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Add targeted_imaging_depth column to get_ophys_experiment_table #2648

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merged 4 commits into from
Jan 23, 2023
Merged

Add targeted_imaging_depth column to get_ophys_experiment_table #2648

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4b0560e
Add targeted_imaging_depth column to get_ophys_experiment_table
mikejhuang Jan 19, 2023
40173c6
update ophys_experiment_table fixture with additional column
mikejhuang Jan 19, 2023
7ef58c1
rollback hdmf for test
mikejhuang Jan 20, 2023
497bbc9
ignore column order in test
mikejhuang Jan 21, 2023
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7 changes: 6 additions & 1 deletion ...rvatory/behavior/behavior_project_cache/project_apis/data_io/behavior_project_lims_api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -359,7 +359,12 @@ def _get_ophys_experiment_table(self) -> pd.DataFrame:
query += where_clause

self.logger.debug(f"get_ophys_experiment_table query: \n{query}")
return self.lims_engine.select(query)
query_df = self.lims_engine.select(query)
targeted_imaging_depth = query_df[
["ophys_container_id", "imaging_depth"]
].groupby("ophys_container_id").mean()
targeted_imaging_depth.columns = ['targeted_imaging_depth']
return query_df.merge(targeted_imaging_depth, on='ophys_container_id')

def _get_ophys_cells_table(self):
"""
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2 changes: 1 addition & 1 deletion ...rain_observatory/behavior/behavior_project_cache/test_behavior_project_metadata_writer.py
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Original file line number Diff line number Diff line change
Expand Up @@ -118,7 +118,7 @@ def test_get_ophys_experiments_table(self):
.sort_values('ophys_experiment_id')\
.reset_index(drop=True)
pd.testing.assert_frame_equal(
obtained, expected)
obtained.sort_index(axis=1), expected.sort_index(axis=1))

@pytest.mark.requires_bamboo
def test_get_ophys_cells_table(self):
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