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
|
/* Copyright (c) 2008-2025 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/.
*
* Covered Software is provided under this License on an "as is"
* basis, without warranty of any kind, either expressed, implied, or
* statutory, including, without limitation, warranties that the
* Covered Software is free of defects, merchantable, fit for a
* particular purpose or non-infringing.
* See the Mozilla Public License v. 2.0 for more details.
*
* For more details, see http://www.mrtrix.org/.
*/
#ifndef __dwi_shells_h__
#define __dwi_shells_h__
#include <fstream>
#include <limits>
#include "app.h"
#include "types.h"
#include "dwi/gradient.h"
#include "misc/bitset.h"
// Don't expect these values to change depending on the particular command that is initialising the Shells class;
// method should be robust to all incoming data
// Maximum absolute difference in b-value for two volumes to be considered to be in the same shell
#define DWI_SHELLS_EPSILON 80
// Minimum number of volumes within DWI_SHELL_EPSILON necessary to continue expansion of the cluster selection
#define DWI_SHELLS_MIN_LINKAGE 3
// Default number of volumes necessary for a shell to be retained
// (note: only applies if function reject_small_shells() is called explicitly)
#define DWI_SHELLS_MIN_DIRECTIONS 6
//CONF option: BValueEpsilon
//CONF default: 80.0
//CONF Specifies the difference between b-values necessary for image
//CONF volumes to be classified as belonging to different shells.
namespace MR
{
namespace App { class OptionGroup; }
namespace DWI
{
extern const App::OptionGroup ShellsOption;
class Shell
{ NOMEMALIGN
public:
Shell() : mean (0.0), stdev (0.0), min (0.0), max (0.0) { }
Shell (const Eigen::MatrixXd& grad, const vector<size_t>& indices);
const vector<size_t>& get_volumes() const { return volumes; }
size_t count() const { return volumes.size(); }
default_type get_mean() const { return mean; }
default_type get_stdev() const { return stdev; }
default_type get_min() const { return min; }
default_type get_max() const { return max; }
bool is_bzero() const { return (mean <= MR::DWI::bzero_threshold()); }
bool operator< (const Shell& rhs) const { return (mean < rhs.mean); }
friend std::ostream& operator<< (std::ostream& stream, const Shell& S)
{
stream << "Shell: " << S.volumes.size() << " volumes, b-value "
<< S.mean << " +- " << S.stdev << " (range [" << S.min << " - " << S.max << "])";
return stream;
}
protected:
vector<size_t> volumes;
default_type mean, stdev, min, max;
};
class Shells
{ NOMEMALIGN
public:
Shells (const Eigen::MatrixXd& grad);
const Shell& operator[] (const size_t i) const { return shells[i]; }
const Shell& smallest() const { return shells.front(); }
const Shell& largest() const { return shells.back(); }
size_t count() const { return shells.size(); }
size_t volumecount() const {
size_t count = 0;
for (const auto& it : shells)
count += it.count();
return count;
}
vector<size_t> get_counts() const {
vector<size_t> c (count());
for (size_t n = 0; n < count(); ++n)
c[n] = shells[n].count();
return c;
}
vector<size_t> get_bvalues() const {
vector<size_t> b (count());
for (size_t n = 0; n < count(); ++n)
b[n] = shells[n].get_mean();
return b;
}
Shells& select_shells (const bool force_singleshell, const bool force_with_bzero, const bool force_without_bzero);
Shells& reject_small_shells (const size_t min_volumes = DWI_SHELLS_MIN_DIRECTIONS);
bool is_single_shell() const {
// only if exactly 1 non-bzero shell
return ((count() == 1 && !has_bzero()) || (count() == 2 && has_bzero()));
}
bool has_bzero() const {
return smallest().is_bzero();
}
friend std::ostream& operator<< (std::ostream& stream, const Shells& S)
{
stream << "Total of " << S.count() << " DWI shells:" << std::endl;
for (const auto& it : S.shells)
stream << it << std::endl;
return stream;
}
protected:
vector<Shell> shells;
private:
using BValueList = decltype(std::declval<const Eigen::MatrixXd>().col(0));
// Functions for current b-value clustering implementation
size_t clusterBvalues (const BValueList&, vector<size_t>&) const;
void regionQuery (const BValueList&, const default_type, vector<size_t>&) const;
};
}
}
#endif
|
