Add scaling factor to fix mean_waveforms and CSD.

AllenInstitute · Nov 30, 2023 · 1c61e26 · 1c61e26
1 parent ef35a6c
commit 1c61e26
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Showing 3 changed files with 18 additions and 3 deletions.
diff --git a/allensdk/brain_observatory/ecephys/_current_source_density.py b/allensdk/brain_observatory/ecephys/_current_source_density.py
@@ -50,9 +50,10 @@ def channel_locations(self) -> np.ndarray:
 
     @classmethod
     def from_json(cls, probe_meta: dict) -> "CurrentSourceDensity":
+        scale = probe_meta.get("scale_mean_waveform_and_csd", 1)
         with h5py.File(probe_meta['csd_path'], "r") as csd_file:
             return CurrentSourceDensity(
-                data=csd_file["current_source_density"][:],
+                data=csd_file["current_source_density"][:] / scale,
                 timestamps=csd_file["timestamps"][:],
                 interpolated_channel_locations=csd_file["csd_locations"][:]
             )

diff --git a/allensdk/brain_observatory/ecephys/_units.py b/allensdk/brain_observatory/ecephys/_units.py
@@ -47,7 +47,8 @@ def from_json(
         )
         mean_waveforms = _read_waveforms_to_dictionary(
             probe['mean_waveforms_path'],
-            local_to_global_unit_map
+            local_to_global_unit_map,
+            mean_waveform_scale=probe.get('scale_mean_waveform_and_csd', 1)
         )
         spike_amplitudes = _read_spike_amplitudes_to_dictionary(
             probe["spike_amplitudes_path"],
@@ -132,6 +133,7 @@ def _read_waveforms_to_dictionary(
         waveforms_path,
         local_to_global_unit_map=None,
         peak_channel_map=None,
+        mean_waveform_scale=1,
 ):
     """ Builds a lookup table for unitwise waveform data
 
@@ -146,6 +148,8 @@ def _read_waveforms_to_dictionary(
         Maps unit identifiers to indices of peak channels. If provided,
         the output will contain only samples on the peak
         channel for each unit.
+    mean_waveform_scale : float, optional
+        Divide out a scaling from the mean_waveform. Default 1.
 
     Returns
     -------
@@ -171,7 +175,7 @@ def _read_waveforms_to_dictionary(
         if peak_channel_map is not None:
             waveform = waveform[:, peak_channel_map[unit_id]]
 
-        output_waveforms[unit_id] = np.squeeze(waveform)
+        output_waveforms[unit_id] = np.squeeze(waveform) / mean_waveform_scale
 
     return output_waveforms
 

diff --git a/allensdk/brain_observatory/ecephys/write_nwb/schemas.py b/allensdk/brain_observatory/ecephys/write_nwb/schemas.py
@@ -204,6 +204,16 @@ class Probe(RaisingSchema):
         help="""amplitude scale factor converting raw amplitudes to Volts.
                 Default converts from bits -> uV -> V""",
     )
+    scale_mean_waveform_and_csd = Float(
+        default=1,
+        allow_none=True,
+        help="""Amount to scale the mean waveform and CSD by. (data / scale).
+                This is a fix for a set of data documented in the change log.
+                The values for unit amplitudes were changed in the input_json
+                file and do not use this scale.
+                If the data in LIMS for these sessions is updated, this scaling
+                is not needed. Default is 1"""
+    )
 
 
 class InvalidEpoch(RaisingSchema):