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fix bug in reader selection #13

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Merged
AurelienJaquier merged 2 commits into from
Aug 21, 2025
Merged

fix bug in reader selection #13

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88ae041
fix bug in reader selection
AurelienJaquier Aug 21, 2025
9d31866
also allow GenericStep in TRTNWB reader
AurelienJaquier Aug 21, 2025
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11 changes: 6 additions & 5 deletions bluepyefe/nwbreader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -278,19 +278,20 @@ def read(self):
"""
data = []

# Only return data if target_protocols is None or includes "step"
# Only return data if target_protocols is None or includes "step" or "genericstep"
if self.target_protocols:
allowed = [p.lower() for p in self.target_protocols]
if "step" not in allowed:
if "step" not in allowed and "genericstep" not in allowed:
logger.warning(
f"TRTNWBReader only supports 'step' protocols, but requested: {self.target_protocols}. Skipping."
"TRTNWBReader only supports 'step' and 'genericstep' protocols, "
f"but requested: {self.target_protocols}. Skipping."
)
return []

# possible paths in content:
# /acquisition/index_00
# or /acquisition/index_000
# or /acquisition/index_0_0_0
# or /acquisition/Index_0_0_0
for voltage_sweep_name, voltage_sweep in list(self.content["acquisition"].items()):
parts = voltage_sweep_name.split("_")
if len(parts) == 2:
Expand All @@ -312,7 +313,7 @@ def read(self):
# possible paths in content:
# /stimulus/presentation/index_01
# or /stimulus/presentation/index_001
# or /stimulus/presentation/index_0_0_1
# or /stimulus/presentation/Index_0_0_1
current_sweep = self.content["stimulus"]["presentation"][current_sweep_name]

data.append(self._format_nwb_trace(
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2 changes: 1 addition & 1 deletion bluepyefe/reader.py
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Original file line number Diff line number Diff line change
Expand Up @@ -215,7 +215,7 @@ def nwb_reader(in_data):
elif "timeseries" in content["acquisition"].keys():
# For data from the Allen Institute
reader = AIBSNWBReader(content, target_protocols)
elif next(iter(content["acquisition"]))[:6] == "index_":
elif next(iter(content["acquisition"]))[:6].lower() == "index_":
# For data from Derek Howard
# (An in vitro whole-cell electrophysiology dataset of human cortical neurons)
reader = TRTNWBReader(content, target_protocols, repetition=None)
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