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/* Copyright (c) 2008-2022 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 "file/config.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
// Default b-value threshold for a shell to be classified as "b=0"
#define DWI_SHELLS_BZERO_THREHSOLD 10.0
//CONF option: BZeroThreshold
//CONF default: 10.0
//CONF Specifies the b-value threshold for determining those image
//CONF volumes that correspond to b=0.
//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;
FORCE_INLINE default_type bzero_threshold () {
static const default_type value = File::Config::get_float ("BZeroThreshold", DWI_SHELLS_BZERO_THREHSOLD);
return value;
}
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 < 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
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