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[clitk.git] / segmentation / clitkMotionMaskGenericFilter.txx

diff --git a/segmentation/clitkMotionMaskGenericFilter.txx b/segmentation/clitkMotionMaskGenericFilter.txx
old mode 100755 (executable)
new mode 100644 (file)
index 50d5269..543bcdb
--- a/segmentation/clitkMotionMaskGenericFilter.txx
+++ b/segmentation/clitkMotionMaskGenericFilter.txx
@@ -3,7 +3,7 @@
 
   Authors belong to:
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - Léon Bérard cancer center       http://www.centreleonberard.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-======================================================================-====*/
+===========================================================================**/
 #ifndef clitkMotionMaskGenericFilter_txx
 #define clitkMotionMaskGenericFilter_txx
 
@@ -97,6 +97,28 @@ MotionMaskGenericFilter::GetAirImage(typename itk::Image<PixelType, Dimension>::
     if (m_Verbose) std::cout<<"Reading the air feature image..."<<std::endl;
     featureReader->Update();
     air=featureReader->GetOutput();
+
+    //---------------------------------
+    // Pad
+    //---------------------------------
+    if(m_ArgsInfo.pad_flag) {
+      typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
+      IteratorType it(air, air->GetLargestPossibleRegion());
+      typename InternalImageType::IndexType index;
+      while(!it.IsAtEnd()) {
+        index=it.GetIndex();
+
+        //Pad borders of all dimensions but 2 (cranio-caudal)
+        for (unsigned int i=0; i<Dimension; i++){
+          if(i==2)
+            continue;
+          if(index[i]==air->GetLargestPossibleRegion().GetIndex()[i]
+              || index[i]==(unsigned int)air->GetLargestPossibleRegion().GetIndex()[i]+ (unsigned int) air->GetLargestPossibleRegion().GetSize()[i]-1)
+            it.Set(1);
+        }
+        ++it;
+      }
+    }
   } else {
     if (m_Verbose) std::cout<<"Extracting the air feature image..."<<std::endl;
     //---------------------------------
@@ -109,12 +131,35 @@ MotionMaskGenericFilter::GetAirImage(typename itk::Image<PixelType, Dimension>::
     if (m_Verbose) std::cout<<"Binarizing the image using thresholds "<<m_ArgsInfo.lowerThresholdAir_arg
                               <<", "<<m_ArgsInfo.upperThresholdAir_arg<<"..."<<std::endl;
     binarizeFilter->Update();
+    air = binarizeFilter->GetOutput();
+
+    //---------------------------------
+    // Pad
+    //---------------------------------
+    if(m_ArgsInfo.pad_flag) {
+      typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
+      IteratorType it(air, air->GetLargestPossibleRegion());
+      typename InternalImageType::IndexType index;
+      while(!it.IsAtEnd()) {
+        index=it.GetIndex();
+
+        //Pad borders of all dimensions but 2 (cranio-caudal)
+        for (unsigned int i=0; i<Dimension; i++){
+          if(i==2)
+            continue;
+          if(index[i]==air->GetLargestPossibleRegion().GetIndex()[i]
+              || index[i]==(unsigned int)air->GetLargestPossibleRegion().GetIndex()[i]+ (unsigned int) air->GetLargestPossibleRegion().GetSize()[i]-1)
+            it.Set(binarizeFilter->GetInsideValue());
+        }
+        ++it;
+      }
+    }
 
     //---------------------------------
     // Remove lungs (in place)
     //---------------------------------
     typedef itk::ImageRegionIterator<InternalImageType> IteratorType;
-    IteratorType itAir(binarizeFilter->GetOutput(), binarizeFilter->GetOutput()->GetLargestPossibleRegion());
+    IteratorType itAir(air, binarizeFilter->GetOutput()->GetLargestPossibleRegion());
     IteratorType itLungs(lungs, binarizeFilter->GetOutput()->GetLargestPossibleRegion()); //lungs padded, used air region
     itAir.GoToBegin();
     itLungs.GoToBegin();
@@ -174,24 +219,7 @@ MotionMaskGenericFilter::GetAirImage(typename itk::Image<PixelType, Dimension>::
   if (m_Verbose) std::cout<<"Mirroring the entire image along the CC axis..."<<std::endl;
   mirrorPadImageFilter->Update();
   air=mirrorPadImageFilter->GetOutput();
-  writeImage<InternalImageType>(air,"/home/srit/tmp/air.mhd");
-
-  //---------------------------------
-  // Pad
-  //---------------------------------
-  if(m_ArgsInfo.pad_flag) {
-    typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
-    IteratorType it(air, air->GetLargestPossibleRegion());
-    typename InternalImageType::IndexType index;
-    while(!it.IsAtEnd()) {
-      index=it.GetIndex();
-      for (unsigned int i=0; i<Dimension; i++)
-        if(index[i]==air->GetLargestPossibleRegion().GetIndex()[i]
-            || index[i]==(unsigned int)air->GetLargestPossibleRegion().GetIndex()[i]+ (unsigned int) air->GetLargestPossibleRegion().GetSize()[i]-1)
-          it.Set(0);
-      ++it;
-    }
-  }
+  //writeImage<InternalImageType>(air,"/home/srit/tmp/air.mhd");
 
   return air;
 }
@@ -349,6 +377,8 @@ MotionMaskGenericFilter::GetLungsImage(typename itk::Image<PixelType, Dimension>
     connectFilter->SetBackgroundValue(0);
     connectFilter->SetFullyConnected(true);
     if (m_Verbose) std::cout<<"Labeling the connected components..."<<std::endl;
+    connectFilter->Update();
+    if (m_Verbose) std::cout<<"found "<< connectFilter->GetObjectCount() << std::endl;
 
     //---------------------------------
     // Sort the labels according to size
@@ -356,7 +386,7 @@ MotionMaskGenericFilter::GetLungsImage(typename itk::Image<PixelType, Dimension>
     typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
     relabelFilter->SetInput(connectFilter->GetOutput());
     if (m_Verbose) std::cout<<"Sorting the labels..."<<std::endl;
-    // writeImage<InternalImageType> (relabelFilter->GetOutput(), "/home/jef/tmp/labels.mhd");
+    // writeImage<InternalImageType> (relabelFilter->GetOutput(), "/home/vdelmon/tmp/labels.mhd");
 
     //---------------------------------
     // Keep the label