1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://www.centreleonberard.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
9 This software is distributed WITHOUT ANY WARRANTY; without even
10 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11 PURPOSE. See the copyright notices for more information.
13 It is distributed under dual licence
15 - BSD See included LICENSE.txt file
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ===========================================================================**/
23 #include <QApplication>
27 #if GDCM_MAJOR_VERSION == 2
28 #include <gdcmReader.h>
30 #include <gdcmAttribute.h>
33 #include <gdcmSQItem.h>
37 #include <vtkVersion.h>
38 #include <vtkSmartPointer.h>
39 #include <vtkAppendPolyData.h>
40 #include <vtkCellArray.h>
41 #include <vtkMetaImageWriter.h>
42 #include <vtkMetaImageReader.h>
43 #include <vtkPolyDataWriter.h>
44 #include <vtkImageData.h>
45 #include <vtkImageCast.h>
46 #include <vtkImageGaussianSmooth.h>
49 #include "clitkCommon.h"
50 #include "clitkCommon.h"
51 #include "clitkDicomRT_StructureSet.h"
52 #include "vvMeshReader.h"
53 #include "vvProgressDialog.h"
55 //------------------------------------------------------------------------------
56 vvMeshReader::vvMeshReader() :
59 //------------------------------------------------------------------------------
62 //------------------------------------------------------------------------------
63 void vvMeshReader::Update()
65 //Show a progress bar only when opening a DC-struct (ie. multiple contours)
66 vvProgressDialog progress("Opening " + filename,(!vtk_mode) && (selected_contours.size()>1));
68 while (this->isRunning()) {
69 progress.SetProgress(result.size(),selected_contours.size());
71 qApp->processEvents();
74 //------------------------------------------------------------------------------
77 //------------------------------------------------------------------------------
78 void vvMeshReader::run()
80 ///Verify the important stuff has been set
81 assert(filename != "");
82 if (vtk_mode) { //Read vtkPolyData
83 vvMesh::Pointer m=vvMesh::New();
84 m->ReadFromVTK(filename.c_str());
85 if (vf) m->propagateContour(vf);
86 m->ComputeMasks(image->GetVTKImages()[0],false); //don't extrude the contour
88 } else { //Read a Dicom-struct file
89 assert(selected_contours.size() > 0);
91 std::vector<vvMesh::Pointer> contour_stacks=readSelectedContours();
92 for (std::vector<vvMesh::Pointer>::iterator i=contour_stacks.begin();
93 i!=contour_stacks.end(); i++) {
94 (*i)->ComputeMasks(image->GetVTKImages()[0],true); //Remesh the contour
95 (*i)->ComputeMeshes();
96 if (vf) (*i)->propagateContour(vf);
101 //------------------------------------------------------------------------------
104 //------------------------------------------------------------------------------
105 std::vector<std::pair<int,std::string> > vvMeshReader::GetROINames()
107 assert(filename!="");
108 std::vector<std::pair<int, std::string> > roi_names;
110 #if CLITK_USE_SYSTEM_GDCM == 1
112 // Read RT-struct data
113 vtkSmartPointer<vtkGDCMPolyDataReader> areader = vtkGDCMPolyDataReader::New();
114 areader->SetFileName(filename.c_str());
117 // get info on roi names
118 vtkRTStructSetProperties * p = areader->GetRTStructSetProperties();
119 int n = p->GetNumberOfStructureSetROIs();
121 for(unsigned int i=0; i<n; i++) {
122 std::string name = p->GetStructureSetROIName(i);
123 int nb = p->GetStructureSetROINumber(i);
124 roi_names.push_back(make_pair(nb,name));
128 #if GDCM_MAJOR_VERSION == 2
130 // duplicate code from clitk::DicomRT_StructureSet::Read
131 gdcm::Reader * reader = new gdcm::Reader;
132 reader->SetFileName( filename.c_str() );
135 const gdcm::DataSet &ds = reader->GetFile().GetDataSet();
138 //Verify if the file is a RT-Structure-Set dicom file
139 gdcm::File * mFile = &(reader->GetFile());
140 gdcm::MediaStorage ms;
141 ms.SetFromFile(*mFile);
142 if( ms != gdcm::MediaStorage::RTStructureSetStorage )
144 std::cerr << "Error. the file " << filename
145 << " 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])"
150 gdcm::Attribute<0x8,0x60> modality;
151 modality.SetFromDataSet( ds );
152 if( modality.GetValue() != "RTSTRUCT" )
154 std::cerr << "Error. the file " << filename
155 << " is not a Dicom Struct ? (must have 0x0008,0x0060 = RTSTRUCT [RT Structure Set Storage])"
160 gdcm::Attribute<0x20,0x10> studyid;
161 studyid.SetFromDataSet( ds );
163 gdcm::Tag tssroisq(0x3006,0x0020);
164 // 0x3006,0x0020 = [ Structure Set ROI Sequence ]
165 bool b = ds.FindDataElement(tssroisq);
167 clitkExceptionMacro("Error: tag 0x3006,0x0020 [ Structure Set ROI Sequence ] not found");
170 const gdcm::DataElement &ssroisq = ds.GetDataElement( tssroisq );
171 gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ssroisq.GetValueAsSQ();
172 assert(roi_seq); // FIXME error message
174 for(unsigned int ridx = 0; ridx < roi_seq->GetNumberOfItems(); ++ridx)
176 gdcm::Item & item = roi_seq->GetItem( ridx + 1); // Item starts at 1
178 const gdcm::Item & sitem = roi_seq->GetItem(ridx+1); // Item start at #1
180 const gdcm::DataSet& snestedds = sitem.GetNestedDataSet();
181 const gdcm::DataSet& nestedds = item.GetNestedDataSet();
183 if( snestedds.FindDataElement( gdcm::Tag(0x3006,0x22) ) )
185 // const gdcm::DataElement & a = nestedds.GetDataElement(gdcm::Tag(0x3006,0x26));
188 gdcm::Attribute<0x3006,0x26> roiname;
189 roiname.SetFromDataSet( snestedds );
190 std::string name = roiname.GetValue(); // 0x3006,0x0026 = [ROI Name]
191 gdcm::Attribute<0x3006,0x0022> roinumber;
192 roinumber.SetFromDataSet( snestedds );
193 int nb = roinumber.GetValue(); // 0x3006,0x0022 = [ROI Number]
195 roi_names.push_back(make_pair(nb,name));
203 reader.SetFileName(filename.c_str());
204 reader.SetMaxSizeLoadEntry(16384);
207 gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
211 for (gdcm::SQItem* i=roi_info->GetFirstSQItem(); i!=0; i=roi_info->GetNextSQItem())
212 if (i->GetEntryValue(0x3006,0x0022)!= gdcm::GDCM_UNFOUND)
213 roi_names.push_back(make_pair(atoi(i->GetEntryValue(0x3006,0x0022).c_str()),i->GetEntryValue(0x3006,0x0026)));
219 //------------------------------------------------------------------------------
222 //------------------------------------------------------------------------------
223 std::vector<vvMesh::Pointer> vvMeshReader::readSelectedContours()
225 std::vector<vvMesh::Pointer> result;
226 #if GDCM_MAJOR_VERSION == 2
228 reader.SetFileName(filename.c_str());
231 const gdcm::DataSet &ds = reader.GetFile().GetDataSet();
233 gdcm::SmartPointer<gdcm::SequenceOfItems> rois = ds.GetDataElement(gdcm::Tag(0x3006,0x39)).GetValueAsSQ();
234 gdcm::SmartPointer<gdcm::SequenceOfItems> roi_info = ds.GetDataElement(gdcm::Tag(0x3006,0x20)).GetValueAsSQ();
235 assert(rois); // TODO error message
236 assert(roi_info); // TODO error message
237 assert(rois->GetNumberOfItems() == roi_info->GetNumberOfItems());
239 for (unsigned ridx = 0; ridx < rois->GetNumberOfItems(); ++ridx)
241 vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
242 const gdcm::DataSet& ds_rois = rois->GetItem( ridx + 1).GetNestedDataSet();
243 const gdcm::DataSet& ds_roi_info = roi_info->GetItem( ridx + 1).GetNestedDataSet();
245 gdcm::Attribute<0x3006,0x84> roinumber;
246 roinumber.SetFromDataSet(ds_rois);
247 if (std::find(selected_contours.begin(), selected_contours.end(), roinumber.GetValue()) != selected_contours.end()) //Only read selected ROIs
249 gdcm::Attribute<0x3006,0x2a> trgb;
250 trgb.SetFromDataSet(ds_rois);
251 vvMesh::Pointer current_roi=vvMesh::New();
252 current_roi->r = trgb[0] / 255.0;
253 current_roi->g = trgb[1] / 255.0;
254 current_roi->b = trgb[2] / 255.0;
256 gdcm::Attribute<0x3006,0x26> tstructure_name;
257 tstructure_name.SetFromDataSet(ds_roi_info);
258 current_roi->structure_name = tstructure_name.GetValue();
260 gdcm::SmartPointer<gdcm::SequenceOfItems> roi_seq = ds_rois.GetDataElement(gdcm::Tag(0x3006,0x40)).GetValueAsSQ();
261 double z0=-1; //Used to determine spacing between slices, assumed to be constant
262 for (unsigned j = 0; j < roi_seq->GetNumberOfItems(); ++j)
264 gdcm::Item & item_roi_seq = roi_seq->GetItem(j + 1); // Item starts at 1
265 const gdcm::DataSet& ds_roi_seq = item_roi_seq.GetNestedDataSet();
266 gdcm::Attribute<0x3006,0x42> tcontour_type;
267 tcontour_type.SetFromDataSet(ds_roi_seq);
268 std::string contour_type = tcontour_type.GetValue();
269 if (contour_type=="CLOSED_PLANAR ")
271 gdcm::Attribute<0x3006,0x46> tpoint_number;
272 tpoint_number.SetFromDataSet(ds_roi_seq);
273 const gdcm::DataElement & points_data = ds_roi_seq.GetDataElement(gdcm::Tag(0x3006,0x50));
274 gdcm::Attribute<0x3006,0x50> tpoints;
275 tpoints.SetFromDataElement(points_data);
276 assert(tpoints.GetNumberOfValues() == static_cast<unsigned int>(tpoint_number.GetValue()) * 3);
277 const double* points = tpoints.GetValues();
278 if (z0 == -1) //First contour
281 if (current_roi->GetSpacing()==-1 && points[2] != z0 )
282 current_roi->SetSpacing(points[2]-z0);
283 vtkPolyData * contour=vtkPolyData::New();
284 contour->Allocate(); //for cell structures
285 contour->SetPoints(vtkPoints::New());
287 for (unsigned idx = 0; idx < tpoints.GetNumberOfValues(); idx += 3)
289 contour->GetPoints()->InsertNextPoint(points[idx], points[idx+1], points[idx+2]);
291 ids[1] = (ids[0] + 1) % tpoint_number.GetValue(); //0-1,1-2,...,n-1-0
292 contour->GetLines()->InsertNextCell(2, ids);
294 #if VTK_MAJOR_VERSION <= 5
295 append->AddInput(contour);
297 append->AddInputData(contour);
301 if (contour_type == "POINT ")
302 ; // silently ignore POINT type since we don't need them at the moment
304 std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
307 current_roi->AddMesh(append->GetOutput());
308 result.push_back(current_roi);
312 //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
317 reader.SetFileName(filename.c_str());
318 reader.SetMaxSizeLoadEntry(16384);
321 gdcm::SeqEntry * rois=reader.GetSeqEntry(0x3006,0x0039);
322 ///We need to iterate both on the contours themselves, and on the contour info
323 gdcm::SeqEntry * roi_info=reader.GetSeqEntry(0x3006,0x0020);
324 gdcm::SQItem* k=roi_info->GetFirstSQItem();
325 for(gdcm::SQItem* i=rois->GetFirstSQItem(); i!=0; i=rois->GetNextSQItem()) { //loop over ROIS
327 vtkSmartPointer<vtkAppendPolyData> append=vtkSmartPointer<vtkAppendPolyData>::New();
328 std::istringstream ss(i->GetEntryValue(0x3006,0x0084));
331 if (std::find(selected_contours.begin(),selected_contours.end(),roi_number) != selected_contours.end()) { //Only read selected ROIs
332 vvMesh::Pointer current_roi=vvMesh::New();
333 std::vector<double> rgb=clitk::parse_string<double>(i->GetEntryValue(0x3006,0x002a),'\\');
334 assert(rgb.size()==3);
335 current_roi->r=rgb[0]/255;
336 current_roi->g=rgb[1]/255;
337 current_roi->b=rgb[2]/255;
338 current_roi->structure_name=k->GetEntryValue(0x3006,0x0026);
339 gdcm::SeqEntry * contours=i->GetSeqEntry(0x3006,0x0040);
340 double z0=-1; //Used to determine spacing between slices, assumed to be constant
341 for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) { //loop over 2D contours
342 std::string contour_type=j->GetEntryValue(0x3006,0x0042);
343 if (contour_type=="CLOSED_PLANAR ") {
344 int point_number=clitk::parse_value<int>(j->GetEntryValue(0x3006,0x0046));
345 std::vector<float> points=clitk::parse_string<float>(j->GetEntryValue(0x3006,0x0050),'\\');
346 assert(points.size() == static_cast<unsigned int>(point_number)*3);
347 if (z0 == -1) //First contour
349 //2nd contour, spacing not yet set. Need to be sure we are on a different slice,
350 //sometimes there is more than one closed contour per slice
351 else if (current_roi->GetSpacing()==-1 && points[2] != z0 )
352 current_roi->SetSpacing(points[2]-z0);
353 vtkPolyData * contour=vtkPolyData::New();
354 contour->Allocate(); //for cell structures
355 contour->SetPoints(vtkPoints::New());
357 for (unsigned int idx=0; idx<points.size(); idx+=3) {
358 contour->GetPoints()->InsertNextPoint(points[idx],points[idx+1],points[idx+2]);
360 ids[1]=(ids[0]+1)%point_number; //0-1,1-2,...,n-1-0
361 contour->GetLines()->InsertNextCell(2,ids);
363 append->AddInput(contour);
364 } else if (contour_type == "POINT ")
365 ; // silently ignore POINT type since we don't need them at the moment
367 std::cerr << "Warning: contour type " << contour_type << " not handled!" << std::endl;
370 current_roi->AddMesh(append->GetOutput());
371 result.push_back(current_roi);
373 //std::cerr << "Warning: ignoring ROI #" << roi_number << std::endl;
375 k=roi_info->GetNextSQItem(); //increment the second loop variable