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
|
/*=========================================================================
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 "itkMedianImageFilter.h"
#include "itkSmoothingRecursiveGaussianImageFilter.h"
#include "ReadWriteData.h"
namespace ants
{
template <unsigned int ImageDimension>
int
SmoothImage(int argc, char * argv[])
{
using PixelType = float;
using ImageType = itk::Image<PixelType, ImageDimension>;
std::vector<float> sigmaVector = ConvertVector<float>(argv[3]);
typename ImageType::Pointer image1 = nullptr;
typename ImageType::Pointer varimage = nullptr;
ReadImage<ImageType>(image1, argv[2]);
using rgf = itk::SmoothingRecursiveGaussianImageFilter<ImageType, ImageType>;
using medf = itk::MedianImageFilter<ImageType, ImageType>;
typename rgf::Pointer filter = rgf::New();
typename medf::Pointer filter2 = medf::New();
typename rgf::SigmaArrayType sigmaArray;
auto & spacing = image1->GetSpacing();
// If true, sigma is in spacing units (usually mm), not voxels
// The recursive filter wants a sigma in mm so we convert if given voxels
bool sigmaInSpacingUnits = false;
if (argc > 5)
{
sigmaInSpacingUnits = std::stoi(argv[5]);
}
bool usemedian = false;
if (argc > 6)
{
usemedian = std::stoi(argv[6]);
}
if (!usemedian)
{
if ((sigmaVector.size() == ImageDimension) || (sigmaVector.size() == 1))
{
for (unsigned int d = 0; d < ImageDimension; d++)
{
if (sigmaVector.size() == 1)
{
if (sigmaInSpacingUnits)
{
sigmaArray[d] = sigmaVector[0];
}
else
{
sigmaArray[d] = sigmaVector[0] * static_cast<float>(spacing[d]);
}
}
else if (sigmaInSpacingUnits)
{
sigmaArray[d] = sigmaVector[d];
}
else
{
sigmaArray[d] = sigmaVector[d] * static_cast<float>(spacing[d]);
}
}
filter->SetSigmaArray(sigmaArray);
}
else
{
std::cerr << "Incorrect sigma vector size. Must either be of size 1 or ImageDimension." << std::endl;
}
filter->SetInput(image1);
filter->Update();
varimage = filter->GetOutput();
}
else
{
typename ImageType::SizeType rad;
if (sigmaVector.size() == 1)
{
rad.Fill(static_cast<unsigned long>(sigmaVector[0]));
}
else if (sigmaVector.size() == ImageDimension)
{
for (unsigned int d = 0; d < ImageDimension; d++)
{
rad[d] = sigmaVector[d];
}
}
else
{
std::cerr << "Incorrect sigma vector size. Must either be of size 1 or ImageDimension." << std::endl;
}
filter2->SetRadius(rad);
filter2->SetInput(image1);
filter2->Update();
varimage = filter2->GetOutput();
}
ANTs::WriteImage<ImageType>(varimage, argv[4]);
return EXIT_SUCCESS;
}
// entry point for the library; parameter 'args' is equivalent to 'argv' in (argc,argv) of commandline parameters to
// 'main()'
int
SmoothImage(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(), "SmoothImage");
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: " << std::endl;
std::cout
<< argv[0]
<< " ImageDimension image.ext smoothingsigma outimage.ext {sigma-is-in-spacing-units-(0)/1} {medianfilter-(0)/1}"
<< std::endl;
std::cout << " If using median filter, sigma is the radius of filtering, in voxels " << std::endl;
std::cout << " A separate sigma can be specified for each dimension, e.g., 1.5x1x2 " << 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;
}
switch (std::stoi(argv[1]))
{
case 2:
{
return SmoothImage<2>(argc, argv);
}
break;
case 3:
{
return SmoothImage<3>(argc, argv);
}
break;
case 4:
{
return SmoothImage<4>(argc, argv);
}
break;
default:
std::cout << "Unsupported dimension" << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
} // namespace ants
|
