some utilities for segmentation

[clitk.git] / itk / clitkSegmentationFunctions.txx

diff --git a/itk/clitkSegmentationFunctions.txx b/itk/clitkSegmentationFunctions.txx
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+++ b/itk/clitkSegmentationFunctions.txx
@@ -0,0 +1,139 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to: 
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+  ======================================================================-====*/
+
+// clitk
+#include "clitkSetBackgroundImageFilter.h"
+
+// itk
+#include <itkConnectedComponentImageFilter.h>
+#include <itkRelabelComponentImageFilter.h>
+#include <itkBinaryThresholdImageFilter.h>
+
+//--------------------------------------------------------------------
+template<class TImageType, class TMaskImageType>
+typename TImageType::Pointer
+clitk::SetBackground(typename TImageType::ConstPointer input, 
+                     typename TMaskImageType::ConstPointer mask, 
+                     typename TMaskImageType::PixelType maskBG,
+                     typename TImageType::PixelType outValue) {
+  typedef clitk::SetBackgroundImageFilter<TImageType, TMaskImageType, TImageType> SetBackgroundImageFilterType;
+  typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
+  setBackgroundFilter->SetInput(input);
+  setBackgroundFilter->SetInput2(mask);
+  setBackgroundFilter->SetMaskValue(maskBG);
+  setBackgroundFilter->SetOutsideValue(outValue);
+  setBackgroundFilter->Update();
+  return setBackgroundFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class TImageType>
+typename TImageType::Pointer
+clitk::Labelize(typename TImageType::Pointer input, 
+                typename TImageType::PixelType BG, 
+                bool isFullyConnected, 
+                int minimalComponentSize) {
+
+  // Connected Component label 
+  typedef itk::ConnectedComponentImageFilter<TImageType, TImageType> ConnectFilterType;
+  typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
+  connectFilter->SetInput(input);
+  connectFilter->SetBackgroundValue(BG);
+  connectFilter->SetFullyConnected(isFullyConnected);
+  
+  // Sort by size and remove too small area.
+  typedef itk::RelabelComponentImageFilter<TImageType, TImageType> RelabelFilterType;
+  typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
+  relabelFilter->InPlaceOn();
+  relabelFilter->SetInput(connectFilter->GetOutput());
+  relabelFilter->SetMinimumObjectSize(minimalComponentSize);
+  relabelFilter->Update();
+
+  // Return result
+  return relabelFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class TImageType>
+typename TImageType::Pointer
+clitk::RemoveLabels(typename TImageType::Pointer input, 
+                    typename TImageType::PixelType BG,
+                    std::vector<typename TImageType::PixelType> & labelsToRemove) {
+  typename TImageType::Pointer working_image = input;
+  for (unsigned int i=0; i <labelsToRemove.size(); i++) {
+    typedef clitk::SetBackgroundImageFilter<TImageType, TImageType> SetBackgroundImageFilterType;
+    typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
+    setBackgroundFilter->SetInput(input);
+    setBackgroundFilter->SetInput2(input);
+    setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
+    setBackgroundFilter->SetOutsideValue(BG);
+    setBackgroundFilter->Update();
+    working_image = setBackgroundFilter->GetOutput();
+  }
+  return working_image;
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class TImageType>
+typename TImageType::Pointer
+clitk::KeepLabels(typename TImageType::Pointer input, 
+                  typename TImageType::PixelType BG, 
+                  typename TImageType::PixelType FG, 
+                  typename TImageType::PixelType firstKeep, 
+                  typename TImageType::PixelType lastKeep, 
+                  bool useLastKeep) {
+  typedef itk::BinaryThresholdImageFilter<TImageType, TImageType> BinarizeFilterType; 
+  typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
+  binarizeFilter->SetInput(input);
+  binarizeFilter->SetLowerThreshold(firstKeep);
+  if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
+  binarizeFilter->SetInsideValue(FG);
+  binarizeFilter->SetOutsideValue(BG);
+  binarizeFilter->Update();
+  return binarizeFilter->GetOutput();
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template<class TImageType>
+typename TImageType::Pointer
+clitk::LabelizeAndSelectLabels(typename TImageType::Pointer input,
+                               typename TImageType::PixelType BG, 
+                               typename TImageType::PixelType FG, 
+                               bool isFullyConnected,
+                               int minimalComponentSize,
+                               LabelizeParameters<typename TImageType::PixelType> * param)
+{
+  typename TImageType::Pointer working_image;
+  working_image = Labelize<TImageType>(input, BG, isFullyConnected, minimalComponentSize);
+  working_image = RemoveLabels<TImageType>(working_image, BG, param->GetLabelsToRemove());
+  working_image = KeepLabels<TImageType>(working_image, 
+                                         BG, FG, 
+                                         param->GetFirstKeep(), 
+                                         param->GetLastKeep(), 
+                                         param->GetUseLastKeep());
+  return working_image;
+}
+//--------------------------------------------------------------------