X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkDicom2Image.cxx;h=6410714293c69e769b12eceae618f9c26a5abf94;hb=bec6f659babc742382ca007b53800e7305fa298f;hp=421d456b945ab4b990b0f79c556828048f73d363;hpb=3651402ef8b7936f79264cba79c284343c704aa2;p=clitk.git

diff --git a/tools/clitkDicom2Image.cxx b/tools/clitkDicom2Image.cxx
index 421d456..6410714 100644
--- a/tools/clitkDicom2Image.cxx
+++ b/tools/clitkDicom2Image.cxx
@@ -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
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
 
 // clitk includes
 #include "clitkDicom2Image_ggo.h"
@@ -22,6 +22,13 @@
 #include "clitkImageCommon.h"
 #include "vvImageReader.h"
 #include "vvImageWriter.h"
+#include <gdcmFile.h>
+#include <vtkImageChangeInformation.h>
+#if GDCM_MAJOR_VERSION == 2
+  #include <gdcmImageHelper.h>
+  #include <gdcmAttribute.h>
+  #include <gdcmReader.h>
+#endif
 
 //====================================================================
 int main(int argc, char * argv[])
@@ -45,16 +52,40 @@ int main(int argc, char * argv[])
 
   //===========================================
   /// Get slices locations ...
+  std::vector<double> theorigin(3);
   std::vector<double> sliceLocations;
   for(unsigned int i=0; i<args_info.inputs_num; i++) {
     //std::cout << "Reading <" << input_files[i] << std::endl;
-    gdcm::File * header = clitk::readDicomHeader(input_files[i]);
-    sliceLocations.push_back(header->GetZOrigin());
-    if (header->GetPixelSize() != 2) {
+#if GDCM_MAJOR_VERSION == 2
+    gdcm::Reader hreader;
+    hreader.SetFileName(input_files[i].c_str());
+    hreader.Read();
+    theorigin = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
+    sliceLocations.push_back(theorigin[2]);
+    gdcm::Attribute<0x28, 0x100> pixel_size;
+    gdcm::DataSet& ds = hreader.GetFile().GetDataSet();
+    pixel_size.SetFromDataSet(ds);
+    if (pixel_size.GetValue() != 16)
+    {
       std::cerr << "Pixel type 2 bytes ! " << std::endl;
       std::cerr << "In file " << input_files[i] << std::endl;
       exit(0);
     }
+#else
+  gdcm::File *header = new gdcm::File();
+  header->SetFileName(input_files[i]);
+  header->SetMaxSizeLoadEntry(16384); // required ?
+  header->Load();
+  theorigin[0] = header->GetXOrigin();
+  theorigin[1] = header->GetYOrigin();
+  theorigin[2] = header->GetZOrigin();
+  sliceLocations.push_back(theorigin[2]);
+  if (header->GetPixelSize() != 2) {
+    std::cerr << "Pixel type 2 bytes ! " << std::endl;
+    std::cerr << "In file " << input_files[i] << std::endl;
+    exit(0);
+  }
+#endif
   }
 
   //===========================================
@@ -117,11 +148,29 @@ int main(int argc, char * argv[])
     std::cerr << reader->GetLastError() << std::endl;
     return 1;
   }
+  
+  vvImage::Pointer image = reader->GetOutput();
+  vtkImageData* vtk_image = image->GetFirstVTKImageData();
+  vtkImageChangeInformation* modifier = vtkImageChangeInformation::New();
+  if  (args_info.focal_origin_given) {
+    std::vector<double> spacing = image->GetSpacing();
+    std::vector<int> size = image->GetSize();
+    theorigin[0] = -spacing[0]*size[0]/2.0;
+    theorigin[1] = -spacing[1]*size[1]/2.0;
+    modifier->SetInput(vtk_image);
+    modifier->SetOutputOrigin(theorigin[0], theorigin[1], sliceLocations[sliceIndex[0]]);
+    modifier->Update();
+    vvImage::Pointer focal_image = vvImage::New();
+    focal_image->AddVtkImage(modifier->GetOutput());
+    image = focal_image;
+  }
 
   vvImageWriter::Pointer writer = vvImageWriter::New();
-  writer->SetInput(reader->GetOutput());
+  writer->SetInput(image);
   writer->SetOutputFileName(args_info.output_arg);
   writer->Update();
 
+  modifier->Delete();
+
   return 0;
 }