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
|
#ifndef itkantsReadWriteTransform_h
#define itkantsReadWriteTransform_h
#include "itkDisplacementFieldTransform.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "itkTransformFileReader.h"
#include "itkTransformFileWriter.h"
#include "itkCompositeTransform.h"
namespace itk
{
namespace ants
{
template <class T, unsigned VImageDimension>
typename itk::Transform<T, VImageDimension, VImageDimension>::Pointer
ReadTransform(const std::string & filename,
const bool useStaticCastForR = false) // This parameter changes to true by the programs that use R, so this code
// returns a different output for them.
{
// We must explicitly check for file existance because failed reading is an acceptable
// state for non-displacment feilds.
if( !itksys::SystemTools::FileExists( filename.c_str() ) )
{
std::cerr << "Transform file does not exist: " << filename << std::endl;
return ITK_NULLPTR;
}
bool hasTransformBeenRead = false;
typedef typename itk::DisplacementFieldTransform<T, VImageDimension> DisplacementFieldTransformType;
typedef typename DisplacementFieldTransformType::DisplacementFieldType DisplacementFieldType;
typedef itk::ImageFileReader<DisplacementFieldType> DisplacementFieldReaderType;
typename DisplacementFieldReaderType::Pointer fieldReader = DisplacementFieldReaderType::New();
// There are known tranform type extentions that should not be considered as imaging files
// That would be used as deformatino feilds
// If file is an hdf5 file, assume it is a tranform instead of an image.
if( filename.find(".h5") == std::string::npos
&& filename.find(".hdf5") == std::string::npos
&& filename.find(".hdf4") == std::string::npos
&& filename.find(".mat") == std::string::npos
&& filename.find(".txt") == std::string::npos
)
{
try
{
fieldReader->SetFileName( filename.c_str() );
fieldReader->Update();
hasTransformBeenRead = true;
}
catch( ... )
{
hasTransformBeenRead = false;
}
}
typedef typename itk::Transform<T, VImageDimension, VImageDimension> TransformType;
typename TransformType::Pointer transform;
if( hasTransformBeenRead )
{
typename DisplacementFieldTransformType::Pointer displacementFieldTransform =
DisplacementFieldTransformType::New();
displacementFieldTransform->SetDisplacementField( fieldReader->GetOutput() );
transform = dynamic_cast<TransformType *>( displacementFieldTransform.GetPointer() );
}
else
{
typename itk::TransformFileReaderTemplate<T>::Pointer transformReader
= itk::TransformFileReaderTemplate<T>::New();
transformReader->SetFileName( filename.c_str() );
try
{
transformReader->Update();
}
catch( const itk::ExceptionObject & e )
{
std::cerr << "Transform reader for "
<< filename << " caught an ITK exception:\n";
e.Print( std::cerr );
return transform;
}
catch( const std::exception & e )
{
std::cerr << "Transform reader for "
<< filename << " caught an exception:\n";
std::cerr << e.what() << std::endl;
return transform;
}
catch( ... )
{
std::cerr << "Transform reader for "
<< filename << " caught an unknown exception!!!\n";
return transform;
}
const typename itk::TransformFileReaderTemplate<T>::TransformListType * const listOfTransforms =
transformReader->GetTransformList();
transform = dynamic_cast<TransformType *>( listOfTransforms->front().GetPointer() );
/** below is a bad thing but it's the only temporary fix i could find for ANTsR on unix --- B.A. */
if ( transform.IsNull() && ( useStaticCastForR == true ) )
{
transform = static_cast<TransformType *>( listOfTransforms->front().GetPointer() );
}
}
return transform;
}
template <class T, unsigned int VImageDimension>
int
WriteTransform(typename itk::Transform<T, VImageDimension, VImageDimension>::Pointer & xfrm,
const std::string & filename)
{
typedef typename itk::DisplacementFieldTransform<T, VImageDimension> DisplacementFieldTransformType;
typedef typename DisplacementFieldTransformType::DisplacementFieldType DisplacementFieldType;
typedef typename itk::ImageFileWriter<DisplacementFieldType> DisplacementFieldWriter;
typedef itk::TransformFileWriterTemplate<T> TransformWriterType;
DisplacementFieldTransformType *dispXfrm =
dynamic_cast<DisplacementFieldTransformType *>(xfrm.GetPointer() );
// if it's a displacement field transform
try
{
if( dispXfrm != ITK_NULLPTR )
{
typename DisplacementFieldType::Pointer dispField = dispXfrm->GetModifiableDisplacementField();
typename DisplacementFieldWriter::Pointer writer = DisplacementFieldWriter::New();
writer->SetInput(dispField);
writer->SetFileName(filename.c_str() );
writer->Update();
}
else
// regular transform
{
typename TransformWriterType::Pointer transformWriter = TransformWriterType::New();
transformWriter->SetInput(xfrm);
transformWriter->SetFileName(filename.c_str() );
transformWriter->Update();
}
}
catch( itk::ExceptionObject & err )
{
std::cerr << "Can't write transform file " << filename << std::endl;
std::cerr << "Exception Object caught: " << std::endl;
std::cerr << err << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
} // namespace itk
#endif // itkantsReadWriteTransform_h
|
