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
=========================================================================*/
-#include "clitkDicomRT_StructureSet.h"
+#include "clitkDicomRT_StructureSet.h"
#include <vtksys/SystemTools.hxx>
+#include "gdcmFile.h"
//--------------------------------------------------------------------
-clitk::DicomRT_StructureSet::DicomRT_StructureSet() {
+clitk::DicomRT_StructureSet::DicomRT_StructureSet()
+{
mStudyID = "NoStudyID";
mStudyTime = "NoStudyTime";
mStudyDate = "NoStudyDate";
mName = "NoName";
mDate = "NoDate";
mTime = "NoTime";
+ mFile = NULL;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-clitk::DicomRT_StructureSet::~DicomRT_StructureSet() {
-
+clitk::DicomRT_StructureSet::~DicomRT_StructureSet()
+{
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-const std::string & clitk::DicomRT_StructureSet::GetStudyID() const {
+const std::string & clitk::DicomRT_StructureSet::GetStudyID() const
+{
return mStudyID;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-const std::string & clitk::DicomRT_StructureSet::GetStudyTime() const{
+const std::string & clitk::DicomRT_StructureSet::GetStudyTime() const
+{
return mStudyTime;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-const std::string & clitk::DicomRT_StructureSet::GetStudyDate() const {
+const std::string & clitk::DicomRT_StructureSet::GetStudyDate() const
+{
return mStudyDate;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-const std::string & clitk::DicomRT_StructureSet::GetLabel() const {
+const std::string & clitk::DicomRT_StructureSet::GetLabel() const
+{
return mLabel;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-const std::string & clitk::DicomRT_StructureSet::GetName() const {
+const std::string & clitk::DicomRT_StructureSet::GetName() const
+{
return mName;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-const std::string & clitk::DicomRT_StructureSet::GetDate() const {
+const std::string & clitk::DicomRT_StructureSet::GetDate() const
+{
return mDate;
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-const std::string & clitk::DicomRT_StructureSet::GetTime() const {
- return mTime;
+void clitk::DicomRT_StructureSet::SetTransformMatrix(vtkMatrix4x4* matrix)
+{
+ mTransformMatrix = matrix;
}
//--------------------------------------------------------------------
-
-
+
+
//--------------------------------------------------------------------
-const std::vector<clitk::DicomRT_ROI*> & clitk::DicomRT_StructureSet::GetListOfROI() const {
- return mListOfROI;
+const std::string & clitk::DicomRT_StructureSet::GetTime() const
+{
+ return mTime;
}
//--------------------------------------------------------------------
-
-
+
+
//--------------------------------------------------------------------
-clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROI(int n) {
- if (mMapOfROIIndex.find(n) == mMapOfROIIndex.end()) {
+// const std::vector<clitk::DicomRT_ROI::Pointer> & clitk::DicomRT_StructureSet::GetListOfROI() const
+// {
+// return mListOfROI;
+// }
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROIFromROINumber(int n)
+{
+ if (mROIs.find(n) == mROIs.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]];
+ return mROIs[n];
}
//--------------------------------------------------------------------
-
-
+
+//--------------------------------------------------------------------
+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::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; i<mListOfROI.size(); i++) {
- mListOfROI[i]->Print(os);
+ << "Number of ROI = " << mROIs.size() << std::endl;
+ for(ROIConstIteratorType iter = mROIs.begin(); iter != mROIs.end(); iter++) {
+ iter->second->Print(os);
}
}
//--------------------------------------------------------------------
+#if GDCM_MAJOR_VERSION >= 2
//--------------------------------------------------------------------
-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();
+int clitk::DicomRT_StructureSet::ReadROINumber(const gdcm::Item & item)
+{
+ // 0x3006,0x0022 = [ROI Number]
+ const gdcm::DataSet & nestedds = item.GetNestedDataSet();
+ gdcm::Attribute<0x3006,0x0022> roinumber;
+ roinumber.SetFromDataSet( nestedds );
+ return roinumber.GetValue();
+}
+//--------------------------------------------------------------------
+#endif
- // 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);
- }
+//--------------------------------------------------------------------
+void clitk::DicomRT_StructureSet::Write(const std::string & filename)
+{
+#if GDCM_MAJOR_VERSION >= 2
+
+ // Assert that the gdcm file is still open (we can write only if it was readed)
+ if (mFile == NULL) {
+ //assert(mFile != NULL);
+ FATAL("Sorry, I can write DICOM only if it was read first from a file with 'Read' function");
+ }
+
+ // 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
+ gdcm::DataSet & ds = mFile->GetDataSet();
+ gdcm::Tag tssroisq(0x3006,0x0020);
+ const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+ gdcm::DataElement de(ssroisq);
+ de.SetValue(*mROIInfoSequenceOfItems);
+ ds.Replace(de);
+
+ // Write [ ROI Contour Sequence ] = 0x3006,0x0039
+ DD("ici");
+ gdcm::Tag troicsq(0x3006,0x0039);
+ const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
+ gdcm::DataElement de2(roicsq);
+ de2.SetValue(*mROIContoursSequenceOfItems);
+ ds.Replace(de2);
+
+ //DEBUG
+ gdcm::DataSet & a = mROIContoursSequenceOfItems->GetItem(1).GetNestedDataSet();
+ gdcm::Tag tcsq(0x3006,0x0040);
+ const gdcm::DataElement& csq = a.GetDataElement( tcsq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> sqi2 = csq.GetValueAsSQ();
+ gdcm::Item & j = sqi2->GetItem(1);
+ gdcm::DataSet & b = j.GetNestedDataSet();
+ gdcm::Attribute<0x3006,0x0050> at;
+ gdcm::Tag tcontourdata(0x3006,0x0050);
+ gdcm::DataElement contourdata = b.GetDataElement( tcontourdata );
+ at.SetFromDataElement( contourdata );
+ const double* points = at.GetValues();
+ DD(points[0]);
+
+
+ // Write dicom
+ gdcm::Writer writer;
+ //writer.CheckFileMetaInformationOff();
+ writer.SetFileName(filename.c_str());
+ writer.SetFile(*mFile);
+ DD("before write");
+ writer.Write();
+ DD("End write");
+#else
+ FATAL("Sorry not compatible with GDCM1, use GDCM2");
+#endif
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+void clitk::DicomRT_StructureSet::Read(const std::string & filename)
+{
+
+//Try to avoid to use extern GDCM library
+
+ //check the RS file is available before conversion
+ gdcm::Reader RTreader;
+ RTreader.SetFileName( filename.c_str() );
+ if( !RTreader.Read() )
+ {
+ std::cout << "Problem reading file: " << filename << std::endl;
+ return;
+ }
+
+ const gdcm::DataSet& ds = RTreader.GetFile().GetDataSet();
+
+ gdcm::MediaStorage ms;
+ ms.SetFromFile( RTreader.GetFile() );
+
+ // (3006,0020) SQ (Sequence with explicit length #=4) # 370, 1 StructureSetROISequence
+ gdcm::Tag tssroisq(0x3006,0x0020);
+ if( !ds.FindDataElement( tssroisq ) )
+ {
+ std::cout << "Problem locating 0x3006,0x0020 - Is this a valid RT Struct file?" << std::endl;
+ return;
+ }
+ gdcm::Tag troicsq(0x3006,0x0039);
+ if( !ds.FindDataElement( troicsq ) )
+ {
+ std::cout << "Problem locating 0x3006,0x0039 - Is this a valid RT Struct file?" << std::endl;
+ return;
+ }
+ const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
+
+ gdcm::SmartPointer<gdcm::SequenceOfItems> sqi = roicsq.GetValueAsSQ();
+ if( !sqi || !sqi->GetNumberOfItems() )
+ {
+ return;
+ }
+ const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> ssqi = ssroisq.GetValueAsSQ();
+ if( !ssqi || !ssqi->GetNumberOfItems() )
+ {
+ return;
+ }
+
// 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();
+ gdcm::Attribute<0x20,0x10> studyid;
+ studyid.SetFromDataSet( ds );
+ gdcm::Attribute<0x8,0x20> studytime;
+ studytime.SetFromDataSet( ds );
+ gdcm::Attribute<0x8,0x30> studydate;
+ studydate.SetFromDataSet( ds );
+ gdcm::Attribute<0x3006,0x02> label;
+ label.SetFromDataSet( ds );
+ gdcm::Attribute<0x3006,0x04> atname;
+ atname.SetFromDataSet( ds );
+ gdcm::Attribute<0x3006,0x09> time;
+ time.SetFromDataSet( ds );
+
+ mStudyID = studyid.GetValue();
+ mStudyTime = studytime.GetValue();
+ mStudyDate = studydate.GetValue();
+ mLabel = label.GetValue();
+ mName = atname.GetValue();
+ mTime = time.GetValue();
+
+ // Temporary store the list of items
+ std::map<int, gdcm::Item*> mMapOfROIInfo;
+ std::map<int, gdcm::Item*> mMapOfROIContours;
+
//----------------------------------
// Read all ROI Names and number
// 0x3006,0x0020 = [ Structure Set ROI Sequence ]
- gdcm::SeqEntry * roi_seq=reader.GetSeqEntry(0x3006,0x0020);
+ //gdcm::Tag tssroisq(0x3006,0x0020);
+ //const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+ mROIInfoSequenceOfItems = ssroisq.GetValueAsSQ();
+ gdcm::SmartPointer<gdcm::SequenceOfItems> & roi_seq = mROIInfoSequenceOfItems;
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
+ for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx)
+ {
+ gdcm::Item & item = roi_seq->GetItem( ridx + 1); // Item starts at 1
+ const gdcm::DataSet& nestedds = item.GetNestedDataSet();
+
+ gdcm::Attribute<0x3006,0x26> roiname;
+ roiname.SetFromDataSet( nestedds );
+ std::string name = roiname.GetValue(); // 0x3006,0x0026 = [ROI Name]
+
+ // 0x3006,0x0022 = [ROI Number]
+ int nb = ReadROINumber(item);
+
+ // Store the item
+ mMapOfROIInfo[nb] = &item;
// 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;
+ 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
+ // Read all ROI item
// 0x3006,0x0039 = [ ROI Contour Sequence ]
- gdcm::SeqEntry * roi_contour_seq=reader.GetSeqEntry(0x3006,0x0039);
+ //gdcm::Tag troicsq(0x3006,0x0039);
+ //const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_contour_seq = roicsq.GetValueAsSQ();
+ mROIContoursSequenceOfItems = roi_contour_seq;
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++;
+ for(unsigned int ridx = 0; ridx < roi_contour_seq->GetNumberOfItems(); ++ridx) {
+ gdcm::Item & item = roi_contour_seq->GetItem( ridx + 1); // Item starts at 1
+ // ROI number [Referenced ROI Number]
+ const gdcm::DataSet& nestedds = item.GetNestedDataSet();
+ gdcm::Attribute<0x3006,0x0084> referencedroinumber;
+ referencedroinumber.SetFromDataSet( nestedds );
+ int nb = referencedroinumber.GetValue();
+ // Store the item
+ mMapOfROIContours[nb] = &item;
+ }
+
+ //----------------------------------
+ // Create the ROIs
+ for(std::map<int, gdcm::Item*>::iterator i = mMapOfROIInfo.begin(); i != mMapOfROIInfo.end(); i++) {
+ int nb = i->first;//ReadROINumber(i);//mROIIndex[i];
+ // Create the roi
+ mROIs[nb] = DicomRT_ROI::New();
+ mROIs[nb]->SetTransformMatrix(mTransformMatrix);
+ mROIs[nb]->Read(mMapOfROIInfo[nb], mMapOfROIContours[nb]);
}
+
+ return;
+
+}
+//--------------------------------------------------------------------
+
+//--------------------------------------------------------------------
+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::Pointer im, std::string n) {
- DD("AddBinaryImageAsNewROI");
+int clitk::DicomRT_StructureSet::AddBinaryImageAsNewROI(vvImage * im, std::string n)
+{
// Search max ROI number
int max = -1;
- for(unsigned int i=0; i<mListOfROI.size(); i++) {
- if (mListOfROI[i]->GetROINumber() > max)
- max = mListOfROI[i]->GetROINumber();
+ for(ROIConstIteratorType iter = mROIs.begin(); iter != mROIs.end(); iter++) {
+ // for(unsigned int i=0; i<mListOfROI.size(); i++) {
+ clitk::DicomRT_ROI::Pointer roi = iter->second;
+ if (roi->GetROINumber() > max)
+ max = roi->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());
+ oss << vtksys::SystemTools::GetFilenameName(vtksys::SystemTools::GetFilenameWithoutLastExtension(n));
mMapOfROIName[max] = oss.str();
// Set 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);
- mListOfROI.push_back(roi);
- mMapOfROIIndex[mListOfROI.size()-1] = max;
- DD(mMapOfROIIndex[mListOfROI.size()-1]);
+ DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
+ roi->SetFromBinaryImage(im, max, oss.str(), color, n);
+ mROIs[max] = roi;
return max;
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff