def create(path, density):
""" Write a new MixtureDensity object to disk.
:param path: Path to the storage location, which will be created as a directory.
:type path: str
:param density: Mixture density.
:type density: pypmc.density.MixtureDensity
"""
description = {}
description['version'] = eos.version()
description['type'] = 'MixtureDensity'
description['components'] = []
for c in density.components:
if type(c) is pypmc.density.gauss.Gauss:
description['components'].append({
'type': 'gauss',
'mu': c.mu.tolist(),
'sigma': c.sigma.tolist()
})
else:
raise RuntimeError(
'Unsupported type of MixtureDensity component: {}'.format(
type(c)))
description['weights'] = density.weights.tolist()
os.makedirs(path, exist_ok=True)
with open(os.path.join(path, 'description.yaml'),
'w') as description_file:
yaml.dump(description, description_file, default_flow_style=False)
def plot_eos_watermark(self, item):
xdelta, ydelta = (0.04, 0.04)
hpos, vpos = item['position'] if 'position' in item else ['right', 'top']
if hpos == 'right':
x = 1 - xdelta
elif hpos == 'left':
x = xdelta
elif hpos == 'center':
x = 0.5
else:
raise ValueError('invalid horizontal position \'{}\''.format(hpos))
if vpos == 'bottom':
y = 0 + ydelta
elif vpos == 'top':
y = 1 - ydelta
elif vpos == 'center':
y = 0.5
else:
raise ValueError('invalid vertical position \'{}\''.format(hpos))
logofont = matplotlib.font_manager.FontProperties(family='sans-serif', size='15')
ax = plt.gca()
ax.text(x, y, r'\textsf{{\textbf{{EOS v{version}}}}}'.format(version=eos.version()),
transform=ax.transAxes, fontproperties=logofont,
color='OrangeRed', alpha=0.5, bbox=dict(facecolor='white', alpha=0.5, lw=0),
horizontalalignment=hpos, verticalalignment=vpos, zorder=+5)
def plot(self):
item = self.item
xdelta, ydelta = (0.04, 0.04)
hpos, vpos = item['position'] if 'position' in item else ['right', 'top']
if hpos == 'right':
x = 1 - xdelta
elif hpos == 'left':
x = xdelta
elif hpos == 'center':
x = 0.5
else:
raise ValueError('invalid horizontal position \'{}\''.format(hpos))
if vpos == 'bottom':
y = 0 + ydelta
elif vpos == 'top':
y = 1 - ydelta
elif vpos == 'center':
y = 0.5
else:
raise ValueError('invalid vertical position \'{}\''.format(hpos))
ax = plt.gca()
color = 'OrangeRed'
version = 'v{version}'.format(version=eos.version())
if 'preliminary' in item and item['preliminary']:
color = 'red'
version = 'Preliminary'
ax.text(x, y, r'\textsf{{\textbf{{EOS {version}}}}}'.format(version=version),
transform=ax.transAxes,
color=color, alpha=0.5, bbox=dict(facecolor='white', alpha=0.5, lw=0),
horizontalalignment=hpos, verticalalignment=vpos, zorder=+5)
def create(path, parameters, samples, weights, proposal):
""" Write a new PMCSampler object to disk.
:param path: Path to the storage location, which will be created as a directory.
:type path: str
:param parameters: Parameter descriptions as a 1D array of shape (N, ).
:type parameters: list or iterable of eos.Parameter
:param samples: Samples as a 2D array of shape (N, P).
:type samples: 2D numpy array
:param weights: Weights on a linear scale as a 2D array of shape (N, 1).
:type weights: 1D numpy array, optional
"""
description = {}
description['version'] = eos.version()
description['type'] = 'PMCSampler'
description['parameters'] = [{
'name': p.name(),
'min': p.min(),
'max': p.max()
} for p in parameters]
description['proposal'] = {
'components': [{
'mu': c.mu.tolist(),
'sigma': c.sigma.tolist()
} for c in proposal.components],
'weights':
proposal.weights.tolist()
}
if not samples.shape[1] == len(parameters):
raise RuntimeError(
'Shape of samples {} incompatible with number of parameters {}'
.format(samples.shape, len(parameters)))
if not weights is None and not samples.shape[0] == weights.shape[0]:
raise RuntimeError(
'Shape of weights {} incompatible with shape of samples {}'.
format(weights.shape, samples.shape))
os.makedirs(path, exist_ok=True)
with open(os.path.join(path, 'description.yaml'),
'w') as description_file:
yaml.dump(description, description_file, default_flow_style=False)
_np.save(os.path.join(path, 'samples.npy'), samples)
_np.save(os.path.join(path, 'weights.npy'), weights)
def create(path, observables, samples, weights):
""" Write a new Prediction object to disk.
:param path: Path to the storage location, which will be created as a directory.
:type path: str
:param observables: Observables as a 1D array of shape (O, ).
:type observables: list or iterable of eos.Observable
:param samples: Samples as a 2D array of shape (N, O).
:type samples: 2D numpy array
:param weights: Weights on a linear scale as a 1D array of shape (N, ).
:type weights: 1D numpy array
"""
description = {}
description['version'] = eos.version()
description['type'] = 'Prediction'
description['observables'] = [{
'name': str(o.name()),
'kinematics': {k.name(): float(k)
for k in o.kinematics()}
} for o in observables]
if not samples.shape[1] == len(observables):
raise RuntimeError(
'Shape of samples {} incompatible with number of observables {}'
.format(samples.shape, len(observables)))
if not samples.shape[0] == weights.shape[0]:
raise RuntimeError(
'Shape of weights {} incompatible with shape of samples {}'.
format(weights.shape, samples.shape))
os.makedirs(path, exist_ok=True)
with open(os.path.join(path, 'description.yaml'),
'w') as description_file:
yaml.dump(description, description_file, default_flow_style=False)
_np.save(os.path.join(path, 'samples.npy'), samples)
_np.save(os.path.join(path, 'weights.npy'), weights)
import eos
import re
observables = eos.Observables()
def latex_to_rst(s):
return(re.sub(r'\$([^\$]*)\$', r':math:`\1`', s))
all_data = []
page_title = 'List of Observables'
print('#' * len(page_title))
print(page_title)
print('#' * len(page_title))
print('\n')
print('The following is a list of observables that is available in EOS v{}.\n\n'.format(eos.version()))
for section in observables.sections():
section_title = latex_to_rst(section.name())
print('*' * len(section_title))
print(section_title)
print('*' * len(section_title))
for group in section:
group_title = latex_to_rst(group.name())
print(group_title)
print('=' * len(group_title))
print('\n')
translation = {
ord(':'): 'co', ord('@'): 'at', ord('/'): 'sl', ord('_'): 'un',
ord('('): 'po', ord(')'): 'pc', ord('+'): 'pp', ord('-'): 'mm',
#
# import os
# import sys
# sys.path.insert(0, os.path.abspath('.'))
# -- Project information -----------------------------------------------------
import eos
project = 'EOS'
copyright = '2019, Danny van Dyk and others'
author = 'Danny van Dyk and others'
master_doc = 'index'
# The full version, including alpha/beta/rc tags
release = eos.version()
# -- General configuration ---------------------------------------------------
# Add any Sphinx extension module names here, as strings. They can be
# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
# ones.
extensions = [
'sphinx.ext.autodoc',
'sphinx.ext.mathjax',
'sphinx.ext.todo',
'sphinx.ext.autosectionlabel',
]
# Add any paths that contain templates here, relative to this directory.
templates_path = ['_templates']
def id_to_eprint_url(eprint_id):
if eprint_id.startswith('oai:arXiv.org:'):
return 'arXiv:' + eprint_id.lstrip(
'oai:arXiv.org:'), 'https://arxiv.org/abs/' + eprint_id.lstrip(
'oai:arXiv.org:')
return None, None
page_title = 'List of References'
print('#' * len(page_title))
print(page_title)
print('#' * len(page_title))
print('\n')
print(
'The following the full list of parameters and their values as of EOS v{}.\n\n'
.format(eos.version()))
for handle, reference in eos.References():
title = latex_to_rst(reference.title())
eprint, url = id_to_eprint_url(reference.eprint_id())
print('.. [{handle}] {authors} {delim}'.format(
handle=handle,
authors=reference.authors(),
delim='--' if title else ''))
print(' {title} {delim}'.format(title=title,
delim='--' if eprint else ''))
if eprint:
print(' `{eprint} <{url}>`_'.format(eprint=eprint, url=url))
print()
result = s
for regexp, repl in replacements:
result = regexp.sub(repl, result)
return(result)
def id_to_eprint_url(eprint_id):
if eprint_id.startswith('oai:arXiv.org:'):
return 'arXiv:' + eprint_id.lstrip('oai:arXiv.org:'), 'https://arxiv.org/abs/' + eprint_id.lstrip('oai:arXiv.org:')
return None, None
page_title = 'List of References'
print('#' * len(page_title))
print(page_title)
print('#' * len(page_title))
print('\n')
print('''
The following is the full list of references that were used to implement theory codes and provide likelihood constraints
or parameter values within EOS v{}.\n\n'''.format(eos.version()))
for handle, reference in eos.References():
title = latex_to_rst(reference.title())
eprint, url = id_to_eprint_url(reference.eprint_id())
print('.. [{handle}] {authors} {delim}'.format(handle=handle, authors=reference.authors(), delim='--' if title else ''))
print(' {title} {delim}'.format(title=title, delim='--' if eprint else ''))
if eprint:
print(' `{eprint} <{url}>`_'.format(eprint=eprint,url=url))
print()
