New commands: peaksconvert, peakscheck #2918
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| // TODO Do we need to support both mathematics and physics conventions for spherical coordinates? | ||
| // And if so, where do we do it? | ||
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| const char *const formats[] = {"unitspherical", "spherical", "unit3vector", "3vector", nullptr}; |
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warning: do not declare C-style arrays, use std::array<> instead [cppcoreguidelines-avoid-c-arrays]
const char *const formats[] = {"unitspherical", "spherical", "unit3vector", "3vector", nullptr};
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| const char *const formats[] = {"unitspherical", "spherical", "unit3vector", "3vector", nullptr}; | ||
| enum class format_t { UNITSPHERICAL, SPHERICAL, UNITTHREEVECTOR, THREEVECTOR }; | ||
| const char *const references[] = {"xyz", "ijk", "bvec", nullptr}; |
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warning: do not declare C-style arrays, use std::array<> instead [cppcoreguidelines-avoid-c-arrays]
const char *const references[] = {"xyz", "ijk", "bvec", nullptr};
^| OPTIONS | ||
| + OptionGroup ("Options providing information about the input image") | ||
| + Option ("in_format", "specify the format in which the input directions are specified") | ||
| + Argument("choice").type_choice(formats) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("choice").type_choice(formats)
^| + Argument("choice").type_choice(formats) | ||
| + Option ("in_reference", "specify the reference axes against which the input directions are specified" | ||
| " (assumed to be real / scanner space if omitted)") | ||
| + Argument("choice").type_choice(references) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("choice").type_choice(references)
^| + OptionGroup ("Options providing information about the output image") | ||
| + Option ("out_format", "specify the format in which the output directions will be specified" | ||
| " (will default to 3-vectors if omitted)") | ||
| + Argument("choice").type_choice(formats) |
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warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]
+ Argument("choice").type_choice(formats)
^| } | ||
| }; | ||
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| class ThreeVector : public FormatBase<3> { |
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warning: destructor of 'ThreeVector' is public and non-virtual [cppcoreguidelines-virtual-class-destructor]
class ThreeVector : public FormatBase<3> {
^Additional context
cmd/peaksconvert.cpp:160: make it public and virtual
class ThreeVector : public FormatBase<3> {
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| class ThreeVector : public FormatBase<3> { | ||
| public: | ||
| ThreeVector(Eigen::Matrix<default_type, 3, 1> in) : FormatBase(in), threevector(in) {} |
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warning: the parameter 'in' is copied for each invocation but only used as a const reference; consider making it a const reference [performance-unnecessary-value-param]
| ThreeVector(Eigen::Matrix<default_type, 3, 1> in) : FormatBase(in), threevector(in) {} | |
| ThreeVector(const Eigen::Matrix<default_type, 3, 1>& in) : FormatBase(in), threevector(in) {} |
| Eigen::Matrix<default_type, 3, 1> operator()() const override { return threevector; } | ||
| Eigen::Matrix<default_type, 3, 1> normalized() const { return threevector.normalized(); } | ||
| default_type radius() const { return threevector.norm(); } | ||
| Eigen::Vector3d threevector; |
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warning: member variable 'threevector' has public visibility [misc-non-private-member-variables-in-classes]
Eigen::Vector3d threevector;
^| Eigen::Vector3d unit_threevector_xyz; | ||
| default_type radius; | ||
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| static transform_linear_type in_ijk2xyz; |
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warning: variable 'in_ijk2xyz' is non-const and globally accessible, consider making it const [cppcoreguidelines-avoid-non-const-global-variables]
static transform_linear_type in_ijk2xyz;
^| default_type radius; | ||
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| static transform_linear_type in_ijk2xyz; | ||
| static bool in_bvec_flipi; |
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warning: variable 'in_bvec_flipi' is non-const and globally accessible, consider making it const [cppcoreguidelines-avoid-non-const-global-variables]
static bool in_bvec_flipi;
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Draft PR.
Depends on #2917 (uses that as base branch).
This is work that I deemed necessary for BIDS BEP016 DWI models (bids-standard/bids-bep016#24).
To have any kind of confidence around robust encoding of the outcomes of diffusion model fits on the filesystem, in my mind there are two requirements:
This necessitates a broader set of data. Showing that for one data instance, the purported coordinate system seems reasonable, is not evidence that in some other use case the interpretation will be incorrect.
Here I've created two new commands, that are requisite for later parts of this validation tool.
peaksconvertconverts both between different reference frames, and between 3-vector versus spherical coordinate encodings. This for instance should allow loading the outcomes of diffusion model fits from FSL and MRtrix in the converse software.peakscheckdoes something similar todwigradcheck, just usingpeaksimages andtckgen -algorithm fact. Similar to dwigradcheck: Enhancements #2902 (which happened during the course of generating this changeset) the set of possible errors in encoding that are evaluated can be more complex than just axis permutations and flips.Outstanding TODOs, many of which are plucked from code comments:
Deep in the spherical coordinates handling, the prospect of a triplet of spherical coefficients appears, where the third element is inferred to be a radius. This is however contrary to ISO convention, where the first element should be the radius. Would need to audit what code uses it, but I would like to consider changing that behaviour. Potentially to avoid unexpected errors, revert those functions to only consider unit spherical coordinates, and have newly named functions that deal with the prospect of triplets?
For spherical coordinates, should support for both physics and mathematics conventions be implemented?
peakschecktests for the prospect of swapping the order of the two angles; but permitting explicit specification of which of the two is in use may be preferable (relates to Spherical coordinates convention bids-standard/bids-bep016#96).Give
peaksconvertability to change fill value of absent fixelsGive
peaksconvertability to reduce maximal number of fixelsHypothetically, this could be done either by culling volumes, or by first sorting by the value per fixel (as 3-vector norm or spherical radius) and then removing
Multi-thread
peaksconvertCheck whether
peaksconvertworks across bootstrap realisations, if those realisations appear along the fifth image axis(In BEP016 I want to define explicitly if an image axis is used to encode orientation information vs. if an image axis is used to encode bootstrap realisations; see Bootstrapping bids-standard/bids-bep016#38. But that may not necessarily propagate to MRtrix)
peakscheck: Try to catch case where upstream there has been an erroneous transformation; eg. someone has orientations in IJK, they erroneously applied an XYZ2IJK transformation, and so now they need to apply the IJK2XYZ transformation twice to get their orientations in MRtrix's expected XYZpeakscheck: Reduce doubling-up between ijk and bvec reference frames.Ideally evaluate each unique transformation only once; there may however be multiple interpretations to a unique transformation.
peakscheck: Add-in_referenceoption; the variant that includes the corresponding transformation to XYZ should then be considered the "expected" interpretation of the input data, used to determine whether the return code should be non-zero.Add ability to disable internal transform realignment on image load via environment variable; make use of this in
peakscheck