X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=common%2FclitkDicomRT_ROI.cxx;h=d8af8c313e10cbd64a5ae92d649f4001ea9f6ce9;hb=d55f025b18f68066a52b8f33c2dc6481e82c2580;hp=73d25b99cf038934b5479b61edca6237e74e9075;hpb=8427d8dc328ffb0f528df6ab1da1a45c6f5b6b59;p=clitk.git

diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx
index 73d25b9..d8af8c3 100644
--- a/common/clitkDicomRT_ROI.cxx
+++ b/common/clitkDicomRT_ROI.cxx
@@ -20,8 +20,12 @@
 #include "clitkDicomRT_ROI.h"
 #include <vtkSmartPointer.h>
 #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
@@ -31,12 +35,14 @@ clitk::DicomRT_ROI::DicomRT_ROI()
 {
   mName = "NoName";
   mNumber = -1;
+  mImage = NULL;
   mColor.resize(3);
   mColor[0] = mColor[1] = mColor[2] = 0;
   mMeshIsUpToDate = false;
   mBackgroundValue = 0;
   mForegroundValue = 1;
   SetDicomUptodateFlag(false);
+  mFilename = "";
 }
 //--------------------------------------------------------------------
 
@@ -67,6 +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
 {
@@ -134,9 +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;
@@ -185,7 +200,8 @@ bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
       return false;
     }
   const gdcm::DataElement& csq = nestedds.GetDataElement( tcsq );
-  gdcm::SmartPointer<gdcm::SequenceOfItems> sqi2 = csq.GetValueAsSQ();
+  mContoursSequenceOfItems = csq.GetValueAsSQ();
+  gdcm::SmartPointer<gdcm::SequenceOfItems> & sqi2 = mContoursSequenceOfItems;
   if( !sqi2 || !sqi2->GetNumberOfItems() )
     {
     }
@@ -193,9 +209,10 @@ bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
 
   for(unsigned int i = 0; i < nitems; ++i)
     {
-      const gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1
+      gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1
       DicomRT_Contour::Pointer c = DicomRT_Contour::New();
-      bool b = c->Read(j);
+      c->SetTransformMatrix(mTransformMatrix);
+      bool b = c->Read(&j);
       if (b) {
         mListOfContours.push_back(c);
       }
@@ -221,6 +238,7 @@ 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);
@@ -238,7 +256,7 @@ void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem *
 
 
 //--------------------------------------------------------------------
-void clitk::DicomRT_ROI::SetImage(vvImage * image)
+void clitk::DicomRT_ROI::SetImage(vvImage::Pointer image)
 {
   mImage = image;
 }
@@ -249,7 +267,7 @@ void clitk::DicomRT_ROI::SetImage(vvImage * image)
 vtkPolyData * clitk::DicomRT_ROI::GetMesh()
 {
   if (!mMeshIsUpToDate) {
-    ComputeMesh();
+    ComputeMeshFromContour();
   }
   return mMesh;
 }
@@ -265,11 +283,15 @@ clitk::DicomRT_Contour * clitk::DicomRT_ROI::GetContour(int n)
 
 
 //--------------------------------------------------------------------
-void clitk::DicomRT_ROI::ComputeMesh()
+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();
  
@@ -280,11 +302,12 @@ void clitk::DicomRT_ROI::ComputeMesh()
 //--------------------------------------------------------------------
 
 
-#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());  
@@ -298,23 +321,47 @@ void clitk::DicomRT_ROI::UpdateDicomItem()
   gdcm::DataSet & ds = mItemInfo->GetNestedDataSet();  
   ds.Replace(de);
 
+  // From MESH to CONTOURS
+  ComputeContoursFromImage();
+
   // Update contours
+  DD(mListOfContours.size());
   for(uint i=0; i<mListOfContours.size(); i++) {
     DD(i);
-    DicomRT_Contour::Pointer roi = mListOfContours[i];
-    roi->UpdateDicomItem(mItemContour);
+    DicomRT_Contour::Pointer contour = mListOfContours[i];
+    contour->UpdateDicomItem();//mItemContour);
   }
+
+  // Nb of contours
+  unsigned int nitems = mContoursSequenceOfItems->GetNumberOfItems();
+  DD(nitems);
+
+  // Write [Contour Sequence] = 0x3006,0x0040)
+  gdcm::DataSet & dsc = mItemContour->GetNestedDataSet();
+  gdcm::Tag tcsq(0x3006,0x0040);
+  const gdcm::DataElement& csq = dsc.GetDataElement( tcsq );
+  gdcm::DataElement dec(csq);
+  dec.SetValue(*mContoursSequenceOfItems);
+  dsc.Replace(dec);
+
+  gdcm::DataSet & a = mContoursSequenceOfItems->GetItem(1).GetNestedDataSet();
+  gdcm::Attribute<0x3006,0x0050> at;
+  gdcm::Tag tcontourdata(0x3006,0x0050);
+  gdcm::DataElement contourdata = a.GetDataElement( tcontourdata );
+  at.SetFromDataElement( contourdata );
+  const double* points = at.GetValues();
+  DD(points[0]);
+
 }
 //--------------------------------------------------------------------
 #endif
 
 //--------------------------------------------------------------------
-void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage * image, int n,
+void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage::Pointer image, int n,
                                             std::string name,
                                             std::vector<double> color, 
                                             std::string filename)
 {
-
   // ROI number [Referenced ROI Number]
   mNumber = n;
 
@@ -340,3 +387,152 @@ vvImage * clitk::DicomRT_ROI::GetImage() const
   return mImage;
 }
 //--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+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
+  if (!mImage) return;
+
+  // Only consider 3D here
+  if (mImage->GetNumberOfDimensions() != 3) {
+    FATAL("DicomRT_ROI::ComputeMeshFromImage only work with 3D images");
+  }
+
+  // Get the VTK image
+  vtkImageData * image = mImage->GetVTKImages()[0];
+  
+  // 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;
+
+
+  // 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]); 
+
+    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
+//--------------------------------------------------------------------
+