added comments to tables

Author: Thinh Nguyen

element_array_ephys/ephys.py

@@ -97,8 +97,9 @@ class AcquisitionSoftware(dj.Lookup):
 
 
 @schema
-class ProbeInsertion(dj.Manual):  # (acute)
+class ProbeInsertion(dj.Manual):
     definition = """
+    # Probe insertion implanted into an animal for a given session.
     -> Session
     insertion_number: tinyint unsigned
     ---
@@ -109,6 +110,7 @@ class ProbeInsertion(dj.Manual):  # (acute)
 @schema
 class InsertionLocation(dj.Manual):
     definition = """
+    # Brain Location of a given probe insertion.
     -> ProbeInsertion
     ---
     -> SkullReference
@@ -124,6 +126,7 @@ class InsertionLocation(dj.Manual):
 @schema
 class EphysRecording(dj.Imported):
     definition = """
+    # Ephys recording from a probe insertion for a given session.
     -> ProbeInsertion      
     ---
     -> probe.ElectrodeConfig
@@ -133,6 +136,7 @@ class EphysRecording(dj.Imported):
 
     class EphysFile(dj.Part):
         definition = """
+        # Paths of files of a given EphysRecording round.
         -> master
         file_path: varchar(255)  # filepath relative to root data directory
         """
@@ -233,6 +237,7 @@ def make(self, key):
 @schema
 class LFP(dj.Imported):
     definition = """
+    # Acquired local field potential (LFP) from a given Ephys recording.
     -> EphysRecording
     ---
     lfp_sampling_rate: float   # (Hz)
@@ -325,6 +330,7 @@ def make(self, key):
 @schema
 class ClusteringMethod(dj.Lookup):
     definition = """
+    # Method for clustering
     clustering_method: varchar(16)
     ---
     clustering_method_desc: varchar(1000)
@@ -337,6 +343,7 @@ class ClusteringMethod(dj.Lookup):
 @schema
 class ClusteringParamSet(dj.Lookup):
     definition = """
+    # Parameter set to be used in a clustering procedure
     paramset_idx:  smallint
     ---
     -> ClusteringMethod    
@@ -387,6 +394,7 @@ class ClusterQualityLabel(dj.Lookup):
 @schema
 class ClusteringTask(dj.Manual):
     definition = """
+    # Manual table for defining a clustering task ready to be run
     -> EphysRecording
     -> ClusteringParamSet
     ---
@@ -404,6 +412,7 @@ class Clustering(dj.Imported):
     + If `task_mode == "load"`: verify output
     """
     definition = """
+    # Clustering Procedure
     -> ClusteringTask
     ---
     clustering_time: datetime  # time of generation of this set of clustering results 
@@ -430,6 +439,7 @@ def make(self, key):
 @schema
 class Curation(dj.Manual):
     definition = """
+    # Manual curation procedure
     -> Clustering
     curation_id: int
     ---
@@ -465,12 +475,14 @@ def create1_from_clustering_task(self, key, curation_note=''):
 @schema
 class CuratedClustering(dj.Imported):
     definition = """
+    # Clustering results of a curation.
     -> Curation    
     """
 
     class Unit(dj.Part):
         definition = """   
         -> master
+        # Properties of a given unit from a round of clustering (and curation)
         unit: int
         ---
         -> probe.ElectrodeConfig.Electrode  # electrode with highest waveform amplitude for this unit
@@ -535,19 +547,22 @@ def make(self, key):
 @schema
 class WaveformSet(dj.Imported):
     definition = """
+    # A set of spike waveforms for units out of a given CuratedClustering
     -> CuratedClustering
     """
 
     class PeakWaveform(dj.Part):
         definition = """
+        # Mean waveform across spikes for a given unit at its representative electrode
         -> master
         -> CuratedClustering.Unit
         ---
-        peak_electrode_waveform: longblob  # (uV) mean waveform for this unit's peak electrode
+        peak_electrode_waveform: longblob  # (uV) mean waveform for a given unit at its representative electrode
         """
 
     class Waveform(dj.Part):
         definition = """
+        # Spike waveforms and their mean across spikes for the given unit
         -> master
         -> CuratedClustering.Unit
         -> probe.ElectrodeConfig.Electrode  

element_array_ephys/probe.py

@@ -26,6 +26,7 @@ def activate(schema_name, *, create_schema=True, create_tables=True):
 @schema
 class ProbeType(dj.Lookup):
     definition = """
+    # Type of probe, with specific electrodes geometry defined
     probe_type: varchar(32)  # e.g. neuropixels_1.0
     """
 
@@ -136,7 +137,8 @@ def build_electrodes(site_count, col_spacing, row_spacing,
 
 @schema
 class Probe(dj.Lookup):
-    definition = """  # represent a physical probe
+    definition = """
+    # Represent a physical probe with unique identification
     probe: varchar(32)  # unique identifier for this model of probe (e.g. serial number)
     ---
     -> ProbeType
@@ -147,6 +149,7 @@ class Probe(dj.Lookup):
 @schema
 class ElectrodeConfig(dj.Lookup):
     definition = """
+    # The electrode configuration setting on a given probe
     electrode_config_hash: uuid  
     ---
     -> ProbeType