Clean up IO classes

Author: rly

src/pynwb/io/icephys.py

@@ -26,11 +26,6 @@ def __init__(self, spec):
 
 @register_map(IntracellularRecordingsTable)
 class IntracellularRecordingsTableMap(AlignedDynamicTableMap):
-    """
-    Customize the mapping for AlignedDynamicTable
-    """
-    def __init__(self, spec):
-        super().__init__(spec)
 
     @DynamicTableMap.object_attr('electrodes')
     def electrodes(self, container, manager):

src/pynwb/io/misc.py

@@ -7,8 +7,6 @@
 
 @register_map(DecompositionSeries)
 class DecompositionSeriesMap(TimeSeriesMap):
-    def __init__(self, spec):
-        super().__init__(spec)
 
     @TimeSeriesMap.constructor_arg('bands')
     def bands(self, builder, manager):
@@ -23,9 +21,6 @@ def bands(self, builder, manager):
 @register_map(Units)
 class UnitsMap(DynamicTableMap):
 
-    def __init__(self, spec):
-        super().__init__(spec)
-
     @DynamicTableMap.constructor_arg('resolution')
     def resolution_carg(self, builder, manager):
         if 'spike_times' in builder:

units.py

@@ -0,0 +1,56 @@
+from datetime import datetime
+from uuid import uuid4
+
+import numpy as np
+from dateutil import tz
+
+from pynwb import NWBHDF5IO, NWBFile, TimeSeries
+
+
+nwbfile = NWBFile(
+    session_description="Mouse exploring an open field",  # required
+    identifier=str(uuid4()),  # required
+    session_start_time=datetime(2018, 4, 25, 2, 30, 3, tzinfo=tz.gettz("US/Pacific")),  # required
+    experimenter=[
+        "Baggins, Bilbo",
+    ],  # optional
+ )
+
+waveforms_list = [
+    np.array([  # unit 1
+        [  # electrode 1
+            [1, 2, 3, 4, 5],  # spike time 1 [sample 1, sample 2, ...]
+            [2, 3, 4, 5, 6],  # spike time 2
+        ],
+        [  # electrode 2
+            [3, 4, 5, 6, 7],  # spike time 1 [sample 1, sample 2, ...]
+            [2, 3, 4, 5, 6],  # spike time 2
+        ],
+    ]),
+    np.array([  # unit 2
+        [  # electrode 1
+            [10, 20, 30, 40, 50],  # spike time 1 [sample 1, sample 2, ...]
+        ],
+        [  # electrode 2
+            [100, 200, 300, 400, 500],  # spike time 1 [sample 1, sample 2, ...]
+        ],
+    ]),
+]
+# mean and sd across spike times
+waveform_mean_list = [np.mean(i, axis=1) for i in waveforms_list]
+waveform_sd_list = [np.std(i, axis=1) for i in waveforms_list]
+
+electrodes_list = [[1, 2], [3]]
+for unit_id in range(2):
+    nwbfile.add_unit(
+        id=unit_id,
+        electrodes=electrodes_list[unit_id],
+        waveforms=waveforms_list[unit_id],
+        waveform_mean=waveform_mean_list[unit_id],  # does not support different number of electrodes
+        waveform_sd=waveform_sd_list[unit_id],  # does not support different number of electrodes
+    )
+
+    breakpoint()
+
+with NWBHDF5IO("temp.nwb", "w") as io:
+    io.write(nwbfile)