diff --git a/CHANGELOG.md b/CHANGELOG.md index 8509f24b0..449ccd8de 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -76,7 +76,8 @@ PositionGroup.alter() `spikesorting.v1.SpikeSorting` #1009 - Remove deprecated dependencies on kachery_client #1014 - Add `UnitAnnotation` table and naming convention for units #1027, #1052 - + - Set `sparse` parameter to waveform extraction step in `spikesorting.v1` + #1039 ## [0.5.2] (April 22, 2024) ### Infrastructure diff --git a/src/spyglass/decoding/v1/clusterless.py b/src/spyglass/decoding/v1/clusterless.py index 3694a550f..f9e149df1 100644 --- a/src/spyglass/decoding/v1/clusterless.py +++ b/src/spyglass/decoding/v1/clusterless.py @@ -147,7 +147,6 @@ def make(self, key): classifier = ClusterlessDetector(**decoding_params) if key["estimate_decoding_params"]: - # if estimating parameters, then we need to treat times outside # decoding interval as missing this means that times outside the # decoding interval will not use the spiking data a better approach diff --git a/src/spyglass/decoding/v1/sorted_spikes.py b/src/spyglass/decoding/v1/sorted_spikes.py index bd44f8eb6..9dbdd015b 100644 --- a/src/spyglass/decoding/v1/sorted_spikes.py +++ b/src/spyglass/decoding/v1/sorted_spikes.py @@ -114,7 +114,6 @@ def make(self, key): classifier = SortedSpikesDetector(**decoding_params) if key["estimate_decoding_params"]: - # if estimating parameters, then we need to treat times outside # decoding interval as missing this means that times outside the # decoding interval will not use the spiking data a better approach diff --git a/src/spyglass/position/v1/position_dlc_pose_estimation.py b/src/spyglass/position/v1/position_dlc_pose_estimation.py index 4b82918a0..8fa3df922 100644 --- a/src/spyglass/position/v1/position_dlc_pose_estimation.py +++ b/src/spyglass/position/v1/position_dlc_pose_estimation.py @@ -118,7 +118,6 @@ def insert_estimation_task( def _insert_est_with_log( self, key, task_mode, params, check_crop, skip_duplicates, output_dir ): - v_path, v_fname, _, _ = get_video_info(key) if not v_path: raise FileNotFoundError(f"Video file not found for {key}") @@ -215,7 +214,6 @@ def make(self, key): @file_log(logger, console=True) def _logged_make(self, key): - METERS_PER_CM = 0.01 logger.info("----------------------") diff --git a/src/spyglass/position/v1/position_dlc_position.py b/src/spyglass/position/v1/position_dlc_position.py index cfad61c15..01b732612 100644 --- a/src/spyglass/position/v1/position_dlc_position.py +++ b/src/spyglass/position/v1/position_dlc_position.py @@ -169,7 +169,6 @@ def make(self, key): @file_log(logger, console=False) def _logged_make(self, key): - METERS_PER_CM = 0.01 logger.info("-----------------------") diff --git a/src/spyglass/spikesorting/v1/metric_curation.py b/src/spyglass/spikesorting/v1/metric_curation.py index 836de018d..b03c7fa9c 100644 --- a/src/spyglass/spikesorting/v1/metric_curation.py +++ b/src/spyglass/spikesorting/v1/metric_curation.py @@ -242,6 +242,7 @@ def make(self, key): waveforms = si.extract_waveforms( recording=recording, sorting=sorting, + sparse=waveform_params.get("sparse", False), folder=waveforms_dir, overwrite=True, **waveform_params, diff --git a/tests/common/test_position.py b/tests/common/test_position.py index f2d882cba..e5f39c20c 100644 --- a/tests/common/test_position.py +++ b/tests/common/test_position.py @@ -183,7 +183,6 @@ def rename_default_cols(common_position): ], ) def test_rename_columns(rename_default_cols, col_type, cols): - _fix_col_names, defaults = rename_default_cols df = pd.DataFrame([range(len(cols) + 1)], columns=["junk"] + cols) result = _fix_col_names(df).columns.tolist() diff --git a/tests/utils/conftest.py b/tests/utils/conftest.py index 726b6b8a7..3723f191c 100644 --- a/tests/utils/conftest.py +++ b/tests/utils/conftest.py @@ -233,7 +233,6 @@ class MergeChild(SpyglassMixin, dj.Manual): @pytest.fixture(scope="module") def graph_tables(dj_conn, graph_schema): - schema = dj.Schema(context=graph_schema) for table in graph_schema.values():