Adding ability to record ECP to nwb files.

bmtk/simulator/bionet/modules/ecp.py

@@ -30,9 +30,10 @@
 from dateutil.tz import tzlocal
 from uuid import uuid4
 
+
 from bmtk.simulator.bionet.modules.sim_module import SimulatorMod
 from bmtk.utils.sonata.utils import add_hdf5_magic, add_hdf5_version
-
+from bmtk.simulator.bionet.io_tools import io
 
 pc = h.ParallelContext()
 MPI_RANK = int(pc.id())
@@ -83,8 +84,12 @@ def __init__(self, tmp_dir, file_name, electrode_positions, file_name_nwb=None,
 
         self._nwb_path = None
         if file_name_nwb:
-            self._nwb_path = file_name_nwb if os.path.isabs(file_name_nwb) else os.path.join(tmp_dir, file_name_nwb)
-
+            try:
+                import pynwb
+                self._nwb_path = file_name_nwb if os.path.isabs(file_name_nwb) else os.path.join(tmp_dir, file_name_nwb)
+
+            except ImportError as ie:
+                io.log_warning('pynwb library is not installed, simulation cannot be saved to {file_name_nwb}.')      
 
         self._local_gids = []
 
@@ -246,26 +251,26 @@ def finalize(self, sim):
         self._delete_tmp_files()
         pc.barrier()
 
-        if self._nwb_path:
+        if self._nwb_path and MPI_RANK == 0:
             convert2nwb(self._nwb_path, self._ecp_output, self._positions_file)
 
+        pc.barrier()
 
 
 def convert2nwb(nwb_path, orig_hdf5_lfp, electrodes_file):
     import pynwb
 
+    # io.log_debug('Writing to NWB format in {nwb_path}')
     if os.path.exists(nwb_path):
         io = pynwb.NWBHDF5IO(nwb_path, 'a')
         nwbfile = io.read()
-        print('appending lfp')
     else:
         io = pynwb.NWBHDF5IO(nwb_path, "w")
         nwbfile = pynwb.NWBFile(
             session_start_time=datetime.now(tzlocal()),
             session_description="test time",
             identifier=str(uuid4()),
         )
-        print('new nwb file')
 
     electrodes_metdata_df = pd.read_csv(electrodes_file, sep=' ').set_index('channel')
 
@@ -281,14 +286,11 @@ def convert2nwb(nwb_path, orig_hdf5_lfp, electrodes_file):
     )
 
     # electrodes_file
-
     nwbfile.add_electrode_column(name="channel_id", description="label of electrode")
     with h5py.File(orig_hdf5_lfp, 'r') as orig_h5:
         channels = orig_h5['ecp/channel_id'][()]
         for chan in channels:
             chan_data = electrodes_metdata_df.loc[chan]
-            # print(chan_data.get('location', 'None'))
-            # print(chan_data.get('x_pos', 'Not Avail'))
             nwbfile.add_electrode(
                 group=electrode_group,
                 channel_id=chan,
@@ -327,8 +329,6 @@ def convert2nwb(nwb_path, orig_hdf5_lfp, electrodes_file):
 
     io.write(nwbfile)
 
-    # print(nwb_path)
-
 
 class RecXElectrode(object):
     """Extracellular electrode

bmtk/utils/reports/spike_trains/spikes_file_writers.py

@@ -159,12 +159,11 @@ def write_nwb(path, spiketrain_reader, mode='a', include_population=True, units=
     if MPI_rank == 0:
         # Last checked pynwb doesn't support writing on multiple cores, must let first core do all the
         # writing to NWB.
-
         if os.path.exists(path) and mode != 'w':
             io = pynwb.NWBHDF5IO(path, 'a')
             nwbfile = io.read()
         else:
-            io = pynwb.NWBHDF5IO(path, mode)
+            io = pynwb.NWBHDF5IO(path, 'w')
             nwbfile = pynwb.NWBFile(
                 session_description='BMTK {} generated NWB spikes file'.format(bmtk.__version__),
                 identifier='Generated in-silico, no session id',  # TODO: No idea what to put here?
@@ -180,20 +179,22 @@ def write_nwb(path, spiketrain_reader, mode='a', include_population=True, units=
 
         nwbfile.add_unit_column(name="node_id", description="id of each node within a population")
 
-        for population in spiketrain_reader.populations:
-            for node_id in spiketrain_reader.node_ids(population=population):
-                spikes_times = spiketrain_reader.get_times(node_id=node_id, population=population)
-                if spikes_times is None or len(spikes_times) == 0:
-                    # No spikes for given node, don't try to write to nwb 
-                    continue
-
-                # sometimes bmtk/sonata may default to use different 32 or unsigned data-types which will cause
-                # nwb to throw a fit. Need to explicity convert data-types just in case.
-                spikes_times = spikes_times.astype('float64')
-                node_id = int(node_id)
+    for population in spiketrain_reader.populations:
+        for node_id in spiketrain_reader.node_ids(population=population):
+            spikes_times = spiketrain_reader.get_times(node_id=node_id, population=population)
+            if spikes_times is None or len(spikes_times) == 0:
+                # No spikes for given node, don't try to write to nwb 
+                continue
+
+            # sometimes bmtk/sonata may default to use different 32 or unsigned data-types which will cause
+            # nwb to throw a fit. Need to explicity convert data-types just in case.
+            spikes_times = np.array(spikes_times).astype('float64')
+            node_id = int(node_id)
+            if MPI_rank == 0:
                 add_unit(node_id, population, spikes_times)
 
-        # with pynwb.NWBHDF5IO(path, mode) as io:
+    # with pynwb.NWBHDF5IO(path, mode) as io:
+    if MPI_rank == 0:
         io.write(nwbfile)
 
     comm_barrier()

docs/autodocs/source/bionet.rst

@@ -237,6 +237,29 @@ And in the config
   cell’s ECP.
 
 
+**Saving ECP to NWB (Neurodata without Borders) format**
+
+You can save the recorded extraceullar field to NWB format by specifying the "file_name_nwb" option.
+
+.. code:: json
+
+    {
+        "ecp": {
+            "cells": "all",
+            "variable_name": "v",
+            "module": "extracellular",
+            "electrode_positions": "components/xelectrode/linear_probe.csv",
+            "file_name": "ecp.h5",
+            "file_name_nwb": "session_data.nwb"
+        }
+    }
+
+In the above case will create an ElectricalSeries acquistion in the session_data.nwb file which can be analyzed
+using pynwb, Matlab, pynapple, or other tools that support the reading of the NWB ecephys data. If the same session
+nwb is also being used to write spikes or membrane properties, BMTK will attempt to append all data of the same
+simulation "session" into a single file. 
+
+
 Synaptic Variables
 ++++++++++++++++++
 Similar to recording from membrane potential, by setting the ``module`` parameter to ``netcon_report``, you can record the