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 ======================================================================-====*/
20 #include "clitkSetBackgroundImageFilter.h"
21 #include "clitkSliceBySliceRelativePositionFilter.h"
22 #include "clitkCropLikeImageFilter.h"
23 #include "clitkMemoryUsage.h"
26 #include <itkConnectedComponentImageFilter.h>
27 #include <itkRelabelComponentImageFilter.h>
28 #include <itkBinaryThresholdImageFilter.h>
29 #include <itkPasteImageFilter.h>
30 #include <itkStatisticsLabelMapFilter.h>
31 #include <itkBinaryBallStructuringElement.h>
32 #include <itkBinaryDilateImageFilter.h>
33 #include <itkConstantPadImageFilter.h>
34 #include <itkImageSliceIteratorWithIndex.h>
35 #include <itkBinaryMorphologicalOpeningImageFilter.h>
36 #include <itkImageDuplicator.h>
40 //--------------------------------------------------------------------
41 template<class ImageType>
42 void ComputeBBFromImageRegion(const ImageType * image,
43 typename ImageType::RegionType region,
44 typename itk::BoundingBox<unsigned long,
45 ImageType::ImageDimension>::Pointer bb) {
46 typedef typename ImageType::IndexType IndexType;
49 for(unsigned int i=0; i<image->GetImageDimension(); i++) {
50 firstIndex[i] = region.GetIndex()[i];
51 lastIndex[i] = firstIndex[i]+region.GetSize()[i];
54 typedef itk::BoundingBox<unsigned long,
55 ImageType::ImageDimension> BBType;
56 typedef typename BBType::PointType PointType;
59 image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
60 image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
62 bb->SetMaximum(lastPoint);
63 bb->SetMinimum(firstPoint);
65 //--------------------------------------------------------------------
68 //--------------------------------------------------------------------
69 template<int Dimension>
70 void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
71 typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
72 typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
74 typedef itk::BoundingBox<unsigned long, Dimension> BBType;
75 typedef typename BBType::PointType PointType;
79 for(unsigned int i=0; i<Dimension; i++) {
80 firstPoint[i] = std::max(bbi1->GetMinimum()[i],
81 bbi2->GetMinimum()[i]);
82 lastPoint[i] = std::min(bbi1->GetMaximum()[i],
83 bbi2->GetMaximum()[i]);
86 bbo->SetMaximum(lastPoint);
87 bbo->SetMinimum(firstPoint);
89 //--------------------------------------------------------------------
92 //--------------------------------------------------------------------
93 template<class ImageType>
94 void ComputeRegionFromBB(const ImageType * image,
95 const typename itk::BoundingBox<unsigned long,
96 ImageType::ImageDimension>::Pointer bb,
97 typename ImageType::RegionType & region) {
99 typedef typename ImageType::IndexType IndexType;
100 typedef typename ImageType::PointType PointType;
101 typedef typename ImageType::RegionType RegionType;
102 typedef typename ImageType::SizeType SizeType;
104 // Region starting point
105 IndexType regionStart;
106 PointType start = bb->GetMinimum();
107 image->TransformPhysicalPointToIndex(start, regionStart);
111 PointType maxs = bb->GetMaximum();
112 PointType mins = bb->GetMinimum();
113 for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
114 regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
118 region.SetIndex(regionStart);
119 region.SetSize(regionSize);
121 //--------------------------------------------------------------------
123 //--------------------------------------------------------------------
124 template<class ImageType, class TMaskImageType>
125 typename ImageType::Pointer
126 SetBackground(const ImageType * input,
127 const TMaskImageType * mask,
128 typename TMaskImageType::PixelType maskBG,
129 typename ImageType::PixelType outValue,
131 typedef SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
132 SetBackgroundImageFilterType;
133 typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
134 = SetBackgroundImageFilterType::New();
135 // if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
136 setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
137 setBackgroundFilter->SetInput(input);
138 setBackgroundFilter->SetInput2(mask);
139 setBackgroundFilter->SetMaskValue(maskBG);
140 setBackgroundFilter->SetOutsideValue(outValue);
141 setBackgroundFilter->Update();
142 return setBackgroundFilter->GetOutput();
144 //--------------------------------------------------------------------
147 //--------------------------------------------------------------------
148 template<class ImageType>
149 int GetNumberOfConnectedComponentLabels(const ImageType * input,
150 typename ImageType::PixelType BG,
151 bool isFullyConnected) {
152 // Connected Component label
153 typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
154 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
155 connectFilter->SetInput(input);
156 connectFilter->SetBackgroundValue(BG);
157 connectFilter->SetFullyConnected(isFullyConnected);
158 connectFilter->Update();
161 return connectFilter->GetObjectCount();
163 //--------------------------------------------------------------------
165 //--------------------------------------------------------------------
167 Warning : in this cas, we consider outputType like inputType, not
168 InternalImageType. Be sure it fits.
170 template<class ImageType>
171 typename ImageType::Pointer
172 Labelize(const ImageType * input,
173 typename ImageType::PixelType BG,
174 bool isFullyConnected,
175 int minimalComponentSize) {
176 // InternalImageType for storing large number of component
177 typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
179 // Connected Component label
180 typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
181 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
182 // connectFilter->ReleaseDataFlagOn();
183 connectFilter->SetInput(input);
184 connectFilter->SetBackgroundValue(BG);
185 connectFilter->SetFullyConnected(isFullyConnected);
187 // Sort by size and remove too small area.
188 typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
189 typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
190 // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
191 relabelFilter->SetInput(connectFilter->GetOutput());
192 relabelFilter->SetMinimumObjectSize(minimalComponentSize);
193 relabelFilter->Update();
196 typename ImageType::Pointer output = relabelFilter->GetOutput();
199 //--------------------------------------------------------------------
202 //--------------------------------------------------------------------
204 Warning : in this cas, we consider outputType like inputType, not
205 InternalImageType. Be sure it fits.
207 template<class ImageType>
208 typename ImageType::Pointer
209 LabelizeAndCountNumberOfObjects(const ImageType * input,
210 typename ImageType::PixelType BG,
211 bool isFullyConnected,
212 int minimalComponentSize,
214 // InternalImageType for storing large number of component
215 typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
217 // Connected Component label
218 typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
219 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
220 // connectFilter->ReleaseDataFlagOn();
221 connectFilter->SetInput(input);
222 connectFilter->SetBackgroundValue(BG);
223 connectFilter->SetFullyConnected(isFullyConnected);
225 // Sort by size and remove too small area.
226 typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
227 typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
228 // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
229 relabelFilter->SetInput(connectFilter->GetOutput());
230 relabelFilter->SetMinimumObjectSize(minimalComponentSize);
231 relabelFilter->Update();
233 nb = relabelFilter->GetNumberOfObjects();
234 // DD(relabelFilter->GetOriginalNumberOfObjects());
235 // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
238 typename ImageType::Pointer output = relabelFilter->GetOutput();
241 //--------------------------------------------------------------------
245 //--------------------------------------------------------------------
246 template<class ImageType>
247 typename ImageType::Pointer
248 RemoveLabels(const ImageType * input,
249 typename ImageType::PixelType BG,
250 std::vector<typename ImageType::PixelType> & labelsToRemove) {
251 assert(labelsToRemove.size() != 0);
252 typename ImageType::Pointer working_image;// = input;
253 for (unsigned int i=0; i <labelsToRemove.size(); i++) {
254 typedef SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
255 typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
256 setBackgroundFilter->SetInput(input);
257 setBackgroundFilter->SetInput2(input);
258 setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
259 setBackgroundFilter->SetOutsideValue(BG);
260 setBackgroundFilter->Update();
261 working_image = setBackgroundFilter->GetOutput();
263 return working_image;
265 //--------------------------------------------------------------------
268 //--------------------------------------------------------------------
269 template<class ImageType>
270 typename ImageType::Pointer
271 KeepLabels(const ImageType * input,
272 typename ImageType::PixelType BG,
273 typename ImageType::PixelType FG,
274 typename ImageType::PixelType firstKeep,
275 typename ImageType::PixelType lastKeep,
277 typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
278 typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
279 binarizeFilter->SetInput(input);
280 binarizeFilter->SetLowerThreshold(firstKeep);
281 if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
282 binarizeFilter->SetInsideValue(FG);
283 binarizeFilter->SetOutsideValue(BG);
284 binarizeFilter->Update();
285 return binarizeFilter->GetOutput();
287 //--------------------------------------------------------------------
290 //--------------------------------------------------------------------
291 template<class ImageType>
292 typename ImageType::Pointer
293 LabelizeAndSelectLabels(const ImageType * input,
294 typename ImageType::PixelType BG,
295 typename ImageType::PixelType FG,
296 bool isFullyConnected,
297 int minimalComponentSize,
298 LabelizeParameters<typename ImageType::PixelType> * param)
300 typename ImageType::Pointer working_image;
301 working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
302 if (param->GetLabelsToRemove().size() != 0)
303 working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
304 working_image = KeepLabels<ImageType>(working_image,
306 param->GetFirstKeep(),
307 param->GetLastKeep(),
308 param->GetUseLastKeep());
309 return working_image;
311 //--------------------------------------------------------------------
314 //--------------------------------------------------------------------
315 template<class ImageType>
316 typename ImageType::Pointer
317 ResizeImageLike(const ImageType * input,
318 const itk::ImageBase<ImageType::ImageDimension> * like,
319 typename ImageType::PixelType backgroundValue)
321 typedef CropLikeImageFilter<ImageType> CropFilterType;
322 typename CropFilterType::Pointer cropFilter = CropFilterType::New();
323 cropFilter->SetInput(input);
324 cropFilter->SetCropLikeImage(like);
325 cropFilter->SetBackgroundValue(backgroundValue);
326 cropFilter->Update();
327 return cropFilter->GetOutput();
329 //--------------------------------------------------------------------
332 //--------------------------------------------------------------------
333 template<class MaskImageType>
334 typename MaskImageType::Pointer
335 SliceBySliceRelativePosition(const MaskImageType * input,
336 const MaskImageType * object,
339 std::string orientation,
340 bool uniqueConnectedComponent,
343 bool singleObjectCCL)
345 typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
346 typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
347 sliceRelPosFilter->VerboseStepFlagOff();
348 sliceRelPosFilter->WriteStepFlagOff();
349 sliceRelPosFilter->SetInput(input);
350 sliceRelPosFilter->SetInputObject(object);
351 sliceRelPosFilter->SetDirection(direction);
352 sliceRelPosFilter->SetFuzzyThreshold(threshold);
353 sliceRelPosFilter->AddOrientationTypeString(orientation);
354 sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
355 sliceRelPosFilter->SetIntermediateSpacing(spacing);
356 sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
357 sliceRelPosFilter->SetUseASingleObjectConnectedComponentBySliceFlag(singleObjectCCL);
358 // sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
359 sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
360 sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
361 sliceRelPosFilter->Update();
362 return sliceRelPosFilter->GetOutput();
364 //--------------------------------------------------------------------
366 //--------------------------------------------------------------------
367 template<class ImageType>
369 FindExtremaPointInAGivenDirection(const ImageType * input,
370 typename ImageType::PixelType bg,
371 int direction, bool opposite,
372 typename ImageType::PointType & point)
374 typename ImageType::PointType dummy;
375 return FindExtremaPointInAGivenDirection(input, bg, direction,
376 opposite, dummy, 0, point);
378 //--------------------------------------------------------------------
380 //--------------------------------------------------------------------
381 template<class ImageType>
383 FindExtremaPointInAGivenDirection(const ImageType * input,
384 typename ImageType::PixelType bg,
385 int direction, bool opposite,
386 typename ImageType::PointType refpoint,
388 typename ImageType::PointType & point)
391 loop over input pixels, store the index in the fg that is max
392 according to the given direction.
394 typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
395 IteratorType iter(input, input->GetLargestPossibleRegion());
397 typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
398 if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
400 while (!iter.IsAtEnd()) {
401 if (iter.Get() != bg) {
402 bool test = iter.GetIndex()[direction] > max[direction];
403 if (opposite) test = !test;
405 typename ImageType::PointType p;
406 input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
407 if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
408 max = iter.GetIndex();
415 if (!found) return false;
416 input->TransformIndexToPhysicalPoint(max, point);
419 //--------------------------------------------------------------------
422 //--------------------------------------------------------------------
423 template<class ImageType>
424 typename ImageType::Pointer
425 CropImageRemoveGreaterThan(const ImageType * image,
426 int dim, double min, bool autoCrop,
427 typename ImageType::PixelType BG)
429 return CropImageAlongOneAxis<ImageType>(image, dim,
430 image->GetOrigin()[dim],
434 //--------------------------------------------------------------------
437 //--------------------------------------------------------------------
438 template<class ImageType>
439 typename ImageType::Pointer
440 CropImageRemoveLowerThan(const ImageType * image,
441 int dim, double max, bool autoCrop,
442 typename ImageType::PixelType BG)
444 typename ImageType::PointType p;
445 image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
446 image->GetLargestPossibleRegion().GetSize(), p);
447 return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
449 //--------------------------------------------------------------------
452 //--------------------------------------------------------------------
453 template<class ImageType>
454 typename ImageType::Pointer
455 CropImageAlongOneAxis(const ImageType * image,
456 int dim, double min, double max,
457 bool autoCrop, typename ImageType::PixelType BG)
459 // Compute region size
460 typename ImageType::RegionType region;
461 typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
462 typename ImageType::PointType p = image->GetOrigin();
464 typename ImageType::IndexType start;
465 image->TransformPhysicalPointToIndex(p, start);
467 typename ImageType::IndexType end;
468 image->TransformPhysicalPointToIndex(p, end);
469 size[dim] = abs(end[dim]-start[dim]);
470 region.SetIndex(start);
471 region.SetSize(size);
474 typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
475 typename CropFilterType::Pointer cropFilter = CropFilterType::New();
476 cropFilter->SetInput(image);
477 cropFilter->SetRegionOfInterest(region);
478 cropFilter->Update();
479 typename ImageType::Pointer result = cropFilter->GetOutput();
483 result = AutoCrop<ImageType>(result, BG);
487 //--------------------------------------------------------------------
490 //--------------------------------------------------------------------
491 template<class ImageType>
493 ComputeCentroids(const ImageType * image,
494 typename ImageType::PixelType BG,
495 std::vector<typename ImageType::PointType> & centroids)
497 typedef long LabelType;
498 static const unsigned int Dim = ImageType::ImageDimension;
499 typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
500 typedef itk::LabelMap< LabelObjectType > LabelMapType;
501 typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
502 typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
503 typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
504 typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
505 imageToLabelFilter->SetBackgroundValue(BG);
506 imageToLabelFilter->SetInput(image);
507 statFilter->SetInput(imageToLabelFilter->GetOutput());
508 statFilter->Update();
509 typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
512 typename ImageType::PointType dummy;
513 centroids.push_back(dummy); // label 0 -> no centroid, use dummy point for BG
514 //DS FIXME (not useful ! to change ..)
515 for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
516 int label = labelMap->GetLabels()[i];
517 centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
520 //--------------------------------------------------------------------
523 //--------------------------------------------------------------------
524 template<class ImageType, class LabelType>
525 typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
526 ComputeLabelMap(const ImageType * image,
527 typename ImageType::PixelType BG,
528 bool computePerimeterFlag)
530 static const unsigned int Dim = ImageType::ImageDimension;
531 typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
532 typedef itk::LabelMap< LabelObjectType > LabelMapType;
533 typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
534 typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
535 typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
536 typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
537 imageToLabelFilter->SetBackgroundValue(BG);
538 imageToLabelFilter->SetInput(image);
539 statFilter->SetInput(imageToLabelFilter->GetOutput());
540 statFilter->SetComputePerimeter(computePerimeterFlag);
541 statFilter->Update();
542 return statFilter->GetOutput();
544 //--------------------------------------------------------------------
547 //--------------------------------------------------------------------
548 template<class ImageType>
550 ComputeCentroids2(const ImageType * image,
551 typename ImageType::PixelType BG,
552 std::vector<typename ImageType::PointType> & centroids)
554 typedef long LabelType;
555 static const unsigned int Dim = ImageType::ImageDimension;
556 typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
557 typedef itk::LabelMap< LabelObjectType > LabelMapType;
558 typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
559 typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
560 typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
561 typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
562 imageToLabelFilter->SetBackgroundValue(BG);
563 imageToLabelFilter->SetInput(image);
564 statFilter->SetInput(imageToLabelFilter->GetOutput());
565 statFilter->Update();
566 typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
569 typename ImageType::PointType dummy;
570 centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
571 for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
572 centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
575 for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
576 DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
577 DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
578 DD(labelMap->GetLabelObject(i)->GetRoundness ());
580 // search for the point on the boundary alog PA
585 //--------------------------------------------------------------------
588 //--------------------------------------------------------------------
589 template<class ImageType>
591 PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
592 const ImageType * image,
597 index3D[0] = index3D[1] = 0;
598 index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
599 image->TransformIndexToPhysicalPoint(index3D, p3D);
602 // p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
603 // + image->GetOrigin()[2];
605 //--------------------------------------------------------------------
608 //--------------------------------------------------------------------
609 template<class ImageType>
611 PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map,
612 const ImageType * image,
613 VectorPoint3DType & list)
615 typename MapPoint2DType::const_iterator iter = map.begin();
616 while (iter != map.end()) {
618 Convert2DTo3D(iter->second, image, iter->first, p);
623 //--------------------------------------------------------------------
626 //--------------------------------------------------------------------
627 template<class ImageType>
629 PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D,
631 const ImageType * image,
632 VectorPoint3DType & list)
634 for(uint i=0; i<p2D.size(); i++) {
636 Convert2DTo3D(p2D[i], image, slice, p);
640 //--------------------------------------------------------------------
643 //--------------------------------------------------------------------
644 template<class ImageType>
646 WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
647 std::string filename)
650 openFileForWriting(os, filename);
651 os << "LANDMARKS1" << std::endl;
652 for(uint i=0; i<points.size(); i++) {
653 const typename ImageType::PointType & p = points[i];
654 // Write it in the file
655 os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
659 //--------------------------------------------------------------------
662 //--------------------------------------------------------------------
663 template<class ImageType>
664 typename ImageType::Pointer
665 Dilate(const ImageType * image, double radiusInMM,
666 typename ImageType::PixelType BG,
667 typename ImageType::PixelType FG,
670 typename ImageType::SizeType r;
671 for(uint i=0; i<ImageType::ImageDimension; i++)
672 r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
673 return Dilate<ImageType>(image, r, BG, FG, extendSupport);
675 //--------------------------------------------------------------------
678 //--------------------------------------------------------------------
679 template<class ImageType>
680 typename ImageType::Pointer
681 Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
682 typename ImageType::PixelType BG,
683 typename ImageType::PixelType FG,
686 typename ImageType::SizeType r;
687 for(uint i=0; i<ImageType::ImageDimension; i++)
688 r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
689 return Dilate<ImageType>(image, r, BG, FG, extendSupport);
691 //--------------------------------------------------------------------
694 //--------------------------------------------------------------------
695 template<class ImageType>
696 typename ImageType::Pointer
697 Dilate(const ImageType * image, typename ImageType::SizeType radius,
698 typename ImageType::PixelType BG,
699 typename ImageType::PixelType FG,
702 // Create kernel for dilatation
703 typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
704 ImageType::ImageDimension> KernelType;
705 KernelType structuringElement;
706 structuringElement.SetRadius(radius);
707 structuringElement.CreateStructuringElement();
709 typename ImageType::Pointer output;
711 typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
712 typename PadFilterType::Pointer padFilter = PadFilterType::New();
713 padFilter->SetInput(image);
714 typename ImageType::SizeType lower;
715 typename ImageType::SizeType upper;
716 for(uint i=0; i<3; i++) {
717 lower[i] = upper[i] = 2*(radius[i]+1);
719 padFilter->SetPadLowerBound(lower);
720 padFilter->SetPadUpperBound(upper);
722 output = padFilter->GetOutput();
726 typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
727 typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
728 dilateFilter->SetBackgroundValue(BG);
729 dilateFilter->SetForegroundValue(FG);
730 dilateFilter->SetBoundaryToForeground(false);
731 dilateFilter->SetKernel(structuringElement);
732 dilateFilter->SetInput(output);
733 dilateFilter->Update();
734 return dilateFilter->GetOutput();
736 //--------------------------------------------------------------------
739 //--------------------------------------------------------------------
740 template<class ImageType>
741 typename ImageType::Pointer
742 Opening(const ImageType * image, typename ImageType::SizeType radius,
743 typename ImageType::PixelType BG,
744 typename ImageType::PixelType FG)
747 typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
748 ImageType::ImageDimension> KernelType;
749 KernelType structuringElement;
750 structuringElement.SetRadius(radius);
751 structuringElement.CreateStructuringElement();
754 typedef itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType , KernelType> OpeningFilterType;
755 typename OpeningFilterType::Pointer open = OpeningFilterType::New();
756 open->SetInput(image);
757 open->SetBackgroundValue(BG);
758 open->SetForegroundValue(FG);
759 open->SetKernel(structuringElement);
761 return open->GetOutput();
763 //--------------------------------------------------------------------
767 //--------------------------------------------------------------------
768 template<class ValueType, class VectorType>
769 void ConvertOption(std::string optionName, uint given,
770 ValueType * values, VectorType & p,
771 uint dim, bool required)
773 if (required && (given == 0)) {
774 clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
775 << dim << " values.");
778 for(uint i=0; i<dim; i++) p[i] = values[0];
782 for(uint i=0; i<dim; i++) p[i] = values[i];
785 if (given == 0) return;
786 clitkExceptionMacro("The option --" << optionName << " must have 1 or "
787 << dim << " values.");
789 //--------------------------------------------------------------------
792 //--------------------------------------------------------------------
794 http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
795 Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
796 (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
797 This will equal zero if the point C is on the line formed by
798 points A and B, and will have a different sign depending on the
799 side. Which side this is depends on the orientation of your (x,y)
800 coordinates, but you can plug test values for A,B and C into this
801 formula to determine whether negative values are to the left or to
803 => to accelerate, start with formula, when change sign -> stop and fill
805 offsetToKeep = is used to determine which side of the line we
806 keep. The point along the mainDirection but 'offsetToKeep' mm away
810 template<class ImageType>
812 SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
813 std::vector<typename ImageType::PointType> & lA,
814 std::vector<typename ImageType::PointType> & lB,
815 typename ImageType::PixelType BG,
819 typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
820 SliceIteratorType siter = SliceIteratorType(input,
821 input->GetLargestPossibleRegion());
822 siter.SetFirstDirection(0);
823 siter.SetSecondDirection(1);
826 typename ImageType::PointType A;
827 typename ImageType::PointType B;
828 typename ImageType::PointType C;
829 assert(lA.size() == lB.size());
830 while ((i<lA.size()) && (!siter.IsAtEnd())) {
831 // Check that the current slice correspond to the current point
832 input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
836 if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
839 // Define A,B,C points
847 // Check that the line is not a point (A=B)
848 bool p = (A[0] == B[0]) && (A[1] == B[1]);
851 C[mainDirection] += offsetToKeep; // I know I must keep this point
852 double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
853 bool isPositive = s<0;
854 while (!siter.IsAtEndOfSlice()) {
855 while (!siter.IsAtEndOfLine()) {
856 // Very slow, I know ... but image should be very small
857 input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
858 double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
859 if (s == 0) siter.Set(BG); // on the line, we decide to remove
861 if (s > 0) siter.Set(BG);
864 if (s < 0) siter.Set(BG);
873 } // End of current slice
877 //--------------------------------------------------------------------
879 //--------------------------------------------------------------------
880 template<class ImageType>
882 AndNot(ImageType * input,
883 const ImageType * object,
884 typename ImageType::PixelType BG)
886 typename ImageType::Pointer o;
888 if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
889 o = clitk::ResizeImageLike<ImageType>(object, input, BG);
893 typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
894 typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
895 boolFilter->InPlaceOn();
896 boolFilter->SetInput1(input);
897 if (resized) boolFilter->SetInput2(o);
898 else boolFilter->SetInput2(object);
899 boolFilter->SetBackgroundValue1(BG);
900 boolFilter->SetBackgroundValue2(BG);
901 boolFilter->SetOperationType(BoolFilterType::AndNot);
902 boolFilter->Update();
904 //--------------------------------------------------------------------
907 //--------------------------------------------------------------------
908 template<class ImageType>
909 typename ImageType::Pointer
910 Binarize(const ImageType * input,
911 typename ImageType::PixelType lower,
912 typename ImageType::PixelType upper,
913 typename ImageType::PixelType BG,
914 typename ImageType::PixelType FG)
916 typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
917 typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
918 binarizeFilter->SetInput(input);
919 binarizeFilter->InPlaceOff();
920 binarizeFilter->SetLowerThreshold(lower);
921 binarizeFilter->SetUpperThreshold(upper);
922 binarizeFilter->SetInsideValue(FG);
923 binarizeFilter->SetOutsideValue(BG);
924 binarizeFilter->Update();
925 return binarizeFilter->GetOutput();
927 //--------------------------------------------------------------------
930 //--------------------------------------------------------------------
931 template<class ImageType>
933 GetMinMaxPointPosition(const ImageType * input,
934 typename ImageType::PointType & min,
935 typename ImageType::PointType & max)
937 typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
938 input->TransformIndexToPhysicalPoint(index, min);
939 index = index+input->GetLargestPossibleRegion().GetSize();
940 input->TransformIndexToPhysicalPoint(index, max);
942 //--------------------------------------------------------------------
945 //--------------------------------------------------------------------
946 template<class ImageType>
947 typename ImageType::PointType
948 FindExtremaPointInAGivenLine(const ImageType * input,
951 typename ImageType::PointType p,
952 typename ImageType::PixelType BG,
955 // Which direction ? Increasing or decreasing.
959 // Transform to pixel index
960 typename ImageType::IndexType index;
961 input->TransformPhysicalPointToIndex(p, index);
963 // Loop while inside the mask;
964 while (input->GetPixel(index) != BG) {
965 index[dimension] += d;
968 // Transform back to Physical Units
969 typename ImageType::PointType result;
970 input->TransformIndexToPhysicalPoint(index, result);
972 // Check that is is not too far away
973 double distance = p.EuclideanDistanceTo(result);
974 if (distance > distanceMax) {
975 result = p; // Get back to initial value
980 //--------------------------------------------------------------------
983 //--------------------------------------------------------------------
984 template<class PointType>
986 IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
988 // Look at the position of point 'like' according to the AB line
989 double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
992 // Look the C position
993 s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
995 if (negative && (s<=0)) return true;
996 if (!negative && (s>=0)) return true;
999 //--------------------------------------------------------------------
1002 //--------------------------------------------------------------------
1003 /* Consider an input object, for each slice, find the extrema
1004 position according to a given direction and build a line segment
1005 passing throught this point in a given direction. Output is a
1006 vector of line (from point A to B), for each slice;
1008 template<class ImageType>
1010 SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
1011 typename ImageType::PixelType BG,
1013 int extremaDirection,
1014 bool extremaOppositeFlag,
1017 std::vector<typename ImageType::PointType> & A,
1018 std::vector<typename ImageType::PointType> & B)
1021 typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1023 // Build the list of slices
1024 std::vector<typename SliceType::Pointer> slices;
1025 clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
1027 // Build the list of 2D points
1028 std::map<int, typename SliceType::PointType> position2D;
1029 for(uint i=0; i<slices.size(); i++) {
1030 typename SliceType::PointType p;
1032 clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
1033 extremaDirection, extremaOppositeFlag, p);
1039 // Convert 2D points in slice into 3D points
1040 clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
1042 // Create additional point just right to the previous ones, on the
1043 // given lineDirection, in order to create a horizontal/vertical line.
1044 for(uint i=0; i<A.size(); i++) {
1045 typename ImageType::PointType p = A[i];
1046 p[lineDirection] += 10;
1054 //--------------------------------------------------------------------
1057 //--------------------------------------------------------------------
1058 template<class ImageType>
1059 typename ImageType::Pointer
1060 SliceBySliceKeepMainCCL(const ImageType * input,
1061 typename ImageType::PixelType BG,
1062 typename ImageType::PixelType FG) {
1065 const int d = ImageType::ImageDimension-1;
1066 typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
1067 std::vector<typename SliceType::Pointer> slices;
1068 clitk::ExtractSlices<ImageType>(input, d, slices);
1070 // Labelize and keep the main one
1071 std::vector<typename SliceType::Pointer> o;
1072 for(uint i=0; i<slices.size(); i++) {
1073 o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
1074 o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
1078 typename ImageType::Pointer output;
1079 output = clitk::JoinSlices<ImageType>(o, input, d);
1082 //--------------------------------------------------------------------
1085 //--------------------------------------------------------------------
1086 template<class ImageType>
1087 typename ImageType::Pointer
1088 Clone(const ImageType * input) {
1089 typedef itk::ImageDuplicator<ImageType> DuplicatorType;
1090 typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
1091 duplicator->SetInputImage(input);
1092 duplicator->Update();
1093 return duplicator->GetOutput();
1095 //--------------------------------------------------------------------
1098 } // end of namespace