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
|
/*
* Copyright (c) 2008-2018 the MRtrix3 contributors.
*
* This Source Code Form is subject to the terms of the Mozilla Public
* License, v. 2.0. If a copy of the MPL was not distributed with this
* file, you can obtain one at http://mozilla.org/MPL/2.0/
*
* MRtrix3 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
*
* For more details, see http://www.mrtrix.org/
*/
#include "command.h"
#include "datatype.h"
#include "image.h"
#include "adapter/replicate.h"
#include "algo/loop.h"
#include "file/ofstream.h"
using namespace MR;
using namespace App;
void usage ()
{
AUTHOR = "Robert E. Smith (robert.smith@florey.edu.au)";
SYNOPSIS = "Print out the values within an image";
DESCRIPTION
+ "If no destination file is specified, the voxel locations will be "
"printed to stdout.";
ARGUMENTS
+ Argument ("input", "the input image.").type_image_in()
+ Argument ("output", "the (optional) output text file.").type_file_out().optional();
OPTIONS
+ Option ("mask", "only write the image values within voxels specified by a mask image")
+ Argument ("image").type_image_in();
}
template <typename T, class StreamType>
void write (Image<T>& image, StreamType& out)
{
for (auto l = Loop(image) (image); l; ++l)
out << image.value() << "\n";
}
template <typename T, class StreamType>
void write (Image<T> image, Image<bool>& mask, StreamType& out)
{
if (!mask.valid()) {
write (image, out);
return;
}
Adapter::Replicate<Image<bool>> replicate (mask, image);
for (auto l = Loop(image) (image, replicate); l; ++l) {
if (replicate.value())
out << image.value() << "\n";
}
}
template <class StreamType>
void write (Header& header, Image<bool>& mask, StreamType& out)
{
switch (uint8_t(DataType(header.datatype())()) & ~(DataType::BigEndian | DataType::LittleEndian | DataType::Complex)) {
case DataType::Bit: case DataType::UInt8: case DataType::UInt16: case DataType::UInt32:
write (header.get_image<uint32_t>(), mask, out);
break;
case DataType::Int8: case DataType::Int16: case DataType::Int32:
write (header.get_image<int32_t>(), mask, out);
break;
case DataType::UInt64: write (header.get_image<uint64_t>(), mask, out); break;
case DataType::Int64: write (header.get_image<int64_t>(), mask, out); break;
case DataType::Float32:
if (header.datatype().is_complex())
write (header.get_image<cfloat>(), mask, out);
else
write (header.get_image<float>(), mask, out);
break;
case DataType::Float64:
if (header.datatype().is_complex())
write (header.get_image<cdouble>(), mask, out);
else
write (header.get_image<double>(), mask, out);
break;
default:
throw Exception ("Unknown data type: " + std::string(header.datatype().description()) + " (" + str(uint32_t(uint8_t(DataType(header.datatype())()))) + ")");
}
}
void run ()
{
auto H = Header::open (argument[0]);
Image<bool> mask;
auto opt = get_options ("mask");
if (opt.size())
mask = Image<bool>::open (opt[0][0]);
if (argument.size() == 2) {
File::OFStream out (argument[1]);
write (H, mask, out);
} else {
write (H, mask, std::cout);
}
}
|
