Merge remote-tracking branch 'cbroz1/ben' into convert_to_nwb

# Conflicts:
#	element_array_ephys/export/nwb/nwb.py

Author: bendichter

element_array_ephys/__init__.py

@@ -0,0 +1,16 @@
+import datajoint as dj
+import logging
+import os
+
+
+dj.config['enable_python_native_blobs'] = True
+
+
+def get_logger(name):
+    log = logging.getLogger(name)
+    log.setLevel(os.getenv('LOGLEVEL', 'INFO'))
+    return log
+
+
+# ephys_acute as default
+import element_array_ephys.ephys_acute as ephys

element_array_ephys/ephys.py renamed to element_array_ephys/ephys_acute.py

@@ -57,9 +57,9 @@ def activate(ephys_schema_name, probe_schema_name=None, *, create_schema=True,
 
 def get_ephys_root_data_dir() -> list:
     """
-    All data paths, directories in DataJoint Elements are recommended to be 
-    stored as relative paths, with respect to some user-configured "root" 
-    directory, which varies from machine to machine (e.g. different mounted 
+    All data paths, directories in DataJoint Elements are recommended to be
+    stored as relative paths, with respect to some user-configured "root"
+    directory, which varies from machine to machine (e.g. different mounted
     drive locations)
 
     get_ephys_root_data_dir() -> list
@@ -142,7 +142,7 @@ class EphysFile(dj.Part):
 
     def make(self, key):
 
-        session_dir = find_full_path(get_ephys_root_data_dir(), 
+        session_dir = find_full_path(get_ephys_root_data_dir(),
                                      get_session_directory(key))
 
         inserted_probe_serial_number = (ProbeInsertion * probe.Probe & key).fetch1('probe')
@@ -191,7 +191,7 @@ def make(self, key):
                           'acq_software': acq_software,
                           'sampling_rate': spikeglx_meta.meta['imSampRate']})
 
-            root_dir = find_root_directory(get_ephys_root_data_dir(), 
+            root_dir = find_root_directory(get_ephys_root_data_dir(),
                                            meta_filepath)
             self.EphysFile.insert1({
                 **key,
@@ -294,8 +294,8 @@ def make(self, key):
                 shank, shank_col, shank_row, _ = spikeglx_recording.apmeta.shankmap['data'][recorded_site]
                 electrode_keys.append(probe_electrodes[(shank, shank_col, shank_row)])
         elif acq_software == 'Open Ephys':
-            
-            session_dir = find_full_path(get_ephys_root_data_dir(), 
+
+            session_dir = find_full_path(get_ephys_root_data_dir(),
                                          get_session_directory(key))
 
             loaded_oe = openephys.OpenEphys(session_dir)
@@ -457,8 +457,14 @@ class Curation(dj.Manual):
 
     def create1_from_clustering_task(self, key, curation_note=''):
         """
-        A function to create a new corresponding "Curation" for a particular 
+<<<<<<< HEAD
+        A function to create a new corresponding "Curation" for a particular
         "ClusteringTask"
+=======
+        A function to create a new corresponding "Curation" for a particular
+        "ClusteringTask", which assumes that no curation was performed on the
+        dataset
+>>>>>>> dee1c29 (Rebase, squashed. See Details)
         """
         if key not in Clustering():
             raise ValueError(f'No corresponding entry in Clustering available'
@@ -472,9 +478,9 @@ def create1_from_clustering_task(self, key, curation_note=''):
         # Synthesize curation_id
         curation_id = dj.U().aggr(self & key, n='ifnull(max(curation_id)+1,1)').fetch1('n')
         self.insert1({**key, 'curation_id': curation_id,
-                      'curation_time': creation_time, 
+                      'curation_time': creation_time,
                       'curation_output_dir': output_dir,
-                      'quality_control': is_qc, 
+                      'quality_control': is_qc,
                       'manual_curation': is_curated,
                       'curation_note': curation_note})
 
@@ -622,7 +628,7 @@ def yield_unit_waveforms():
                 spikeglx_meta_filepath = get_spikeglx_meta_filepath(key)
                 neuropixels_recording = spikeglx.SpikeGLX(spikeglx_meta_filepath.parent)
             elif acq_software == 'Open Ephys':
-                session_dir = find_full_path(get_ephys_root_data_dir(), 
+                session_dir = find_full_path(get_ephys_root_data_dir(),
                                              get_session_directory(key))
                 openephys_dataset = openephys.OpenEphys(session_dir)
                 neuropixels_recording = openephys_dataset.probes[probe_serial_number]
@@ -669,7 +675,7 @@ def get_spikeglx_meta_filepath(ephys_recording_key):
     except FileNotFoundError:
         # if not found, search in session_dir again
         if not spikeglx_meta_filepath.exists():
-            session_dir = find_full_path(get_ephys_root_data_dir(), 
+            session_dir = find_full_path(get_ephys_root_data_dir(),
                                          get_session_directory(
                                              ephys_recording_key))
             inserted_probe_serial_number = (ProbeInsertion * probe.Probe
@@ -708,7 +714,7 @@ def get_neuropixels_channel2electrode_map(ephys_recording_key, acq_software):
             for recorded_site, (shank, shank_col, shank_row, _) in enumerate(
                 spikeglx_meta.shankmap['data'])}
     elif acq_software == 'Open Ephys':
-        session_dir = find_full_path(get_ephys_root_data_dir(), 
+        session_dir = find_full_path(get_ephys_root_data_dir(),
                                      get_session_directory(ephys_recording_key))
         openephys_dataset = openephys.OpenEphys(session_dir)
         probe_serial_number = (ProbeInsertion & ephys_recording_key).fetch1('probe')