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[ENH]: Complexity features #145

Merged
merged 94 commits into from
Nov 15, 2023
Merged

[ENH]: Complexity features #145

merged 94 commits into from
Nov 15, 2023

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omidvarnia
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@omidvarnia omidvarnia commented Nov 24, 2022

This PR adds seven complexity measures, i.e., range entropy and its AUC, permutation entropy, sample entropy, multiscale entropy and its AUC, and Hurst exponent.

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codecov bot commented Nov 24, 2022

Codecov Report

Merging #145 (563acde) into main (69d17a7) will decrease coverage by 0.24%.
The diff coverage is 85.94%.

Additional details and impacted files

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@@            Coverage Diff             @@
##             main     #145      +/-   ##
==========================================
- Coverage   90.04%   89.80%   -0.24%     
==========================================
  Files          90       99       +9     
  Lines        4118     4367     +249     
  Branches      811      842      +31     
==========================================
+ Hits         3708     3922     +214     
- Misses        286      305      +19     
- Partials      124      140      +16     
Flag Coverage Δ
docs 100.00% <ø> (ø)
junifer 89.80% <85.94%> (-0.24%) ⬇️

Flags with carried forward coverage won't be shown. Click here to find out more.

Files Coverage Δ
docs/conf.py 100.00% <ø> (ø)
junifer/markers/utils.py 90.47% <ø> (ø)
junifer/markers/complexity/complexity_base.py 96.00% <96.00%> (ø)
junifer/markers/complexity/__init__.py 81.81% <81.81%> (ø)
...nifer/markers/complexity/multiscale_entropy_auc.py 87.09% <87.09%> (ø)
junifer/markers/complexity/perm_entropy.py 85.71% <85.71%> (ø)
junifer/markers/complexity/range_entropy.py 86.66% <86.66%> (ø)
junifer/markers/complexity/range_entropy_auc.py 89.18% <89.18%> (ø)
junifer/markers/complexity/sample_entropy.py 87.09% <87.09%> (ø)
...unifer/markers/complexity/weighted_perm_entropy.py 85.71% <85.71%> (ø)
... and 1 more

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github-actions bot commented Nov 24, 2022

PR Preview Action v1.4.4
Preview removed because the pull request was closed.
2023-11-15 17:28 UTC

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@omidvarnia Can you create one marker per measure? The way it is right now is one marker to rule them all. Junifer's philosophy is to have specific markers with minimal parametrisation.

@synchon synchon added enhancement New feature or request marker Issues or pull requests related to markers WIP Work in progress and removed marker Issues or pull requests related to markers labels Jan 17, 2023
@synchon synchon force-pushed the complexity_features branch 3 times, most recently from 5ab727d to df5c96e Compare January 19, 2023 16:07
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@omidvarnia

  • The tests are failing for storage and I believe it has something to do with how the marker computation output is being manipulated, would be good if you take a look.
  • Would be great if you also take a look at [ENH]: Support for multiple computed masks #175 for handling the mask parameter.

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@synchon synchon requested a review from fraimondo January 19, 2023 16:18
@synchon synchon added ready Pull request is ready for review and merge and removed WIP Work in progress labels Jan 19, 2023
@synchon synchon force-pushed the complexity_features branch from d9633f6 to 5ea9195 Compare January 30, 2023 09:55
@synchon synchon force-pushed the complexity_features branch from 951f9d0 to 83a2fa5 Compare March 3, 2023 13:06
@synchon synchon added the marker Issues or pull requests related to markers label Mar 3, 2023
@fraimondo fraimondo marked this pull request as draft March 30, 2023 16:28
@synchon synchon removed the ready Pull request is ready for review and merge label Jul 7, 2023
@synchon synchon force-pushed the complexity_features branch from 736a65b to 486c6db Compare October 27, 2023 15:21
@synchon synchon changed the title Complexity features [ENH]: Complexity features Oct 27, 2023
@synchon synchon marked this pull request as ready for review October 27, 2023 15:24
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synchon commented Oct 27, 2023

Needs to wait for #269, but should be good for review.

junifer/markers/complexity/hurst_exponent.py Show resolved Hide resolved
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junifer/markers/__init__.py Outdated Show resolved Hide resolved
…opy, permutation entropy, and weighted permutation entropy. To be tested and verified.
…ropy and its weighted version, sample entropy, AUC od multiscale entropy, and Hurst exponent) were added to the Complexity class of markers.
@synchon synchon force-pushed the complexity_features branch from eb174fb to a8fb07d Compare November 13, 2023 11:53
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synchon commented Nov 13, 2023

@fraimondo I've adapted the imports and everything else as we discussed, should be good for a review. I'll fix the tests in the meantime.

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@synchon synchon merged commit 50d0f97 into main Nov 15, 2023
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@synchon synchon deleted the complexity_features branch November 17, 2023 09:46
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[MARKER]: Add complexity features
3 participants