]> Creatis software - clitk.git/blob - tools/clitkVFMerge.cxx
hide inputselector option
[clitk.git] / tools / clitkVFMerge.cxx
1 /*=========================================================================
2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
3
4   Authors belong to:
5   - University of LYON              http://www.universite-lyon.fr/
6   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
8
9   This software is distributed WITHOUT ANY WARRANTY; without even
10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
11   PURPOSE.  See the copyright notices for more information.
12
13   It is distributed under dual licence
14
15   - BSD        See included LICENSE.txt file
16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17 ======================================================================-====*/
18 #ifndef CLITKVFMERGE_CXX
19 #define CLITKVFMERGE_CXX
20
21 /**
22  * @file   clitkVFMerge.cxx
23  * @author Jef Vandemeulebroucke <jefvdmb@gmail.com>
24  * @date   June 15  10:14:53 2007
25  *
26  * @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 .
27  *
28  *
29  */
30
31 // clitk include
32 #include "clitkVFMerge_ggo.h"
33 #include "clitkIO.h"
34 #include "clitkImageCommon.h"
35
36 // itk include
37 //#include "itkReadTransform.h"
38 #include "itkImageFileWriter.h"
39 #include <iostream>
40 #include "itkImageFileReader.h"
41 //#include "itkRawImageIO.h"
42 //#include "macro.h"
43
44 int main( int argc, char *argv[] )
45 {
46
47   // Init command line
48   GGO(clitkVFMerge, args_info);
49   CLITK_INIT;
50
51   const unsigned int SpaceDimension = 3;
52   const unsigned int ModelDimension = 4;
53   typedef itk::Vector< float, SpaceDimension > Displacement;
54   typedef itk::Image< Displacement, SpaceDimension > DeformationFieldType;
55   typedef itk::Image< Displacement, ModelDimension > DynamicDeformationFieldType;
56   typedef itk::ImageFileReader< DeformationFieldType > DeformationFieldReaderType;
57   typedef itk::ImageFileWriter< DynamicDeformationFieldType > DynamicDeformationFieldWriterType;
58
59
60 //declare the dynamic
61   DynamicDeformationFieldType::Pointer  dynamicDeformationField=DynamicDeformationFieldType::New();
62
63
64 //declare their iterators
65   typedef itk::ImageRegionIterator< DynamicDeformationFieldType> DynamicDeformationFieldIteratorType;
66   DynamicDeformationFieldIteratorType *dynamicIteratorPointer= new DynamicDeformationFieldIteratorType;
67
68   for (unsigned int i=0 ; i< args_info.inputs_num ; i ++) {
69     //read in the deformation field i
70     DeformationFieldReaderType::Pointer deformationFieldReader = DeformationFieldReaderType::New();
71     deformationFieldReader->SetFileName( args_info.inputs[i]);
72     if (args_info.verbose_flag) std::cout<<"Reading VF number "<< i+1 << std::endl;
73     deformationFieldReader->Update();
74     DeformationFieldType::Pointer currentDeformationField = deformationFieldReader->GetOutput();
75
76     //create an iterator for the current deformation field
77     typedef itk::ImageRegionIterator<DeformationFieldType> FieldIteratorType;
78     FieldIteratorType fieldIterator(currentDeformationField, currentDeformationField->GetLargestPossibleRegion());
79
80     //Allocate memory for the dynamic components
81     if (i==0) {
82       DynamicDeformationFieldType::RegionType dynamicDeformationFieldRegion;
83       DynamicDeformationFieldType::RegionType::SizeType dynamicDeformationFieldSize;
84       DeformationFieldType::RegionType::SizeType deformationFieldSize;
85       deformationFieldSize= currentDeformationField->GetLargestPossibleRegion().GetSize();
86       dynamicDeformationFieldSize[0]=deformationFieldSize[0];
87       dynamicDeformationFieldSize[1]=deformationFieldSize[1];
88       dynamicDeformationFieldSize[2]=deformationFieldSize[2];
89       dynamicDeformationFieldSize[3]=args_info.inputs_num;
90       dynamicDeformationFieldRegion.SetSize(dynamicDeformationFieldSize);
91       DynamicDeformationFieldType::IndexType start;
92       start.Fill(0);
93       dynamicDeformationFieldRegion.SetIndex(start);
94       dynamicDeformationField->SetRegions(dynamicDeformationFieldRegion);
95       dynamicDeformationField->Allocate();
96
97
98       //Set the spacing
99       DeformationFieldType::SpacingType spacing= currentDeformationField->GetSpacing();
100       DynamicDeformationFieldType::SpacingType dynamicSpacing;
101       dynamicSpacing[0]=spacing[0];
102       dynamicSpacing[1]=spacing[1];
103       dynamicSpacing[2]=spacing[2];
104       dynamicSpacing[3]=args_info.spacing_arg; //JV par exemple
105       dynamicDeformationField->SetSpacing(dynamicSpacing);
106       DynamicDeformationFieldType::PointType origin;
107       origin[0]=args_info.xorigin_arg;
108       origin[1]=args_info.yorigin_arg;
109       origin[2]=args_info.zorigin_arg;
110       origin[3]=0; //temporal origin is always 0
111       dynamicDeformationField->SetOrigin(origin);
112
113       // Creating iterators for the currentDeformationField and the DynamicDeformationField
114       DynamicDeformationFieldIteratorType *dynamicIterator= new DynamicDeformationFieldIteratorType(dynamicDeformationField, dynamicDeformationField->GetLargestPossibleRegion());
115       dynamicIteratorPointer=dynamicIterator;
116       dynamicIteratorPointer->GoToBegin();
117     }
118     if (args_info.verbose_flag) std::cout<<"Merging VF number "<< i+1 << std::endl;
119     //Copy the current component of the input into dynamicDeformationFieldComponent
120     fieldIterator.GoToBegin();
121     while(!fieldIterator.IsAtEnd()) {
122       dynamicIteratorPointer->Set(fieldIterator.Get());
123       ++fieldIterator;
124       ++(*dynamicIteratorPointer);
125     }
126   }
127
128
129 //Write the vector field
130   DynamicDeformationFieldWriterType::Pointer writer = DynamicDeformationFieldWriterType::New();
131   writer->SetInput( dynamicDeformationField );
132   writer->SetFileName( args_info.output_arg );
133   if (args_info.verbose_flag) std::cout<<"Writing the dynamic VF"<< std::endl;
134
135
136   try {
137
138     writer->Update( );
139   } catch( itk::ExceptionObject & excp ) {
140     std::cerr << "Problem writing the output file" << std::endl;
141     std::cerr << excp << std::endl;
142     return EXIT_FAILURE;
143   }
144   return EXIT_SUCCESS;
145 }
146 #endif
147
148