"""Visual impression of current exploration."""
from __future__ import print_function, division
import sys
import shutil
from numpy import log10
import numpy as np
import string
from xml.sax.saxutils import escape as html_escape
clusteridstrings = ['%d' % i for i in range(10)] + list(string.ascii_uppercase) + list(string.ascii_lowercase)
spearman = None
try:
import scipy.stats
spearman = scipy.stats.spearmanr
except ImportError:
pass
def round_parameterlimits(plo, phi, paramlimitguess=None):
"""Guess the current parameter range.
Parameters
-----------
plo: array of floats
for each parameter, current minimum value
phi: array of floats
for each parameter, current maximum value
paramlimitguess: array of float tuples
for each parameter, guess of parameter range if available
Returns
-------
plo_rounded: array of floats
for each parameter, rounded minimum value
phi_rounded: array of floats
for each parameter, rounded maximum value
formats: array of float tuples
for each parameter, string format for representing it.
"""
with np.errstate(divide='ignore'):
expos = log10(np.abs([plo, phi]))
expolo = np.floor(np.min(expos, axis=0))
expohi = np.ceil(np.max(expos, axis=0))
is_negative = plo < 0
plo_rounded = np.where(is_negative, -10**expohi, 0)
phi_rounded = np.where(is_negative, 10**expohi, 10**expohi)
if paramlimitguess is not None:
for i, (plo_guess, phi_guess) in enumerate(paramlimitguess):
# if plo_guess is higher than what we thought, we can increase to match
if plo_guess <= plo[i] and plo_guess >= plo_rounded[i]:
plo_rounded[i] = plo_guess
if phi_guess >= phi[i] and phi_guess <= phi_rounded[i]:
phi_rounded[i] = phi_guess
formats = []
for i in range(len(plo)):
fmt = '%+.1e'
if -1 <= expolo[i] <= 2 and -1 <= expohi[i] <= 2:
fmt = '%+.1f'
if -4 <= expolo[i] <= 0 and -4 <= expohi[i] <= 0:
fmt = '%%+.%df' % (max(0, -min(expolo[i], expohi[i])))
if phi[i] == plo[i]:
fmt = '%+.1f'
elif fmt % plo[i] == fmt % phi[i]:
fmt = '%%+.%df' % (max(0, -int(np.floor(log10(phi[i] - plo[i])))))
formats.append(fmt)
return plo_rounded, phi_rounded, formats
def nicelogger(points, info, region, transformLayer, region_fresh=False):
"""Log current live points and integration progress to stdout.
Parameters
-----------
points: dict with keys "u", "p", "logl"
live points (u: cube coordinates, p: transformed coordinates,
logl: loglikelihood values)
info: dict
integration information. Keys are:
- paramlims (optional): parameter ranges
- logvol: expected volume at this iteration
region: MLFriends
Current region.
transformLayer: ScaleLayer or AffineLayer
Current transformLayer (for clustering information).
region_fresh: bool
Whether the region was just updated.
"""
p = points['p']
paramnames = info['paramnames']
# print()
# print('lnZ = %.1f, remainder = %.1f, lnLike = %.1f | Efficiency: %d/%d = %.4f%%\r' % (
# logz, logz_remain, np.max(logl), ncall, it, it * 100 / ncall))
plo = p.min(axis=0)
phi = p.max(axis=0)
plo_rounded, phi_rounded, paramformats = round_parameterlimits(plo, phi, paramlimitguess=info.get('paramlims'))
if sys.stderr.isatty() and hasattr(shutil, 'get_terminal_size'):
columns, _rows = shutil.get_terminal_size(fallback=(80, 25))
else:
columns, _rows = 80, 25
paramwidth = max([len(pname) for pname in paramnames])
width = columns - 23 - paramwidth
width = max(width, 10)
indices = ((p - plo_rounded) * width / (phi_rounded - plo_rounded).reshape((1, -1))).astype(int)
indices[indices >= width] = width - 1
indices[indices < 0] = 0
ndim = len(plo)
print()
print()
clusterids = transformLayer.clusterids % len(clusteridstrings)
nmodes = transformLayer.nclusters
print(
"Mono-modal" if nmodes == 1 else "Have %d modes" % nmodes,
"Volume: ~exp(%.2f)" % region.estimate_volume(), '*' if region_fresh else ' ',
"Expected Volume: exp(%.2f)" % info['logvol'],
'' if 'order_test_correlation' not in info else
("Quality: correlation length: %d (%s)" % (info['order_test_correlation'], '+' if info['order_test_direction'] >= 0 else '-'))
if np.isfinite(info['order_test_correlation']) else "Quality: ok",
)
print()
if ndim == 1:
pass
elif ndim == 2 and spearman is not None:
rho, pval = spearman(p)
if pval < 0.01 and abs(rho) > 0.75:
print(" %s between %s and %s: rho=%.2f" % (
'positive degeneracy' if rho > 0 else 'negative degeneracy',
paramnames[0], paramnames[1], rho))
elif spearman is not None:
rho, pval = spearman(p)
if np.isfinite(pval).all() and pval.ndim == 2:
for i, param in enumerate(paramnames):
for j, param2 in enumerate(paramnames[:i]):
if pval[i,j] < 0.01 and abs(rho[i,j]) > 0.99:
s = 'positive relation' if rho[i,j] > 0 else 'negative relation'
print(" perfect %s between %s and %s" % (s, param, param2))
elif pval[i,j] < 0.01 and abs(rho[i,j]) > 0.75:
s = 'positive degeneracy' if rho[i,j] > 0 else 'negative degeneracy'
print(" %s between %s and %s: rho=%.2f" % (s, param, param2, rho[i,j]))
for i, (param, fmt) in enumerate(zip(paramnames, paramformats)):
if nmodes == 1:
line = [' ' for _ in range(width)]
for j in np.unique(indices[:,i]):
line[j] = '*'
linestr = ''.join(line)
else:
line = [' ' for _ in range(width)]
for clusterid, j in zip(clusterids, indices[:,i]):
if clusterid > 0 and line[j] in (' ', '0'):
# set it to correct cluster id
line[j] = clusteridstrings[clusterid]
elif clusterid == 0 and line[j] == ' ':
# empty, so set it although we don't know the cluster id
line[j] = '0'
# else:
# line[j] = '*'
linestr = ''.join(line)
line = linestr
ilo, ihi = indices[:,i].min(), indices[:,i].max()
if ilo > 10:
assert line[:10] == ' ' * 10
leftstr = fmt % plo[i]
j = ilo - 2 - len(leftstr) # left-bound
if j < width and j > 0:
line = line[:j] + leftstr + line[j + len(leftstr):]
if ihi < width - 10:
rightstr = fmt % phi[i]
j = ihi + 3 # right-bound
if j < width and j > 0:
line = line[:j] + rightstr + line[j + len(rightstr):]
parampadded = ('%%-%ds' % paramwidth) % param
print('%s: %09s|%s|%9s' % (parampadded, fmt % plo_rounded[i], line, fmt % phi_rounded[i]))
print()
def isnotebook():
"""Check if running in a Jupyter notebook."""
try:
shell = get_ipython().__class__.__name__
if shell == 'ZMQInteractiveShell':
return True # Jupyter notebook or qtconsole
elif shell == 'TerminalInteractiveShell':
return False # Terminal running IPython
else:
return False # Other type (?)
except NameError:
return False # Probably standard Python interpreter
class LivePointsWidget(object):
"""
Widget for ipython and jupyter notebooks.
Shows where the live points are currently in parameter space.
"""
def __init__(self):
"""Initialise. To draw, call .initialize()."""
self.grid = None
self.label = None
self.laststatus = None
def initialize(self, paramnames, width):
"""Set up and display widget.
Parameters
----------
paramnames: list of str
Parameter names
width: int
number of html table columns.
"""
from ipywidgets import HTML, VBox, Layout, GridspecLayout
from IPython.display import display
grid = GridspecLayout(len(paramnames), width + 3)
self.laststatus = []
for a, paramname in enumerate(paramnames):
self.laststatus.append('*' * width)
htmlcode = "
"
for b in range(width):
grid[a, b + 2] = HTML(htmlcode, layout=Layout(margin="0"))
htmlcode = "%s
"
grid[a, 0] = HTML(htmlcode % html_escape(paramname), layout=Layout(margin="0"))
grid[a, 1] = HTML("...", layout=Layout(margin="0"))
grid[a,-1] = HTML("...", layout=Layout(margin="0"))
self.grid = grid
self.label = HTML()
box = VBox(children=[self.label, grid])
display(box)
def __call__(self, points, info, region, transformLayer, region_fresh=False):
"""Update widget to show current live points and integration progress to stdout.
Parameters
-----------
points: dict with keys u, p, logl
live points (u: cube coordinates, p: transformed coordinates,
logl: loglikelihood values)
info: dict
integration information. Keys are:
- paramlims (optional): parameter ranges
- logvol: expected volume at this iteration
region: MLFriends
Current region.
transformLayer: ScaleLayer or AffineLayer
Current transformLayer (for clustering information).
region_fresh: bool
Whether the region was just updated.
"""
# t = time.time()
# if self.lastupdate is not None and self.lastupdate < t - 5:
# return
# self.lastupdate = t
# u, p, logl = points['u'], points['p'], points['logl']
p = points['p']
paramnames = info['paramnames']
# print()
# print('lnZ = %.1f, remainder = %.1f, lnLike = %.1f | Efficiency: %d/%d = %.4f%%\r' % (
# logz, logz_remain, np.max(logl), ncall, it, it * 100 / ncall))
plo = p.min(axis=0)
phi = p.max(axis=0)
plo_rounded, phi_rounded, paramformats = round_parameterlimits(plo, phi, paramlimitguess=info.get('paramlims'))
width = 50
if self.grid is None:
self.initialize(paramnames, width)
with np.errstate(invalid="ignore"):
indices = ((p - plo_rounded) * width / (phi_rounded - plo_rounded).reshape((1, -1))).astype(int)
indices[indices >= width] = width - 1
indices[indices < 0] = 0
ndim = len(plo)
clusterids = transformLayer.clusterids % len(clusteridstrings)
nmodes = transformLayer.nclusters
labeltext = ("Mono-modal" if nmodes == 1 else "Have %d modes" % nmodes) + \
(" | Volume: ~exp(%.2f) " % region.estimate_volume()) + ('*' if region_fresh else ' ') + \
" | Expected Volume: exp(%.2f)" % info['logvol'] + \
('' if 'order_test_correlation' not in info else
(" | Quality: correlation length: %d (%s)" % (info['order_test_correlation'], '+' if info['order_test_direction'] >= 0 else '-'))
if np.isfinite(info['order_test_correlation']) else " | Quality: ok")
if ndim == 1:
pass
elif ndim == 2 and spearman is not None:
rho, pval = spearman(p)
if pval < 0.01 and abs(rho) > 0.75:
labeltext += ("
%s between %s and %s: rho=%.2f" % (
'positive degeneracy' if rho > 0 else 'negative degeneracy',
paramnames[0], paramnames[1], rho))
elif spearman is not None:
rho, pval = spearman(p)
for i, param in enumerate(paramnames):
for j, param2 in enumerate(paramnames[:i]):
if pval[i,j] < 0.01 and abs(rho[i,j]) > 0.99:
labeltext += ("
perfect %s between %s and %s" % (
'positive relation' if rho[i,j] > 0 else 'negative relation',
param2, param))
elif pval[i,j] < 0.01 and abs(rho[i,j]) > 0.75:
labeltext += ("
%s between %s and %s: rho=%.2f" % (
'positive degeneracy' if rho[i,j] > 0 else 'negative degeneracy',
param2, param, rho[i,j]))
for i, (param, fmt) in enumerate(zip(paramnames, paramformats)):
if nmodes == 1:
line = [' ' for _ in range(width)]
for j in np.unique(indices[:,i]):
line[j] = '*'
linestr = ''.join(line)
else:
line = [' ' for _ in range(width)]
for clusterid, j in zip(clusterids, indices[:,i]):
if clusterid > 0 and line[j] in (' ', '0'):
# set it to correct cluster id
line[j] = clusteridstrings[clusterid]
elif clusterid == 0 and line[j] == ' ':
# empty, so set it although we don't know the cluster id
line[j] = '0'
# else:
# line[j] = '*'
linestr = ''.join(line)
oldlinestr = self.laststatus[i]
for j, (c, d) in enumerate(zip(linestr, oldlinestr)):
if c != d:
if c == ' ':
self.grid[i, j + 2].value = "
"
else:
self.grid[i, j + 2].value = "%s
" % c.replace('*', ' ')
self.laststatus[i] = linestr
# self.grid[i,0].value = param
self.grid[i, 1].value = fmt % plo_rounded[i]
self.grid[i,-1].value = fmt % phi_rounded[i]
self.label.value = labeltext
def get_default_viz_callback():
"""Get default callback.
LivePointsWidget for Jupyter notebook, nicelogger otherwise.
"""
if isnotebook():
return LivePointsWidget()
else:
return nicelogger