#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
mBackgroundValue = 0;
mForegroundValue = 1;
SetDicomUptodateFlag(false);
+ mFilename = "";
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::SetROINumber(int number)
+{
+ mNumber = number;
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
const std::string & clitk::DicomRT_ROI::GetName() 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;
gdcm::SmartPointer<gdcm::SequenceOfItems> & sqi2 = mContoursSequenceOfItems;
if( !sqi2 || !sqi2->GetNumberOfItems() )
{
+ return false;
}
unsigned int nitems = sqi2->GetNumberOfItems();
{
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);
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);
//--------------------------------------------------------------------
-void clitk::DicomRT_ROI::SetImage(vvImage * image)
+void clitk::DicomRT_ROI::SetImage(vvImage::Pointer image)
{
mImage = image;
}
{
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();
//--------------------------------------------------------------------
-#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());
#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;
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+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
// 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
+//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff