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Merged
merged 6 commits into from
Mar 21, 2022
Merged

Add attributes and rename module #58

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6b17239
Increase datatype size
kabilar Mar 11, 2022
b13995e
Merge branch 'main' of https://github.com/datajoint/element-array-eph…
kabilar Mar 11, 2022
65b9ece
Add recording metadata
kabilar Mar 11, 2022
1104ab4
Rename module `ephys` to `ephys_acute`
kabilar Mar 19, 2022
0d56f2e
Update string formatting
kabilar Mar 19, 2022
fc38bb5
Ensure backwards compatibility
kabilar Mar 21, 2022
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1 change: 1 addition & 0 deletions element_array_ephys/__init__.py
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Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
import element_array_ephys.ephys_acute as ephys
13 changes: 10 additions & 3 deletions element_array_ephys/ephys.py → element_array_ephys/ephys_acute.py
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Original file line number Diff line number Diff line change
Expand Up @@ -130,7 +130,9 @@ class EphysRecording(dj.Imported):
---
-> probe.ElectrodeConfig
-> AcquisitionSoftware
sampling_rate: float # (Hz)
sampling_rate: float # (Hz)
recording_datetime: datetime # datetime of the recording from this probe
recording_duration: float # (seconds) duration of the recording from this probe
"""

class EphysFile(dj.Part):
Expand Down Expand Up @@ -189,7 +191,10 @@ def make(self, key):
self.insert1({**key,
**generate_electrode_config(probe_type, electrode_group_members),
'acq_software': acq_software,
'sampling_rate': spikeglx_meta.meta['imSampRate']})
'sampling_rate': spikeglx_meta.meta['imSampRate'],
'recording_datetime': spikeglx_meta.recording_time,
'recording_duration': (spikeglx_meta.recording_duration
or spikeglx.retrieve_recording_duration(meta_filepath))})

root_dir = find_root_directory(get_ephys_root_data_dir(),
meta_filepath)
Expand Down Expand Up @@ -223,7 +228,9 @@ def make(self, key):
self.insert1({**key,
**generate_electrode_config(probe_type, electrode_group_members),
'acq_software': acq_software,
'sampling_rate': probe_data.ap_meta['sample_rate']})
'sampling_rate': probe_data.ap_meta['sample_rate'],
'recording_datetime': probe_data.recording_info['recording_datetimes'][0],
'recording_duration': np.sum(probe_data.recording_info['recording_durations'])})

root_dir = find_root_directory(get_ephys_root_data_dir(),
probe_data.recording_info['recording_files'][0])
Expand Down
16 changes: 12 additions & 4 deletions element_array_ephys/ephys_chronic.py
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Original file line number Diff line number Diff line change
Expand Up @@ -132,7 +132,9 @@ class EphysRecording(dj.Imported):
---
-> probe.ElectrodeConfig
-> AcquisitionSoftware
sampling_rate: float # (Hz)
sampling_rate: float # (Hz)
recording_datetime: datetime # datetime of the recording from this probe
recording_duration: float # (seconds) duration of the recording from this probe
"""

class EphysFile(dj.Part):
Expand Down Expand Up @@ -168,7 +170,8 @@ def make(self, key):
break
else:
raise FileNotFoundError(
'No SpikeGLX data found for probe insertion: {}'.format(key))
f'No SpikeGLX data found for probe insertion: {key}' +
' The probe serial number does not match.')

if re.search('(1.0|2.0)', spikeglx_meta.probe_model):
probe_type = spikeglx_meta.probe_model
Expand All @@ -190,7 +193,10 @@ def make(self, key):
self.insert1({**key,
**generate_electrode_config(probe_type, electrode_group_members),
'acq_software': acq_software,
'sampling_rate': spikeglx_meta.meta['imSampRate']})
'sampling_rate': spikeglx_meta.meta['imSampRate'],
'recording_datetime': spikeglx_meta.recording_time,
'recording_duration': (spikeglx_meta.recording_duration
or spikeglx.retrieve_recording_duration(meta_filepath))})

root_dir = find_root_directory(get_ephys_root_data_dir(),
meta_filepath)
Expand Down Expand Up @@ -224,7 +230,9 @@ def make(self, key):
self.insert1({**key,
**generate_electrode_config(probe_type, electrode_group_members),
'acq_software': acq_software,
'sampling_rate': probe_data.ap_meta['sample_rate']})
'sampling_rate': probe_data.ap_meta['sample_rate'],
'recording_datetime': probe_data.recording_info['recording_datetimes'][0],
'recording_duration': np.sum(probe_data.recording_info['recording_durations'])})

root_dir = find_root_directory(get_ephys_root_data_dir(),
probe_data.recording_info['recording_files'][0])
Expand Down
2 changes: 1 addition & 1 deletion element_array_ephys/probe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@ class ElectrodeConfig(dj.Lookup):
electrode_config_hash: uuid
---
-> ProbeType
electrode_config_name: varchar(64) # user friendly name
electrode_config_name: varchar(4000) # user friendly name
"""

class Electrode(dj.Part):
Expand Down