}
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROIFromROIName(const std::string& name)
+{
+ std::map<int, std::string>::iterator it = mMapOfROIName.begin();
+ int number = -1;
+ while (it != mMapOfROIName.end() && number == -1) {
+ if (it->second == name)
+ number = it->first;
+ else
+ it++;
+ }
+
+ if (number == -1) {
+ std::cerr << "No ROI name " << name << std::endl;
+ return NULL;
+ }
+
+ return mROIs[number];
+}
+//--------------------------------------------------------------------
+/*
+// RP: 08/02/2013
+// RegEx version shall be available when C++x11 supports it propely
+//
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROIFromROINameRegEx(const std::string& regEx)
+{
+ std::map<int, std::string>::iterator it = mMapOfROIName.begin();
+ int number = -1;
+
+ while (it != mMapOfROIName.end() && number == -1) {
+ if (std::tr1::regex_match (it->second, std::tr1::regex(regEx)))
+ number = it->first;
+ else
+ it++;
+ }
+
+ if (number == -1) {
+ std::cerr << "No ROI name " << number << std::endl;
+ return NULL;
+ }
+
+ return mROIs[number];
+}
+//--------------------------------------------------------------------
+*/
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROIFromROINameSubstr(const std::string& s)
+{
+ std::map<int, std::string>::iterator it = mMapOfROIName.begin();
+ int number = -1;
+
+ while (it != mMapOfROIName.end() && number == -1) {
+ if (it->second.find(s) != std::string::npos)
+ number = it->first;
+ else
+ it++;
+ }
+
+ if (number == -1) {
+ std::cerr << "No ROI name " << s << std::endl;
+ return NULL;
+ }
+
+ return mROIs[number];
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+clitk::DicomRT_StructureSet::ROIMapContainer *
+clitk::DicomRT_StructureSet::GetROIsFromROINameSubstr(const std::string& s)
+{
+ static ROIMapContainer rois;
+ rois.clear();
+
+ ROIMapContainer::iterator it = mROIs.begin();
+ int number = -1;
+
+ while (it != mROIs.end()) {
+ if (it->second->GetName().find(s) != std::string::npos) {
+ number = it->first;
+ rois[number] = it->second;
+ }
+ it++;
+ }
+
+ if (number == -1) {
+ std::cerr << "No ROI name " << s << std::endl;
+ return NULL;
+ }
+
+ return &rois;
+
+}
+//--------------------------------------------------------------------
//--------------------------------------------------------------------
void clitk::DicomRT_StructureSet::Print(std::ostream & os) const
void clitk::DicomRT_StructureSet::Write(const std::string & filename)
{
#if GDCM_MAJOR_VERSION == 2
- DD("DCM RT Writer");
// Assert that the gdcm file is still open (we can write only if it was readed)
if (mFile == NULL) {
}
// Loop and update each ROI
+ int i=0;
for(ROIIteratorType iter = mROIs.begin(); iter != mROIs.end(); iter++) {
iter->second->UpdateDicomItem();
+ i++;
}
// Write [ Structure Set ROI Sequence ] = 0x3006,0x0020
//--------------------------------------------------------------------
void clitk::DicomRT_StructureSet::Read(const std::string & filename)
{
+#if CLITK_USE_SYSTEM_GDCM == 1
+ vtkSmartPointer<vtkGDCMPolyDataReader> reader = vtkGDCMPolyDataReader::New();
+ reader->SetFileName(filename.c_str());
+ reader->Update();
+
+ // Get global information
+ vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
+ mStudyID = p->GetStudyInstanceUID();
+ mStudyDate = p->GetStructureSetDate();
+ mLabel = p->GetStructureSetLabel();
+ mName = p->GetStructureSetName();
+ mTime = p->GetStructureSetTime();
+
+ int n = p->GetNumberOfStructureSetROIs();
+ for(unsigned int i=0; i<n; i++) {
+ // Get the roi number
+ int roinumber = p->GetStructureSetROINumber(i);
+ // Create the roi
+ DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
+ roi->Read(reader, i);
+ // Insert in the map
+ mROIs[roinumber] = roi;
+ }
+ return;
+#endif // END version with system gdcm (vtkGDCMPolyDataReader)
+
+
// Open DICOM
#if GDCM_MAJOR_VERSION == 2
+ FATAL("Error : compile vv with itk4 + external gdcm");
+
// Read gdcm file
mReader = new gdcm::Reader;
mReader->SetFileName(filename.c_str());
// Temporary store the list of items
std::map<int, gdcm::Item*> mMapOfROIInfo;
std::map<int, gdcm::Item*> mMapOfROIContours;
+
+std::map<int, clitk::DicomRT_ROI::Pointer> mROIs;
+ std::map<int, std::string> mMapOfROIName;
+#if GDCM_MAJOR_VERSION == 2
+ gdcm::Reader * mReader;
+ gdcm::SmartPointer<gdcm::SequenceOfItems> mROIInfoSequenceOfItems;
+ gdcm::SmartPointer<gdcm::SequenceOfItems> mROIContoursSequenceOfItems;
+#endif
+ gdcm::File * mFile;
+
//----------------------------------
// Read all ROI Names and number
//--------------------------------------------------------------------
+//--------------------------------------------------------------------
+bool clitk::DicomRT_StructureSet::IsDicomRTStruct(const std::string & filename)
+{
+ // Open DICOM
+#if GDCM_MAJOR_VERSION == 2
+ // Read gdcm file
+ mReader = new gdcm::Reader;
+ mReader->SetFileName(filename.c_str());
+ mReader->Read();
+ mFile = &(mReader->GetFile());
+ const gdcm::DataSet & ds = mFile->GetDataSet();
+
+ // Check file type
+ //Verify if the file is a RT-Structure-Set dicom file
+ gdcm::MediaStorage ms;
+ ms.SetFromFile(*mFile);
+ if( ms != gdcm::MediaStorage::RTStructureSetStorage ) return false;
+
+ gdcm::Attribute<0x8,0x60> modality;
+ modality.SetFromDataSet( ds );
+ if( modality.GetValue() != "RTSTRUCT" ) return false;
+
+ return true;
+
+ //----------------------------------------------------------------------------------------
+#else
+ mFile = new gdcm::File;
+ mFile->SetFileName(filename.c_str());
+ mFile->SetMaxSizeLoadEntry(16384); // Needed ...
+ mFile->SetLoadMode(gdcm::LD_NOSHADOW); // don't load shadow tags (in order to save memory)
+ mFile->Load();
+
+ // Check file type
+ //Verify if the file is a RT-Structure-Set dicom file
+ if (!gdcm::Util::DicomStringEqual(mFile->GetEntryValue(0x0008,0x0016),"1.2.840.10008.5.1.4.1.1.481.3"))
+ return false;
+ if (!gdcm::Util::DicomStringEqual(mFile->GetEntryValue(0x0008,0x0060),"RTSTRUCT"))
+ return false;
+
+ return true;
+
+#endif
+}
+//--------------------------------------------------------------------
+
+
//--------------------------------------------------------------------
int clitk::DicomRT_StructureSet::AddBinaryImageAsNewROI(vvImage * im, std::string n)
{
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff