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Add sample SLEAP data containing mixed (user/predicted) labels #85

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merged 3 commits into from
Nov 14, 2023
Merged

Add sample SLEAP data containing mixed (user/predicted) labels #85

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d8bc10b
Update poses registry
lochhh Nov 14, 2023
19791e2
Update tests to use reusable SLEAP file fixture
lochhh Nov 14, 2023
78705f3
Configure sphinx gallery to rerun examples
lochhh Nov 14, 2023
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3 changes: 2 additions & 1 deletion docs/source/conf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,7 @@
"examples_dirs": ["../../examples"],
"filename_pattern": "/*.py", # which files to execute before inclusion
"gallery_dirs": ["examples"], # output directory
"run_stale_examples": True, # re-run examples on each build
}

# -- Options for HTML output -------------------------------------------------
Expand Down Expand Up @@ -133,7 +134,7 @@
# so a file named "default.css" will overwrite the builtin "default.css".
# html_static_path = ['_static']

# The linkcheck builder will skip verifying that anchors exist when checking
# The linkcheck builder will skip verifying that anchors exist when checking
# these URLs
linkcheck_anchors_ignore_for_url = [
"https://gin.g-node.org/G-Node/Info/wiki/",
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2 changes: 2 additions & 0 deletions movement/datasets.py
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Expand Up @@ -36,6 +36,8 @@
"SLEAP_two-mice_social-interaction.predictions.slp": "45881affde9704c045e70b8d4b3f6bbb8d9bd8ef9f4cdea6d173cfe35857549b", # noqa: E501
"SLEAP_three-mice_Aeon_proofread.analysis.h5": "82ebd281c406a61536092863bc51d1a5c7c10316275119f7daf01c1ff33eac2a", # noqa: E501
"SLEAP_three-mice_Aeon_proofread.predictions.slp": "7b7436a52dfd5f4d80d7c66919ad1a1732e5435fe33faf9011ec5f7b7074e788", # noqa: E501
"SLEAP_three-mice_Aeon_mixed-labels.analysis.h5": "899651ec027eb8fd6181246f89142ad1c0a40f14394fc8144d44ea093c0e137d", # noqa: E501
"SLEAP_three-mice_Aeon_mixed-labels.predictions.slp": "6d3f2c5446e9c12aabf28d5a9470835736b0419dcefebba89c305114f83b82d1", # noqa: E501
},
)

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17 changes: 17 additions & 0 deletions tests/conftest.py
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Expand Up @@ -26,6 +26,8 @@ def pytest_configure():
"SLEAP_single-mouse_EPM.predictions.slp",
"SLEAP_three-mice_Aeon_proofread.analysis.h5",
"SLEAP_three-mice_Aeon_proofread.predictions.slp",
"SLEAP_three-mice_Aeon_mixed-labels.analysis.h5",
"SLEAP_three-mice_Aeon_mixed-labels.predictions.slp",
]
}

Expand Down Expand Up @@ -167,6 +169,21 @@ def dlc_style_df():
return pd.read_hdf(pytest.POSE_DATA.get("DLC_single-wasp.predictions.h5"))


@pytest.fixture(
params=[
"SLEAP_single-mouse_EPM.analysis.h5",
"SLEAP_single-mouse_EPM.predictions.slp",
"SLEAP_three-mice_Aeon_proofread.analysis.h5",
"SLEAP_three-mice_Aeon_proofread.predictions.slp",
"SLEAP_three-mice_Aeon_mixed-labels.analysis.h5",
"SLEAP_three-mice_Aeon_mixed-labels.predictions.slp",
]
)
def sleap_file(request):
"""Return the file path for a SLEAP .h5 or .slp file."""
return pytest.POSE_DATA.get(request.param)


@pytest.fixture
def valid_tracks_array():
"""Return a function that generate different kinds
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16 changes: 3 additions & 13 deletions tests/test_unit/test_load_poses.py
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Expand Up @@ -42,21 +42,11 @@ def assert_dataset(
)
assert dataset.fps is None

@pytest.mark.parametrize(
"file_name",
[
"SLEAP_single-mouse_EPM.analysis.h5",
"SLEAP_single-mouse_EPM.predictions.slp",
"SLEAP_three-mice_Aeon_proofread.analysis.h5",
"SLEAP_three-mice_Aeon_proofread.predictions.slp",
],
)
def test_load_from_slp_file(self, file_name):
def test_load_from_slp_file(self, sleap_file):
"""Test that loading pose tracks from valid SLEAP files
returns a proper Dataset."""
file_path = POSE_DATA.get(file_name)
ds = load_poses.from_sleap_file(file_path)
self.assert_dataset(ds, file_path, "SLEAP")
ds = load_poses.from_sleap_file(sleap_file)
self.assert_dataset(ds, sleap_file, "SLEAP")

@pytest.mark.parametrize(
"file_name",
Expand Down