/*=========================================================================
+ Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Program: vv
- Language: C++
- Author : Joel Schaerer (joel.schaerer@insa-lyon.fr)
+ Authors belong to:
+ - University of LYON http://www.universite-lyon.fr/
+ - Léon Bérard cancer center http://www.centreleonberard.fr
+ - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
-Copyright (C) 2008
-Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
-CREATIS-LRMN 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.
-This program is free software: you can redistribute it and/or modify
-it under the terms of the GNU General Public License as published by
-the Free Software Foundation, version 3 of the License.
+ It is distributed under dual licence
-This program is distributed in the hope that it will be useful,
-but WITHOUT ANY WARRANTY; without even the implied warranty of
-MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
-GNU General Public License for more details.
+ - BSD See included LICENSE.txt file
+ - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+ ===========================================================================**/
-You should have received a copy of the GNU General Public License
-along with this program. If not, see <http://www.gnu.org/licenses/>.
-
-=========================================================================*/
+// std
#include <algorithm>
+// qt
#include <QApplication>
+// gdcm
+#include <gdcmFile.h>
+#if GDCM_MAJOR_VERSION >= 2
+#include <gdcmReader.h>
+#include <gdcmTag.h>
+#include <gdcmAttribute.h>
+#else
#include <gdcm.h>
#include <gdcmSQItem.h>
+#endif
+// vtk
+#include <vtkVersion.h>
#include <vtkSmartPointer.h>
#include <vtkAppendPolyData.h>
#include <vtkCellArray.h>
#include <vtkImageCast.h>
#include <vtkImageGaussianSmooth.h>
+// clitk
+#include "clitkCommon.h"
#include "clitkCommon.h"
+#include "clitkDicomRT_StructureSet.h"
#include "vvMeshReader.h"
#include "vvProgressDialog.h"
+//------------------------------------------------------------------------------
vvMeshReader::vvMeshReader() :
- vtk_mode(false)
+vtk_mode(false)
{}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvMeshReader::Update()
{
- //Show a progress bar only when opening a DC-struct (ie. multiple contours)
- vvProgressDialog progress("Opening " + filename,(!vtk_mode) && (selected_contours.size()>1));
- this->start();
- while (this->isRunning())
- {
- progress.SetProgress(result.size(),selected_contours.size());
- this->wait(50);
- qApp->processEvents();
- }
+ //Show a progress bar only when opening a DC-struct (ie. multiple contours)
+ vvProgressDialog progress("Opening " + filename,(!vtk_mode) && (selected_contours.size()>1));
+ this->start();
+ while (this->isRunning()) {
+ progress.SetProgress(result.size(),selected_contours.size());
+ this->wait(50);
+ qApp->processEvents();
+ }
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
void vvMeshReader::run()
{
- ///Verify the important stuff has been set
- assert(filename != "");
- if (vtk_mode) //Read vtkPolyData
- {
- vvMesh::Pointer m=vvMesh::New();
- m->ReadFromVTK(filename.c_str());
- if (vf) m->propagateContour(vf);
- m->ComputeMasks(image->GetVTKImages()[0],true);
- result.push_back(m);
- }
- else //Read a Dicom-struct file
- {
- assert(selected_contours.size() > 0);
- assert(image);
- std::vector<vvMesh::Pointer> contour_stacks=readSelectedContours();
- for (std::vector<vvMesh::Pointer>::iterator i=contour_stacks.begin();
- i!=contour_stacks.end();i++)
- {
- (*i)->ComputeMasks(image->GetVTKImages()[0],true); //Remesh the contour
- (*i)->ComputeMeshes();
- if (vf) (*i)->propagateContour(vf);
- result.push_back(*i);
- }
+ ///Verify the important stuff has been set
+ assert(filename != "");
+ if (vtk_mode) { //Read vtkPolyData
+ vvMesh::Pointer m=vvMesh::New();
+ m->ReadFromVTK(filename.c_str());
+ if (vf) m->propagateContour(vf);
+ m->ComputeMasks(image->GetVTKImages()[0],false); //don't extrude the contour
+ result.push_back(m);
+ } else { //Read a Dicom-struct file
+ assert(selected_contours.size() > 0);
+ assert(image);
+ std::vector<vvMesh::Pointer> contour_stacks=readSelectedContours();
+ for (std::vector<vvMesh::Pointer>::iterator i=contour_stacks.begin();
+ i!=contour_stacks.end(); i++) {
+ (*i)->ComputeMasks(image->GetVTKImages()[0],true); //Remesh the contour
+ (*i)->ComputeMeshes();
+ if (vf) (*i)->propagateContour(vf);
+ result.push_back(*i);
}
+ }
}
+//------------------------------------------------------------------------------
-template<class ElementType>
-ElementType parse_value(std::string str)
-{
- std::istringstream parser(str);
- ElementType value;
- parser >> value;
- assert(!parser.fail());
- return value;
-}
-template<class ElementType>
-std::vector<ElementType> parse_string(std::string str,char delim)
+//------------------------------------------------------------------------------
+std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
{
- std::istringstream ss(str);
- std::string token;
- std::vector<ElementType> result;
- while (getline(ss,token,delim))
- {
- result.push_back(parse_value<ElementType>(token));
+ assert(filename!="");
+ std::vector<std::pair<int, std::string> > roi_names;
+
+#if CLITK_USE_SYSTEM_GDCM == 1
+
+ // Read RT-struct data
+ vtkSmartPointer<vtkGDCMPolyDataReader> areader = vtkGDCMPolyDataReader::New();
+ areader->SetFileName(filename.c_str());
+ areader->Update();
+
+ // get info on roi names
+ vtkRTStructSetProperties * p = areader->GetRTStructSetProperties();
+ int n = p->GetNumberOfStructureSetROIs();
+
+ for(unsigned int i=0; i<n; i++) {
+ std::string name = p->GetStructureSetROIName(i);
+ int nb = p->GetStructureSetROINumber(i);
+ roi_names.push_back(make_pair(nb,name));
+ }
+
+#else
+#if GDCM_MAJOR_VERSION >= 2
+
+ // duplicate code from clitk::DicomRT_StructureSet::Read
+ gdcm::Reader * reader = new gdcm::Reader;
+ reader->SetFileName( filename.c_str() );
+ reader->Read();
+
+ const gdcm::DataSet &ds = reader->GetFile().GetDataSet();
+
+ // Check file type
+ //Verify if the file is a RT-Structure-Set dicom file
+ gdcm::File * mFile = &(reader->GetFile());
+ gdcm::MediaStorage ms;
+ ms.SetFromFile(*mFile);
+ 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);
+ }
+
+ gdcm::Attribute<0x20,0x10> studyid;
+ studyid.SetFromDataSet( ds );
+
+ gdcm::Tag tssroisq(0x3006,0x0020);
+ // 0x3006,0x0020 = [ Structure Set ROI Sequence ]
+ bool b = ds.FindDataElement(tssroisq);
+ if (!b) { // FIXME
+ clitkExceptionMacro("Error: tag 0x3006,0x0020 [ Structure Set ROI Sequence ] not found");
}
- return result;
-}
+
+ const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ssroisq.GetValueAsSQ();
+ assert(roi_seq); // FIXME error message
+
+ for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx)
+ {
+ gdcm::Item & item = roi_seq->GetItem( ridx + 1); // Item starts at 1
-std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
-{
- assert(filename!="");
- gdcm::File reader;
- reader.SetFileName(filename.c_str());
- reader.SetMaxSizeLoadEntry(16384);
- reader.Load();
-
- gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
- assert(roi_info);
- std::vector<std::pair<int, std::string> > roi_names;
- // DD("ici");
- //int n=0;
- for (gdcm::SQItem* i=roi_info->GetFirstSQItem();i!=0;i=roi_info->GetNextSQItem())
- if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
- roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
- return roi_names;
+ const gdcm::Item & sitem = roi_seq->GetItem(ridx+1); // Item start at #1
+
+ const gdcm::DataSet& snestedds = sitem.GetNestedDataSet();
+ const gdcm::DataSet& nestedds = item.GetNestedDataSet();
+
+ if( snestedds.FindDataElement( gdcm::Tag(0x3006,0x22) ) )
+ {
+ // const gdcm::DataElement & a = nestedds.GetDataElement(gdcm::Tag(0x3006,0x26));
+ // DD(a.GetValue());
+
+ gdcm::Attribute<0x3006,0x26> roiname;
+ roiname.SetFromDataSet( snestedds );
+ std::string name = roiname.GetValue(); // 0x3006,0x0026 = [ROI Name]
+ gdcm::Attribute<0x3006,0x0022> roinumber;
+ roinumber.SetFromDataSet( snestedds );
+ int nb = roinumber.GetValue(); // 0x3006,0x0022 = [ROI Number]
+
+ roi_names.push_back(make_pair(nb,name));
+ }
+ }
+
+ delete reader;
+
+#else
+ gdcm::File reader;
+ reader.SetFileName(filename.c_str());
+ reader.SetMaxSizeLoadEntry(16384);
+ reader.Load();
+
+ gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
+ assert(roi_info);
+ // DD("ici");
+ //int n=0;
+ for (gdcm::SQItem* i=roi_info->GetFirstSQItem(); i!=0; i=roi_info->GetNextSQItem())
+ if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
+ roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
+#endif
+#endif
+
+ return roi_names;
}
+//------------------------------------------------------------------------------
+
+//------------------------------------------------------------------------------
std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
{
- gdcm::File reader;
- reader.SetFileName(filename.c_str());
- reader.SetMaxSizeLoadEntry(16384);
- reader.Load();
-
- std::vector<vvMesh::Pointer> result;
- gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
- ///We need to iterate both on the contours themselves, and on the contour info
- gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
- gdcm::SQItem* k=roi_info->GetFirstSQItem();
- for(gdcm::SQItem* i=rois->GetFirstSQItem();i!=0;i=rois->GetNextSQItem()) //loop over ROIS
+ std::vector<vvMesh::Pointer> result;
+#if GDCM_MAJOR_VERSION >= 2
+ gdcm::Reader reader;
+ reader.SetFileName(filename.c_str());
+ reader.Read();
+
+ const gdcm::DataSet &ds = reader.GetFile().GetDataSet();
+
+ gdcm::SmartPointer<gdcm::SequenceOfItems> rois = ds.GetDataElement(gdcm::Tag(0x3006,0x39)).GetValueAsSQ();
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_info = ds.GetDataElement(gdcm::Tag(0x3006,0x20)).GetValueAsSQ();
+ assert(rois); // TODO error message
+ assert(roi_info); // TODO error message
+ assert(rois->GetNumberOfItems() == roi_info->GetNumberOfItems());
+
+ for (unsigned ridx = 0; ridx < rois->GetNumberOfItems(); ++ridx)
{
- assert(k!=0);
- vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
- std::istringstream ss(i->GetEntryValue(0x3006,0x0084));
- int roi_number;ss >> roi_number;
- if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end())//Only read selected ROIs
+ vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
+ const gdcm::DataSet& ds_rois = rois->GetItem( ridx + 1).GetNestedDataSet();
+ const gdcm::DataSet& ds_roi_info = roi_info->GetItem( ridx + 1).GetNestedDataSet();
+
+ gdcm::Attribute<0x3006,0x84> roinumber;
+ roinumber.SetFromDataSet(ds_rois);
+ if (std::find(selected_contours.begin(), selected_contours.end(), roinumber.GetValue()) != selected_contours.end()) //Only read selected ROIs
{
- vvMesh::Pointer current_roi=vvMesh::New();
- std::vector<double> rgb=parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
- assert(rgb.size()==3);
- current_roi->r=rgb[0]/255; current_roi->g=rgb[1]/255; current_roi->b=rgb[2]/255;
- current_roi->structure_name=k->GetEntryValue(0x3006,0x0026);
- gdcm::SeqEntry * contours=i->GetSeqEntry(0x3006,0x0040);
- double z0=-1; //Used to determine spacing between slices, assumed to be constant
- for(gdcm::SQItem* j=contours->GetFirstSQItem();j!=0;j=contours->GetNextSQItem()) //loop over 2D contours
+ gdcm::Attribute<0x3006,0x2a> trgb;
+ trgb.SetFromDataSet(ds_rois);
+ vvMesh::Pointer current_roi=vvMesh::New();
+ current_roi->r = trgb[0] / 255.0;
+ current_roi->g = trgb[1] / 255.0;
+ current_roi->b = trgb[2] / 255.0;
+
+ gdcm::Attribute<0x3006,0x26> tstructure_name;
+ tstructure_name.SetFromDataSet(ds_roi_info);
+ current_roi->structure_name = tstructure_name.GetValue();
+
+ gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ds_rois.GetDataElement(gdcm::Tag(0x3006,0x40)).GetValueAsSQ();
+ double z0=-1; //Used to determine spacing between slices, assumed to be constant
+ for (unsigned j = 0; j < roi_seq->GetNumberOfItems(); ++j)
{
- std::string contour_type=j->GetEntryValue(0x3006,0x0042);
- if (contour_type=="CLOSED_PLANAR ")
+ gdcm::Item & item_roi_seq = roi_seq->GetItem(j + 1); // Item starts at 1
+ const gdcm::DataSet& ds_roi_seq = item_roi_seq.GetNestedDataSet();
+ gdcm::Attribute<0x3006,0x42> tcontour_type;
+ tcontour_type.SetFromDataSet(ds_roi_seq);
+ std::string contour_type = tcontour_type.GetValue();
+ if (contour_type=="CLOSED_PLANAR ")
{
- int point_number=parse_value<int>(j->GetEntryValue(0x3006,0x0046));
- std::vector<float> points=parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
- assert(points.size() == static_cast<unsigned int>(point_number)*3);
- if (z0 == -1) //First contour
- z0=points[2];
- //2nd contour, spacing not yet set. Need to be sure we are on a different slice,
- //sometimes there is more than one closed contour per slice
- else if (current_roi->GetSpacing()==-1 && points[2] != z0 )
- current_roi->SetSpacing(points[2]-z0);
- vtkPolyData * contour=vtkPolyData::New();
- contour->Allocate(); //for cell structures
- contour->SetPoints(vtkPoints::New());
- vtkIdType ids[2];
- for (unsigned int idx=0;idx<points.size();idx+=3)
+ gdcm::Attribute<0x3006,0x46> tpoint_number;
+ tpoint_number.SetFromDataSet(ds_roi_seq);
+ const gdcm::DataElement & points_data = ds_roi_seq.GetDataElement(gdcm::Tag(0x3006,0x50));
+ gdcm::Attribute<0x3006,0x50> tpoints;
+ tpoints.SetFromDataElement(points_data);
+ assert(tpoints.GetNumberOfValues() == static_cast<unsigned int>(tpoint_number.GetValue()) * 3);
+ const double* points = tpoints.GetValues();
+ if (z0 == -1) //First contour
+ z0=points[2];
+ else
+ if (current_roi->GetSpacing()==-1 && points[2] != z0 )
+ current_roi->SetSpacing(points[2]-z0);
+ vtkPolyData * contour=vtkPolyData::New();
+ contour->Allocate(); //for cell structures
+ contour->SetPoints(vtkPoints::New());
+ vtkIdType ids[2];
+ for (unsigned idx = 0; idx < tpoints.GetNumberOfValues(); idx += 3)
{
- contour->GetPoints()->InsertNextPoint(points[idx],points[idx+1],points[idx+2]);
- ids[0]=idx/3;ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
- contour->GetLines()->InsertNextCell(2,ids);
+ contour->GetPoints()->InsertNextPoint(points[idx], points[idx+1], points[idx+2]);
+ ids[0] = idx / 3;
+ ids[1] = (ids[0] + 1) % tpoint_number.GetValue(); //0-1,1-2,...,n-1-0
+ contour->GetLines()->InsertNextCell(2, ids);
}
- append->AddInput(contour);
+#if VTK_MAJOR_VERSION <= 5
+ append->AddInput(contour);
+#else
+ append->AddInputData(contour);
+#endif
}
- else if (contour_type == "POINT ")
- ; // silently ignore POINT type since we don't need them at the moment
+ else
+ if (contour_type == "POINT ")
+ ; // silently ignore POINT type since we don't need them at the moment
else
- std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
+ std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
}
- append->Update();
- current_roi->AddMesh(append->GetOutput());
- result.push_back(current_roi);
+ append->Update();
+ current_roi->AddMesh(append->GetOutput());
+ result.push_back(current_roi);
}
- else
+ else
{
- //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
+ //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
}
- k=roi_info->GetNextSQItem(); //increment the second loop variable
}
- return result;
+#else
+ gdcm::File reader;
+ reader.SetFileName(filename.c_str());
+ reader.SetMaxSizeLoadEntry(16384);
+ reader.Load();
+
+ gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
+ ///We need to iterate both on the contours themselves, and on the contour info
+ gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
+ gdcm::SQItem* k=roi_info->GetFirstSQItem();
+ for(gdcm::SQItem* i=rois->GetFirstSQItem(); i!=0; i=rois->GetNextSQItem()) { //loop over ROIS
+ assert(k!=0);
+ vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
+ std::istringstream ss(i->GetEntryValue(0x3006,0x0084));
+ int roi_number;
+ ss >> roi_number;
+ if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end()) { //Only read selected ROIs
+ vvMesh::Pointer current_roi=vvMesh::New();
+ std::vector<double> rgb=clitk::parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
+ assert(rgb.size()==3);
+ current_roi->r=rgb[0]/255;
+ current_roi->g=rgb[1]/255;
+ current_roi->b=rgb[2]/255;
+ current_roi->structure_name=k->GetEntryValue(0x3006,0x0026);
+ gdcm::SeqEntry * contours=i->GetSeqEntry(0x3006,0x0040);
+ double z0=-1; //Used to determine spacing between slices, assumed to be constant
+ for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { //loop over 2D contours
+ std::string contour_type=j->GetEntryValue(0x3006,0x0042);
+ if (contour_type=="CLOSED_PLANAR ") {
+ int point_number=clitk::parse_value<int>(j->GetEntryValue(0x3006,0x0046));
+ std::vector<float> points=clitk::parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
+ assert(points.size() == static_cast<unsigned int>(point_number)*3);
+ if (z0 == -1) //First contour
+ z0=points[2];
+ //2nd contour, spacing not yet set. Need to be sure we are on a different slice,
+ //sometimes there is more than one closed contour per slice
+ else if (current_roi->GetSpacing()==-1 && points[2] != z0 )
+ current_roi->SetSpacing(points[2]-z0);
+ vtkPolyData * contour=vtkPolyData::New();
+ contour->Allocate(); //for cell structures
+ contour->SetPoints(vtkPoints::New());
+ vtkIdType ids[2];
+ for (unsigned int idx=0; idx<points.size(); idx+=3) {
+ contour->GetPoints()->InsertNextPoint(points[idx],points[idx+1],points[idx+2]);
+ ids[0]=idx/3;
+ ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
+ contour->GetLines()->InsertNextCell(2,ids);
+ }
+ append->AddInput(contour);
+ } else if (contour_type == "POINT ")
+ ; // silently ignore POINT type since we don't need them at the moment
+ else
+ std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
+ }
+ append->Update();
+ current_roi->AddMesh(append->GetOutput());
+ result.push_back(current_roi);
+ } else {
+ //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
+ }
+ k=roi_info->GetNextSQItem(); //increment the second loop variable
+ }
+#endif
+ return result;
}
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff