Slicer  5.0
Slicer is a multi-platform, free and open source software package for visualization and medical image computing
labelMapPreprocessor.h
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1 #ifndef LABELMAPPREPROCESSOR_H
2 #define LABELMAPPREPROCESSOR_H
3 
4 #include "itkImage.h"
5 #include "itkImageRegionIterator.h"
6 
7 #include <algorithm>
8 
9 template <typename pixel_t>
10 typename itk::Image<pixel_t, 3>::Pointer
11 preprocessLabelMap(typename itk::Image<pixel_t, 3>::Pointer originalLabelMap, pixel_t desiredLabel)
12 {
13  /*
14  If there is a single non-zero label in the originalLabelMap, then
15  use that as the label map to feed the segmentor.
16 
17  If originalLabelMap contains multiple labels, extract
18  desiredLabel, forms a new label map containing only desiredLabel
19  to feed the segmentor.
20 
21  If originalLabelMap contains multiple labels, but do NOT contain
22  desiredLabel, then use all the non-zero labels as a single label
23  and output label value is desiredLabel.
24 
25  1. count number of different labels in the originalLabelMap
26 
27  2. if #= 1, return it
28 
29  3. if #= 2, if desiredLabel is not there, then return originalLabelMap itself
30 
31  4. if #= 2, go thru originalLabelMap and fill in a new label map
32  with 1 where the label matches.
33 
34 
35  */
36 
37  typedef itk::Image<pixel_t, 3> image_t;
38 
39  typedef itk::ImageRegionIterator<image_t> imageRegionIterator_t;
40 
41  // 1.
42  imageRegionIterator_t iter(originalLabelMap, originalLabelMap->GetLargestPossibleRegion() );
43  iter.GoToBegin();
44 
45  typename image_t::SizeType sz = originalLabelMap->GetLargestPossibleRegion().GetSize();
46 
47  std::vector<pixel_t> uniqueLabels(sz[0] * sz[1] * sz[2]);
48  long i = 0;
49  for( ; !iter.IsAtEnd(); ++iter )
50  {
51  uniqueLabels[i++] = iter.Get();
52  }
53 
54  std::sort(uniqueLabels.begin(), uniqueLabels.end() );
55  typename std::vector<pixel_t>::iterator itl = std::unique(uniqueLabels.begin(), uniqueLabels.end() );
56  uniqueLabels.resize( itl - uniqueLabels.begin() );
57 
58  if( uniqueLabels[0] != 0 )
59  {
60  std::cerr << "Error: least label is not 0? no background?\n";
61  raise(SIGABRT);
62  }
63 
64  short numOfLabels = uniqueLabels.size() - 1; // 0 not count
65 
66  // 2.
67  if( 1 == numOfLabels )
68  {
69  return originalLabelMap;
70  }
71 
72  // 3.
73  if( !std::binary_search(uniqueLabels.begin(), uniqueLabels.end(), desiredLabel) )
74  {
75  return originalLabelMap;
76  }
77 
78  // 4.
79  typename image_t::Pointer newLabelMap = image_t::New();
80  newLabelMap->CopyInformation(originalLabelMap);
81  newLabelMap->SetRegions( originalLabelMap->GetLargestPossibleRegion() );
82  newLabelMap->Allocate();
83  newLabelMap->FillBuffer(0);
84 
85  imageRegionIterator_t iterNew(newLabelMap, newLabelMap->GetLargestPossibleRegion() );
86  iterNew.GoToBegin();
87  iter.GoToBegin();
88  for( ; !iter.IsAtEnd(); ++iter, ++iterNew )
89  {
90  if( iter.Get() == desiredLabel )
91  {
92  iterNew.Set(1);
93  }
94  }
95 
96  return newLabelMap;
97 }
98 
99 #endif
itk::Image< pixel_t, 3 >::Pointer preprocessLabelMap(typename itk::Image< pixel_t, 3 >::Pointer originalLabelMap, pixel_t desiredLabel)