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 = unit(time[0])
stop = unit(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, pq.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 __getitem__(self, time):
from scipy.interpolate import interp1d
from morphforge.traces.tracetypes.tracefixeddt import TraceFixedDT
if isinstance(time, tuple):
assert len(time) == 2
start = unit(time[0])
stop = unit(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,
pq.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 __init__(self, results, tags=(["Voltage"], ["Current"],
["Conductance"],["State"], ["State (Tau)"], ["State (SteddyState)"],
["Tau"]), figsize=(12, 8), timeranges=(None,), filename=None,
annotation=None, jitter=0.0, tracecolour=None, legendlabel="${result.name} - ${trace.comment}",
haslegend=True,sorttraces = True, colors=None):
#from morphforge.core.pylab import mpl
#from morphforge.core.pylab import mpl
self.sorttraces = sorttraces
self.haslegend = haslegend
# Filter out tag sets which actually have relevant traces:
allTraceObjs = Flatten([ result.traces for result in results ])
self.tags = []
for tgs in tags:
validTraces = allTraceObjs[:]
for tag in tgs:
validTraces = [ trc for trc in validTraces if tag in trc.tags ]
if validTraces != []: self.tags.append(tgs)
self.legendlabel = legendlabel
self.results = results
self.figsize = figsize
self.ignoreInitial = unit("5:ms")
self.axisPadding = 0.3
self.axisPadding = 0.1
self.jitter = float(jitter)
self.timeranges = timeranges #if timeranges else [None]
self.tracecolour = tracecolour
self.colors = colors
self.annotation = annotation
self.filename = filename
self.fig = None
self.subfigs = []
self.Render()
def __init__(
self,
srcs,
plots=None,
additional_plots=None,
figtitle=None,
fig_kwargs=None,
show=True,
linkage=None,
timerange=None,
mpl_tight_bounds=False,
share_x_labels=True,
nxticks=4,
show_xlabel='only-once',
show_xticklabels='only-once',
show_xticklabels_with_units=True,
show_xaxis_position='bottom',
xticks=None
):
"""Plot a set of traces.
Keyword arguments:
plots --
srcs --
plots --
additional_plots --
figtitle --
fig_kwargs --
show --
linkage --
timerange --
mpl_tight_bounds --
share_x_labels --
nxticks=4,
show_xlabel -- which plots should the x-axis be displayed on.
show_xticklabels --
show_xticklabels_with_units --
show_xaxis_position --
xticks --
"""
if fig_kwargs is None:
fig_kwargs = self._default_fig_kwargs
self.linkage = linkage
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),
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=xticks
assert self.show_xlabel in self._options_show_xlabel, 'Invalid'
assert self.show_xticklabels in self._options_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*pq.ms for xtick in self.xticks]
assert self.xticks is None or isinstance(self.xticks, int) or ( is_iterable(self.xticks) and [ unit(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 __init__(self,
srcs,
plots=None,
additional_plots=None,
figtitle=None,
fig_kwargs=None,
show=True,
linkage=None,
timerange=None,
mpl_tight_bounds=False,
share_x_labels=True,
nxticks=4,
show_xlabel='only-once',
show_xticklabels='only-once',
show_xticklabels_with_units=True,
show_xaxis_position='bottom',
xticks=None):
"""Plot a set of traces.
Keyword arguments:
plots --
srcs --
plots --
additional_plots --
figtitle --
fig_kwargs --
show --
linkage --
timerange --
mpl_tight_bounds --
share_x_labels --
nxticks=4,
show_xlabel -- which plots should the x-axis be displayed on.
show_xticklabels --
show_xticklabels_with_units --
show_xaxis_position --
xticks --
"""
if fig_kwargs is None:
fig_kwargs = self._default_fig_kwargs
self.linkage = linkage
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),
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 = xticks
assert self.show_xlabel in self._options_show_xlabel, 'Invalid'
assert self.show_xticklabels in self._options_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 * pq.ms for xtick in self.xticks]
assert self.xticks is None or isinstance(
self.xticks, int) or (is_iterable(self.xticks)
and [unit(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()