From 996c472dd4315215c25890d6b8a9b565413352f7 Mon Sep 17 00:00:00 2001
From: tbaudier <thomas.baudier@creatis.insa-lyon.fr>
Date: Tue, 23 Jan 2018 15:56:59 +0100
Subject: [PATCH] Add localization of max and min in clitkImageStatistics

---
 tools/clitkImageStatistics.ggo              | 25 +++++++++++----------
 tools/clitkImageStatisticsGenericFilter.h   |  3 ++-
 tools/clitkImageStatisticsGenericFilter.txx | 24 +++++++++++++++++++-
 3 files changed, 38 insertions(+), 14 deletions(-)

diff --git a/tools/clitkImageStatistics.ggo b/tools/clitkImageStatistics.ggo
index 7e28e42..60d451a 100644
--- a/tools/clitkImageStatistics.ggo
+++ b/tools/clitkImageStatistics.ggo
@@ -4,17 +4,18 @@ version "2.0"
 #This tool supports multiple images on the input, or even 4D, but all images must be of the same type and dimensions. 
 purpose "Compute statistics on an image, or on part of an image specified by a mask and label(s). The tool also supports multichannel images, which is useful, e.g., for vector fields. All channels are processed (separately) by default, but only one channel may be chosen."
 
-option "config"	  	-	"Config file"			  string  	no
-option "verbose"   	v   	"Verbose"			  flag		off
+option "config"       - "Config file"                                                         string  no
+option "verbose"      v "Verbose"                                                             flag    off
 
-option "input"		i	"Input image filename"		  string  	no multiple
-option "channel"    c "Image channel to be used in statistics (-1 to process all channels)"  int no default="-1"
-option "mask"		m	"Mask image filename (uchar)"		  string  	no
-option "label"		l	"Label(s) in the mask image to consider"	int  	no 	multiple 	default="1"
-option "histogram"	-	"Compute histogram, allows median calculation"	string  no
-option "dvhistogram" -	"Compute dose volume histogram"	string  no
-option "bins"		-	"Number of histogram bins"	  		int  	no 	default="100"
-option "lower"		-	"Lower histogram bound"	double 	no default="-1000"	
-option "upper"		-	"Upper histogram bound"	double 	no default="1000"		
+option "input"        i "Input image filename"                                                string  no  multiple
+option "channel"      c "Image channel to be used in statistics (-1 to process all channels)" int     no  default="-1"
+option "mask"         m "Mask image filename (uchar)"                                         string  no
+option "label"        l "Label(s) in the mask image to consider"                              int     no  multiple 	default="1"
+option "localize"     - "With verbose, write the index coordinates of the max and min"        flag    off
+option "histogram"    - "Compute histogram, allows median calculation"                        string  no
+option "dvhistogram"  - "Compute dose volume histogram"                                       string  no
+option "bins"         - "Number of histogram bins"                                            int     no  default="100"
+option "lower"        - "Lower histogram bound"                                               double  no  default="-1000"
+option "upper"        - "Upper histogram bound"                                               double  no  default="1000"
 
-option "allow_resize"   	r   	"Resize mask if different from input"			  flag		off
+option "allow_resize" r "Resize mask if different from input"                                 flag    off
diff --git a/tools/clitkImageStatisticsGenericFilter.h b/tools/clitkImageStatisticsGenericFilter.h
index 8544d59..26da4e4 100644
--- a/tools/clitkImageStatisticsGenericFilter.h
+++ b/tools/clitkImageStatisticsGenericFilter.h
@@ -61,6 +61,7 @@ namespace clitk
     {
       m_ArgsInfo=a;
       m_Verbose=m_ArgsInfo.verbose_flag;
+      m_Localize=m_ArgsInfo.localize_flag;
 
       if(m_ArgsInfo.input_given)
         m_InputFileName=m_ArgsInfo.input_arg[0];
@@ -98,7 +99,7 @@ namespace clitk
     // Data members
     //----------------------------------------
     args_info_clitkImageStatistics m_ArgsInfo;
-    bool m_Verbose;
+    bool m_Verbose, m_Localize;
     std::string m_InputFileName;
 
   };
diff --git a/tools/clitkImageStatisticsGenericFilter.txx b/tools/clitkImageStatisticsGenericFilter.txx
index b3eff93..82a11ab 100644
--- a/tools/clitkImageStatisticsGenericFilter.txx
+++ b/tools/clitkImageStatisticsGenericFilter.txx
@@ -20,6 +20,7 @@
 
 #include "itkNthElementImageAdaptor.h"
 #include "itkJoinSeriesImageFilter.h"
+#include "itkImageRegionConstIterator.h"
 
 #include "clitkImageStatisticsGenericFilter.h"
 #include "clitkCropLikeImageFilter.h"
@@ -232,8 +233,21 @@ namespace clitk
 
         statisticsFilter->Update();
 
+        //find localization for max and min (the last pixel found)
+        typename InputImageType::IndexType minIndex, maxIndex;
+        if (m_Verbose && m_Localize) {
+          itk::ImageRegionConstIterator<InputImageAdaptorType> imageIterator(input_adaptor,input_adaptor->GetLargestPossibleRegion());
+          while(!imageIterator.IsAtEnd()) {
+            if (imageIterator.Get() == statisticsFilter->GetMinimum(label))
+              minIndex = imageIterator.GetIndex();
+            if (imageIterator.Get() == statisticsFilter->GetMaximum(label))
+              maxIndex = imageIterator.GetIndex();
+            ++imageIterator;
+          }
+        }
+
         // Output
-       if (m_Verbose) std::cout<<"N° of pixels: ";
+        if (m_Verbose) std::cout<<"N° of pixels: ";
         std::cout<<statisticsFilter->GetCount(label)<<std::endl;
         if (m_Verbose) std::cout<<"Mean: ";
         std::cout<<statisticsFilter->GetMean(label)<<std::endl;
@@ -243,8 +257,16 @@ namespace clitk
         std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
         if (m_Verbose) std::cout<<"Min: ";
         std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
+        if (m_Verbose && m_Localize) {
+          std::cout<<"        in voxel of index: ";
+          std::cout<<minIndex<<std::endl;
+        }
         if (m_Verbose) std::cout<<"Max: ";
         std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
+        if (m_Verbose && m_Localize) {
+          std::cout<<"        in voxel of index: ";
+          std::cout<<maxIndex<<std::endl;
+        }
         if (m_Verbose) std::cout<<"Sum: ";
         std::cout<<statisticsFilter->GetSum(label)<<std::endl;
         if (m_Verbose) std::cout<<"Volume (cc): ";
-- 
2.45.1