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>
37 #include <itkSignedMaurerDistanceMapImageFilter.h>
41 //--------------------------------------------------------------------
42 template<class ImageType, class TMaskImageType>
43 typename ImageType::Pointer
44 SetBackground(const ImageType * input,
45 const TMaskImageType * mask,
46 typename TMaskImageType::PixelType maskBG,
47 typename ImageType::PixelType outValue,
49 typedef SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
50 SetBackgroundImageFilterType;
51 typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
52 = SetBackgroundImageFilterType::New();
53 // if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
54 setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
55 setBackgroundFilter->SetInput(input);
56 setBackgroundFilter->SetInput2(mask);
57 setBackgroundFilter->SetMaskValue(maskBG);
58 setBackgroundFilter->SetOutsideValue(outValue);
59 setBackgroundFilter->Update();
60 return setBackgroundFilter->GetOutput();
62 //--------------------------------------------------------------------
65 //--------------------------------------------------------------------
66 template<class ImageType>
67 int GetNumberOfConnectedComponentLabels(const ImageType * input,
68 typename ImageType::PixelType BG,
69 bool isFullyConnected) {
70 // Connected Component label
71 typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
72 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
73 connectFilter->SetInput(input);
74 connectFilter->SetBackgroundValue(BG);
75 connectFilter->SetFullyConnected(isFullyConnected);
76 connectFilter->Update();
79 return connectFilter->GetObjectCount();
81 //--------------------------------------------------------------------
83 //--------------------------------------------------------------------
85 Warning : in this cas, we consider outputType like inputType, not
86 InternalImageType. Be sure it fits.
88 template<class ImageType>
89 typename ImageType::Pointer
90 Labelize(const ImageType * input,
91 typename ImageType::PixelType BG,
92 bool isFullyConnected,
93 int minimalComponentSize) {
94 // InternalImageType for storing large number of component
95 typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
97 // Connected Component label
98 typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
99 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
100 // connectFilter->ReleaseDataFlagOn();
101 connectFilter->SetInput(input);
102 connectFilter->SetBackgroundValue(BG);
103 connectFilter->SetFullyConnected(isFullyConnected);
105 // Sort by size and remove too small area.
106 typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
107 typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
108 // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
109 relabelFilter->SetInput(connectFilter->GetOutput());
110 relabelFilter->SetMinimumObjectSize(minimalComponentSize);
111 relabelFilter->Update();
114 typename ImageType::Pointer output = relabelFilter->GetOutput();
117 //--------------------------------------------------------------------
120 //--------------------------------------------------------------------
122 Warning : in this cas, we consider outputType like inputType, not
123 InternalImageType. Be sure it fits.
125 template<class ImageType>
126 typename ImageType::Pointer
127 LabelizeAndCountNumberOfObjects(const ImageType * input,
128 typename ImageType::PixelType BG,
129 bool isFullyConnected,
130 int minimalComponentSize,
132 // InternalImageType for storing large number of component
133 typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
135 // Connected Component label
136 typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
137 typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
138 // connectFilter->ReleaseDataFlagOn();
139 connectFilter->SetInput(input);
140 connectFilter->SetBackgroundValue(BG);
141 connectFilter->SetFullyConnected(isFullyConnected);
143 // Sort by size and remove too small area.
144 typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
145 typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
146 // relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
147 relabelFilter->SetInput(connectFilter->GetOutput());
148 relabelFilter->SetMinimumObjectSize(minimalComponentSize);
149 relabelFilter->Update();
151 nb = relabelFilter->GetNumberOfObjects();
152 // DD(relabelFilter->GetOriginalNumberOfObjects());
153 // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
156 typename ImageType::Pointer output = relabelFilter->GetOutput();
159 //--------------------------------------------------------------------
163 //--------------------------------------------------------------------
164 template<class ImageType>
165 typename ImageType::Pointer
166 RemoveLabels(const ImageType * input,
167 typename ImageType::PixelType BG,
168 std::vector<typename ImageType::PixelType> & labelsToRemove) {
169 assert(labelsToRemove.size() != 0);
170 typename ImageType::Pointer working_image;// = input;
171 for (unsigned int i=0; i <labelsToRemove.size(); i++) {
172 typedef SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
173 typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
174 setBackgroundFilter->SetInput(input);
175 setBackgroundFilter->SetInput2(input);
176 setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
177 setBackgroundFilter->SetOutsideValue(BG);
178 setBackgroundFilter->Update();
179 working_image = setBackgroundFilter->GetOutput();
181 return working_image;
183 //--------------------------------------------------------------------
186 //--------------------------------------------------------------------
187 template<class ImageType>
188 typename ImageType::Pointer
189 KeepLabels(const ImageType * input,
190 typename ImageType::PixelType BG,
191 typename ImageType::PixelType FG,
192 typename ImageType::PixelType firstKeep,
193 typename ImageType::PixelType lastKeep,
195 typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
196 typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
197 binarizeFilter->SetInput(input);
198 binarizeFilter->SetLowerThreshold(firstKeep);
199 if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
200 binarizeFilter->SetInsideValue(FG);
201 binarizeFilter->SetOutsideValue(BG);
202 binarizeFilter->Update();
203 return binarizeFilter->GetOutput();
205 //--------------------------------------------------------------------
208 //--------------------------------------------------------------------
209 template<class ImageType>
210 typename ImageType::Pointer
211 LabelizeAndSelectLabels(const ImageType * input,
212 typename ImageType::PixelType BG,
213 typename ImageType::PixelType FG,
214 bool isFullyConnected,
215 int minimalComponentSize,
216 LabelizeParameters<typename ImageType::PixelType> * param)
218 typename ImageType::Pointer working_image;
219 working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
220 if (param->GetLabelsToRemove().size() != 0)
221 working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
222 working_image = KeepLabels<ImageType>(working_image,
224 param->GetFirstKeep(),
225 param->GetLastKeep(),
226 param->GetUseLastKeep());
227 return working_image;
229 //--------------------------------------------------------------------
232 //--------------------------------------------------------------------
233 template<class MaskImageType>
234 typename MaskImageType::Pointer
235 SliceBySliceRelativePosition(const MaskImageType * input,
236 const MaskImageType * object,
239 std::string orientation,
240 bool uniqueConnectedComponent,
243 bool singleObjectCCL)
245 typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
246 typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
247 sliceRelPosFilter->VerboseStepFlagOff();
248 sliceRelPosFilter->WriteStepFlagOff();
249 sliceRelPosFilter->SetInput(input);
250 sliceRelPosFilter->SetInputObject(object);
251 sliceRelPosFilter->SetDirection(direction);
252 sliceRelPosFilter->SetFuzzyThreshold(threshold);
253 sliceRelPosFilter->AddOrientationTypeString(orientation);
254 sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
255 sliceRelPosFilter->SetIntermediateSpacing(spacing);
256 sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
257 sliceRelPosFilter->ObjectCCLSelectionFlagOff();
258 sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
259 // sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
260 sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
261 sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
262 sliceRelPosFilter->Update();
263 return sliceRelPosFilter->GetOutput();
265 //--------------------------------------------------------------------
268 //--------------------------------------------------------------------
269 template<class MaskImageType>
270 typename MaskImageType::Pointer
271 SliceBySliceRelativePosition(const MaskImageType * input,
272 const MaskImageType * object,
277 bool uniqueConnectedComponent,
280 bool singleObjectCCL)
282 typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
283 typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
284 sliceRelPosFilter->VerboseStepFlagOff();
285 sliceRelPosFilter->WriteStepFlagOff();
286 sliceRelPosFilter->SetInput(input);
287 sliceRelPosFilter->SetInputObject(object);
288 sliceRelPosFilter->SetDirection(direction);
289 sliceRelPosFilter->SetFuzzyThreshold(threshold);
290 // sliceRelPosFilter->AddOrientationTypeString(orientation);
291 sliceRelPosFilter->AddAngles(angle, 0.0);
292 sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
293 sliceRelPosFilter->SetIntermediateSpacing(spacing);
294 sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
295 sliceRelPosFilter->ObjectCCLSelectionFlagOff();
296 sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
297 sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
298 sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
299 sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
300 sliceRelPosFilter->Update();
301 return sliceRelPosFilter->GetOutput();
303 //--------------------------------------------------------------------
306 //--------------------------------------------------------------------
307 template<class ImageType>
309 FindExtremaPointInAGivenDirection(const ImageType * input,
310 typename ImageType::PixelType bg,
311 int direction, bool opposite,
312 typename ImageType::PointType & point)
314 typename ImageType::PointType dummy;
315 return FindExtremaPointInAGivenDirection(input, bg, direction,
316 opposite, dummy, 0, point);
318 //--------------------------------------------------------------------
321 //--------------------------------------------------------------------
322 template<class ImageType>
324 FindExtremaPointInAGivenDirection(const ImageType * input,
325 typename ImageType::PixelType bg,
326 int direction, bool opposite,
327 typename ImageType::PointType refpoint,
329 typename ImageType::PointType & point)
332 loop over input pixels, store the index in the fg that is max
333 according to the given direction.
335 typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
336 IteratorType iter(input, input->GetLargestPossibleRegion());
338 typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
339 if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
341 while (!iter.IsAtEnd()) {
342 if (iter.Get() != bg) {
343 bool test = iter.GetIndex()[direction] > max[direction];
344 if (opposite) test = !test;
346 typename ImageType::PointType p;
347 input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
348 if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
349 max = iter.GetIndex();
356 if (!found) return false;
357 input->TransformIndexToPhysicalPoint(max, point);
360 //--------------------------------------------------------------------
363 //--------------------------------------------------------------------
364 template<class ImageType>
365 typename ImageType::Pointer
366 CropImageRemoveGreaterThan(const ImageType * image,
367 int dim, double min, bool autoCrop,
368 typename ImageType::PixelType BG)
370 return CropImageAlongOneAxis<ImageType>(image, dim,
371 image->GetOrigin()[dim],
375 //--------------------------------------------------------------------
378 //--------------------------------------------------------------------
379 template<class ImageType>
380 typename ImageType::Pointer
381 CropImageRemoveLowerThan(const ImageType * image,
382 int dim, double max, bool autoCrop,
383 typename ImageType::PixelType BG)
385 typename ImageType::PointType p;
386 image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
387 image->GetLargestPossibleRegion().GetSize(), p);
388 return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
390 //--------------------------------------------------------------------
393 //--------------------------------------------------------------------
394 template<class ImageType>
395 typename ImageType::Pointer
396 CropImageAlongOneAxis(const ImageType * image,
397 int dim, double min, double max,
398 bool autoCrop, typename ImageType::PixelType BG)
400 // Compute region size
401 typename ImageType::RegionType region;
402 typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
403 typename ImageType::PointType p = image->GetOrigin();
404 if (min > p[dim]) p[dim] = min; // Check if not outside the image
405 typename ImageType::IndexType start;
406 image->TransformPhysicalPointToIndex(p, start);
407 double m = image->GetOrigin()[dim] + size[dim]*image->GetSpacing()[dim];
408 if (max > m) p[dim] = m; // Check if not outside the image
410 typename ImageType::IndexType end;
411 image->TransformPhysicalPointToIndex(p, end);
412 size[dim] = abs(end[dim]-start[dim]);
413 region.SetIndex(start);
414 region.SetSize(size);
417 typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
418 typename CropFilterType::Pointer cropFilter = CropFilterType::New();
419 cropFilter->SetInput(image);
420 cropFilter->SetRegionOfInterest(region);
421 cropFilter->Update();
422 typename ImageType::Pointer result = cropFilter->GetOutput();
426 result = AutoCrop<ImageType>(result, BG);
430 //--------------------------------------------------------------------
433 //--------------------------------------------------------------------
434 template<class ImageType>
436 ComputeCentroids(const ImageType * image,
437 typename ImageType::PixelType BG,
438 std::vector<typename ImageType::PointType> & centroids)
440 typedef long LabelType;
441 static const unsigned int Dim = ImageType::ImageDimension;
442 typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
443 typedef itk::LabelMap< LabelObjectType > LabelMapType;
444 typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
445 typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
446 typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
447 typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
448 imageToLabelFilter->SetBackgroundValue(BG);
449 imageToLabelFilter->SetInput(image);
450 statFilter->SetInput(imageToLabelFilter->GetOutput());
451 statFilter->Update();
452 typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
455 typename ImageType::PointType dummy;
456 centroids.push_back(dummy); // label 0 -> no centroid, use dummy point for BG
457 //DS FIXME (not useful ! to change ..)
458 for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
459 int label = labelMap->GetLabels()[i];
460 centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
463 //--------------------------------------------------------------------
466 //--------------------------------------------------------------------
467 template<class ImageType, class LabelType>
468 typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
469 ComputeLabelMap(const ImageType * image,
470 typename ImageType::PixelType BG,
471 bool computePerimeterFlag)
473 static const unsigned int Dim = ImageType::ImageDimension;
474 typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
475 typedef itk::LabelMap< LabelObjectType > LabelMapType;
476 typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
477 typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
478 typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
479 typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
480 imageToLabelFilter->SetBackgroundValue(BG);
481 imageToLabelFilter->SetInput(image);
482 statFilter->SetInput(imageToLabelFilter->GetOutput());
483 statFilter->SetComputePerimeter(computePerimeterFlag);
484 statFilter->Update();
485 return statFilter->GetOutput();
487 //--------------------------------------------------------------------
490 //--------------------------------------------------------------------
491 template<class ImageType>
493 ComputeCentroids2(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
514 for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
515 centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
518 for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
519 DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
520 DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
521 DD(labelMap->GetLabelObject(i)->GetRoundness ());
523 // search for the point on the boundary alog PA
528 //--------------------------------------------------------------------
531 //--------------------------------------------------------------------
532 template<class ImageType>
534 PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
535 const ImageType * image,
540 index3D[0] = index3D[1] = 0;
541 index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
542 image->TransformIndexToPhysicalPoint(index3D, p3D);
545 // p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
546 // + image->GetOrigin()[2];
548 //--------------------------------------------------------------------
551 //--------------------------------------------------------------------
552 template<class ImageType>
554 PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map,
555 const ImageType * image,
556 VectorPoint3DType & list)
558 typename MapPoint2DType::const_iterator iter = map.begin();
559 while (iter != map.end()) {
561 Convert2DTo3D(iter->second, image, iter->first, p);
566 //--------------------------------------------------------------------
569 //--------------------------------------------------------------------
570 template<class ImageType>
572 PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D,
574 const ImageType * image,
575 VectorPoint3DType & list)
577 for(uint i=0; i<p2D.size(); i++) {
579 Convert2DTo3D(p2D[i], image, slice, p);
583 //--------------------------------------------------------------------
586 //--------------------------------------------------------------------
587 template<class ImageType>
589 WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
590 std::string filename)
593 openFileForWriting(os, filename);
594 os << "LANDMARKS1" << std::endl;
595 for(uint i=0; i<points.size(); i++) {
596 const typename ImageType::PointType & p = points[i];
597 // Write it in the file
598 os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
602 //--------------------------------------------------------------------
605 //--------------------------------------------------------------------
606 template<class ImageType>
607 typename ImageType::Pointer
608 Dilate(const ImageType * image, double radiusInMM,
609 typename ImageType::PixelType BG,
610 typename ImageType::PixelType FG,
613 typename ImageType::SizeType r;
614 for(uint i=0; i<ImageType::ImageDimension; i++)
615 r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
616 return Dilate<ImageType>(image, r, BG, FG, extendSupport);
618 //--------------------------------------------------------------------
621 //--------------------------------------------------------------------
622 template<class ImageType>
623 typename ImageType::Pointer
624 Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
625 typename ImageType::PixelType BG,
626 typename ImageType::PixelType FG,
629 typename ImageType::SizeType r;
630 for(uint i=0; i<ImageType::ImageDimension; i++)
631 r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
632 return Dilate<ImageType>(image, r, BG, FG, extendSupport);
634 //--------------------------------------------------------------------
637 //--------------------------------------------------------------------
638 template<class ImageType>
639 typename ImageType::Pointer
640 Dilate(const ImageType * image, typename ImageType::SizeType radius,
641 typename ImageType::PixelType BG,
642 typename ImageType::PixelType FG,
645 // Create kernel for dilatation
646 typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
647 ImageType::ImageDimension> KernelType;
648 KernelType structuringElement;
649 structuringElement.SetRadius(radius);
650 structuringElement.CreateStructuringElement();
652 typename ImageType::Pointer output;
654 typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
655 typename PadFilterType::Pointer padFilter = PadFilterType::New();
656 padFilter->SetInput(image);
657 typename ImageType::SizeType lower;
658 typename ImageType::SizeType upper;
659 for(uint i=0; i<3; i++) {
660 lower[i] = upper[i] = 2*(radius[i]+1);
662 padFilter->SetPadLowerBound(lower);
663 padFilter->SetPadUpperBound(upper);
665 output = padFilter->GetOutput();
669 typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
670 typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
671 dilateFilter->SetBackgroundValue(BG);
672 dilateFilter->SetForegroundValue(FG);
673 dilateFilter->SetBoundaryToForeground(false);
674 dilateFilter->SetKernel(structuringElement);
675 if (extendSupport) dilateFilter->SetInput(output);
676 else dilateFilter->SetInput(image);
677 dilateFilter->Update();
678 return dilateFilter->GetOutput();
680 //--------------------------------------------------------------------
683 //--------------------------------------------------------------------
684 template<class ImageType>
685 typename ImageType::Pointer
686 Opening(const ImageType * image, typename ImageType::SizeType radius,
687 typename ImageType::PixelType BG,
688 typename ImageType::PixelType FG)
691 typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
692 ImageType::ImageDimension> KernelType;
693 KernelType structuringElement;
694 structuringElement.SetRadius(radius);
695 structuringElement.CreateStructuringElement();
698 typedef itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType , KernelType> OpeningFilterType;
699 typename OpeningFilterType::Pointer open = OpeningFilterType::New();
700 open->SetInput(image);
701 open->SetBackgroundValue(BG);
702 open->SetForegroundValue(FG);
703 open->SetKernel(structuringElement);
705 return open->GetOutput();
707 //--------------------------------------------------------------------
711 //--------------------------------------------------------------------
712 template<class ValueType, class VectorType>
713 void ConvertOption(std::string optionName, uint given,
714 ValueType * values, VectorType & p,
715 uint dim, bool required)
717 if (required && (given == 0)) {
718 clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
719 << dim << " values.");
722 for(uint i=0; i<dim; i++) p[i] = values[0];
726 for(uint i=0; i<dim; i++) p[i] = values[i];
729 if (given == 0) return;
730 clitkExceptionMacro("The option --" << optionName << " must have 1 or "
731 << dim << " values.");
733 //--------------------------------------------------------------------
736 //--------------------------------------------------------------------
738 http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
739 Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
740 (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
741 This will equal zero if the point C is on the line formed by
742 points A and B, and will have a different sign depending on the
743 side. Which side this is depends on the orientation of your (x,y)
744 coordinates, but you can plug test values for A,B and C into this
745 formula to determine whether negative values are to the left or to
747 => to accelerate, start with formula, when change sign -> stop and fill
749 offsetToKeep = is used to determine which side of the line we
750 keep. The point along the mainDirection but 'offsetToKeep' mm away
754 template<class ImageType>
756 SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
757 std::vector<typename ImageType::PointType> & lA,
758 std::vector<typename ImageType::PointType> & lB,
759 typename ImageType::PixelType BG,
763 assert((mainDirection==0) || (mainDirection==1));
764 typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
765 SliceIteratorType siter = SliceIteratorType(input,
766 input->GetLargestPossibleRegion());
767 siter.SetFirstDirection(0);
768 siter.SetSecondDirection(1);
771 typename ImageType::PointType A;
772 typename ImageType::PointType B;
773 typename ImageType::PointType C;
774 assert(lA.size() == lB.size());
775 while ((i<lA.size()) && (!siter.IsAtEnd())) {
776 // Check that the current slice correspond to the current point
777 input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
778 if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
781 // Define A,B,C points
786 // Check that the line is not a point (A=B)
787 bool p = (A[0] == B[0]) && (A[1] == B[1]);
790 C[mainDirection] += offsetToKeep; // I know I must keep this point
791 double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
792 bool isPositive = s<0;
793 while (!siter.IsAtEndOfSlice()) {
794 while (!siter.IsAtEndOfLine()) {
795 // Very slow, I know ... but image should be very small
796 input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
797 double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
798 if (s == 0) siter.Set(BG); // on the line, we decide to remove
800 if (s > 0) siter.Set(BG);
803 if (s < 0) siter.Set(BG);
812 } // End of current slice
816 //--------------------------------------------------------------------
819 //--------------------------------------------------------------------
820 template<class ImageType>
822 AndNot(ImageType * input,
823 const ImageType * object,
824 typename ImageType::PixelType BG)
826 typename ImageType::Pointer o;
828 if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
829 o = clitk::ResizeImageLike<ImageType>(object, input, BG);
833 typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
834 typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
835 boolFilter->InPlaceOn();
836 boolFilter->SetInput1(input);
837 if (resized) boolFilter->SetInput2(o);
838 else boolFilter->SetInput2(object);
839 boolFilter->SetBackgroundValue1(BG);
840 boolFilter->SetBackgroundValue2(BG);
841 boolFilter->SetOperationType(BoolFilterType::AndNot);
842 boolFilter->Update();
844 //--------------------------------------------------------------------
847 //--------------------------------------------------------------------
848 template<class ImageType>
850 And(ImageType * input,
851 const ImageType * object,
852 typename ImageType::PixelType BG)
854 typename ImageType::Pointer o;
856 if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
857 o = clitk::ResizeImageLike<ImageType>(object, input, BG);
861 typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
862 typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
863 boolFilter->InPlaceOn();
864 boolFilter->SetInput1(input);
865 if (resized) boolFilter->SetInput2(o);
866 else boolFilter->SetInput2(object);
867 boolFilter->SetBackgroundValue1(BG);
868 boolFilter->SetBackgroundValue2(BG);
869 boolFilter->SetOperationType(BoolFilterType::And);
870 boolFilter->Update();
872 //--------------------------------------------------------------------
875 //--------------------------------------------------------------------
876 template<class ImageType>
878 Or(ImageType * input,
879 const ImageType * object,
880 typename ImageType::PixelType BG)
882 typename ImageType::Pointer o;
884 if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
885 o = clitk::ResizeImageLike<ImageType>(object, input, BG);
889 typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
890 typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
891 boolFilter->InPlaceOn();
892 boolFilter->SetInput1(input);
893 if (resized) boolFilter->SetInput2(o);
894 else boolFilter->SetInput2(object);
895 boolFilter->SetBackgroundValue1(BG);
896 boolFilter->SetBackgroundValue2(BG);
897 boolFilter->SetOperationType(BoolFilterType::Or);
898 boolFilter->Update();
900 //--------------------------------------------------------------------
903 //--------------------------------------------------------------------
904 template<class ImageType>
905 typename ImageType::Pointer
906 Binarize(const ImageType * input,
907 typename ImageType::PixelType lower,
908 typename ImageType::PixelType upper,
909 typename ImageType::PixelType BG,
910 typename ImageType::PixelType FG)
912 typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
913 typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
914 binarizeFilter->SetInput(input);
915 binarizeFilter->InPlaceOff();
916 binarizeFilter->SetLowerThreshold(lower);
917 binarizeFilter->SetUpperThreshold(upper);
918 binarizeFilter->SetInsideValue(FG);
919 binarizeFilter->SetOutsideValue(BG);
920 binarizeFilter->Update();
921 return binarizeFilter->GetOutput();
923 //--------------------------------------------------------------------
926 //--------------------------------------------------------------------
927 template<class ImageType>
929 GetMinMaxPointPosition(const ImageType * input,
930 typename ImageType::PointType & min,
931 typename ImageType::PointType & max)
933 typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
934 input->TransformIndexToPhysicalPoint(index, min);
935 index = index+input->GetLargestPossibleRegion().GetSize();
936 input->TransformIndexToPhysicalPoint(index, max);
938 //--------------------------------------------------------------------
941 //--------------------------------------------------------------------
942 template<class ImageType>
943 typename ImageType::PointType
944 FindExtremaPointInAGivenLine(const ImageType * input,
947 typename ImageType::PointType p,
948 typename ImageType::PixelType BG,
951 // Which direction ? Increasing or decreasing.
955 // Transform to pixel index
956 typename ImageType::IndexType index;
957 input->TransformPhysicalPointToIndex(p, index);
959 // Loop while inside the mask;
960 while (input->GetPixel(index) != BG) {
961 index[dimension] += d;
964 // Transform back to Physical Units
965 typename ImageType::PointType result;
966 input->TransformIndexToPhysicalPoint(index, result);
968 // Check that is is not too far away
969 double distance = p.EuclideanDistanceTo(result);
970 if (distance > distanceMax) {
971 result = p; // Get back to initial value
976 //--------------------------------------------------------------------
979 //--------------------------------------------------------------------
980 template<class PointType>
982 IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
984 // Look at the position of point 'like' according to the AB line
985 double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
988 // Look the C position
989 s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
991 if (negative && (s<=0)) return true;
992 if (!negative && (s>=0)) return true;
995 //--------------------------------------------------------------------
998 //--------------------------------------------------------------------
999 /* Consider an input object, for each slice, find the extrema
1000 position according to a given direction and build a line segment
1001 passing throught this point in a given direction. Output is a
1002 vector of line (from point A to B), for each slice;
1004 template<class ImageType>
1006 SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
1007 typename ImageType::PixelType BG,
1009 int extremaDirection,
1010 bool extremaOppositeFlag,
1013 std::vector<typename ImageType::PointType> & A,
1014 std::vector<typename ImageType::PointType> & B)
1017 typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1019 // Build the list of slices
1020 std::vector<typename SliceType::Pointer> slices;
1021 clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
1023 // Build the list of 2D points
1024 std::map<int, typename SliceType::PointType> position2D;
1025 for(uint i=0; i<slices.size(); i++) {
1026 typename SliceType::PointType p;
1028 clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
1029 extremaDirection, extremaOppositeFlag, p);
1035 // Convert 2D points in slice into 3D points
1036 clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
1038 // Create additional point just right to the previous ones, on the
1039 // given lineDirection, in order to create a horizontal/vertical line.
1040 for(uint i=0; i<A.size(); i++) {
1041 typename ImageType::PointType p = A[i];
1042 p[lineDirection] += 10;
1045 A[i][extremaDirection] += margin;
1046 B[i][extremaDirection] += margin;
1050 //--------------------------------------------------------------------
1053 //--------------------------------------------------------------------
1054 template<class ImageType>
1055 typename ImageType::Pointer
1056 SliceBySliceKeepMainCCL(const ImageType * input,
1057 typename ImageType::PixelType BG,
1058 typename ImageType::PixelType FG) {
1061 const int d = ImageType::ImageDimension-1;
1062 typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
1063 std::vector<typename SliceType::Pointer> slices;
1064 clitk::ExtractSlices<ImageType>(input, d, slices);
1066 // Labelize and keep the main one
1067 std::vector<typename SliceType::Pointer> o;
1068 for(uint i=0; i<slices.size(); i++) {
1069 o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
1070 o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
1074 typename ImageType::Pointer output;
1075 output = clitk::JoinSlices<ImageType>(o, input, d);
1078 //--------------------------------------------------------------------
1081 //--------------------------------------------------------------------
1082 template<class ImageType>
1083 typename ImageType::Pointer
1084 Clone(const ImageType * input) {
1085 typedef itk::ImageDuplicator<ImageType> DuplicatorType;
1086 typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
1087 duplicator->SetInputImage(input);
1088 duplicator->Update();
1089 return duplicator->GetOutput();
1091 //--------------------------------------------------------------------
1094 //--------------------------------------------------------------------
1095 /* Consider an input object, start at A, for each slice (dim1):
1096 - compute the intersection between the AB line and the current slice
1097 - remove what is at lower or greater according to dim2 of this point
1100 template<class ImageType>
1101 typename ImageType::Pointer
1102 SliceBySliceSetBackgroundFromSingleLine(const ImageType * input,
1103 typename ImageType::PixelType BG,
1104 typename ImageType::PointType & A,
1105 typename ImageType::PointType & B,
1106 int dim1, int dim2, bool removeLowerPartFlag)
1110 typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1111 typedef typename SliceType::Pointer SlicePointer;
1112 std::vector<SlicePointer> slices;
1113 clitk::ExtractSlices<ImageType>(input, dim1, slices);
1115 // Start at slice that contains A, and stop at B
1116 typename ImageType::IndexType Ap;
1117 typename ImageType::IndexType Bp;
1118 input->TransformPhysicalPointToIndex(A, Ap);
1119 input->TransformPhysicalPointToIndex(B, Bp);
1121 // Determine slice largest region
1122 typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1123 typename SliceType::SizeType size = region.GetSize();
1124 typename SliceType::IndexType index = region.GetIndex();
1127 double a = (Bp[dim2]-Ap[dim2])/(Bp[dim1]-Ap[dim1]);
1128 double b = Ap[dim2];
1130 // Loop from slice A to slice B
1131 for(uint i=0; i<(Bp[dim1]-Ap[dim1]); i++) {
1132 // Compute intersection between line AB and current slice for the dim2
1134 // Change region (lower than dim2)
1135 if (removeLowerPartFlag) {
1136 size[dim2] = p-Ap[dim2];
1139 size[dim2] = slices[0]->GetLargestPossibleRegion().GetSize()[dim2]-p;
1142 region.SetSize(size);
1143 region.SetIndex(index);
1144 // Fill region with BG (simple region iterator)
1145 FillRegionWithValue<SliceType>(slices[i+Ap[dim1]], BG, region);
1147 typedef itk::ImageRegionIterator<SliceType> IteratorType;
1148 IteratorType iter(slices[i+Ap[dim1]], region);
1150 while (!iter.IsAtEnd()) {
1159 typename ImageType::Pointer output;
1160 output = clitk::JoinSlices<ImageType>(slices, input, dim1);
1163 //--------------------------------------------------------------------
1165 //--------------------------------------------------------------------
1166 /* Consider an input object, slice by slice, use the point A and set
1167 pixel to BG according to their position relatively to A
1169 template<class ImageType>
1170 typename ImageType::Pointer
1171 SliceBySliceSetBackgroundFromPoints(const ImageType * input,
1172 typename ImageType::PixelType BG,
1174 std::vector<typename ImageType::PointType> & A,
1175 bool removeGreaterThanXFlag,
1176 bool removeGreaterThanYFlag)
1180 typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1181 typedef typename SliceType::Pointer SlicePointer;
1182 std::vector<SlicePointer> slices;
1183 clitk::ExtractSlices<ImageType>(input, sliceDim, slices);
1185 // Start at slice that contains A
1186 typename ImageType::IndexType Ap;
1188 // Determine slice largest region
1189 typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1190 typename SliceType::SizeType size = region.GetSize();
1191 typename SliceType::IndexType index = region.GetIndex();
1193 // Loop from slice A to slice B
1194 for(uint i=0; i<A.size(); i++) {
1195 input->TransformPhysicalPointToIndex(A[i], Ap);
1196 uint sliceIndex = Ap[2] - input->GetLargestPossibleRegion().GetIndex()[2];
1197 if ((sliceIndex < 0) || (sliceIndex >= slices.size())) {
1198 continue; // do not consider this slice
1201 // Compute region for BG
1202 if (removeGreaterThanXFlag) {
1204 size[0] = region.GetSize()[0]-(index[0]-region.GetIndex()[0]);
1207 index[0] = region.GetIndex()[0];
1208 size[0] = Ap[0] - index[0];
1211 if (removeGreaterThanYFlag) {
1213 size[1] = region.GetSize()[1]-(index[1]-region.GetIndex()[1]);
1216 index[1] = region.GetIndex()[1];
1217 size[1] = Ap[1] - index[1];
1221 region.SetSize(size);
1222 region.SetIndex(index);
1224 // Fill region with BG (simple region iterator)
1225 FillRegionWithValue<SliceType>(slices[sliceIndex], BG, region);
1230 typename ImageType::Pointer output;
1231 output = clitk::JoinSlices<ImageType>(slices, input, sliceDim);
1234 //--------------------------------------------------------------------
1237 //--------------------------------------------------------------------
1238 template<class ImageType>
1240 FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, typename ImageType::RegionType & region)
1242 typedef itk::ImageRegionIterator<ImageType> IteratorType;
1243 IteratorType iter(input, region);
1245 while (!iter.IsAtEnd()) {
1250 //--------------------------------------------------------------------
1253 //--------------------------------------------------------------------
1254 template<class ImageType>
1256 GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min,
1257 typename ImageType::PointType & max)
1259 typedef typename ImageType::PointType PointType;
1260 typedef typename ImageType::IndexType IndexType;
1261 IndexType min_i, max_i;
1262 min_i = input->GetLargestPossibleRegion().GetIndex();
1263 for(uint i=0; i<ImageType::ImageDimension; i++)
1264 max_i[i] = input->GetLargestPossibleRegion().GetSize()[i] + min_i[i];
1265 input->TransformIndexToPhysicalPoint(min_i, min);
1266 input->TransformIndexToPhysicalPoint(max_i, max);
1268 //--------------------------------------------------------------------
1271 //--------------------------------------------------------------------
1272 template<class ImageType>
1273 typename itk::Image<float, ImageType::ImageDimension>::Pointer
1274 DistanceMap(const ImageType * input, typename ImageType::PixelType BG)//,
1275 // typename itk::Image<float, ImageType::ImageDimension>::Pointer dmap)
1277 typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
1278 typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, FloatImageType> DistanceMapFilterType;
1279 typename DistanceMapFilterType::Pointer filter = DistanceMapFilterType::New();
1280 filter->SetInput(input);
1281 filter->SetUseImageSpacing(true);
1282 filter->SquaredDistanceOff();
1283 filter->SetBackgroundValue(BG);
1285 return filter->GetOutput();
1287 //--------------------------------------------------------------------
1290 //--------------------------------------------------------------------
1291 template<class ImageType>
1293 SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures(const ImageType * S1,
1294 const ImageType * S2,
1295 typename ImageType::PixelType BG,
1297 std::vector<typename ImageType::PointType> & A,
1298 std::vector<typename ImageType::PointType> & B)
1301 typedef typename itk::Image<typename ImageType::PixelType, 2> SliceType;
1302 typedef typename SliceType::Pointer SlicePointer;
1303 std::vector<SlicePointer> slices_s1;
1304 std::vector<SlicePointer> slices_s2;
1305 clitk::ExtractSlices<ImageType>(S1, sliceDimension, slices_s1);
1306 clitk::ExtractSlices<ImageType>(S2, sliceDimension, slices_s2);
1308 assert(slices_s1.size() == slices_s2.size());
1311 typedef itk::Image<float,2> FloatImageType;
1312 typedef itk::SignedMaurerDistanceMapImageFilter<SliceType, FloatImageType> DistanceMapFilterType;
1313 std::vector<typename FloatImageType::Pointer> dmaps1;
1314 std::vector<typename FloatImageType::Pointer> dmaps2;
1315 typename FloatImageType::Pointer dmap;
1318 for(uint i=0; i<slices_s1.size(); i++) {
1319 // Compute dmap for S1 *TO PUT IN FONCTION*
1320 dmap = clitk::DistanceMap<SliceType>(slices_s1[i], BG);
1321 dmaps1.push_back(dmap);
1322 writeImage<FloatImageType>(dmap, "dmap1.mha");
1323 // Compute dmap for S2
1324 dmap = clitk::DistanceMap<SliceType>(slices_s2[i], BG);
1325 dmaps2.push_back(dmap);
1326 writeImage<FloatImageType>(dmap, "dmap2.mha");
1328 // Look in S2 for the point the closest to S1
1329 typename SliceType::PointType p = ComputeClosestPoint<SliceType>(slices_s1[i], dmaps2[i], BG);
1330 typename ImageType::PointType p3D;
1331 clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S1, i, p3D);
1334 // Look in S2 for the point the closest to S1
1335 p = ComputeClosestPoint<SliceType>(slices_s2[i], dmaps1[i], BG);
1336 clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S2, i, p3D);
1343 typedef itk::Image<float,3> FT;
1344 FT::Pointer f = FT::New();
1345 typename FT::Pointer d1 = clitk::JoinSlices<FT>(dmaps1, S1, 2);
1346 typename FT::Pointer d2 = clitk::JoinSlices<FT>(dmaps2, S2, 2);
1347 writeImage<FT>(d1, "d1.mha");
1348 writeImage<FT>(d2, "d2.mha");
1351 //--------------------------------------------------------------------
1354 //--------------------------------------------------------------------
1355 template<class ImageType>
1356 typename ImageType::PointType
1357 ComputeClosestPoint(const ImageType * input,
1358 const itk::Image<float, ImageType::ImageDimension> * dmap,
1359 typename ImageType::PixelType & BG)
1361 // Loop dmap + S2, if FG, get min
1362 typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
1363 typedef itk::ImageRegionConstIteratorWithIndex<ImageType> ImageIteratorType;
1364 typedef itk::ImageRegionConstIterator<FloatImageType> DMapIteratorType;
1365 ImageIteratorType iter1(input, input->GetLargestPossibleRegion());
1366 DMapIteratorType iter2(dmap, dmap->GetLargestPossibleRegion());
1370 double dmin = 100000.0;
1371 typename ImageType::IndexType indexmin;
1372 while (!iter1.IsAtEnd()) {
1373 if (iter1.Get() != BG) {
1374 double d = iter2.Get();
1376 indexmin = iter1.GetIndex();
1385 typename ImageType::PointType p;
1386 input->TransformIndexToPhysicalPoint(indexmin, p);
1389 //--------------------------------------------------------------------
1394 } // end of namespace