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://oncora1.lyon.fnclcc.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 ======================================================================-====*/
19 #ifndef CLITKSEGMENTATIONUTILS_H
20 #define CLITKSEGMENTATIONUTILS_H
23 #include "clitkCommon.h"
24 #include "clitkAutoCropFilter.h"
25 #include "clitkLabelizeParameters.h"
26 #include "clitkExtractSliceFilter.h"
29 #include <itkBoundingBox.h>
30 #include <itkJoinSeriesImageFilter.h>
31 #include <itkChangeInformationImageFilter.h>
35 http://answerpot.com/showthread.php?357451-Itk::SmartPointer%20-%20problem%20making%20code%20const-correct
36 it is better to take raw pointer as argument instead of SmartPointer.
41 //--------------------------------------------------------------------
42 template<class TInternalImageType, class TMaskInternalImageType>
43 typename TInternalImageType::Pointer
44 SetBackground(const TInternalImageType * input,
45 const TMaskInternalImageType * mask,
46 typename TMaskInternalImageType::PixelType maskBG,
47 typename TInternalImageType::PixelType outValue,
49 //--------------------------------------------------------------------
52 //--------------------------------------------------------------------
53 template<class ImageType>
54 int GetNumberOfConnectedComponentLabels(const ImageType * input,
55 typename ImageType::PixelType BG,
56 bool isFullyConnected);
57 //--------------------------------------------------------------------
60 //--------------------------------------------------------------------
61 template<class TImageType>
62 typename TImageType::Pointer
63 Labelize(const TImageType * input, typename TImageType::PixelType BG,
64 bool isFullyConnected, int minimalComponentSize);
65 template<class TImageType>
66 typename TImageType::Pointer
67 LabelizeAndCountNumberOfObjects(const TImageType * input,
68 typename TImageType::PixelType BG,
69 bool isFullyConnected,
70 int minimalComponentSize,
72 //--------------------------------------------------------------------
75 //--------------------------------------------------------------------
76 template<class ImageType>
77 typename ImageType::Pointer
78 RemoveLabels(const ImageType * input,
79 typename ImageType::PixelType BG,
80 std::vector<typename ImageType::PixelType> & labelsToRemove);
81 //--------------------------------------------------------------------
84 //--------------------------------------------------------------------
85 template<class ImageType>
86 typename ImageType::Pointer
87 AutoCrop(const ImageType * input,
88 typename ImageType::PixelType BG,
89 const bool useBorderFlag=false) {
90 typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
91 typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
92 autoCropFilter->SetInput(input);
93 autoCropFilter->SetBackgroundValue(BG);
94 autoCropFilter->SetUseBorder(useBorderFlag);
95 autoCropFilter->Update();
96 return autoCropFilter->GetOutput();
98 //--------------------------------------------------------------------
101 //--------------------------------------------------------------------
102 template<class TImageType>
103 typename TImageType::Pointer
104 KeepLabels(const TImageType * input,
105 typename TImageType::PixelType BG,
106 typename TImageType::PixelType FG,
107 typename TImageType::PixelType firstKeep,
108 typename TImageType::PixelType lastKeep,
110 //--------------------------------------------------------------------
113 //--------------------------------------------------------------------
114 template<class TImageType>
115 typename TImageType::Pointer
116 LabelizeAndSelectLabels(const TImageType * input,
117 typename TImageType::PixelType BG,
118 typename TImageType::PixelType FG,
119 bool isFullyConnected,
120 int minimalComponentSize,
121 LabelizeParameters<typename TImageType::PixelType> * param);
124 //--------------------------------------------------------------------
125 template<class MaskImageType>
126 typename MaskImageType::Pointer
127 SliceBySliceRelativePosition(const MaskImageType * input,
128 const MaskImageType * object,
131 std::string orientation,
132 bool uniqueConnectedComponent=false,
134 bool autocropflag=true,
135 bool singleObjectCCL=true);
136 template<class MaskImageType>
137 typename MaskImageType::Pointer
138 SliceBySliceRelativePosition(const MaskImageType * input,
139 const MaskImageType * object,
144 bool uniqueConnectedComponent=false,
146 bool autocropflag=true,
147 bool singleObjectCCL=true);
149 //--------------------------------------------------------------------
150 // In a binary image, search for the point belonging to the FG that
151 // is the most exterma in the direction 'direction' (or in the
152 // opposite if notFlag is given).
153 template<class ImageType>
155 FindExtremaPointInAGivenDirection(const ImageType * input,
156 typename ImageType::PixelType bg,
157 int direction, bool opposite,
158 typename ImageType::PointType & p);
160 //--------------------------------------------------------------------
162 //--------------------------------------------------------------------
163 // Same as above but check that the found point is not more than
164 // 'distanceMax' away from 'refPoint'
165 template<class ImageType>
167 FindExtremaPointInAGivenDirection(const ImageType * input,
168 typename ImageType::PixelType bg,
169 int direction, bool opposite,
170 typename ImageType::PointType refPoint,
172 typename ImageType::PointType & p);
174 //--------------------------------------------------------------------
176 //--------------------------------------------------------------------
177 template<class ImageType>
178 typename ImageType::Pointer
179 CropImageAlongOneAxis(const ImageType * image,
180 int dim, double min, double max,
181 bool autoCrop = false,
182 typename ImageType::PixelType BG=0);
183 template<class ImageType>
184 typename ImageType::Pointer
185 CropImageRemoveGreaterThan(const ImageType * image,
186 int dim, double min, bool autoCrop = false,
187 typename ImageType::PixelType BG=0);
188 template<class ImageType>
189 typename ImageType::Pointer
190 CropImageRemoveLowerThan(const ImageType * image,
191 int dim, double max,bool autoCrop = false,
192 typename ImageType::PixelType BG=0);
193 //--------------------------------------------------------------------
196 //--------------------------------------------------------------------
197 template<class ImageType, class LabelType>
198 typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
199 ComputeLabelMap(const ImageType * image,
200 typename ImageType::PixelType BG,
201 bool computePerimeterFlag=false);
202 template<class ImageType>
204 ComputeCentroids(const ImageType * image,
205 typename ImageType::PixelType BG,
206 std::vector<typename ImageType::PointType> & centroids);
207 template<class ImageType>
209 ComputeCentroids2(const ImageType * image,
210 typename ImageType::PixelType BG,
211 std::vector<typename ImageType::PointType> & centroids);
212 //--------------------------------------------------------------------
215 //--------------------------------------------------------------------
216 template<class ImageType>
218 ExtractSlices(const ImageType * image, int direction,
219 std::vector<typename itk::Image<typename ImageType::PixelType,
220 ImageType::ImageDimension-1>::Pointer > & slices)
222 typedef ExtractSliceFilter<ImageType> ExtractSliceFilterType;
223 typedef typename ExtractSliceFilterType::SliceType SliceType;
224 typename ExtractSliceFilterType::Pointer
225 extractSliceFilter = ExtractSliceFilterType::New();
226 extractSliceFilter->SetInput(image);
227 extractSliceFilter->SetDirection(direction);
228 extractSliceFilter->Update();
229 extractSliceFilter->GetOutputSlices(slices);
231 //--------------------------------------------------------------------
234 //--------------------------------------------------------------------
235 template<class ImageType>
236 typename ImageType::Pointer
237 JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
238 ImageType::ImageDimension-1>::Pointer > & slices,
239 const itk::ImageBase<ImageType::ImageDimension> * input, //const ImageType * input,
241 typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
242 typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JoinSeriesFilterType;
243 typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
244 joinFilter->SetOrigin(input->GetOrigin()[direction]);
245 joinFilter->SetSpacing(input->GetSpacing()[direction]);
246 for(unsigned int i=0; i<slices.size(); i++) {
247 joinFilter->PushBackInput(slices[i]);
249 joinFilter->Update();
250 return joinFilter->GetOutput();
252 //--------------------------------------------------------------------
255 //--------------------------------------------------------------------
256 // Set of tools to manage 3D points and 2D points in slices
257 template<class ImageType>
260 typedef typename ImageType::PointType PointType3D;
261 typedef typename ImageType::IndexType IndexType3D;
262 typedef typename ImageType::PixelType PixelType;
263 typedef typename ImageType::Pointer ImagePointer;
264 typedef typename ImageType::ConstPointer ImageConstPointer;
265 typedef itk::Image<PixelType, 2> SliceType;
266 typedef typename SliceType::PointType PointType2D;
267 typedef typename SliceType::IndexType IndexType2D;
269 typedef std::map<int, PointType2D> MapPoint2DType;
270 typedef std::vector<PointType3D> VectorPoint3DType;
271 typedef std::vector<PointType2D> VectorPoint2DType;
274 static void Convert2DTo3D(const PointType2D & p2D,
275 const ImageType * image,
278 static void Convert2DMapTo3DList(const MapPoint2DType & map,
279 const ImageType * image,
280 VectorPoint3DType & list);
281 static void Convert2DListTo3DList(const VectorPoint2DType & p,
283 const ImageType * image,
284 VectorPoint3DType & list);
287 //--------------------------------------------------------------------
288 template<class ImageType>
290 WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
291 std::string filename);
292 //--------------------------------------------------------------------
295 //--------------------------------------------------------------------
296 template<class ImageType>
297 typename ImageType::Pointer
298 Dilate(const ImageType * image, double radiusInMM,
299 typename ImageType::PixelType BG,
300 typename ImageType::PixelType FG,
302 template<class ImageType>
303 typename ImageType::Pointer
304 Dilate(const ImageType * image, typename ImageType::SizeType radius,
305 typename ImageType::PixelType BG,
306 typename ImageType::PixelType FG,
308 template<class ImageType>
309 typename ImageType::Pointer
310 Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
311 typename ImageType::PixelType BG,
312 typename ImageType::PixelType FG,
314 //--------------------------------------------------------------------
317 //--------------------------------------------------------------------
318 template<class ImageType>
319 typename ImageType::Pointer
320 Opening(const ImageType * image, typename ImageType::SizeType radius,
321 typename ImageType::PixelType BG, typename ImageType::PixelType FG);
322 //--------------------------------------------------------------------
325 //--------------------------------------------------------------------
326 template<class ValueType, class VectorType>
327 void ConvertOption(std::string optionName, uint given,
328 ValueType * values, VectorType & p,
329 uint dim, bool required);
330 #define ConvertOptionMacro(OPTIONNAME, VAR, DIM, REQUIRED) \
331 ConvertOption(#OPTIONNAME, OPTIONNAME##_given, OPTIONNAME##_arg, VAR, DIM, REQUIRED);
332 //--------------------------------------------------------------------
334 //--------------------------------------------------------------------
335 template<class ImageType>
337 SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
338 std::vector<typename ImageType::PointType> & lA,
339 std::vector<typename ImageType::PointType> & lB,
340 typename ImageType::PixelType BG,
342 double offsetToKeep);
343 //--------------------------------------------------------------------
346 //--------------------------------------------------------------------
347 template<class ImageType>
348 void AndNot(ImageType * input,
349 const ImageType * object,
350 typename ImageType::PixelType BG=0);
351 template<class ImageType>
352 void And(ImageType * input,
353 const ImageType * object,
354 typename ImageType::PixelType BG=0);
355 template<class ImageType>
356 void Or(ImageType * input,
357 const ImageType * object,
358 typename ImageType::PixelType BG=0);
359 //--------------------------------------------------------------------
362 //--------------------------------------------------------------------
363 template<class ImageType>
364 typename ImageType::Pointer
365 Binarize(const ImageType * input,
366 typename ImageType::PixelType lower,
367 typename ImageType::PixelType upper,
368 typename ImageType::PixelType BG=0,
369 typename ImageType::PixelType FG=1);
370 //--------------------------------------------------------------------
373 //--------------------------------------------------------------------
374 template<class ImageType>
376 GetMinMaxPointPosition(const ImageType * input,
377 typename ImageType::PointType & min,
378 typename ImageType::PointType & max);
379 //--------------------------------------------------------------------
381 //--------------------------------------------------------------------
382 template<class ImageType>
383 typename ImageType::PointType
384 FindExtremaPointInAGivenLine(const ImageType * input,
385 int dimension, bool inverse,
386 typename ImageType::PointType p,
387 typename ImageType::PixelType BG,
389 //--------------------------------------------------------------------
392 //--------------------------------------------------------------------
393 template<class PointType>
395 IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like);
396 //--------------------------------------------------------------------
399 //--------------------------------------------------------------------
400 template<class ImageType>
402 SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
403 typename ImageType::PixelType BG,
405 int extremaDirection,
406 bool extremaOppositeFlag,
409 std::vector<typename ImageType::PointType> & A,
410 std::vector<typename ImageType::PointType> & B);
411 template<class ImageType>
413 SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures(const ImageType * S1,
414 const ImageType * S2,
415 typename ImageType::PixelType BG,
417 std::vector<typename ImageType::PointType> & A,
418 std::vector<typename ImageType::PointType> & B);
419 //--------------------------------------------------------------------
422 //--------------------------------------------------------------------
423 template<class ImageType>
424 typename ImageType::Pointer
425 SliceBySliceKeepMainCCL(const ImageType * input,
426 typename ImageType::PixelType BG,
427 typename ImageType::PixelType FG);
428 //--------------------------------------------------------------------
431 //--------------------------------------------------------------------
432 template<class ImageType>
433 typename ImageType::Pointer
434 Clone(const ImageType * input);
435 //--------------------------------------------------------------------
438 //--------------------------------------------------------------------
439 template<class ImageType>
440 typename ImageType::Pointer
441 SliceBySliceSetBackgroundFromSingleLine(const ImageType * input,
442 typename ImageType::PixelType BG,
443 typename ImageType::PointType & A,
444 typename ImageType::PointType & B,
445 int dim1, int dim2, bool removeLowerPartFlag);
446 //--------------------------------------------------------------------
449 //--------------------------------------------------------------------
450 template<class ImageType>
451 typename ImageType::Pointer
452 SliceBySliceSetBackgroundFromPoints(const ImageType * input,
453 typename ImageType::PixelType BG,
455 std::vector<typename ImageType::PointType> & A,
456 bool removeGreaterThanXFlag,
457 bool removeGreaterThanYFlag);
458 //--------------------------------------------------------------------
461 //--------------------------------------------------------------------
462 template<class ImageType>
464 FillRegionWithValue(ImageType * input, typename ImageType::PixelType value,
465 typename ImageType::RegionType & region);
466 //--------------------------------------------------------------------
469 //--------------------------------------------------------------------
470 template<class ImageType>
472 GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min,
473 typename ImageType::PointType & max);
474 //--------------------------------------------------------------------
477 //--------------------------------------------------------------------
478 template<class ImageType>
479 typename itk::Image<float, ImageType::ImageDimension>::Pointer//void
480 DistanceMap(const ImageType * input, typename ImageType::PixelType BG);//,
481 //--------------------------------------------------------------------
484 //--------------------------------------------------------------------
485 template<class ImageType>
486 typename ImageType::PointType
487 ComputeClosestPoint(const ImageType * input,
488 const itk::Image<float, ImageType::ImageDimension> * dmap,
489 typename ImageType::PixelType & BG);
490 //--------------------------------------------------------------------
492 //--------------------------------------------------------------------
493 template<class ImageType>
494 typename ImageType::Pointer
495 RemoveNegativeIndexFromRegion(ImageType * input);
496 //--------------------------------------------------------------------
499 } // end clitk namespace
501 #include "clitkSegmentationUtils.txx"