def setup(parameter_set,
generate=False,
duration=1080, #Match time run in Figure 1C of Kato et. al, Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.09.034
dt=0.1,
target_directory='examples',
include_muscles = True):
exec('from parameters_%s import ParameterisedModel'%parameter_set)
params = ParameterisedModel()
# Match the labelled cells in Figure 1C of Kato et. al, Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.09.034
cells_to_stimulate = ["AVAR", "AVAL", "RIMR", "RIML", "AVER", "VA01", "SABVL", "OLQVL", "DB01", "VB01", "DB02", "RMER", "RMEL", "RID", "AVBR", "RIBL", "VB02", "RMED", "RMEV", "AVBL", "SMDVL", "SMDVR", "RIVL", "RIVR", "OLQVR", "OLQDL", "AIBL", "AIBR", "OLQDR", "RIFR", "SMBDR"]
# Plot some directly stimulated & some not stimulated
cells_to_plot = ["AVAR", "AVAL", "RIMR", "RIML", "AVER", "VA01", "SABVL", "OLQVL", "DB01", "VB01", "DB02", "RMER", "RMEL", "RID", "AVBR", "RIBL", "VB02", "RMED", "RMEV", "AVBL", "SMDVL", "SMDVR", "RIVL", "RIVR", "OLQVR", "OLQDL", "AIBL", "AIBR", "OLQDR", "RIFR", "SMBDR"]
reference = "c302_%s_Kato"%parameter_set
cell_names, conns = c302.get_cell_names_and_connection()
if generate:
c302.generate(reference,
params,
cells_to_plot=cells_to_plot,
cells_to_stimulate=cells_to_stimulate,
include_muscles = include_muscles,
duration=duration,
dt=dt,
vmin=-72 if parameter_set=='A' else -52,
vmax=-48 if parameter_set=='A' else -28,
validate=(parameter_set!='B'),
target_directory=target_directory)
return cell_names, cells_to_stimulate, params, include_muscles
def setup(parameter_set,
generate=False,
duration=500,
dt=0.1,
target_directory='examples',
include_muscles = True):
exec('from parameters_%s import ParameterisedModel'%parameter_set)
params = ParameterisedModel()
# Some random set of neurons
cells_to_stimulate = ["ADAL", "ADAR", "M1","M2L","M3L","M3R","M4","I1R","I2L","I5","I6","MI","NSMR","MCL","ASEL", "AVEL", "AWAR", "DB1", "DVC", "RIAR", "RMDDL"]
# Plot some directly stimulated & some not stimulated
cells_to_plot = ["ADAL", "ADAR", "PVDR", "BDUR","I1R","I2L"]
reference = "c302_%s_Full"%parameter_set
cell_names, conns = c302.get_cell_names_and_connection()
if generate:
c302.generate(reference,
params,
cells_to_plot=cells_to_plot,
cells_to_stimulate=cells_to_stimulate,
include_muscles = include_muscles,
duration=duration,
dt=dt,
vmin=-72 if parameter_set=='A' else -52,
vmax=-48 if parameter_set=='A' else -28,
validate=(parameter_set!='B'),
target_directory=target_directory)
return cell_names, cells_to_stimulate, params, include_muscles
def setup(
parameter_set,
generate=False,
duration=1000,
dt=0.05,
target_directory='examples',
muscles_to_include=None, # None => All!
data_reader="SpreadsheetDataReader",
param_overrides={},
config_param_overrides={},
verbose=True):
exec('from parameters_%s import ParameterisedModel' % parameter_set,
globals())
params = ParameterisedModel()
# Some random set of neurons
cells_to_stimulate = [
"ADAL", "ADAR", "M1", "M2L", "M3L", "M3R", "M4", "I1R", "I2L", "I5",
"I6", "MI", "NSMR", "MCL", "ASEL", "AVEL", "AWAR", "DB1", "DVC",
"RIAR", "RMDDL"
]
cells_to_stimulate = ['PVCL', 'PVCR']
cells_to_stimulate = ['PLML', 'PLMR']
#cells_to_stimulate = ['AVBL','AVBR']
# Plot some directly stimulated & some not stimulated
cells_to_plot = ["ADAL", "ADAR", "PVDR", "BDUR", "I1R", "I2L"]
cells_to_plot = [
'AVBL', 'AVBR', 'PVCL', 'PVCR', 'DB1', 'DB2', 'VB1', 'VB2', 'DD1',
'DD2', 'VD1', 'VD2'
]
reference = "c302_%s_Full" % parameter_set
cell_names, conns = c302.get_cell_names_and_connection()
nml_doc = None
if generate:
nml_doc = c302.generate(reference,
params,
cells_to_plot=cells_to_plot,
cells_to_stimulate=cells_to_stimulate,
muscles_to_include=muscles_to_include,
duration=duration,
dt=dt,
vmin=-72 if parameter_set == 'A' else -52,
vmax=-48 if parameter_set == 'A' else -28,
target_directory=target_directory,
param_overrides=param_overrides,
verbose=verbose,
data_reader=data_reader)
return cell_names, cells_to_stimulate, params, muscles_to_include, nml_doc
def setup(
parameter_set,
generate=False,
duration=1080, #Match time run in Figure 1C of Kato et. al, Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.09.034
dt=0.1,
target_directory='examples',
muscles_to_include=None,
data_reader="SpreadsheetDataReader",
param_overrides={},
config_param_overrides={},
verbose=True):
exec('from parameters_%s import ParameterisedModel' % parameter_set)
params = ParameterisedModel()
# Match the labelled cells in Figure 1C of Kato et. al, Cell 2015 http://dx.doi.org/10.1016/j.cell.2015.09.034
cells_to_stimulate = [
"AVAR", "AVAL", "RIMR", "RIML", "AVER", "VA01", "SABVL", "OLQVL",
"DB01", "VB01", "DB02", "RMER", "RMEL", "RID", "AVBR", "RIBL", "VB02",
"RMED", "RMEV", "AVBL", "SMDVL", "SMDVR", "RIVL", "RIVR", "OLQVR",
"OLQDL", "AIBL", "AIBR", "OLQDR", "RIFR", "SMBDR"
]
# Plot some directly stimulated & some not stimulated
cells_to_plot = [
"AVAR", "AVAL", "RIMR", "RIML", "AVER", "VA01", "SABVL", "OLQVL",
"DB01", "VB01", "DB02", "RMER", "RMEL", "RID", "AVBR", "RIBL", "VB02",
"RMED", "RMEV", "AVBL", "SMDVL", "SMDVR", "RIVL", "RIVR", "OLQVR",
"OLQDL", "AIBL", "AIBR", "OLQDR", "RIFR", "SMBDR"
]
reference = "c302_%s_Kato" % parameter_set
cell_names, conns = c302.get_cell_names_and_connection()
if generate:
c302.generate(reference,
params,
cells_to_plot=cells_to_plot,
cells_to_stimulate=cells_to_stimulate,
muscles_to_include=muscles_to_include,
duration=duration,
dt=dt,
vmin=-72 if parameter_set == 'A' else -52,
vmax=-48 if parameter_set == 'A' else -28,
target_directory=target_directory,
param_overrides=param_overrides,
verbose=verbose,
data_reader=data_reader)
return cell_names, cells_to_stimulate, params, muscles_to_include
def setup(parameter_set,
generate=False,
duration=1000,
dt=0.05,
target_directory='examples',
muscles_to_include = None, # None => All!
data_reader="SpreadsheetDataReader",
param_overrides={},
config_param_overrides={},
verbose=True):
exec('from parameters_%s import ParameterisedModel'%parameter_set, globals())
params = ParameterisedModel()
# Some random set of neurons
cells_to_stimulate = ["ADAL", "ADAR", "M1","M2L","M3L","M3R","M4","I1R","I2L","I5","I6","MI","NSMR","MCL","ASEL", "AVEL", "AWAR", "DB1", "DVC", "RIAR", "RMDDL"]
cells_to_stimulate = ['PVCL','PVCR']
cells_to_stimulate = ['PLML','PLMR']
#cells_to_stimulate = ['AVBL','AVBR']
# Plot some directly stimulated & some not stimulated
cells_to_plot = ["ADAL", "ADAR", "PVDR", "BDUR","I1R","I2L"]
cells_to_plot = ['AVBL','AVBR','PVCL', 'PVCR', 'DB1','DB2','VB1','VB2','DD1','DD2','VD1','VD2']
reference = "c302_%s_Full"%parameter_set
cell_names, conns = c302.get_cell_names_and_connection()
nml_doc = None
if generate:
nml_doc = c302.generate(reference,
params,
cells_to_plot=cells_to_plot,
cells_to_stimulate=cells_to_stimulate,
muscles_to_include = muscles_to_include,
duration=duration,
dt=dt,
vmin=-72 if parameter_set=='A' else -52,
vmax=-48 if parameter_set=='A' else -28,
target_directory=target_directory,
param_overrides=param_overrides,
verbose=verbose,
data_reader=data_reader)
return cell_names, cells_to_stimulate, params, muscles_to_include, nml_doc
def setup(parameter_set,
generate=False,
duration=1000,
dt=0.05,
target_directory='examples',
include_muscles=True):
exec('from parameters_%s import ParameterisedModel' % parameter_set)
params = ParameterisedModel()
# Some random set of neurons
cells_to_stimulate = [
"ADAL", "ADAR", "M1", "M2L", "M3L", "M3R", "M4", "I1R", "I2L", "I5",
"I6", "MI", "NSMR", "MCL", "ASEL", "AVEL", "AWAR", "DB1", "DVC",
"RIAR", "RMDDL"
]
cells_to_stimulate = ['PVCL', 'PVCR']
# Plot some directly stimulated & some not stimulated
cells_to_plot = ["ADAL", "ADAR", "PVDR", "BDUR", "I1R", "I2L"]
cells_to_plot = [
'AVBL', 'AVBR', 'PVCL', 'PVCR', 'DB1', 'DB2', 'VB1', 'VB2', 'DD1',
'DD2', 'VD1', 'VD2'
]
reference = "c302_%s_Full" % parameter_set
cell_names, conns = c302.get_cell_names_and_connection()
if generate:
c302.generate(reference,
params,
cells_to_plot=cells_to_plot,
cells_to_stimulate=cells_to_stimulate,
include_muscles=include_muscles,
duration=duration,
dt=dt,
vmin=-72 if parameter_set == 'A' else -52,
vmax=-48 if parameter_set == 'A' else -28,
validate=(parameter_set != 'B'),
target_directory=target_directory)
return cell_names, cells_to_stimulate, params, include_muscles