/*========================================================================= Program: vv http://www.creatis.insa-lyon.fr/rio/vv Main authors : XX XX XX Authors belongs to: - University of LYON http://www.universite-lyon.fr/ - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the copyright notices for more information. It is distributed under dual licence - BSD http://www.opensource.org/licenses/bsd-license.php - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html =========================================================================*/ #include "clitkDicomRT_StructureSet.h" #include //-------------------------------------------------------------------- clitk::DicomRT_StructureSet::DicomRT_StructureSet() { mStudyID = "NoStudyID"; mStudyTime = "NoStudyTime"; mStudyDate = "NoStudyDate"; mLabel = "NoLabel"; mName = "NoName"; mDate = "NoDate"; mTime = "NoTime"; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- clitk::DicomRT_StructureSet::~DicomRT_StructureSet() { } //-------------------------------------------------------------------- //-------------------------------------------------------------------- const std::string & clitk::DicomRT_StructureSet::GetStudyID() const { return mStudyID; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- const std::string & clitk::DicomRT_StructureSet::GetStudyTime() const { return mStudyTime; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- const std::string & clitk::DicomRT_StructureSet::GetStudyDate() const { return mStudyDate; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- const std::string & clitk::DicomRT_StructureSet::GetLabel() const { return mLabel; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- const std::string & clitk::DicomRT_StructureSet::GetName() const { return mName; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- const std::string & clitk::DicomRT_StructureSet::GetDate() const { return mDate; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- const std::string & clitk::DicomRT_StructureSet::GetTime() const { return mTime; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- const std::vector & clitk::DicomRT_StructureSet::GetListOfROI() const { return mListOfROI; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROI(int n) { if (mMapOfROIIndex.find(n) == mMapOfROIIndex.end()) { std::cerr << "No ROI number " << n << std::endl; return NULL; } // DD(mListOfROI[mMapOfROIIndex[n]]->GetName()); //DD(mListOfROI[mMapOfROIIndex[n]]->GetROINumber()); return mListOfROI[mMapOfROIIndex[n]]; } //-------------------------------------------------------------------- //-------------------------------------------------------------------- void clitk::DicomRT_StructureSet::Print(std::ostream & os) const { os << "Study ID = " << mStudyID << std::endl << "Study Date = " << mStudyDate << std::endl << "Study Time = " << mStudyTime << std::endl << "Struct Label = " << mLabel << std::endl << "Struct Name = " << mName << std::endl << "Struct Time = " << mTime << std::endl << "Number of ROI = " << mListOfROI.size() << std::endl; for(unsigned int i=0; iPrint(os); } } //-------------------------------------------------------------------- //-------------------------------------------------------------------- void clitk::DicomRT_StructureSet::Read(const std::string & filename) { // Open DICOM gdcm::File reader; reader.SetFileName(filename.c_str()); reader.SetMaxSizeLoadEntry(16384); // Needed ... reader.SetLoadMode(gdcm::LD_NOSHADOW); // don't load shadow tags (in order to save memory) reader.Load(); // Check file type //Verify if the file is a RT-Structure-Set dicom file if (!gdcm::Util::DicomStringEqual(reader.GetEntryValue(0x0008,0x0016),"1.2.840.10008.5.1.4.1.1.481.3")) { //SOP clas UID std::cerr << "Error. the file " << filename << " is not a Dicom Struct ? (must have a SOP Class UID [0008|0016] = 1.2.840.10008.5.1.4.1.1.481.3 ==> [RT Structure Set Storage])" << std::endl; exit(0); } if (!gdcm::Util::DicomStringEqual(reader.GetEntryValue(0x0008,0x0060),"RTSTRUCT")) { //SOP clas UID std::cerr << "Error. the file " << filename << " is not a Dicom Struct ? (must have 0x0008,0x0060 = RTSTRUCT [RT Structure Set Storage])" << std::endl; exit(0); } // Read global info mStudyID = reader.GetValEntry(0x0020,0x0010)->GetValue(); mStudyTime = reader.GetValEntry(0x008,0x0020)->GetValue(); mStudyDate = reader.GetValEntry(0x008,0x0030)->GetValue(); mLabel = reader.GetValEntry(0x3006,0x002)->GetValue(); mName = reader.GetValEntry(0x3006,0x004)->GetValue(); mTime = reader.GetValEntry(0x3006,0x009)->GetValue(); //---------------------------------- // Read all ROI Names and number // 0x3006,0x0020 = [ Structure Set ROI Sequence ] gdcm::SeqEntry * roi_seq=reader.GetSeqEntry(0x3006,0x0020); assert(roi_seq); // TODO error message for (gdcm::SQItem* r=roi_seq->GetFirstSQItem(); r!=0; r=roi_seq->GetNextSQItem()) { std::string name = r->GetEntryValue(0x3006,0x0026); // 0x3006,0x0026 = [ROI Name] int nb = atoi(r->GetEntryValue(0x3006,0x0022).c_str()); // 0x3006,0x0022 = [ROI Number] // Change number if needed //TODO // Check if such a number already exist if (mMapOfROIName.find(nb) != mMapOfROIName.end()) { std::cerr << "WARNING. A Roi already exist with the number " << nb << ". I replace." << std::endl; } // Add in map mMapOfROIName[nb] = name; } // DD(mMapOfROIName.size()); //---------------------------------- // Read all ROI // 0x3006,0x0039 = [ ROI Contour Sequence ] gdcm::SeqEntry * roi_contour_seq=reader.GetSeqEntry(0x3006,0x0039); assert(roi_contour_seq); // TODO error message int n=0; for (gdcm::SQItem* r=roi_contour_seq->GetFirstSQItem(); r!=0; r=roi_contour_seq->GetNextSQItem()) { DicomRT_ROI * roi = new DicomRT_ROI; roi->Read(mMapOfROIName, r); mListOfROI.push_back(roi); mMapOfROIIndex[roi->GetROINumber()] = n; n++; } } //-------------------------------------------------------------------- //-------------------------------------------------------------------- int clitk::DicomRT_StructureSet::AddBinaryImageAsNewROI(vvImage::Pointer im, std::string n) { //DD("AddBinaryImageAsNewROI"); // Search max ROI number int max = -1; for(unsigned int i=0; iGetROINumber() > max) max = mListOfROI[i]->GetROINumber(); } // DD(max); ++max; //DD(max); // Compute name std::ostringstream oss; oss << vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(n)); // << "_roi_" << max << vtksys::SystemTools::GetFilenameLastExtension(n); //DD(oss.str()); mMapOfROIName[max] = oss.str(); // Set color std::vector color; color.push_back(1); color.push_back(0); color.push_back(0); // Create ROI DicomRT_ROI * roi = new DicomRT_ROI; roi->SetFromBinaryImage(im, max, oss.str(), color, n); mListOfROI.push_back(roi); mMapOfROIIndex[mListOfROI.size()-1] = max; //DD(mMapOfROIIndex[mListOfROI.size()-1]); return max; } //--------------------------------------------------------------------