127 implement mims by frey-perez · Pull Request #193 · childmindresearch/wristpy

frey-perez · 2025-05-06T18:22:01Z

Resolves Task: Implement Monitor Independent Monitor Summary unit (MIMS) #127

* testing time values, adding test data from R. * testing values * changed interpolate test to correlation * doc strings * ruff error. * failing matrix test for older version of polars. * interpolation correction * testing values * review changes + added md file from old branch. * typo. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* step 1: find maxed out probabilities * All major steps before final interpolation. * minor renaming * working version, partially updated doc strings. * initial testing * Doc strings * further testing, doc strings changes. * Final testing, error checks in metrics. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Superfluous print statements, doc string edit. * minor parameter changes * scipy ruff error * removing.whl * github actions- ruff- scipy issue. * initial changes. * superfluous * formatting --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* step 1: find maxed out probabilities * All major steps before final interpolation. * minor renaming * working version, partially updated doc strings. * initial testing * Doc strings * further testing, doc strings changes. * Final testing, error checks in metrics. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Superfluous print statements, doc string edit. * minor parameter changes * scipy ruff error * removing.whl * github actions- ruff- scipy issue. * initial changes. * superfluous * formatting * butterworth_filter * aggregate+filter * basic test, test data. * further testing. * Final testing, doc strings. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * set sorted error * np.trapezoid error, imports error. * mypy errors * numpy timestamps normalization. * max value issue * max_value second fix. * Max value aggregatoin bug. * scipy trapezoid replacing numpy implementation * missed an instance of np.trapezoid. * variable name change. * doc string change. * tuple fix, other comments. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

* independent mims module. * combined_mims * sample_data * overall test * paramertrize * documentation * note on extra timestamp * spacing. * documentation * test error * Update src/wristpy/processing/mims.py Co-authored-by: Adam Santorelli <148909356+Asanto32@users.noreply.github.com> * seperate mims testing. * moving fixtures, reorganized testing. * epochs are floats, truncation moved, new truncation argument. * doc change. * doc string, type hinting. * typing error. * updated markdown. * markdown capitalization. * doc string --------- Co-authored-by: Adam Santorelli <148909356+Asanto32@users.noreply.github.com>

…arch/wristpy into 127-implement-mims

codecov · 2025-05-06T18:31:21Z

Codecov Report

Attention: Patch coverage is 95.37037% with 10 lines in your changes missing coverage. Please review.

Project coverage is 95.96%. Comparing base (8ae0163) to head (4f04c46).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
src/wristpy/processing/mims.py	95.74%	8 Missing ⚠️
src/wristpy/core/orchestrator.py	85.71%	1 Missing ⚠️
src/wristpy/io/readers/readers.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #193      +/-   ##
==========================================
- Coverage   96.14%   95.96%   -0.19%     
==========================================
  Files          13       14       +1     
  Lines         778      991     +213     
==========================================
+ Hits          748      951     +203     
- Misses         30       40      +10

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Asanto32 · 2025-05-20T14:36:28Z

        thresholds = thresholds or (0.029, 0.338, 0.604)
    elif activity_metric == "ag_count":
        thresholds = thresholds or (100, 3000, 5200)
+    elif activity_metric == "mims":


Can probably add a test for mims in test_orchestrator? To make sure it handles the dynamic range/thresholds properly?

Co-authored-by: Adam Santorelli <148909356+Asanto32@users.noreply.github.com>

…arch/wristpy into 127-implement-mims

reindervdw-cmi · 2025-05-21T13:47:01Z

+
+            else:
+                right = right[1:]
+


should this have an elif abs(len(left) - len(right)) > 1 error handler?

should be covered by the error handling at the top of the function right?

if np.abs(len(left) - len(right)) >= 2: raise ValueError( f"Mismatch in {sign} edges. # left: {len(left)}, # right: {len(right)}" )

reindervdw-cmi · 2025-05-21T13:48:18Z

+
+    Args:
+        marker_length: Length of marker array.
+        left: indices indicating the left edge of a potential maxed-out region.


Define that these are vectors (assuming that they are indeed 1-dimensional vectors)

reindervdw-cmi · 2025-05-21T13:49:57Z

+    non_maxed_out_mask = np.abs(marker) < confidence_threshold
+    num_non_maxed = np.sum(non_maxed_out_mask)
+
+    if num_non_maxed / len(marker) < 0.3:


where does this 0.3 "magic" value come from

https://github.com/mHealthGroup/MIMSunit/blob/master/R/extrapolate.R#L686-L689

That's the threshold they used for this here, didn't find any particular justification.

reindervdw-cmi · 2025-05-21T14:15:27Z


+    dynamic_range = _extract_dynamic_range(
+        metadata=data["metadata"],
+        file_type=file_type,  # type: ignore


make the type ignore specific

frey-perez and others added 13 commits January 17, 2025 10:33

first portion of algorithm

e45a2d3

interpolation correction

a41a24d

removing place holders

3def235

removing placeholder

f86e31a

All changes for implementing MIMS

4257962

Merge branch '127-implement-mims' of https://github.com/childmindrese…

c8eba12

…arch/wristpy into 127-implement-mims

organize imports

3fbf9af

regenerating lock file.

14a335a

ruff error.

122f597

frey-perez added 14 commits May 8, 2025 16:26

adding mims to cli, adding device range to watchdata.

4fb8aec

documentation

a65f83f

citation for threshold values for mims.

b95ce39

deleted leftover truncation, truncation happens in aggregate_mims.

3cdc786

timestamp fix

cf98353

metric added to run_dir

24a91f9

testing for readerss helper function.

63a76dd

ruff error.

68c8aa1

dynamic range change, literal casting.

7e33a83

import block

0a8fc3a

doc string.

b9b293c

Merge remote-tracking branch 'origin/main' into 127-implement-mims

a58181e

mypy issue with float vs np. float

94950db

mypy literal issue

c08fc68

frey-perez marked this pull request as ready for review May 16, 2025 15:54

frey-perez requested a review from Asanto32 May 16, 2025 15:54

frey-perez requested a review from reindervdw-cmi May 16, 2025 15:54

Merge remote-tracking branch 'origin/main' into 127-implement-mims

b78e02e

Asanto32 reviewed May 20, 2025

View reviewed changes

Comment thread tests/unit/test_readers.py Outdated

Asanto32 reviewed May 20, 2025

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Comment thread src/wristpy/core/cli.py Outdated

Asanto32 reviewed May 20, 2025

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Comment thread src/wristpy/core/orchestrator.py Outdated

frey-perez and others added 3 commits May 20, 2025 17:58

Update src/wristpy/core/orchestrator.py

d9b66dc

Co-authored-by: Adam Santorelli <148909356+Asanto32@users.noreply.github.com>

adam review.

7bee464

Merge branch '127-implement-mims' of https://github.com/childmindrese…

023ec70

…arch/wristpy into 127-implement-mims

reindervdw-cmi requested changes May 21, 2025

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reindervdw-cmi reviewed May 21, 2025

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frey-perez added 3 commits May 23, 2025 13:22

review changes.

b178ed3

unused import.

4f1374b

doc change.

4f04c46

frey-perez requested review from Asanto32 and reindervdw-cmi May 23, 2025 18:39

reindervdw-cmi approved these changes Jun 3, 2025

View reviewed changes

frey-perez merged commit 4ed8686 into main Jun 6, 2025
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frey-perez deleted the 127-implement-mims branch June 6, 2025 17:27

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127 implement mims#193

127 implement mims#193
frey-perez merged 34 commits into
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frey-perez commented May 6, 2025 •

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