def _get_history(source, ids=None):
"""get params and cost from the given source
source is the name of the trajectory logfile (or solver instance)
if provided, ids are the list of 'run ids' to select
"""
try: # if it's a logfile, it might be multi-id
from mystic.munge import read_trajectories
step, param, cost = read_trajectories(source)
except: # it's not a logfile, so read and return
from mystic.munge import read_history
param, cost = read_history(source)
return [param], [cost]
# split (i,id) into iteration and id
multinode = len(step[0]) - 1 #XXX: what if step = []?
if multinode: id = [i[1] for i in step]
else: id = [0 for i in step]
params = [[] for i in range(max(id) + 1)]
costs = [[] for i in range(len(params))]
# populate params for each id with the corresponding (param,cost)
for i in range(len(id)):
if ids is None or id[i] in ids: # take only the selected 'id'
params[id[i]].append(param[i])
costs[id[i]].append(cost[i])
params = [r for r in params if len(r)] # only keep selected 'ids'
costs = [r for r in costs if len(r)] # only keep selected 'ids'
# convert to support format
from mystic.munge import raw_to_support
for i in range(len(params)):
params[i], costs[i] = raw_to_support(params[i], costs[i])
return params, costs
def _get_history(source, ids=None):
"""get params and cost from the given source
source is the name of the trajectory logfile (or solver instance)
if provided, ids are the list of 'run ids' to select
"""
try: # if it's a logfile, it might be multi-id
from mystic.munge import read_trajectories
step, param, cost = read_trajectories(source)
except: # it's not a logfile, so read and return
from mystic.munge import read_history
param, cost = read_history(source)
return [param],[cost]
# split (i,id) into iteration and id
multinode = len(step[0]) - 1 #XXX: what if step = []?
if multinode: id = [i[1] for i in step]
else: id = [0 for i in step]
params = [[] for i in range(max(id) + 1)]
costs = [[] for i in range(len(params))]
# populate params for each id with the corresponding (param,cost)
for i in range(len(id)):
if ids is None or id[i] in ids: # take only the selected 'id'
params[id[i]].append(param[i])
costs[id[i]].append(cost[i])
params = [r for r in params if len(r)] # only keep selected 'ids'
costs = [r for r in costs if len(r)] # only keep selected 'ids'
# convert to support format
from mystic.munge import raw_to_support
for i in range(len(params)):
params[i], costs[i] = raw_to_support(params[i], costs[i])
return params, costs
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("-s","--scale",action="store",dest="scale",\
metavar="INT",default=1.0,
help="grayscale contrast multiplier for points in plot")
parser.add_option("-f","--flat",action="store_true",dest="flatten",\
default=False,help="show selected iterations in a single plot")
parsed_opts, parsed_args = parser.parse_args()
# get the name of the parameter log file
from mystic.munge import read_history
params, _cost = read_history(parsed_args[0])
# would be nice to use meta = ['wx','wx2','x','x2','wy',...]
# exec "from %s import meta" % file
try: # select the bounds
bounds = parsed_opts.bounds.split(",") # format is "60:105, 0:30, 2.1:2.8"
bounds = [tuple(float(j) for j in i.split(':')) for i in bounds]
except:
bounds = [(0,1),(0,1),(0,1)]
try: # select which params are along which axes
xyz = parsed_opts.xyz.split(",") # format is "0 1, 4 5, 8 9"
xyz = [tuple(int(j) for j in i.split()) for i in xyz]
except:
xyz = [(1,),(3,),(5,)]
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("-s","--scale",action="store",dest="scale",\
metavar="INT",default=1.0,
help="grayscale contrast multiplier for points in plot")
parser.add_option("-f","--flat",action="store_true",dest="flatten",\
default=False,help="show selected iterations in a single plot")
parsed_opts, parsed_args = parser.parse_args()
# get the name of the parameter log file
from mystic.munge import read_history
params, _cost = read_history(parsed_args[0])
# would be nice to use meta = ['wx','wx2','x','x2','wy',...]
# exec "from %s import meta" % file
try: # select the bounds
bounds = parsed_opts.bounds.split(
",") # format is "60:105, 0:30, 2.1:2.8"
bounds = [tuple(float(j) for j in i.split(':')) for i in bounds]
except:
bounds = [(0, 1), (0, 1), (0, 1)]
try: # select which params are along which axes
xyz = parsed_opts.xyz.split(",") # format is "0 1, 4 5, 8 9"
xyz = [tuple(int(j) for j in i.split()) for i in xyz]
except:
xyz = [(0, ), (1, ), (2, )]
def collapse_plotter(filename, **kwds):
"""
generate cost convergence rate plots from file written with 'write_support_file'
Available from the command shell as:
mystic_collapse_plotter.py filename [options]
or as a function call as:
mystic.collapse_plotter(filename, **options)
The option "col" takes a string of comma-separated integers indicating
iteration numbers where parameter collapse has occurred. If a second set of
integers is provided (delineated by a semicolon), the additional set of integers
will be plotted with a different linestyle (to indicate a different type of
collapse).
The option "label" takes a label string. For example, label = "y"
will label the y-axis plot with 'y'. LaTeX is also accepted. For example,
label = " log-cost, $ log_{10}(\hat{P} - \hat{P}_{max})$" will label the
y-axis with standard LaTeX math formatting. Note that the leading space is
required, and the text is aligned along the axis.
Required Inputs:
filename name of the python convergence logfile (e.g paramlog.py)
"""
import shlex
global __quit
__quit = False
instance = None
# handle the special case where list is provided by sys.argv
if isinstance(filename, (list, tuple)) and not kwds:
cmdargs = filename # (above is used by script to parse command line)
elif isinstance(filename, basestring) and not kwds:
cmdargs = shlex.split(filename)
# 'everything else' is essentially the functional interface
else:
cmdargs = kwds.get('kwds', '')
if not cmdargs:
out = kwds.get('out', None)
dots = kwds.get('dots', False)
#line = kwds.get('line', False)
linear = kwds.get('linear', False)
iter = kwds.get('iter', None)
label = kwds.get('label', None)
col = kwds.get('col', None)
# process "commandline" arguments
cmdargs = ''
cmdargs += '' if out is None else '--out={} '.format(out)
cmdargs += '' if dots == False else '--dots '
cmdargs += '' if linear == False else '--linear '
#cmdargs += '' if line == False else '--line '
cmdargs += '' if iter is None else '--iter={} '.format(iter)
cmdargs += '' if label == None else '--label={} '.format(label)
cmdargs += '' if col is None else '--col="{}" '.format(col)
else:
cmdargs = ' ' + cmdargs
if isinstance(filename, basestring):
cmdargs = filename.split() + shlex.split(cmdargs)
else: # special case of passing in monitor instance
instance = filename
cmdargs = 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=collapse_plotter.__doc__.split('\n\nOptions:')[0])
parser.add_option("-d","--dots",action="store_true",dest="dots",\
default=False,help="show data points in plot")
#parser.add_option("-l","--line",action="store_true",dest="line",\
# default=False,help="connect data points with a line")
parser.add_option("-y","--linear",action="store_true",dest="linear",\
default=False,help="plot y-axis in linear scale")
parser.add_option("-u","--out",action="store",dest="out",\
metavar="STR",default=None,
help="filepath to save generated plot")
parser.add_option("-i","--iter",action="store",dest="stop",metavar="INT",\
default=None,help="the largest iteration to plot")
parser.add_option("-l","--label",action="store",dest="label",\
metavar="STR",default="",\
help="string to assign label to y-axis")
parser.add_option("-c","--col",action="store",dest="collapse",\
metavar="STR",default="",
help="string to indicate collapse indices")
# import sys
# if 'mystic_collapse_plotter.py' not in sys.argv:
from StringIO import StringIO
f = StringIO()
parser.print_help(file=f)
f.seek(0)
if 'Options:' not in collapse_plotter.__doc__:
collapse_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
style = '-' # default linestyle
if parsed_opts.dots:
mark = 'o'
# when using 'dots', also turn off 'line'
#if not parsed_opts.line:
# style = 'None'
else:
mark = ''
try: # select labels for the axes
label = parsed_opts.label # format is "x" or " $x$"
except:
label = 'log-cost, $log_{10}(y - y_{min})$'
try: # get logfile name
filename = parsed_args[0]
except:
raise IOError, "please provide log file name"
try: # select which iteration to stop plotting at
stop = int(parsed_opts.stop)
except:
stop = None
try: # select collapse boundaries to plot
collapse = parsed_opts.collapse.split(
';') # format is "2, 3; 4, 5, 6; 7"
collapse = [eval("(%s,)" % i) if i.strip() else () for i in collapse]
except:
collapse = []
# read file
from mystic.munge import read_history
params, cost = read_history(filename)
# ignore everything after 'stop'
cost = cost[:stop]
params = params[:stop]
# get the minimum cost
import numpy as np
cost_min = min(cost)
# convert to log scale
x = np.arange(len(cost))
settings = np.seterr(all='ignore')
if parsed_opts.linear:
y = np.array(cost)
#y = np.abs(cost_min - np.array(cost))
else:
y = np.log10(np.abs(cost_min - np.array(cost)))
np.seterr(**settings)
import matplotlib.pyplot as plt
fig = plt.figure()
plt.plot(x, y, linestyle=style, marker=mark, markersize=1)
colors = ['orange', 'red', 'brown', 'pink']
linestyles = ['--', '-.', ':', '-']
for param, color, style in zip(collapse, colors, linestyles):
for clps in set(param):
plt.axvline(x=clps,
ymin=-10,
ymax=1,
hold=None,
linestyle=style,
linewidth=param.count(clps),
color=color)
if label:
#plt.title('convergence rate')
plt.xlabel('iteration number, $n$')
plt.ylabel(label)
#plt.ylabel('$log-error,\; log_{10}(\hat{P} - \hat{P}_{max})$')
if not parsed_opts.out:
plt.show()
else:
fig.savefig(parsed_opts.out)
def collapse_plotter(filename, **kwds):
"""
generate cost convergence rate plots from file written with 'write_support_file'
Available from the command shell as:
mystic_collapse_plotter.py filename [options]
or as a function call as:
mystic.collapse_plotter(filename, **options)
The option "col" takes a string of comma-separated integers indicating
iteration numbers where parameter collapse has occurred. If a second set of
integers is provided (delineated by a semicolon), the additional set of integers
will be plotted with a different linestyle (to indicate a different type of
collapse).
The option "label" takes a label string. For example, label = "y"
will label the y-axis plot with 'y'. LaTeX is also accepted. For example,
label = " log-cost, $ log_{10}(\hat{P} - \hat{P}_{max})$" will label the
y-axis with standard LaTeX math formatting. Note that the leading space is
required, and the text is aligned along the axis.
Required Inputs:
filename name of the python convergence logfile (e.g paramlog.py)
"""
import shlex
try:
basestring
from StringIO import StringIO
except NameError:
basestring = str
from io import StringIO
global __quit
__quit = False
instance = None
# handle the special case where list is provided by sys.argv
if isinstance(filename, (list,tuple)) and not kwds:
cmdargs = filename # (above is used by script to parse command line)
elif isinstance(filename, basestring) and not kwds:
cmdargs = shlex.split(filename)
# 'everything else' is essentially the functional interface
else:
cmdargs = kwds.get('kwds', '')
if not cmdargs:
out = kwds.get('out', None)
dots = kwds.get('dots', False)
#line = kwds.get('line', False)
linear = kwds.get('linear', False)
iter = kwds.get('iter', None)
label = kwds.get('label', None)
col = kwds.get('col', None)
# process "commandline" arguments
cmdargs = ''
cmdargs += '' if out is None else '--out={} '.format(out)
cmdargs += '' if dots == False else '--dots '
cmdargs += '' if linear == False else '--linear '
#cmdargs += '' if line == False else '--line '
cmdargs += '' if iter is None else '--iter={} '.format(iter)
cmdargs += '' if label == None else '--label={} '.format(label)
cmdargs += '' if col is None else '--col="{}" '.format(col)
else:
cmdargs = ' ' + cmdargs
if isinstance(filename, basestring):
cmdargs = filename.split() + shlex.split(cmdargs)
else: # special case of passing in monitor instance
instance = filename
cmdargs = 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=collapse_plotter.__doc__.split('\n\nOptions:')[0])
parser.add_option("-d","--dots",action="store_true",dest="dots",\
default=False,help="show data points in plot")
#parser.add_option("-l","--line",action="store_true",dest="line",\
# default=False,help="connect data points with a line")
parser.add_option("-y","--linear",action="store_true",dest="linear",\
default=False,help="plot y-axis in linear scale")
parser.add_option("-u","--out",action="store",dest="out",\
metavar="STR",default=None,
help="filepath to save generated plot")
parser.add_option("-i","--iter",action="store",dest="stop",metavar="INT",\
default=None,help="the largest iteration to plot")
parser.add_option("-l","--label",action="store",dest="label",\
metavar="STR",default="",\
help="string to assign label to y-axis")
parser.add_option("-c","--col",action="store",dest="collapse",\
metavar="STR",default="",
help="string to indicate collapse indices")
# import sys
# if 'mystic_collapse_plotter.py' not in sys.argv:
if PY3:
f = StringIO()
parser.print_help(file=f)
f.seek(0)
if 'Options:' not in collapse_plotter.__doc__:
collapse_plotter.__doc__ += '\nOptions:%s' % f.read().split('Options:')[-1]
f.close()
else:
if 'Options:' not in collapse_plotter.__doc__:
collapse_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
style = '-' # default linestyle
if parsed_opts.dots:
mark = 'o'
# when using 'dots', also turn off 'line'
#if not parsed_opts.line:
# style = 'None'
else:
mark = ''
try: # select labels for the axes
label = parsed_opts.label # format is "x" or " $x$"
except:
label = 'log-cost, $log_{10}(y - y_{min})$'
try: # get logfile name
filename = parsed_args[0]
except:
raise IOError("please provide log file name")
try: # select which iteration to stop plotting at
stop = int(parsed_opts.stop)
except:
stop = None
try: # select collapse boundaries to plot
collapse = parsed_opts.collapse.split(';') # format is "2, 3; 4, 5, 6; 7"
collapse = [eval("(%s,)" % i) if i.strip() else () for i in collapse]
except:
collapse = []
# read file
from mystic.munge import read_history
params, cost = read_history(filename)
# ignore everything after 'stop'
cost = cost[:stop]
params = params[:stop]
# get the minimum cost
import numpy as np
cost_min = min(cost)
# convert to log scale
x = np.arange(len(cost))
settings = np.seterr(all='ignore')
if parsed_opts.linear:
y = np.array(cost)
#y = np.abs(cost_min - np.array(cost))
else:
y = np.log10(np.abs(cost_min - np.array(cost)))
np.seterr(**settings)
import matplotlib.pyplot as plt
fig = plt.figure()
plt.plot(x, y, linestyle=style, marker=mark, markersize=1)
colors = ['orange','red','brown','pink']
linestyles = ['--','-.',':','-']
for param,color,style in zip(collapse,colors,linestyles):
for clps in set(param):
plt.axvline(x=clps, ymin=-10, ymax=1, hold=None, linestyle=style, linewidth=param.count(clps), color=color)
if label:
#plt.title('convergence rate')
plt.xlabel('iteration number, $n$')
plt.ylabel(label)
#plt.ylabel('$log-error,\; log_{10}(\hat{P} - \hat{P}_{max})$')
if not parsed_opts.out:
plt.show()
else:
fig.savefig(parsed_opts.out)