Rename sh2power to sh2metric, new "entropy" operation #2985

Lestropie · 2024-09-03T06:20:14Z

Had previously thought about this from the perspective of registration, but have also been looking at a collaborator dataset where doing satisfactory masking for FBA has been difficult, and using that to revised FBA documentation (#2685).

Here is the WM FOD l=0 image, which you can see doesn't do a very good job of separating what one would like to analyse vs. not:

Then this is the entropy of the WM FOD template (normalised & inverted):

Implement the Spherical Harmonic Entropy (SHE) metric as per:
https://arxiv.org/pdf/1805.08084
This may yield the same or similar result much faster
Add command-line option to modify the direction set that's used for amplitude sampling
Implement entropy operations for:
- mrmath
- fixel2voxel
Revisit templated entropy calculation code
For some reason had trouble specifying the logarithm function as a template. The switch statement should get optimised out by the compiler, but maybe I'll have another go before merging.

Includes checking out a new test data commit that moves existing test data and adds new test data.

github-actions

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github-actions · 2024-09-03T06:24:25Z

cmd/sh2metric.cpp

+
+constexpr size_t default_direction_set = 1281;
+
+std::vector<std::string> metrics = {"entropy", "power"};


warning: variable 'metrics' is non-const and globally accessible, consider making it const [cppcoreguidelines-avoid-non-const-global-variables]

std::vector<std::string> metrics = {"entropy", "power"}; ^

github-actions · 2024-09-03T06:24:26Z

cmd/sh2metric.cpp

+}
+// clang-format on
+
+void run_entropy() {


warning: function 'run_entropy' has cognitive complexity of 30 (threshold 25) [readability-function-cognitive-complexity]

void run_entropy() { ^

Additional context

cmd/sh2metric.cpp:83: +1, including nesting penalty of 0, nesting level increased to 1

for (size_t i = 0; i != argument.size() - 2; ++i) { ^

cmd/sh2metric.cpp:87: +2, including nesting penalty of 1, nesting level increased to 2

if (i == 0) { ^

cmd/sh2metric.cpp:89: +1, nesting level increased to 2

} else { ^

cmd/sh2metric.cpp:90: +3, including nesting penalty of 2, nesting level increased to 3

if (!voxel_grids_match_in_scanner_space(header, H_out)) ^

cmd/sh2metric.cpp:105: nesting level increased to 1

Processor(const std::vector<Image<float>> &SH_images, ^

cmd/sh2metric.cpp:112: +2, including nesting penalty of 1, nesting level increased to 2

for (const auto &i : SH_images) ^

cmd/sh2metric.cpp:116: nesting level increased to 1

Processor(const Processor &that) ^

cmd/sh2metric.cpp:118: +2, including nesting penalty of 1, nesting level increased to 2

for (const auto &i : that.images) ^

cmd/sh2metric.cpp:122: nesting level increased to 1

bool operator()(Iterator &pos) { ^

cmd/sh2metric.cpp:124: +2, including nesting penalty of 1, nesting level increased to 2

for (auto &image : images) { ^

cmd/sh2metric.cpp:128: +3, including nesting penalty of 2, nesting level increased to 3

for (auto l = Loop(3)(image); l; ++l) ^

cmd/sh2metric.cpp:136: +2, including nesting penalty of 1, nesting level increased to 2

} catch (Exception &) { ^

cmd/sh2metric.cpp:154: nesting level increased to 1

Shared(const std::vector<Image<float>> &SH_images, const DWI::Directions::Set &dirs, const bool normalise) ^

cmd/sh2metric.cpp:157: +2, including nesting penalty of 1, nesting level increased to 2

for (ssize_t row = 0; row != dirs.size(); ++row) ^

cmd/sh2metric.cpp:160: +2, including nesting penalty of 1, nesting level increased to 2

for (const auto &i : SH_images) { ^

cmd/sh2metric.cpp:162: +3, including nesting penalty of 2, nesting level increased to 3

if (transforms.find(lmax) == transforms.end()) ^

cmd/sh2metric.cpp:166: +2, including nesting penalty of 1, nesting level increased to 2

if (normalise) ^

cmd/sh2metric.cpp:169: nesting level increased to 1

vector_type operator()(vector_type &SH_coefs) const { ^

cmd/sh2metric.cpp:175: nesting level increased to 1

size_t get_num_dirs() const { return num_dirs; } ^

cmd/sh2metric.cpp:176: nesting level increased to 1

default_type normalise(const default_type in) const { return normalisation(in); } ^

cmd/sh2metric.cpp:184: nesting level increased to 1

Normalisation() ^

cmd/sh2metric.cpp:187: nesting level increased to 1

void initialise(const size_t num_images, const DWI::Directions::Set &dirs, const transform_type transform) { ^

cmd/sh2metric.cpp:200: nesting level increased to 1

default_type operator()(const default_type in) const { ^

cmd/sh2metric.cpp:201: +2, including nesting penalty of 1, nesting level increased to 2

if (!std::isfinite(lower) || !std::isfinite(upper)) ^

cmd/sh2metric.cpp:201: +1

if (!std::isfinite(lower) || !std::isfinite(upper)) ^

cmd/sh2metric.cpp:182: nesting level increased to 1

class Normalisation { ^

cmd/sh2metric.cpp:182: nesting level increased to 1

class Normalisation { ^

cmd/sh2metric.cpp:182: nesting level increased to 1

class Normalisation { ^

cmd/sh2metric.cpp:151: nesting level increased to 1

class Shared { ^

cmd/sh2metric.cpp:151: nesting level increased to 1

class Shared { ^

cmd/sh2metric.cpp:151: nesting level increased to 1

class Shared { ^

cmd/sh2metric.cpp:151: nesting level increased to 1

class Shared { ^

cmd/sh2metric.cpp:151: nesting level increased to 1

class Shared { ^

cmd/sh2metric.cpp:102: nesting level increased to 1

class Processor { ^

cmd/sh2metric.cpp:102: nesting level increased to 1

class Processor { ^

github-actions · 2024-09-03T06:24:26Z

cmd/sh2metric.cpp

+  for (size_t i = 0; i != argument.size() - 2; ++i) {
+    Header header(Header::open(argument[i]));
+    Math::SH::check(header);
+    max_lmax = std::max(max_lmax, Math::SH::LforN(header.size(3)));


warning: narrowing conversion from 'ssize_t' (aka 'long') to signed type 'int' is implementation-defined [bugprone-narrowing-conversions]

max_lmax = std::max(max_lmax, Math::SH::LforN(header.size(3))); ^

github-actions · 2024-09-03T06:24:26Z

cmd/sh2metric.cpp

+  }
+  H_out.ndim() = 3;
+
+  DWI::Directions::Set dirs(default_direction_set);


warning: variable 'dirs' of type 'DWI::Directions::Set' can be declared 'const' [misc-const-correctness]

Suggested change

DWI::Directions::Set dirs(default_direction_set);

DWI::Directions::Set const dirs(default_direction_set);

github-actions · 2024-09-03T06:24:26Z

cmd/sh2metric.cpp

+  H_out.ndim() = 3;
+
+  DWI::Directions::Set dirs(default_direction_set);
+  Image<float> image_out(Image<float>::create(argument[argument.size() - 1], H_out));


warning: variable 'image_out' of type 'Image' can be declared 'const' [misc-const-correctness]

Suggested change

Image<float> image_out(Image<float>::create(argument[argument.size() - 1], H_out));

Image<float> const image_out(Image<float>::create(argument[argument.size() - 1], H_out));

github-actions · 2024-09-03T06:24:27Z

cmd/sh2metric.cpp

+        Normalisation()
+            : lower(std::numeric_limits<default_type>::quiet_NaN()),
+              upper(std::numeric_limits<default_type>::quiet_NaN()) {}
+        void initialise(const size_t num_images, const DWI::Directions::Set &dirs, const transform_type transform) {


warning: the const qualified parameter 'transform' is copied for each invocation; consider making it a reference [performance-unnecessary-value-param]

Suggested change

void initialise(const size_t num_images, const DWI::Directions::Set &dirs, const transform_type transform) {

void initialise(const size_t num_images, const DWI::Directions::Set &dirs, const transform_type& transform) {

github-actions · 2024-09-03T06:24:27Z

cmd/sh2metric.cpp

+        void initialise(const size_t num_images, const DWI::Directions::Set &dirs, const transform_type transform) {
+          Eigen::Matrix<default_type, Eigen::Dynamic, 1> delta_coefs;
+          Math::SH::delta(
+              delta_coefs, Eigen::Matrix<default_type, 3, 1>({0.0, 0.0, 1.0}), Math::SH::LforN(transform.cols()));


warning: narrowing conversion from 'size_t' (aka 'unsigned long') to signed type 'int' is implementation-defined [bugprone-narrowing-conversions]

delta_coefs, Eigen::Matrix<default_type, 3, 1>({0.0, 0.0, 1.0}), Math::SH::LforN(transform.cols())); ^

github-actions · 2024-09-03T06:24:27Z

cmd/sh2metric.cpp

+        void initialise(const size_t num_images, const DWI::Directions::Set &dirs, const transform_type transform) {
+          Eigen::Matrix<default_type, Eigen::Dynamic, 1> delta_coefs;
+          Math::SH::delta(
+              delta_coefs, Eigen::Matrix<default_type, 3, 1>({0.0, 0.0, 1.0}), Math::SH::LforN(transform.cols()));


warning: narrowing conversion from 'Index' (aka 'long') to signed type 'int' is implementation-defined [bugprone-narrowing-conversions]

delta_coefs, Eigen::Matrix<default_type, 3, 1>({0.0, 0.0, 1.0}), Math::SH::LforN(transform.cols())); ^

github-actions · 2024-09-03T06:24:27Z

cmd/sh2metric.cpp

+          //   and pad out zeroes to simulate all other input SH functions being zero
+          Eigen::Matrix<default_type, Eigen::Dynamic, 1> amps = transform * delta_coefs;
+          amps.conservativeResizeLike(
+              Eigen::Matrix<default_type, Eigen::Dynamic, 1>::Zero(num_images * transform.rows()));


warning: narrowing conversion from 'size_t' (aka 'unsigned long') to signed type 'Index' (aka 'long') is implementation-defined [bugprone-narrowing-conversions]

Eigen::Matrix<default_type, Eigen::Dynamic, 1>::Zero(num_images * transform.rows())); ^

github-actions · 2024-09-03T06:24:28Z

cmd/sh2metric.cpp

+              Eigen::Matrix<default_type, Eigen::Dynamic, 1>::Zero(num_images * transform.rows()));
+          lower = Math::Entropy::nits(amps);
+          upper = Math::Entropy::nits(
+              Eigen::Matrix<default_type, Eigen::Dynamic, 1>::Constant(num_images * transform.rows(), 1.0));


warning: narrowing conversion from 'size_t' (aka 'unsigned long') to signed type 'Index' (aka 'long') is implementation-defined [bugprone-narrowing-conversions]

Eigen::Matrix<default_type, Eigen::Dynamic, 1>::Constant(num_images * transform.rows(), 1.0)); ^

Lestropie · 2024-10-08T01:07:30Z

Was potentially a little too idealistic about this metric being useful as a scalar surrogate for multi-contrast registration (as multiple SH images can be provided as input to the entropy calculation). Kind of interesting, and maybe useful in specific use cases such as the unusual template above, but not a game-changer.

Single-subject HCP data:

Rename sh2power to sh2metric, new "entropy" operation

fe604e9

Includes checking out a new test data commit that moves existing test data and adds new test data.

Lestropie added the enhancement label Sep 3, 2024

Lestropie self-assigned this Sep 3, 2024

github-actions bot reviewed Sep 3, 2024

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Rename sh2power to sh2metric, new "entropy" operation #2985

Rename sh2power to sh2metric, new "entropy" operation #2985

Lestropie commented Sep 3, 2024 •

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Lestropie commented Oct 8, 2024


		constexpr size_t default_direction_set = 1281;

		std::vector<std::string> metrics = {"entropy", "power"};

	DWI::Directions::Set dirs(default_direction_set);
	DWI::Directions::Set const dirs(default_direction_set);

	Image<float> image_out(Image<float>::create(argument[argument.size() - 1], H_out));
	Image<float> const image_out(Image<float>::create(argument[argument.size() - 1], H_out));

	void initialise(const size_t num_images, const DWI::Directions::Set &dirs, const transform_type transform) {
	void initialise(const size_t num_images, const DWI::Directions::Set &dirs, const transform_type& transform) {

Rename sh2power to sh2metric, new "entropy" operation #2985

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Rename sh2power to sh2metric, new "entropy" operation #2985

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Lestropie commented Sep 3, 2024 • edited Loading

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Lestropie commented Oct 8, 2024

Lestropie commented Sep 3, 2024 •

edited

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