X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=common%2FclitkDicomRT_ROI.cxx;h=75fc8e97fdbc517bdc61da7dc5b60bd672d9ffe9;hb=2300716104b55267692efc2c0e506b3c5c45df38;hp=f65dc6298a90cdfc084ed7e2b960eb0d3e34f47e;hpb=163fa80ef3873595f3e3cf75fb03e53536d1a6ee;p=clitk.git diff --git a/common/clitkDicomRT_ROI.cxx b/common/clitkDicomRT_ROI.cxx index f65dc62..75fc8e9 100644 --- a/common/clitkDicomRT_ROI.cxx +++ b/common/clitkDicomRT_ROI.cxx @@ -2,9 +2,9 @@ Program: vv http://www.creatis.insa-lyon.fr/rio/vv Main authors : XX XX XX - Authors belongs to: + 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 @@ -17,53 +17,87 @@ =========================================================================*/ -#include "clitkDicomRT_ROI.h" +#include "clitkDicomRT_ROI.h" #include #include +#include +#include + +#if GDCM_MAJOR_VERSION == 2 +#include "gdcmAttribute.h" +#include "gdcmItem.h" +#endif //-------------------------------------------------------------------- -clitk::DicomRT_ROI::DicomRT_ROI() { +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; + SetDicomUptodateFlag(false); } //-------------------------------------------------------------------- //-------------------------------------------------------------------- -clitk::DicomRT_ROI::~DicomRT_ROI() { - +clitk::DicomRT_ROI::~DicomRT_ROI() +{ +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +void clitk::DicomRT_ROI::SetDisplayColor(double r, double v, double b) +{ + mColor.resize(3); + mColor[0] = r; + mColor[1] = v; + mColor[2] = b; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- -int clitk::DicomRT_ROI::GetROINumber() const { +int clitk::DicomRT_ROI::GetROINumber() const +{ return mNumber; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- -const std::string & clitk::DicomRT_ROI::GetName() const { +const std::string & clitk::DicomRT_ROI::GetName() const +{ return mName; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- -const std::vector & clitk::DicomRT_ROI::GetDisplayColor() const { +const std::string & clitk::DicomRT_ROI::GetFilename() const +{ + return mFilename; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +const std::vector & clitk::DicomRT_ROI::GetDisplayColor() const +{ return mColor; } //-------------------------------------------------------------------- - //-------------------------------------------------------------------- -void clitk::DicomRT_ROI::Print(std::ostream & os) const { - os << "ROI " << mNumber << "\t" << mName +void clitk::DicomRT_ROI::Print(std::ostream & os) const +{ + os << "ROI " << mNumber << "\t" << mName << "\t(" << mColor[0] << " " << mColor[1] << " " << mColor[2] << ")" << "\t Contours = " << mListOfContours.size() << std::endl; } @@ -71,15 +105,114 @@ void clitk::DicomRT_ROI::Print(std::ostream & os) const { //-------------------------------------------------------------------- -void clitk::DicomRT_ROI::Read(std::map & rois, gdcm::SQItem * item) { +void clitk::DicomRT_ROI::SetBackgroundValueLabelImage(double bg) +{ + mBackgroundValue = bg; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +double clitk::DicomRT_ROI::GetBackgroundValueLabelImage() const +{ + return mBackgroundValue; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +void clitk::DicomRT_ROI::SetForegroundValueLabelImage(double bg) +{ + mForegroundValue = bg; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +double clitk::DicomRT_ROI::GetForegroundValueLabelImage() const +{ + return mForegroundValue; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +#if GDCM_MAJOR_VERSION == 2 +bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour) +{ + // 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(); - // Change number if needed + // Check this is the same with the other item + const gdcm::DataSet & nestedds = mItemContour->GetNestedDataSet(); + gdcm::Attribute<0x3006,0x0084> referencedroinumber; + referencedroinumber.SetFromDataSet( nestedds ); + int nb2 = referencedroinumber.GetValue(); - // TODO + // Must never be different + if (nb1 != nb2) { + DD(nb2); + DD(nb1); + FATAL("nb1 must equal nb2" << std::endl); + } + mNumber = nb1; + + // 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 = {}; + color.SetFromDataSet( nestedds ); + assert( color.GetNumberOfValues() == 3 ); + mColor[0] = color.GetValue(0); + mColor[1] = color.GetValue(1); + mColor[2] = color.GetValue(2); + + // Read contours [Contour Sequence] + 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 ); + mContoursSequenceOfItems = csq.GetValueAsSQ(); + gdcm::SmartPointer & sqi2 = mContoursSequenceOfItems; + if( !sqi2 || !sqi2->GetNumberOfItems() ) + { + } + unsigned int nitems = sqi2->GetNumberOfItems(); + for(unsigned int i = 0; i < nitems; ++i) + { + 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) +{ // ROI number [Referenced ROI Number] mNumber = atoi(item->GetEntryValue(0x3006,0x0084).c_str()); - + // Retrieve ROI Name mName = rois[mNumber]; @@ -88,19 +221,39 @@ void clitk::DicomRT_ROI::Read(std::map & rois, gdcm::SQItem * // Read contours [Contour Sequence] gdcm::SeqEntry * contours=item->GetSeqEntry(0x3006,0x0040); - for(gdcm::SQItem* j=contours->GetFirstSQItem();j!=0;j=contours->GetNextSQItem()) { - DicomRT_Contour * c = new DicomRT_Contour; - bool b = c->Read(j); - if (b) mListOfContours.push_back(c); + 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 //-------------------------------------------------------------------- //-------------------------------------------------------------------- -vtkPolyData * clitk::DicomRT_ROI::GetMesh() { +void clitk::DicomRT_ROI::SetImage(vvImage * image) +{ + mImage = image; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +vtkPolyData * clitk::DicomRT_ROI::GetMesh() +{ if (!mMeshIsUpToDate) { - ComputeMesh(); + ComputeMeshFromContour(); } return mMesh; } @@ -108,29 +261,96 @@ vtkPolyData * clitk::DicomRT_ROI::GetMesh() { //-------------------------------------------------------------------- -void clitk::DicomRT_ROI::ComputeMesh() { - vtkAppendPolyData * append = vtkAppendPolyData::New(); +clitk::DicomRT_Contour * clitk::DicomRT_ROI::GetContour(int n) +{ + return mListOfContours[n]; +} +//-------------------------------------------------------------------- + + +//-------------------------------------------------------------------- +void clitk::DicomRT_ROI::ComputeMeshFromContour() +{ + vtkSmartPointer append = vtkSmartPointer::New(); for(unsigned int i=0; iAddInput(mListOfContours[i]->GetMesh()); } append->Update(); - mMesh = append->GetOutput(); + + mMesh = vtkSmartPointer::New(); + mMesh->DeepCopy(append->GetOutput()); mMeshIsUpToDate = true; } //-------------------------------------------------------------------- +#if GDCM_MAJOR_VERSION == 2 + //-------------------------------------------------------------------- -void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage::Pointer image, int n, - std::string name, - std::vector color) { - +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; 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) +{ + // ROI number [Referenced ROI Number] mNumber = n; - + // ROI Name mName = name; - + mFilename = filename; + // ROI Color [ROI Display Color] mColor = color; @@ -144,7 +364,54 @@ void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage::Pointer image, int n, //-------------------------------------------------------------------- -const vvImage::Pointer clitk::DicomRT_ROI::GetImage() const { +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()); + } +} +//--------------------------------------------------------------------