Set sparse=False during waveform extraction (#1039)

* Save LFP as pynwb.ecephys.LFP * Fix formatting * Fix formatting * Set sparse False during wf extraciton * Black * Update Changelog * Black --------- Co-authored-by: Eric Denovellis <[email protected]> Co-authored-by: Eric Denovellis <[email protected]>
LorenFrankLab · Aug 5, 2024 · 907098a · 907098a
1 parent 24793f5
commit 907098a
Show file tree

Hide file tree

Showing 8 changed files with 3 additions and 8 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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():