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"
+#if GDCM_MAJOR_VERSION == 2
+#include "gdcmReader.h"
+#include "gdcmAttribute.h"
+#endif
//--------------------------------------------------------------------
-clitk::DicomRT_StructureSet::DicomRT_StructureSet() {
+clitk::DicomRT_StructureSet::DicomRT_StructureSet()
+{
mStudyID = "NoStudyID";
mStudyTime = "NoStudyTime";
mStudyDate = "NoStudyDate";
//--------------------------------------------------------------------
-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 {
+const std::string & clitk::DicomRT_StructureSet::GetTime() const
+{
return mTime;
}
//--------------------------------------------------------------------
-
-
+
+
//--------------------------------------------------------------------
-const std::vector<clitk::DicomRT_ROI*> & clitk::DicomRT_StructureSet::GetListOfROI() const {
+const std::vector<clitk::DicomRT_ROI::Pointer> & clitk::DicomRT_StructureSet::GetListOfROI() const
+{
return mListOfROI;
}
//--------------------------------------------------------------------
-
-
+
+
//--------------------------------------------------------------------
-clitk::DicomRT_ROI* clitk::DicomRT_StructureSet::GetROI(int n) {
+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());
+ // DD(mListOfROI[mMapOfROIIndex[n]]->GetName());
+ //DD(mListOfROI[mMapOfROIIndex[n]]->GetROINumber());
return mListOfROI[mMapOfROIIndex[n]];
}
//--------------------------------------------------------------------
-
-
+
+
//--------------------------------------------------------------------
-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
//--------------------------------------------------------------------
-void clitk::DicomRT_StructureSet::Read(const std::string & filename) {
+void clitk::DicomRT_StructureSet::Read(const std::string & filename)
+{
// Open DICOM
+#if GDCM_MAJOR_VERSION == 2
+ gdcm::Reader reader;
+ reader.SetFileName(filename.c_str());
+ reader.Read();
+
+ const gdcm::File & file = reader.GetFile();
+ const gdcm::DataSet & ds = file.GetDataSet();
+
+ // Check file type
+ //Verify if the file is a RT-Structure-Set dicom file
+ gdcm::MediaStorage ms;
+ ms.SetFromFile(file);
+ if( ms != gdcm::MediaStorage::RTStructureSetStorage )
+ {
+ 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);
+ }
+
+ gdcm::Attribute<0x8,0x60> modality;
+ modality.SetFromDataSet( ds );
+ if( modality.GetValue() != "RTSTRUCT" )
+ {
+ 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
+ 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();
+
+ //----------------------------------
+ // Read all ROI Names and number
+ // 0x3006,0x0020 = [ Structure Set ROI Sequence ]
+ gdcm::Tag tssroisq(0x3006,0x0020);
+ const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ssroisq.GetValueAsSQ();
+ assert(roi_seq); // TODO error message
+ 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]
+ gdcm::Attribute<0x3006,0x0022> roinumber;
+ roinumber.SetFromDataSet( nestedds );
+ int nb = roinumber.GetValue(); // 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::Tag troicsq(0x3006,0x0039);
+ const gdcm::DataElement &roicsq = ds.GetDataElement( troicsq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_contour_seq = roicsq.GetValueAsSQ();
+ assert(roi_contour_seq); // TODO error message
+ int n=0;
+ for(unsigned int ridx = 0; ridx < roi_contour_seq->GetNumberOfItems(); ++ridx)
+ {
+ gdcm::Item & item = roi_contour_seq->GetItem( ridx + 1); // Item starts at 1
+
+ DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
+ roi->Read(mMapOfROIName, item);
+ mListOfROI.push_back(roi);
+ mMapOfROIIndex[roi->GetROINumber()] = n;
+ n++;
+ }
+
+#else
gdcm::File reader;
reader.SetFileName(filename.c_str());
reader.SetMaxSizeLoadEntry(16384); // Needed ...
// 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
+ 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
+ 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();
+ if (!reader.GetValEntry(0x3006,0x004)) {
+ mName = "Anonymous";
+ }
+ else {
+ 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]
+ 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;
+ 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
// 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;
+ for (gdcm::SQItem* r=roi_contour_seq->GetFirstSQItem(); r!=0; r=roi_contour_seq->GetNextSQItem()) {
+ DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
roi->Read(mMapOfROIName, r);
mListOfROI.push_back(roi);
mMapOfROIIndex[roi->GetROINumber()] = n;
n++;
}
+#endif
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-int clitk::DicomRT_StructureSet::AddBinaryImageAsNewROI(vvImage::Pointer im, std::string n) {
- DD("AddBinaryImageAsNewROI");
+int clitk::DicomRT_StructureSet::AddBinaryImageAsNewROI(vvImage * im, std::string n)
+{
+ //DD("AddBinaryImageAsNewROI");
// Search max ROI number
int max = -1;
for(unsigned int i=0; i<mListOfROI.size(); i++) {
- if (mListOfROI[i]->GetROINumber() > max)
+ if (mListOfROI[i]->GetROINumber() > max)
max = mListOfROI[i]->GetROINumber();
}
- DD(max);
+ // DD(max);
++max;
- DD(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));
+ // << "_roi_" << max << vtksys::SystemTools::GetFilenameLastExtension(n);
+ //DD(oss.str());
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);
+ DicomRT_ROI::Pointer roi = DicomRT_ROI::New();
+ roi->SetFromBinaryImage(im, max, oss.str(), color, n);
mListOfROI.push_back(roi);
mMapOfROIIndex[mListOfROI.size()-1] = max;
- DD(mMapOfROIIndex[mListOfROI.size()-1]);
+ //DD(mMapOfROIIndex[mListOfROI.size()-1]);
return max;
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff