#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;
mBackgroundValue = 0;
mForegroundValue = 1;
+ SetDicomUptodateFlag(false);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
#if GDCM_MAJOR_VERSION == 2
-void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::Item const & item)
+bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
{
- const gdcm::DataSet& nestedds = item.GetNestedDataSet();
-
+ // 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
+ int nb2 = referencedroinumber.GetValue();
+
+ // Must never be different
+ if (nb1 != nb2) {
+ DD(nb2);
+ DD(nb1);
+ FATAL("nb1 must equal nb2" << std::endl);
+ }
+ mNumber = nb1;
- // ROI number [Referenced ROI Number]
- mNumber = referencedroinumber.GetValue();
-
- // 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() )
{
}
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);
}
}
+ 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());
else {
std::cerr << "Warning. Could not read contour for structure <" << mName << ">, number" << mNumber << " ? I ignore it" << std::endl;
}
+ SetDicomUptodateFlag(true);
}
#endif
//--------------------------------------------------------------------
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++) {
//--------------------------------------------------------------------
+#if GDCM_MAJOR_VERSION == 2
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_ROI::UpdateDicomItem()
+{
+ 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 * image, int n,
std::string name,
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());
+ }
+}
+//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff