# Copyright 2017. Allen Institute. All rights reserved
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
# following conditions are met:
#
# 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following
# disclaimer.
#
# 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided with the distribution.
#
# 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
# INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
# SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
import os
from bmtk.simulator.bionet.modules.sim_module import SimulatorMod
from bmtk.utils.reports.spike_trains import SpikeTrains, sort_order, sort_order_lu
from neuron import h
pc = h.ParallelContext()
MPI_RANK = int(pc.id())
N_HOSTS = int(pc.nhost())
[docs]class SpikesMod(SimulatorMod):
"""Module use for saving spikes
"""
def __init__(self, tmp_dir, spikes_file_csv=None, spikes_file=None, spikes_file_nwb=None, cache_to_disk=True,
spikes_sort_order=None, mode='a', compression='gzip'):
# TODO: Have option to turn off caching spikes to csv.
def _file_path(file_name):
if file_name is None:
return None
if os.path.isabs(file_name):
return file_name
else:
rel_tmp = os.path.realpath(tmp_dir)
rel_fname = os.path.realpath(file_name)
if not rel_fname.startswith(rel_tmp):
return os.path.join(tmp_dir, file_name)
else:
return file_name
# return file_name if os.path.isabs(file_name) else os.path.join(tmp_dir, file_name)
self._csv_fname = _file_path(spikes_file_csv)
self._save_csv = spikes_file_csv is not None
self._h5_fname = _file_path(spikes_file)
self._save_h5 = spikes_file is not None
self._mode = mode
self._nwb_fname = _file_path(spikes_file_nwb)
self._save_nwb = spikes_file_nwb is not None
self._tmpdir = tmp_dir
self._sort_order = sort_order_lu.get(spikes_sort_order, sort_order.none)
cache_name = os.path.basename(self._h5_fname or self._csv_fname or self._nwb_fname)
self._spike_writer = SpikeTrains(cache_dir=tmp_dir, cache_name=cache_name, cache_to_disk=cache_to_disk)
self._spike_writer.compression = compression
self._gid_map = None
[docs] def initialize(self, sim):
# TODO: since it's possible that other modules may need to access spikes, set_spikes_recordings() should
# probably be called in the simulator itself.
sim.set_spikes_recording()
self._gid_map = sim.net.gid_pool
[docs] def block(self, sim, block_interval):
# take spikes from Simulator spikes vector and save to the tmp file
for gid, tVec in sim.spikes_table.items():
pop_id = self._gid_map.get_pool_id(gid)
for t in tVec:
self._spike_writer.add_spike(node_id=pop_id.node_id, timestamp=t, population=pop_id.population)
pc.barrier() # wait until all ranks have been saved
sim.set_spikes_recording() # reset recording vector
[docs] def finalize(self, sim):
# TODO: Get ride of flush/barrier calls, spike_trains should take care of it
self._spike_writer.flush()
pc.barrier()
if self._save_csv:
self._spike_writer.to_csv(self._csv_fname, sort_order=self._sort_order)
pc.barrier()
if self._save_h5:
self._spike_writer.to_sonata(self._h5_fname, sort_order=self._sort_order, mode=self._mode,
compression=self._spike_writer.compression)
pc.barrier()
if self._save_nwb:
self._spike_writer.to_nwb(self._nwb_fname, sort_order=self._sort_order)
pc.barrier()
self._spike_writer.close()
