From 327ed9a4c0398e274453754d4ec27ca9633810dd Mon Sep 17 00:00:00 2001
From: David Sarrut <david.sarrut@gmail.com>
Date: Tue, 20 Mar 2012 14:23:24 +0100
Subject: [PATCH] Add dice with reference image

---
 segmentation/clitkStructuresExtractionFilter.h   | 2 +-
 segmentation/clitkStructuresExtractionFilter.txx | 8 +++++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/segmentation/clitkStructuresExtractionFilter.h b/segmentation/clitkStructuresExtractionFilter.h
index 3e7d303..9bf57d0 100644
--- a/segmentation/clitkStructuresExtractionFilter.h
+++ b/segmentation/clitkStructuresExtractionFilter.h
@@ -88,7 +88,7 @@ namespace clitk {
     
     // RelativePositionList management 
     void AddRelativePositionListFilename(std::string s);    
-    MaskImagePointer ApplyRelativePositionList(std::string name, MaskImageType * input);
+    MaskImagePointer ApplyRelativePositionList(std::string name, MaskImageType * input, bool overlap=false);
     
    protected:
     StructuresExtractionFilter();
diff --git a/segmentation/clitkStructuresExtractionFilter.txx b/segmentation/clitkStructuresExtractionFilter.txx
index 3a3e0ab..9559d4c 100644
--- a/segmentation/clitkStructuresExtractionFilter.txx
+++ b/segmentation/clitkStructuresExtractionFilter.txx
@@ -47,7 +47,7 @@ AddRelativePositionListFilename(std::string s) {
 template <class TImageType>
 typename clitk::StructuresExtractionFilter<TImageType>::MaskImagePointer
 clitk::StructuresExtractionFilter<TImageType>::
-ApplyRelativePositionList(std::string name, MaskImageType * input) 
+ApplyRelativePositionList(std::string name, MaskImageType * input, bool overlap) 
 { 
   // Create all RelativePositionList
   for(unsigned int i=0; i<mListOfRelativePositionListFilename.size(); i++) {
@@ -71,8 +71,14 @@ ApplyRelativePositionList(std::string name, MaskImageType * input)
     relpos->SetCurrentStepNumber(GetCurrentStepNumber());
     relpos->SetWriteStepFlag(GetWriteStepFlag());
     relpos->SetInput(input);
+    if (overlap) {
+      std::string n = name.substr(8,2);
+      MaskImagePointer ref = this->GetAFDB()->template GetImage <MaskImageType>("S"+n+"_Ref");
+      relpos->SetReferenceImageForOverlapMeasure(ref);
+    }
     relpos->Update();
     input = relpos->GetOutput();
+
     SetCurrentStepNumber(relpos->GetCurrentStepNumber());
   }
   return input;
-- 
2.47.1