From 7b7aa6a850620a9932b5a65ec035845c5800319e Mon Sep 17 00:00:00 2001
From: grevillot <grevillot>
Date: Thu, 10 Mar 2011 07:54:53 +0000
Subject: [PATCH] *** empty log message ***
---
tools/clitkImageExtractLine.cxx | 103 ++++++++++++++++++++++++++++++--
tools/clitkImageExtractLine.ggo | 1 +
2 files changed, 99 insertions(+), 5 deletions(-)
diff --git a/tools/clitkImageExtractLine.cxx b/tools/clitkImageExtractLine.cxx
index bd7c978..a4040dd 100644
--- a/tools/clitkImageExtractLine.cxx
+++ b/tools/clitkImageExtractLine.cxx
@@ -22,6 +22,10 @@
* @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
@@ -43,6 +47,7 @@ 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) {
@@ -75,16 +80,104 @@ 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
diff --git a/tools/clitkImageExtractLine.ggo b/tools/clitkImageExtractLine.ggo
index 988c0f5..96a76cc 100644
--- a/tools/clitkImageExtractLine.ggo
+++ b/tools/clitkImageExtractLine.ggo
@@ -10,6 +10,7 @@ option "verbose" v "Verbose" flag off
option "firstIndex" f "First index value (in voxels)" int yes multiple
option "lastIndex" l "Last index value (in voxels" int yes multiple
+option "integral" I "Integrate the image along the line" int no default = "0"
option "mm" m "Last/first index are in mm" flag off
--
2.49.0