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ASTIM_sim_batch.py
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text/x-python
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R4670 PySONIC (old)
ASTIM_sim_batch.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2017-02-13 18:16:09
# @Email: theo.lemaire@epfl.ch
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2017-08-23 16:25:04
""" Run batch acoustic simulations of the NICE model. """
import
logging
import
numpy
as
np
from
PointNICE.solvers
import
runSimBatch
from
PointNICE.channels
import
*
from
PointNICE.utils
import
LoadParams
,
CheckBatchLog
# Set logging options
logging
.
basicConfig
(
format
=
'
%(asctime)s
%(message)s
'
,
datefmt
=
'
%d
/%m/%Y %H:%M:%S:'
)
logger
=
logging
.
getLogger
(
'PointNICE'
)
logger
.
setLevel
(
logging
.
DEBUG
)
# BLS parameters
bls_params
=
LoadParams
()
# Geometry of NBLS structure
a
=
32e-9
# in-plane radius (m)
d
=
0.0e-6
# embedding tissue thickness (m)
geom
=
{
"a"
:
a
,
"d"
:
d
}
# Channels mechanisms
neurons
=
[
CorticalRS
()]
# Stimulation parameters
stim_params
=
{
'freqs'
:
[
3.5e5
],
# Hz
'amps'
:
[
100e3
],
# Pa
'durations'
:
[
50e-3
],
# s
'PRFs'
:
[
1e2
],
# Hz
'DFs'
:
[
1.0
]
}
stim_params
[
'offsets'
]
=
[
30e-3
]
*
len
(
stim_params
[
'durations'
])
# s
# stim_params = {
# 'freqs': np.array([200, 400, 600, 800, 1000]) * 1e3, # Hz
# 'amps': np.array([10, 20, 40, 80, 150, 300, 600]) * 1e3, # Pa
# 'durs': np.array([20, 40, 60, 80, 100, 150, 200, 250, 300]) * 1e-3, # s
# 'PRFs': np.array([0.1, 0.2, 0.5, 1, 2, 5, 10]) * 1e3, # Hz
# 'DFs': np.array([1, 2, 5, 10, 25, 50, 75, 100]) / 100
# }
# stim_params['offsets'] = 350e-3 - stim_params['durations'] # s
# Simulation type
sim_type
=
'effective'
# Select output directory
try
:
(
batch_dir
,
log_filepath
)
=
CheckBatchLog
(
'elec'
)
except
AssertionError
as
err
:
logger
.
error
(
err
)
quit
()
# Run simulation batch
runSimBatch
(
batch_dir
,
log_filepath
,
neurons
,
bls_params
,
geom
,
stim_params
,
sim_type
)
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