Merge branch 'master' into main

CBroz1 · Dec 14, 2023 · 4a1aa6c · 4a1aa6c
2 parents 45710f8 + 0d66ea9
commit 4a1aa6c
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Showing 5 changed files with 15 additions and 12 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,7 +8,8 @@
 - Add Mixin class to centralize `fetch_nwb` functionality. #692
 - Minor fixes to LinearizedPositionV1 pipeline #695
 - Add SpikeSorting V1 pipeline #651
-- Refactor restriction use in `delete_downstream_merge`
+- Refactor restriction use in `delete_downstream_merge` #703
+- Minor fixes to LFPBandV1 populator #706
 
 ## [0.4.3] (November 7, 2023)
 

diff --git a/src/spyglass/common/common_filter.py b/src/spyglass/common/common_filter.py
@@ -461,7 +461,8 @@ def filter_data(
             frm, to = self._time_bound_check(
                 a_start, a_stop, timestamps, n_samples
             )
-
+            if np.isclose(frm, to, rtol=0, atol=1e-8):
+                continue
             indices.append((frm, to))
 
             shape, _ = gsp.filter_data_fir(

diff --git a/src/spyglass/lfp/analysis/v1/lfp_band.py b/src/spyglass/lfp/analysis/v1/lfp_band.py
@@ -355,6 +355,9 @@ def make(self, key):
                 }
             )
         else:
+            lfp_band_valid_times = interval_list_censor(
+                lfp_band_valid_times, new_timestamps
+            )
             # check that the valid times are the same
             assert np.isclose(
                 tmp_valid_times[0], lfp_band_valid_times

diff --git a/src/spyglass/lfp/v1/lfp.py b/src/spyglass/lfp/v1/lfp.py
@@ -32,15 +32,17 @@ class LFPSelection(dj.Manual):
     The interval list is used to select the times from the raw data that will be
     filtered.  The user can also specify the filter to be used.
 
-    The LFP data is filtered and downsampled to 1 KHz.  The filtered data is stored
-    in the AnalysisNwbfile table.  The valid times for the filtered data are stored
-    in the IntervalList table.
+    The LFP data is filtered and downsampled to the user-defined sampling rate, specified
+    as lfp_sampling_rate.  The filtered data is stored in the AnalysisNwbfile table.
+    The valid times for the filtered data are stored in the IntervalList table.
     """
 
     definition = """
      -> LFPElectrodeGroup                                                  # the group of electrodes to be filtered
      -> IntervalList.proj(target_interval_list_name='interval_list_name')  # the original set of times to be filtered
      -> FirFilterParameters                                                # the filter to be used
+     ---
+     target_sampling_rate = 1000 : float                                     # the desired output sampling rate, in HZ                                                                                                                                                                                                                
      """
 
 
@@ -58,7 +60,6 @@ class LFPV1(SpyglassMixin, dj.Computed):
     """
 
     def make(self, key):
-        DECIMATION_FACTOR = 1000
         # get the NWB object with the data
         nwbf_key = {"nwb_file_name": key["nwb_file_name"]}
         rawdata = (Raw & nwbf_key).fetch_nwb()[0]["raw"]
@@ -94,8 +95,8 @@ def make(self, key):
             f"LFP: found {len(valid_times)} intervals > {MIN_LFP_INTERVAL_DURATION} sec long."
         )
 
-        # target 1 KHz sampling rate
-        decimation = sampling_rate // DECIMATION_FACTOR
+        # target user-specified sampling rate
+        decimation = sampling_rate // key["target_sampling_rate"]
 
         # get the LFP filter that matches the raw data
         filter = (

diff --git a/src/spyglass/spikesorting/v1/curation.py b/src/spyglass/spikesorting/v1/curation.py
@@ -150,10 +150,7 @@ def insert_metric_curation(cls, key: Dict, apply_merge=False):
             labels=MetricCuration.get_labels(key) or None,
             merge_groups=MetricCuration.get_merge_groups(key) or None,
             apply_merge=apply_merge,
-            description=(
-                "metric curation of sorting id "
-                + f"{sorting_id}, curation id {parent_curation_id}"
-            ),
+            description=(f"metric_curation_id: {key['metric_curation_id']}"),
         )
 
         return curation_key