def set_ylim(self, *args, **kwargs):
x0 = x1 = None
if args is not None:
if len(args) == 1:
x0, x1 = args[0]
else:
x0, x1 = args
else:
x0 = kwargs.get('bottom', None)
x1 = kwargs.get('top', None)
# So we can forward arguments:
if 'bottom' in kwargs:
del kwargs['bottom']
if 'top' in kwargs:
del kwargs['top']
#Convert strings to units
if x0 is not None and isinstance(x0, basestring):
x0 = qty(x0)
if x1 is not None and isinstance(x1, basestring):
x1 = qty(x1)
# Are the baseunits set? If not, then lets set them:
if self.xyUnitBase[1] is None:
self._setxyUnitDisplay(unitY=x0)
# Set the limits
if x0 is not None:
self.ax.set_ylim(bottom = x0.rescale(self.xyUnitBase[1]).magnitude, **kwargs)
if x1 is not None:
self.ax.set_ylim(top = x1.rescale(self.xyUnitBase[1]).magnitude, **kwargs)
def __getitem__(self, time):
from scipy.interpolate import interp1d
from morphforge.traces.tracetypes.tracefixeddt import TraceFixedDT
if isinstance(time, tuple):
assert len(time) == 2
start = qty(time[0])
stop = qty(time[1])
if start < self._time[0]:
assert False, 'Time out of bounds'
if stop > self._time[-1]:
assert False, 'Time out of bounds'
mask = np.logical_and(start < self.time_pts, self._time < stop)
if len(np.nonzero(mask)[0]) < 2:
assert False
return TraceFixedDT(time=self._time[np.nonzero(mask)[0]],
data=self.data_pts[np.nonzero(mask)[0]])
assert isinstance(time, units.quantity.Quantity), "Times should be quantity. Found: %s %s"%(time, type(time))
# Rebase the Time:
time.rescale(self._time.units)
interpolator = interp1d(self.time_pts_np,
self.data_pts_np)
d_mag = interpolator(time.magnitude)
return d_mag * self.data_unit
def _setxyUnitDisplay(self, unitX=None, unitY=None):
if unitX is not None:
unitX = (qty(unitX) if isinstance(unitX, basestring) else unitX)
if unitY is not None:
unitY = (qty(unitY) if isinstance(unitY, basestring) else unitY)
# Set the base units, if they are not already set:
if unitX is not None and self.xyUnitBase[0] is None:
self._setxyUnitBase(unitX=unitX)
if unitY is not None and self.xyUnitBase[1] is None:
self._setxyUnitBase(unitY=unitY)
if unitX is not None:
self.xyUnitDisplay[0] = unitX.units
# Update the axis ticks:
symbol = self.getSymbolFromUnit(self.xyUnitDisplay[0])
scaling = (self.xyUnitBase[0]/self.xyUnitDisplay[0]).rescale(pq.dimensionless)
xFormatterFunc = self.xTickFormatGenerator(scaling=scaling, symbol=symbol, ticklabel_quantisation=None)
self.ax.xaxis.set_major_formatter(xFormatterFunc)
if unitY is not None:
self.xyUnitDisplay[1] = unitY.units
symbol = self.getSymbolFromUnit(self.xyUnitDisplay[1])
scaling = (self.xyUnitBase[1]/self.xyUnitDisplay[1]).rescale(pq.dimensionless)
yFormatterFunc = self.yTickFormatGenerator(scaling=scaling, symbol=symbol, ticklabel_quantisation=None)
self.ax.yaxis.set_major_formatter(yFormatterFunc)
# Update the labels
self._update_labels()
def set_xlim(self, *args, **kwargs):
x0 = x1 = None
if args is not None:
if len(args) == 1:
x0, x1 =args[0]
else:
x0, x1 = args
else:
x0 = kwargs.get('left', None)
x1 = kwargs.get('right', None)
# So we can forward arguments:
if 'left' in kwargs:
del kwargs['left']
if 'left' in kwargs:
del kwargs['left']
#
if x0 is not None and isinstance(x0, basestring):
x0 = qty(x0)
if x1 is not None and isinstance(x1, basestring):
x1 = qty(x1)
# Are the baseunits set? If not, then lets set them:
if self.xyUnitBase[0] is None:
self._setxyUnitDisplay(unitX=x0)
# Set the limits
if x0 is not None:
self.ax.set_xlim(left = x0.rescale(self.xyUnitBase[0]).magnitude, **kwargs)
if x1 is not None:
self.ax.set_xlim(right = x1.rescale(self.xyUnitBase[0]).magnitude, **kwargs)
def __init__(self, equation, conductance, reversalpotential, statevars_new={}, **kwargs):
super(MM_InfTauInterpolatedChannel, self).__init__(**kwargs)
self.eqn = equation
self.conductance = qty(conductance)
self.reversalpotential = qty(reversalpotential)
self.statevars_new = statevars_new.copy()
def __init__(self, name, ion, equation, conductance, reversalpotential, statevars, beta2threshold, **kwargs):
super(StdChlAlphaBetaBeta, self).__init__(name=name, **kwargs)
#self.name = name
self.ion = ion
self.eqn = equation
self.conductance = qty(conductance)
self.beta2threshold = qty(beta2threshold)
self.statevars = dict([(s, (sDict['alpha'], sDict['beta1'], sDict['beta2'])) for s, sDict in statevars.iteritems()])
self.reversalpotential = qty(reversalpotential)
def get_sample_k(env):
kStateVars = {'n': {'alpha': [-0.55, -0.01, -1.00, 55.0, -10.00],
'beta': [0.125, 0, 0, 65, 80]}}
k_chl = env.Channel(
StdChlAlphaBeta,
name='KChl',
ion='k',
equation='n*n*n*n',
conductance=qty('36:mS/cm2'),
reversalpotential=qty('-77:mV'),
statevars=kStateVars,
)
return k_chl
def _setxyUnitBase(self, unitX=None, unitY=None):
if unitX is not None:
unitX = (qty(unitX) if isinstance(unitX, basestring) else unitX)
if unitY is not None:
unitY = (qty(unitY) if isinstance(unitY, basestring) else unitY)
if unitX is not None:
assert self.xyUnitBase[0] == None
unitX = (qty(unitX) if isinstance(unitX, basestring) else unitX)
self.xyUnitBase[0] = unitX.units.simplified.units
if unitY is not None:
assert self.xyUnitBase[1] == None
unitY = (qty(unitY) if isinstance(unitY, basestring) else unitY)
self.xyUnitBase[1] = unitY.units.simplified.units
def __init__(self, equation, conductance, reversalpotential, statevars=None, name=None, ion=None, **kwargs):
super(StdChlAlphaBeta, self).__init__(name=name, **kwargs)
# TODO: FIXED DEFAULT PARAMETER 'statevars'
if statevars is None:
statevars = {}
self.ion = ion
self.eqn = equation
self.conductance = qty(conductance)
self.statevars = dict([(s, (sDict['alpha'], sDict['beta'])) for s, sDict in statevars.iteritems()])
self.reversalpotential = qty(reversalpotential)
self.conductance = self.conductance.rescale('S/cm2')
self.reversalpotential = self.reversalpotential.rescale('mV')
def main():
l1 = TracePiecewise(pieces = [
TracePieceFunctionFlat(time_window=(0, 50)*units.ms, x=qty("0:pA")),
TracePieceFunctionFlat(time_window=(50, 150)*units.ms, x=qty("110:pA")),
TracePieceFunctionFlat(time_window=(150, 350)*units.ms, x=qty("0:pA")),
])
sel1 = LevelSelectorGroup(" A, { 10:65 @ -1:1 }, B, { 10: @ 90:111 }, C", xunit=qty("ms"), yunit=qty("pA"))
matches = sel1.matchall(l1)
for m in matches:
print m
def reduce_to_variable_dt_trace(cls, original_trace, epsilon):
assert isinstance(original_trace, TracePointBased)
epsilon = qty(epsilon)
time_units = original_trace.time_unit
time_data = original_trace.time_pts_np
data_units = original_trace.data_unit
data_data = original_trace.data_pts_np
pts = zip(time_data.tolist(), data_data.tolist())
newpts = _simplify_points(pts, epsilon)
(new_time, new_data) = zip(*newpts)
new_trace = TraceVariableDT(np.array(new_time) * time_units,
np.array(new_data) * data_units,
name=original_trace.name,
comment=original_trace.comment,
tags=original_trace.tags)
print 'Simplified from N=%d to N=%d' % (original_trace.get_n(),
new_trace.get_n())
return new_trace
def __init__(self, morphology=None, area=None, segmenter=None, initial_voltage=None, cell_tags=None, cell_type=None, **kwargs):
if area is not None:
assert morphology is None
morphology = MorphologyBuilder.get_single_section_soma(area=area)
if cell_tags == None:
cell_tags = []
from morphforge.simulation.base.segmentation.cellsegmenter import CellSegmenter_MaxCompartmentLength
super(Cell, self).__init__(**kwargs)
self.morphology = morphology
self._cell_type = cell_type
self.cell_segmenter = (segmenter if segmenter else CellSegmenter_MaxCompartmentLength())
#self.cell_segmenter.connect_to_cell(self)
self.biophysics = CellBiophysics(self)
self.initial_voltage = initial_voltage or qty('-51:mV')
self.cell_tags = cell_tags
if self.name:
self.cell_tags = self.cell_tags + [self.name]
self.population = None
def get_defaults(cls):
defs = {NEURONSimulationSettings.dt: qty('0.01:ms'),
NEURONSimulationSettings.tstop: qty('500:ms'),
NEURONSimulationSettings.reltol: 0.0,
NEURONSimulationSettings.abstol: 1e-2,
#NEURONSimulationSettings.reltol: 1e-12,
#NEURONSimulationSettings.abstol: 1e-12,
NEURONSimulationSettings.cvode: True,
NEURONSimulationSettings.strict_modlunit: True,
# This options automatically simplifies traces after recoding,
# which can make intermediate files much smaller.
NEURONSimulationSettings.simplify_traces: None
}
# Check we have defaults for all parameters:
for parameter in NEURONSimulationSettings.allparams:
assert parameter in defs
return defs
def get_sample_na(env):
na_state_vars = { 'm': {
'alpha': [-4.00,-0.10,-1.00,40.00,-10.00],
'beta': [4.00, 0.00, 0.00,65.00, 18.00]},
'h': {
'alpha': [0.07,0.00,0.00,65.00,20.00],
'beta': [1.00,0.00,1.00,35.00,-10.00]}
}
na_chl = env.Channel(
StdChlAlphaBeta,
name='NaChl',
ion='na',
equation='m*m*m*h',
conductance=qty('120:mS/cm2'),
reversalpotential=qty('50:mV'),
statevars=na_state_vars,
)
return na_chl
def _convert_to_unit(o, default_unit):
assert not isinstance(default_unit, units.Quantity)
if isinstance(o, units.Quantity):
return o.rescale(default_unit)
elif is_float(o) or is_int(o):
return o * morphforge.units.parse_unit_str(default_unit)#.rescale(default_unit)
elif isinstance(o, (str, unicode)) and ':' in o:
return qty(o).rescale(default_unit)
else:
raise ValueError()
def build_traces(cls, header_info, data_array):
n_cols = data_array.shape[1]
# Get the time column:
time_data_raw = data_array[:, 0]
time_unit = qty(str(header_info.column_data[0]['unit']))
time_data = time_data_raw * time_unit
# Do we build as fixed or variable array:
trace_builder = (TraceFixedDT if TraceFixedDT.is_array_fixed_dt(time_data) else TraceVariableDT)
trcs = []
for i in range(1, n_cols):
d_i = data_array[:, i]
column_metadict = header_info.column_data[i]
dataUnit = qty(str(column_metadict.get('unit', '')))
data_label = str(column_metadict.get('label', 'Column%d' % i))
data_tags = str(column_metadict.get('tags', '')).split(',')
d = d_i * dataUnit
tr = trace_builder(time_data, d, name=data_label, tags=data_tags)
trcs.append(tr)
return trcs
def build_passive_cell(sim, input_resistance, capacitance=None, area=None, name=None, reversalpotential=None):
import morphforgecontrib.stdimports as mfc
env = sim.environment
if area is None:
area = qty('1000:um2')
if capacitance is None:
capacitance = qty('10:pF')
if reversalpotential is None:
reversalpotential = qty('-60:mV')
lk = env.Channel( mfc.StdChlLeak,
conductance = ((1/input_resistance) / area ),
reversalpotential = reversalpotential,
)
cell = sim.create_cell(area=area, name=name, initial_voltage=reversalpotential)
cell.apply_channel(lk)
cell.set_passive(mf.PassiveProperty.SpecificCapacitance, capacitance / area)
return cell
def __init__(self, name, ion, equation, permeability, intracellular_concentration, extracellular_concentration, temperature, beta2threshold, statevars, **kwargs):
super( StdChlCalciumAlphaBetaBeta, self).__init__(name=name, **kwargs)
self.ion = ion
self.permeability = qty(permeability)
self.intracellular_concentration = qty(intracellular_concentration)
self.extracellular_concentration = qty(extracellular_concentration)
self.eqn = equation
self.statevars = dict([(s, (sDict['alpha'], sDict['beta1'], sDict['beta2'])) for s, sDict in statevars.iteritems()])
self.beta2threshold = qty(beta2threshold)
self.F = qty('96485.3365:C/mol')
self.R = qty('8.314421:J/(K mol)')
self.CaZ = qty('2.0:')
self.T = qty(temperature)
def build_hh_cell(sim, cell_area=None, name=None):
if cell_area is None:
cell_area = qty('5000:um2')
morphology = MorphologyBuilder.get_single_section_soma(area = cell_area)
cell = sim.create_cell(morphology=morphology,name=name)
# Apply the channels uniformly over the cell
env = sim.environment
modelsrc=StandardModels.HH52
cell.apply_channel( ChannelLibrary.get_channel(modelsrc=modelsrc, celltype=None, channeltype="Na", env=env) )
cell.apply_channel( ChannelLibrary.get_channel(modelsrc=modelsrc, celltype=None, channeltype="K", env=env) )
cell.apply_channel( ChannelLibrary.get_channel(modelsrc=modelsrc, celltype=None, channeltype="Lk", env=env) )
return cell
def newFunctor(env, _voltage_interpolation_values=voltage_interpolation_values):
old_chl = chl_functor(env)
assert isinstance(
old_chl, (StdChlAlphaBeta, StdChlAlphaBetaBeta)
) # or issubclass(StdChlAlphaBetaBeta, old_chl)
# New Name
if new_name is not None:
chl_name = new_name
else:
chl_name = old_chl.name + clone_name_suffix
# Interpolation voltages:
# voltage_interpolation_values=voltage_interpolation_values
if _voltage_interpolation_values is None:
_voltage_interpolation_values = np.linspace(-80, 60, 10) * qty("mV")
# Copy the state variables
new_state_vars = {}
for state_var in old_chl.get_state_variables():
alpha, beta = old_chl.get_alpha_beta_at_voltage(statevar=state_var, V=_voltage_interpolation_values)
inf, tau = InfTauCalculator.alpha_beta_to_inf_tau(alpha, beta)
V = _voltage_interpolation_values.rescale("mV").magnitude
inf = inf.rescale(units.dimensionless).magnitude
tau = tau.rescale("ms").magnitude
new_state_vars[state_var] = InfTauInterpolation(V=V, inf=inf, tau=tau)
chl = env.Channel(
MM_InfTauInterpolatedChannel,
name=chl_name,
ion=old_chl.ion,
equation=old_chl.eqn,
conductance=old_chl.conductance,
reversalpotential=old_chl.reversalpotential,
statevars_new=new_state_vars,
)
return chl
def build_voltageclamp_soma_simulation(env, V, channel_functor, morphology):
sim = env.Simulation(name='SimXX', cvode=False, dt= qty('0.01:ms'))
cell = sim.create_cell(name='Cell1', morphology=morphology)
cell.apply_channel( channel=channel_functor(env=sim.environment))
sim.record( cell, what=cell.Recordables.MembraneVoltage, name='SomaVoltage' , cell_location=cell.soma)
vc = sim.create_voltageclamp(
name='Stim1',
amp1=qty('-81.5:mV'),
amp2=qty(V),
amp3=qty('-81.5:mV'),
dur1=qty('100:ms'),
dur2=qty('100:ms'),
dur3=qty('100:ms'),
cell_location=cell.soma,
)
sim.record(vc, what=vc.Recordables.Current, name='VCCurrent')
return sim
def __init__(
self,
dur1,
amp1,
dur2='0:ms',
dur3='0:ms',
amp2='0:mV',
amp3='0:mV',
rs='0.01:MOhm',
**kwargs
):
super(VoltageClampStepChange, self).__init__(**kwargs)
self.dur1 = qty(dur1)
self.dur2 = qty(dur2)
self.dur3 = qty(dur3)
self.amp1 = qty(amp1)
self.amp2 = qty(amp2)
self.amp3 = qty(amp3)
self.rs = qty(rs)
def get_unit(self):
return qty('')
def p_unit_definiton(p):
""" unit_def : CURLY_LBRACE D COLON ID CURLY_RBRACE """
p[0] = qty(p[4])
def __init__(
self,
srcs,
plots=None,
additional_plots=None,
figtitle=None,
fig_kwargs=None,
show=True,
linkage=None,
timerange=None,
mpl_tight_bounds=False,
decimate_points=False,
share_x_labels=True,
nxticks=4,
show_xlabel='only-once',
show_xticklabels='only-once',
show_xticklabels_with_units=True,
show_xaxis_position='bottom',
xticklabel_quantisation = False,
xticks=None,
xlabel='Time'
):
self.xlabel = xlabel
if fig_kwargs is None:
fig_kwargs = self._default_fig_kwargs
self.linkage = linkage
self.decimate_points = decimate_points
if not is_iterable(srcs):
srcs = [srcs]
# For each type of input (in 'srcs'); this should return a list of traces:
self.all_trace_objs = []
self.all_event_set_objs = []
trace_extractors = {
SimulationResult: lambda obj: (self.all_trace_objs.extend(obj.traces),self.all_event_set_objs.extend(obj.evsets)),
TraceFixedDT: lambda obj: self.all_trace_objs.append(obj),
TraceVariableDT: lambda obj: self.all_trace_objs.append(obj),
TracePiecewise: lambda obj: self.all_trace_objs.append(obj),
EventSet: lambda obj: self.all_event_set_objs.append(obj)
}
for obj in srcs:
tr_extractor = trace_extractors[type(obj)]
tr_extractor(obj)
# Use the new PlotSpec architecture:
# Filter out which plots are actually going to display something,
# and filter out the rest:
plots = plots if plots is not None else TagViewer._default_plot_specs
if additional_plots:
plots = tuple(list(plots) + list(additional_plots))
self.plot_specs = [plotspec for plotspec in plots if
[tr for tr in self.all_trace_objs if plotspec.addtrace_predicate(tr)] or \
[evset for evset in self.all_event_set_objs if plotspec.addeventset_predicate(evset)] \
]
self.fig_kwargs = fig_kwargs
self.figtitle = figtitle
self.mpl_tight_bounds = mpl_tight_bounds
self.timerange = timerange
#self.share_x_labels = share_x_labels
self.nxticks = nxticks
# X-axis configuration:
self.show_xlabel = show_xlabel
self.show_xticklabels = show_xticklabels
self.show_xticklabels_with_units = show_xticklabels_with_units
self.show_xaxis_position = show_xaxis_position
#self.xticks_as_ints = xticks_as_ints
self.xticklabel_quantisation = xticklabel_quantisation
self.xticks=xticks
assert self.show_xlabel in self._options_show_xlabel, 'Invalid'
assert self.show_xticklabels in self._options_show_xticklabels, 'Invalid: %s' % show_xticklabels
assert self.show_xticklabels_with_units in self._options_show_xticklabels_with_units
assert self.show_xaxis_position in self._options_show_xaxis_position
if is_iterable( self.xticks ) and all( [isinstance(xtick, (int, float)) for xtick in self.xticks]):
self.xticks = [ xtick*units.ms for xtick in self.xticks]
assert self.xticks is None or isinstance(self.xticks, int) or ( is_iterable(self.xticks) and [ qty(xtick) for xtick in self.xticks] )
self.fig = None
self.subaxes = []
self.create_figure()
if TagViewer.MPL_AUTO_SHOW and show:
import pylab
pylab.show()
def get_sample_lk(env):
lk_chl = env.Channel(StdChlLeak, name='LkChl',
conductance=qty('0.3:mS/cm2'),
reversalpotential=qty('-54.3:mV') )
return lk_chl
def __init__(self, conductance, reversalpotential, **kwargs):
super(StdChlLeak, self).__init__(**kwargs)
self.conductance = qty(conductance)
self.reversalpotential = qty(reversalpotential)
def get_defaults(self):
return {'gBar': self.conductance,
'e_rev': self.reversalpotential,
'gScale': qty('1.0')}
def get_unit(self):
return qty('S/cm2')
def __init__(self, amp, dur, delay, **kwargs):
super(CurrentClampStepChange, self).__init__(**kwargs)
self.amp = qty(amp)
self.dur = qty(dur)
self.delay = qty(delay)