ElectrodesTable

src/pynwb/ecephys.py

@@ -1,9 +1,9 @@
 import warnings
 from collections.abc import Iterable
 
-from hdmf.common import DynamicTableRegion
+from hdmf.common import DynamicTableRegion, DynamicTable, VectorData
 from hdmf.data_utils import DataChunkIterator, assertEqualShape
-from hdmf.utils import docval, popargs, get_docval, popargs_to_dict, get_data_shape
+from hdmf.utils import docval, popargs, getargs, get_docval, popargs_to_dict, get_data_shape
 
 from . import register_class, CORE_NAMESPACE
 from .base import TimeSeries
@@ -37,6 +37,47 @@ def __init__(self, **kwargs):
             setattr(self, key, val)
 
 
+@register_class('ElectrodesTable', CORE_NAMESPACE)
+class ElectrodesTable(DynamicTable):
+    """TODO"""
+
+    __columns__ = (
+        {'name': 'location', 'description': 'TODO', 'required': True},
+        {'name': 'group', 'description': 'TODO', 'required': True})
+
+    @docval({'name': 'group_name', 'type': VectorData, 'doc':'TODO', 'default': None},
+            {'name': 'x', 'type': float, 'doc':'TODO', 'default': None},
+            {'name': 'y', 'type': float, 'doc':'TODO', 'default': None},
+            {'name': 'z', 'type': float, 'doc':'TODO', 'default': None},
+            {'name': 'imp', 'type': float, 'doc':'TODO', 'default': None},
+            {'name': 'filtering', 'type': str, 'doc':'TODO', 'default': None},
+            {'name': 'rel_x', 'type': float, 'doc':'TODO', 'default': None},
+            {'name': 'rel_y', 'type': float, 'doc':'TODO', 'default': None},
+            {'name': 'rel_z', 'type': float, 'doc':'TODO', 'default': None},
+            {'name': 'reference', 'type': VectorData, 'doc':'TODO', 'default': None},)
+    def __init__(self, **kwargs):
+        kwargs['name'] = 'electrodes'
+        kwargs['description'] = 'metadata about extracellular electrodes'
+
+        # optional fields
+        keys_to_set = (
+            'group_name',
+            'x',
+            'y',
+            'z',
+            'imp',
+            'filtering',
+            'rel_x',
+            'rel_y',
+            'rel_z',
+            'reference')
+        args_to_set = popargs_to_dict(keys_to_set, kwargs)
+        for key, val in args_to_set.items():
+            setattr(self, key, val)
+
+        super().__init__(**kwargs)
+
+
 @register_class('ElectricalSeries', CORE_NAMESPACE)
 class ElectricalSeries(TimeSeries):
     """

src/pynwb/file.py

@@ -15,7 +15,7 @@
 from .base import TimeSeries, ProcessingModule
 from .device import Device
 from .epoch import TimeIntervals
-from .ecephys import ElectrodeGroup
+from .ecephys import ElectrodeGroup, ElectrodesTable
 from .icephys import (IntracellularElectrode, SweepTable, PatchClampSeries, IntracellularRecordingsTable,
                       SimultaneousRecordingsTable, SequentialRecordingsTable, RepetitionsTable,
                       ExperimentalConditionsTable)
@@ -377,7 +377,7 @@ class NWBFile(MultiContainerInterface, HERDManager):
             {'name': 'lab_meta_data', 'type': (list, tuple), 'default': None,
              'doc': 'an extension that contains lab-specific meta-data'},
             {'name': 'electrodes', 'type': DynamicTable,
-             'doc': 'the ElectrodeTable that belongs to this NWBFile', 'default': None},
+             'doc': 'the ElectrodesTable that belongs to this NWBFile', 'default': None},
             {'name': 'electrode_groups', 'type': Iterable,
              'doc': 'the ElectrodeGroups that belong to this NWBFile', 'default': None},
             {'name': 'ic_electrodes', 'type': (list, tuple),
@@ -644,7 +644,7 @@ def add_epoch(self, **kwargs):
 
     def __check_electrodes(self):
         if self.electrodes is None:
-            self.electrodes = ElectrodeTable()
+            self.electrodes = ElectrodesTable()
 
     @docval(*get_docval(DynamicTable.add_column), allow_extra=True)
     def add_electrode_column(self, **kwargs):
@@ -701,8 +701,8 @@ def add_electrode(self, **kwargs):
             raise ValueError("The 'location' argument is required when creating an electrode.")
         if not kwargs['group']:
             raise ValueError("The 'group' argument is required when creating an electrode.")
-        if d.get('group_name', None) is None:
-            d['group_name'] = d['group'].name
+        # if d.get('group_name', None) is None:
+        #     d['group_name'] = d['group'].name
 
         new_cols = [('x', 'the x coordinate of the position (+x is posterior)'),
                     ('y', 'the y coordinate of the position (+y is inferior)'),
@@ -738,7 +738,7 @@ def create_electrode_table_region(self, **kwargs):
         for idx in region:
             if idx < 0 or idx >= len(self.electrodes):
                 raise IndexError('The index ' + str(idx) +
-                                 ' is out of range for the ElectrodeTable of length '
+                                 ' is out of range for the ElectrodesTable of length '
                                  + str(len(self.electrodes)))
         desc = getargs('description', kwargs)
         name = getargs('name', kwargs)
@@ -820,13 +820,13 @@ def add_invalid_time_interval(self, **kwargs):
         self.__check_invalid_times()
         self.invalid_times.add_interval(**kwargs)
 
-    @docval({'name': 'electrode_table', 'type': DynamicTable, 'doc': 'the ElectrodeTable for this file'})
+    @docval({'name': 'electrode_table', 'type': DynamicTable, 'doc': 'the ElectrodesTable for this file'})
     def set_electrode_table(self, **kwargs):
         """
-        Set the electrode table of this NWBFile to an existing ElectrodeTable
+        Set the electrode table of this NWBFile to an existing ElectrodesTable
         """
         if self.electrodes is not None:
-            msg = 'ElectrodeTable already exists, cannot overwrite'
+            msg = 'ElectrodesTable already exists, cannot overwrite'
             raise ValueError(msg)
         electrode_table = getargs('electrode_table', kwargs)
         self.electrodes = electrode_table
@@ -1179,14 +1179,14 @@ def _tablefunc(table_name, description, columns):
     return t
 
 
-def ElectrodeTable(name='electrodes',
-                   description='metadata about extracellular electrodes'):
-    return _tablefunc(name, description,
-                      [('location', 'the location of channel within the subject e.g. brain region'),
-                       ('group', 'a reference to the ElectrodeGroup this electrode is a part of'),
-                       ('group_name', 'the name of the ElectrodeGroup this electrode is a part of')
-                       ]
-                      )
+# def ElectrodesTable(name='electrodes',
+#                    description='metadata about extracellular electrodes'):
+#     return _tablefunc(name, description,
+#                       [('location', 'the location of channel within the subject e.g. brain region'),
+#                        ('group', 'a reference to the ElectrodeGroup this electrode is a part of'),
+#                        ('group_name', 'the name of the ElectrodeGroup this electrode is a part of')
+#                        ]
+#                       )
 
 
 def TrialTable(name='trials', description='metadata about experimental trials'):

src/pynwb/io/file.py

@@ -34,6 +34,7 @@ def __init__(self, spec):
         # map "stimulus" to NWBDataInterface and DynamicTable and unmap the spec for TimeSeries because it is
         # included in the mapping to NWBDataInterface
         self.unmap(stimulus_spec.get_group('presentation').get_neurodata_type('TimeSeries'))
+        # breakpoint()
         self.map_spec('stimulus', stimulus_spec.get_group('presentation').get_neurodata_type('NWBDataInterface'))
         self.map_spec('stimulus', stimulus_spec.get_group('presentation').get_neurodata_type('DynamicTable'))
         self.map_spec('stimulus_template', stimulus_spec.get_group('templates').get_neurodata_type('TimeSeries'))
@@ -73,6 +74,7 @@ def __init__(self, spec):
 
         ecephys_spec = general_spec.get_group('extracellular_ephys')
         self.unmap(ecephys_spec)
+        # breakpoint()
         self.map_spec('electrodes', ecephys_spec.get_group('electrodes'))
         self.map_spec('electrode_groups', ecephys_spec.get_neurodata_type('ElectrodeGroup'))
 

tests/unit/foo.py

@@ -0,0 +1,64 @@
+from datetime import datetime
+from uuid import uuid4
+
+import numpy as np
+from dateutil.tz import tzlocal
+from hdmf.common import VectorData
+
+from pynwb import NWBHDF5IO, NWBFile
+from pynwb.ecephys import LFP, ElectricalSeries, ElectrodeGroup, ElectrodesTable
+
+nwbfile = NWBFile(
+    session_description="my first synthetic recording",
+    identifier=str(uuid4()),
+    session_start_time=datetime.now(tzlocal()),
+    experimenter=[
+        "Baggins, Bilbo",
+    ],
+    lab="Bag End Laboratory",
+    institution="University of Middle Earth at the Shire",
+    experiment_description="I went on an adventure to reclaim vast treasures.",
+    session_id="LONELYMTN001",
+)
+
+device = nwbfile.create_device(
+    name="array", description="the best array", manufacturer="Probe Company 9000"
+)
+
+group = ElectrodeGroup( name='foo',
+        description="electrode group",
+        device=device,
+        location="brain area",)
+# location_col = VectorData(name='location', description='foo', data=['brain area'])
+# group_col = VectorData(name='groups', description='foo', data=[group])
+
+# table = ElectrodesTable()
+# nwbfile.electrodes = table
+# nwbfile.add_electrode(group=group, location='brain')
+# breakpoint()
+# nwbfile.add_electrode_column(name="label", description="label of electrode")
+
+nshanks = 4
+nchannels_per_shank = 3
+electrode_counter = 0
+#
+for ishank in range(nshanks):
+    # create an electrode group for this shank
+    electrode_group = nwbfile.create_electrode_group(
+        name="shank{}".format(ishank),
+        description="electrode group for shank {}".format(ishank),
+        device=device,
+        location="brain area",
+    )
+    # add electrodes to the electrode table
+    for ielec in range(nchannels_per_shank):
+        nwbfile.add_electrode(
+            group=electrode_group,
+            label="shank{}elec{}".format(ishank, ielec),
+            location="brain area",
+        )
+        electrode_counter += 1
+# breakpoint()
+with NWBHDF5IO("ecephys_tutorial.nwb", "w") as io:
+    io.write(nwbfile)
+breakpoint()