X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkImageArithmGenericFilter.txx;h=37fa000d3c3e402a1dac421696e070ed8f4f4e90;hb=dad5c078062d820e3fc4c2b6c47b822245487cb9;hp=1dd236f1f9e24fb44abd2f83bee7251e0dfc1f13;hpb=b1f5d6c99d0263700df2ddb2c6d1bf348709cd92;p=clitk.git

diff --git a/tools/clitkImageArithmGenericFilter.txx b/tools/clitkImageArithmGenericFilter.txx
old mode 100755
new mode 100644
index 1dd236f..37fa000
--- a/tools/clitkImageArithmGenericFilter.txx
+++ b/tools/clitkImageArithmGenericFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.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
@@ -14,12 +14,14 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
 #ifndef CLITKIMAGEARITHMGENERICFILTER_TXX
 #define CLITKIMAGEARITHMGENERICFILTER_TXX
 
 #include "clitkImageCommon.h"
 
+#include "itkMinimumMaximumImageCalculator.h"
+
 namespace clitk
 {
 
@@ -63,7 +65,7 @@ void ImageArithmGenericFilter<args_info_type>::SetArgsInfo(const args_info_type
   mArgsInfo=a;
 
   // Set value
-  SetIOVerbose(mArgsInfo.verbose_flag);
+  this->SetIOVerbose(mArgsInfo.verbose_flag);
   mTypeOfOperation = mArgsInfo.operation_arg;
   mDefaultPixelValue = mArgsInfo.pixelValue_arg;
   mScalar = mArgsInfo.scalar_arg;
@@ -71,13 +73,13 @@ void ImageArithmGenericFilter<args_info_type>::SetArgsInfo(const args_info_type
 
   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
 
-  if (mArgsInfo.input1_given) AddInputFilename(mArgsInfo.input1_arg);
+  if (mArgsInfo.input1_given) this->AddInputFilename(mArgsInfo.input1_arg);
   if (mArgsInfo.input2_given) {
     mIsOperationUseASecondImage = true;
-    AddInputFilename(mArgsInfo.input2_arg);
+    this->AddInputFilename(mArgsInfo.input2_arg);
   }
 
-  if (mArgsInfo.output_given) SetOutputFilename(mArgsInfo.output_arg);
+  if (mArgsInfo.output_given) this->SetOutputFilename(mArgsInfo.output_arg);
 
   // Check type of operation (with scalar or with other image)
   if ((mArgsInfo.input2_given) && (mArgsInfo.scalar_given)) {
@@ -110,6 +112,15 @@ void ImageArithmGenericFilter<args_info_type>::UpdateWithInputImageType()
   typename ImageType::Pointer input2 = NULL;
   IteratorType it2;
 
+  // Special case for normalisation
+  if (mTypeOfOperation == 12) {
+    typedef itk::MinimumMaximumImageCalculator<ImageType> MinMaxFilterType;
+    typename MinMaxFilterType::Pointer ff = MinMaxFilterType::New();
+    ff->SetImage(input1);
+    ff->ComputeMaximum();
+    mScalar = ff->GetMaximum();
+    mTypeOfOperation = 11; // divide
+  }
 
   if (mIsOperationUseASecondImage) {
       // Read input2
@@ -117,9 +128,12 @@ void ImageArithmGenericFilter<args_info_type>::UpdateWithInputImageType()
       // Set input image iterator
       it2 = IteratorType(input2, input2->GetLargestPossibleRegion());
       // Check dimension
-      if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input1, input2)) {
-          std::cerr << "* ERROR * the images (input and input2) must have the same size & spacing";
-          return;
+      if (!clitk::HaveSameSize<ImageType, ImageType>(input1, input2)) {
+        itkExceptionMacro(<< "The images (input and input2) must have the same size");
+      }
+      if(!clitk::HaveSameSpacing<ImageType, ImageType>(input1, input2)) {
+        itkWarningMacro(<< "The images (input and input2) do not have the same spacing. "
+                        << "Using first input's information.");
       }
   }
 
@@ -364,9 +378,27 @@ void clitk::ImageArithmGenericFilter<args_info_type>::ComputeImage(Iter1 it, Ite
     }
     break;
   case 10: // exp
-    static const double c = std::pow(2,16);
     while (!it.IsAtEnd()) {
-      ito.Set(PixelTypeDownCast<double, PixelType>((c - (double)it.Get())/mScalar));
+      ito.Set(PixelTypeDownCast<double, PixelType>((0x10000 - (double)it.Get())/mScalar));
+      ++it;
+      ++ito;
+    }
+    break;
+  case 11: // divide
+    while (!it.IsAtEnd()) {
+      ito.Set(PixelTypeDownCast<double, PixelType>((double)it.Get() / mScalar) );
+      ++it;
+      ++ito;
+    }
+    break;
+  case 13: // -ln I/I0
+    while (!it.IsAtEnd()) {
+      if (it.Get() == 0) { // special case for fluence image with 0 value in a pixel -> consider 0.5
+        ito.Set(-log(0.5 / mScalar) );
+      }
+      else {
+        ito.Set(PixelTypeDownCast<double, PixelType>(-log((double)it.Get() / mScalar)) );
+      }
       ++it;
       ++ito;
     }
@@ -378,6 +410,8 @@ void clitk::ImageArithmGenericFilter<args_info_type>::ComputeImage(Iter1 it, Ite
 }
 //--------------------------------------------------------------------
 
+
+
 } // end namespace
 
 #endif  //#define CLITKIMAGEARITHMGENERICFILTER_TXX