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
def read_logfile(filename):
"""read 'parameters' and 'cost' from LoggingMonitor archive
Inputs:
filename: str path to location of klepto.archives.dir_archive
"""
from mystic.munge import read_trajectories
param, param, cost = read_trajectories(filename)
return param, cost
def Trajectories(self): #XXX: better/alternate, read from evalmon?
from mystic.munge import read_trajectories
if not self.traj:
try: #NOTE: FRAGILE (if absolute path is not used)
filename = self.solver._stepmon._filename
step, param, cost = read_trajectories(filename)
except AttributeError:
msg = "a LoggingMonitor or UseTrajectories is required"
raise RuntimeError(msg)
else:
step = []; cost = []; param = [];
for sprayer in self._allSolvers: #XXX: slow? better thread.map?
for seeker in sprayer._allSolvers:
values = read_trajectories(seeker._stepmon)
step.extend(values[0])
param.extend(values[1])
cost.extend(values[2])
#XXX: (not from archive, so) if self._inv: use -cost
return step, param, cost
def Trajectories(self): #XXX: better/alternate, read from evalmon?
from mystic.munge import read_trajectories
if not self.traj:
try: #NOTE: FRAGILE (if absolute path is not used)
filename = self.solver._stepmon._filename
step, param, cost = read_trajectories(filename)
except AttributeError:
msg = "a LoggingMonitor or UseTrajectories is required"
raise RuntimeError(msg)
else:
step = []
cost = []
param = []
for sprayer in self._allSolvers: #XXX: slow? better thread.map?
for seeker in sprayer._allSolvers:
values = read_trajectories(seeker._stepmon)
step.extend(values[0])
param.extend(values[1])
cost.extend(values[2])
#XXX: (not from archive, so) if self._inv: use -cost
return step, param, cost
def Trajectories(self, all=False):
"""return tuple (iteration, coordinates, cost) of all trajectories
"""
mon = '_evalmon' if all else '_stepmon'
from mystic.munge import read_trajectories
if not self.traj:
try: #NOTE: FRAGILE (if absolute path is not used)
filename = getattr(self.solver, mon)._filename
step, param, cost = read_trajectories(filename)
except AttributeError:
msg = "a LoggingMonitor or UseTrajectories is required"
raise RuntimeError(msg)
else:
step = []; cost = []; param = [];
for sprayer in self._allSolvers: #XXX: slow? better thread.map?
for seeker in sprayer._allSolvers:
values = read_trajectories(getattr(seeker,mon))
step.extend(values[0])
param.extend(values[1])
cost.extend(values[2])
#XXX: (not from archive, so) if self._inv: use -cost
return step, param, cost
def Trajectories(self, all=False):
"""return tuple (iteration, coordinates, cost) of all trajectories
"""
mon = '_evalmon' if all else '_stepmon'
from mystic.munge import read_trajectories
if not self.traj:
try: #NOTE: FRAGILE (if absolute path is not used)
filename = getattr(self.solver, mon)._filename
step, param, cost = read_trajectories(filename)
except AttributeError:
msg = "a LoggingMonitor or UseTrajectories is required"
raise RuntimeError(msg)
else:
step = []; cost = []; param = [];
for sprayer in self._allSolvers: #XXX: slow? better thread.map?
for seeker in sprayer._allSolvers:
values = read_trajectories(getattr(seeker,mon))
step.extend(values[0])
param.extend(values[1])
cost.extend(values[2])
#XXX: (not from archive, so) if self._inv: use -cost
return step, param, cost
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)