def __init__(self, objective, sampler=None, **kwds):
"""response surface interpolator, where data is sampled from objective
Input:
objective: function of the form z=f(x)
sampler: mystic.search.Searcher instance
Additional Inputs:
maxpts: int, maximum number of points to use from (x,z)
noise: float, amplitude of gaussian noise to remove duplicate x
method: string for kind of interpolator
dim: number of parameters in the input for the objective function
filter: a data filter produced with mystic.filters.generate_filter
penalty: mystic.penalty instance of the form y' = k*p(x)
constraints: mystic.constraints instance of the form x' = c(x)
NOTE:
if scipy is not installed, will use np.interp for 1D (non-rbf),
or mystic's rbf otherwise. default method is 'nearest' for
1D and 'linear' otherwise. method can be one of ('rbf','linear',
'nearest','cubic','inverse','gaussian','quintic','thin_plate').
"""
# sampler configuration
from mystic.search import Searcher
self.sampler = Searcher() if sampler is None else sampler
self.maxpts = kwds.pop('maxpts', None) # N = 1000
self.noise = kwds.pop('noise', 1e-8)
self.filter = kwds.pop('filter', None)
self.penalty = kwds.pop('penalty', None)
self.constraints = kwds.pop('constraints', None)
# monitor, archive, and trajectories
self._minmon = self._maxmon = None #XXX: better default?
self._minarch = self._maxarch = None #XXX: better default?
self.x = None # params (x)
self.z = None # cost (objective(x))
# point generator(s) and interpolated model(s) #XXX: better names?
self.dim = kwds.pop('dim', None) #XXX: should be (or set) len(x)
self.objective = objective # original F(x)
self.surrogate = None # interpolated F(*x)
# interpolator configuration
self.args = {} #dict(smooth=0, function='thin_plate')
self.args.update(kwds)
return
def __init__(self, objective, sampler=None, **kwds):
# sampler configuration
from mystic.search import Searcher
self.sampler = Searcher() if sampler is None else sampler
self.maxpts = kwds.pop('maxpts', None) # N = 1000
self.noise = kwds.pop('noise', 1e-8)
# monitor, archive, and trajectories
self._minmon = self._maxmon = None #XXX: better default?
self._minarch = self._maxarch = None #XXX: better default?
self.x = None # params (x)
self.z = None # cost (objective(x))
# point generator(s) and interpolated model(s) #XXX: better names?
self.dim = kwds.pop('dim', None) #XXX: should be (or set) len(x)
self.objective = objective # original F(x)
self.surrogate = None # interpolated F(*x)
# interpolator configuration
self.args = {} #dict(smooth=0, function='thin_plate')
self.args.update(kwds)
return
def __init__(self, objective, sampler=None, **kwds):
# sampler configuration
from mystic.search import Searcher
self.sampler = Searcher() if sampler is None else sampler
self.maxpts = kwds.pop('maxpts', None) # N = 1000
self.noise = kwds.pop('noise', 1e-8)
# monitor, archive, and trajectories
self._minmon = self._maxmon = None #XXX: better default?
self._minarch = self._maxarch = None #XXX: better default?
self.x = None # params (x)
self.z = None # cost (objective(x))
# point generator(s) and interpolated model(s) #XXX: better names?
self.dim = kwds.pop('dim', None) #XXX: should be (or set) len(x)
self.objective = objective # original F(x)
self.surrogate = None # interpolated F(*x)
# interpolator configuration
self.args = {}#dict(smooth=0, function='thin_plate')
self.args.update(kwds)
return
def __init__(self, objective, sampler=None, **kwds):
"""response surface interpolator, where data is sampled from objective
Input:
objective: function of the form z=f(x)
sampler: mystic.search.Searcher instance
Additional Inputs:
maxpts: int, maximum number of points to use from (x,z)
noise: float, amplitude of gaussian noise to remove duplicate x
method: string for kind of interpolator
dim: number of parameters in the input for the objective function
NOTE:
if scipy is not installed, will use np.interp for 1D (non-rbf),
or mystic's rbf otherwise. default method is 'nearest' for
1D and 'linear' otherwise. method can be one of ('rbf','linear',
'nearest','cubic','inverse','gaussian','quintic','thin_plate').
"""
# sampler configuration
from mystic.search import Searcher
self.sampler = Searcher() if sampler is None else sampler
self.maxpts = kwds.pop('maxpts', None) # N = 1000
self.noise = kwds.pop('noise', 1e-8)
# monitor, archive, and trajectories
self._minmon = self._maxmon = None #XXX: better default?
self._minarch = self._maxarch = None #XXX: better default?
self.x = None # params (x)
self.z = None # cost (objective(x))
# point generator(s) and interpolated model(s) #XXX: better names?
self.dim = kwds.pop('dim', None) #XXX: should be (or set) len(x)
self.objective = objective # original F(x)
self.surrogate = None # interpolated F(*x)
# interpolator configuration
self.args = {}#dict(smooth=0, function='thin_plate')
self.args.update(kwds)
return
class Surface(object): #FIXME: should be subclass of Interpolator (?)
#surface has:
# args - interpolation configuration (smooth, function, ...)
# sampler - a search algorithm
# maxpts - a maximum number of sampling points
# noise - a noise coefficient
# dim - dimensionality of the model
# function - target function [F(*x)]
# objective - target function [F(x)]
# surrogate - interpolated function [F(*x)]
# model - interpolated function [F(x)]
# x,y,z - sampled points(*)
#
#surface (or sampler) has:
# _minmon,_maxmon - step monitor(*)
# _minarch,_maxarch - sampled point archives(*)
#
#surface can:
# Sample - populate sampled point archive with solver trajectories
# Interpolate - build interpolated function from sampled points
# Plot - plot sampled points and interpolated surface
#
#surface (or sampler) can:
# UseMonitor - track trajectories with a monitor(s)
# UseArchive - track sampled points in an archive(s)
# _max - fetch (x,y,z,model(x,y)) for maximal z of sampled points
# _min - fetch (x,y,z,model(x,y)) for minimal z of sampled points
def __init__(self, objective, sampler=None, **kwds):
"""response surface interpolator, where data is sampled from objective
Input:
objective: function of the form z=f(x)
sampler: mystic.search.Searcher instance
Additional Inputs:
maxpts: int, maximum number of points to use from (x,z)
noise: float, amplitude of gaussian noise to remove duplicate x
method: string for kind of interpolator
dim: number of parameters in the input for the objective function
filter: a data filter produced with mystic.filters.generate_filter
penalty: mystic.penalty instance of the form y' = k*p(x)
constraints: mystic.constraints instance of the form x' = c(x)
NOTE:
if scipy is not installed, will use np.interp for 1D (non-rbf),
or mystic's rbf otherwise. default method is 'nearest' for
1D and 'linear' otherwise. method can be one of ('rbf','linear',
'nearest','cubic','inverse','gaussian','quintic','thin_plate').
"""
# sampler configuration
from mystic.search import Searcher
self.sampler = Searcher() if sampler is None else sampler
self.maxpts = kwds.pop('maxpts', None) # N = 1000
self.noise = kwds.pop('noise', 1e-8)
self.filter = kwds.pop('filter', None)
self.penalty = kwds.pop('penalty', None)
self.constraints = kwds.pop('constraints', None)
# monitor, archive, and trajectories
self._minmon = self._maxmon = None #XXX: better default?
self._minarch = self._maxarch = None #XXX: better default?
self.x = None # params (x)
self.z = None # cost (objective(x))
# point generator(s) and interpolated model(s) #XXX: better names?
self.dim = kwds.pop('dim', None) #XXX: should be (or set) len(x)
self.objective = objective # original F(x)
self.surrogate = None # interpolated F(*x)
# interpolator configuration
self.args = {} #dict(smooth=0, function='thin_plate')
self.args.update(kwds)
return
# XXX: useful?
# def _invert_model:
# takes model and returns inverted_model (maxmodel or invmodel?)
# def _invert_trajectories:
# takes (xyz) trajectories and returns inverted trajectories (xy-z)
def UseMonitor(self, min=None, max=None):
"""track parameter trajectories with a monitor(s)
Input:
min: monitor instance to track minima; if True, use a new Monitor
max: monitor instance to track maxima; if True, use a new Monitor
Output:
None
"""
from mystic.monitors import Monitor
if type(min) is bool: self._minmon = Monitor() if min else None
elif min is not None: self._minmon = min
if type(max) is bool: self._maxmon = Monitor() if max else None
elif max is not None: self._maxmon = max
return
def UseArchive(self, min=None, max=None):
"""track sampled points in an archive(s)
Input:
min: archive instance to store minima; if True, use a new archive
max: archive instance to store maxima; if True, use a new archive
Output:
None
"""
from klepto.archives import dict_archive as d
if type(min) is bool: self._minarch = d(cached=False) if min else None
elif min is not None: self._minarch = min
if type(max) is bool: self._maxarch = d(cached=False) if max else None
elif max is not None: self._maxarch = max
return
"""
def doit(self, bounds, stop, step=200, scale=False, shift=False,
density=9, axes=(), vals=(), maxpts=maxpts, **kwds):
if not self.sampler.traj: self.sampler.UseTrajectories()
# get trajectories
self.Sample(bounds, stop)
# get interpolated function
self.Interpolate(**kwds)
# check extrema #XXX: put _min,_max in Interpolate? (downsampled)
f = lambda x,z: (z,surface.surrogate(*x))
print("min: {}; min@f: {}".format(*f(*surface._min())))
print("max: {}; max@f: {}".format(*f(*urfacef._max())))
# plot surface
self.Plot(step=step, scale=scale, shift=shift, density=density, axes=axes, vals=vals, maxpts=maxpts)
return
"""
def Sample(self,
bounds,
stop,
clear=False,
verbose=False,
all=False,
**kwds):
"""sample data (x,z) using objective function z=f(x)
Input:
bounds: tuple of floats (min,max), bounds on the search region
stop: termination condition
clear: if True, clear the archive of stored points
verbose: if True, print a summary of search/sampling results
all: if True, use solver EvalMonitor, else use StepMonitor
filter: a data filter produced with mystic.filters.generate_filter
penalty: mystic.penalty instance of the form y' = k*p(x)
constraints: mystic.constraints instance of the form x' = c(x)
Output:
x: an array of shape (npts, dim) or (npts,)
z: an array of shape (npts,)
"""
#XXX: does the strategy of finding min/max always apply?
import numpy as np
penalty = kwds.get('penalty', self.penalty)
constraints = kwds.get('constraints', self.constraints)
kwargs = dict(stop=stop, penalty=penalty, constraints=constraints)
# get model (for minima)
model = self.objective
self.dim = len(bounds)
### get mins ###
monitor = self._minmon
archive = None if clear else self._minarch
inverse = False
if all: #FIXME: better define role/use of Reset/Archive/clear...
self.sampler.Reset(None, inv=inverse) # reset the sampler
self.sampler.archive = archive
self.sampler.Search(model, bounds, evalmon=monitor, **kwargs)
else:
self.sampler.Reset(archive, inv=inverse) # reset the sampler
self.sampler.Search(model, bounds, monitor=monitor, **kwargs)
if verbose: self.sampler._summarize()
# read trajectories from log (or monitor)
xyz = self.sampler.Samples(all=all)
if clear: self.sampler.Reset() # reset the sampler
### end mins ###
# invert model (for maxima)
imodel = lambda *args, **kwds: -model(*args, **kwds)
if penalty is not None: # also invert penalty
kwargs['penalty'] = lambda *args, **kwds: -penalty(*args, **kwds)
### get maxs ###
monitor = self._maxmon
archive = None if clear else self._maxarch
inverse = True
if all: #FIXME: better define role/use of Reset/Archive/clear...
self.sampler.Reset(None, inv=inverse) # reset the sampler
self.sampler.archive = archive
self.sampler.Search(imodel, bounds, evalmon=monitor, **kwargs)
else:
self.sampler.Reset(archive, inv=inverse) # reset the sampler
self.sampler.Search(imodel, bounds, monitor=monitor, **kwargs)
if verbose: self.sampler._summarize()
xyz = np.hstack((xyz, self.sampler.Samples(all=all)))
if clear: self.sampler.Reset() # reset the sampler
### end maxs ###
# split into params and cost
self.x = xyz.T[:, :-1]
self.z = xyz.T[:, -1]
# apply any filter, and return
filter = kwds.pop('filter', self.filter)
if filter: #XXX: better here, or in Interpolate???
self.x, self.z = filter(self.x, self.z)
return self.x, self.z
def Interpolate(self, **kwds): #XXX: refactor so use self.interpolator ?
"""interpolate data (x,z) to generate response function z=f(*x)
Input:
maxpts: int, maximum number of points to use from (x,z)
noise: float, amplitude of gaussian noise to remove duplicate x
method: string for kind of interpolator
extrap: if True, extrapolate a bounding box (can reduce # of nans)
arrays: if True, return a numpy array; otherwise don't return arrays
Output:
interpolated response function, where z=f(*x.T)
NOTE:
if scipy is not installed, will use np.interp for 1D (non-rbf),
or mystic's rbf otherwise. default method is 'nearest' for
1D and 'linear' otherwise. method can be one of ('rbf','linear',
'nearest','cubic','inverse','gaussian','quintic','thin_plate').
"""
from interpolator import Interpolator
args = self.args.copy()
args.update(kwds)
maxpts, noise = self.maxpts, self.noise
ii = Interpolator(self.x, self.z, maxpts=maxpts, noise=noise, **args)
self.surrogate = ii.Interpolate(**args)
# build the surrogate
self.surrogate.__doc__ = self.objective.__doc__
return self.surrogate
def _max(self): #XXX: remove?
"""get the x[i],z[i] corresponding to the max(z)
"""
import numpy as np
mz = np.argmax(self.z)
return self.x[mz], self.z[mz]
def _min(self): #XXX: remove?
"""get the x[i],z[i] corresponding to the min(z)
"""
import numpy as np
mz = np.argmin(self.z)
return self.x[mz], self.z[mz]
def Plot(self, **kwds):
"""produce a scatterplot of (x,z) and the surface z = function(*x.T)
Input:
step: int, plot every 'step' points on the grid [default: 200]
scale: float, scaling factor for the z-axis [default: False]
shift: float, additive shift for the z-axis [default: False]
density: int, density of wireframe for the plot surface [default: 9]
axes: tuple, indicies of the axes to plot [default: ()]
vals: list of values (one per axis) for unplotted axes [default: ()]
maxpts: int, maximum number of (x,z) points to use [default: None]
kernel: function transforming x to x', where x' = kernel(x)
vtol: float, maximum distance outside bounds hypercube to plot data
"""
# get interpolted function
fx = self.surrogate
# plot interpolated surface
from plotter import Plotter
p = Plotter(self.x, self.z, fx, **kwds)
p.Plot()
# if plotter interpolated the function, get the function
self.surrogate = fx or p.function
def __set_function(self,
function): #XXX: deal w/ selector (2D)? ExtraArgs?
# convert to 'model' format (i.e. takes a parameter vector)
from mystic.math.interpolate import _to_objective
_objective = _to_objective(function)
def objective(x, *args, **kwds):
result = _objective(x, *args, **kwds)
return result.tolist() if hasattr(result, 'tolist') else result
self.objective = objective
self.objective.__doc__ = function.__doc__
return
def __function(self): #XXX: deal w/ selector (2D)? ExtraArgs? _to_function
# convert model to 'args' format (i.e. takes positional args)
from mystic.math.interpolate import _to_function
function = _to_function(self.objective, ndim=self.dim)
function.__doc__ = self.objective.__doc__
return function
def __model(self): #XXX: deal w/ selector (2D)? ExtraArgs? _to_objective
# convert to 'model' format (i.e. takes a parameter vector)
if self.surrogate is None: return None
from mystic.math.interpolate import _to_objective
_objective = _to_objective(self.surrogate)
def objective(x, *args, **kwds):
result = _objective(x, *args, **kwds)
return result.tolist() if hasattr(result, 'tolist') else result
objective.__doc__ = self.objective.__doc__
return objective
# interface
function = property(__function, __set_function)
model = property(__model)
class Surface(object):
#surface has:
# args - interpolation configuration (smooth, function, ...)
# sampler - a search algorithm
# maxpts - a maximum number of sampling points
# noise - a noise coefficient
# dim - dimensionality of the model
# function - target function [F(*x)]
# objective - target function [F(x)]
# surrogate - interpolated function [F(*x)]
# model - interpolated function [F(x)]
# x,y,z - sampled points(*)
#
#surface (or sampler) has:
# _minmon,_maxmon - step monitor(*)
# _minarch,_maxarch - sampled point archives(*)
#
#surface can:
# Sample - populate sampled point archive with solver trajectories
# Interpolate - build interpolated function from sampled points
# Plot - plot sampled points and interpolated surface
#
#surface (or sampler) can:
# UseMonitor - track trajectories with a monitor(s)
# UseArchive - track sampled points in an archive(s)
# _noise - remove duplicate sampled points (x) by adding noise to x
# _downsample - skip sampled points at a regular interval (for speed)
# _max - fetch (x,y,z,model(x,y)) for maximal z of sampled points
# _min - fetch (x,y,z,model(x,y)) for minimal z of sampled points
def __init__(self, objective, sampler=None, **kwds):
# sampler configuration
from mystic.search import Searcher
self.sampler = Searcher() if sampler is None else sampler
self.maxpts = kwds.pop('maxpts', None) # N = 1000
self.noise = kwds.pop('noise', 1e-8)
# monitor, archive, and trajectories
self._minmon = self._maxmon = None #XXX: better default?
self._minarch = self._maxarch = None #XXX: better default?
self.x = None # params (x)
self.z = None # cost (objective(x))
# point generator(s) and interpolated model(s) #XXX: better names?
self.dim = kwds.pop('dim', None) #XXX: should be (or set) len(x)
self.objective = objective # original F(x)
self.surrogate = None # interpolated F(*x)
# interpolator configuration
self.args = {} #dict(smooth=0, function='thin_plate')
self.args.update(kwds)
return
# XXX: useful?
# def _invert_model:
# takes model and returns inverted_model (maxmodel or invmodel?)
# def _invert_trajectories:
# takes (xyz) trajectories and returns inverted trajectories (xy-z)
def UseMonitor(self, min=None, max=None):
from mystic.monitors import Monitor
if type(min) is bool: self._minmon = Monitor() if min else None
elif min is not None: self._minmon = min
if type(max) is bool: self._maxmon = Monitor() if max else None
elif max is not None: self._maxmon = max
return
def UseArchive(self, min=None, max=None):
from klepto.archives import dict_archive as d
if type(min) is bool: self._minarch = d(cached=False) if min else None
elif min is not None: self._minarch = min
if type(max) is bool: self._maxarch = d(cached=False) if max else None
elif max is not None: self._maxarch = max
return
"""
def doit(self, bounds, stop, step=200, scale=False, shift=False,
density=9, axes=(), vals=(), maxpts=maxpts, **kwds):
if not self.sampler.traj: self.sampler.UseTrajectories()
# get trajectories
self.Sample(bounds, stop)
# get interpolated function
self.Interpolate(**kwds)
# check extrema #XXX: put _min,_max in Interpolate? (downsampled)
f = lambda x,z: (z,surface.surrogate(*x))
print("min: {}; min@f: {}".format(*f(*surface._min())))
print("max: {}; max@f: {}".format(*f(*urfacef._max())))
# plot surface
self.Plot(step, scale, shift, density, axes, vals, maxpts)
return
"""
def Sample(self, bounds, stop, clear=False, verbose=False):
#XXX: does the strategy of finding min/max always apply?
import numpy as np
# get model (for minima)
model = self.objective
self.dim = len(bounds)
### get mins ###
stepmon = self._minmon
archive = None if clear else self._minarch
inverse = False
self.sampler.Reset(archive, inv=inverse) # reset the sampler
self.sampler.Search(model, bounds, stop=stop, monitor=stepmon)
if verbose: self.sampler._summarize()
# read trajectories from log (or monitor)
xyz = self.sampler.Samples()
if clear: self.sampler.Reset() # reset the sampler
### end mins ###
# invert model (for maxima)
imodel = lambda *args, **kwds: -model(*args, **kwds)
### get maxs ###
stepmon = self._maxmon
archive = None if clear else self._maxarch
inverse = True
self.sampler.Reset(archive, inv=inverse) # reset the sampler
self.sampler.Search(imodel, bounds, stop=stop, monitor=stepmon)
if verbose: self.sampler._summarize()
xyz = np.hstack((xyz, self.sampler.Samples()))
if clear: self.sampler.Reset() # reset the sampler
### end maxs ###
# split into params and cost
self.x = xyz.T[:, :-1]
self.z = xyz.T[:, -1]
return self.x, self.z
def _noise(self, scale=None, x=None):
#HACK: remove any duplicate points by adding noise
import numpy as np
if x is None: x = self.x
if scale is None: scale = self.noise
if not scale: return x
return x + np.random.normal(scale=scale, size=x.shape)
def _downsample(self, maxpts=None, x=None, z=None):
if maxpts is None: maxpts = self.maxpts
if x is None: x = self.x
if z is None: z = self.z
if len(x) != len(z):
raise ValueError("the input array lengths must match exactly")
if maxpts is not None and len(z) > maxpts:
N = max(int(round(len(z) / float(maxpts))), 1)
# print("for speed, sampling {} down to {}".format(len(z),len(z)/N))
# ax.plot(x[:,0], x[:,1], z, 'ko', linewidth=2, markersize=4)
x = x[::N]
z = z[::N]
# plt.show()
# exit()
return x, z
def _interpolate(self, x, z, **kwds):
import numpy as np
from scipy.interpolate import Rbf as interpolate
return interpolate(*np.vstack((x.T, z)), **kwds)
def Interpolate(self, **kwds): #XXX: better take a strategy?
maxpts = kwds.pop('maxpts', self.maxpts)
noise = kwds.pop('noise', self.noise)
args = self.args.copy()
args.update(kwds)
x, z = self._downsample(maxpts)
#NOTE: really only need to add noise when have duplicate x,y coords
x = self._noise(noise, x)
# build the surrogate
self.surrogate = self._interpolate(x, z, **args)
self.surrogate.__doc__ = self.function.__doc__
return self.surrogate
def _max(self):
import numpy as np
x = self.x
z = self.z
mz = np.argmax(z)
return x[mz], z[mz]
def _min(self):
import numpy as np
x = self.x
z = self.z
mz = np.argmin(z)
return x[mz], z[mz]
def Plot(self, step=200, scale=False, shift=False, \
density=9, axes=(), vals=(), maxpts=None):
# plot interpolated surface
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt
from matplotlib import cm
import numpy as np
figure = plt.figure()
kwds = {'projection': '3d'}
ax = figure.gca(**kwds)
ax.autoscale(tight=True)
if maxpts is None: maxpts = self.maxpts
x, z = self._downsample(maxpts)
# get two axes to plot, and indices of the remaining axes
axes = axes[:2] #XXX: error if wrong size?
ix = [i for i in range(len(x.T)) if i not in axes]
n = 2 - len(axes)
axes, ix = list(axes) + ix[:n], ix[n:]
# build list of fixed values (default mins), override with user input
#fix = np.zeros(len(ix))
fix = enumerate(self._min()[0])
fix = np.array(tuple(j for (i, j) in fix if i not in axes))
fix[:len(vals)] = vals
# build grid of points, one for each param, apply fixed values
grid = np.ones((len(x.T), step, step))
grid[ix] = fix[:, None, None]
del ix, fix
# build sub-surface of surrogate(x) to display, apply to the grid
xy = x.T[axes]
M = complex('{}j'.format(step))
grid[axes] = np.mgrid[xy[0].min():xy[0].max():M,
xy[1].min():xy[1].max():M]
del xy
# evaluate the surrogate on the sub-surface
z_ = self.surrogate(*grid)
# scaling used by model plotter
if scale:
if shift:
z_ = np.asarray(z_) + shift
z_ = np.log(4 * np.asarray(z_) * scale + 1) + 2
# plot surface
d = max(11 - density, 1)
x_ = grid[axes[0]]
y_ = grid[axes[-1]]
ax.plot_wireframe(x_, y_, z_, rstride=d, cstride=d)
#ax.plot_surface(x_, y_, z_, rstride=d, cstride=d, cmap=cm.jet, linewidth=0, antialiased=False)
# use the sampled values
z_ = z
# scaling used by model plotter
if scale:
if shift:
z_ = np.asarray(z_) + shift
z_ = np.log(4 * np.asarray(z_) * scale + 1) + 2
# plot data points
x_ = x.T[axes[0]]
y_ = x.T[axes[-1]]
ax.plot(x_, y_, z_, 'ko', linewidth=2, markersize=4)
plt.show() #XXX: show or don't show?... or return?
# figure.savefig('griewangk.png')
def __set_function(self,
function): #XXX: deal w/ selector (2D)? ExtraArgs?
# convert to 'model' format (i.e. takes a parameter vector)
def objective(x, *args, **kwds):
return function(*(tuple(x) + args), **kwds).tolist()
self.objective = objective
self.objective.__doc__ = function.__doc__
return
def __function(self): #XXX: deal w/ selector (2D)? ExtraArgs?
# convert model to 'args' format (i.e. takes positional args)
def function(*args, **kwds):
len = self.dim # or kwds.pop('len', None)
if len is None: return self.objective(args, **kwds)
return self.objective(args[:len], *args[len:], **kwds)
function.__doc__ = self.objective.__doc__
return function
def __model(self): #XXX: deal w/ selector (2D)? ExtraArgs?
# convert to 'model' format (i.e. takes a parameter vector)
if self.surrogate is None: return None
def objective(x, *args, **kwds):
return self.surrogate(*(tuple(x) + args), **kwds).tolist()
objective.__doc__ = self.objective.__doc__
return objective
# interface
function = property(__function, __set_function)
model = property(__model)
class Surface(object):
#surface has:
# args - interpolation configuration (smooth, function, ...)
# sampler - a search algorithm
# maxpts - a maximum number of sampling points
# noise - a noise coefficient
# dim - dimensionality of the model
# function - target function [F(*x)]
# objective - target function [F(x)]
# surrogate - interpolated function [F(*x)]
# model - interpolated function [F(x)]
# x,y,z - sampled points(*)
#
#surface (or sampler) has:
# _minmon,_maxmon - step monitor(*)
# _minarch,_maxarch - sampled point archives(*)
#
#surface can:
# Sample - populate sampled point archive with solver trajectories
# Interpolate - build interpolated function from sampled points
# Plot - plot sampled points and interpolated surface
#
#surface (or sampler) can:
# UseMonitor - track trajectories with a monitor(s)
# UseArchive - track sampled points in an archive(s)
# _noise - remove duplicate sampled points (x) by adding noise to x
# _downsample - skip sampled points at a regular interval (for speed)
# _max - fetch (x,y,z,model(x,y)) for maximal z of sampled points
# _min - fetch (x,y,z,model(x,y)) for minimal z of sampled points
def __init__(self, objective, sampler=None, **kwds):
# sampler configuration
from mystic.search import Searcher
self.sampler = Searcher() if sampler is None else sampler
self.maxpts = kwds.pop('maxpts', None) # N = 1000
self.noise = kwds.pop('noise', 1e-8)
# monitor, archive, and trajectories
self._minmon = self._maxmon = None #XXX: better default?
self._minarch = self._maxarch = None #XXX: better default?
self.x = None # params (x)
self.z = None # cost (objective(x))
# point generator(s) and interpolated model(s) #XXX: better names?
self.dim = kwds.pop('dim', None) #XXX: should be (or set) len(x)
self.objective = objective # original F(x)
self.surrogate = None # interpolated F(*x)
# interpolator configuration
self.args = {}#dict(smooth=0, function='thin_plate')
self.args.update(kwds)
return
# XXX: useful?
# def _invert_model:
# takes model and returns inverted_model (maxmodel or invmodel?)
# def _invert_trajectories:
# takes (xyz) trajectories and returns inverted trajectories (xy-z)
def UseMonitor(self, min=None, max=None):
from mystic.monitors import Monitor
if type(min) is bool: self._minmon = Monitor() if min else None
elif min is not None: self._minmon = min
if type(max) is bool: self._maxmon = Monitor() if max else None
elif max is not None: self._maxmon = max
return
def UseArchive(self, min=None, max=None):
from klepto.archives import dict_archive as d
if type(min) is bool: self._minarch = d(cached=False) if min else None
elif min is not None: self._minarch = min
if type(max) is bool: self._maxarch = d(cached=False) if max else None
elif max is not None: self._maxarch = max
return
"""
def doit(self, bounds, stop, step=200, scale=False, shift=False,
density=9, axes=(), vals=(), maxpts=maxpts, **kwds):
if not self.sampler.traj: self.sampler.UseTrajectories()
# get trajectories
self.Sample(bounds, stop)
# get interpolated function
self.Interpolate(**kwds)
# check extrema #XXX: put _min,_max in Interpolate? (downsampled)
f = lambda x,z: (z,surface.surrogate(*x))
print "min: {}; min@f: {}".format(*f(*surface._min()))
print "max: {}; max@f: {}".format(*f(*urfacef._max()))
# plot surface
self.Plot(step, scale, shift, density, axes, vals, maxpts)
return
"""
def Sample(self, bounds, stop, clear=False, verbose=False):
#XXX: does the strategy of finding min/max always apply?
import numpy as np
# get model (for minima)
model = self.objective
self.dim = len(bounds)
### get mins ###
stepmon = self._minmon
archive = None if clear else self._minarch
inverse = False
self.sampler.Reset(archive, inv=inverse) # reset the sampler
self.sampler.Search(model, bounds, stop=stop, monitor=stepmon)
if verbose: self.sampler._summarize()
# read trajectories from log (or monitor)
xyz = self.sampler.Samples()
if clear: self.sampler.Reset() # reset the sampler
### end mins ###
# invert model (for maxima)
imodel = lambda *args, **kwds: -model(*args, **kwds)
### get maxs ###
stepmon = self._maxmon
archive = None if clear else self._maxarch
inverse = True
self.sampler.Reset(archive, inv=inverse) # reset the sampler
self.sampler.Search(imodel, bounds, stop=stop, monitor=stepmon)
if verbose: self.sampler._summarize()
xyz = np.hstack((xyz, self.sampler.Samples()))
if clear: self.sampler.Reset() # reset the sampler
### end maxs ###
# split into params and cost
self.x = xyz.T[:,:-1]
self.z = xyz.T[:,-1]
return self.x, self.z
def _noise(self, scale=None, x=None):
#HACK: remove any duplicate points by adding noise
import numpy as np
if x is None: x = self.x
if scale is None: scale = self.noise
if not scale: return x
return x + np.random.normal(scale=scale, size=x.shape)
def _downsample(self, maxpts=None, x=None, z=None):
if maxpts is None: maxpts = self.maxpts
if x is None: x = self.x
if z is None: z = self.z
if len(x) != len(z):
raise ValueError("the input array lengths must match exactly")
if maxpts is not None and len(z) > maxpts:
N = max(int(round(len(z)/float(maxpts))),1)
# print "for speed, sampling {} down to {}".format(len(z),len(z)/N)
# ax.plot(x[:,0], x[:,1], z, 'ko', linewidth=2, markersize=4)
x = x[::N]
z = z[::N]
# plt.show()
# exit()
return x, z
def _interpolate(self, x, z, **kwds):
import numpy as np
from scipy.interpolate import Rbf as interpolate
return interpolate(*np.vstack((x.T, z)), **kwds)
def Interpolate(self, **kwds): #XXX: better take a strategy?
maxpts = kwds.pop('maxpts', self.maxpts)
noise = kwds.pop('noise', self.noise)
args = self.args.copy()
args.update(kwds)
x, z = self._downsample(maxpts)
#NOTE: really only need to add noise when have duplicate x,y coords
x = self._noise(noise, x)
# build the surrogate
self.surrogate = self._interpolate(x, z, **args)
self.surrogate.__doc__ = self.function.__doc__
return self.surrogate
def _max(self):
import numpy as np
x = self.x
z = self.z
mz = np.argmax(z)
return x[mz],z[mz]
def _min(self):
import numpy as np
x = self.x
z = self.z
mz = np.argmin(z)
return x[mz],z[mz]
def Plot(self, step=200, scale=False, shift=False, \
density=9, axes=(), vals=(), maxpts=None):
# plot interpolated surface
from mpl_toolkits.mplot3d import axes3d
import matplotlib.pyplot as plt
from matplotlib import cm
import numpy as np
figure = plt.figure()
kwds = {'projection':'3d'}
ax = figure.gca(**kwds)
ax.autoscale(tight=True)
if maxpts is None: maxpts = self.maxpts
x, z = self._downsample(maxpts)
# get two axes to plot, and indices of the remaining axes
axes = axes[:2] #XXX: error if wrong size?
ix = [i for i in range(len(x.T)) if i not in axes]
n = 2-len(axes)
axes, ix = list(axes)+ix[:n], ix[n:]
# build list of fixed values (default mins), override with user input
#fix = np.zeros(len(ix))
fix = enumerate(self._min()[0])
fix = np.array(tuple(j for (i,j) in fix if i not in axes))
fix[:len(vals)] = vals
# build grid of points, one for each param, apply fixed values
grid = np.ones((len(x.T),step,step))
grid[ix] = fix[:,None,None]
del ix, fix
# build sub-surface of surrogate(x) to display, apply to the grid
xy = x.T[axes]
M = complex('{}j'.format(step))
grid[axes] = np.mgrid[xy[0].min():xy[0].max():M,
xy[1].min():xy[1].max():M]
del xy
# evaluate the surrogate on the sub-surface
z_ = self.surrogate(*grid)
# scaling used by model plotter
if scale:
if shift:
z_ = np.asarray(z_)+shift
z_ = np.log(4*np.asarray(z_)*scale+1)+2
# plot surface
d = max(11 - density, 1)
x_ = grid[axes[0]]
y_ = grid[axes[-1]]
ax.plot_wireframe(x_, y_, z_, rstride=d, cstride=d)
#ax.plot_surface(x_, y_, z_, rstride=d, cstride=d, cmap=cm.jet, linewidth=0, antialiased=False)
# use the sampled values
z_ = z
# scaling used by model plotter
if scale:
if shift:
z_ = np.asarray(z_)+shift
z_ = np.log(4*np.asarray(z_)*scale+1)+2
# plot data points
x_ = x.T[axes[0]]
y_ = x.T[axes[-1]]
ax.plot(x_, y_, z_, 'ko', linewidth=2, markersize=4)
plt.show() #XXX: show or don't show?... or return?
# figure.savefig('griewangk.png')
def __set_function(self, function): #XXX: deal w/ selector (2D)? ExtraArgs?
# convert to 'model' format (i.e. takes a parameter vector)
def objective(x, *args, **kwds):
return function(*(tuple(x)+args), **kwds).tolist()
self.objective = objective
self.objective.__doc__ = function.__doc__
return
def __function(self): #XXX: deal w/ selector (2D)? ExtraArgs?
# convert model to 'args' format (i.e. takes positional args)
def function(*args, **kwds):
len = self.dim # or kwds.pop('len', None)
if len is None: return self.objective(args, **kwds)
return self.objective(args[:len], *args[len:], **kwds)
function.__doc__ = self.objective.__doc__
return function
def __model(self): #XXX: deal w/ selector (2D)? ExtraArgs?
# convert to 'model' format (i.e. takes a parameter vector)
if self.surrogate is None: return None
def objective(x, *args, **kwds):
return self.surrogate(*(tuple(x)+args), **kwds).tolist()
objective.__doc__ = self.objective.__doc__
return objective
# interface
function = property(__function, __set_function )
model = property(__model )
#CUTE: 'configure' monitor and archive if they are desired
if stepmon:
stepmon = LoggingMonitor(1) # montor for all runs
itermon = LoggingMonitor(1, filename='inv.txt') #XXX: log.txt?
else:
stepmon = itermon = None
if archive: #python2.5
ar_name = '__%s_%sD_cache__' % (model.__self__.__class__.__name__,ndim)
archive = dir_archive(ar_name, serialized=True, cached=False)
ar_name = '__%s_%sD_invcache__' % (model.__self__.__class__.__name__,ndim)
ivcache = dir_archive(ar_name, serialized=True, cached=False)
else:
archive = ivcache = None
from mystic.search import Searcher #XXX: init w/ archive, then UseArchive?
sampler = Searcher(npts, retry, tol, mem, _map, archive, sprayer, seeker)
sampler.Verbose(disp)
sampler.UseTrajectories(traj)
### doit ###
maxpts = 1000. #10000.
surface = Surface(model, sampler, maxpts=maxpts, dim=ndim)
surface.UseMonitor(stepmon, itermon)
surface.UseArchive(archive, ivcache)
density = 9
shift = 0
scale = 0
step = 200
args = {
'smooth': 0,
seeker = PowellDirectionalSolver
npts = 25 # number of solvers
_map = Pool().map
retry = 1 # max consectutive iteration retries without a cache 'miss'
tol = 8 # rounding precision
mem = 1 # cache rounding precision
#CUTE: 'configure' monitor and archive if they are desired
if stepmon: stepmon = LoggingMonitor(1) # montor for all runs
else: stepmon = None
if archive: #python2.5
ar_name = '__%s_%sD_cache__' % (model.__self__.__class__.__name__,ndim)
archive = dir_archive(ar_name, serialized=True, cached=False)
else: archive = None
searcher = Searcher(npts, retry, tol, mem, _map, archive, sprayer, seeker)
searcher.Verbose(disp)
searcher.UseTrajectories(traj)
searcher.Reset(archive, inv=False)
searcher.Search(model, bounds, stop=stop, monitor=stepmon)
searcher._summarize()
##### extract results #####
xyz = searcher.Samples()
##### invert the model, and get the maxima #####
imodel = lambda *args, **kwds: -model(*args, **kwds)
#CUTE: 'configure' monitor and archive if they are desired
if stepmon not in (None, False):
repeat = 0 # number of times to repeat the search
tol = 8 # rounding precision
mem = 1 # cache rounding precision
size = 0 # max in-memory cache size
#CUTE: 'configure' monitor and archive if they are desired
if evalmon: evalmon = LoggingMonitor(1) # montor for all runs
else: evalmon = None
if archive: #python2.5
name = getattr(model,'__name__','model')
ar_name = '__%s_%sD_cache__' % (name,ndim)
archive = dir_archive(ar_name, serialized=True, cached=False)
else: archive = None
# configure a Searcher to use a "evaluation archive"
searcher = Searcher(npts, retry, tol, mem, size, _map, archive, None, sprayer, seeker, repeat=repeat)
searcher.Verbose(disp)
searcher.UseTrajectories(traj)
searcher.Reset(None, inv=False) #XXX: careful, can replace searcher.cache
searcher.Search(model, bounds, stop=stop, evalmon=evalmon)
searcher._summarize()
##### extract results #####
xyz = searcher.Samples(all=True)
##### invert the model, and get the maxima #####
imodel = lambda *args, **kwds: -model(*args, **kwds)
#CUTE: 'configure' monitor and archive if they are desired
if evalmon not in (None, False):
if stepmon: stepmon = LoggingMonitor(1) # montor for all runs
else: stepmon = None
if archive: #python2.5
name = getattr(model, '__name__', 'model')
ar_name = '__%s_%sD_cache__' % (name, ndim)
archive = dir_archive(ar_name, serialized=True, cached=False)
else:
archive = None
# configure a Searcher to use a "trajectory cache"
searcher = Searcher(npts,
retry,
tol,
mem,
size,
_map,
None,
archive,
sprayer,
seeker,
repeat=repeat)
searcher.Verbose(disp)
searcher.UseTrajectories(traj)
searcher.Reset(archive, inv=False)
searcher.Search(model, bounds, stop=stop, monitor=stepmon)
searcher._summarize()
##### extract results #####
xyz = searcher.Samples()
class Surface(object): #FIXME: should be subclass of Interpolator (?)
#surface has:
# args - interpolation configuration (smooth, function, ...)
# sampler - a search algorithm
# maxpts - a maximum number of sampling points
# noise - a noise coefficient
# dim - dimensionality of the model
# function - target function [F(*x)]
# objective - target function [F(x)]
# surrogate - interpolated function [F(*x)]
# model - interpolated function [F(x)]
# x,y,z - sampled points(*)
#
#surface (or sampler) has:
# _minmon,_maxmon - step monitor(*)
# _minarch,_maxarch - sampled point archives(*)
#
#surface can:
# Sample - populate sampled point archive with solver trajectories
# Interpolate - build interpolated function from sampled points
# Plot - plot sampled points and interpolated surface
#
#surface (or sampler) can:
# UseMonitor - track trajectories with a monitor(s)
# UseArchive - track sampled points in an archive(s)
# _max - fetch (x,y,z,model(x,y)) for maximal z of sampled points
# _min - fetch (x,y,z,model(x,y)) for minimal z of sampled points
def __init__(self, objective, sampler=None, **kwds):
"""response surface interpolator, where data is sampled from objective
Input:
objective: function of the form z=f(x)
sampler: mystic.search.Searcher instance
Additional Inputs:
maxpts: int, maximum number of points to use from (x,z)
noise: float, amplitude of gaussian noise to remove duplicate x
method: string for kind of interpolator
dim: number of parameters in the input for the objective function
NOTE:
if scipy is not installed, will use np.interp for 1D (non-rbf),
or mystic's rbf otherwise. default method is 'nearest' for
1D and 'linear' otherwise. method can be one of ('rbf','linear',
'nearest','cubic','inverse','gaussian','quintic','thin_plate').
"""
# sampler configuration
from mystic.search import Searcher
self.sampler = Searcher() if sampler is None else sampler
self.maxpts = kwds.pop('maxpts', None) # N = 1000
self.noise = kwds.pop('noise', 1e-8)
# monitor, archive, and trajectories
self._minmon = self._maxmon = None #XXX: better default?
self._minarch = self._maxarch = None #XXX: better default?
self.x = None # params (x)
self.z = None # cost (objective(x))
# point generator(s) and interpolated model(s) #XXX: better names?
self.dim = kwds.pop('dim', None) #XXX: should be (or set) len(x)
self.objective = objective # original F(x)
self.surrogate = None # interpolated F(*x)
# interpolator configuration
self.args = {}#dict(smooth=0, function='thin_plate')
self.args.update(kwds)
return
# XXX: useful?
# def _invert_model:
# takes model and returns inverted_model (maxmodel or invmodel?)
# def _invert_trajectories:
# takes (xyz) trajectories and returns inverted trajectories (xy-z)
def UseMonitor(self, min=None, max=None):
"""track parameter trajectories with a monitor(s)
Input:
min: monitor instance to track minima; if True, use a new Monitor
max: monitor instance to track maxima; if True, use a new Monitor
Output:
None
"""
from mystic.monitors import Monitor
if type(min) is bool: self._minmon = Monitor() if min else None
elif min is not None: self._minmon = min
if type(max) is bool: self._maxmon = Monitor() if max else None
elif max is not None: self._maxmon = max
return
def UseArchive(self, min=None, max=None):
"""track sampled points in an archive(s)
Input:
min: archive instance to store minima; if True, use a new archive
max: archive instance to store maxima; if True, use a new archive
Output:
None
"""
from klepto.archives import dict_archive as d
if type(min) is bool: self._minarch = d(cached=False) if min else None
elif min is not None: self._minarch = min
if type(max) is bool: self._maxarch = d(cached=False) if max else None
elif max is not None: self._maxarch = max
return
"""
def doit(self, bounds, stop, step=200, scale=False, shift=False,
density=9, axes=(), vals=(), maxpts=maxpts, **kwds):
if not self.sampler.traj: self.sampler.UseTrajectories()
# get trajectories
self.Sample(bounds, stop)
# get interpolated function
self.Interpolate(**kwds)
# check extrema #XXX: put _min,_max in Interpolate? (downsampled)
f = lambda x,z: (z,surface.surrogate(*x))
print("min: {}; min@f: {}".format(*f(*surface._min())))
print("max: {}; max@f: {}".format(*f(*urfacef._max())))
# plot surface
self.Plot(step=step, scale=scale, shift=shift, density=density, axes=axes, vals=vals, maxpts=maxpts)
return
"""
def Sample(self, bounds, stop, clear=False, verbose=False, all=False):
"""sample data (x,z) using objective function z=f(x)
Input:
bounds: tuple of floats (min,max), bounds on the search region
stop: termination condition
clear: if True, clear the archive of stored points
verbose: if True, print a summary of search/sampling results
all: if True, use solver EvalMonitor, else use StepMonitor
Output:
x: an array of shape (npts, dim) or (npts,)
z: an array of shape (npts,)
"""
#XXX: does the strategy of finding min/max always apply?
import numpy as np
# get model (for minima)
model = self.objective
self.dim = len(bounds)
### get mins ###
monitor = self._minmon
archive = None if clear else self._minarch
inverse = False
if all: #FIXME: better define role/use of Reset/Archive/clear...
self.sampler.Reset(None, inv=inverse) # reset the sampler
self.sampler.archive = archive
self.sampler.Search(model, bounds, stop=stop, evalmon=monitor)
else:
self.sampler.Reset(archive, inv=inverse) # reset the sampler
self.sampler.Search(model, bounds, stop=stop, monitor=monitor)
if verbose: self.sampler._summarize()
# read trajectories from log (or monitor)
xyz = self.sampler.Samples(all=all)
if clear: self.sampler.Reset() # reset the sampler
### end mins ###
# invert model (for maxima)
imodel = lambda *args, **kwds: -model(*args, **kwds)
### get maxs ###
monitor = self._maxmon
archive = None if clear else self._maxarch
inverse = True
if all: #FIXME: better define role/use of Reset/Archive/clear...
self.sampler.Reset(None, inv=inverse) # reset the sampler
self.sampler.archive = archive
self.sampler.Search(imodel, bounds, stop=stop, evalmon=monitor)
else:
self.sampler.Reset(archive, inv=inverse) # reset the sampler
self.sampler.Search(imodel, bounds, stop=stop, monitor=monitor)
if verbose: self.sampler._summarize()
xyz = np.hstack((xyz, self.sampler.Samples(all=all)))
if clear: self.sampler.Reset() # reset the sampler
### end maxs ###
# split into params and cost
self.x = xyz.T[:,:-1]
self.z = xyz.T[:,-1]
return self.x, self.z
def Interpolate(self, **kwds): #XXX: refactor so use self.interpolator ?
"""interpolate data (x,z) to generate response function z=f(*x)
Input:
maxpts: int, maximum number of points to use from (x,z)
noise: float, amplitude of gaussian noise to remove duplicate x
method: string for kind of interpolator
extrap: if True, extrapolate a bounding box (can reduce # of nans)
arrays: if True, return a numpy array; otherwise don't return arrays
Output:
interpolated response function, where z=f(*x.T)
NOTE:
if scipy is not installed, will use np.interp for 1D (non-rbf),
or mystic's rbf otherwise. default method is 'nearest' for
1D and 'linear' otherwise. method can be one of ('rbf','linear',
'nearest','cubic','inverse','gaussian','quintic','thin_plate').
"""
from interpolator import Interpolator
args = self.args.copy()
args.update(kwds)
maxpts, noise = self.maxpts, self.noise
ii = Interpolator(self.x, self.z, maxpts=maxpts, noise=noise, **args)
self.surrogate = ii.Interpolate(**args)
# build the surrogate
self.surrogate.__doc__ = self.objective.__doc__
return self.surrogate
def _max(self): #XXX: remove?
"""get the x[i],z[i] corresponding to the max(z)
"""
import numpy as np
mz = np.argmax(self.z)
return self.x[mz], self.z[mz]
def _min(self): #XXX: remove?
"""get the x[i],z[i] corresponding to the min(z)
"""
import numpy as np
mz = np.argmin(self.z)
return self.x[mz], self.z[mz]
def Plot(self, **kwds):
"""produce a scatterplot of (x,z) and the surface z = function(*x.T)
Input:
step: int, plot every 'step' points on the grid [default: 200]
scale: float, scaling factor for the z-axis [default: False]
shift: float, additive shift for the z-axis [default: False]
density: int, density of wireframe for the plot surface [default: 9]
axes: tuple, indicies of the axes to plot [default: ()]
vals: list of values (one per axis) for unplotted axes [default: ()]
maxpts: int, maximum number of (x,z) points to use [default: None]
kernel: function transforming x to x', where x' = kernel(x)
"""
# get interpolted function
fx = self.surrogate
# plot interpolated surface
from plotter import Plotter
p = Plotter(self.x, self.z, fx, **kwds)
p.Plot()
# if plotter interpolated the function, get the function
self.surrogate = fx or p.function
def __set_function(self, function): #XXX: deal w/ selector (2D)? ExtraArgs?
# convert to 'model' format (i.e. takes a parameter vector)
from mystic.math.interpolate import _to_objective
_objective = _to_objective(function)
def objective(x, *args, **kwds):
result = _objective(x, *args, **kwds)
return result.tolist() if hasattr(result, 'tolist') else result
self.objective = objective
self.objective.__doc__ = function.__doc__
return
def __function(self): #XXX: deal w/ selector (2D)? ExtraArgs? _to_function
# convert model to 'args' format (i.e. takes positional args)
from mystic.math.interpolate import _to_function
function = _to_function(self.objective, ndim=self.dim)
function.__doc__ = self.objective.__doc__
return function
def __model(self): #XXX: deal w/ selector (2D)? ExtraArgs? _to_objective
# convert to 'model' format (i.e. takes a parameter vector)
if self.surrogate is None: return None
from mystic.math.interpolate import _to_objective
_objective = _to_objective(self.surrogate)
def objective(x, *args, **kwds):
result = _objective(x, *args, **kwds)
return result.tolist() if hasattr(result, 'tolist') else result
objective.__doc__ = self.objective.__doc__
return objective
# interface
function = property(__function, __set_function )
model = property(__model )
costmon = LoggingMonitor(1, filename='inv.txt') #XXX: log.txt?
else:
monitor = costmon = None
if archive: #python2.5
name = getattr(model,'__name__','model')
ar_name = '__%s_%sD_cache__' % (name,ndim)
archive = dir_archive(ar_name, serialized=True, cached=False)
ar_name = '__%s_%sD_invcache__' % (name,ndim)
ivcache = dir_archive(ar_name, serialized=True, cached=False)
else:
archive = ivcache = None
from mystic.search import Searcher #XXX: init w/ archive, then UseArchive?
expts,evals = (None,archive) if all else (archive, None)
#expts,evals = (archive, None) #XXX: don't override the sample archive
sampler = Searcher(npts, retry, tol, mem, size, _map, evals, expts, sprayer, seeker, repeat=repeat)
sampler.Verbose(disp)
sampler.UseTrajectories(traj)
### doit ###
maxpts = 1000. #10000.
surface = Surface(model, sampler, maxpts=maxpts, dim=ndim)
surface.UseMonitor(monitor, costmon)
surface.UseArchive(archive, ivcache)
density = 9
shift = 0
scale = 0
step = 200
args = {
#'smooth': 0,
if evalmon: evalmon = LoggingMonitor(1) # montor for all runs
else: evalmon = None
if archive: #python2.5
name = getattr(model, '__name__', 'model')
ar_name = '__%s_%sD_cache__' % (name, ndim)
archive = dir_archive(ar_name, serialized=True, cached=False)
else:
archive = None
# configure a Searcher to use a "evaluation archive"
searcher = Searcher(npts,
retry,
tol,
mem,
size,
_map,
archive,
None,
sprayer,
seeker,
repeat=repeat)
searcher.Verbose(disp)
searcher.UseTrajectories(traj)
searcher.Reset(None, inv=False) #XXX: careful, can replace searcher.cache
searcher.Search(model, bounds, stop=stop, evalmon=evalmon)
searcher._summarize()
##### extract results #####
xyz = searcher.Samples(all=True)