#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
{
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 = "";
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::SetROINumber(int number)
+{
+ mNumber = number;
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
const std::string & clitk::DicomRT_ROI::GetName() const
{
//--------------------------------------------------------------------
-#if GDCM_MAJOR_VERSION == 2
-void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::Item const & item)
+#if GDCM_MAJOR_VERSION >= 2
+bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
{
- const gdcm::DataSet& nestedds = item.GetNestedDataSet();
-
+ //FATAL("Error : compile vv with itk4 + external gdcm");
+ // Keep dicom item
+ mItemInfo = itemInfo;
+ mItemContour = itemContour;
+ // DD(mItemInfo);
+
+ // ROI number [Referenced ROI Number]
+ const gdcm::DataSet & nesteddsInfo = mItemInfo->GetNestedDataSet();
+ gdcm::Attribute<0x3006,0x0022> roinumber;
+ roinumber.SetFromDataSet( nesteddsInfo );
+ int nb1 = roinumber.GetValue();
+
+ // Check this is the same with the other item
+ const gdcm::DataSet & nestedds = mItemContour->GetNestedDataSet();
gdcm::Attribute<0x3006,0x0084> referencedroinumber;
referencedroinumber.SetFromDataSet( nestedds );
- // Change number if needed
-
- // TODO
-
- // ROI number [Referenced ROI Number]
- mNumber = referencedroinumber.GetValue();
+ int nb2 = referencedroinumber.GetValue();
+
+ // Must never be different
+ if (nb1 != nb2) {
+ DD(nb2);
+ DD(nb1);
+ FATAL("nb1 must equal nb2" << std::endl);
+ }
+ mNumber = nb1;
- // Retrieve ROI Name
- mName = rois[mNumber];
+ // Retrieve ROI Name (in the info item)
+ gdcm::Attribute<0x3006,0x26> roiname;
+ roiname.SetFromDataSet( nesteddsInfo );
+ mName = roiname.GetValue();
+ // DD(mName);
// ROI Color [ROI Display Color]
gdcm::Attribute<0x3006,0x002a> color = {};
if( !nestedds.FindDataElement( tcsq ) )
{
std::cerr << "Warning. Could not read contour for structure <" << mName << ">, number" << mNumber << " ? I ignore it" << std::endl;
- return;
+ SetDicomUptodateFlag(true);
+ 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() )
{
+ return false;
}
unsigned int nitems = 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);
+ c->SetTransformMatrix(mTransformMatrix);
+ bool b = c->Read(&j);
if (b) {
mListOfContours.push_back(c);
}
}
+ SetDicomUptodateFlag(true);
+ return true;
}
#else
void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem * item)
{
-
- // Change number if needed
-
- // TODO
-
// ROI number [Referenced ROI Number]
mNumber = atoi(item->GetEntryValue(0x3006,0x0084).c_str());
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);
else {
std::cerr << "Warning. Could not read contour for structure <" << mName << ">, number" << mNumber << " ? I ignore it" << std::endl;
}
+ SetDicomUptodateFlag(true);
}
#endif
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-void clitk::DicomRT_ROI::SetImage(vvImage * image)
+void clitk::DicomRT_ROI::SetImage(vvImage::Pointer image)
{
mImage = image;
}
vtkPolyData * clitk::DicomRT_ROI::GetMesh()
{
if (!mMeshIsUpToDate) {
- ComputeMesh();
+ ComputeMeshFromContour();
}
return mMesh;
}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
clitk::DicomRT_Contour * clitk::DicomRT_ROI::GetContour(int n)
{
return mListOfContours[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();
//--------------------------------------------------------------------
+#if GDCM_MAJOR_VERSION >= 2
//--------------------------------------------------------------------
-void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage * image, int n,
+void clitk::DicomRT_ROI::UpdateDicomItem()
+{
+ FATAL("Error : compile vv with itk4 + external gdcm");
+
+ if (GetDicomUptoDateFlag()) return;
+ DD("ROI::UpdateDicomItem");
+ DD(GetName());
+
+ // From now, only some item can be modified
+
+ // Set ROI Name 0x3006,0x26>
+ gdcm::Attribute<0x3006,0x26> roiname;
+ roiname.SetValue(GetName());
+ gdcm::DataElement de = roiname.GetAsDataElement();
+ 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 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::Pointer image, int n,
std::string name,
std::vector<double> color,
std::string filename)
{
-
// ROI number [Referenced ROI Number]
mNumber = n;
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
+//--------------------------------------------------------------------
+
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff