Merge pull request #70 from ttngu207/no-curation

bugfix for LFP electrode mapping

Author: sidhulyalkar

element_array_ephys/ephys_acute.py

@@ -407,7 +407,7 @@ def make(self, key):
                                 for key in electrode_query.fetch('KEY')}
 
             electrode_keys.extend(probe_electrodes[channel_idx]
-                                  for channel_idx in oe_probe.lfp_meta['channels_indices'])
+                                  for channel_idx in lfp_channel_ind)
         else:
             raise NotImplementedError(f'LFP extraction from acquisition software'
                                       f' of type {acq_software} is not yet implemented')
@@ -428,7 +428,8 @@ class ClusteringMethod(dj.Lookup):
     clustering_method_desc: varchar(1000)
     """
 
-    contents = [('kilosort2.5', 'kilosort2.5 clustering method'),
+    contents = [('kilosort2', 'kilosort2 clustering method'),
+                ('kilosort2.5', 'kilosort2.5 clustering method'),
                 ('kilosort3', 'kilosort3 clustering method')]
 
 

element_array_ephys/ephys_chronic.py

@@ -4,11 +4,15 @@
 import numpy as np
 import inspect
 import importlib
+from decimal import Decimal
 
 from element_interface.utils import find_root_directory, find_full_path, dict_to_uuid
 
 from .readers import spikeglx, kilosort, openephys
-from . import probe
+from . import probe, get_logger
+
+
+log = get_logger(__name__)
 
 schema = dj.schema()
 
@@ -350,7 +354,7 @@ def make(self, key):
                                 for key in electrode_query.fetch('KEY')}
 
             electrode_keys.extend(probe_electrodes[channel_idx]
-                                  for channel_idx in oe_probe.lfp_meta['channels_indices'])
+                                  for channel_idx in lfp_channel_ind)
         else:
             raise NotImplementedError(f'LFP extraction from acquisition software'
                                       f' of type {acq_software} is not yet implemented')
@@ -371,7 +375,8 @@ class ClusteringMethod(dj.Lookup):
     clustering_method_desc: varchar(1000)
     """
 
-    contents = [('kilosort2.5', 'kilosort2.5 clustering method'),
+    contents = [('kilosort2', 'kilosort2 clustering method'),
+                ('kilosort2.5', 'kilosort2.5 clustering method'),
                 ('kilosort3', 'kilosort3 clustering method')]
 
 

element_array_ephys/ephys_no_curation.py

@@ -406,7 +406,7 @@ def make(self, key):
                                 for key in electrode_query.fetch('KEY')}
 
             electrode_keys.extend(probe_electrodes[channel_idx]
-                                  for channel_idx in oe_probe.lfp_meta['channels_indices'])
+                                  for channel_idx in lfp_channel_ind)
         else:
             raise NotImplementedError(f'LFP extraction from acquisition software'
                                       f' of type {acq_software} is not yet implemented')
@@ -427,7 +427,8 @@ class ClusteringMethod(dj.Lookup):
     clustering_method_desc: varchar(1000)
     """
 
-    contents = [('kilosort2.5', 'kilosort2.5 clustering method'),
+    contents = [('kilosort2', 'kilosort2 clustering method'),
+                ('kilosort2.5', 'kilosort2.5 clustering method'),
                 ('kilosort3', 'kilosort3 clustering method')]
 
 

requirements.txt

@@ -1,5 +1,5 @@
 datajoint>=0.13
-pyopenephys @ git+https://github.com/ttngu207/pyopenephys.git
+pyopenephys @ git+https://github.com/datajoint-company/pyopenephys.git
 openpyxl
 pynwb==1.4.0
 element-interface @ git+https://github.com/datajoint/element-interface.git