X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkImageExtractLine.cxx;h=a4040dd2b05f1a6ce39ab52eb873e277286970f7;hb=91dc23d0440db7c36cabdb46271bebe30a28819c;hp=4edc0133d6ee32d6da105deb582e929c3b472a89;hpb=eb2ea680811676c925bc37c6ddb2981f193fae8c;p=clitk.git

diff --git a/tools/clitkImageExtractLine.cxx b/tools/clitkImageExtractLine.cxx
index 4edc013..a4040dd 100644
--- a/tools/clitkImageExtractLine.cxx
+++ b/tools/clitkImageExtractLine.cxx
@@ -1,33 +1,43 @@
-/*-------------------------------------------------------------------------
-                                                                                
-  Copyright (c) CREATIS (Centre de Recherche et d'Applications en Traitement de
-  l'Image). All rights reserved. See Doc/License.txt or
-  http://www.creatis.insa-lyon.fr/Public/Gdcm/License.html for details.
-                                                                                
+/*=========================================================================
+  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 above copyright notices for more information.
-                                                                             
-  -------------------------------------------------------------------------*/
+  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
+======================================================================-====*/
 #ifndef CLITKIMAGEEXTRACTLINE_CXX
 #define CLITKIMAGEEXTRACTLINE_CXX
-
 /**
    -------------------------------------------------
    * @file   clitkImageExtractLine.cxx
    * @author David Sarrut <David.Sarrut@creatis.insa-lyon.fr>
    * @date   23 Feb 2008 08:37:53
+   * @modified by Loïc Grevillot <Loic.Grevillot@creatis.insa-lyon.fr>
+   * @date   10 March 2011
+      * Option -I added, in order to integrate plans perpendicular to a line
+   
    -------------------------------------------------*/
 
 // clitk include
 #include "clitkImageExtractLine_ggo.h"
 #include "clitkIO.h"
 #include "clitkImageCommon.h"
+#include "clitkCommon.h"
 #include <itkLineConstIterator.h>
 
 //--------------------------------------------------------------------
-int main(int argc, char * argv[]) {
+int main(int argc, char * argv[])
+{
 
   // Init command line
   GGO(clitkImageExtractLine, args_info);
@@ -37,7 +47,8 @@ int main(int argc, char * argv[]) {
   typedef float PixelType;
   const unsigned int Dimension=3;
   typedef itk::Image<PixelType, Dimension> ImageType;
-  
+  typedef itk::Size<Dimension> SizeType;
+
   // Check options
   if (args_info.firstIndex_given != Dimension) {
     std::cerr << "Please give " << Dimension << "values to --firstIndex option" << std::endl;
@@ -59,7 +70,7 @@ int main(int argc, char * argv[]) {
   double length = 0.0;
   for(unsigned int i=0; i<Dimension; i++) {
     firstIndex[i] = args_info.firstIndex_arg[i];
-    lastIndex[i] = args_info.lastIndex_arg[i];    
+    lastIndex[i] = args_info.lastIndex_arg[i];
     if (args_info.mm_flag) {
       firstIndex[i] /= spacing[i];
       lastIndex[i] /= spacing[i];
@@ -69,22 +80,110 @@ int main(int argc, char * argv[]) {
   length = sqrt(length);
 
   // Loop
+//   std::vector<double> depth;
+//   std::vector<double> values;
+//   itk::LineConstIterator<ImageType> iter(input, firstIndex, lastIndex);
+//   iter.GoToBegin();
+//   while (!iter.IsAtEnd()) {
+//     values.push_back(iter.Get());
+//     ++iter;
+//   }
+//   double step = length/values.size();
+
   std::vector<double> depth;
   std::vector<double> values;
   itk::LineConstIterator<ImageType> iter(input, firstIndex, lastIndex);
-  iter.GoToBegin();
-  while (!iter.IsAtEnd()) {
-    values.push_back(iter.Get());
-    ++iter;
+  int direction=0;
+  
+  // args_info.integral_arg=0, so, it does not compute the integral
+  if (args_info.integral_arg==0){
+    iter.GoToBegin();
+    while (!iter.IsAtEnd()) {
+      values.push_back(iter.Get());
+      ++iter;
+    }
   }
+  // args_info.integral_arg=1, so, it computes the integral
+  else if (lastIndex[0]-firstIndex[0]==0 && lastIndex[1]-firstIndex[1]==0 && lastIndex[2]-firstIndex[2]>0)
+    direction=1;
+  else if (lastIndex[0]-firstIndex[0]==0 && lastIndex[1]-firstIndex[1]>0 && lastIndex[2]-firstIndex[2]==0)
+    direction=2;
+  else if (lastIndex[0]-firstIndex[0]>0 && lastIndex[1]-firstIndex[1]==0 && lastIndex[2]-firstIndex[2]==0)
+    direction=3;
+  else{
+    //std::cout<<lastIndex[0]-firstIndex[0]<<"  "<<lastIndex[1]-firstIndex[1]<<"  "<<lastIndex[3]-firstIndex[3]<<std::endl;
+    std::cout<<"Index are not defined along a straight along x or y or z axis."<<std::endl;
+    std::cout<<"The line cannot be extracted."<<std::endl;
+    exit(0);
+  }
+  
+  if (args_info.integral_arg!=0){
+    SizeType dim;
+    dim=input->GetLargestPossibleRegion().GetSize();
+    DD(dim);
+    DD(direction);
+    
+    int a=0, b=0, c=0;
+    
+    if (direction==2){
+      a=0;
+      b=1;
+      c=2;
+    }
+    if (direction==1){
+      a=0;
+      b=2;
+      c=1;
+    }    
+    if (direction==3){
+      a=2;
+      b=0;
+      c=1;
+    } 
+    
+    double val[dim[b]];
+      for (int i=0; i<dim[b]; i++)
+	val[i]=0;
+      
+    int k;
+    for (int i=0; i<dim[a]; i++){
+      for (int j=0; j<dim[c]; j++){
+  //      std::cout<<"i "<<i<<"  j "<<j<<std::endl;
+	k=0;
+	firstIndex[a]=i;
+	firstIndex[c]=j;
+	lastIndex[a]=i;
+	lastIndex[c]=j;
+  //      std::cout<<"A"<<std::endl;
+	itk::LineConstIterator<ImageType> iter(input, firstIndex, lastIndex);
+	iter.GoToBegin();
+  //      std::cout<<"B"<<std::endl;
+	val[k]+=iter.Get();
+	k++;
+  //      std::cout<<"C"<<std::endl;
+	while (!iter.IsAtEnd()) {
+  //	std::cout<<"D "<<k<<std::endl;
+	  val[k]+=iter.Get();
+	  ++iter;
+	  k++;
+	}
+      }
+    }
+  
+    for (unsigned int i=0; i<dim[b]; i++){
+      values.push_back(val[i]);
+    }
+  }
+  
   double step = length/values.size();
+  DD(values.size());
   
   // If isocenter is used
   double isoDistance = 0.0;
   if (args_info.isocenter_given) { // isoCenter is in mm
     IndexType isoCenter;
-    for(unsigned int i=0; i<Dimension; i++) { 
-      isoCenter[i] = args_info.isocenter_arg[i]; 
+    for(unsigned int i=0; i<Dimension; i++) {
+      isoCenter[i] = args_info.isocenter_arg[i];
       isoDistance += pow(isoCenter[i] - firstIndex[i]*spacing[i],2);
     }
     DD(isoCenter);
@@ -107,15 +206,14 @@ int main(int argc, char * argv[]) {
       lg += step;
     }
     os.close();
-  }
-  else {
+  } else {
     for(unsigned int i=0; i<values.size(); i++) {
       os << values[i] << std::endl;
     }
     os.close();
   }
 
-  // this is the end my friend  
+  // this is the end my friend
   return 0;
 } // end main