#include "clitkDicomRT_ROI.h"
#include <vtkSmartPointer.h>
#include <vtkAppendPolyData.h>
+#include <vtkImageClip.h>
+#include <vtkMarchingSquares.h>
#if GDCM_MAJOR_VERSION == 2
#include "gdcmAttribute.h"
{
mName = "NoName";
mNumber = -1;
+ mImage = NULL;
mColor.resize(3);
mColor[0] = mColor[1] = mColor[2] = 0;
mMeshIsUpToDate = false;
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() )
{
}
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);
+ bool b = c->Read(&j);
if (b) {
mListOfContours.push_back(c);
}
vtkPolyData * clitk::DicomRT_ROI::GetMesh()
{
if (!mMeshIsUpToDate) {
- ComputeMesh();
+ ComputeMeshFromContour();
}
return mMesh;
}
//--------------------------------------------------------------------
-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++) {
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
return mImage;
}
//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::ComputeContoursFromImage()
+{
+ 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();
+ clipper->SetInput(image);
+ 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);
+ for(uint i=0; i<n; i++) {
+ // Clip to the current slice
+ extent[4] = extent[5] = image->GetOrigin()[2]+i*image->GetSpacing()[2];
+ DDV(extent, 6);
+ clipper->SetOutputWholeExtent(extent[0],extent[1],extent[2],
+ extent[3],extent[4],extent[5]);
+
+
+ squares->Update();
+ DD(squares->GetNumberOfContours());
+ mListOfContours[i]->SetMesh(squares->GetOutput());
+ }
+}
+//--------------------------------------------------------------------