forked from InsightSoftwareConsortium/ITK
-
Notifications
You must be signed in to change notification settings - Fork 0
/
DeformableRegistration10.cxx
218 lines (174 loc) · 7.93 KB
/
DeformableRegistration10.cxx
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
/*=========================================================================
Program: Insight Segmentation & Registration Toolkit
Module: DeformableRegistration10.cxx
Language: C++
Date: $Date$
Version: $Revision$
Copyright (c) Insight Software Consortium. All rights reserved.
See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm for details.
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.
=========================================================================*/
#ifndef USE_FFTW
#error "This program needs FFTW to work."
#endif
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkCurvatureRegistrationFilter.h"
#include "itkFastSymmetricForcesDemonsRegistrationFunction.h"
#include "itkMultiResolutionPDEDeformableRegistration.h"
#include "itkHistogramMatchingImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkWarpImageFilter.h"
#include "itkLinearInterpolateImageFunction.h"
#include "itkExceptionObject.h"
const unsigned int Dimension = 3;
// The following section of code implements a Command observer
// that will monitor the evolution of the registration process.
//
class CommandIterationUpdate : public itk::Command
{
public:
typedef CommandIterationUpdate Self;
typedef itk::Command Superclass;
typedef itk::SmartPointer<CommandIterationUpdate> Pointer;
itkNewMacro( CommandIterationUpdate );
protected:
CommandIterationUpdate() {};
typedef itk::Image< float, Dimension > InternalImageType;
typedef itk::Vector< float, Dimension > VectorPixelType;
typedef itk::Image< VectorPixelType, Dimension > DeformationFieldType;
typedef itk::CurvatureRegistrationFilter<
InternalImageType,
InternalImageType,
DeformationFieldType,
itk::FastSymmetricForcesDemonsRegistrationFunction<InternalImageType,InternalImageType,DeformationFieldType> > RegistrationFilterType;
public:
void Execute(itk::Object *caller, const itk::EventObject & event)
{
Execute( (const itk::Object *)caller, event);
}
void Execute(const itk::Object * object, const itk::EventObject & event)
{
const RegistrationFilterType * filter =
dynamic_cast< const RegistrationFilterType * >( object );
if( !(itk::IterationEvent().CheckEvent( &event )) )
{
return;
}
std::cout << filter->GetMetric() << std::endl;
}
};
int main( int argc, char *argv[] )
{
if( argc < 4 )
{
std::cerr << "Missing Parameters " << std::endl;
std::cerr << "Usage: " << argv[0];
std::cerr << " fixedImageFile movingImageFile ";
std::cerr << " outputImageFile " << std::endl;
return 1;
}
typedef short PixelType;
typedef itk::Image< PixelType, Dimension > FixedImageType;
typedef itk::Image< PixelType, Dimension > MovingImageType;
typedef itk::Image< float, Dimension > JacobianImageType;
typedef itk::ImageFileReader< FixedImageType > FixedImageReaderType;
typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
FixedImageReaderType::Pointer fixedImageReader =
FixedImageReaderType::New();
MovingImageReaderType::Pointer movingImageReader =
MovingImageReaderType::New();
fixedImageReader->SetFileName( argv[1] );
movingImageReader->SetFileName( argv[2] );
typedef float InternalPixelType;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
typedef itk::CastImageFilter< FixedImageType,
InternalImageType > FixedImageCasterType;
typedef itk::CastImageFilter< MovingImageType,
InternalImageType > MovingImageCasterType;
FixedImageCasterType::Pointer fixedImageCaster =
FixedImageCasterType::New();
MovingImageCasterType::Pointer movingImageCaster =
MovingImageCasterType::New();
fixedImageCaster->SetInput( fixedImageReader->GetOutput() );
movingImageCaster->SetInput( movingImageReader->GetOutput() );
typedef itk::HistogramMatchingImageFilter<
InternalImageType,
InternalImageType > MatchingFilterType;
MatchingFilterType::Pointer matcher = MatchingFilterType::New();
matcher->SetInput( movingImageCaster->GetOutput() );
matcher->SetReferenceImage( fixedImageCaster->GetOutput() );
matcher->SetNumberOfHistogramLevels( 1024 );
matcher->SetNumberOfMatchPoints( 7 );
matcher->ThresholdAtMeanIntensityOn();
typedef itk::Vector< float, Dimension > VectorPixelType;
typedef itk::Image< VectorPixelType, Dimension > DeformationFieldType;
typedef itk::CurvatureRegistrationFilter<
InternalImageType,
InternalImageType,
DeformationFieldType,
itk::FastSymmetricForcesDemonsRegistrationFunction<InternalImageType,InternalImageType,DeformationFieldType> > RegistrationFilterType;
RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
filter->SetTimeStep( 1 );
filter->SetConstraintWeight( 0.1 );
CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
filter->AddObserver( itk::IterationEvent(), observer );
typedef itk::MultiResolutionPDEDeformableRegistration<
InternalImageType,
InternalImageType,
DeformationFieldType > MultiResRegistrationFilterType;
MultiResRegistrationFilterType::Pointer multires = MultiResRegistrationFilterType::New();
multires->SetRegistrationFilter( filter );
multires->SetNumberOfLevels( 3 );
multires->SetFixedImage( fixedImageCaster->GetOutput() );
multires->SetMovingImage( matcher->GetOutput() );
unsigned int nIterations[4] = { 10, 20, 50, 50 };
multires->SetNumberOfIterations( nIterations );
multires->Update();
typedef itk::WarpImageFilter<
MovingImageType,
MovingImageType,
DeformationFieldType > WarperType;
typedef itk::LinearInterpolateImageFunction<
MovingImageType,
double > InterpolatorType;
WarperType::Pointer warper = WarperType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
warper->SetInput( movingImageReader->GetOutput() );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( fixedImage->GetSpacing() );
warper->SetOutputOrigin( fixedImage->GetOrigin() );
warper->SetDeformationField( multires->GetOutput() );
// Write warped image out to file
typedef unsigned short OutputPixelType;
typedef itk::Image< OutputPixelType, Dimension > OutputImageType;
typedef itk::CastImageFilter<
MovingImageType,
OutputImageType > CastFilterType;
typedef itk::ImageFileWriter< OutputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName( argv[3] );
caster->SetInput( warper->GetOutput() );
writer->SetInput( caster->GetOutput() );
writer->Update();
if( argc > 4 ) // if a fourth line argument has been provided...
{
typedef itk::ImageFileWriter< DeformationFieldType > FieldWriterType;
FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
fieldWriter->SetFileName( argv[4] );
fieldWriter->SetInput( multires->GetOutput() );
try
{
fieldWriter->Update();
}
catch ( itk::ExceptionObject e )
{
e.Print( std::cerr );
}
}
return 0;
}