Update Main from Dev by AlbertoCasasOrtiz · Pull Request #297 · opencap-org/opencap-core

AlbertoCasasOrtiz · 2026-08-06T19:20:22Z

PRs in dev:

Addiotional PRs:

Add exhaustive calibration fallback

Test main pipeline regressions

Close utility file handles

AlbertoCasasOrtiz · 2026-08-06T22:02:07Z

@carmichaelong @csherry04 I just reviewed all files and run tests. I got one test failing because of an assertion error, and I think it is because a really small error in a few values while doing scaling. This seems like float point precision issue or differences in a library version?

OS: Ubuntu 20.04.6 LTS

E           AssertionError:
E           Not equal to tolerance rtol=0, atol=1e-05
E           ('pelvis', 'pelvis_geom_1')
E           Mismatched elements: 3 / 3 (100%)
E           Max absolute difference: 0.00099501
E           Max relative difference: 0.00073795
E            x: array([1.349348, 1.349348, 1.478875])
E            y: array([1.348353, 1.348353, 1.479606])

This is the full test output:

(opencap-core-dev-alberto) clarkadmin@clarkadmin-Alienware-Aurora-Ryzen-Edition:~/Documents/repos-alberto/opencap-core-dev$ python -m pytest ./tests/
============================================================================================== test session starts ==============================================================================================
platform linux -- Python 3.9.20, pytest-8.4.2, pluggy-1.5.0
rootdir: /home/clarkadmin/Documents/repos-alberto/opencap-core-dev
collected 55 items

tests/test_api.py ...                                                                                                                                                                                     [  5%]
tests/test_calibration.py ........                                                                                                                                                                        [ 20%]
tests/test_main.py .......F..                                                                                                                                                                             [ 38%]
tests/test_sync.py ..................................                                                                                                                                                     [100%]

=================================================================================================== FAILURES ====================================================================================================
_____________________________________________________________________________________________ test_neutral_scaling ______________________________________________________________________________________________

tmp_path = PosixPath('/tmp/pytest-of-clarkadmin/pytest-7/test_neutral_scaling0')

    def test_neutral_scaling(tmp_path):
        sessionName = 'sync_2-cameras'
        trialName = 'neutral'
        trialID = trialName
        dataDir = tmp_path
        sessionDir = os.path.join(dataDir, 'Data', sessionName)

        prepare_test_session(
            SYNC_2CAM_DIR,
            sessionDir,
            trialName,
            ['Cam0', 'Cam1'],
            'OutputPkl_default',
        )

        main(
            sessionName,
            trialName,
            trialID,
            cameras_to_use=SYNC_2CAM_NEUTRAL_ORDER,
            dataDir=dataDir,
            genericFolderNames=True,
            scaleModel=True,
            syncVer='1.1',
        )

        output_post_augmentation_trc = os.path.join(
            sessionDir,
            'MarkerData',
            'PostAugmentation',
            f'{trialName}.trc',
        )
        ref_post_augmentation_trc = os.path.join(
            SYNC_2CAM_DIR,
            'MarkerData',
            f'{trialName}.trc',
        )
        compare_trc(output_post_augmentation_trc, ref_post_augmentation_trc, atol=1e-5)

        scaled_model = os.path.join(
            sessionDir,
            'OpenSimData',
            'Model',
            'LaiUhlrich2022_scaled.osim',
        )
        assert os.path.exists(scaled_model)
        ref_scaled_model = os.path.join(
            SYNC_2CAM_DIR,
            'OpenSimData',
            'Model',
            'LaiUhlrich2022_scaled.osim',
        )
>       compare_osim_scales(scaled_model, ref_scaled_model, atol=1e-5)

tests/test_main.py:387:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _

output_osim = '/tmp/pytest-of-clarkadmin/pytest-7/test_neutral_scaling0/Data/sync_2-cameras/OpenSimData/Model/LaiUhlrich2022_scaled.osim'
ref_osim = '/home/clarkadmin/Documents/repos-alberto/opencap-core-dev/tests/opencap-test-data/Data/sync_2-cameras/OpenSimData/Model/LaiUhlrich2022_scaled.osim', atol = 1e-05

    def compare_osim_scales(output_osim, ref_osim, atol=5e-3):
        output_scale_factors = load_osim_scales(output_osim)
        ref_scale_factors = load_osim_scales(ref_osim)
        assert output_scale_factors.keys() == ref_scale_factors.keys()
        for mesh_key in ref_scale_factors:
>           np.testing.assert_allclose(
                output_scale_factors[mesh_key],
                ref_scale_factors[mesh_key],
                rtol=0,
                atol=atol,
                err_msg=str(mesh_key),
            )
E           AssertionError:
E           Not equal to tolerance rtol=0, atol=1e-05
E           ('pelvis', 'pelvis_geom_1')
E           Mismatched elements: 3 / 3 (100%)
E           Max absolute difference: 0.00099501
E           Max relative difference: 0.00073795
E            x: array([1.349348, 1.349348, 1.478875])
E            y: array([1.348353, 1.348353, 1.479606])

tests/test_main.py:96: AssertionError
--------------------------------------------------------------------------------------------- Captured stdout call ----------------------------------------------------------------------------------------------
Using cameras: ['Cam1', 'Cam0']
Running OpenPose for Cam1
Running OpenPose for Cam0
You tried to filter 30 Hz signal with cutoff freq of 500. Will filter at 15 instead.
You tried to filter 30 Hz signal with cutoff freq of 500. Will filter at 15 instead.
Writing synchronized videos
1/1 - 1s - 616ms/epoch - 616ms/step
1/1 - 1s - 950ms/epoch - 950ms/step
Static phase of 0.10s detected in staticPose between [0.67, 0.77].
writing Neutral video
=============================================================================================== warnings summary ================================================================================================
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:10
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:10: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    _nlv = LooseVersion(_np_version)

../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:11
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:11: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    _np_version_under1p16 = _nlv < LooseVersion("1.16")

../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:12
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:12: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    _np_version_under1p17 = _nlv < LooseVersion("1.17")

../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:13
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:13: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    _np_version_under1p18 = _nlv < LooseVersion("1.18")

../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:14
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:14: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    _np_version_under1p19 = _nlv < LooseVersion("1.19")

../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:15
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/__init__.py:15: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    _np_version_under1p20 = _nlv < LooseVersion("1.20")

../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/setuptools/_distutils/version.py:337
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/setuptools/_distutils/version.py:337
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/setuptools/_distutils/version.py:337
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/setuptools/_distutils/version.py:337
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/setuptools/_distutils/version.py:337
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/setuptools/_distutils/version.py:337
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/setuptools/_distutils/version.py:337: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    other = LooseVersion(other)

../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/function.py:125
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/function.py:125
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/pandas/compat/numpy/function.py:125: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    if LooseVersion(_np_version) >= LooseVersion("1.17.0"):

../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/matplotlib/__init__.py:169
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/matplotlib/__init__.py:169
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/matplotlib/__init__.py:169
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/matplotlib/__init__.py:169
../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/matplotlib/__init__.py:169
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/matplotlib/__init__.py:169: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.
    if LooseVersion(module.__version__) < minver:

../../../anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/flatbuffers/compat.py:19
  /home/clarkadmin/anaconda3/envs/opencap-core-dev-alberto/lib/python3.9/site-packages/flatbuffers/compat.py:19: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses
    import imp

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html
============================================================================================ short test summary info ============================================================================================
FAILED tests/test_main.py::test_neutral_scaling - AssertionError:
============================================================================= 1 failed, 54 passed, 20 warnings in 91.21s (0:01:31) ==============================================================================

Update CHANGELOG.md

AlbertoCasasOrtiz · 2026-08-06T22:20:41Z

I also updated changelog with these changes in this PR.

Updated README.md with tests.

Revised main pipeline regression tests

carmichaelong · 2026-08-07T23:00:56Z

@AlbertoCasasOrtiz I merged the update to the tests from @csherry04 into dev. Let us know if that addresses your concerns, or if there are any other remaining (in case you have to pass it off to us before your vacation).

AlbertoCasasOrtiz · 2026-08-08T01:53:59Z

By relaxing the tolerance, tests are passing now both on the Ubuntu and Windows machine. If there is nothing else to test, I thinkg this should be ready to merge.

AlbertoCasasOrtiz · 2026-08-24T17:16:59Z

@carmichaelong Feel free to merge this one when ready. I checked the code again and everything seems ok.

carmichaelong · 2026-08-25T00:20:43Z

Tests look good in my environment as well

csherry04 and others added 10 commits June 26, 2026 15:49

Add exhaustive calibration fallback

28ca289

Close utility file handles

f5ba989

Resolve exhaustive fallback merge conflict

69b73ce

Address calibration fallback review comments

9028579

Merge pull request #286 from csherry04/exhaustive-fallback-change

228e6e7

Add exhaustive calibration fallback

Add main pipeline regression tests

86313a5

Address main pipeline test review comments

a92e37b

Rename main test session helper

bf401c6

Merge pull request #290 from csherry04/test-main-pipeline-regressions

df6a990

Test main pipeline regressions

Merge pull request #293 from csherry04/fix/254-close-file-handles

fb0f282

Close utility file handles

AlbertoCasasOrtiz added 2 commits August 6, 2026 15:19

Update CHANGELOG.md

d14dbfd

Merge pull request #298 from opencap-org/update-changelog

e3abb87

Update CHANGELOG.md

AlbertoCasasOrtiz requested a review from carmichaelong August 6, 2026 22:21

AlbertoCasasOrtiz and others added 5 commits August 6, 2026 16:01

Updated README.md with tests.

5329554

Merge pull request #299 from opencap-org/update-readme-tests

9dc299b

Updated README.md with tests.

Isolate main pipeline regression tests

9f3204e

Clarify main test keypoint fixture formats

1b11cf9

Merge pull request #301 from csherry04/test-main-pipeline-regressions

c37cbd1

Revised main pipeline regression tests

AlbertoCasasOrtiz self-assigned this Aug 24, 2026

carmichaelong approved these changes Aug 25, 2026

View reviewed changes

carmichaelong merged commit 85fc927 into main Aug 25, 2026
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