1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
3 Main authors : XX XX XX
6 - University of LYON http://www.universite-lyon.fr/
7 - Léon Bérard cancer center http://www.centreleonberard.fr
8 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
10 This software is distributed WITHOUT ANY WARRANTY; without even
11 the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
12 PURPOSE. See the copyright notices for more information.
14 It is distributed under dual licence
15 - BSD http://www.opensource.org/licenses/bsd-license.php
16 - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
18 =========================================================================*/
20 #include "clitkDicomRT_ROI.h"
21 #include <vtkSmartPointer.h>
22 #include <vtkAppendPolyData.h>
23 #include <vtkImageClip.h>
24 #include <vtkMarchingSquares.h>
25 #include <vtkPolyDataWriter.h>
26 #include <vtkVersion.h>
28 #if GDCM_MAJOR_VERSION == 2
29 #include "gdcmAttribute.h"
33 //--------------------------------------------------------------------
34 clitk::DicomRT_ROI::DicomRT_ROI()
40 mColor[0] = mColor[1] = mColor[2] = 0;
41 mMeshIsUpToDate = false;
44 SetDicomUptodateFlag(false);
47 //--------------------------------------------------------------------
50 //--------------------------------------------------------------------
51 clitk::DicomRT_ROI::~DicomRT_ROI()
54 //--------------------------------------------------------------------
57 //--------------------------------------------------------------------
58 void clitk::DicomRT_ROI::SetDisplayColor(double r, double v, double b)
65 //--------------------------------------------------------------------
68 //--------------------------------------------------------------------
69 int clitk::DicomRT_ROI::GetROINumber() const
73 //--------------------------------------------------------------------
76 //--------------------------------------------------------------------
77 void clitk::DicomRT_ROI::SetROINumber(int number)
81 //--------------------------------------------------------------------
84 //--------------------------------------------------------------------
85 const std::string & clitk::DicomRT_ROI::GetName() const
89 //--------------------------------------------------------------------
92 //--------------------------------------------------------------------
93 const std::string & clitk::DicomRT_ROI::GetFilename() const
97 //--------------------------------------------------------------------
100 //--------------------------------------------------------------------
101 const std::vector<double> & clitk::DicomRT_ROI::GetDisplayColor() const
105 //--------------------------------------------------------------------
108 //--------------------------------------------------------------------
109 void clitk::DicomRT_ROI::Print(std::ostream & os) const
111 os << "ROI " << mNumber << "\t" << mName
112 << "\t(" << mColor[0] << " " << mColor[1] << " " << mColor[2] << ")"
113 << "\t Contours = " << mListOfContours.size() << std::endl;
115 //--------------------------------------------------------------------
118 //--------------------------------------------------------------------
119 void clitk::DicomRT_ROI::SetBackgroundValueLabelImage(double bg)
121 mBackgroundValue = bg;
123 //--------------------------------------------------------------------
126 //--------------------------------------------------------------------
127 double clitk::DicomRT_ROI::GetBackgroundValueLabelImage() const
129 return mBackgroundValue;
131 //--------------------------------------------------------------------
134 //--------------------------------------------------------------------
135 void clitk::DicomRT_ROI::SetForegroundValueLabelImage(double bg)
137 mForegroundValue = bg;
139 //--------------------------------------------------------------------
142 //--------------------------------------------------------------------
143 double clitk::DicomRT_ROI::GetForegroundValueLabelImage() const
145 return mForegroundValue;
147 //--------------------------------------------------------------------
150 //--------------------------------------------------------------------
151 #if GDCM_MAJOR_VERSION == 2
152 bool clitk::DicomRT_ROI::Read(gdcm::Item * itemInfo, gdcm::Item * itemContour)
154 //FATAL("Error : compile vv with itk4 + external gdcm");
156 mItemInfo = itemInfo;
157 mItemContour = itemContour;
160 // ROI number [Referenced ROI Number]
161 const gdcm::DataSet & nesteddsInfo = mItemInfo->GetNestedDataSet();
162 gdcm::Attribute<0x3006,0x0022> roinumber;
163 roinumber.SetFromDataSet( nesteddsInfo );
164 int nb1 = roinumber.GetValue();
166 // Check this is the same with the other item
167 const gdcm::DataSet & nestedds = mItemContour->GetNestedDataSet();
168 gdcm::Attribute<0x3006,0x0084> referencedroinumber;
169 referencedroinumber.SetFromDataSet( nestedds );
170 int nb2 = referencedroinumber.GetValue();
172 // Must never be different
176 FATAL("nb1 must equal nb2" << std::endl);
180 // Retrieve ROI Name (in the info item)
181 gdcm::Attribute<0x3006,0x26> roiname;
182 roiname.SetFromDataSet( nesteddsInfo );
183 mName = roiname.GetValue();
186 // ROI Color [ROI Display Color]
187 gdcm::Attribute<0x3006,0x002a> color = {};
188 color.SetFromDataSet( nestedds );
189 assert( color.GetNumberOfValues() == 3 );
190 mColor[0] = color.GetValue(0);
191 mColor[1] = color.GetValue(1);
192 mColor[2] = color.GetValue(2);
194 // Read contours [Contour Sequence]
195 gdcm::Tag tcsq(0x3006,0x0040);
196 if( !nestedds.FindDataElement( tcsq ) )
198 std::cerr << "Warning. Could not read contour for structure <" << mName << ">, number" << mNumber << " ? I ignore it" << std::endl;
199 SetDicomUptodateFlag(true);
202 const gdcm::DataElement& csq = nestedds.GetDataElement( tcsq );
203 mContoursSequenceOfItems = csq.GetValueAsSQ();
204 gdcm::SmartPointer<gdcm::SequenceOfItems> & sqi2 = mContoursSequenceOfItems;
205 if( !sqi2 || !sqi2->GetNumberOfItems() )
208 unsigned int nitems = sqi2->GetNumberOfItems();
210 for(unsigned int i = 0; i < nitems; ++i)
212 gdcm::Item & j = sqi2->GetItem(i+1); // Item start at #1
213 DicomRT_Contour::Pointer c = DicomRT_Contour::New();
214 c->SetTransformMatrix(mTransformMatrix);
215 bool b = c->Read(&j);
217 mListOfContours.push_back(c);
220 SetDicomUptodateFlag(true);
224 void clitk::DicomRT_ROI::Read(std::map<int, std::string> & rois, gdcm::SQItem * item)
226 // ROI number [Referenced ROI Number]
227 mNumber = atoi(item->GetEntryValue(0x3006,0x0084).c_str());
230 mName = rois[mNumber];
232 // ROI Color [ROI Display Color]
233 mColor = clitk::parse_string<double>(item->GetEntryValue(0x3006,0x002a),'\\');
235 // Read contours [Contour Sequence]
236 gdcm::SeqEntry * contours=item->GetSeqEntry(0x3006,0x0040);
239 for(gdcm::SQItem* j=contours->GetFirstSQItem(); j!=0; j=contours->GetNextSQItem()) {
240 DicomRT_Contour::Pointer c = DicomRT_Contour::New();
241 c->SetTransformMatrix(mTransformMatrix);
244 mListOfContours.push_back(c);
250 std::cerr << "Warning. Could not read contour for structure <" << mName << ">, number" << mNumber << " ? I ignore it" << std::endl;
252 SetDicomUptodateFlag(true);
255 //--------------------------------------------------------------------
258 //--------------------------------------------------------------------
259 void clitk::DicomRT_ROI::SetImage(vvImage::Pointer image)
263 //--------------------------------------------------------------------
266 //--------------------------------------------------------------------
267 vtkPolyData * clitk::DicomRT_ROI::GetMesh()
269 if (!mMeshIsUpToDate) {
270 ComputeMeshFromContour();
274 //--------------------------------------------------------------------
277 //--------------------------------------------------------------------
278 clitk::DicomRT_Contour * clitk::DicomRT_ROI::GetContour(int n)
280 return mListOfContours[n];
282 //--------------------------------------------------------------------
285 //--------------------------------------------------------------------
286 void clitk::DicomRT_ROI::ComputeMeshFromContour()
288 vtkSmartPointer<vtkAppendPolyData> append = vtkSmartPointer<vtkAppendPolyData>::New();
289 for(unsigned int i=0; i<mListOfContours.size(); i++) {
290 #if VTK_MAJOR_VERSION <= 5
291 append->AddInput(mListOfContours[i]->GetMesh());
293 append->AddInputData(mListOfContours[i]->GetMesh());
298 mMesh = vtkSmartPointer<vtkPolyData>::New();
299 mMesh->DeepCopy(append->GetOutput());
300 mMeshIsUpToDate = true;
302 //--------------------------------------------------------------------
305 #if GDCM_MAJOR_VERSION == 2
306 //--------------------------------------------------------------------
307 void clitk::DicomRT_ROI::UpdateDicomItem()
309 FATAL("Error : compile vv with itk4 + external gdcm");
311 if (GetDicomUptoDateFlag()) return;
312 DD("ROI::UpdateDicomItem");
315 // From now, only some item can be modified
317 // Set ROI Name 0x3006,0x26>
318 gdcm::Attribute<0x3006,0x26> roiname;
319 roiname.SetValue(GetName());
320 gdcm::DataElement de = roiname.GetAsDataElement();
321 gdcm::DataSet & ds = mItemInfo->GetNestedDataSet();
324 // From MESH to CONTOURS
325 ComputeContoursFromImage();
328 DD(mListOfContours.size());
329 for(uint i=0; i<mListOfContours.size(); i++) {
331 DicomRT_Contour::Pointer contour = mListOfContours[i];
332 contour->UpdateDicomItem();//mItemContour);
336 unsigned int nitems = mContoursSequenceOfItems->GetNumberOfItems();
339 // Write [Contour Sequence] = 0x3006,0x0040)
340 gdcm::DataSet & dsc = mItemContour->GetNestedDataSet();
341 gdcm::Tag tcsq(0x3006,0x0040);
342 const gdcm::DataElement& csq = dsc.GetDataElement( tcsq );
343 gdcm::DataElement dec(csq);
344 dec.SetValue(*mContoursSequenceOfItems);
347 gdcm::DataSet & a = mContoursSequenceOfItems->GetItem(1).GetNestedDataSet();
348 gdcm::Attribute<0x3006,0x0050> at;
349 gdcm::Tag tcontourdata(0x3006,0x0050);
350 gdcm::DataElement contourdata = a.GetDataElement( tcontourdata );
351 at.SetFromDataElement( contourdata );
352 const double* points = at.GetValues();
356 //--------------------------------------------------------------------
359 //--------------------------------------------------------------------
360 void clitk::DicomRT_ROI::SetFromBinaryImage(vvImage::Pointer image, int n,
362 std::vector<double> color,
363 std::string filename)
365 // ROI number [Referenced ROI Number]
370 mFilename = filename;
372 // ROI Color [ROI Display Color]
375 // No contours [Contour Sequence]
376 mListOfContours.clear();
381 //--------------------------------------------------------------------
384 //--------------------------------------------------------------------
385 vvImage * clitk::DicomRT_ROI::GetImage() const
389 //--------------------------------------------------------------------
392 //--------------------------------------------------------------------
393 void clitk::DicomRT_ROI::SetTransformMatrix(vtkMatrix4x4* matrix)
395 mTransformMatrix = matrix;
397 //--------------------------------------------------------------------
400 //--------------------------------------------------------------------
401 void clitk::DicomRT_ROI::ComputeContoursFromImage()
403 FATAL("ComputeContoursFromImage should not be call. To be replace");
404 DD("ComputeMeshFromImage");
406 // Check that an image is loaded
409 // Only consider 3D here
410 if (mImage->GetNumberOfDimensions() != 3) {
411 FATAL("DicomRT_ROI::ComputeMeshFromImage only work with 3D images");
415 vtkImageData * image = mImage->GetVTKImages()[0];
417 // Get initial extend for the clipping
418 vtkSmartPointer<vtkImageClip> clipper = vtkSmartPointer<vtkImageClip>::New();
419 #if VTK_MAJOR_VERSION <= 5
420 clipper->SetInput(image);
422 clipper->SetInputData(image);
425 int* extent = image->GetExtent();
427 // std::vector<int> extend;
431 uint n = image->GetDimensions()[2];
433 DD(mListOfContours.size());
434 mListOfContours.resize(n); /// ???FIXME
435 DD(mListOfContours.size());
436 std::vector<vtkSmartPointer<vtkPolyData> > contours;
437 for(uint i=0; i<n; i++) {
440 // FIXME vtkDiscreteMarchingCubes INSTEAD
443 vtkSmartPointer<vtkMarchingSquares> squares = vtkSmartPointer<vtkMarchingSquares>::New();
444 #if VTK_MAJOR_VERSION <= 5
445 squares->SetInput(image);
447 squares->SetInputData(image);
449 squares->SetImageRange(extent[0], extent[1], extent[2], extent[3], i, i);
450 squares->SetValue(1, 1.0);
452 DD(squares->GetNumberOfContours());
454 //clitk::DicomRT_Contour * contour = new clitk::DicomRT_Contour();
455 //mListOfContours[i]->SetMesh(squares->GetOutput());
458 vtkSmartPointer<vtkPolyData> m = squares->GetOutput();
459 contours.push_back(m);
462 // Clip to the current slice
463 extent[4] = extent[5] = image->GetOrigin()[2]+i*image->GetSpacing()[2];
465 // Prepare the marching squares
466 vtkSmartPointer<vtkMarchingSquares> squares = vtkSmartPointer<vtkMarchingSquares>::New();
467 clipper->SetOutputWholeExtent(extent[0],extent[1],extent[2],
468 extent[3],extent[4],extent[5]);
470 squares->SetInput(clipper->GetOutput());
472 DD(squares->GetNumberOfContours());
473 mListOfContours[i]->SetMesh(squares->GetOutput());
478 vtkSmartPointer<vtkAppendPolyData> append = vtkSmartPointer<vtkAppendPolyData>::New();
479 for(unsigned int i=0; i<n; i++) {
480 #if VTK_MAJOR_VERSION <= 5
481 append->AddInput(contours[i]);
483 append->AddInputData(contours[i]);
488 mMesh = vtkSmartPointer<vtkPolyData>::New();
489 mMesh->DeepCopy(append->GetOutput());
492 vtkPolyDataWriter * w = vtkPolyDataWriter::New();
493 #if VTK_MAJOR_VERSION <= 5
496 w->SetInputData(mMesh);
498 w->SetFileName("toto.vtk");
503 //--------------------------------------------------------------------
506 //--------------------------------------------------------------------
507 #if CLITK_USE_SYSTEM_GDCM == 1
508 void clitk::DicomRT_ROI::Read(vtkSmartPointer<vtkGDCMPolyDataReader> & reader, int roiindex)
510 vtkRTStructSetProperties * p = reader->GetRTStructSetProperties();
512 mName = p->GetStructureSetROIName(roiindex);
513 mNumber = p->GetStructureSetROINumber(roiindex);
515 //mColor = //FIXME !!
517 // gdcm::Attribute<0x3006,0x002a> color = {};
519 // const gdcm::DataSet & nestedds = mItemContour->GetNestedDataSet();
520 // color.SetFromDataSet( nestedds );
521 // assert( color.GetNumberOfValues() == 3 );
522 // mColor[0] = color.GetValue(0);
523 // mColor[1] = color.GetValue(1);
524 // mColor[2] = color.GetValue(2);
527 SetDicomUptodateFlag(true);
529 mMesh = reader->GetOutput(roiindex);
530 DicomRT_Contour::Pointer c = DicomRT_Contour::New();
531 c->SetTransformMatrix(mTransformMatrix);
532 c->SetMesh(mMesh); // FIXME no GetZ, not GetPoints
533 mMeshIsUpToDate = true;
534 mListOfContours.push_back(c);
537 //--------------------------------------------------------------------