Merge branch 'master' of git.creatis.insa-lyon.fr:clitk

[clitk.git] / tools / clitkDicom2Image.cxx

diff --git a/tools/clitkDicom2Image.cxx b/tools/clitkDicom2Image.cxx
index 0390c60d553adde38959f994a328ba6043e81e0a..07a85653edc37eba8c30262676b860b5d1038207 100644 (file)
--- a/tools/clitkDicom2Image.cxx
+++ b/tools/clitkDicom2Image.cxx
@@ -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 +52,44 @@ 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
+    if (args_info.verbose_flag)
+      std::cout << "Using GDCM-2.x" << std::endl;
+    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
+    if (args_info.verbose_flag)
+      std::cout << "Not using GDCM-2.x" << std::endl;
+  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 +152,29 @@ 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;
 }