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>
38 //--------------------------------------------------------------------
39 template<class ImageType>
40 void ComputeBBFromImageRegion(const ImageType * image,
41 typename ImageType::RegionType region,
42 typename itk::BoundingBox<unsigned long,
43 ImageType::ImageDimension>::Pointer bb) {
44 typedef typename ImageType::IndexType IndexType;
47 for(unsigned int i=0; i<image->GetImageDimension(); i++) {
48 firstIndex[i] = region.GetIndex()[i];
49 lastIndex[i] = firstIndex[i]+region.GetSize()[i];
52 typedef itk::BoundingBox<unsigned long,
53 ImageType::ImageDimension> BBType;
54 typedef typename BBType::PointType PointType;
57 image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
58 image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
60 bb->SetMaximum(lastPoint);
61 bb->SetMinimum(firstPoint);
63 //--------------------------------------------------------------------
66 //--------------------------------------------------------------------
67 template<int Dimension>
68 void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
69 typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
70 typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
72 typedef itk::BoundingBox<unsigned long, Dimension> BBType;
73 typedef typename BBType::PointType PointType;
77 for(unsigned int i=0; i<Dimension; i++) {
78 firstPoint[i] = std::max(bbi1->GetMinimum()[i],
79 bbi2->GetMinimum()[i]);
80 lastPoint[i] = std::min(bbi1->GetMaximum()[i],
81 bbi2->GetMaximum()[i]);
84 bbo->SetMaximum(lastPoint);
85 bbo->SetMinimum(firstPoint);
87 //--------------------------------------------------------------------
90 //--------------------------------------------------------------------
91 template<class ImageType>
92 void ComputeRegionFromBB(const ImageType * image,
93 const typename itk::BoundingBox<unsigned long,
94 ImageType::ImageDimension>::Pointer bb,
95 typename ImageType::RegionType & region) {
97 typedef typename ImageType::IndexType IndexType;
98 typedef typename ImageType::PointType PointType;
99 typedef typename ImageType::RegionType RegionType;
100 typedef typename ImageType::SizeType SizeType;
102 // Region starting point
103 IndexType regionStart;
104 PointType start = bb->GetMinimum();
105 image->TransformPhysicalPointToIndex(start, regionStart);
109 PointType maxs = bb->GetMaximum();
110 PointType mins = bb->GetMinimum();
111 for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
112 regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
116 region.SetIndex(regionStart);
117 region.SetSize(regionSize);
119 //--------------------------------------------------------------------
121 //--------------------------------------------------------------------
122 template<class ImageType, class TMaskImageType>
123 typename ImageType::Pointer
124 SetBackground(const ImageType * input,
125 const TMaskImageType * mask,
126 typename TMaskImageType::PixelType maskBG,
127 typename ImageType::PixelType outValue,
129 typedef SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
130 SetBackgroundImageFilterType;
131 typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
132 = SetBackgroundImageFilterType::New();
133 // if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
134 setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
135 setBackgroundFilter->SetInput(input);
136 setBackgroundFilter->SetInput2(mask);
137 setBackgroundFilter->SetMaskValue(maskBG);
138 setBackgroundFilter->SetOutsideValue(outValue);
139 setBackgroundFilter->Update();
140 return setBackgroundFilter->GetOutput();
142 //--------------------------------------------------------------------
145 //--------------------------------------------------------------------
146 template<class ImageType>
147 int GetNumberOfConnectedComponentLabels(const ImageType * input,
148 typename ImageType::PixelType BG,
149 bool isFullyConnected) {
150 // Connected Component label
151 typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
152 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
153 connectFilter->SetInput(input);
154 connectFilter->SetBackgroundValue(BG);
155 connectFilter->SetFullyConnected(isFullyConnected);
156 connectFilter->Update();
159 return connectFilter->GetObjectCount();
161 //--------------------------------------------------------------------
163 //--------------------------------------------------------------------
165 Warning : in this cas, we consider outputType like inputType, not
166 InternalImageType. Be sure it fits.
168 template<class ImageType>
169 typename ImageType::Pointer
170 Labelize(const ImageType * input,
171 typename ImageType::PixelType BG,
172 bool isFullyConnected,
173 int minimalComponentSize) {
174 // InternalImageType for storing large number of component
175 typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
177 // Connected Component label
178 typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
179 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
180 // connectFilter->ReleaseDataFlagOn();
181 connectFilter->SetInput(input);
182 connectFilter->SetBackgroundValue(BG);
183 connectFilter->SetFullyConnected(isFullyConnected);
185 // Sort by size and remove too small area.
186 typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
187 typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
188 // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
189 relabelFilter->SetInput(connectFilter->GetOutput());
190 relabelFilter->SetMinimumObjectSize(minimalComponentSize);
191 relabelFilter->Update();
194 typename ImageType::Pointer output = relabelFilter->GetOutput();
197 //--------------------------------------------------------------------
200 //--------------------------------------------------------------------
202 Warning : in this cas, we consider outputType like inputType, not
203 InternalImageType. Be sure it fits.
205 template<class ImageType>
206 typename ImageType::Pointer
207 LabelizeAndCountNumberOfObjects(const ImageType * input,
208 typename ImageType::PixelType BG,
209 bool isFullyConnected,
210 int minimalComponentSize,
212 // InternalImageType for storing large number of component
213 typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
215 // Connected Component label
216 typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
217 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
218 // connectFilter->ReleaseDataFlagOn();
219 connectFilter->SetInput(input);
220 connectFilter->SetBackgroundValue(BG);
221 connectFilter->SetFullyConnected(isFullyConnected);
223 // Sort by size and remove too small area.
224 typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
225 typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
226 // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
227 relabelFilter->SetInput(connectFilter->GetOutput());
228 relabelFilter->SetMinimumObjectSize(minimalComponentSize);
229 relabelFilter->Update();
231 nb = relabelFilter->GetNumberOfObjects();
232 // DD(relabelFilter->GetOriginalNumberOfObjects());
233 // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
236 typename ImageType::Pointer output = relabelFilter->GetOutput();
239 //--------------------------------------------------------------------
243 //--------------------------------------------------------------------
244 template<class ImageType>
245 typename ImageType::Pointer
246 RemoveLabels(const ImageType * input,
247 typename ImageType::PixelType BG,
248 std::vector<typename ImageType::PixelType> & labelsToRemove) {
249 assert(labelsToRemove.size() != 0);
250 typename ImageType::Pointer working_image;// = input;
251 for (unsigned int i=0; i <labelsToRemove.size(); i++) {
252 typedef SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
253 typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
254 setBackgroundFilter->SetInput(input);
255 setBackgroundFilter->SetInput2(input);
256 setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
257 setBackgroundFilter->SetOutsideValue(BG);
258 setBackgroundFilter->Update();
259 working_image = setBackgroundFilter->GetOutput();
261 return working_image;
263 //--------------------------------------------------------------------
266 //--------------------------------------------------------------------
267 template<class ImageType>
268 typename ImageType::Pointer
269 KeepLabels(const ImageType * input,
270 typename ImageType::PixelType BG,
271 typename ImageType::PixelType FG,
272 typename ImageType::PixelType firstKeep,
273 typename ImageType::PixelType lastKeep,
275 typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
276 typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
277 binarizeFilter->SetInput(input);
278 binarizeFilter->SetLowerThreshold(firstKeep);
279 if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
280 binarizeFilter->SetInsideValue(FG);
281 binarizeFilter->SetOutsideValue(BG);
282 binarizeFilter->Update();
283 return binarizeFilter->GetOutput();
285 //--------------------------------------------------------------------
288 //--------------------------------------------------------------------
289 template<class ImageType>
290 typename ImageType::Pointer
291 LabelizeAndSelectLabels(const ImageType * input,
292 typename ImageType::PixelType BG,
293 typename ImageType::PixelType FG,
294 bool isFullyConnected,
295 int minimalComponentSize,
296 LabelizeParameters<typename ImageType::PixelType> * param)
298 typename ImageType::Pointer working_image;
299 working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
300 if (param->GetLabelsToRemove().size() != 0)
301 working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
302 working_image = KeepLabels<ImageType>(working_image,
304 param->GetFirstKeep(),
305 param->GetLastKeep(),
306 param->GetUseLastKeep());
307 return working_image;
309 //--------------------------------------------------------------------
312 //--------------------------------------------------------------------
313 template<class ImageType>
314 typename ImageType::Pointer
315 ResizeImageLike(const ImageType * input,
316 const itk::ImageBase<ImageType::ImageDimension> * like,
317 typename ImageType::PixelType backgroundValue)
319 typedef CropLikeImageFilter<ImageType> CropFilterType;
320 typename CropFilterType::Pointer cropFilter = CropFilterType::New();
321 cropFilter->SetInput(input);
322 cropFilter->SetCropLikeImage(like);
323 cropFilter->SetBackgroundValue(backgroundValue);
324 cropFilter->Update();
325 return cropFilter->GetOutput();
327 //--------------------------------------------------------------------
330 //--------------------------------------------------------------------
331 template<class MaskImageType>
332 typename MaskImageType::Pointer
333 SliceBySliceRelativePosition(const MaskImageType * input,
334 const MaskImageType * object,
337 std::string orientation,
338 bool uniqueConnectedComponent,
341 bool singleObjectCCL)
343 typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
344 typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
345 sliceRelPosFilter->VerboseStepFlagOff();
346 sliceRelPosFilter->WriteStepFlagOff();
347 sliceRelPosFilter->SetInput(input);
348 sliceRelPosFilter->SetInputObject(object);
349 sliceRelPosFilter->SetDirection(direction);
350 sliceRelPosFilter->SetFuzzyThreshold(threshold);
351 sliceRelPosFilter->AddOrientationTypeString(orientation);
352 sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
353 sliceRelPosFilter->SetIntermediateSpacing(spacing);
354 sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
355 sliceRelPosFilter->SetUseASingleObjectConnectedComponentBySliceFlag(singleObjectCCL);
356 // sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
357 sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
358 sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
359 sliceRelPosFilter->Update();
360 return sliceRelPosFilter->GetOutput();
362 //--------------------------------------------------------------------
364 //--------------------------------------------------------------------
365 template<class ImageType>
367 FindExtremaPointInAGivenDirection(const ImageType * input,
368 typename ImageType::PixelType bg,
369 int direction, bool opposite,
370 typename ImageType::PointType & point)
372 typename ImageType::PointType dummy;
373 return FindExtremaPointInAGivenDirection(input, bg, direction,
374 opposite, dummy, 0, point);
376 //--------------------------------------------------------------------
378 //--------------------------------------------------------------------
379 template<class ImageType>
381 FindExtremaPointInAGivenDirection(const ImageType * input,
382 typename ImageType::PixelType bg,
383 int direction, bool opposite,
384 typename ImageType::PointType refpoint,
386 typename ImageType::PointType & point)
389 loop over input pixels, store the index in the fg that is max
390 according to the given direction.
392 typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
393 IteratorType iter(input, input->GetLargestPossibleRegion());
395 typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
396 if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
398 while (!iter.IsAtEnd()) {
399 if (iter.Get() != bg) {
400 bool test = iter.GetIndex()[direction] > max[direction];
401 if (opposite) test = !test;
403 typename ImageType::PointType p;
404 input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
405 if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
406 max = iter.GetIndex();
413 if (!found) return false;
414 input->TransformIndexToPhysicalPoint(max, point);
417 //--------------------------------------------------------------------
420 //--------------------------------------------------------------------
421 template<class ImageType>
422 typename ImageType::Pointer
423 CropImageAbove(const ImageType * image,
424 int dim, double min, bool autoCrop,
425 typename ImageType::PixelType BG)
427 return CropImageAlongOneAxis<ImageType>(image, dim,
428 image->GetOrigin()[dim],
432 //--------------------------------------------------------------------
435 //--------------------------------------------------------------------
436 template<class ImageType>
437 typename ImageType::Pointer
438 CropImageBelow(const ImageType * image,
439 int dim, double max, bool autoCrop,
440 typename ImageType::PixelType BG)
442 typename ImageType::PointType p;
443 image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
444 image->GetLargestPossibleRegion().GetSize(), p);
445 return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
447 //--------------------------------------------------------------------
450 //--------------------------------------------------------------------
451 template<class ImageType>
452 typename ImageType::Pointer
453 CropImageAlongOneAxis(const ImageType * image,
454 int dim, double min, double max,
455 bool autoCrop, typename ImageType::PixelType BG)
457 // Compute region size
458 typename ImageType::RegionType region;
459 typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
460 typename ImageType::PointType p = image->GetOrigin();
462 typename ImageType::IndexType start;
463 image->TransformPhysicalPointToIndex(p, start);
465 typename ImageType::IndexType end;
466 image->TransformPhysicalPointToIndex(p, end);
467 size[dim] = fabs(end[dim]-start[dim]);
468 region.SetIndex(start);
469 region.SetSize(size);
472 typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
473 typename CropFilterType::Pointer cropFilter = CropFilterType::New();
474 cropFilter->SetInput(image);
475 cropFilter->SetRegionOfInterest(region);
476 cropFilter->Update();
477 typename ImageType::Pointer result = cropFilter->GetOutput();
481 result = AutoCrop<ImageType>(result, BG);
485 //--------------------------------------------------------------------
488 //--------------------------------------------------------------------
489 template<class ImageType>
491 ComputeCentroids(const ImageType * image,
492 typename ImageType::PixelType BG,
493 std::vector<typename ImageType::PointType> & centroids)
495 typedef long LabelType;
496 static const unsigned int Dim = ImageType::ImageDimension;
497 typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
498 typedef itk::LabelMap< LabelObjectType > LabelMapType;
499 typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
500 typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
501 typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
502 typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
503 imageToLabelFilter->SetBackgroundValue(BG);
504 imageToLabelFilter->SetInput(image);
505 statFilter->SetInput(imageToLabelFilter->GetOutput());
506 statFilter->Update();
507 typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
510 typename ImageType::PointType dummy;
511 centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
512 for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
513 centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
516 //--------------------------------------------------------------------
519 //--------------------------------------------------------------------
520 template<class ImageType>
522 ExtractSlices(const ImageType * image, int direction,
523 std::vector<typename itk::Image<typename ImageType::PixelType,
524 ImageType::ImageDimension-1>::Pointer > & slices)
526 typedef ExtractSliceFilter<ImageType> ExtractSliceFilterType;
527 typedef typename ExtractSliceFilterType::SliceType SliceType;
528 typename ExtractSliceFilterType::Pointer
529 extractSliceFilter = ExtractSliceFilterType::New();
530 extractSliceFilter->SetInput(image);
531 extractSliceFilter->SetDirection(direction);
532 extractSliceFilter->Update();
533 extractSliceFilter->GetOutputSlices(slices);
535 //--------------------------------------------------------------------
538 //--------------------------------------------------------------------
539 template<class ImageType>
541 PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
542 const ImageType * image,
547 index3D[0] = index3D[1] = 0;
548 index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
549 image->TransformIndexToPhysicalPoint(index3D, p3D);
552 // p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
553 // + image->GetOrigin()[2];
555 //--------------------------------------------------------------------
558 //--------------------------------------------------------------------
559 template<class ImageType>
561 PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map,
562 const ImageType * image,
563 VectorPoint3DType & list)
565 typename MapPoint2DType::const_iterator iter = map.begin();
566 while (iter != map.end()) {
568 Convert2DTo3D(iter->second, image, iter->first, p);
573 //--------------------------------------------------------------------
575 //--------------------------------------------------------------------
576 template<class ImageType>
578 WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
579 std::string filename)
582 openFileForWriting(os, filename);
583 os << "LANDMARKS1" << std::endl;
584 for(uint i=0; i<points.size(); i++) {
585 const typename ImageType::PointType & p = points[i];
586 // Write it in the file
587 os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
591 //--------------------------------------------------------------------
594 //--------------------------------------------------------------------
595 template<class ImageType>
596 typename ImageType::Pointer
597 Dilate(const ImageType * image, double radiusInMM,
598 typename ImageType::PixelType BG,
599 typename ImageType::PixelType FG,
602 typename ImageType::SizeType r;
603 for(uint i=0; i<ImageType::ImageDimension; i++)
604 r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
605 return Dilate<ImageType>(image, r, BG, FG, extendSupport);
607 //--------------------------------------------------------------------
610 //--------------------------------------------------------------------
611 template<class ImageType>
612 typename ImageType::Pointer
613 Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
614 typename ImageType::PixelType BG,
615 typename ImageType::PixelType FG,
618 typename ImageType::SizeType r;
619 for(uint i=0; i<ImageType::ImageDimension; i++)
620 r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
621 return Dilate<ImageType>(image, r, BG, FG, extendSupport);
623 //--------------------------------------------------------------------
626 //--------------------------------------------------------------------
627 template<class ImageType>
628 typename ImageType::Pointer
629 Dilate(const ImageType * image, typename ImageType::SizeType radius,
630 typename ImageType::PixelType BG,
631 typename ImageType::PixelType FG,
634 // Create kernel for dilatation
635 typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
636 ImageType::ImageDimension> KernelType;
637 KernelType structuringElement;
638 structuringElement.SetRadius(radius);
639 structuringElement.CreateStructuringElement();
641 typename ImageType::Pointer output;
643 typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
644 typename PadFilterType::Pointer padFilter = PadFilterType::New();
645 padFilter->SetInput(image);
646 typename ImageType::SizeType lower;
647 typename ImageType::SizeType upper;
648 for(uint i=0; i<3; i++) {
649 lower[i] = upper[i] = 2*(radius[i]+1);
651 padFilter->SetPadLowerBound(lower);
652 padFilter->SetPadUpperBound(upper);
654 output = padFilter->GetOutput();
658 typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
659 typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
660 dilateFilter->SetBackgroundValue(BG);
661 dilateFilter->SetForegroundValue(FG);
662 dilateFilter->SetBoundaryToForeground(false);
663 dilateFilter->SetKernel(structuringElement);
664 dilateFilter->SetInput(output);
665 dilateFilter->Update();
666 return dilateFilter->GetOutput();
668 //--------------------------------------------------------------------
671 //--------------------------------------------------------------------
672 template<class ValueType, class VectorType>
673 void ConvertOption(std::string optionName, uint given,
674 ValueType * values, VectorType & p,
675 uint dim, bool required)
677 if (required && (given == 0)) {
678 clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
679 << dim << " values.");
682 for(uint i=0; i<dim; i++) p[i] = values[0];
686 for(uint i=0; i<dim; i++) p[i] = values[i];
689 if (given == 0) return;
690 clitkExceptionMacro("The option --" << optionName << " must have 1 or "
691 << dim << " values.");
693 //--------------------------------------------------------------------
696 //--------------------------------------------------------------------
698 http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
699 Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
700 (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
701 This will equal zero if the point C is on the line formed by
702 points A and B, and will have a different sign depending on the
703 side. Which side this is depends on the orientation of your (x,y)
704 coordinates, but you can plug test values for A,B and C into this
705 formula to determine whether negative values are to the left or to
707 => to accelerate, start with formula, when change sign -> stop and fill
709 offsetToKeep = is used to determine which side of the line we
710 keep. The point along the mainDirection but 'offsetToKeep' mm away
714 template<class ImageType>
716 SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
717 std::vector<typename ImageType::PointType> & lA,
718 std::vector<typename ImageType::PointType> & lB,
719 typename ImageType::PixelType BG,
723 typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
724 SliceIteratorType siter = SliceIteratorType(input,
725 input->GetLargestPossibleRegion());
726 siter.SetFirstDirection(0);
727 siter.SetSecondDirection(1);
730 typename ImageType::PointType A;
731 typename ImageType::PointType B;
732 typename ImageType::PointType C;
733 assert(lA.size() == lB.size());
734 while ((i<lA.size()) && (!siter.IsAtEnd())) {
735 // Check that the current slice correspond to the current point
736 input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
740 if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
743 // Define A,B,C points
751 // Check that the line is not a point (A=B)
752 bool p = (A[0] == B[0]) && (A[1] == B[1]);
755 C[mainDirection] += offsetToKeep; // I know I must keep this point
756 double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
757 bool isPositive = s<0;
758 while (!siter.IsAtEndOfSlice()) {
759 while (!siter.IsAtEndOfLine()) {
760 // Very slow, I know ... but image should be very small
761 input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
762 double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
763 if (s == 0) siter.Set(BG); // on the line, we decide to remove
765 if (s > 0) siter.Set(BG);
768 if (s < 0) siter.Set(BG);
777 } // End of current slice
781 //--------------------------------------------------------------------
783 //--------------------------------------------------------------------
784 template<class ImageType>
786 AndNot(ImageType * input,
787 const ImageType * object,
788 typename ImageType::PixelType BG)
790 typename ImageType::Pointer o;
792 if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
793 o = clitk::ResizeImageLike<ImageType>(object, input, BG);
797 typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
798 typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
799 boolFilter->InPlaceOn();
800 boolFilter->SetInput1(input);
801 if (resized) boolFilter->SetInput2(o);
802 else boolFilter->SetInput2(object);
803 boolFilter->SetBackgroundValue1(BG);
804 boolFilter->SetBackgroundValue2(BG);
805 boolFilter->SetOperationType(BoolFilterType::AndNot);
806 boolFilter->Update();
808 //--------------------------------------------------------------------
811 //--------------------------------------------------------------------
812 template<class ImageType>
813 typename ImageType::Pointer
814 Binarize(const ImageType * input,
815 typename ImageType::PixelType lower,
816 typename ImageType::PixelType upper,
817 typename ImageType::PixelType BG,
818 typename ImageType::PixelType FG)
820 typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
821 typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
822 binarizeFilter->SetInput(input);
823 binarizeFilter->SetLowerThreshold(lower);
824 binarizeFilter->SetUpperThreshold(upper);
825 binarizeFilter->SetInsideValue(FG);
826 binarizeFilter->SetOutsideValue(BG);
827 binarizeFilter->Update();
828 return binarizeFilter->GetOutput();
830 //--------------------------------------------------------------------
833 //--------------------------------------------------------------------
834 template<class ImageType>
836 GetMinMaxPointPosition(const ImageType * input,
837 typename ImageType::PointType & min,
838 typename ImageType::PointType & max)
840 typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
841 input->TransformIndexToPhysicalPoint(index, min);
842 index = index+input->GetLargestPossibleRegion().GetSize();
843 input->TransformIndexToPhysicalPoint(index, max);
845 //--------------------------------------------------------------------
848 //--------------------------------------------------------------------
849 template<class ImageType>
850 typename ImageType::PointType
851 FindExtremaPointInAGivenLine(const ImageType * input,
854 typename ImageType::PointType p,
855 typename ImageType::PixelType BG,
858 // Which direction ? Increasing or decreasing.
862 // Transform to pixel index
863 typename ImageType::IndexType index;
864 input->TransformPhysicalPointToIndex(p, index);
866 // Loop while inside the mask;
867 while (input->GetPixel(index) != BG) {
868 index[dimension] += d;
871 // Transform back to Physical Units
872 typename ImageType::PointType result;
873 input->TransformIndexToPhysicalPoint(index, result);
875 // Check that is is not too far away
876 double distance = p.EuclideanDistanceTo(result);
877 if (distance > distanceMax) {
878 result = p; // Get back to initial value
883 //--------------------------------------------------------------------
886 //--------------------------------------------------------------------
887 template<class PointType>
889 IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
891 // Look at the position of point 'like' according to the AB line
892 double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
895 // Look the C position
896 s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
898 if (negative && (s<=0)) return true;
899 if (!negative && (s>=0)) return true;
902 //--------------------------------------------------------------------
905 //--------------------------------------------------------------------
906 /* Consider an input object, for each slice, find the extrema
907 position according to a given direction and build a line segment
908 passing throught this point in a given direction. Output is a
909 vector of line (from point A to B), for each slice;
911 template<class ImageType>
913 SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
914 typename ImageType::PixelType BG,
916 int extremaDirection,
917 bool extremaOppositeFlag,
920 std::vector<typename ImageType::PointType> & A,
921 std::vector<typename ImageType::PointType> & B)
924 typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
926 // Build the list of slices
927 std::vector<typename SliceType::Pointer> slices;
928 clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
930 // Build the list of 2D points
931 std::map<int, typename SliceType::PointType> position2D;
932 for(uint i=0; i<slices.size(); i++) {
933 typename SliceType::PointType p;
935 clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
936 extremaDirection, extremaOppositeFlag, p);
942 // Convert 2D points in slice into 3D points
943 clitk::PointsUtils<ImageType>::Convert2DTo3DList(position2D, input, A);
945 // Create additional point just right to the previous ones, on the
946 // given lineDirection, in order to create a horizontal/vertical line.
947 for(uint i=0; i<A.size(); i++) {
948 typename ImageType::PointType p = A[i];
949 p[lineDirection] += 10;
957 //--------------------------------------------------------------------
960 } // end of namespace