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import os
from neuron import h
import h5py
import numpy as np
from bmtk.simulator.bionet.modules.sim_module import SimulatorMod
from bmtk.utils.reports.current_writer import CurrentWriterv01
pc = h.ParallelContext()
MPI_RANK = int(pc.id())
N_HOSTS = int(pc.nhost())
[docs]class ClampReport(SimulatorMod):
def __init__(self, tmp_dir, file_name, variable_name, buffer_data=True, **kwargs):
"""Module used for saving NEURON clamp currents at each given step of the simulation.
:param variable_name: which type of clamp it is a report of. As of now options are se, ic, and f_ic.
:param clamps: indexes of the clamp list to make a report of.
:param tmp_dir:
:param file_name: name of h5 file to save variable to.
:param buffer_data: Set to true then data will be saved to memory until written to disk during each block, reqs.
more memory but faster. Set to false and data will be written to disk on each step (default: True)
"""
self._tmp_dir = tmp_dir
self._file_name = file_name if os.path.isabs(file_name) else os.path.join(tmp_dir, file_name)
if N_HOSTS > 1:
self._tmp_files = []
for i in range(N_HOSTS):
tmp_name = variable_name + str(i)
self._tmp_files.append(os.path.join(self._tmp_dir, tmp_name))
self._rank_file = self._tmp_files[MPI_RANK]
else:
self._rank_file = self._file_name
self._var_recorder = None
self._variable_name = variable_name
self._buffer_data = buffer_data
@property
def variable(self):
return self._variable_name
[docs] def initialize(self, sim, clamps):
self._clamps = clamps
self._var_recorder = CurrentWriterv01(self._rank_file, num_currents=len(self._clamps),
buffer_size=sim.nsteps_block, buffer_data=self._buffer_data, tstart=0.0,
tstop=sim.tstop, dt=sim.dt)
self._var_recorder.initialize()
[docs] def step(self, sim, tstep):
# save the current of each clamp at the current time-step.
vals = []
for clamp in self._clamps:
vals.append(clamp._stim.i)
self._var_recorder.record_clamps(vals, tstep)
[docs] def block(self, sim, block_interval):
# write variables in memory to file
self._var_recorder.flush()
[docs] def finalize(self, sim):
# TODO: Build in mpi signaling into var_recorder
pc.barrier()
self._var_recorder.close()
if MPI_RANK == 0:
self.merge()
[docs] def merge(self):
if N_HOSTS > 1:
h5final = h5py.File(self._file_name, 'w')
all_currents = []
for i in range(N_HOSTS):
tmp_file = h5py.File(self._tmp_files[i], 'r')
data = tmp_file['data'][()]
for current in data:
if len(current) > 0:
all_currents.append(current)
tmp_file.close()
os.remove(self._tmp_files[i])
h5final.create_dataset('data', data=np.array(all_currents))
h5final.close()
