Make sampling rate for LFP user-defined instead of hard-coded to 1000…

… Hz (#705) * Make sampling rate for LFP user-defined rather than hard-coded to 1000 Hz * Fixed default lfp_sampling_rate and moved decimation factor line * Update src/spyglass/lfp/v1/lfp.py --------- Co-authored-by: Sharon Chiang <[email protected]> Co-authored-by: Eric Denovellis <[email protected]> Co-authored-by: Chris Brozdowski <[email protected]>
LorenFrankLab · Dec 14, 2023 · 0d66ea9 · 0d66ea9
1 parent 06f292e
commit 0d66ea9
Showing 1 changed file with 7 additions and 6 deletions.
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 = (