labelMapPreprocessor.h

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#ifndef LABELMAPPREPROCESSOR_H
#define LABELMAPPREPROCESSOR_H
 
#include "itkImage.h"
#include "itkImageRegionIterator.h"
 
#include <algorithm>
#include <iostream>
 
template <typename pixel_t>
typename itk::Image<pixel_t, 3>::Pointer preprocessLabelMap(typename itk::Image<pixel_t, 3>::Pointer originalLabelMap, pixel_t desiredLabel)
{
  /*
    If there is a single non-zero label in the originalLabelMap, then
    use that as the label map to feed the segmentor.
 
    If originalLabelMap contains multiple labels, extract
    desiredLabel, forms a new label map containing only desiredLabel
    to feed the segmentor.
 
    If originalLabelMap contains multiple labels, but do NOT contain
    desiredLabel, then use all the non-zero labels as a single label
    and output label value is desiredLabel.
 
    1. count number of different labels in the originalLabelMap
 
    2. if #= 1, return it
 
    3. if #= 2, if desiredLabel is not there, then return originalLabelMap itself
 
    4. if #= 2, go thru originalLabelMap and fill in a new label map
       with 1 where the label matches.
 
 
   */
 
  typedef itk::Image<pixel_t, 3> image_t;
 
  typedef itk::ImageRegionIterator<image_t> imageRegionIterator_t;
 
  // 1.
  imageRegionIterator_t iter(originalLabelMap, originalLabelMap->GetLargestPossibleRegion());
  iter.GoToBegin();
 
  typename image_t::SizeType sz = originalLabelMap->GetLargestPossibleRegion().GetSize();
 
  std::vector<pixel_t> uniqueLabels(sz[0] * sz[1] * sz[2]);
  long i = 0;
  for (; !iter.IsAtEnd(); ++iter)
  {
    uniqueLabels[i++] = iter.Get();
  }
 
  std::sort(uniqueLabels.begin(), uniqueLabels.end());
  typename std::vector<pixel_t>::iterator itl = std::unique(uniqueLabels.begin(), uniqueLabels.end());
  uniqueLabels.resize(itl - uniqueLabels.begin());
 
  if (uniqueLabels[0] != 0)
  {
    std::cerr << "Error: least label is not 0? no background?\n";
    raise(SIGABRT);
  }
 
  short numOfLabels = uniqueLabels.size() - 1; // 0 not count
 
  // 2.
  if (1 == numOfLabels)
  {
    return originalLabelMap;
  }
 
  // 3.
  if (!std::binary_search(uniqueLabels.begin(), uniqueLabels.end(), desiredLabel))
  {
    return originalLabelMap;
  }
 
  // 4.
  typename image_t::Pointer newLabelMap = image_t::New();
  newLabelMap->CopyInformation(originalLabelMap);
  newLabelMap->SetRegions(originalLabelMap->GetLargestPossibleRegion());
  newLabelMap->Allocate();
  newLabelMap->FillBuffer(0);
 
  imageRegionIterator_t iterNew(newLabelMap, newLabelMap->GetLargestPossibleRegion());
  iterNew.GoToBegin();
  iter.GoToBegin();
  for (; !iter.IsAtEnd(); ++iter, ++iterNew)
  {
    if (iter.Get() == desiredLabel)
    {
      iterNew.Set(1);
    }
  }
 
  return newLabelMap;
}
 
#endif