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Update ephys_acute to latest version in modular-clustering #180

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merged 2 commits into from
Jan 11, 2024
Merged

Update ephys_acute to latest version in modular-clustering #180

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7242a1d
Minor fixes
kushalbakshi Jan 10, 2024
942897d
Black formatting
kushalbakshi Jan 10, 2024
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17 changes: 11 additions & 6 deletions element_array_ephys/ephys_acute.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,10 +10,10 @@
import pandas as pd
from element_interface.utils import dict_to_uuid, find_full_path, find_root_directory

from . import ephys_report, get_logger, probe
from . import ephys_report, probe
from .readers import kilosort, openephys, spikeglx

log = get_logger(__name__)
log = dj.logger

schema = dj.schema()

Expand Down Expand Up @@ -126,7 +126,7 @@ class AcquisitionSoftware(dj.Lookup):
acq_software ( varchar(24) ): Acquisition software, e.g,. SpikeGLX, OpenEphys
"""

definition = """ # Software used for recording of neuropixels probes
definition = """ # Name of software used for recording of neuropixels probes - SpikeGLX or Open Ephys
acq_software: varchar(24)
"""
contents = zip(["SpikeGLX", "Open Ephys"])
Expand Down Expand Up @@ -180,7 +180,10 @@ def auto_generate_entries(cls, session_key):
"probe_type": spikeglx_meta.probe_model,
"probe": spikeglx_meta.probe_SN,
}
if probe_key["probe"] not in [p["probe"] for p in probe_list]:
if (
probe_key["probe"] not in [p["probe"] for p in probe_list]
and probe_key not in probe.Probe()
):
probe_list.append(probe_key)

probe_dir = meta_filepath.parent
Expand All @@ -204,7 +207,10 @@ def auto_generate_entries(cls, session_key):
"probe_type": oe_probe.probe_model,
"probe": oe_probe.probe_SN,
}
if probe_key["probe"] not in [p["probe"] for p in probe_list]:
if (
probe_key["probe"] not in [p["probe"] for p in probe_list]
and probe_key not in probe.Probe()
):
probe_list.append(probe_key)
probe_insertion_list.append(
{
Expand Down Expand Up @@ -533,7 +539,6 @@ def make(self, key):
- 1 : 0 : -self._skip_channel_counts
]

# (sample x channel)
lfp = oe_probe.lfp_timeseries[:, lfp_channel_ind]
lfp = (
lfp * np.array(oe_probe.lfp_meta["channels_gains"])[lfp_channel_ind]
Expand Down
2 changes: 1 addition & 1 deletion element_array_ephys/spike_sorting/ecephys_spike_sorting.py
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Original file line number Diff line number Diff line change
Expand Up @@ -337,4 +337,4 @@ def _get_execution_duration(modules_input_hash_fp, modules_to_run):
dur = modules_status[m]["duration"] or 0
logged_exec_dur += int(dur)

return logged_exec_dur, modules_status
return logged_exec_dur, modules_status