X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=vv%2FvvMeshReader.cxx;h=fb0baf47a10c0edd5cd9ef7edb01dbab36db1bf6;hb=431fea9a7c825943b07fc4b4f3423355a5fee501;hp=d5100b1e336218485b608022da329ade80515765;hpb=1e034c70105f0926939acaaa27ddb46e904ae8bf;p=clitk.git

diff --git a/vv/vvMeshReader.cxx b/vv/vvMeshReader.cxx
index d5100b1..fb0baf4 100644
--- a/vv/vvMeshReader.cxx
+++ b/vv/vvMeshReader.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
@@ -14,13 +14,20 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
 #include <algorithm>
 
 #include <QApplication>
 
-#include <gdcm.h>
-#include <gdcmSQItem.h>
+#include <gdcmFile.h>
+#if GDCM_MAJOR_VERSION == 2
+  #include <gdcmReader.h>
+  #include <gdcmTag.h>
+  #include <gdcmAttribute.h>
+#else
+  #include <gdcm.h>
+  #include <gdcmSQItem.h>
+#endif
 
 #include <vtkSmartPointer.h>
 #include <vtkAppendPolyData.h>
@@ -35,6 +42,7 @@
 #include "clitkCommon.h"
 #include "vvMeshReader.h"
 #include "vvProgressDialog.h"
+#include <clitkCommon.h>
 
 vvMeshReader::vvMeshReader() :
   vtk_mode(false)
@@ -60,7 +68,7 @@ void vvMeshReader::run()
     vvMesh::Pointer m=vvMesh::New();
     m->ReadFromVTK(filename.c_str());
     if (vf) m->propagateContour(vf);
-    m->ComputeMasks(image->GetVTKImages()[0],true);
+    m->ComputeMasks(image->GetVTKImages()[0],false); //don't extrude the contour
     result.push_back(m);
   } else { //Read a Dicom-struct file
     assert(selected_contours.size() > 0);
@@ -76,31 +84,39 @@ void vvMeshReader::run()
   }
 }
 
-template<class ElementType>
-ElementType parse_value(std::string str)
-{
-  std::istringstream parser(str);
-  ElementType value;
-  parser >> value;
-  assert(!parser.fail());
-  return value;
-}
-
-template<class ElementType>
-std::vector<ElementType> parse_string(std::string str,char delim)
-{
-  std::istringstream ss(str);
-  std::string token;
-  std::vector<ElementType> result;
-  while (getline(ss,token,delim)) {
-    result.push_back(parse_value<ElementType>(token));
-  }
-  return result;
-}
-
 std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
 {
   assert(filename!="");
+  std::vector<std::pair<int, std::string> > roi_names;
+#if GDCM_MAJOR_VERSION == 2
+  // duplicate code from  clitk::DicomRT_StructureSet::Read
+  gdcm::Reader reader;
+  reader.SetFileName( filename.c_str() );
+  reader.Read();
+
+  const gdcm::DataSet &ds = reader.GetFile().GetDataSet();
+
+  gdcm::Tag tssroisq(0x3006,0x0020);
+  const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+  gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ssroisq.GetValueAsSQ();
+  assert(roi_seq); // TODO error message
+  for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx)
+    {
+    gdcm::Item & item = roi_seq->GetItem( ridx + 1); // Item starts at 1
+    const gdcm::DataSet& nestedds = item.GetNestedDataSet();
+    if( nestedds.FindDataElement( gdcm::Tag(0x3006,0x22) ) )
+      {
+      gdcm::Attribute<0x3006,0x26> roiname;
+      roiname.SetFromDataSet( nestedds );
+      std::string name = roiname.GetValue();      // 0x3006,0x0026 = [ROI Name]
+      gdcm::Attribute<0x3006,0x0022> roinumber;
+      roinumber.SetFromDataSet( nestedds );
+      int nb = roinumber.GetValue();  // 0x3006,0x0022 = [ROI Number]
+
+      roi_names.push_back(make_pair(nb,name));
+      }
+    }
+#else
   gdcm::File reader;
   reader.SetFileName(filename.c_str());
   reader.SetMaxSizeLoadEntry(16384);
@@ -108,23 +124,25 @@ std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
 
   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
   assert(roi_info);
-  std::vector<std::pair<int, std::string> > roi_names;
   // DD("ici");
   //int n=0;
   for (gdcm::SQItem* i=roi_info->GetFirstSQItem(); i!=0; i=roi_info->GetNextSQItem())
     if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
       roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
+#endif
   return roi_names;
 }
 
 std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
 {
+  std::vector<vvMesh::Pointer> result;
+#if GDCM_MAJOR_VERSION == 2
+#else
   gdcm::File reader;
   reader.SetFileName(filename.c_str());
   reader.SetMaxSizeLoadEntry(16384);
   reader.Load();
 
-  std::vector<vvMesh::Pointer> result;
   gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
   ///We need to iterate both on the contours themselves, and on the contour info
   gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
@@ -137,7 +155,7 @@ std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
     ss >> roi_number;
     if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end()) { //Only read selected ROIs
       vvMesh::Pointer current_roi=vvMesh::New();
-      std::vector<double> rgb=parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
+      std::vector<double> rgb=clitk::parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
       assert(rgb.size()==3);
       current_roi->r=rgb[0]/255;
       current_roi->g=rgb[1]/255;
@@ -148,8 +166,8 @@ std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
       for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { //loop over 2D contours
         std::string contour_type=j->GetEntryValue(0x3006,0x0042);
         if (contour_type=="CLOSED_PLANAR ") {
-          int point_number=parse_value<int>(j->GetEntryValue(0x3006,0x0046));
-          std::vector<float> points=parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
+          int point_number=clitk::parse_value<int>(j->GetEntryValue(0x3006,0x0046));
+          std::vector<float> points=clitk::parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
           assert(points.size() == static_cast<unsigned int>(point_number)*3);
           if (z0 == -1) //First contour
             z0=points[2];
@@ -181,6 +199,7 @@ std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
     }
     k=roi_info->GetNextSQItem(); //increment the second loop variable
   }
+#endif
   return result;
 }