Merge pull request #17 from ttngu207/main

specify a separate `get_clustering_root_data_dir()` - handle cases where raw ephys and clustering results are stored at different root locations (e.g. different mount points)

Author: dimitri-yatsenko

element_array_ephys/__init__.py

@@ -1,5 +1,3 @@
-__author__ = "DataJoint NEURO"
-__date__ = "December 15, 2020"
-__version__ = "0.0.1"
+import datajoint as dj
 
-__all__ = ['__author__', '__version__', '__date__']
+dj.config['enable_python_native_blobs'] = True

element_array_ephys/ephys.py

@@ -17,6 +17,11 @@ def activate(schema_name, create_schema=True, create_tables=True):
     """
     schema.activate(schema_name, create_schema=create_schema, create_tables=create_tables)
 
+    # Add neuropixels probes
+    for probe_type in ('neuropixels 1.0 - 3A', 'neuropixels 1.0 - 3B',
+                       'neuropixels 2.0 - SS', 'neuropixels 2.0 - MS'):
+        ProbeType.create_neuropixels_probe(probe_type)
+
 
 @schema
 class ProbeType(dj.Lookup):

element_array_ephys/probe.py

@@ -33,10 +33,10 @@ class OpenEphys:
     def __init__(self, experiment_dir):
         self.sess_dir = pathlib.Path(experiment_dir)
 
-        oe_file = pyopenephys.File(self.sess_dir.parent)  # this is on the Record Node level
+        openephys_file = pyopenephys.File(self.sess_dir.parent)  # this is on the Record Node level
 
         # extract the "recordings" for this session
-        self.experiment = next(experiment for experiment in oe_file.experiments
+        self.experiment = next(experiment for experiment in openephys_file.experiments
                                if pathlib.Path(experiment.absolute_foldername) == self.sess_dir)
 
         self.recording_time = self.experiment.datetime
@@ -58,47 +58,50 @@ def load_probe_data(self):
         probes = {}
         for processor in self.experiment.settings['SIGNALCHAIN']['PROCESSOR']:
             if processor['@pluginName'] in ('Neuropix-PXI', 'Neuropix-3a'):
-                if processor['@pluginName'] == 'Neuropix-3a':
-                    oe_probe = Probe(processor)
-                    probes[oe_probe.probeSN] = oe_probe
+                if (processor['@pluginName'] == 'Neuropix-3a'
+                        or 'NP_PROBE' not in processor['EDITOR']):
+                    probe = Probe(processor)
+                    probes[probe.probe_SN] = probe
                 else:
                     for probe_index in range(len(processor['EDITOR']['NP_PROBE'])):
-                        oe_probe = Probe(processor, probe_index)
-                        probes[oe_probe.probe_SN] = oe_probe
+                        probe = Probe(processor, probe_index)
+                        probes[probe.probe_SN] = probe
 
-        for probe_index, probe_SN in enumerate(probes.keys()):
+        for probe_index, probe_SN in enumerate(probes):
 
-            oe_probe = probes[probe_SN]
+            probe = probes[probe_SN]
 
             for rec in self.experiment.recordings:
-                for cont_info, analog_signal in zip(rec._oebin['continuous'],
-                                                    rec.analog_signals):
-                    if cont_info['source_processor_id'] != oe_probe.processor_id:
+                for continuous_info, analog_signal in zip(rec._oebin['continuous'],
+                                                          rec.analog_signals):
+                    if continuous_info['source_processor_id'] != probe.processor_id:
                         continue
 
-                    if cont_info['source_processor_sub_idx'] == probe_index * 2:  # ap data
-                        assert cont_info['sample_rate'] == analog_signal.sample_rate == 30000
-                        cont_type = 'ap'
+                    if continuous_info['source_processor_sub_idx'] == probe_index * 2:  # ap data
+                        assert continuous_info['sample_rate'] == analog_signal.sample_rate == 30000
+                        continuous_type = 'ap'
 
-                        oe_probe.recording_info['recording_count'] += 1
-                        oe_probe.recording_info['recording_datetimes'].append(
+                        probe.recording_info['recording_count'] += 1
+                        probe.recording_info['recording_datetimes'].append(
                             rec.datetime)
-                        oe_probe.recording_info['recording_durations'].append(
+                        probe.recording_info['recording_durations'].append(
                             float(rec.duration))
-                        oe_probe.recording_info['recording_files'].append(
-                            rec.absolute_foldername / 'continuous' / cont_info['folder_name'])
+                        probe.recording_info['recording_files'].append(
+                            rec.absolute_foldername / 'continuous' / continuous_info['folder_name'])
 
-                    elif cont_info['source_processor_sub_idx'] == probe_index * 2 + 1:  # lfp data
-                        assert cont_info['sample_rate'] == analog_signal.sample_rate == 2500
-                        cont_type = 'lfp'
+                    elif continuous_info['source_processor_sub_idx'] == probe_index * 2 + 1:  # lfp data
+                        assert continuous_info['sample_rate'] == analog_signal.sample_rate == 2500
+                        continuous_type = 'lfp'
 
-                    if getattr(oe_probe, cont_type + '_meta') is None:
-                        cont_info['channels_ids'] = analog_signal.channel_ids
-                        cont_info['channels_names'] = analog_signal.channel_names
-                        cont_info['channels_gains'] = analog_signal.gains
-                        setattr(oe_probe, cont_type + '_meta', cont_info)
+                    meta = getattr(probe, continuous_type + '_meta')
+                    if not meta:
+                        meta.update(**continuous_info,
+                                    channels_ids=analog_signal.channel_ids,
+                                    channels_names=analog_signal.channel_names,
+                                    channels_gains=analog_signal.gains)
 
-                    oe_probe.__dict__[f'{cont_type}_analog_signals'].append(analog_signal)
+                    signal = getattr(probe, continuous_type + '_analog_signals')
+                    signal.append(analog_signal)
 
         return probes
 
@@ -108,18 +111,19 @@ class Probe:
     def __init__(self, processor, probe_index=0):
         self.processor_id = int(processor['@NodeId'])
 
-        if processor['@pluginName'] == 'Neuropix-3a':
-            
+        if processor['@pluginName'] == 'Neuropix-3a' or 'NP_PROBE' not in processor['EDITOR']:
             self.probe_info = processor['EDITOR']['PROBE']
             self.probe_SN = self.probe_info['@probe_serial_number']
-            self.probe_model = "Neuropixels 3A"
+            self.probe_model = {
+                "Neuropix-PXI": "neuropixels 1.0 - 3B",
+                "Neuropix-3a": "neuropixels 1.0 - 3A"}[processor['@pluginName']]
         else:
             self.probe_info = processor['EDITOR']['NP_PROBE'][probe_index]
             self.probe_SN = self.probe_info['@probe_serial_number']
             self.probe_model = self.probe_info['@probe_name']
 
-        self.ap_meta = None
-        self.lfp_meta = None
+        self.ap_meta = {}
+        self.lfp_meta = {}
 
         self.ap_analog_signals = []
         self.lfp_analog_signals = []

element_array_ephys/readers/openephys.py

@@ -0,0 +1,2 @@
+"""Package metadata."""
+__version__ = '0.1.1'

element_array_ephys/version.py

@@ -1,6 +1,7 @@
 from setuptools import setup, find_packages
 from os import path
 
+pkg_name = 'element_array_ephys'
 here = path.abspath(path.dirname(__file__))
 
 long_description = """"
@@ -10,9 +11,12 @@
 with open(path.join(here, 'requirements.txt')) as f:
     requirements = f.read().splitlines()
 
+with open(path.join(here, pkg_name, 'version.py')) as f:
+    exec(f.read())
+
 setup(
     name='element-array-ephys',
-    version='0.0.1',
+    version=__version__,
     description="DataJoint Element for Extracellular Array Electrophysiology",
     long_description=long_description,
     author='DataJoint NEURO',