X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkDicom2Image.cxx;h=aa63b0489bd50505255c2610640e8bbb4615c70e;hb=b7b8f2b040d1772c30c34653ee3fe0c27bc8fa71;hp=b1b105d676746bc70817053004cad8e76208cd15;hpb=60850f3574637676931f327adee41d29f94bc067;p=clitk.git

diff --git a/tools/clitkDicom2Image.cxx b/tools/clitkDicom2Image.cxx
index b1b105d..aa63b04 100644
--- a/tools/clitkDicom2Image.cxx
+++ b/tools/clitkDicom2Image.cxx
@@ -17,6 +17,7 @@
 ===========================================================================**/
 
 // clitk includes
+#include "clitkIO.h"
 #include "clitkDicom2Image_ggo.h"
 #include "clitkCommon.h"
 #include "clitkImageCommon.h"
@@ -25,7 +26,7 @@
 #include <gdcmFile.h>
 #include <vtkVersion.h>
 #include <vtkImageChangeInformation.h>
-#if GDCM_MAJOR_VERSION == 2
+#if GDCM_MAJOR_VERSION >= 2
   #include <gdcmImageHelper.h>
   #include <gdcmAttribute.h>
   #include <gdcmReader.h>
@@ -38,6 +39,8 @@ int main(int argc, char * argv[])
 {
   // init command line
   GGO(clitkDicom2Image, args_info);
+  CLITK_INIT;
+
   std::vector<std::string> input_files;
   ///if std_input is given, read the input files from stdin
   if (args_info.std_input_given) {
@@ -61,7 +64,7 @@ int main(int argc, char * argv[])
   std::map< int, std::vector<double> > theorientation;
   std::map< int, std::vector<double> > sliceLocations;
   std::map< int, std::vector<std::string> > seriesFiles;
-#if GDCM_MAJOR_VERSION == 2
+#if GDCM_MAJOR_VERSION >= 2
   if (args_info.verbose_flag)
     std::cout << "Using GDCM-2.x" << std::endl;
 #else
@@ -73,7 +76,7 @@ int main(int argc, char * argv[])
   for(unsigned int i=0; i<args_info.inputs_num; i++) {
     if (args_info.verbose_flag)
         std::cout << "Reading <" << input_files[i] << std::endl;
-#if GDCM_MAJOR_VERSION == 2
+#if GDCM_MAJOR_VERSION >= 2
     gdcm::Reader hreader;
     hreader.SetFileName(input_files[i].c_str());
     hreader.Read();
@@ -84,22 +87,25 @@ int main(int argc, char * argv[])
       series_number_att.SetFromDataSet(ds);
       series_number = series_number_att.GetValue();
     }
-    
+
     series_numbers.insert(series_number);
     theorigin[series_number] = gdcm::ImageHelper::GetOriginValue(hreader.GetFile());
     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);
+    if (args_info.patientSystem_flag) {
+      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);
+    } else
+      sliceLocations[series_number].push_back(theorigin[series_number][2]);
     seriesFiles[series_number].push_back(input_files[i]);
-    
+
     gdcm::Attribute<0x28, 0x100> pixel_size;
     pixel_size.SetFromDataSet(ds);
     /* if (pixel_size.GetValue() != 16)
@@ -118,7 +124,7 @@ 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();
@@ -200,7 +206,7 @@ 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();
@@ -226,34 +232,24 @@ 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);
-    }
+    if (args_info.patientSystem_flag && !image->GetTransform().empty())
+      writer->SetSaveTransform(true);
     writer->SetOutputFileName(outfile);
     writer->Update();
 
     modifier->Delete();
-    
+
     sn++;
   }
-  
+
   return 0;
 }