X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkDicom2Image.cxx;h=e08f0def68acd476d1731cbbd1a6d722e4c2b441;hb=09189117040bdb0c9d46a5132671567efea31632;hp=b25b001dea3a19c75edec04b1bcf790891c5cf6a;hpb=4eb6f95e59a7602564b15f9d0715650dc91442a2;p=clitk.git

diff --git a/tools/clitkDicom2Image.cxx b/tools/clitkDicom2Image.cxx
index b25b001..e08f0de 100644
--- a/tools/clitkDicom2Image.cxx
+++ b/tools/clitkDicom2Image.cxx
@@ -23,6 +23,7 @@
 #include "vvImageReader.h"
 #include "vvImageWriter.h"
 #include <gdcmFile.h>
+#include <vtkVersion.h>
 #include <vtkImageChangeInformation.h>
 #if GDCM_MAJOR_VERSION == 2
   #include <gdcmImageHelper.h>
@@ -57,13 +58,22 @@ int main(int argc, char * argv[])
   int series_number = -1;
   std::set<int> series_numbers;
   std::map< int, std::vector<double> > theorigin;
+  std::map< int, std::vector<double> > theorientation;
   std::map< int, std::vector<double> > sliceLocations;
   std::map< int, std::vector<std::string> > seriesFiles;
-  for(unsigned int i=0; i<args_info.inputs_num; i++) {
-    //std::cout << "Reading <" << input_files[i] << std::endl;
 #if GDCM_MAJOR_VERSION == 2
+  if (args_info.verbose_flag)
+    std::cout << "Using GDCM-2.x" << std::endl;
+#else
+  if (args_info.verbose_flag) {
+    std::cout << "Not using GDCM-2.x" << std::endl;
+    std::cout<< "The image orientation is not supported with this version of GDCM" <<std::endl;
+  }
+#endif
+  for(unsigned int i=0; i<args_info.inputs_num; i++) {
     if (args_info.verbose_flag)
-      std::cout << "Using GDCM-2.x" << std::endl;
+        std::cout << "Reading <" << input_files[i] << std::endl;
+#if GDCM_MAJOR_VERSION == 2
     gdcm::Reader hreader;
     hreader.SetFileName(input_files[i].c_str());
     hreader.Read();
@@ -71,15 +81,25 @@ int main(int argc, char * argv[])
 
     if (args_info.extract_series_flag) {
       gdcm::Attribute<0x20,0x11> series_number_att;
-      series_number_att.SetFromDataSet(hreader.GetFile().GetDataSet());
+      series_number_att.SetFromDataSet(ds);
       series_number = series_number_att.GetValue();
     }
-    
+
     series_numbers.insert(series_number);
     theorigin[series_number] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
-    sliceLocations[series_number].push_back(theorigin[series_number][2]);
+    theorientation[series_number] = gdcm::ImageHelper::GetDirectionCosinesValue(hreader.GetFile());
+    double n1 = theorientation[series_number][1]*theorientation[series_number][5]-
+                theorientation[series_number][2]*theorientation[series_number][4];
+    double n2 = theorientation[series_number][3]*theorientation[series_number][2]-
+                theorientation[series_number][5]*theorientation[series_number][0];
+    double n3 = theorientation[series_number][0]*theorientation[series_number][4]-
+                theorientation[series_number][1]*theorientation[series_number][3];
+    double sloc = theorigin[series_number][0]*n1+
+                  theorigin[series_number][1]*n2+
+                  theorigin[series_number][2]*n3;
+    sliceLocations[series_number].push_back(sloc);
     seriesFiles[series_number].push_back(input_files[i]);
-    
+
     gdcm::Attribute<0x28, 0x100> pixel_size;
     pixel_size.SetFromDataSet(ds);
     /* if (pixel_size.GetValue() != 16)
@@ -90,8 +110,6 @@ int main(int argc, char * argv[])
        }
     */
 #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 ?
@@ -100,7 +118,7 @@ int main(int argc, char * argv[])
   if (args_info.extract_series_flag) {
     series_number = atoi(header->GetEntryValue(0x20,0x11).c_str());
   }
-  
+
   series_numbers.insert(series_number);
   theorigin[series_number].resize(3);
   theorigin[series_number][0] = header->GetXOrigin();
@@ -126,7 +144,7 @@ int main(int argc, char * argv[])
     std::vector<std::string> files = seriesFiles[*sn];
     std::vector<int> sliceIndex;
     clitk::GetSortedIndex(locs, sliceIndex);
-    if (args_info.verboseSliceLocation_flag) {
+    if (args_info.verbose_flag) {
       std::cout << locs[sliceIndex[0]] << " -> "
                 << sliceIndex[0] << " / " << 0 << " => "
                 << "0 mm "
@@ -182,7 +200,7 @@ 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();
@@ -191,7 +209,11 @@ int main(int argc, char * argv[])
       std::vector<int> size = image->GetSize();
       origin[0] = -spacing[0]*size[0]/2.0;
       origin[1] = -spacing[1]*size[1]/2.0;
+#if VTK_MAJOR_VERSION <= 5
       modifier->SetInput(vtk_image);
+#else
+      modifier->SetInputData(vtk_image);
+#endif
       modifier->SetOutputOrigin(origin[0], origin[1], locs[sliceIndex[0]]);
       modifier->Update();
       vvImage::Pointer focal_image = vvImage::New();
@@ -204,18 +226,38 @@ int main(int argc, char * argv[])
       outfile = args_info.output_arg;
     else {
       std::ostringstream name;
-      name << *sn << "_" << args_info.output_arg;
+      std::vector<std::string> directory = clitk::SplitFilename(args_info.output_arg);
+      if (directory.size() == 2)
+        name << directory[0] << *sn << "_" << directory[1];
+      else
+        name << *sn << "_" << args_info.output_arg;
       outfile = name.str();
     }
+    //Check on transform
+    bool bId = true;
+    for(unsigned int i=0; i<4; i++) {
+      for(unsigned int j=0; j<4; j++) {
+        double elt = image->GetTransform()[0]->GetMatrix()->GetElement(i,j);
+        if(i==j && elt!=1.) {
+          bId = false;
+        }
+        if(i!=j && elt!=0.) {
+          bId = false;
+        }
+      }
+    }
     vvImageWriter::Pointer writer = vvImageWriter::New();
     writer->SetInput(image);
+    if(!bId) {
+        writer->SetSaveTransform(true);
+    }
     writer->SetOutputFileName(outfile);
     writer->Update();
 
     modifier->Delete();
-    
+
     sn++;
   }
-  
+
   return 0;
 }