Add ability to set smoothing sigma in get_firing_rate (#994)

* add option to set spike smoothing sigma * update changelog
LorenFrankLab · Jun 3, 2024 · 04ec37a · 04ec37a
1 parent 00ce118
commit 04ec37a
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -28,6 +28,8 @@
     - `DLCPosVideo` table now inserts into self after `make` #966
 - Common
     - Don't insert lab member when creating lab team #983
+- Spikesorting
+    - Allow user to set smoothing timescale in `SortedSpikesGroup.get_firing_rate` #994
 
 ## [0.5.2] (April 22, 2024)
 

diff --git a/src/spyglass/spikesorting/analysis/v1/group.py b/src/spyglass/spikesorting/analysis/v1/group.py
@@ -189,7 +189,11 @@ def get_spike_indicator(cls, key: dict, time: np.ndarray) -> np.ndarray:
 
     @classmethod
     def get_firing_rate(
-        cls, key: dict, time: np.ndarray, multiunit: bool = False
+        cls,
+        key: dict,
+        time: np.ndarray,
+        multiunit: bool = False,
+        smoothing_sigma: float = 0.015,
     ) -> np.ndarray:
         spike_indicator = cls.get_spike_indicator(key, time)
         if spike_indicator.ndim == 1:
@@ -202,7 +206,9 @@ def get_firing_rate(
         return np.stack(
             [
                 get_multiunit_population_firing_rate(
-                    indicator[:, np.newaxis], sampling_frequency
+                    indicator[:, np.newaxis],
+                    sampling_frequency,
+                    smoothing_sigma,
                 )
                 for indicator in spike_indicator.T
             ],