Merge pull request #393 from kerautret/FixITK2vol

Fix itk2vol (issue #390)
DGtal-team · Apr 7, 2021 · dda16f1 · dda16f1
2 parents 33480a8 + 8ee04a6
commit dda16f1
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Showing 4 changed files with 38 additions and 22 deletions.
diff --git a/.travis/install_deps_macos.sh b/.travis/install_deps_macos.sh
@@ -3,6 +3,9 @@
 #
 # Note: gmp and boost already installed
 #
+brew install ccache
+export PATH="/usr/local/opt/ccache/libexec:$PATH"
+
 brew update > brew.log
 #brew install qt5 doxygen homebrew/science/hdf5 graphviz graphicsmagick fftw eigen
 brew install qt5 graphicsmagick fftw eigen

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -69,6 +69,13 @@ SET(VERSION ${DGtalTools_VERSION_MAJOR}.${DGtalTools_VERSION_MINOR}.${DGtalTools
 
 
 
+#-----------------------------------------------------------------------------
+# ITK setting
+#-----------------------------------------------------------------------------
+if (  WITH_ITK )
+    include(${ITK_USE_FILE})
+ENDIF( WITH_ITK )
+
 
 # -----------------------------------------------------------------------------
 # Documentation

diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,9 +1,16 @@
 # DGtalTools 1.2
 - *global*
+  - Fix itk2vol and fix ITK cmake configuaration that was making wrong the ITK image read.
+  (Bertrand Kerautret [#393](https://github.com/DGtal-team/DGtalTools/pull/393))
+<<<<<<< HEAD
 
+
+
+
+=======
   - Travis: Fix old default osx_image with xcode12.2 and remove non used boost
     cmake references. (Bertrand Kerautret [#394](https://github.com/DGtal-team/DGtalTools/pull/394)) 
-    
+>>>>>>> bf6f26204de31698d991a81f19627f225426d146
 
 # DGtalTools 1.1
 

diff --git a/converters/itk2vol.cpp b/converters/itk2vol.cpp
@@ -73,6 +73,7 @@ using namespace DGtal;
 
 */
 
+typedef ImageContainerBySTLVector < Z3i::Domain, unsigned char > Image3DChar;
 
 
 template<typename TImage, typename TImageMask>
@@ -90,12 +91,22 @@ applyMaskImage( TImage &imageInput,  const  TImageMask &maskImage,
 
 }
 
+template<typename TImage, typename TRescale>
+void
+exportImageUCHAR(TImage img, const std::string resName, TRescale rScale)
+{
+  Image3DChar res ( img.domain() );
+
+  for (const auto p: img.domain() ) {
+    res.setValue(p, rScale(img(p)));
+  }
+  DGtal::GenericWriter<Image3DChar, 3, unsigned char>::exportFile(resName, res);
+}
 
 
 
 int main( int argc, char** argv )
 {
-  typedef ImageContainerBySTLVector < Z3i::Domain, unsigned char > Image3DChar;
   typedef ImageContainerBySTLVector < Z3i::Domain,  double > Image3D_D;
   typedef ImageContainerBySTLVector < Z3i::Domain,  int > Image3D_I;
 
@@ -119,7 +130,7 @@ int main( int argc, char** argv )
    app.add_option("-r,--maskRemoveLabel", maskRemoveLabel,"Change the label value that defines the part of input image to be removed by the option --maskImage." );
    app.add_option("--inputMin", inputMin, "set minimum density threshold on Hounsfield scale.");
    app.add_option("--inputMax", inputMax, "set maximum density threshold on Hounsfield scale.");
-   app.add_option("-t,--inputType", inputType, "to sepcify the input image type (int or double).")
+   app.add_option("-t,--inputType", inputType, "to specify the input image type (int or double).")
      -> check(CLI::IsMember({"int", "double"}));
 
    app.get_formatter()->column_width(40);
@@ -129,39 +140,27 @@ int main( int argc, char** argv )
 
   if (inputType == "double") {
       typedef DGtal::functors::Rescaling<double ,unsigned char > RescalFCT;
-      trace.info() << "Reading input input file " << inputFileName ; 
-      Image3D_D inputImage = ITKReader< Image3D_D  >::importITK(inputFileName);
+      trace.info() << "Reading input file (of type double)" << inputFileName ;
+      Image3D_D inputImage = ITKReader< Image3D_D  >::importITK(inputFileName, true);
       trace.info() << " [done] " << std::endl ; 
       trace.info() << " converting into vol file... " ; 
       if ( inputMask != "")
       {
         Image3D_I maskImage = ITKReader< Image3D_I  >::importITK(inputMask);
         applyMaskImage(inputImage, maskImage, maskRemoveLabel);
       }
-
       RescalFCT rescaleCustom(inputMin, inputMax, 0, 255);
-      DGtal::GenericWriter<Image3D_D, 3, unsigned char, RescalFCT>::exportFile(outputFileName,
-                                                                               inputImage,
-                                                                               "UInt8Array3D",
-                                                                               rescaleCustom);
+      exportImageUCHAR(inputImage,outputFileName, rescaleCustom );
   }else {
      typedef DGtal::functors::Rescaling<int ,unsigned char > RescalFCT;
-      trace.info() << "Reading input input file " << inputFileName ; 
-      Image3D_I inputImage = ITKReader< Image3D_I  >::importITK(inputFileName);
+      trace.info() << "Reading input file (of type int) " << inputFileName ;
+      Image3D_I inputImage = ITKReader< Image3D_I  >::importITK(inputFileName, true);
       trace.info() << " [done] " << std::endl ; 
       trace.info() << " converting into vol file... " ; 
       RescalFCT rescaleCustom(inputMin, inputMax, 0, 255);
-      if (inputMask != "")
-      {
-        Image3D_I maskImage = ITKReader< Image3D_I  >::importITK(inputMask);
-        applyMaskImage(inputImage, maskImage, maskRemoveLabel);
+      exportImageUCHAR(inputImage,outputFileName, rescaleCustom );
+
       }
-
-      DGtal::GenericWriter<Image3D_I, 3, unsigned char, RescalFCT>::exportFile(outputFileName,
-                                                                               inputImage,
-                                                                               "UInt8Array3D",
-                                                                               rescaleCustom);
-  }
   trace.info() << " [done] " << std::endl ;   
   return EXIT_SUCCESS;  
 }