X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=common%2FclitkDicomRT_ROI.cxx;h=af8bee67a77a769e680c3ea892e91fd98e235a47;hb=HEAD;hp=98f9f59d1519bd0c8e5a99ca8ae631c3b8d0a1fa;hpb=f6ec1c5f4f1c2105b428fe2d87e794417897a4e8;p=clitk.git

diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx
index 98f9f59..af8bee6 100644
--- a/common/clitkDicomRT_ROI.cxx
+++ b/common/clitkDicomRT_ROI.cxx
@@ -22,8 +22,10 @@
 #include <vtkAppendPolyData.h>
 #include <vtkImageClip.h>
 #include <vtkMarchingSquares.h>
+#include <vtkPolyDataWriter.h>
+#include <vtkVersion.h>
 
-#if GDCM_MAJOR_VERSION == 2
+#if GDCM_MAJOR_VERSION >= 2
 #include "gdcmAttribute.h"
 #include "gdcmItem.h"
 #endif
@@ -40,6 +42,7 @@ clitk::DicomRT_ROI::DicomRT_ROI()
   mBackgroundValue = 0;
   mForegroundValue = 1;
   SetDicomUptodateFlag(false);
+  mFilename = "";
 }
 //--------------------------------------------------------------------
 
@@ -70,6 +73,14 @@ int clitk::DicomRT_ROI::GetROINumber() const
 //--------------------------------------------------------------------
 
 
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::SetROINumber(int number)
+{
+  mNumber = number;
+}
+//--------------------------------------------------------------------
+
+
 //--------------------------------------------------------------------
 const std::string & clitk::DicomRT_ROI::GetName() const
 {
@@ -137,9 +148,10 @@ double clitk::DicomRT_ROI::GetForegroundValueLabelImage() const
 
 
 //--------------------------------------------------------------------
-#if GDCM_MAJOR_VERSION == 2
+#if GDCM_MAJOR_VERSION >= 2
 bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
 {
+  //FATAL("Error : compile vv with itk4 + external gdcm");
   // Keep dicom item
   mItemInfo = itemInfo;
   mItemContour = itemContour;
@@ -192,6 +204,7 @@ bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
   gdcm::SmartPointer<gdcm::SequenceOfItems> & sqi2 = mContoursSequenceOfItems;
   if( !sqi2 || !sqi2->GetNumberOfItems() )
     {
+    return false;
     }
   unsigned int nitems = sqi2->GetNumberOfItems();
 
@@ -199,6 +212,7 @@ bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
     {
       gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1
       DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+      c->SetTransformMatrix(mTransformMatrix);
       bool b = c->Read(&j);
       if (b) {
         mListOfContours.push_back(c);
@@ -225,6 +239,7 @@ void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem *
     int i=0;
     for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) {
       DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+      c->SetTransformMatrix(mTransformMatrix);
       bool b = c->Read(j);
       if (b) {
         mListOfContours.push_back(c);
@@ -273,7 +288,11 @@ void clitk::DicomRT_ROI::ComputeMeshFromContour()
 {
   vtkSmartPointer<vtkAppendPolyData> append = vtkSmartPointer<vtkAppendPolyData>::New();
   for(unsigned int i=0; i<mListOfContours.size(); i++) {
-    append->AddInput(mListOfContours[i]->GetMesh());
+#if VTK_MAJOR_VERSION <= 5
+  	append->AddInput(mListOfContours[i]->GetMesh());
+#else
+  	append->AddInputData(mListOfContours[i]->GetMesh());
+#endif
   }
   append->Update();
  
@@ -284,11 +303,12 @@ void clitk::DicomRT_ROI::ComputeMeshFromContour()
 //--------------------------------------------------------------------
 
 
-#if GDCM_MAJOR_VERSION == 2
-
+#if GDCM_MAJOR_VERSION >= 2
 //--------------------------------------------------------------------
 void clitk::DicomRT_ROI::UpdateDicomItem()
 {
+  FATAL("Error : compile vv with itk4 + external gdcm");
+
   if (GetDicomUptoDateFlag()) return;
   DD("ROI::UpdateDicomItem");
   DD(GetName());  
@@ -343,7 +363,6 @@ void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage::Pointer image, int n,
                                             std::vector<double> color, 
                                             std::string filename)
 {
-
   // ROI number [Referenced ROI Number]
   mNumber = n;
 
@@ -371,9 +390,18 @@ vvImage * clitk::DicomRT_ROI::GetImage() const
 //--------------------------------------------------------------------
 
 
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::SetTransformMatrix(vtkMatrix4x4* matrix)
+{
+  mTransformMatrix = matrix;
+}
+//--------------------------------------------------------------------
+
+
 //--------------------------------------------------------------------
 void clitk::DicomRT_ROI::ComputeContoursFromImage()
 {
+  FATAL("ComputeContoursFromImage should not be call. To be replace");
   DD("ComputeMeshFromImage");
 
   // Check that an image is loaded
@@ -389,29 +417,123 @@ void clitk::DicomRT_ROI::ComputeContoursFromImage()
   
   // Get initial extend for the clipping
   vtkSmartPointer<vtkImageClip> clipper = vtkSmartPointer<vtkImageClip>::New();
+#if VTK_MAJOR_VERSION <= 5
   clipper->SetInput(image);
+#else
+  clipper->SetInputData(image);
+#endif
+  
   int* extent = image->GetExtent();
   DDV(extent, 6);
   //  std::vector<int> extend;
 
-  // Prepare the marching squares
-  vtkSmartPointer<vtkMarchingSquares> squares = vtkSmartPointer<vtkMarchingSquares>::New();
-  squares->SetInput(clipper->GetOutput());
 
   // Loop on slice
   uint n = image->GetDimensions()[2];
   DD(n);
+  DD(mListOfContours.size());
+  mListOfContours.resize(n); /// ???FIXME
+  DD(mListOfContours.size());
+  std::vector<vtkSmartPointer<vtkPolyData> > contours;
   for(uint i=0; i<n; i++) {
+    DD(i);
+
+    // FIXME     vtkDiscreteMarchingCubes INSTEAD
+
+
+    vtkSmartPointer<vtkMarchingSquares> squares = vtkSmartPointer<vtkMarchingSquares>::New();
+#if VTK_MAJOR_VERSION <= 5
+    squares->SetInput(image);
+#else
+    squares->SetInputData(image);
+#endif
+    squares->SetImageRange(extent[0], extent[1], extent[2], extent[3], i, i);
+    squares->SetValue(1, 1.0);
+    squares->Update();
+    DD(squares->GetNumberOfContours());
+    
+    //clitk::DicomRT_Contour * contour = new clitk::DicomRT_Contour();
+    //mListOfContours[i]->SetMesh(squares->GetOutput());
+
+    
+    vtkSmartPointer<vtkPolyData> m = squares->GetOutput();
+    contours.push_back(m);
+
+    /*
     // Clip to the current slice
     extent[4] = extent[5] = image->GetOrigin()[2]+i*image->GetSpacing()[2];
     DDV(extent, 6);
+    // Prepare the marching squares
+    vtkSmartPointer<vtkMarchingSquares> squares = vtkSmartPointer<vtkMarchingSquares>::New();
     clipper->SetOutputWholeExtent(extent[0],extent[1],extent[2],
-                                extent[3],extent[4],extent[5]);
-    
+                                extent[3],extent[4],extent[5]); 
 
+    squares->SetInput(clipper->GetOutput());
     squares->Update();
     DD(squares->GetNumberOfContours());
     mListOfContours[i]->SetMesh(squares->GetOutput());
+    */
+  }
+  DD("done");
+ 
+  vtkSmartPointer<vtkAppendPolyData> append = vtkSmartPointer<vtkAppendPolyData>::New();
+  for(unsigned int i=0; i<n; i++) {
+#if VTK_MAJOR_VERSION <= 5
+    append->AddInput(contours[i]);
+#else
+    append->AddInputData(contours[i]);
+#endif
   }
+  append->Update();
+ 
+  mMesh = vtkSmartPointer<vtkPolyData>::New();
+  mMesh->DeepCopy(append->GetOutput());
+  
+  // Write vtk
+  vtkPolyDataWriter * w = vtkPolyDataWriter::New();
+#if VTK_MAJOR_VERSION <= 5
+  w->SetInput(mMesh);
+#else
+  w->SetInputData(mMesh);
+#endif
+  w->SetFileName("toto.vtk");
+  w->Write();
+
+  DD("done");
 }
 //--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+#if CLITK_USE_SYSTEM_GDCM == 1
+void clitk::DicomRT_ROI::Read(vtkSmartPointer<vtkGDCMPolyDataReader> & reader, int roiindex)
+{
+  vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
+  
+  mName = p->GetStructureSetROIName(roiindex);
+  mNumber = p->GetStructureSetROINumber(roiindex);
+
+  //mColor = //FIXME !!  
+
+  // gdcm::Attribute<0x3006,0x002a> color = {};
+  
+  // const gdcm::DataSet & nestedds = mItemContour->GetNestedDataSet();
+  // color.SetFromDataSet( nestedds );
+  // assert( color.GetNumberOfValues() == 3 );
+  // mColor[0] = color.GetValue(0);
+  // mColor[1] = color.GetValue(1);
+  // mColor[2] = color.GetValue(2);
+
+
+  SetDicomUptodateFlag(true);
+  // Get the contour
+  mMesh =  reader->GetOutput(roiindex);  
+  DicomRT_Contour::Pointer c = DicomRT_Contour::New();
+  c->SetTransformMatrix(mTransformMatrix);
+  c->SetMesh(mMesh); // FIXME no GetZ, not GetPoints  
+  mMeshIsUpToDate = true;
+  mListOfContours.push_back(c);
+}
+#endif
+//--------------------------------------------------------------------
+