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Some bug fix #89

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merged 1 commit into from
Sep 6, 2022
Merged

Some bug fix #89

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10 changes: 5 additions & 5 deletions bluepyefe/extract.py
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Original file line number Diff line number Diff line change
Expand Up @@ -186,10 +186,10 @@ def read_recordings(


def extract_efeatures_at_targets(
cells,
targets,
map_function=map,
efel_settings=None
cells,
targets,
map_function=map,
efel_settings=None
):
"""
Extract efeatures from recordings following the protocols, amplitudes and
Expand Down Expand Up @@ -809,7 +809,7 @@ def extract_efeatures(
the path contains data coming from different stimuli (eg: for NWB).
targets (list): define the efeatures to extract as well as which
protocols and current amplitude they should be extracted for. If
targets are not probided, automatic targets will be used.
targets are not provided, automatic targets will be used.
Of the form:
[{
"efeature": "AP_amplitude",
Expand Down
13 changes: 10 additions & 3 deletions bluepyefe/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -269,9 +269,7 @@ def _nwb_reader_BBP(content, target_protocols, repetition):
for cell_id in content["data_organization"].keys():

if ecode not in content["data_organization"][cell_id]:
logger.info(
f"No eCode {ecode} in nwb {in_data['filepath']}."
)
logger.debug(f"No eCode {ecode} in nwb.")
continue

ecode_content = content["data_organization"][cell_id][ecode]
Expand All @@ -292,6 +290,15 @@ def _nwb_reader_BBP(content, target_protocols, repetition):
else:
continue

if key_current not in content["stimulus"]["presentation"]:
logger.debug(f"Ignoring {key_current} not"
" present in the stimulus presentation")
continue
if trace_name not in content["acquisition"]:
logger.debug(f"Ignoring {trace_name} not"
" present in the acquisition")
continue

data.append(_format_nwb_trace(
voltage=content["acquisition"][trace_name]["data"],
current=content["stimulus"]["presentation"][key_current]["data"],
Expand Down