X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=common%2FclitkDicomRT_ROI.cxx;h=75fc8e97fdbc517bdc61da7dc5b60bd672d9ffe9;hb=4f4d79533d2bdd0c13d90cde6bbb67e5f313b638;hp=cd8af0c9b7833843ec0b118112a5670fec7f2562;hpb=b3f649f6e833485a45e94f99bd78d1dce03b3852;p=clitk.git diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx index cd8af0c..75fc8e9 100644 --- a/common/clitkDicomRT_ROI.cxx +++ b/common/clitkDicomRT_ROI.cxx @@ -4,7 +4,7 @@ Authors belongs to: - University of LYON http://www.universite-lyon.fr/ - - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr + - Léon Bérard cancer center http://www.centreleonberard.fr - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr This software is distributed WITHOUT ANY WARRANTY; without even @@ -20,6 +20,8 @@ #include "clitkDicomRT_ROI.h" #include #include +#include +#include #if GDCM_MAJOR_VERSION == 2 #include "gdcmAttribute.h" @@ -31,12 +33,13 @@ 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; - mZDelta = 0; + SetDicomUptodateFlag(false); } //-------------------------------------------------------------------- @@ -135,21 +138,38 @@ double clitk::DicomRT_ROI::GetForegroundValueLabelImage() const //-------------------------------------------------------------------- #if GDCM_MAJOR_VERSION == 2 -void clitk::DicomRT_ROI::Read(std::map & 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 = {}; @@ -163,45 +183,33 @@ void clitk::DicomRT_ROI::Read(std::map & rois, gdcm::Item cons gdcm::Tag tcsq(0x3006,0x0040); if( !nestedds.FindDataElement( tcsq ) ) { + std::cerr << "Warning. Could not read contour for structure <" << mName << ">, number" << mNumber << " ? I ignore it" << std::endl; + SetDicomUptodateFlag(true); + return false; } const gdcm::DataElement& csq = nestedds.GetDataElement( tcsq ); - gdcm::SmartPointer sqi2 = csq.GetValueAsSQ(); + mContoursSequenceOfItems = csq.GetValueAsSQ(); + gdcm::SmartPointer & sqi2 = mContoursSequenceOfItems; if( !sqi2 || !sqi2->GetNumberOfItems() ) { } unsigned int nitems = sqi2->GetNumberOfItems(); - bool contour_processed=false; - bool delta_computed=false; - double last_z=0; for(unsigned int i = 0; i < nitems; ++i) { - const gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1 - DicomRT_Contour::Pointer c = DicomRT_Contour::New(); - bool b = c->Read(j); - if (b) { - mListOfContours.push_back(c); - if (contour_processed) { - double delta=c->GetZ() - last_z; - if (delta_computed) - assert(mZDelta == delta); - else - mZDelta = delta; - } else - contour_processed=true; - last_z=c->GetZ(); + gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1 + DicomRT_Contour::Pointer c = DicomRT_Contour::New(); + bool b = c->Read(&j); + if (b) { + mListOfContours.push_back(c); + } } - } - + SetDicomUptodateFlag(true); + return true; } #else void clitk::DicomRT_ROI::Read(std::map & rois, gdcm::SQItem * item) { - - // Change number if needed - - // TODO - // ROI number [Referenced ROI Number] mNumber = atoi(item->GetEntryValue(0x3006,0x0084).c_str()); @@ -213,25 +221,21 @@ void clitk::DicomRT_ROI::Read(std::map & rois, gdcm::SQItem * // Read contours [Contour Sequence] gdcm::SeqEntry * contours=item->GetSeqEntry(0x3006,0x0040); - bool contour_processed=false; - bool delta_computed=false; - double last_z=0; - for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { - DicomRT_Contour::Pointer c = DicomRT_Contour::New(); - bool b = c->Read(j); - if (b) { - mListOfContours.push_back(c); - if (contour_processed) { - double delta=c->GetZ() - last_z; - if (delta_computed) - assert(mZDelta == delta); - else - mZDelta = delta; - } else - contour_processed=true; - last_z=c->GetZ(); + if (contours) { + int i=0; + for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { + DicomRT_Contour::Pointer c = DicomRT_Contour::New(); + bool b = c->Read(j); + if (b) { + mListOfContours.push_back(c); + } + ++i; } } + else { + std::cerr << "Warning. Could not read contour for structure <" << mName << ">, number" << mNumber << " ? I ignore it" << std::endl; + } + SetDicomUptodateFlag(true); } #endif //-------------------------------------------------------------------- @@ -249,18 +253,23 @@ void clitk::DicomRT_ROI::SetImage(vvImage * 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 append = vtkSmartPointer::New(); for(unsigned int i=0; i + 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; iUpdateDicomItem();//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, - std::vector color, - std::string filename) + std::string name, + std::vector color, + std::string filename) { // ROI number [Referenced ROI Number] @@ -307,3 +369,49 @@ vvImage * clitk::DicomRT_ROI::GetImage() const 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 clipper = vtkSmartPointer::New(); + clipper->SetInput(image); + int* extent = image->GetExtent(); + DDV(extent, 6); + // std::vector extend; + + // Prepare the marching squares + vtkSmartPointer squares = vtkSmartPointer::New(); + squares->SetInput(clipper->GetOutput()); + + // Loop on slice + uint n = image->GetDimensions()[2]; + DD(n); + for(uint i=0; iGetOrigin()[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()); + } +} +//--------------------------------------------------------------------