def clear(erase=True, all=False):
'''
Clears all Brian objects.
Specifically, it stops all existing Brian objects from being collected by
:class:`MagicNetwork` (objects created after clearing will still be collected).
If ``erase`` is ``True`` then it will also delete all data from these objects.
This is useful in, for example, ``ipython`` which stores persistent references
to objects in any given session, stopping the data and memory from being freed
up. If ``all=True`` then all Brian objects will be cleared. See also
:func:`forget`.
'''
if all is False:
net = MagicNetwork(level=2)
objs = net.groups + net.connections + net.operations
else:
groups, _ = magic.find_instances(NeuronGroup, all=True)
connections, _ = magic.find_instances(Connection, all=True)
operations, _ = magic.find_instances(NetworkOperation, all=True)
objs = groups+connections+operations
for o in objs:
o.set_instance_id(-1)
if erase:
for k, v in o.__dict__.iteritems():
object.__setattr__(o, k, None)
gc.collect()
def clear(erase=True, all=False):
'''
Clears all Brian objects.
Specifically, it stops all existing Brian objects from being collected by
:class:`MagicNetwork` (objects created after clearing will still be collected).
If ``erase`` is ``True`` then it will also delete all data from these objects.
This is useful in, for example, ``ipython`` which stores persistent references
to objects in any given session, stopping the data and memory from being freed
up. If ``all=True`` then all Brian objects will be cleared. See also
:func:`forget`.
'''
if all is False:
net = MagicNetwork(level=2)
objs = net.groups + net.connections + net.operations
else:
groups, _ = magic.find_instances(NeuronGroup, all=True)
connections, _ = magic.find_instances(Connection, all=True)
operations, _ = magic.find_instances(NetworkOperation, all=True)
objs = groups + connections + operations
for o in objs:
o.set_instance_id(-1)
if erase:
for k, v in o.__dict__.iteritems():
object.__setattr__(o, k, None)
gc.collect()
def __init__(self, verbose=False, level=1):
'''
Set verbose=False to turn off comments.
The level variable contains the location of the namespace.
'''
(groups, groupnames) = magic.find_instances(NeuronGroup)
groups = [g for g in groups if g._owner is g]
groupnames = [gn for g, gn in zip(groups, groupnames) if g._owner is g]
(connections, connectionnames) = magic.find_instances(Connection)
(operations, operationnames) = magic.find_instances(NetworkOperation)
if verbose:
print "[MagicNetwork] Groups:", groupnames
print "[MagicNetwork] Connections:", connectionnames
print "[MagicNetwork] Operations:", operationnames
# Use set() to discard duplicates
Network.__init__(self, list(set(groups)), list(set(connections)), list(set(operations)))
def __init__(self, verbose=False, level=1):
'''
Set verbose=False to turn off comments.
The level variable contains the location of the namespace.
'''
(groups, groupnames) = magic.find_instances(NeuronGroup)
groups = [g for g in groups if g._owner is g]
groupnames = [gn for g, gn in zip(groups, groupnames) if g._owner is g]
(connections, connectionnames) = magic.find_instances(Connection)
(operations, operationnames) = magic.find_instances(NetworkOperation)
if verbose:
print "[MagicNetwork] Groups:", groupnames
print "[MagicNetwork] Connections:", connectionnames
print "[MagicNetwork] Operations:", operationnames
# Use set() to discard duplicates
Network.__init__(self, list(set(groups)), list(set(connections)),
list(set(operations)))
def hist_plot(histmon=None, **plotoptions):
"""Plot a histogram
**Usage**
``hist_plot(histmon,options...)``
Plot the given histogram monitor
``hist_plot(options...)``
Guesses which histogram monitor to use
with argument:
``histmon``
is a monitor of histogram type
**Notes**
Plots only the first n-1 of n bars in the histogram, because
the nth bar is for the interval (-,infinity).
**Options**
Any of PyLab options for bar can be given, as well as:
``showplot=False``
set to ``True`` to run pylab's ``show()`` function
``newfigure=True``
set to ``False`` not to create a new figure with pylab's ``figure()`` function
``xlabel``
label for the x-axis
``ylabel``
label for the y-axis
``title``
title for the plot
"""
if histmon is None:
(histmons, histmonnames) = magic.find_instances(HistogramMonitorBase)
if len(histmons) == 0:
raise TypeError, "No histogram monitors found."
elif len(histmons) > 1:
log_info("brian.hist_plot", "Found more than one histogram monitor, using first one.")
histmon = histmons[0]
# OPTIONS
# Defaults
myopts = {"title": "", "xlabel": "Time (ms)", "ylabel": "Count", "showplot": False, "newfigure": True}
# User options
_take_options(myopts, plotoptions)
# PLOTTING ROUTINE
if myopts["newfigure"]:
pylab.figure()
pylab.bar(histmon.bins[:-1] / ms, histmon.count[:-1], (histmon.bins[1:] - histmon.bins[:-1]) / ms, **plotoptions)
pylab.ylabel(myopts["ylabel"])
pylab.xlabel(myopts["xlabel"])
pylab.title(myopts["title"])
if myopts["showplot"]:
pylab.show()
def hist_plot(histmon=None, **plotoptions):
"""Plot a histogram
**Usage**
``hist_plot(histmon,options...)``
Plot the given histogram monitor
``hist_plot(options...)``
Guesses which histogram monitor to use
with argument:
``histmon``
is a monitor of histogram type
**Notes**
Plots only the first n-1 of n bars in the histogram, because
the nth bar is for the interval (-,infinity).
**Options**
Any of PyLab options for bar can be given, as well as:
``showplot=False``
set to ``True`` to run pylab's ``show()`` function
``newfigure=True``
set to ``False`` not to create a new figure with pylab's ``figure()`` function
``xlabel``
label for the x-axis
``ylabel``
label for the y-axis
``title``
title for the plot
"""
if histmon is None:
(histmons, histmonnames) = magic.find_instances(HistogramMonitorBase)
if len(histmons) == 0:
raise TypeError, "No histogram monitors found."
elif len(histmons) > 1:
log_info('brian.hist_plot', "Found more than one histogram monitor, using first one.")
histmon = histmons[0]
# OPTIONS
# Defaults
myopts = {"title":"", "xlabel":"Time (ms)", "ylabel":"Count", "showplot":False, 'newfigure':True }
# User options
_take_options(myopts, plotoptions)
# PLOTTING ROUTINE
if myopts['newfigure']:
pylab.figure()
pylab.bar(histmon.bins[:-1] / ms, histmon.count[:-1], (histmon.bins[1:] - histmon.bins[:-1]) / ms, **plotoptions)
pylab.ylabel(myopts['ylabel'])
pylab.xlabel(myopts['xlabel'])
pylab.title(myopts["title"])
if myopts["showplot"]:
pylab.show()
def guess_clock(clock=None):
'''
Tries to guess the clock from global and local namespaces
from the caller.
Selects the most local clock.
Raises an error if several clocks coexist in the same namespace.
If a non-None clock is passed, then it is returned (simplifies the code).
'''
if clock:
return clock
# Get variables from the stack
(clocks, clocknames) = magic.find_instances(Clock)
if len(clocks) > 1: # several clocks: ambiguous
# What type of error?
raise TypeError("Clock is ambiguous. Please specify it explicitly.")
if len(clocks) == 1:
return clocks[0]
# Fall back on default clock
if exists_global_preference('defaultclock'): return get_global_preference('defaultclock')
# No clock found
raise TypeError("No clock found. Please define a clock.")
def guess_clock(clock=None):
'''
Tries to guess the clock from global and local namespaces
from the caller.
Selects the most local clock.
Raises an error if several clocks coexist in the same namespace.
If a non-None clock is passed, then it is returned (simplifies the code).
'''
if clock:
return clock
# Get variables from the stack
(clocks, clocknames) = magic.find_instances(Clock)
if len(clocks) > 1: # several clocks: ambiguous
# What type of error?
raise TypeError("Clock is ambiguous. Please specify it explicitly.")
if len(clocks) == 1:
return clocks[0]
# Fall back on default clock
if exists_global_preference('defaultclock'):
return get_global_preference('defaultclock')
# No clock found
raise TypeError("No clock found. Please define a clock.")
def raster_plot(*monitors, **additionalplotoptions):
"""Raster plot of a :class:`SpikeMonitor`
**Usage**
``raster_plot(monitor,options...)``
Plots the spike times of the monitor
on the x-axis, and the neuron number on the y-axis
``raster_plot(monitor0,monitor1,...,options...)``
Plots the spike times
for all the monitors given, with y-axis defined by placing a spike
from neuron n of m in monitor i at position i+n/m
``raster_plot(options...)``
Guesses the monitors to plot automagically
**Options**
Any of PyLab options for the ``plot`` command can be given, as well as:
``showplot=False``
set to ``True`` to run pylab's ``show()`` function
``newfigure=False``
set to ``True`` to create a new figure with pylab's ``figure()`` function
``xlabel``
label for the x-axis
``ylabel``
label for the y-axis
``title``
title for the plot
``showgrouplines=False``
set to ``True`` to show a line between each monitor
``grouplinecol``
colour for group lines
``spacebetweengroups``
value between 0 and 1 to insert a space between
each group on the y-axis
``refresh``
Specify how often (in simulation time) you would like the plot to
refresh. Note that this will only work if pylab is in interactive mode,
to ensure this call the pylab ``ion()`` command.
``showlast``
If you are using the ``refresh`` option above, plots are much quicker
if you specify a fixed time window to display (e.g. the last 100ms).
``redraw``
If you are using more than one realtime monitor, only one of them needs
to issue a redraw command, therefore set this to ``False`` for all but
one of them.
Note that with some IDEs, interactive plotting will not work with the
default matplotlib backend, try doing something like this at the
beginning of your script (before importing brian)::
import matplotlib
matplotlib.use('WXAgg')
You may need to experiment, try WXAgg, GTKAgg, QTAgg, TkAgg.
"""
if len(monitors) == 0:
(monitors, monitornames) = magic.find_instances(SpikeMonitor)
if len(monitors):
# OPTIONS
# Defaults
myopts = {
"title": "",
"xlabel": "Time (ms)",
"showplot": False,
"showgrouplines": False,
"spacebetweengroups": 0.0,
"grouplinecol": "k",
'newfigure': False,
'refresh': None,
'showlast': None,
'redraw': True
}
plotoptions = {'mew': 0}
if len(monitors) == 1:
myopts["ylabel"] = 'Neuron number'
else:
myopts["ylabel"] = 'Group number'
# User options
_take_options(myopts, additionalplotoptions)
plotoptions.update(additionalplotoptions)
# PLOTTING ROUTINE
spacebetween = myopts['spacebetweengroups']
class SecondTupleArray(object):
def __init__(self, obj):
self.obj = obj
def __getitem__(self, i):
return float(self.obj[i][1])
def __len__(self):
return len(self.obj)
def get_plot_coords(tmin=None, tmax=None):
allsn = []
allst = []
for i, m in enumerate(monitors):
mspikes = m.spikes
if tmin is not None and tmax is not None:
x = SecondTupleArray(mspikes)
imin = bisect.bisect_left(x, tmin)
imax = bisect.bisect_right(x, tmax)
mspikes = mspikes[imin:imax]
if len(mspikes):
sn, st = array(mspikes).T
else:
sn, st = array([]), array([])
st /= ms
if len(monitors) == 1:
allsn = [sn]
else:
allsn.append(i + (
(1. - spacebetween) / float(len(m.source))) * sn)
allst.append(st)
sn = hstack(allsn)
st = hstack(allst)
if len(monitors) == 1:
nmax = len(monitors[0].source)
else:
nmax = len(monitors)
return st, sn, nmax
st, sn, nmax = get_plot_coords()
if myopts['newfigure']:
pylab.figure()
if myopts['refresh'] is None:
line, = pylab.plot(st, sn, '.', **plotoptions)
else:
line, = pylab.plot([], [], '.', **plotoptions)
if myopts['refresh'] is not None:
pylab.axis(ymin=0, ymax=nmax)
if myopts['showlast'] is not None:
pylab.axis(xmin=-myopts['showlast'] / ms, xmax=0)
ax = pylab.gca()
if myopts['showgrouplines']:
for i in range(len(monitors)):
pylab.axhline(i, color=myopts['grouplinecol'])
pylab.axhline(i + (1 - spacebetween),
color=myopts['grouplinecol'])
pylab.ylabel(myopts['ylabel'])
pylab.xlabel(myopts['xlabel'])
pylab.title(myopts["title"])
if myopts["showplot"]:
pylab.show()
if myopts['refresh'] is not None:
@network_operation(clock=EventClock(dt=myopts['refresh']))
def refresh_raster_plot(clk):
if matplotlib.is_interactive():
if myopts['showlast'] is None:
st, sn, nmax = get_plot_coords()
line.set_xdata(st)
line.set_ydata(sn)
ax.set_xlim(0, amax(st))
else:
st, sn, nmax = get_plot_coords(
clk._t - float(myopts['showlast']), clk._t)
ax.set_xlim((clk.t - myopts['showlast']) / ms,
clk.t / ms)
line.set_xdata(array(st))
line.set_ydata(sn)
if myopts['redraw']:
pylab.draw()
pylab.get_current_fig_manager().canvas.flush_events()
monitors[0].contained_objects.append(refresh_raster_plot)
def raster_plot(*monitors, **additionalplotoptions):
"""Raster plot of a :class:`SpikeMonitor`
**Usage**
``raster_plot(monitor,options...)``
Plots the spike times of the monitor
on the x-axis, and the neuron number on the y-axis
``raster_plot(monitor0,monitor1,...,options...)``
Plots the spike times
for all the monitors given, with y-axis defined by placing a spike
from neuron n of m in monitor i at position i+n/m
``raster_plot(options...)``
Guesses the monitors to plot automagically
**Options**
Any of PyLab options for the ``plot`` command can be given, as well as:
``showplot=False``
set to ``True`` to run pylab's ``show()`` function
``newfigure=False``
set to ``True`` to create a new figure with pylab's ``figure()`` function
``xlabel``
label for the x-axis
``ylabel``
label for the y-axis
``title``
title for the plot
``showgrouplines=False``
set to ``True`` to show a line between each monitor
``grouplinecol``
colour for group lines
``spacebetweengroups``
value between 0 and 1 to insert a space between
each group on the y-axis
``refresh``
Specify how often (in simulation time) you would like the plot to
refresh. Note that this will only work if pylab is in interactive mode,
to ensure this call the pylab ``ion()`` command.
``showlast``
If you are using the ``refresh`` option above, plots are much quicker
if you specify a fixed time window to display (e.g. the last 100ms).
``redraw``
If you are using more than one realtime monitor, only one of them needs
to issue a redraw command, therefore set this to ``False`` for all but
one of them.
Note that with some IDEs, interactive plotting will not work with the
default matplotlib backend, try doing something like this at the
beginning of your script (before importing brian)::
import matplotlib
matplotlib.use('WXAgg')
You may need to experiment, try WXAgg, GTKAgg, QTAgg, TkAgg.
"""
if len(monitors) == 0:
(monitors, monitornames) = magic.find_instances(SpikeMonitor)
if len(monitors):
# OPTIONS
# Defaults
myopts = {
"title": "",
"xlabel": "Time (ms)",
"showplot": False,
"showgrouplines": False,
"spacebetweengroups": 0.0,
"grouplinecol": "k",
"newfigure": False,
"refresh": None,
"showlast": None,
"redraw": True,
}
plotoptions = {"mew": 0}
if len(monitors) == 1:
myopts["ylabel"] = "Neuron number"
else:
myopts["ylabel"] = "Group number"
# User options
_take_options(myopts, additionalplotoptions)
plotoptions.update(additionalplotoptions)
# PLOTTING ROUTINE
spacebetween = myopts["spacebetweengroups"]
class SecondTupleArray(object):
def __init__(self, obj):
self.obj = obj
def __getitem__(self, i):
return float(self.obj[i][1])
def __len__(self):
return len(self.obj)
def get_plot_coords(tmin=None, tmax=None):
allsn = []
allst = []
for i, m in enumerate(monitors):
mspikes = m.spikes
if tmin is not None and tmax is not None:
x = SecondTupleArray(mspikes)
imin = bisect.bisect_left(x, tmin)
imax = bisect.bisect_right(x, tmax)
mspikes = mspikes[imin:imax]
if len(mspikes):
sn, st = array(mspikes).T
else:
sn, st = array([]), array([])
st /= ms
if len(monitors) == 1:
allsn = [sn]
else:
allsn.append(i + ((1.0 - spacebetween) / float(len(m.source))) * sn)
allst.append(st)
sn = hstack(allsn)
st = hstack(allst)
if len(monitors) == 1:
nmax = len(monitors[0].source)
else:
nmax = len(monitors)
return st, sn, nmax
st, sn, nmax = get_plot_coords()
if myopts["newfigure"]:
pylab.figure()
if myopts["refresh"] is None:
line, = pylab.plot(st, sn, ".", **plotoptions)
else:
line, = pylab.plot([], [], ".", **plotoptions)
if myopts["refresh"] is not None:
pylab.axis(ymin=0, ymax=nmax)
if myopts["showlast"] is not None:
pylab.axis(xmin=-myopts["showlast"] / ms, xmax=0)
ax = pylab.gca()
if myopts["showgrouplines"]:
for i in range(len(monitors)):
pylab.axhline(i, color=myopts["grouplinecol"])
pylab.axhline(i + (1 - spacebetween), color=myopts["grouplinecol"])
pylab.ylabel(myopts["ylabel"])
pylab.xlabel(myopts["xlabel"])
pylab.title(myopts["title"])
if myopts["showplot"]:
pylab.show()
if myopts["refresh"] is not None:
@network_operation(clock=EventClock(dt=myopts["refresh"]))
def refresh_raster_plot(clk):
if matplotlib.is_interactive():
if myopts["showlast"] is None:
st, sn, nmax = get_plot_coords()
line.set_xdata(st)
line.set_ydata(sn)
ax.set_xlim(0, amax(st))
else:
st, sn, nmax = get_plot_coords(clk._t - float(myopts["showlast"]), clk._t)
ax.set_xlim((clk.t - myopts["showlast"]) / ms, clk.t / ms)
line.set_xdata(array(st))
line.set_ydata(sn)
if myopts["redraw"]:
pylab.draw()
pylab.get_current_fig_manager().canvas.flush_events()
monitors[0].contained_objects.append(refresh_raster_plot)
