juaml / junifer

Forschungszentrum Jülich Neuroimaging Feature Extractor
https://juaml.github.io/junifer
GNU Affero General Public License v3.0
14 stars 13 forks source link

[ENH]: Introduce `JuniferConnectivityMeasure` #348

Closed synchon closed 1 month ago

synchon commented 2 months ago

This PR introduces JuniferConnectivityMeasure, tailored nilearn.connectome.ConnectivityMeasure for junifer. This sets sklearn.covariance.EmpiricalCovariance as the default covariance estimator and correlation as the default connectivity matrix kind, which is what junifer users mostly do. It also sets the ground to add custom connectivity matrix kinds and correlation metrics. Required by #333 and #335 as of now.

codecov[bot] commented 2 months ago

Codecov Report

Attention: Patch coverage is 93.38843% with 8 lines in your changes missing coverage. Please review.

Project coverage is 88.67%. Comparing base (f80c685) to head (6b792b9).

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/juaml/junifer/pull/348/graphs/tree.svg?width=650&height=150&src=pr&token=5H21JuZXMw&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml)](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) ```diff @@ Coverage Diff @@ ## main #348 +/- ## ========================================== + Coverage 88.58% 88.67% +0.08% ========================================== Files 114 115 +1 Lines 5028 5138 +110 Branches 983 1019 +36 ========================================== + Hits 4454 4556 +102 - Misses 418 422 +4 - Partials 156 160 +4 ``` | [Flag](https://app.codecov.io/gh/juaml/junifer/pull/348/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [docs](https://app.codecov.io/gh/juaml/junifer/pull/348/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `100.00% <ø> (ø)` | | | [junifer](https://app.codecov.io/gh/juaml/junifer/pull/348/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | `88.67% <93.38%> (+0.08%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#carryforward-flags-in-the-pull-request-comment) to find out more. | [Files](https://app.codecov.io/gh/juaml/junifer/pull/348?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml) | Coverage Δ | | |---|---|---| | [docs/conf.py](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&filepath=docs%2Fconf.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-ZG9jcy9jb25mLnB5) | `100.00% <ø> (ø)` | | | [junifer/external/nilearn/\_\_init\_\_.py](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&filepath=junifer%2Fexternal%2Fnilearn%2F__init__.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9leHRlcm5hbC9uaWxlYXJuL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [...ivity/crossparcellation\_functional\_connectivity.py](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffunctional_connectivity%2Fcrossparcellation_functional_connectivity.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5L2Nyb3NzcGFyY2VsbGF0aW9uX2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5LnB5) | `100.00% <100.00%> (ø)` | | | [...nnectivity/edge\_functional\_connectivity\_parcels.py](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffunctional_connectivity%2Fedge_functional_connectivity_parcels.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5L2VkZ2VfZnVuY3Rpb25hbF9jb25uZWN0aXZpdHlfcGFyY2Vscy5weQ==) | `100.00% <ø> (ø)` | | | [...nnectivity/edge\_functional\_connectivity\_spheres.py](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffunctional_connectivity%2Fedge_functional_connectivity_spheres.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5L2VkZ2VfZnVuY3Rpb25hbF9jb25uZWN0aXZpdHlfc3BoZXJlcy5weQ==) | `89.47% <ø> (ø)` | | | [...ional\_connectivity/functional\_connectivity\_base.py](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffunctional_connectivity%2Ffunctional_connectivity_base.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5L2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5X2Jhc2UucHk=) | `96.42% <100.00%> (+0.13%)` | :arrow_up: | | [...al\_connectivity/functional\_connectivity\_parcels.py](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffunctional_connectivity%2Ffunctional_connectivity_parcels.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5L2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5X3BhcmNlbHMucHk=) | `100.00% <ø> (ø)` | | | [...al\_connectivity/functional\_connectivity\_spheres.py](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&filepath=junifer%2Fmarkers%2Ffunctional_connectivity%2Ffunctional_connectivity_spheres.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9tYXJrZXJzL2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5L2Z1bmN0aW9uYWxfY29ubmVjdGl2aXR5X3NwaGVyZXMucHk=) | `100.00% <ø> (ø)` | | | [...r/external/nilearn/junifer\_connectivity\_measure.py](https://app.codecov.io/gh/juaml/junifer/pull/348?src=pr&el=tree&filepath=junifer%2Fexternal%2Fnilearn%2Fjunifer_connectivity_measure.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=juaml#diff-anVuaWZlci9leHRlcm5hbC9uaWxlYXJuL2p1bmlmZXJfY29ubmVjdGl2aXR5X21lYXN1cmUucHk=) | `92.52% <92.52%> (ø)` | |
github-actions[bot] commented 2 months ago

PR Preview Action v1.4.7 :---: Preview removed because the pull request was closed. 2024-07-19 10:27 UTC