-/*-------------------------------------------------------------------------
-
- 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);
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;
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];
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);
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
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff