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
|
/*=========================================================================
Program: Advanced Normalization Tools
Copyright (c) ConsortiumOfANTS. All rights reserved.
See accompanying COPYING.txt or
https://github.com/stnava/ANTs/blob/master/ANTSCopyright.txt 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.
=========================================================================*/
#include "antsUtilities.h"
#include <algorithm>
#include <iostream>
#include <fstream>
#include <cstdio>
#include "itkImage.h"
#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "itkCastImageFilter.h"
#include "itkRescaleIntensityImageFilter.h"
#include "ReadWriteData.h"
#include "TensorFunctions.h"
namespace ants
{
template <unsigned int ImageDimension>
int
CopyImageHeaderInformation(int argc, char * argv[])
{
using inPixelType = float;
using ImageType = itk::Image<inPixelType, ImageDimension>;
using readertype = itk::ImageFileReader<ImageType>;
typename readertype::Pointer reader = readertype::New();
reader->SetFileName(argv[1]);
reader->Update();
// std::cout << " Spacing " << reader->GetOutput()->GetSpacing() << std::endl;
// std::cout << " Origin " << reader->GetOutput()->GetOrigin() << std::endl;
// std::cout << " Direction " << std::endl << reader->GetOutput()->GetDirection() << std::endl;
// std::cout << " Size " << std::endl << reader->GetOutput()->GetLargestPossibleRegion().GetSize() << std::endl;
bool istensor = false;
if (argc > 7)
{
if (std::stoi(argv[7]))
{
istensor = true;
}
}
if (istensor)
{
using TensorType = itk::Vector<float, 6>;
using TensorFieldType = itk::Image<TensorType, ImageDimension>;
typename TensorFieldType::Pointer timage;
ReadTensorImage<TensorFieldType>(timage, argv[2], false);
// std::cout<< " tim dir " << timage->GetDirection() << std::endl;
if (argc > 6)
{
if (std::stoi(argv[6]))
{
timage->SetSpacing(reader->GetOutput()->GetSpacing());
}
}
if (argc > 5)
{
if (std::stoi(argv[5]))
{
timage->SetOrigin(reader->GetOutput()->GetOrigin());
}
}
if (argc > 4)
{
if (std::stoi(argv[4]))
{
timage->SetDirection(reader->GetOutput()->GetDirection());
}
}
// std::cout<< " tim dir " << timage->GetDirection() << std::endl;
WriteTensorImage<TensorFieldType>(timage, argv[3], false);
return EXIT_SUCCESS;
}
typename readertype::Pointer reader2 = readertype::New();
reader2->SetFileName(argv[2]);
reader2->Update();
// MakeNewImage(typename TImage::Pointer image1, typename TImage::PixelType initval)
typename ImageType::Pointer newimage = MakeNewImage<ImageType>(reader2->GetOutput(), -1);
if (argc > 6)
{
if (std::stoi(argv[6]))
{
newimage->SetSpacing(reader->GetOutput()->GetSpacing());
}
}
if (argc > 5)
{
if (std::stoi(argv[5]))
{
newimage->SetOrigin(reader->GetOutput()->GetOrigin());
}
}
if (argc > 4)
{
if (std::stoi(argv[4]))
{
newimage->SetDirection(reader->GetOutput()->GetDirection());
}
}
ANTs::WriteImage<ImageType>(newimage, argv[3]);
return EXIT_FAILURE;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
CopyImageHeaderInformation(std::vector<std::string> args, std::ostream * /*out_stream = nullptr */)
{
// put the arguments coming in as 'args' into standard (argc,argv) format;
// 'args' doesn't have the command name as first, argument, so add it manually;
// 'args' may have adjacent arguments concatenated into one argument,
// which the parser should handle
args.insert(args.begin(), "CopyImageHeaderInformation");
int argc = args.size();
char ** argv = new char *[args.size() + 1];
for (unsigned int i = 0; i < args.size(); ++i)
{
// allocate space for the string plus a null character
argv[i] = new char[args[i].length() + 1];
std::strncpy(argv[i], args[i].c_str(), args[i].length());
// place the null character in the end
argv[i][args[i].length()] = '\0';
}
argv[argc] = nullptr;
// class to automatically cleanup argv upon destruction
class Cleanup_argv
{
public:
Cleanup_argv(char ** argv_, int argc_plus_one_)
: argv(argv_)
, argc_plus_one(argc_plus_one_)
{}
~Cleanup_argv()
{
for (unsigned int i = 0; i < argc_plus_one; ++i)
{
delete[] argv[i];
}
delete[] argv;
}
private:
char ** argv;
unsigned int argc_plus_one;
};
Cleanup_argv cleanup_argv(argv, argc + 1);
// antscout->set_stream( out_stream );
if (argc < 4)
{
std::cout << "Usage: " << argv[0]
<< " refimage.ext imagetocopyrefimageinfoto.ext imageout.ext boolcopydirection boolcopyorigin "
"boolcopyspacing {bool-Image2-IsTensor}"
<< std::endl;
if (argc >= 2 && (std::string(argv[1]) == std::string("--help") || std::string(argv[1]) == std::string("-h")))
{
return EXIT_SUCCESS;
}
return EXIT_FAILURE;
}
// Get the image dimension
std::string fn = std::string(argv[1]);
itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(fn.c_str(), itk::IOFileModeEnum::ReadMode);
imageIO->SetFileName(fn.c_str());
imageIO->ReadImageInformation();
unsigned int dim = imageIO->GetNumberOfDimensions();
switch (dim)
{
case 2:
{
CopyImageHeaderInformation<2>(argc, argv);
}
break;
case 3:
{
CopyImageHeaderInformation<3>(argc, argv);
}
break;
case 4:
{
CopyImageHeaderInformation<4>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension : " << dim << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
|
