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Move strange units warning to get traces #761

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Merged
merged 3 commits into from
Jul 1, 2022
Merged

Move strange units warning to get traces #761

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acec02f
move warning to get_traces
h-mayorquin Jun 30, 2022
7eb7288
Merge branch 'master' into move_warning_to_get_traces
h-mayorquin Jun 30, 2022
ae85710
Merge branch 'master' into move_warning_to_get_traces
h-mayorquin Jun 30, 2022
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8 changes: 8 additions & 0 deletions spikeinterface/core/baserecording.py
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Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
from typing import Iterable, List, Union
from pathlib import Path
import warnings

import numpy as np

Expand Down Expand Up @@ -103,6 +104,13 @@ def get_traces(self,
assert order in ["C", "F"]
traces = np.asanyarray(traces, order=order)
if return_scaled:
if hasattr(self, "NeoRawIOClass"):
if self.has_non_standard_units:
message = (
f'This extractor based on neo.{self.NeoRawIOClass} has channels with units not in (V, mV, uV)'
)
warnings.warn(message)

if not self.has_scaled_traces():
raise ValueError('This recording do not support return_scaled=True (need gain_to_uV and offset_'
'to_uV properties)')
Expand Down
9 changes: 5 additions & 4 deletions spikeinterface/extractors/neoextractors/neobaseextractor.py
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Expand Up @@ -64,11 +64,12 @@ def __init__(self, stream_id=None, all_annotations=False, **neo_kwargs):
offsets = signal_channels['offset']

units = signal_channels['units']
if not np.all(np.isin(units, ['V', 'Volt', 'mV', 'uV'])):
# check that units are V, mV or uV
message = f'This extractor based on neo.{self.NeoRawIOClass} have strange units not in (V, mV, uV) {units}'
warnings.warn(message)

# mark that units are V, mV or uV
self.has_non_standard_units = False
if not np.all(np.isin(units, ['V', 'Volt', 'mV', 'uV'])):
self.has_non_standard_units = True

additional_gain = np.ones(units.size, dtype='float')
additional_gain[units == 'V'] = 1e6
additional_gain[units == 'Volt'] = 1e6
Expand Down