def _decorate_objective(self, cost, ExtraArgs=None):
"""decorate the cost function with bounds, penalties, monitors, etc"""
#print("@%r %r %r" % (cost, ExtraArgs, max))
evalmon = self._evalmon
raw = cost
if ExtraArgs is None: ExtraArgs = ()
self._fcalls, cost = wrap_function(cost, ExtraArgs, evalmon)
if self._useStrictRange:
if self.generations:
#NOTE: pop[0] was best, may not be after resetting simplex
for i, j in enumerate(self._setSimplexWithinRangeBoundary()):
self.population[i + 1] = self.population[0].copy()
self.population[i + 1][i] = j
else:
self.population[0] = self._clipGuessWithinRangeBoundary(
self.population[0])
cost = wrap_bounds(cost, self._strictMin, self._strictMax)
cost = wrap_penalty(cost, self._penalty)
cost = wrap_nested(cost, self._constraints)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' and 'raw' cost function
self._cost = (cost, raw, ExtraArgs)
self._live = True
return cost
def _decorate_objective(self, cost, ExtraArgs=None):
"""decorate cost function with bounds, penalties, monitors, etc"""
#print("@%r %r %r" % (cost, ExtraArgs, max))
raw = cost
if ExtraArgs is None: ExtraArgs = ()
from mystic.python_map import python_map
if self._map != python_map:
#FIXME: EvaluationMonitor fails for MPI, throws error for 'pp'
from mystic.monitors import Null
evalmon = Null()
else:
evalmon = self._evalmon
fcalls, cost = wrap_function(cost, ExtraArgs, evalmon)
if self._useStrictRange:
indx = list(self.popEnergy).index(self.bestEnergy)
ngen = self.generations #XXX: no random if generations=0 ?
for i in range(self.nPop):
self.population[i] = self._clipGuessWithinRangeBoundary(
self.population[i], (not ngen) or (i is indx))
cost = wrap_bounds(cost, self._strictMin, self._strictMax)
cost = wrap_penalty(cost, self._penalty)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' and 'raw' cost function
self._cost = (cost, raw, ExtraArgs)
self._live = True
return cost
def _decorate_objective(self, cost, ExtraArgs=None):
"""decorate cost function with bounds, penalties, monitors, etc"""
#print ("@", cost, ExtraArgs, max)
raw = cost
if ExtraArgs is None: ExtraArgs = ()
from python_map import python_map
if self._map != python_map:
#FIXME: EvaluationMonitor fails for MPI, throws error for 'pp'
from mystic.monitors import Null
evalmon = Null()
else: evalmon = self._evalmon
fcalls, cost = wrap_function(cost, ExtraArgs, evalmon)
if self._useStrictRange:
indx = list(self.popEnergy).index(self.bestEnergy)
ngen = self.generations #XXX: no random if generations=0 ?
for i in range(self.nPop):
self.population[i] = self._clipGuessWithinRangeBoundary(self.population[i], (not ngen) or (i is indx))
cost = wrap_bounds(cost, self._strictMin, self._strictMax)
cost = wrap_penalty(cost, self._penalty)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' and 'raw' cost function
self._cost = (cost, raw, ExtraArgs)
self._live = True
return cost
def _decorate_objective(self, cost, ExtraArgs=None):
"""decorate the cost function with bounds, penalties, monitors, etc
input::
- cost is the objective function, of the form y = cost(x, *ExtraArgs),
where x is a candidate solution, and ExtraArgs is the tuple of positional
arguments required to evaluate the objective."""
#print("@%r %r %r" % (cost, ExtraArgs, max))
evalmon = self._evalmon
raw = cost
if ExtraArgs is None: ExtraArgs = ()
self._fcalls, cost = wrap_function(cost, ExtraArgs, evalmon)
if self._useStrictRange:
indx = list(self.popEnergy).index(self.bestEnergy)
ngen = self.generations #XXX: no random if generations=0 ?
for i in range(self.nPop):
self.population[i] = self._clipGuessWithinRangeBoundary(
self.population[i], (not ngen) or (i == indx))
cost = wrap_bounds(cost, self._strictMin,
self._strictMax) #XXX: remove?
from mystic.constraints import and_
constraints = and_(self._constraints,
self._strictbounds,
onfail=self._strictbounds)
else:
constraints = self._constraints
cost = wrap_penalty(cost, self._penalty)
cost = wrap_nested(cost, constraints)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' and 'raw' cost function
self._cost = (cost, raw, ExtraArgs)
self._live = True
return cost
def _RegisterObjective(self, cost, ExtraArgs=None):
"""decorate cost function with bounds, penalties, monitors, etc"""
if ExtraArgs == None: ExtraArgs = ()
self._fcalls, cost = wrap_function(cost, ExtraArgs, self._evalmon)
if self._useStrictRange:
for i in range(self.nPop):
self.population[i] = self._clipGuessWithinRangeBoundary(self.population[i])
cost = wrap_bounds(cost, self._strictMin, self._strictMax)
cost = wrap_penalty(cost, self._penalty)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' cost function
self._cost = (cost, ExtraArgs)
return cost
def _RegisterObjective(self, cost, ExtraArgs=None):
"""decorate cost function with bounds, penalties, monitors, etc"""
if ExtraArgs == None: ExtraArgs = ()
#FIXME: EvaluationMonitor fails for MPI, throws error for 'pp'
from python_map import python_map
if self._map != python_map:
self._fcalls = [0] #FIXME: temporary patch for removing the following line
else:
self._fcalls, cost = wrap_function(cost, ExtraArgs, self._evalmon)
if self._useStrictRange:
for i in range(self.nPop):
self.population[i] = self._clipGuessWithinRangeBoundary(self.population[i])
cost = wrap_bounds(cost, self._strictMin, self._strictMax)
cost = wrap_penalty(cost, self._penalty)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' cost function
self._cost = (cost, ExtraArgs)
return cost
def _decorate_objective(self, cost, ExtraArgs=None):
"""decorate cost function with bounds, penalties, monitors, etc"""
#print ("@", cost, ExtraArgs, max)
raw = cost
if ExtraArgs is None: ExtraArgs = ()
self._fcalls, cost = wrap_function(cost, ExtraArgs, self._evalmon)
if self._useStrictRange:
indx = list(self.popEnergy).index(self.bestEnergy)
ngen = self.generations #XXX: no random if generations=0 ?
for i in range(self.nPop):
self.population[i] = self._clipGuessWithinRangeBoundary(self.population[i], (not ngen) or (i is indx))
cost = wrap_bounds(cost, self._strictMin, self._strictMax)
cost = wrap_penalty(cost, self._penalty)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' and 'raw' cost function
self._cost = (cost, raw, ExtraArgs)
self._live = True
return cost
def _decorate_objective(self, cost, ExtraArgs=None):
"""decorate cost function with bounds, penalties, monitors, etc"""
#print("@%r %r %r" % (cost, ExtraArgs, max))
raw = cost
if ExtraArgs is None: ExtraArgs = ()
self._fcalls, cost = wrap_function(cost, ExtraArgs, self._evalmon)
if self._useStrictRange:
indx = list(self.popEnergy).index(self.bestEnergy)
ngen = self.generations #XXX: no random if generations=0 ?
for i in range(self.nPop):
self.population[i] = self._clipGuessWithinRangeBoundary(self.population[i], (not ngen) or (i is indx))
cost = wrap_bounds(cost, self._strictMin, self._strictMax)
cost = wrap_penalty(cost, self._penalty)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' and 'raw' cost function
self._cost = (cost, raw, ExtraArgs)
self._live = True
return cost
def _decorate_objective(self, cost, ExtraArgs=None):
"""decorate the cost function with bounds, penalties, monitors, etc
input::
- cost is the objective function, of the form y = cost(x, *ExtraArgs),
where x is a candidate solution, and ExtraArgs is the tuple of positional
arguments required to evaluate the objective."""
#print("@%r %r %r" % (cost, ExtraArgs, max))
evalmon = self._evalmon
raw = cost
if ExtraArgs is None: ExtraArgs = ()
self._fcalls, cost = wrap_function(cost, ExtraArgs, evalmon)
if self._useStrictRange:
if self.generations:
#NOTE: pop[0] was best, may not be after resetting simplex
for i, j in enumerate(self._setSimplexWithinRangeBoundary()):
self.population[i + 1] = self.population[0].copy()
self.population[i + 1][i] = j
else:
self.population[0] = self._clipGuessWithinRangeBoundary(
self.population[0])
cost = wrap_bounds(cost, self._strictMin,
self._strictMax) #XXX: remove?
from mystic.constraints import and_
constraints = and_(self._constraints,
self._strictbounds,
onfail=self._strictbounds)
else:
constraints = self._constraints
cost = wrap_penalty(cost, self._penalty)
cost = wrap_nested(cost, constraints)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' and 'raw' cost function
self._cost = (cost, raw, ExtraArgs)
self._live = True
return cost
def _decorate_objective(self, cost, ExtraArgs=None):
"""decorate the cost function with bounds, penalties, monitors, etc"""
#print ("@", cost, ExtraArgs, max)
raw = cost
if ExtraArgs is None: ExtraArgs = ()
self._fcalls, cost = wrap_function(cost, ExtraArgs, self._evalmon)
if self._useStrictRange:
if self.generations:
#NOTE: pop[0] was best, may not be after resetting simplex
for i,j in enumerate(self._setSimplexWithinRangeBoundary()):
self.population[i+1] = self.population[0].copy()
self.population[i+1][i] = j
else:
self.population[0] = self._clipGuessWithinRangeBoundary(self.population[0])
cost = wrap_bounds(cost, self._strictMin, self._strictMax)
cost = wrap_penalty(cost, self._penalty)
cost = wrap_nested(cost, self._constraints)
if self._reducer:
#cost = reduced(*self._reducer)(cost) # was self._reducer = (f,bool)
cost = reduced(self._reducer, arraylike=True)(cost)
# hold on to the 'wrapped' and 'raw' cost function
self._cost = (cost, raw, ExtraArgs)
self._live = True
return cost
def model_plotter(model, logfile=None, **kwds):
"""
generate surface contour plots for model, specified by full import path
generate model trajectory from logfile (or solver restart file), if provided
Available from the command shell as:
mystic_model_plotter.py model (filename) [options]
or as a function call as:
mystic.model_plotter(model, filename=None, **options)
The option "bounds" takes an indicator string, where the bounds should
be given as comma-separated slices. For example, using bounds = "-1:10, 0:20"
will set the lower and upper bounds for x to be (-1,10) and y to be (0,20).
The "step" can also be given, to control the number of lines plotted in the
grid. Thus "-1:10:.1, 0:20" would set the bounds as above, but use increments
of .1 along x and the default step along y. For models with > 2D, the bounds
can be used to specify 2 dimensions plus fixed values for remaining dimensions.
Thus, "-1:10, 0:20, 1.0" would plot the 2D surface where the z-axis was fixed
at z=1.0. When called from a script, slice objects can be used instead of a
string, thus "-1:10:.1, 0:20, 1.0" becomes (slice(-1,10,.1), slice(20), 1.0).
The option "label" takes comma-separated strings. For example, label = "x,y,"
will place 'x' on the x-axis, 'y' on the y-axis, and nothing on the z-axis.
LaTeX is also accepted. For example, label = "$ h $, $ {\\alpha}$, $ v$" will
label the axes with standard LaTeX math formatting. Note that the leading
space is required, while a trailing space aligns the text with the axis
instead of the plot frame.
The option "reduce" can be given to reduce the output of a model to a scalar,
thus converting 'model(params)' to 'reduce(model(params))'. A reducer is given
by the import path (e.g. 'numpy.add'). The option "scale" will convert the plot
to log-scale, and scale the cost by 'z=log(4*z*scale+1)+2'. This is useful for
visualizing small contour changes around the minimium. If using log-scale
produces negative numbers, the option "shift" can be used to shift the cost
by 'z=z+shift'. Both shift and scale are intended to help visualize contours.
Required Inputs:
model full import path for the model (e.g. mystic.models.rosen)
Additional Inputs:
filename name of the convergence logfile (e.g. log.txt)
"""
#FIXME: should be able to:
# - apply a constraint as a region of NaN -- apply when 'xx,yy=x[ij],y[ij]'
# - apply a penalty by shifting the surface (plot w/alpha?) -- as above
# - build an appropriately-sized default grid (from logfile info)
# - move all mulit-id param/cost reading into read_history
#FIXME: current issues:
# - 1D slice and projection work for 2D function, but aren't "pretty"
# - 1D slice and projection for 1D function, is it meaningful and correct?
# - should be able to plot from solver.genealogy (multi-monitor?) [1D,2D,3D?]
# - should be able to scale 'z-axis' instead of scaling 'z' itself
# (see https://github.com/matplotlib/matplotlib/issues/209)
# - if trajectory outside contour grid, will increase bounds
# (see support_hypercube.py for how to fix bounds)
import shlex
global __quit
__quit = False
_model = None
_reducer = None
_solver = None
instance = None
# handle the special case where list is provided by sys.argv
if isinstance(model, (list, tuple)) and not logfile and not kwds:
cmdargs = model # (above is used by script to parse command line)
elif isinstance(model, basestring) and not logfile and not kwds:
cmdargs = shlex.split(model)
# 'everything else' is essentially the functional interface
else:
cmdargs = kwds.get('kwds', '')
if not cmdargs:
out = kwds.get('out', None)
bounds = kwds.get('bounds', None)
label = kwds.get('label', None)
nid = kwds.get('nid', None)
iter = kwds.get('iter', None)
reduce = kwds.get('reduce', None)
scale = kwds.get('scale', None)
shift = kwds.get('shift', None)
fill = kwds.get('fill', False)
depth = kwds.get('depth', False)
dots = kwds.get('dots', False)
join = kwds.get('join', False)
verb = kwds.get('verb', False)
# special case: bounds passed as list of slices
if not isinstance(bounds, (basestring, type(None))):
cmdargs = ''
for b in bounds:
if isinstance(b, slice):
cmdargs += "{}:{}:{}, ".format(b.start, b.stop, b.step)
else:
cmdargs += "{}, ".format(b)
bounds = cmdargs[:-2]
cmdargs = ''
if callable(reduce): _reducer, reduce = reduce, None
# special case: model passed as model instance
#model.__doc__.split('using::')[1].split()[0].strip()
if callable(model): _model, model = model, "None"
# handle logfile if given
if logfile:
if isinstance(logfile, basestring):
model += ' ' + logfile
else: # special case of passing in monitor instance
instance = logfile
# process "commandline" arguments
if not cmdargs:
cmdargs = ''
cmdargs += '' if out is None else '--out={} '.format(out)
cmdargs += '' if bounds is None else '--bounds="{}" '.format(
bounds)
cmdargs += '' if label is None else '--label={} '.format(label)
cmdargs += '' if nid is None else '--nid={} '.format(nid)
cmdargs += '' if iter is None else '--iter={} '.format(iter)
cmdargs += '' if reduce is None else '--reduce={} '.format(reduce)
cmdargs += '' if scale is None else '--scale={} '.format(scale)
cmdargs += '' if shift is None else '--shift={} '.format(shift)
cmdargs += '' if fill == False else '--fill '
cmdargs += '' if depth == False else '--depth '
cmdargs += '' if dots == False else '--dots '
cmdargs += '' if join == False else '--join '
cmdargs += '' if verb == False else '--verb '
else:
cmdargs = ' ' + cmdargs
cmdargs = model.split() + shlex.split(cmdargs)
#XXX: note that 'argparse' is new as of python2.7
from optparse import OptionParser
def _exit(self, errno=None, msg=None):
global __quit
__quit = True
if errno or msg:
msg = msg.split(': error: ')[-1].strip()
raise IOError(msg)
OptionParser.exit = _exit
parser = OptionParser(usage=model_plotter.__doc__.split('\n\nOptions:')[0])
parser.add_option("-u","--out",action="store",dest="out",\
metavar="STR",default=None,
help="filepath to save generated plot")
parser.add_option("-b","--bounds",action="store",dest="bounds",\
metavar="STR",default="-5:5:.1, -5:5:.1",
help="indicator string to set plot bounds and density")
parser.add_option("-l","--label",action="store",dest="label",\
metavar="STR",default=",,",
help="string to assign label to axis")
parser.add_option("-n","--nid",action="store",dest="id",\
metavar="INT",default=None,
help="id # of the nth simultaneous points to plot")
parser.add_option("-i","--iter",action="store",dest="stop",\
metavar="STR",default=":",
help="string for smallest:largest iterations to plot")
parser.add_option("-r","--reduce",action="store",dest="reducer",\
metavar="STR",default="None",
help="import path of output reducer function")
parser.add_option("-x","--scale",action="store",dest="zscale",\
metavar="INT",default=0.0,
help="scale plotted cost by z=log(4*z*scale+1)+2")
parser.add_option("-z","--shift",action="store",dest="zshift",\
metavar="INT",default=0.0,
help="shift plotted cost by z=z+shift")
parser.add_option("-f","--fill",action="store_true",dest="fill",\
default=False,help="plot using filled contours")
parser.add_option("-d","--depth",action="store_true",dest="surface",\
default=False,help="plot contours showing depth in 3D")
parser.add_option("-o","--dots",action="store_true",dest="dots",\
default=False,help="show trajectory points in plot")
parser.add_option("-j","--join",action="store_true",dest="line",\
default=False,help="connect trajectory points in plot")
parser.add_option("-v","--verb",action="store_true",dest="verbose",\
default=False,help="print model documentation string")
# import sys
# if 'mystic_model_plotter.py' not in sys.argv:
from StringIO import StringIO
f = StringIO()
parser.print_help(file=f)
f.seek(0)
if 'Options:' not in model_plotter.__doc__:
model_plotter.__doc__ += '\nOptions:%s' % f.read().split(
'Options:')[-1]
f.close()
try:
parsed_opts, parsed_args = parser.parse_args(cmdargs)
except UnboundLocalError:
pass
if __quit: return
# get the import path for the model
model = parsed_args[0] # e.g. 'mystic.models.rosen'
if "None" == model: model = None
try: # get the name of the parameter log file
source = parsed_args[1] # e.g. 'log.txt'
except:
source = None
try: # select the bounds
options = parsed_opts.bounds # format is "-1:10:.1, -1:10:.1, 1.0"
except:
options = "-5:5:.1, -5:5:.1"
try: # plot using filled contours
fill = parsed_opts.fill
except:
fill = False
try: # plot contours showing depth in 3D
surface = parsed_opts.surface
except:
surface = False
#XXX: can't do '-x' with no argument given (use T/F instead?)
try: # scale plotted cost by z=log(4*z*scale+1)+2
scale = float(parsed_opts.zscale)
if not scale: scale = False
except:
scale = False
#XXX: can't do '-z' with no argument given
try: # shift plotted cost by z=z+shift
shift = float(parsed_opts.zshift)
if not shift: shift = False
except:
shift = False
try: # import path of output reducer function
reducer = parsed_opts.reducer # e.g. 'numpy.add'
if "None" == reducer: reducer = None
except:
reducer = None
style = '-' # default linestyle
if parsed_opts.dots:
mark = 'o' # marker=mark
# when using 'dots', also can turn off 'line'
if not parsed_opts.line:
style = '' # linestyle='None'
else:
mark = ''
color = 'w' if fill else 'k'
style = color + style + mark
try: # select labels for the axes
label = parsed_opts.label.split(',') # format is "x, y, z"
except:
label = ['', '', '']
try: # select which 'id' to plot results for
ids = (int(parsed_opts.id), ) #XXX: allow selecting more than one id ?
except:
ids = None # i.e. 'all'
try: # select which iteration to stop plotting at
stop = parsed_opts.stop # format is "1:10:1"
stop = stop if ":" in stop else ":" + stop
except:
stop = ":"
try: # select whether to be verbose about model documentation
verbose = bool(parsed_opts.verbose)
except:
verbose = False
#################################################
solver = None # set to 'mystic.solvers.fmin' (or similar) for 'live' fits
#NOTE: 'live' runs constrain params explicitly in the solver, then reduce
# dimensions appropriately so results can be 2D contour plotted.
# When working with legacy results that have more than 2 params,
# the trajectory WILL NOT follow the masked surface generated
# because the masked params were NOT fixed when the solver was run.
#################################################
from mystic.tools import reduced, masked, partial
# process inputs
if _model: model = _model
if _reducer: reducer = _reducer
if _solver: solver = _solver
select, spec, mask = _parse_input(options)
x, y = _parse_axes(spec, grid=True) # grid=False for 1D plots
#FIXME: does grid=False still make sense here...?
if reducer: reducer = _reducer or _get_instance(reducer)
if solver and (not source or not model): #XXX: not instance?
raise RuntimeError('a model and results filename are required')
elif not source and not model and not instance:
raise RuntimeError('a model or a results file is required')
if model:
model = _model or _get_instance(model)
if verbose: print model.__doc__
# need a reducer if model returns an array
if reducer: model = reduced(reducer, arraylike=False)(model)
if solver:
# if 'live'... pick a solver
solver = 'mystic.solvers.fmin'
solver = _solver or _get_instance(solver)
xlen = len(select) + len(mask)
if solver.__name__.startswith('diffev'):
initial = [(-1, 1)] * xlen
else:
initial = [0] * xlen
from mystic.monitors import VerboseLoggingMonitor
if instance:
itermon = VerboseLoggingMonitor(new=True)
itermon.prepend(instance)
else:
itermon = VerboseLoggingMonitor(filename=source, new=True)
# explicitly constrain parameters
model = partial(mask)(model)
# solve
sol = solver(model, x0=initial, itermon=itermon)
#-OVERRIDE-INPUTS-#
import numpy
# read trajectories from monitor (comment out to use logfile)
source = itermon
# if negative minimum, shift by the 'solved minimum' plus an epsilon
shift = max(-numpy.min(itermon.y), 0.0) + 0.5 # a good guess
#-----------------#
if model: # for plotting, implicitly constrain by reduction
model = masked(mask)(model)
## plot the surface in 1D
#if solver: v=sol[-1]
#elif source: v=cost[-1]
#else: v=None
#fig0 = _draw_slice(model, x=x, y=v, scale=scale, shift=shift)
# plot the surface in 2D or 3D
fig = _draw_contour(model,
x,
y,
surface=surface,
fill=fill,
scale=scale,
shift=shift)
else:
#fig0 = None
fig = None
if instance: source = instance
if source:
# params are the parameter trajectories
# cost is the solution trajectory
params, cost = _get_history(source, ids)
if len(cost) > 1: style = style[1:] # 'auto-color' #XXX: or grayscale?
for p, c in zip(params, cost):
## project trajectory on a 1D slice of model surface #XXX: useful?
#s = select[0] if len(select) else 0
#px = p[int(s)] # _draw_projection requires one parameter
## ignore everything after 'stop'
#_c = eval('c[%s]' % stop)
#_x = eval('px[%s]' % stop)
#fig0 = _draw_projection(_x,_c, style=style, scale=scale, shift=shift, figure=fig0)
# plot the trajectory on the model surface (2D or 3D)
# get two selected params #XXX: what if len(select)<2? or len(p)<2?
p = [p[int(i)] for i in select[:2]]
px, py = p # _draw_trajectory requires two parameters
# ignore everything after 'stop'
_x = eval('px[%s]' % stop)
_y = eval('py[%s]' % stop)
_c = eval('c[%s]' % stop) if surface else None
fig = _draw_trajectory(_x,
_y,
_c,
style=style,
scale=scale,
shift=shift,
figure=fig)
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import axes3d
# add labels to the axes
if surface: kwds = {'projection': '3d'} # 3D
else: kwds = {} # 2D
ax = fig.gca(**kwds)
ax.set_xlabel(label[0])
ax.set_ylabel(label[1])
if surface: ax.set_zlabel(label[2])
if not parsed_opts.out:
plt.show()
else:
fig.savefig(parsed_opts.out)
def model_plotter(model, logfile=None, **kwds):
"""
generate surface contour plots for model, specified by full import path
generate model trajectory from logfile (or solver restart file), if provided
Available from the command shell as:
mystic_model_plotter.py model (filename) [options]
or as a function call as:
mystic.model_plotter(model, filename=None, **options)
The option "bounds" takes an indicator string, where the bounds should
be given as comma-separated slices. For example, using bounds = "-1:10, 0:20"
will set the lower and upper bounds for x to be (-1,10) and y to be (0,20).
The "step" can also be given, to control the number of lines plotted in the
grid. Thus "-1:10:.1, 0:20" would set the bounds as above, but use increments
of .1 along x and the default step along y. For models with > 2D, the bounds
can be used to specify 2 dimensions plus fixed values for remaining dimensions.
Thus, "-1:10, 0:20, 1.0" would plot the 2D surface where the z-axis was fixed
at z=1.0. When called from a script, slice objects can be used instead of a
string, thus "-1:10:.1, 0:20, 1.0" becomes (slice(-1,10,.1), slice(20), 1.0).
The option "label" takes comma-separated strings. For example, label = "x,y,"
will place 'x' on the x-axis, 'y' on the y-axis, and nothing on the z-axis.
LaTeX is also accepted. For example, label = "$ h $, $ {\\alpha}$, $ v$" will
label the axes with standard LaTeX math formatting. Note that the leading
space is required, while a trailing space aligns the text with the axis
instead of the plot frame.
The option "reduce" can be given to reduce the output of a model to a scalar,
thus converting 'model(params)' to 'reduce(model(params))'. A reducer is given
by the import path (e.g. 'numpy.add'). The option "scale" will convert the plot
to log-scale, and scale the cost by 'z=log(4*z*scale+1)+2'. This is useful for
visualizing small contour changes around the minimium. If using log-scale
produces negative numbers, the option "shift" can be used to shift the cost
by 'z=z+shift'. Both shift and scale are intended to help visualize contours.
Required Inputs:
model full import path for the model (e.g. mystic.models.rosen)
Additional Inputs:
filename name of the convergence logfile (e.g. log.txt)
"""
#FIXME: should be able to:
# - apply a constraint as a region of NaN -- apply when 'xx,yy=x[ij],y[ij]'
# - apply a penalty by shifting the surface (plot w/alpha?) -- as above
# - build an appropriately-sized default grid (from logfile info)
# - move all mulit-id param/cost reading into read_history
#FIXME: current issues:
# - 1D slice and projection work for 2D function, but aren't "pretty"
# - 1D slice and projection for 1D function, is it meaningful and correct?
# - should be able to plot from solver.genealogy (multi-monitor?) [1D,2D,3D?]
# - should be able to scale 'z-axis' instead of scaling 'z' itself
# (see https://github.com/matplotlib/matplotlib/issues/209)
# - if trajectory outside contour grid, will increase bounds
# (see support_hypercube.py for how to fix bounds)
import shlex
try:
basestring
from StringIO import StringIO
except NameError:
basestring = str
from io import StringIO
global __quit
__quit = False
_model = None
_reducer = None
_solver = None
instance = None
# handle the special case where list is provided by sys.argv
if isinstance(model, (list,tuple)) and not logfile and not kwds:
cmdargs = model # (above is used by script to parse command line)
elif isinstance(model, basestring) and not logfile and not kwds:
cmdargs = shlex.split(model)
# 'everything else' is essentially the functional interface
else:
cmdargs = kwds.get('kwds', '')
if not cmdargs:
out = kwds.get('out', None)
bounds = kwds.get('bounds', None)
label = kwds.get('label', None)
nid = kwds.get('nid', None)
iter = kwds.get('iter', None)
reduce = kwds.get('reduce', None)
scale = kwds.get('scale', None)
shift = kwds.get('shift', None)
fill = kwds.get('fill', False)
depth = kwds.get('depth', False)
dots = kwds.get('dots', False)
join = kwds.get('join', False)
verb = kwds.get('verb', False)
# special case: bounds passed as list of slices
if not isinstance(bounds, (basestring, type(None))):
cmdargs = ''
for b in bounds:
if isinstance(b, slice):
cmdargs += "{}:{}:{}, ".format(b.start, b.stop, b.step)
else:
cmdargs += "{}, ".format(b)
bounds = cmdargs[:-2]
cmdargs = ''
if isinstance(reduce, collections.Callable): _reducer, reduce = reduce, None
# special case: model passed as model instance
#model.__doc__.split('using::')[1].split()[0].strip()
if isinstance(model, collections.Callable): _model, model = model, "None"
# handle logfile if given
if logfile:
if isinstance(logfile, basestring):
model += ' ' + logfile
else: # special case of passing in monitor instance
instance = logfile
# process "commandline" arguments
if not cmdargs:
cmdargs = ''
cmdargs += '' if out is None else '--out={} '.format(out)
cmdargs += '' if bounds is None else '--bounds="{}" '.format(bounds)
cmdargs += '' if label is None else '--label={} '.format(label)
cmdargs += '' if nid is None else '--nid={} '.format(nid)
cmdargs += '' if iter is None else '--iter={} '.format(iter)
cmdargs += '' if reduce is None else '--reduce={} '.format(reduce)
cmdargs += '' if scale is None else '--scale={} '.format(scale)
cmdargs += '' if shift is None else '--shift={} '.format(shift)
cmdargs += '' if fill == False else '--fill '
cmdargs += '' if depth == False else '--depth '
cmdargs += '' if dots == False else '--dots '
cmdargs += '' if join == False else '--join '
cmdargs += '' if verb == False else '--verb '
else:
cmdargs = ' ' + cmdargs
cmdargs = model.split() + shlex.split(cmdargs)
#XXX: note that 'argparse' is new as of python2.7
from optparse import OptionParser
def _exit(self, errno=None, msg=None):
global __quit
__quit = True
if errno or msg:
msg = msg.split(': error: ')[-1].strip()
raise IOError(msg)
OptionParser.exit = _exit
parser = OptionParser(usage=model_plotter.__doc__.split('\n\nOptions:')[0])
parser.add_option("-u","--out",action="store",dest="out",\
metavar="STR",default=None,
help="filepath to save generated plot")
parser.add_option("-b","--bounds",action="store",dest="bounds",\
metavar="STR",default="-5:5:.1, -5:5:.1",
help="indicator string to set plot bounds and density")
parser.add_option("-l","--label",action="store",dest="label",\
metavar="STR",default=",,",
help="string to assign label to axis")
parser.add_option("-n","--nid",action="store",dest="id",\
metavar="INT",default=None,
help="id # of the nth simultaneous points to plot")
parser.add_option("-i","--iter",action="store",dest="stop",\
metavar="STR",default=":",
help="string for smallest:largest iterations to plot")
parser.add_option("-r","--reduce",action="store",dest="reducer",\
metavar="STR",default="None",
help="import path of output reducer function")
parser.add_option("-x","--scale",action="store",dest="zscale",\
metavar="INT",default=0.0,
help="scale plotted cost by z=log(4*z*scale+1)+2")
parser.add_option("-z","--shift",action="store",dest="zshift",\
metavar="INT",default=0.0,
help="shift plotted cost by z=z+shift")
parser.add_option("-f","--fill",action="store_true",dest="fill",\
default=False,help="plot using filled contours")
parser.add_option("-d","--depth",action="store_true",dest="surface",\
default=False,help="plot contours showing depth in 3D")
parser.add_option("-o","--dots",action="store_true",dest="dots",\
default=False,help="show trajectory points in plot")
parser.add_option("-j","--join",action="store_true",dest="line",\
default=False,help="connect trajectory points in plot")
parser.add_option("-v","--verb",action="store_true",dest="verbose",\
default=False,help="print model documentation string")
# import sys
# if 'mystic_model_plotter.py' not in sys.argv:
if PY3:
f = StringIO()
parser.print_help(file=f)
f.seek(0)
if 'Options:' not in model_plotter.__doc__:
model_plotter.__doc__ += '\nOptions:%s' % f.read().split('Options:')[-1]
f.close()
else:
if 'Options:' not in model_plotter.__doc__:
model_plotter.__doc__ += '\nOptions:%s' % parser.format_help().split('Options:')[-1]
try:
parsed_opts, parsed_args = parser.parse_args(cmdargs)
except UnboundLocalError:
pass
if __quit: return
# get the import path for the model
model = parsed_args[0] # e.g. 'mystic.models.rosen'
if "None" == model: model = None
try: # get the name of the parameter log file
source = parsed_args[1] # e.g. 'log.txt'
except:
source = None
try: # select the bounds
options = parsed_opts.bounds # format is "-1:10:.1, -1:10:.1, 1.0"
except:
options = "-5:5:.1, -5:5:.1"
try: # plot using filled contours
fill = parsed_opts.fill
except:
fill = False
try: # plot contours showing depth in 3D
surface = parsed_opts.surface
except:
surface = False
#XXX: can't do '-x' with no argument given (use T/F instead?)
try: # scale plotted cost by z=log(4*z*scale+1)+2
scale = float(parsed_opts.zscale)
if not scale: scale = False
except:
scale = False
#XXX: can't do '-z' with no argument given
try: # shift plotted cost by z=z+shift
shift = float(parsed_opts.zshift)
if not shift: shift = False
except:
shift = False
try: # import path of output reducer function
reducer = parsed_opts.reducer # e.g. 'numpy.add'
if "None" == reducer: reducer = None
except:
reducer = None
style = '-' # default linestyle
if parsed_opts.dots:
mark = 'o' # marker=mark
# when using 'dots', also can turn off 'line'
if not parsed_opts.line:
style = '' # linestyle='None'
else:
mark = ''
color = 'w' if fill else 'k'
style = color + style + mark
try: # select labels for the axes
label = parsed_opts.label.split(',') # format is "x, y, z"
except:
label = ['','','']
try: # select which 'id' to plot results for
ids = (int(parsed_opts.id),) #XXX: allow selecting more than one id ?
except:
ids = None # i.e. 'all'
try: # select which iteration to stop plotting at
stop = parsed_opts.stop # format is "1:10:1"
stop = stop if ":" in stop else ":"+stop
except:
stop = ":"
try: # select whether to be verbose about model documentation
verbose = bool(parsed_opts.verbose)
except:
verbose = False
#################################################
solver = None # set to 'mystic.solvers.fmin' (or similar) for 'live' fits
#NOTE: 'live' runs constrain params explicitly in the solver, then reduce
# dimensions appropriately so results can be 2D contour plotted.
# When working with legacy results that have more than 2 params,
# the trajectory WILL NOT follow the masked surface generated
# because the masked params were NOT fixed when the solver was run.
#################################################
from mystic.tools import reduced, masked, partial
# process inputs
if _model: model = _model
if _reducer: reducer = _reducer
if _solver: solver = _solver
select, spec, mask = _parse_input(options)
x,y = _parse_axes(spec, grid=True) # grid=False for 1D plots
#FIXME: does grid=False still make sense here...?
if reducer: reducer = _reducer or _get_instance(reducer)
if solver and (not source or not model): #XXX: not instance?
raise RuntimeError('a model and results filename are required')
elif not source and not model and not instance:
raise RuntimeError('a model or a results file is required')
if model:
model = _model or _get_instance(model)
if verbose: print(model.__doc__)
# need a reducer if model returns an array
if reducer: model = reduced(reducer, arraylike=False)(model)
if solver:
# if 'live'... pick a solver
solver = 'mystic.solvers.fmin'
solver = _solver or _get_instance(solver)
xlen = len(select)+len(mask)
if solver.__name__.startswith('diffev'):
initial = [(-1,1)]*xlen
else:
initial = [0]*xlen
from mystic.monitors import VerboseLoggingMonitor
if instance:
itermon = VerboseLoggingMonitor(new=True)
itermon.prepend(instance)
else:
itermon = VerboseLoggingMonitor(filename=source, new=True)
# explicitly constrain parameters
model = partial(mask)(model)
# solve
sol = solver(model, x0=initial, itermon=itermon)
#-OVERRIDE-INPUTS-#
import numpy
# read trajectories from monitor (comment out to use logfile)
source = itermon
# if negative minimum, shift by the 'solved minimum' plus an epsilon
shift = max(-numpy.min(itermon.y), 0.0) + 0.5 # a good guess
#-----------------#
if model: # for plotting, implicitly constrain by reduction
model = masked(mask)(model)
## plot the surface in 1D
#if solver: v=sol[-1]
#elif source: v=cost[-1]
#else: v=None
#fig0 = _draw_slice(model, x=x, y=v, scale=scale, shift=shift)
# plot the surface in 2D or 3D
fig = _draw_contour(model, x, y, surface=surface, fill=fill, scale=scale, shift=shift)
else:
#fig0 = None
fig = None
if instance: source = instance
if source:
# params are the parameter trajectories
# cost is the solution trajectory
params, cost = _get_history(source, ids)
if len(cost) > 1: style = style[1:] # 'auto-color' #XXX: or grayscale?
for p,c in zip(params, cost):
## project trajectory on a 1D slice of model surface #XXX: useful?
#s = select[0] if len(select) else 0
#px = p[int(s)] # _draw_projection requires one parameter
## ignore everything after 'stop'
#_c = eval('c[%s]' % stop)
#_x = eval('px[%s]' % stop)
#fig0 = _draw_projection(_x,_c, style=style, scale=scale, shift=shift, figure=fig0)
# plot the trajectory on the model surface (2D or 3D)
# get two selected params #XXX: what if len(select)<2? or len(p)<2?
p = [p[int(i)] for i in select[:2]]
px,py = p # _draw_trajectory requires two parameters
# ignore everything after 'stop'
locals = dict(px=px, py=py, c=c)
_x = eval('px[%s]' % stop, locals)
_y = eval('py[%s]' % stop, locals)
_c = eval('c[%s]' % stop, locals) if surface else None
fig = _draw_trajectory(_x,_y,_c, style=style, scale=scale, shift=shift, figure=fig)
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import axes3d
# add labels to the axes
if surface: kwds = {'projection':'3d'} # 3D
else: kwds = {} # 2D
ax = fig.gca(**kwds)
ax.set_xlabel(label[0])
ax.set_ylabel(label[1])
if surface: ax.set_zlabel(label[2])
if not parsed_opts.out:
plt.show()
else:
fig.savefig(parsed_opts.out)
from mystic.tools import reduced, masked, partial
# process inputs
select, spec, mask = parse_input(options)
x, y = parse_axes(spec, grid=True) # grid=False for 1D plots
#FIXME: does grid=False still make sense here...?
if reducer: reducer = get_instance(reducer)
if solver and (not source or not model):
raise RuntimeError('a model and results filename are required')
elif not source and not model:
raise RuntimeError('a model or a results file is required')
if model:
model = get_instance(model)
# need a reducer if model returns an array
if reducer: model = reduced(reducer, arraylike=False)(model)
if solver:
# if 'live'... pick a solver
solver = 'mystic.solvers.fmin'
solver = get_instance(solver)
xlen = len(select) + len(mask)
if solver.__name__.startswith('diffev'):
initial = [(-1, 1)] * xlen
else:
initial = [0] * xlen
from mystic.monitors import VerboseLoggingMonitor
itermon = VerboseLoggingMonitor(filename=source, new=True)
# explicitly constrain parameters
model = partial(mask)(model)
# solve
from mystic.tools import reduced, masked, partial
# process inputs
select, spec, mask = parse_input(options)
x,y = parse_axes(spec, grid=True) # grid=False for 1D plots
#FIXME: does grid=False still make sense here...?
if reducer: reducer = get_instance(reducer)
if solver and (not source or not model):
raise RuntimeError('a model and results filename are required')
elif not source and not model:
raise RuntimeError('a model or a results file is required')
if model:
model = get_instance(model)
# need a reducer if model returns an array
if reducer: model = reduced(reducer, arraylike=False)(model)
if solver:
# if 'live'... pick a solver
solver = 'mystic.solvers.fmin'
solver = get_instance(solver)
xlen = len(select)+len(mask)
if solver.__name__.startswith('diffev'):
initial = [(-1,1)]*xlen
else:
initial = [0]*xlen
from mystic.monitors import VerboseLoggingMonitor
itermon = VerboseLoggingMonitor(filename=source, new=True)
# explicitly constrain parameters
model = partial(mask)(model)
# solve