# (i,id) + { (i,) then (i+1,) } + { list [list1, ...] }
# (i,) + { (i,) then (i+1,) } + { list [list1, ...] }
# (i,id) + { (i,) then (0,) } + { float list }
# (i,) + { (i,) then (0,) } + { float list }
# (i,id) + { (i,) then (0,) } + { list [list1, ...] }
# (i,) + { (i,) then (0,) } + { list [list1, ...] }
# NOTES:
# Legend is different for list versus [list1,...]
# Plot should be discontinuous for (i,) then (0,)
# parse file contents to get (i,id), cost, and parameters
from mystic.munge import logfile_reader, read_raw_file
try:
step, param, cost = logfile_reader(filename)
except SyntaxError:
read_raw_file(filename)
msg = "incompatible file format, try 'support_convergence.py'"
raise SyntaxError(msg)
# ignore everything after 'stop'
step = step[:stop]
cost = cost[:stop]
param = param[:stop]
# split (i,id) into iteration and id
multinode = len(step[0]) - 1 #XXX: what if step = []?
iter = [i[0] for i in step]
if multinode:
id = [i[1] for i in step]
else:
id = [0 for i in step]
def log_reader(filename, **kwds):
"""
plot parameter convergence from file written with 'LoggingMonitor'
Available from the command shell as:
mystic_log_reader.py filename [options]
or as a function call as:
mystic.log_reader(filename, **options)
The option "param" takes an indicator string. The indicator string is built
from comma-separated array slices. For example, params = ":" will plot all
parameters. Alternatively, params = ":2, 3:" will plot all parameters except
for the third parameter, while params = "0" will only plot the first parameter.
Required Inputs:
filename name of the convergence logfile (e.g log.txt)
"""
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)
iter = kwds.get('iter', None)
legend = kwds.get('legend', False)
nid = kwds.get('nid', None)
param = kwds.get('param', None)
# process "commandline" arguments
cmdargs = ''
cmdargs += '' if out is None else '--out={} '.format(out)
cmdargs += '' if dots == False else '--dots '
cmdargs += '' if line == False else '--line '
cmdargs += '' if iter is None else '--iter={} '.format(iter)
cmdargs += '' if legend == False else '--legend '
cmdargs += '' if nid is None else '--nid={} '.format(nid)
cmdargs += '' if param is None else '--param="{}" '.format(param)
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=log_reader.__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("-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 in plot with a line")
parser.add_option("-i","--iter",action="store",dest="stop",metavar="INT",\
default=None,help="the largest iteration to plot")
parser.add_option("-g","--legend",action="store_true",dest="legend",\
default=False,help="show the legend")
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("-p","--param",action="store",dest="param",\
metavar="STR",default=":",
help="indicator string to select parameters")
#parser.add_option("-f","--file",action="store",dest="filename",metavar="FILE",\
# default='log.txt',help="log file name")
# import sys
# if 'mystic_log_reader.py' not in sys.argv:
from StringIO import StringIO
f = StringIO()
parser.print_help(file=f)
f.seek(0)
if 'Options:' not in log_reader.__doc__:
log_reader.__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 can turn off 'line'
if not parsed_opts.line:
style = 'None'
else:
mark = ''
try: # get logfile name
if instance:
filename = instance
else:
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 which 'id' to plot results for
runs = (int(parsed_opts.id),
) #XXX: allow selecting more than one id ?
except:
runs = None # i.e. 'all' **or** use id=0, which should be 'best' energy ?
try: # select which parameters to plot
select = parsed_opts.param.split(',') # format is ":2, 2:4, 5, 6:"
except:
select = [':']
# ensure all terms of select have a ":"
for i in range(len(select)):
if isinstance(select[i], int): select[i] = str(select[i])
if select[i] == '-1': select[i] = 'len(params)-1:len(params)'
elif not select[i].count(':'):
select[i] += ':' + str(int(select[i]) + 1)
# == Possible results ==
# iter = (i,id) or (i,)
# split => { (i,) then (i+1,) } or { (i,) then (0,) }
# y x = { float list } or { list [list1, ...] }
# == Use Cases ==
# (i,id) + { (i,) then (i+1,) } + { float list }
# (i,) + { (i,) then (i+1,) } + { float list }
# (i,id) + { (i,) then (i+1,) } + { list [list1, ...] }
# (i,) + { (i,) then (i+1,) } + { list [list1, ...] }
# (i,id) + { (i,) then (0,) } + { float list }
# (i,) + { (i,) then (0,) } + { float list }
# (i,id) + { (i,) then (0,) } + { list [list1, ...] }
# (i,) + { (i,) then (0,) } + { list [list1, ...] }
# NOTES:
# Legend is different for list versus [list1,...]
# Plot should be discontinuous for (i,) then (0,)
# parse file contents to get (i,id), cost, and parameters
try:
instance = instance if instance else filename
from mystic.munge import read_trajectories
step, param, cost = read_trajectories(instance)
except SyntaxError:
from mystic.munge import read_raw_file
read_raw_file(filename)
msg = "incompatible file format, try 'support_convergence.py'"
raise SyntaxError(msg)
# ignore everything after 'stop'
step = step[:stop]
cost = cost[:stop]
param = param[:stop]
# split (i,id) into iteration and id
multinode = len(step[0]) - 1 #XXX: what if step = []?
iter = [i[0] for i in step]
if multinode:
id = [i[1] for i in step]
else:
id = [0 for i in step]
# build the list of selected parameters
params = range(len(param[0]))
selected = []
for i in select:
selected.extend(eval("params[%s]" % i))
selected = list(set(selected))
results = [[] for i in range(max(id) + 1)]
# populate results for each id with the corresponding (iter,cost,param)
for i in range(len(id)):
if runs is None or id[i] in runs: # take only the selected 'id'
results[id[i]].append((iter[i], cost[i], param[i]))
# NOTE: for example... results = [[(0,...)],[(0,...),(1,...)],[],[(0,...)]]
# build list of parameter (and cost) convergences for each id
conv = []
cost_conv = []
iter_conv = []
for i in range(len(results)):
conv.append([]) #; cost_conv.append([]); iter_conv.append([])
if len(results[i]):
for k in range(len(results[i][0][2])):
conv[i].append(
[results[i][j][2][k] for j in range(len(results[i]))])
cost_conv.append(
[results[i][j][1] for j in range(len(results[i]))])
iter_conv.append(
[results[i][j][0] for j in range(len(results[i]))])
else:
conv[i] = [[] for k in range(len(param[0]))]
cost_conv.append([])
iter_conv.append([])
#print "iter_conv = %s" % iter_conv
#print "cost_conv = %s" % cost_conv
#print "conv = %s" % conv
import matplotlib.pyplot as plt
fig = plt.figure()
#FIXME: These may fail when conv[i][j] = [[],[],[]] and cost = []. Verify this.
ax1 = fig.add_subplot(2, 1, 1)
for i in range(len(conv)):
if runs is None or i in runs: # take only the selected 'id'
for j in range(len(param[0])):
if j in selected: # take only the selected 'params'
tag = "%d,%d" % (j, i) # label is 'parameter,id'
ax1.plot(iter_conv[i],
conv[i][j],
label="%s" % tag,
marker=mark,
linestyle=style)
if parsed_opts.legend: plt.legend()
ax2 = fig.add_subplot(2, 1, 2)
for i in range(len(conv)):
if runs is None or i in runs: # take only the selected 'id'
tag = "%d" % i # label is 'cost id'
ax2.plot(iter_conv[i],
cost_conv[i],
label='cost %s' % tag,
marker=mark,
linestyle=style)
if parsed_opts.legend: plt.legend()
if not parsed_opts.out:
plt.show()
else:
fig.savefig(parsed_opts.out)
def log_reader(filename, **kwds):
"""
plot parameter convergence from file written with 'LoggingMonitor'
Available from the command shell as:
mystic_log_reader.py filename [options]
or as a function call as:
mystic.log_reader(filename, **options)
The option "param" takes an indicator string. The indicator string is built
from comma-separated array slices. For example, params = ":" will plot all
parameters. Alternatively, params = ":2, 3:" will plot all parameters except
for the third parameter, while params = "0" will only plot the first parameter.
Required Inputs:
filename name of the convergence logfile (e.g log.txt)
"""
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)
iter = kwds.get('iter', None)
legend = kwds.get('legend', False)
nid = kwds.get('nid', None)
param = kwds.get('param', None)
# process "commandline" arguments
cmdargs = ''
cmdargs += '' if out is None else '--out={} '.format(out)
cmdargs += '' if dots == False else '--dots '
cmdargs += '' if line == False else '--line '
cmdargs += '' if iter is None else '--iter={} '.format(iter)
cmdargs += '' if legend == False else '--legend '
cmdargs += '' if nid is None else '--nid={} '.format(nid)
cmdargs += '' if param is None else '--param="{}" '.format(param)
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=log_reader.__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("-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 in plot with a line")
parser.add_option("-i","--iter",action="store",dest="stop",metavar="INT",\
default=None,help="the largest iteration to plot")
parser.add_option("-g","--legend",action="store_true",dest="legend",\
default=False,help="show the legend")
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("-p","--param",action="store",dest="param",\
metavar="STR",default=":",
help="indicator string to select parameters")
#parser.add_option("-f","--file",action="store",dest="filename",metavar="FILE",\
# default='log.txt',help="log file name")
# import sys
# if 'mystic_log_reader.py' not in sys.argv:
if PY3:
f = StringIO()
parser.print_help(file=f)
f.seek(0)
if 'Options:' not in log_reader.__doc__:
log_reader.__doc__ += '\nOptions:%s' % f.read().split('Options:')[-1]
f.close()
else:
if 'Options:' not in log_reader.__doc__:
log_reader.__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 can turn off 'line'
if not parsed_opts.line:
style = 'None'
else:
mark = ''
try: # get logfile name
if instance:
filename = instance
else:
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 which 'id' to plot results for
runs = (int(parsed_opts.id),) #XXX: allow selecting more than one id ?
except:
runs = None # i.e. 'all' **or** use id=0, which should be 'best' energy ?
try: # select which parameters to plot
select = parsed_opts.param.split(',') # format is ":2, 2:4, 5, 6:"
except:
select = [':']
# ensure all terms of select have a ":"
for i in range(len(select)):
if isinstance(select[i], int): select[i] = str(select[i])
if select[i] == '-1': select[i] = 'len(params)-1:len(params)'
elif not select[i].count(':'):
select[i] += ':' + str(int(select[i])+1)
# == Possible results ==
# iter = (i,id) or (i,)
# split => { (i,) then (i+1,) } or { (i,) then (0,) }
# y x = { float list } or { list [list1, ...] }
# == Use Cases ==
# (i,id) + { (i,) then (i+1,) } + { float list }
# (i,) + { (i,) then (i+1,) } + { float list }
# (i,id) + { (i,) then (i+1,) } + { list [list1, ...] }
# (i,) + { (i,) then (i+1,) } + { list [list1, ...] }
# (i,id) + { (i,) then (0,) } + { float list }
# (i,) + { (i,) then (0,) } + { float list }
# (i,id) + { (i,) then (0,) } + { list [list1, ...] }
# (i,) + { (i,) then (0,) } + { list [list1, ...] }
# NOTES:
# Legend is different for list versus [list1,...]
# Plot should be discontinuous for (i,) then (0,)
# parse file contents to get (i,id), cost, and parameters
try:
instance = instance if instance else filename
from mystic.munge import read_trajectories
step, param, cost = read_trajectories(instance)
except SyntaxError:
from mystic.munge import read_raw_file
read_raw_file(filename)
msg = "incompatible file format, try 'support_convergence.py'"
raise SyntaxError(msg)
# ignore everything after 'stop'
step = step[:stop]
cost = cost[:stop]
param = param[:stop]
# split (i,id) into iteration and id
multinode = len(step[0]) - 1 #XXX: what if step = []?
iter = [i[0] for i in step]
if multinode:
id = [i[1] for i in step]
else:
id = [0 for i in step]
# build the list of selected parameters
params = list(range(len(param[0])))
selected = []
locals = dict(params=params)
for i in select:
selected.extend(eval("params[%s]" % i, locals))
selected = list(set(selected))
results = [[] for i in range(max(id) + 1)]
# populate results for each id with the corresponding (iter,cost,param)
for i in range(len(id)):
if runs is None or id[i] in runs: # take only the selected 'id'
results[id[i]].append((iter[i],cost[i],param[i]))
# NOTE: for example... results = [[(0,...)],[(0,...),(1,...)],[],[(0,...)]]
# build list of parameter (and cost) convergences for each id
conv = []; cost_conv = []; iter_conv = []
for i in range(len(results)):
conv.append([])#; cost_conv.append([]); iter_conv.append([])
if len(results[i]):
for k in range(len(results[i][0][2])):
conv[i].append([results[i][j][2][k] for j in range(len(results[i]))])
cost_conv.append([results[i][j][1] for j in range(len(results[i]))])
iter_conv.append([results[i][j][0] for j in range(len(results[i]))])
else:
conv[i] = [[] for k in range(len(param[0]))]
cost_conv.append([])
iter_conv.append([])
#print("iter_conv = %s" % iter_conv)
#print("cost_conv = %s" % cost_conv)
#print("conv = %s" % conv)
import matplotlib.pyplot as plt
fig = plt.figure()
#FIXME: These may fail when conv[i][j] = [[],[],[]] and cost = []. Verify this.
ax1 = fig.add_subplot(2,1,1)
for i in range(len(conv)):
if runs is None or i in runs: # take only the selected 'id'
for j in range(len(param[0])):
if j in selected: # take only the selected 'params'
tag = "%d,%d" % (j,i) # label is 'parameter,id'
ax1.plot(iter_conv[i],conv[i][j],label="%s" % tag,marker=mark,linestyle=style)
if parsed_opts.legend: plt.legend()
ax2 = fig.add_subplot(2,1,2)
for i in range(len(conv)):
if runs is None or i in runs: # take only the selected 'id'
tag = "%d" % i # label is 'cost id'
ax2.plot(iter_conv[i],cost_conv[i],label='cost %s' % tag,marker=mark,linestyle=style)
if parsed_opts.legend: plt.legend()
if not parsed_opts.out:
plt.show()
else:
fig.savefig(parsed_opts.out)
