Medical Imaging Interaction Toolkit  2024.12.00
Medical Imaging Interaction Toolkit
•All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Properties Friends Macros Modules Pages
mitkCLUtil.h
Go to the documentation of this file.
1 /*============================================================================
2 
3 The Medical Imaging Interaction Toolkit (MITK)
4 
5 Copyright (c) German Cancer Research Center (DKFZ)
6 All rights reserved.
7 
8 Use of this source code is governed by a 3-clause BSD license that can be
9 found in the LICENSE file.
10 
11 ============================================================================*/
12 
13 #ifndef mitkCLUtil_h
14 #define mitkCLUtil_h
15 
16 #include <itkeigen/Eigen/Dense>
17 #include <MitkCLUtilitiesExports.h>
18 #include <itkImageRegionIterator.h>
19 
20 
21 #include <mitkImage.h>
22 #include <mitkImageCast.h>
23 #include <mitkITKImageImport.h>
24 
25 #include <itkConnectedComponentImageFilter.h>
26 namespace mitk
27 {
28 
29 class MITKCLUTILITIES_EXPORT CLUtil
30 {
31 public:
35  enum MorphologicalDimensions
36  {
37  Axial,Coronal,Sagittal,All
38  };
39 
45  static void CreateCheckerboardMask(mitk::Image::Pointer image, mitk::Image::Pointer & outimage);
46 
53  static void InterpolateCheckerboardPrediction(mitk::Image::Pointer checkerboard_prediction, mitk::Image::Pointer & checkerboard_mask, mitk::Image::Pointer & outimage);
54 
60  static void CountVoxel(mitk::Image::Pointer image, std::map<unsigned int, unsigned int> & map);
61 
68  static void CountVoxel(mitk::Image::Pointer image, unsigned int label, unsigned int & count);
69 
75  static void CountVoxel(mitk::Image::Pointer image, unsigned int & count);
76 
84  static void SumVoxelForLabel(mitk::Image::Pointer image, const mitk::Image::Pointer & source , unsigned int label, double & val );
85 
93  static void SqSumVoxelForLabel(mitk::Image::Pointer image, const mitk::Image::Pointer & source, unsigned int label, double & val );
94 
101  static void LogicalAndImages(const Image::Pointer &image1, const Image::Pointer &image2, Image::Pointer &outimage);
102 
103 
110  static void GaussianFilter(mitk::Image::Pointer image, mitk::Image::Pointer & smoothed ,double sigma);
111 
119  static void DifferenceOfGaussianFilter(mitk::Image::Pointer image, mitk::Image::Pointer & smoothed, double sigma1, double sigma2);
120 
127  static void LaplacianOfGaussianFilter(mitk::Image::Pointer image, mitk::Image::Pointer & smoothed, double sigma1);
128 
135  static void HessianOfGaussianFilter(mitk::Image::Pointer image, std::vector<mitk::Image::Pointer> &out, double sigma);
136 
144  static void LocalHistogram(mitk::Image::Pointer image, std::vector<mitk::Image::Pointer> &out, int Bins, int NeighbourhoodSize);
145 
151  template<typename TMatrixElementType>
152  static mitk::Image::Pointer Transform(const Eigen::Matrix<TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic> & matrix, const mitk::Image::Pointer & mask)
153  {
154  itk::Image<unsigned int, 3>::Pointer itkMask;
155  mitk::CastToItkImage(mask,itkMask);
156 
157  typename itk::Image<TMatrixElementType, 3>::Pointer itk_img = itk::Image<TMatrixElementType, 3>::New();
158  itk_img->SetRegions(itkMask->GetLargestPossibleRegion());
159  itk_img->SetOrigin(itkMask->GetOrigin());
160  itk_img->SetSpacing(itkMask->GetSpacing());
161  itk_img->SetDirection(itkMask->GetDirection());
162  itk_img->Allocate();
163 
164 
165  unsigned int n_numSamples = 0;
166  mitk::CLUtil::CountVoxel(mask,n_numSamples);
167 
168  if(n_numSamples != matrix.rows())
169  MITK_ERROR << "Number of samples in matrix and number of points under the masks is not the same!";
170 
171  auto mit = itk::ImageRegionConstIterator<itk::Image<unsigned int, 3> >(itkMask, itkMask->GetLargestPossibleRegion());
172  auto oit = itk::ImageRegionIterator<itk::Image<TMatrixElementType, 3> >(itk_img, itk_img->GetLargestPossibleRegion());
173 
174  unsigned int current_row = 0;
175  while(!mit.IsAtEnd())
176  {
177  if(mit.Value() > 0)
178  oit.Set(matrix(current_row++,0));
179  else
180  oit.Set(0.0);
181  ++mit;
182  ++oit;
183  }
184 
185  mitk::Image::Pointer out_img = mitk::Image::New();
186  mitk::GrabItkImageMemory(itk_img,out_img);
187  return out_img;
188  }
194  template<typename TMatrixElementType>
195  static Eigen::Matrix<TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic> Transform(const mitk::Image::Pointer & img, const mitk::Image::Pointer & mask)
196  {
197  itk::Image<unsigned int, 3>::Pointer current_mask;
198  mitk::CastToItkImage(mask,current_mask);
199 
200  unsigned int n_numSamples = 0;
201  mitk::CLUtil::CountVoxel(mask,n_numSamples);
202 
203  typename itk::Image<TMatrixElementType, 3>::Pointer current_img;
204  mitk::CastToItkImage(img,current_img);
205 
206  Eigen::Matrix<TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic> out_matrix(n_numSamples,1);
207 
208  auto mit = itk::ImageRegionConstIterator<itk::Image<unsigned int, 3> >(current_mask, current_mask->GetLargestPossibleRegion());
209  auto iit = itk::ImageRegionConstIterator<itk::Image<TMatrixElementType, 3> >(current_img,current_img->GetLargestPossibleRegion());
210  unsigned int current_row = 0;
211  while (!mit.IsAtEnd()) {
212  if(mit.Value() > 0)
213  out_matrix(current_row++) = iit.Value();
214  ++mit;
215  ++iit;
216  }
217 
218  return out_matrix;
219  }
220 
228  static void DilateBinary(mitk::Image::Pointer & sourceImage, mitk::Image::Pointer& resultImage, int radius , MorphologicalDimensions d);
229 
237  static void ErodeBinary(mitk::Image::Pointer & sourceImage, mitk::Image::Pointer& resultImage, int radius, MorphologicalDimensions d);
238 
246  static void ClosingBinary(mitk::Image::Pointer & sourceImage, mitk::Image::Pointer& resultImage, int radius, MorphologicalDimensions d);
247 
248 
254  static void MergeLabels(mitk::Image::Pointer & img, const std::map<unsigned int, unsigned int> & map);
255 
263  static void ConnectedComponentsImage(mitk::Image::Pointer & image, mitk::Image::Pointer& mask, mitk::Image::Pointer &outimage, unsigned int& num_components);
264 
271  static void GrabLabel(mitk::Image::Pointer & image, mitk::Image::Pointer & outimage, unsigned int label);
272 
273 
280  static void InsertLabel(mitk::Image::Pointer & image, mitk::Image::Pointer & maskImage, unsigned int label);
281 
289  static void ErodeGrayscale(mitk::Image::Pointer & image, unsigned int radius, mitk::CLUtil::MorphologicalDimensions d, mitk::Image::Pointer & outimage );
290 
298  static void DilateGrayscale(mitk::Image::Pointer & image, unsigned int radius, mitk::CLUtil::MorphologicalDimensions d, mitk::Image::Pointer & outimage );
299 
305  static void FillHoleGrayscale(mitk::Image::Pointer & image, mitk::Image::Pointer & outimage);
306 
314  static void ProbabilityMap(const mitk::Image::Pointer& sourceImage, double mean, double std_dev, mitk::Image::Pointer& resultImage);
315 
316  template<class TImageType>
317  static void itkCountVoxel( TImageType * image, std::map<unsigned int, unsigned int> & map)
318  {
319  auto it = itk::ImageRegionIterator< TImageType >(image,image->GetLargestPossibleRegion());
320  while(!it.IsAtEnd())
321  {
322  if(map.find(it.Value()) == map.end())
323  map[it.Value()] = 0;
324  map[it.Value()]++;
325  ++it;
326  }
327  }
328 
329  template <class TImageType>
330  static void itkCountVoxel(TImageType* image, typename TImageType::PixelType label, unsigned int & count )
331  {
332  itk::ImageRegionConstIterator<TImageType> inputIter(image, image->GetLargestPossibleRegion());
333  while(!inputIter.IsAtEnd())
334  {
335  if(inputIter.Value() == label) ++count;
336  ++inputIter;
337  }
338  }
339 
340  template<typename TImageType>
341  static inline void itkCountVoxel(TImageType * mask, unsigned int & n_numSamples)
342  {
343  auto mit = itk::ImageRegionConstIterator<TImageType>(mask, mask->GetLargestPossibleRegion());
344  while (!mit.IsAtEnd())
345  {
346  if(mit.Value() > 0)
347  n_numSamples++;
348  ++mit;
349  }
350  }
351 
352  template <class TImageType1, class TImageType2>
353  static void itkSampleLabel(TImageType1* image, TImageType2* output, double acceptrate, unsigned int label)
354  {
355  std::srand (time(nullptr));
356 
357  itk::ImageRegionConstIterator< TImageType1 > inputIter(image, image->GetLargestPossibleRegion());
358  itk::ImageRegionIterator< TImageType2 > outputIter(output, output->GetLargestPossibleRegion());
359 
360  while (!inputIter.IsAtEnd())
361  {
362  double r = (double)(rand()) / RAND_MAX;
363  if(inputIter.Get() == label && r < acceptrate)
364  outputIter.Set(label);
365 
366  ++inputIter;
367  ++outputIter;
368  }
369  }
370 
371  template <class TImageType>
372  static void itkSampleLabel(TImageType* image, mitk::Image::Pointer & output, unsigned int n_samples_drawn)
373  {
374  std::srand (time(nullptr));
375 
376  typename TImageType::Pointer itk_out = TImageType::New();
377  itk_out->SetRegions(image->GetLargestPossibleRegion());
378  itk_out->SetDirection(image->GetDirection());
379  itk_out->SetOrigin(image->GetOrigin());
380  itk_out->SetSpacing(image->GetSpacing());
381  itk_out->Allocate();
382  itk_out->FillBuffer(0);
383 
384  itk::ImageRegionConstIterator< TImageType > inputIter(image, image->GetLargestPossibleRegion());
385  itk::ImageRegionIterator< TImageType > outputIter(itk_out, itk_out->GetLargestPossibleRegion());
386 
387  for(unsigned int i = 0 ; i < n_samples_drawn ;)
388  {
389  double r = (double)(rand()) / RAND_MAX;
390  if(inputIter.Value() != 0 && r < 0.01 && outputIter.Value() == 0)
391  {
392  outputIter.Set(inputIter.Value());
393  i++;
394  }
395  ++inputIter;
396  ++outputIter;
397 
398  if(inputIter.IsAtEnd())
399  {
400  inputIter.GoToBegin();
401  outputIter.GoToBegin();
402  }
403 
404  }
405 
406  mitk::CastToMitkImage(itk_out, output);
407  }
408 
409 private:
410 
411  template<class TImageType>
412  static void itkErodeGrayscale(TImageType * image, mitk::Image::Pointer & outimage , unsigned int radius, mitk::CLUtil::MorphologicalDimensions d);
413 
414  template<class TImageType>
415  static void itkDilateGrayscale(TImageType * image, mitk::Image::Pointer & outimage , unsigned int radius, mitk::CLUtil::MorphologicalDimensions d);
416 
417  template<class TImageType>
418  static void itkFillHoleGrayscale(TImageType * image, mitk::Image::Pointer & outimage);
419 
420  template< typename TImageType >
421  static void itkInsertLabel(TImageType * maskImage, mitk::Image::Pointer & outimage, unsigned int label)
422  {
423 
424  typename TImageType::Pointer itk_out;
425 
426  if(outimage.IsNull()) // create if necessary
427  {
428  MITK_INFO << "Initialize new image";
429  itk_out = TImageType::New();
430  itk_out->SetSpacing(maskImage->GetSpacing());
431  itk_out->SetDirection(maskImage->GetDirection());
432  itk_out->SetOrigin(maskImage->GetOrigin());
433  itk_out->SetRegions(maskImage->GetLargestPossibleRegion());
434  itk_out->Allocate();
435  itk_out->FillBuffer(0);
436  }else
437  {
438  mitk::CastToItkImage(outimage, itk_out);
439  }
440 
441  itk::ImageRegionIterator<TImageType> oit(itk_out,itk_out->GetLargestPossibleRegion());
442  itk::ImageRegionConstIterator<TImageType> mit(maskImage,maskImage->GetLargestPossibleRegion());
443 
444  while(!mit.IsAtEnd())
445  {
446  if(mit.Value() != 0)
447  {
448  oit.Set(label);
449  }
450  ++oit;
451  ++mit;
452  }
453 
454  mitk::CastToMitkImage(itk_out,outimage);
455  }
456 
457 
458  template< typename TImageType >
459  static void itkGrabLabel(TImageType * image, mitk::Image::Pointer & outimage, unsigned int label)
460  {
461  typedef itk::Image<unsigned short, 3> TOutType;
462  TOutType::Pointer itk_out = TOutType::New();
463  itk_out->SetRegions(image->GetLargestPossibleRegion());
464  itk_out->SetDirection(image->GetDirection());
465  itk_out->SetOrigin(image->GetOrigin());
466  itk_out->SetSpacing(image->GetSpacing());
467  itk_out->Allocate();
468 
469  itk::ImageRegionConstIterator<TImageType> iit(image, image->GetLargestPossibleRegion());
470  itk::ImageRegionIterator<TOutType> oit(itk_out,itk_out->GetLargestPossibleRegion());
471 
472  while(!iit.IsAtEnd())
473  {
474  if(iit.Value() == static_cast<typename TImageType::PixelType>(label))
475  oit.Set(1);
476  else
477  oit.Set(0);
478 
479  ++iit;
480  ++oit;
481  }
482 
483  mitk::CastToMitkImage(itk_out, outimage);
484  }
485 
486  template<class TImagetype>
487  static void itkMergeLabels(TImagetype * img, const std::map<unsigned int, unsigned int> & map)
488  {
489 
490  auto it = itk::ImageRegionIterator<TImagetype>(img,img->GetLargestPossibleRegion());
491 
492  while(!it.IsAtEnd())
493  {
494  if(map.find(it.Value())!=map.end())
495  it.Set( map.at(it.Value()) );
496  ++it;
497  }
498 
499  }
500 
501  template<typename TImageType>
502  static void itkConnectedComponentsImage(TImageType * image, mitk::Image::Pointer& mask, mitk::Image::Pointer &outimage, unsigned int& num_components)
503  {
504  typedef itk::Image<unsigned short, 3> MaskImageType;
505  MaskImageType::Pointer itk_mask;
506  if(mask.IsNull())
507  {
508  itk_mask = MaskImageType::New();
509  itk_mask->SetRegions(image->GetLargestPossibleRegion());
510  itk_mask->SetDirection(image->GetDirection());
511  itk_mask->SetOrigin(image->GetOrigin());
512  itk_mask->SetSpacing(image->GetSpacing());
513  itk_mask->Allocate();
514  itk_mask->FillBuffer(1);
515  }else{
516  mitk::CastToItkImage(mask,itk_mask);
517  }
518 
519  typedef itk::ConnectedComponentImageFilter<TImageType, MaskImageType, MaskImageType > FilterType;
520  typename FilterType::Pointer cc_filter = FilterType::New();
521  cc_filter->SetMaskImage(itk_mask.GetPointer());
522  cc_filter->SetInput(image);
523  cc_filter->SetBackgroundValue(0);
524  cc_filter->Update();
525 
526  num_components = cc_filter->GetObjectCount();
527  mitk::CastToMitkImage(cc_filter->GetOutput(), outimage);
528  }
529 
530  template< typename TImageType >
531  static void itkCreateCheckerboardMask(TImageType * image, mitk::Image::Pointer & outimage);
532 
533  template< typename TImageType >
534  static void itkInterpolateCheckerboardPrediction(TImageType * checkerboard_prediction, mitk::Image::Pointer & checkerboard_mask, mitk::Image::Pointer & outimage);
535 
536  template <class TImageType>
537  static void itkSumVoxelForLabel(TImageType* image, const mitk::Image::Pointer & source , typename TImageType::PixelType label, double & val );
538 
539  template <class TImageType>
540  static void itkSqSumVoxelForLabel(TImageType* image, const mitk::Image::Pointer & source, typename TImageType::PixelType label, double & val );
541 
542  template<typename TStructuringElement>
543  static void itkFitStructuringElement(TStructuringElement & se, MorphologicalDimensions d, int radius);
544 
545  template<typename TImageType>
546  static void itkDilateBinary(TImageType * sourceImage, mitk::Image::Pointer& resultImage, int radius , MorphologicalDimensions d);
547 
548  template<typename TImageType>
549  static void itkErodeBinary(TImageType * sourceImage, mitk::Image::Pointer& resultImage, int radius, MorphologicalDimensions d);
550 
551  template<typename TImageType>
552  static void itkClosingBinary(TImageType * sourceImage, mitk::Image::Pointer& resultImage, int radius, MorphologicalDimensions d);
553 
554  template<typename TPixel, unsigned int VDimension>
555  static void itkFillHolesBinary(itk::Image<TPixel, VDimension>* sourceImage, mitk::Image::Pointer& resultImage);
556 
557  template<typename TImageType>
558  static void itkLogicalAndImages(const TImageType * image1, const mitk::Image::Pointer & image2, mitk::Image::Pointer & outimage);
559 
560  template<class TImageType>
561  static void itkGaussianFilter(TImageType * image, mitk::Image::Pointer & smoothed ,double sigma);
562 
563  template<class TImageType>
564  static void itkDifferenceOfGaussianFilter(TImageType * image, mitk::Image::Pointer & smoothed, double sigma1, double sigma2);
565 
566  template<typename TImageType>
567  static void itkProbabilityMap(const TImageType * sourceImage, double mean, double std_dev, mitk::Image::Pointer& resultImage);
568 
569  template<typename TPixel, unsigned int VImageDimension>
570  static void itkHessianOfGaussianFilter(itk::Image<TPixel, VImageDimension>* itkImage, double variance, std::vector<mitk::Image::Pointer> &out);
571 
572  template<typename TPixel, unsigned int VImageDimension>
573  static void itkLaplacianOfGaussianFilter(itk::Image<TPixel, VImageDimension>* itkImage, double variance, mitk::Image::Pointer &output);
574 
575  template<typename TPixel, unsigned int VImageDimension>
576  static void itkLocalHistograms(itk::Image<TPixel, VImageDimension>* itkImage, std::vector<mitk::Image::Pointer> &out, int size, int bins);
577 };
578 
579 } //namespace MITK
580 
581 #endif
MITKCLUTILITIES_EXPORT
#define MITKCLUTILITIES_EXPORT
Definition: MitkCLUtilitiesExports.h:15
mitk::GrabItkImageMemory
Image::Pointer GrabItkImageMemory(itk::SmartPointer< ItkOutputImageType > &itkimage, mitk::Image *mitkImage=nullptr, const BaseGeometry *geometry=nullptr, bool update=true)
Grabs the memory of an itk::Image (with a specific type) and puts it into an mitk::Image.
mitk::AnatomicalPlane::Coronal
@ Coronal
MITK_INFO
#define MITK_INFO
Definition: mitkLog.h:209
mitkImage.h
mitk::Image::New
static Pointer New()
mitk::CLUtil::itkSampleLabel
static void itkSampleLabel(TImageType1 *image, TImageType2 *output, double acceptrate, unsigned int label)
Definition: mitkCLUtil.h:353
mitkImageCast.h
mitk::CLUtil::itkSampleLabel
static void itkSampleLabel(TImageType *image, mitk::Image::Pointer &output, unsigned int n_samples_drawn)
Definition: mitkCLUtil.h:372
mitk::CLUtil::itkCountVoxel
static void itkCountVoxel(TImageType *image, typename TImageType::PixelType label, unsigned int &count)
Definition: mitkCLUtil.h:330
mitk::CLUtil::CountVoxel
static void CountVoxel(mitk::Image::Pointer image, std::map< unsigned int, unsigned int > &map)
CountVoxel.
MITK_ERROR
#define MITK_ERROR
Definition: mitkLog.h:211
itk::SmartPointer
Definition: mitkIFileReader.h:30
mitk::CastToMitkImage
void CastToMitkImage(const itk::SmartPointer< ItkOutputImageType > &itkimage, itk::SmartPointer< mitk::Image > &mitkoutputimage)
Cast an itk::Image (with a specific type) to an mitk::Image.
Definition: mitkImageCast.h:74
mitk
Find image slices visible on a given plane.
Definition: RenderingTests.dox:1
mitk::CLUtil::Transform
static Eigen::Matrix< TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic > Transform(const mitk::Image::Pointer &img, const mitk::Image::Pointer &mask)
TransformImageToMatrix.
Definition: mitkCLUtil.h:195
mitk::CLUtil
Definition: mitkCLUtil.h:29
mitk::AnatomicalPlane::Axial
@ Axial
mitk::CLUtil::MorphologicalDimensions
MorphologicalDimensions
The MorphologicalDimensions enum.
Definition: mitkCLUtil.h:35
mitk::CastToItkImage
void MITKCORE_EXPORT CastToItkImage(const mitk::Image *mitkImage, itk::SmartPointer< ItkOutputImageType > &itkOutputImage)
Cast an mitk::Image to an itk::Image with a specific type.
mitkITKImageImport.h
mitk::CLUtil::itkCountVoxel
static void itkCountVoxel(TImageType *image, std::map< unsigned int, unsigned int > &map)
Definition: mitkCLUtil.h:317
mitk::CLUtil::Transform
static mitk::Image::Pointer Transform(const Eigen::Matrix< TMatrixElementType, Eigen::Dynamic, Eigen::Dynamic > &matrix, const mitk::Image::Pointer &mask)
transform
Definition: mitkCLUtil.h:152
map
Definition: mitkFastSymmetricForcesDemonsMultiResDefaultRegistrationAlgorithm_ProfileResource.h:26
mitk::CLUtil::itkCountVoxel
static void itkCountVoxel(TImageType *mask, unsigned int &n_numSamples)
Definition: mitkCLUtil.h:341
MitkCLUtilitiesExports.h
mitk::CLUtil::Sagittal
@ Sagittal
Definition: mitkCLUtil.h:37