+/*=========================================================================
+ 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://www.centreleonberard.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 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 CLITKVFMERGE_CXX
#define CLITKVFMERGE_CXX
* @file clitkVFMerge.cxx
* @author Jef Vandemeulebroucke <jefvdmb@gmail.com>
* @date June 15 10:14:53 2007
- *
+ *
* @brief Read in one VF (ex mhd, vf) and write to another. Transforming from mm to voxels needed for the vf format is implemented in clitkVfImageIO.cxx .
- *
- *
+ *
+ *
*/
// clitk include
#include "clitkVFMerge_ggo.h"
#include "clitkIO.h"
-#include "clitkIOCommon.h"
+#include "clitkImageCommon.h"
+#include "clitkCommon.h"
// itk include
-//#include "itkReadTransform.h"
#include "itkImageFileWriter.h"
#include <iostream>
#include "itkImageFileReader.h"
-//#include "itkRawImageIO.h"
-//#include "macro.h"
int main( int argc, char *argv[] )
{
GGO(clitkVFMerge, args_info);
CLITK_INIT;
-const unsigned int SpaceDimension = 3;
-const unsigned int ModelDimension = 4;
-typedef itk::Vector< float, SpaceDimension > Displacement;
-typedef itk::Image< Displacement, SpaceDimension > DeformationFieldType;
-typedef itk::Image< Displacement, ModelDimension > DynamicDeformationFieldType;
-typedef itk::ImageFileReader< DeformationFieldType > DeformationFieldReaderType;
-typedef itk::ImageFileWriter< DynamicDeformationFieldType > DynamicDeformationFieldWriterType;
+ const unsigned int SpaceDimension = 3;
+ const unsigned int ModelDimension = 4;
+ typedef itk::Vector< float, SpaceDimension > Displacement;
+ typedef itk::Image< Displacement, SpaceDimension > DeformationFieldType;
+ typedef itk::Image< Displacement, ModelDimension > DynamicDeformationFieldType;
+ typedef itk::ImageFileReader< DeformationFieldType > DeformationFieldReaderType;
+ typedef itk::ImageFileWriter< DynamicDeformationFieldType > DynamicDeformationFieldWriterType;
+
-
//declare the dynamic
- DynamicDeformationFieldType::Pointer dynamicDeformationField=DynamicDeformationFieldType::New();
-
-
- //declare their iterators
- typedef itk::ImageRegionIterator< DynamicDeformationFieldType> DynamicDeformationFieldIteratorType;
- DynamicDeformationFieldIteratorType *dynamicIteratorPointer= new DynamicDeformationFieldIteratorType;
-
- for (unsigned int i=0 ; i< args_info.inputs_num ; i ++)
- {
- //read in the deformation field i
- DeformationFieldReaderType::Pointer deformationFieldReader = DeformationFieldReaderType::New();
- deformationFieldReader->SetFileName( args_info.inputs[i]);
- if (args_info.verbose_flag) std::cout<<"Reading VF number "<< i+1 << std::endl;
- deformationFieldReader->Update();
- DeformationFieldType::Pointer currentDeformationField = deformationFieldReader->GetOutput();
-
- //create an iterator for the current deformation field
- typedef itk::ImageRegionIterator<DeformationFieldType> FieldIteratorType;
- FieldIteratorType fieldIterator(currentDeformationField, currentDeformationField->GetLargestPossibleRegion());
-
- //Allocate memory for the dynamic components
- if (i==0)
- {
- DynamicDeformationFieldType::RegionType dynamicDeformationFieldRegion;
- DynamicDeformationFieldType::RegionType::SizeType dynamicDeformationFieldSize;
- DeformationFieldType::RegionType::SizeType deformationFieldSize;
- deformationFieldSize= currentDeformationField->GetLargestPossibleRegion().GetSize();
- dynamicDeformationFieldSize[0]=deformationFieldSize[0];
- dynamicDeformationFieldSize[1]=deformationFieldSize[1];
- dynamicDeformationFieldSize[2]=deformationFieldSize[2];
- dynamicDeformationFieldSize[3]=args_info.inputs_num;
- dynamicDeformationFieldRegion.SetSize(dynamicDeformationFieldSize);
- DynamicDeformationFieldType::IndexType start;
- start.Fill(0);
- dynamicDeformationFieldRegion.SetIndex(start);
- dynamicDeformationField->SetRegions(dynamicDeformationFieldRegion);
- dynamicDeformationField->Allocate();
-
-
- //Set the spacing
- DeformationFieldType::SpacingType spacing= currentDeformationField->GetSpacing();
- DynamicDeformationFieldType::SpacingType dynamicSpacing;
- dynamicSpacing[0]=spacing[0];
- dynamicSpacing[1]=spacing[1];
- dynamicSpacing[2]=spacing[2];
- dynamicSpacing[3]=args_info.spacing_arg; //JV par exemple
- dynamicDeformationField->SetSpacing(dynamicSpacing);
- DynamicDeformationFieldType::PointType origin;
- origin[0]=args_info.xorigin_arg;
- origin[1]=args_info.yorigin_arg;
- origin[2]=args_info.zorigin_arg;
- origin[3]=0; //temporal origin is always 0
- dynamicDeformationField->SetOrigin(origin);
-
- // Creating iterators for the currentDeformationField and the DynamicDeformationField
- DynamicDeformationFieldIteratorType *dynamicIterator= new DynamicDeformationFieldIteratorType(dynamicDeformationField, dynamicDeformationField->GetLargestPossibleRegion());
- dynamicIteratorPointer=dynamicIterator;
- dynamicIteratorPointer->GoToBegin();
- }
- if (args_info.verbose_flag) std::cout<<"Merging VF number "<< i+1 << std::endl;
- //Copy the current component of the input into dynamicDeformationFieldComponent
- fieldIterator.GoToBegin();
- while(!fieldIterator.IsAtEnd())
- {
- dynamicIteratorPointer->Set(fieldIterator.Get());
- ++fieldIterator;
- ++(*dynamicIteratorPointer);
- }
- }
-
+ DynamicDeformationFieldType::Pointer dynamicDeformationField=DynamicDeformationFieldType::New();
+
+
+//declare their iterators
+ typedef itk::ImageRegionIterator< DynamicDeformationFieldType> DynamicDeformationFieldIteratorType;
+ DynamicDeformationFieldIteratorType *dynamicIteratorPointer= new DynamicDeformationFieldIteratorType;
+
+ for (unsigned int i=0 ; i< args_info.inputs_num ; i ++) {
+ //read in the deformation field i
+ DeformationFieldReaderType::Pointer deformationFieldReader = DeformationFieldReaderType::New();
+ deformationFieldReader->SetFileName( args_info.inputs[i]);
+ if (args_info.verbose_flag) std::cout<<"Reading VF number "<< i+1 << std::endl;
+ deformationFieldReader->Update();
+ DeformationFieldType::Pointer currentDeformationField = deformationFieldReader->GetOutput();
+
+ //create an iterator for the current deformation field
+ typedef itk::ImageRegionIterator<DeformationFieldType> FieldIteratorType;
+ FieldIteratorType fieldIterator(currentDeformationField, currentDeformationField->GetLargestPossibleRegion());
+
+ //Allocate memory for the dynamic components
+ if (i==0) {
+ DynamicDeformationFieldType::RegionType dynamicDeformationFieldRegion;
+ DynamicDeformationFieldType::RegionType::SizeType dynamicDeformationFieldSize;
+ DeformationFieldType::RegionType::SizeType deformationFieldSize;
+ deformationFieldSize= currentDeformationField->GetLargestPossibleRegion().GetSize();
+ dynamicDeformationFieldSize[0]=deformationFieldSize[0];
+ dynamicDeformationFieldSize[1]=deformationFieldSize[1];
+ dynamicDeformationFieldSize[2]=deformationFieldSize[2];
+ dynamicDeformationFieldSize[3]=args_info.inputs_num;
+ dynamicDeformationFieldRegion.SetSize(dynamicDeformationFieldSize);
+ DynamicDeformationFieldType::IndexType start;
+ start.Fill(0);
+ dynamicDeformationFieldRegion.SetIndex(start);
+ dynamicDeformationField->SetRegions(dynamicDeformationFieldRegion);
+ dynamicDeformationField->Allocate();
+
+
+ //Set the spacing
+ DeformationFieldType::SpacingType spacing= currentDeformationField->GetSpacing();
+ DynamicDeformationFieldType::SpacingType dynamicSpacing;
+ dynamicSpacing[0]=spacing[0];
+ dynamicSpacing[1]=spacing[1];
+ dynamicSpacing[2]=spacing[2];
+ dynamicSpacing[3]=args_info.spacing_arg; //JV par exemple
+ dynamicDeformationField->SetSpacing(dynamicSpacing);
+ DynamicDeformationFieldType::PointType origin;
+ origin[0]=args_info.xorigin_arg;
+ origin[1]=args_info.yorigin_arg;
+ origin[2]=args_info.zorigin_arg;
+ origin[3]=0; //temporal origin is always 0
+ dynamicDeformationField->SetOrigin(origin);
+
+ // Creating iterators for the currentDeformationField and the DynamicDeformationField
+ DynamicDeformationFieldIteratorType *dynamicIterator= new DynamicDeformationFieldIteratorType(dynamicDeformationField, dynamicDeformationField->GetLargestPossibleRegion());
+ dynamicIteratorPointer=dynamicIterator;
+ dynamicIteratorPointer->GoToBegin();
+ }
+ if (args_info.verbose_flag) std::cout<<"Merging VF number "<< i+1 << std::endl;
+ //Copy the current component of the input into dynamicDeformationFieldComponent
+ fieldIterator.GoToBegin();
+ while(!fieldIterator.IsAtEnd()) {
+ dynamicIteratorPointer->Set(fieldIterator.Get());
+ ++fieldIterator;
+ ++(*dynamicIteratorPointer);
+ }
+ }
+
//Write the vector field
- DynamicDeformationFieldWriterType::Pointer writer = DynamicDeformationFieldWriterType::New();
- writer->SetInput( dynamicDeformationField );
- writer->SetFileName( args_info.output_arg );
- if (args_info.verbose_flag) std::cout<<"Writing the dynamic VF"<< std::endl;
-
-
- try {
-
- writer->Update( );
- }
- catch( itk::ExceptionObject & excp ) {
- std::cerr << "Problem writing the output file" << std::endl;
- std::cerr << excp << std::endl;
- return EXIT_FAILURE;
- }
- return EXIT_SUCCESS;
+ DynamicDeformationFieldWriterType::Pointer writer = DynamicDeformationFieldWriterType::New();
+ writer->SetInput( dynamicDeformationField );
+ writer->SetFileName( args_info.output_arg );
+ if (args_info.verbose_flag) std::cout<<"Writing the dynamic VF"<< std::endl;
+
+
+ try {
+
+ writer->Update( );
+ } catch( itk::ExceptionObject & excp ) {
+ std::cerr << "Problem writing the output file" << std::endl;
+ std::cerr << excp << std::endl;
+ return EXIT_FAILURE;
+ }
+ return EXIT_SUCCESS;
}
#endif
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff