arg[i]<<std::endl;
     varianceArray[i] = mArgsInfo.variance_arg[i];
   }
+  } else {
+      for (unsigned int i = 0; i < dim; i++) {
+          varianceArray[i] = 1.0;
+      }
+  }
   // Reading input
   typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
 
@@ -109,6 +116,8 @@ BlurImageGenericFilter<args_info_type>::UpdateWithInputImageType()
   gaussianFilter->SetVariance(varianceArray);
   gaussianFilter->Update();
 
+  //std::cout<<"variance value="<<gaussianFilter->GetVariance()<<std::endl;
+
   // Write/Save results
   this->template SetNextOutput<OutputImageType>(gaussianFilter->GetOutput());
 }
diff --git a/tools/clitkImageGradientMagnitude.ggo b/tools/clitkImageGradientMagnitude.ggo
index 3863262..90c2073 100644
--- a/tools/clitkImageGradientMagnitude.ggo
+++ b/tools/clitkImageGradientMagnitude.ggo
@@ -12,4 +12,4 @@ option "input"		i	"Input image filename"		  string  	required
 option "mask"		m	"Mask input image filename"       string  	optional
 option "output"    	o   	"Output image filename"		  string 	required
 option "normalize"      n       "Normalize the output image between 0 and 1"    flag off
-option "gaussian_filter" g      "Gaussian filtering"              flag          off
+option "gaussian_filter" g      "Gaussian filtering - default sigma value=1.0"              flag          off
diff --git a/tools/clitkImageGradientMagnitudeGenericFilter.txx b/tools/clitkImageGradientMagnitudeGenericFilter.txx
index 19bf823..1df5601 100644
--- a/tools/clitkImageGradientMagnitudeGenericFilter.txx
+++ b/tools/clitkImageGradientMagnitudeGenericFilter.txx
@@ -141,6 +141,7 @@ namespace clitk
             typename GradientMagnitudeImageFilterType::Pointer gradientFilter=GradientMagnitudeImageFilterType::New();
             gradientFilter->SetInput(input);
             gradientFilter->Update();
+            //std::cout<<"sigma value="<<gradientFilter->GetSigma()<<std::endl;
             outputGradientFilter = gradientFilter->GetOutput();
         }
         // Set iterator
diff --git a/tools/clitkImageLaplacian.ggo b/tools/clitkImageLaplacian.ggo
index 4ba1afd..43b70d1 100644
--- a/tools/clitkImageLaplacian.ggo
+++ b/tools/clitkImageLaplacian.ggo
@@ -12,4 +12,4 @@ option "input"		i	"Input image filename"		  string  	required
 option "mask"		m	"Mask input image filename"       string  	optional
 option "output"    	o   	"Output image filename"		  string 	required
 option "normalize"      n       "Normalize the output image between 0 and 1"    flag off
-option "gaussian_filter" g      "Gaussian filtering"              flag          on
+option "gaussian_filter" g      "Gaussian filtering - default sigma value=1.0"              flag          on
diff --git a/tools/clitkImageLaplacianGenericFilter.txx b/tools/clitkImageLaplacianGenericFilter.txx
index 940e9fc..ba36d18 100644
--- a/tools/clitkImageLaplacianGenericFilter.txx
+++ b/tools/clitkImageLaplacianGenericFilter.txx
@@ -143,6 +143,7 @@ ImageLaplacianGenericFilter<args_info_type>::UpdateWithInputImageType()
         typename LaplacianImageFilterType::Pointer laplacianFilter=LaplacianImageFilterType::New();
         laplacianFilter->SetInput(castFilter->GetOutput());
         laplacianFilter->Update();
+        //std::cout<<"sigma value="<<laplacianFilter->GetSigma()<<std::endl;
         outputLaplacianFilter = laplacianFilter->GetOutput();
     }
     // Set iterator
-- 
2.47.1