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run_lookups.py
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Wed, May 1, 14:52
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text/x-python
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Fri, May 3, 14:52 (2 d)
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17361515
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R4670 PySONIC (old)
run_lookups.py
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# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Email: theo.lemaire@epfl.ch
# @Date: 2017-06-02 17:50:10
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2020-02-03 21:37:09
''' Create lookup table for specific neuron. '''
import
os
import
itertools
import
logging
import
numpy
as
np
from
PySONIC.utils
import
logger
,
isIterable
,
alert
from
PySONIC.core
import
NeuronalBilayerSonophore
,
Batch
,
Lookup
,
AcousticDrive
from
PySONIC.parsers
import
MechSimParser
from
PySONIC.constants
import
DQ_LOOKUP
@alert
def
computeAStimLookup
(
pneuron
,
aref
,
fref
,
Aref
,
Qref
,
fsref
=
None
,
mpi
=
False
,
loglevel
=
logging
.
INFO
):
''' Run simulations of the mechanical system for a multiple combinations of
imposed sonophore radius, US frequencies, acoustic amplitudes charge densities and
(spatially-averaged) sonophore membrane coverage fractions, compute effective
coefficients and store them in a dictionary of n-dimensional arrays.
:param pneuron: point-neuron model
:param aref: array of sonophore radii (m)
:param fref: array of acoustic drive frequencies (Hz)
:param Aref: array of acoustic drive amplitudes (Pa)
:param Qref: array of membrane charge densities (C/m2)
:param fsref: acoustic drive phase (rad)
:param mpi: boolean statting wether or not to use multiprocessing
:param loglevel: logging level
:return: lookups dictionary
'''
descs
=
{
'a'
:
'sonophore radii'
,
'f'
:
'US frequencies'
,
'A'
:
'US amplitudes'
,
'fs'
:
'sonophore membrane coverage fractions'
}
# Populate reference vectors dictionary
refs
=
{
'a'
:
aref
,
# nm
'f'
:
fref
,
# Hz
'A'
:
Aref
,
# Pa
'Q'
:
Qref
# C/m2
}
# If multiple sonophore coverage values, ensure that only 1 value of
# sonophore radius and US frequency are provided
err_fs
=
'cannot span {} for more than 1 {}'
if
fsref
.
size
>
1
or
fsref
[
0
]
!=
1.
:
for
x
in
[
'a'
,
'f'
]:
assert
refs
[
x
]
.
size
==
1
,
err_fs
.
format
(
descs
[
'fs'
],
descs
[
x
])
# Add sonophore coverage vector to references
refs
[
'fs'
]
=
fsref
# Check validity of all reference vectors
for
key
,
values
in
refs
.
items
():
if
not
isIterable
(
values
):
raise
TypeError
(
f
'Invalid {descs[key]} (must be provided as list or numpy array)'
)
if
not
all
(
isinstance
(
x
,
float
)
for
x
in
values
):
raise
TypeError
(
f
'Invalid {descs[key]} (must all be float typed)'
)
if
len
(
values
)
==
0
:
raise
ValueError
(
f
'Empty {key} array'
)
if
key
in
(
'a'
,
'f'
)
and
min
(
values
)
<=
0
:
raise
ValueError
(
f
'Invalid {descs[key]} (must all be strictly positive)'
)
if
key
in
(
'A'
,
'fs'
)
and
min
(
values
)
<
0
:
raise
ValueError
(
f
'Invalid {descs[key]} (must all be positive or null)'
)
# Get references dimensions
dims
=
np
.
array
([
x
.
size
for
x
in
refs
.
values
()])
# Create simulation queue per sonophore radius
drives
=
AcousticDrive
.
createQueue
(
fref
,
Aref
)
queue
=
[]
for
drive
in
drives
:
for
Qm
in
Qref
:
queue
.
append
([
drive
,
Qm
,
refs
[
'fs'
]])
# Run simulations and populate outputs
logger
.
info
(
'Starting simulation batch for
%s
neuron'
,
pneuron
.
name
)
outputs
=
[]
for
a
in
aref
:
nbls
=
NeuronalBilayerSonophore
(
a
,
pneuron
)
batch
=
Batch
(
nbls
.
computeEffVars
,
queue
)
outputs
+=
batch
(
mpi
=
mpi
,
loglevel
=
loglevel
)
# Split comp times and effvars from outputs
effvars
,
tcomps
=
[
list
(
x
)
for
x
in
zip
(
*
outputs
)]
effvars
=
list
(
itertools
.
chain
.
from_iterable
(
effvars
))
# Make sure outputs size matches inputs dimensions product
nout
=
len
(
effvars
)
assert
nout
==
dims
.
prod
(),
'Number of outputs does not match number of combinations'
# Reshape effvars into nD arrays and add them to lookups dictionary
logger
.
info
(
'Reshaping output into lookup tables'
)
varkeys
=
list
(
effvars
[
0
]
.
keys
())
tables
=
{}
for
key
in
varkeys
:
effvar
=
[
effvars
[
i
][
key
]
for
i
in
range
(
nout
)]
tables
[
key
]
=
np
.
array
(
effvar
)
.
reshape
(
dims
)
# Reshape computation times, tile over extra fs dimension, and add it as a lookup table
tcomps
=
np
.
array
(
tcomps
)
.
reshape
(
dims
[:
-
1
])
tcomps
=
np
.
moveaxis
(
np
.
array
([
tcomps
for
i
in
range
(
dims
[
-
1
])]),
0
,
-
1
)
tables
[
'tcomp'
]
=
tcomps
# Construct and return lookup object
return
Lookup
(
refs
,
tables
)
def
main
():
parser
=
MechSimParser
(
outputdir
=
'.'
)
parser
.
addNeuron
()
parser
.
addTest
()
parser
.
defaults
[
'neuron'
]
=
'RS'
parser
.
defaults
[
'radius'
]
=
np
.
array
([
16.0
,
32.0
,
64.0
])
# nm
parser
.
defaults
[
'freq'
]
=
np
.
array
([
20.
,
100.
,
500.
,
1e3
,
2e3
,
3e3
,
4e3
])
# kHz
parser
.
defaults
[
'amp'
]
=
np
.
insert
(
np
.
logspace
(
np
.
log10
(
0.1
),
np
.
log10
(
600
),
num
=
50
),
0
,
0.0
)
# kPa
parser
.
defaults
[
'charge'
]
=
np
.
nan
args
=
parser
.
parse
()
logger
.
setLevel
(
args
[
'loglevel'
])
for
pneuron
in
args
[
'neuron'
]:
# Determine charge vector
charges
=
args
[
'charge'
]
if
charges
.
size
==
1
and
np
.
isnan
(
charges
[
0
]):
Qmin
,
Qmax
=
pneuron
.
Qbounds
charges
=
np
.
arange
(
Qmin
,
Qmax
+
DQ_LOOKUP
,
DQ_LOOKUP
)
# C/m2
# Determine output filename
f
=
NeuronalBilayerSonophore
(
32e-9
,
pneuron
)
.
getLookupFilePath
if
args
[
'fs'
]
.
size
==
1
and
args
[
'fs'
][
0
]
==
1.
:
lookup_fpath
=
f
()
else
:
lookup_fpath
=
f
(
a
=
args
[
'radius'
][
0
],
f
=
args
[
'freq'
][
0
],
fs
=
True
)
# Combine inputs into single list
inputs
=
[
args
[
x
]
for
x
in
[
'radius'
,
'freq'
,
'amp'
]]
+
[
charges
,
args
[
'fs'
]]
# Adapt inputs and output filename if test case
if
args
[
'test'
]:
for
i
,
x
in
enumerate
(
inputs
):
if
x
is
not
None
and
x
.
size
>
1
:
inputs
[
i
]
=
np
.
array
([
x
.
min
(),
x
.
max
()])
fcode
,
fext
=
os
.
path
.
splitext
(
lookup_fpath
)
lookup_fpath
=
f
'{fcode}_test{fext}'
# Check if lookup file already exists
if
os
.
path
.
isfile
(
lookup_fpath
):
logger
.
warning
(
'"
%s
" file already exists and will be overwritten. '
+
'Continue? (y/n)'
,
lookup_fpath
)
user_str
=
input
()
if
user_str
not
in
[
'y'
,
'Y'
]:
logger
.
error
(
'
%s
Lookup creation canceled'
,
pneuron
.
name
)
return
# Compute lookup
lkp
=
computeAStimLookup
(
pneuron
,
*
inputs
,
mpi
=
args
[
'mpi'
],
loglevel
=
args
[
'loglevel'
])
logger
.
info
(
f
'Generated lookup: {lkp}'
)
# Save lookup in PKL file
logger
.
info
(
'Saving
%s
neuron lookup in file: "
%s
"'
,
pneuron
.
name
,
lookup_fpath
)
lkp
.
toPickle
(
lookup_fpath
)
if
__name__
==
'__main__'
:
main
()
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