def test_quantityexpr():
data = []
for (a, b, check_with_gnu) in valid_quantity_exprs:
print 'a:', a
print 'b:', b
A = NeuroUnitParser.QuantityExpr(a)
print 'LOADING B'
B = NeuroUnitParser.QuantityExpr(b)
if check_with_gnu:
verify_equivalence_with_gnuunits(a, b)
print "typeA:", type(A)
print "typeB:", type(B)
pcA = ((A - B) / A).dimensionless()
pcB = ((A - B) / B).dimensionless()
data.append([
a, b,
"$%s$" % (A.FormatLatex()),
"$%s$" % (B.FormatLatex()),
str(pcA),
str(pcB)
])
header = "A|B|Parsed(A)|Parsed(B)|PC(A)|PC(B)".split("|")
return Table(header=header, data=data)
def cmdline_simulate(args):
print 'Simulating'
for arg, arg_value in vars(args).items():
print arg, arg_value
from neurounits import NeuroUnitParser, MQ1
from neurounits.nineml_fe.nineml_fe_utils import get_src_9ml_files
# Load from all the include directories, but only add files once
# to prevent duplicate entries in the library_manager
#src_files = []
#for incl_path in args.include:
# assert os.path.exists(incl_path)
# # Add all the files in a directory:
# if os.path.isdir(incl_path):
# new_files = sorted([ os.path.abspath(fname) for fname in glob.glob(incl_path+'/*.9ml') ] )
# for fname in new_files:
# if not fname in src_files:
# src_files.append(fname)
# # Add an individual file:
# elif os.path.isfile(incl_path):
# if not incl_path in src_files:
# src_files.append(incl_path)
src_files = get_src_9ml_files(args)
# Read all the input files:
library_manager = NeuroUnitParser.Parse9MLFiles(filenames=src_files)
# Get the component:
component = library_manager.get(args.component)
component.summarise()
# Get the start and end times:
t_end = NeuroUnitParser.QuantitySimple(args.endt)
assert t_end.is_compatible(MQ1('1s').units)
t_end = t_end.float_in_si()
dt = NeuroUnitParser.QuantitySimple(args.dt)
assert dt.is_compatible(MQ1('1s').units)
dt = dt.float_in_si()
# OK lets simulate!
res = component.simulate(times=np.arange(0, t_end, dt), )
print 'Simulating'
for arg, arg_value in vars(args).items():
print arg, arg_value
# and plot:
res.auto_plot()
# Shall we pop up?
if args.show_plot:
pylab.show()
print 'Simulating'
for arg, arg_value in vars(args).items():
print arg, arg_value
class NEURONMappings(object):
current_units = {
MechanismType.Distributed: NeuroUnitParser.Unit("mA/cm2"),
MechanismType.Point: NeuroUnitParser.Unit("nA"),
}
supplied_value_names = {
NeuronSuppliedValues.MembraneVoltage: 'v',
NeuronSuppliedValues.Time: 't',
NeuronSuppliedValues.Temperature: 'celsius'
}
supplied_value_units = {
NeuronSuppliedValues.MembraneVoltage: NeuroUnitParser.Unit("mV"),
NeuronSuppliedValues.Time: NeuroUnitParser.Unit("ms"),
NeuronSuppliedValues.Temperature: NeuroUnitParser.Unit("K")
}
def test_quantitysimple():
data = []
for (a, b, check_with_gnu) in valid_quantitysimple:
A = NeuroUnitParser.QuantitySimple(a)
B = NeuroUnitParser.QuantitySimple(b)
if check_with_gnu:
verify_equivalence_with_gnuunits(a, b)
pcA = ((A - B) / A).dimensionless()
pcB = ((A - B) / B).dimensionless()
assert pcA == 0
assert pcB == 0
data.append([a, b, str(A), str(B), str(pcA), str(pcB)])
header = "A|B|Parsed(A)|Parsed(B)|PC(A)|PC(B)".split("|")
return Table(header=header, data=data)
def test5():
library_manager = NeuroUnitParser.Parse9MLFile("""
define_component van_de_pol {
x' = mu * (x-(x*x*x)/3 - y) * {10ms-1}
#x' = mu * (x-(x**3)/3 - y) * {10ms-1}
y' = x/mu * {10ms-1}
#mu = 6.0
initial {
x=1.0
y=6.0
}
<=> PARAMETER mu
}
""")
res = library_manager.get('van_de_pol').simulate(times=np.linspace(
0.0, 0.0200, 10000),
parameters={'mu': "4.0"})
res.auto_plot()
# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
# POSSIBILITY OF SUCH DAMAGE.
#-------------------------------------------------------------------------------
from neurounits import NeuroUnitParser
import quantities as pq
from neurounits.writers.writer_ast_to_simulatable_object import EqnSimulator
es = NeuroUnitParser.EqnSet("""
EQNSET lorenz {
x' = (sigma*(y-x)) * {1s-1}
y' = (x*( rho-z)-y) * {1s-1}
z' = (x*y-beta*z) * {1s-1}
sigma = 1000
beta = 8/3
rho= 28
<=> OUTPUT x:(), y:(), z:()
<=> INITIAL x:1.0
<=> INITIAL y:1.0
<=> INITIAL z:1.0
}
""")
#SimulateEquations(es)
#es.to_redoc().to_pdf(filename="/home/michael/Desktop//out1.pdf")
import numpy as np
evaluator = EqnSimulator(es, )
def run_scenario_filename(fname, code_path_mode='reduced', only_first_paramtuple=False, plot_results=False, short_run=False):
if short_run is True:
only_first_paramtuple = True
print 'Reading from file', fname
conf = configobj.ConfigObj(fname)
units_dict = dict( [(k,NeuroUnitParser.Unit(v).as_quantities_unit() ) for (k,v) in conf['Units'].iteritems() ] )
param_syms = conf['Parameter Values'].keys()
param_vals = [ conf['Parameter Values'][sym] for sym in param_syms]
#description_lines = [ l.strip() for l in conf['description'].split('\n')]
#description_lines = [ l for l in description_lines if l]
description_lines = []
for line in conf['description'].split('\n'):
# Skip blank lines:
if not line.strip():
continue
# If it starts with whitespace, then add it to the previous line
if re.match(r"""^[\s]+""", line):
description_lines[-1] = description_lines[-1] + ' ' + line.strip()
continue
# Otherwise, just add it
description_lines.append(line)
description_lines = [ l.strip() for l in description_lines]
description_lines = [ re.sub(r"\s+", " ", l) for l in description_lines]
code_paths = handler_lib.build_code_paths(description_lines, mode=code_path_mode)
for param_index, param_vals_inst in enumerate(itertools.product(*param_vals)) :
if only_first_paramtuple and param_index != 0:
break
# For each code_path
for code_path_index, code_path in enumerate(code_paths):
# Build the base context:
parameter_values_float = {}
for (param_index,k) in enumerate(param_syms):
parameter_values_float[k] = float(param_vals_inst[param_index])
parameter_values = {}
for (param_index,k) in enumerate(param_syms):
parameter_values[k] = float(param_vals_inst[param_index]) * units_dict[k]
ctx = ActionContext(parameter_values = parameter_values)
# Execute the code-path:
code_path.execute(ctx=ctx)
#Extract the relevant columns and save them to a file:
column_names = conf['Output Format']['columns']
basename = conf['Output Format']['base_filename']
# Get trace data, except time:
data_col_names = column_names[1:]
traces = [ctx.res.get_trace(ctx.records[col])for col in data_col_names]
# Use the time record of the first trace
time = traces[0].time_pts_ms
trace_data = [ tr.data_pts/units_dict[col] for col,tr in zip(data_col_names,traces) ]
trace_data = [tr.rescale(pq.dimensionless).magnitude for tr in trace_data]
data = [time] + trace_data
data_matrix = np.vstack(( data) ).T
opfile = basename.replace('<','{').replace('>','}').format( **parameter_values_float)
opfile = opfile + 'mfcuke_%d' % code_path_index
opdir = os.path.join( simtest_utils.Locations.output_root(), conf['scenario_short'])
opfile = os.path.join(opdir, opfile)
np.savetxt(opfile, data_matrix)
if plot_results:
mf.TagViewer(ctx.res, show=False)
def convert_string_to_quantity(s):
if isinstance(s, basestring):
return NeuroUnitParser.QuantitySimple(s).as_quantities_quantity()
else:
return s
def parse_io_line(line):
from neurounits import NeuroUnitParser
from neurounits.unit_errors import ParsingError
assert isinstance(line, basestring)
print 'Line', line
metadata = {}
if 'METADATA' in line:
(line, metadata) = line.split('METADATA')
metadata = read_json(metadata)
#r = re.compile( r"""<=> \s* (?P<MODE>[a-zA-Z]+) \s* (?P<SYMBOL>[a-zA-Z][a-zA-Z0-9_]*) \s* ([:] \s* (?P<UNIT>[a-zA-Z0-9/()]*) )? """, re.VERBOSE)
r = re.compile( r"""<=> \s* (?P<MODE>[a-zA-Z]+) \s* (?P<DEFS>.*) $""", re.VERBOSE)
m = r.match(line)
if not m:
raise ParsingError('Unable to parse line: "%s"'%line)
g = m.groupdict()
mode = g['MODE']
if mode in ('INPUT', 'OUTPUT', 'PARAMETER'):
defs = []
data = g['DEFS']
for d in data.split(','):
pDef = d.split(':')
if len(pDef) == 1:
(symbol, dimension_str) = (pDef[0], None)
elif len(pDef) == 2:
(symbol, dimension_str) = pDef
else:
raise ParsingError("Can't interpret line: %s" % line)
symbol = symbol.strip()
dimension_str = (dimension_str.strip() if dimension_str else dimension_str)
# Allow units to be specified in '{' '}' too. This is hacky and should be better
# integrated.
if dimension_str:
if dimension_str[0] == '{' and dimension_str[-1] == '}':
dimension_str = '(' + dimension_str[1:-1] + ')'
dimension = NeuroUnitParser.Unit(dimension_str) if dimension_str is not None else None
dimension = dimension.with_no_powerten() if dimension is not None else dimension
io_data = IODataDimensionSpec(symbol=symbol.strip(),
iotype=IOType.LUT[mode], dimension=dimension,
metadata=metadata)
defs.append(io_data)
return defs
elif mode == "INITIAL":
defs = []
data = g['DEFS']
for d in data.split(','):
pDef = d.split(':')
ic = IODataInitialCondition(symbol=pDef[0], value=pDef[1])
defs.append(ic)
return defs
else:
raise ParsingError('Unexpected Mode: %s' % mode)
# 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.
#-------------------------------------------------------------------------------
from neurounits import NeuroUnitParser
import quantities as pq
from neurounits.writers.writer_ast_to_simulatable_object import EqnSimulator
es = NeuroUnitParser.EqnSet("""
EQNSET van_de_pol {
x' = mu * (x-(x**3)/3 - y) * {10ms-1}
y' = x/mu * {10ms-1}
#mu = 6.0
<=> PARAMETER mu
<=> INITIAL x:0
<=> INITIAL y:0
}
""")
#SimulateEquations(es)
#es.to_redoc().to_pdf(filename="/home/michael/Desktop//out1.pdf")
import numpy as np
evaluator = EqnSimulator(es, )
one = es.library_manager.backend.Quantity(1.0,
es.library_manager.backend.Unit())
six = es.library_manager.backend.Quantity(6.0,
library_manager = neurounits.NeuroUnitParser.File(neuron_def)
from neurounits import NeuroUnitParser as P
print library_manager
evaluator = EqnSimulator( library_manager.eqnsets[0] )
res = evaluator(
time_data = np.linspace(0.0, 0.100, 1000),
params={
},
state0In={
'V':P.QuantityExpr('-52mV'),
'm':P.QuantityExpr('0'),
'h':P.QuantityExpr('0'),
'kf':P.QuantityExpr('0'),
'ks':P.QuantityExpr('0'),
'ca_m':P.QuantityExpr('0'),
}
)
print 'Done Simulating'
print res
print res.keys()
#pylab.figure()
#pylab.plot(res['x'], res['y'])
def build_eqnset(chlmlinfo, eqnsetname=None):
assert type(chlmlinfo) == ChannelMLInfo
if not eqnsetname:
eqnsetname = chlmlinfo.name
unit_mode = {
'Physiological Units': NeuroMLUnitsMode.Physiological,
"SI Units": NeuroMLUnitsMode.SI
}[chlmlinfo.units]
# Some sanity checks on what is supported:
# ------------------------------------------
# Check we are dealing with an IV law, not an IAF type mechanism:
if chlmlinfo.iv_cond_law and chlmlinfo.iv_cond_law != 'ohmic':
raise NeuroUnitsImportNeuroMLNotImplementedException(
"Non-IV Cond law-type Channels")
if chlmlinfo.iv_default_gmax is None or chlmlinfo.iv_default_erev is None:
raise NeuroUnitsImportNeuroMLNotImplementedException(
"Can't find default reversal potentials/conductances")
if chlmlinfo.unsupported_tags is not None:
raise NeuroUnitsImportNeuroMLNotImplementedException(
chlmlinfo.unsupported_tags)
if chlmlinfo.parameters:
raise NeuroUnitsImportNeuroMLNotImplementedException(
"Can't deal with parameters")
neuroml_dt = {
NeuroMLUnitsMode.Physiological: "{1ms}",
NeuroMLUnitsMode.SI: "{1s}",
}[unit_mode]
neuroml_v_unit = {
NeuroMLUnitsMode.Physiological: "{1mV}",
NeuroMLUnitsMode.SI: "{1V}",
}[unit_mode]
eqns = []
# Build the Q10 Info:
q10gateadjustments, q10_eqns = build_gate_q10_settings_dict(chlmlinfo)
eqns.extend(q10_eqns)
# Build the conductance and current equations:
eqns.append('%s = %s * %s' %
(Name.Conductance, Name.OpenConductance, Name.PropGatesOpen))
eqns.append('%s = %s * ( (%s) - (%s) ) ' %
(Name.MembraneCurrent, Name.Conductance, Name.Voltage,
Name.ReversalPotential))
gate_prop_names = dict([(gate, '%s' % gate.name)
for gate in chlmlinfo.gates])
gate_prop_terms = dict([
(gate, '*'.join([gate_prop_names[gate]] * gate.instances))
for gate in chlmlinfo.gates
])
if gate_prop_terms:
eqns.append('%s = %s' %
(Name.PropGatesOpen, '*'.join(gate_prop_terms.values())))
else:
eqns.append('%s = 1.0' % (Name.PropGatesOpen))
# Build Eqns for individual gates:
for g in chlmlinfo.gates:
q10tempadjustmentName = q10gateadjustments.get(
g.name, q10gateadjustments[None])
# Gate with alpha/beta rate variables specified:
if g.transitions:
gate_eqns = _build_gate_alphabetainftau(
g=g,
q10tempadjustmentName=q10tempadjustmentName,
neuroml_dt=neuroml_dt)
eqns.extend(gate_eqns)
# Gate specified as an inf-tau value:
elif len(g.time_courses) == 1 and len(g.steady_states) == 1:
gate_eqns = _build_gate_inftau(
g=g,
q10tempadjustmentName=q10tempadjustmentName,
neuroml_dt=neuroml_dt)
eqns.extend(gate_eqns)
else:
raise NeuroUnitsImportNeuroMLNotImplementedException(
'Non-Standard Gate/Transtions')
#Voltage Offsets:
vOffset = None
if chlmlinfo.offset:
vOffset = "( %f * %s )" % (chlmlinfo.offset, neuroml_v_unit)
vOffsetTerm = "-%s" % vOffset if vOffset is not None else ""
# OK, use regular expressions to remap variables
# to the variable with the unit:
remaps = [
lambda e: re.sub(r"""\bcelsius\b""", "(celsius/{1K})", e),
lambda e: re.sub(r"""\b__VGate__\b""", "((V %s)/%s)" %
(vOffsetTerm, neuroml_v_unit), e),
lambda e: re.sub(r"""\b__V__\b""", "(V)", e),
]
# Apply the remappings:
for r in remaps:
eqns = [r(e) for e in eqns]
io_string = Template("""
<=> PARAMETER $OpenConductance : (S/m2)
<=> PARAMETER $ReversalPotential : (mV)
<=> OUTPUT $MembraneCurrent :(A/m2) METADATA {"mf":{"role":"TRANSMEMBRANECURRENT"} }
<=> INPUT V:(V) METADATA {"mf":{"role":"MEMBRANEVOLTAGE"} }
<=> INPUT $Temperature :(K) METADATA {"mf":{"role":"TEMPERATURE"} } """
).substitute(**Name.__dict__)
import_string = """
from std.math import exp
from std.math import pow
from std.math import fabs """
neuroEqn = """
eqnset %s{
%s
%s
%s
}""" % (eqnsetname, import_string, "\n\t\t".join(eqns), io_string)
neuroEqn = "\n".join([l for l in neuroEqn.split("\n") if l.strip()])
options = NeuroUnitParserOptions(
allow_unused_parameter_declarations=True,
allow_unused_suppliedvalue_declarations=True)
eqnset = NeuroUnitParser.NineMLComponent(text=neuroEqn, options=options)
default_params = {
NeuroMLUnitsMode.Physiological: {
"GMAX":
NeuroUnitParser.QuantitySimple("%s mS/cm2" %
(chlmlinfo.iv_default_gmax)),
"VREV":
NeuroUnitParser.QuantitySimple("%s mV" %
(chlmlinfo.iv_default_erev)),
},
NeuroMLUnitsMode.SI: {
"GMAX":
NeuroUnitParser.QuantitySimple("%s S/m2" %
(chlmlinfo.iv_default_gmax)),
"VREV":
NeuroUnitParser.QuantitySimple("%s V" %
(chlmlinfo.iv_default_erev)),
},
}[unit_mode]
return eqnset, default_params
def cmdline_summarise(args):
import mredoc
print 'Summarise'
from neurounits import NeuroUnitParser, MQ1
from neurounits.nineml_fe.nineml_fe_utils import get_src_9ml_files
src_files = get_src_9ml_files(args)
# Read all the input files:
library_manager = NeuroUnitParser.Parse9MLFiles(filenames=src_files)
print args.what
if not args.what:
objs = list(library_manager.objects)
else:
objs = [ library_manager.get(name) for name in args.what ]
summaries = []
for o in objs:
print 'Summarising:', repr(o)
summaries.append( o.to_redoc() )
summary_obj = mredoc.Section(