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WangWenjun559/Weiss | summary/sumy/sklearn/ensemble/tests/test_weight_boosting.py | 32 | 15697 | """Testing for the boost module (sklearn.ensemble.boost)."""
import numpy as np
from sklearn.utils.testing import assert_array_equal, assert_array_less
from sklearn.utils.testing import assert_array_almost_equal
from sklearn.utils.testing import assert_equal
from sklearn.utils.testing import assert_raises, assert_raises_regexp
from sklearn.cross_validation import train_test_split
from sklearn.grid_search import GridSearchCV
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import AdaBoostRegressor
from scipy.sparse import csc_matrix
from scipy.sparse import csr_matrix
from scipy.sparse import coo_matrix
from scipy.sparse import dok_matrix
from scipy.sparse import lil_matrix
from sklearn.svm import SVC, SVR
from sklearn.tree import DecisionTreeClassifier, DecisionTreeRegressor
from sklearn.utils import shuffle
from sklearn import datasets
# Common random state
rng = np.random.RandomState(0)
# Toy sample
X = [[-2, -1], [-1, -1], [-1, -2], [1, 1], [1, 2], [2, 1]]
y_class = ["foo", "foo", "foo", 1, 1, 1] # test string class labels
y_regr = [-1, -1, -1, 1, 1, 1]
T = [[-1, -1], [2, 2], [3, 2]]
y_t_class = ["foo", 1, 1]
y_t_regr = [-1, 1, 1]
# Load the iris dataset and randomly permute it
iris = datasets.load_iris()
perm = rng.permutation(iris.target.size)
iris.data, iris.target = shuffle(iris.data, iris.target, random_state=rng)
# Load the boston dataset and randomly permute it
boston = datasets.load_boston()
boston.data, boston.target = shuffle(boston.data, boston.target,
random_state=rng)
def test_classification_toy():
# Check classification on a toy dataset.
for alg in ['SAMME', 'SAMME.R']:
clf = AdaBoostClassifier(algorithm=alg, random_state=0)
clf.fit(X, y_class)
assert_array_equal(clf.predict(T), y_t_class)
assert_array_equal(np.unique(np.asarray(y_t_class)), clf.classes_)
assert_equal(clf.predict_proba(T).shape, (len(T), 2))
assert_equal(clf.decision_function(T).shape, (len(T),))
def test_regression_toy():
# Check classification on a toy dataset.
clf = AdaBoostRegressor(random_state=0)
clf.fit(X, y_regr)
assert_array_equal(clf.predict(T), y_t_regr)
def test_iris():
# Check consistency on dataset iris.
classes = np.unique(iris.target)
clf_samme = prob_samme = None
for alg in ['SAMME', 'SAMME.R']:
clf = AdaBoostClassifier(algorithm=alg)
clf.fit(iris.data, iris.target)
assert_array_equal(classes, clf.classes_)
proba = clf.predict_proba(iris.data)
if alg == "SAMME":
clf_samme = clf
prob_samme = proba
assert_equal(proba.shape[1], len(classes))
assert_equal(clf.decision_function(iris.data).shape[1], len(classes))
score = clf.score(iris.data, iris.target)
assert score > 0.9, "Failed with algorithm %s and score = %f" % \
(alg, score)
# Somewhat hacky regression test: prior to
# ae7adc880d624615a34bafdb1d75ef67051b8200,
# predict_proba returned SAMME.R values for SAMME.
clf_samme.algorithm = "SAMME.R"
assert_array_less(0,
np.abs(clf_samme.predict_proba(iris.data) - prob_samme))
def test_boston():
# Check consistency on dataset boston house prices.
clf = AdaBoostRegressor(random_state=0)
clf.fit(boston.data, boston.target)
score = clf.score(boston.data, boston.target)
assert score > 0.85
def test_staged_predict():
# Check staged predictions.
rng = np.random.RandomState(0)
iris_weights = rng.randint(10, size=iris.target.shape)
boston_weights = rng.randint(10, size=boston.target.shape)
# AdaBoost classification
for alg in ['SAMME', 'SAMME.R']:
clf = AdaBoostClassifier(algorithm=alg, n_estimators=10)
clf.fit(iris.data, iris.target, sample_weight=iris_weights)
predictions = clf.predict(iris.data)
staged_predictions = [p for p in clf.staged_predict(iris.data)]
proba = clf.predict_proba(iris.data)
staged_probas = [p for p in clf.staged_predict_proba(iris.data)]
score = clf.score(iris.data, iris.target, sample_weight=iris_weights)
staged_scores = [
s for s in clf.staged_score(
iris.data, iris.target, sample_weight=iris_weights)]
assert_equal(len(staged_predictions), 10)
assert_array_almost_equal(predictions, staged_predictions[-1])
assert_equal(len(staged_probas), 10)
assert_array_almost_equal(proba, staged_probas[-1])
assert_equal(len(staged_scores), 10)
assert_array_almost_equal(score, staged_scores[-1])
# AdaBoost regression
clf = AdaBoostRegressor(n_estimators=10, random_state=0)
clf.fit(boston.data, boston.target, sample_weight=boston_weights)
predictions = clf.predict(boston.data)
staged_predictions = [p for p in clf.staged_predict(boston.data)]
score = clf.score(boston.data, boston.target, sample_weight=boston_weights)
staged_scores = [
s for s in clf.staged_score(
boston.data, boston.target, sample_weight=boston_weights)]
assert_equal(len(staged_predictions), 10)
assert_array_almost_equal(predictions, staged_predictions[-1])
assert_equal(len(staged_scores), 10)
assert_array_almost_equal(score, staged_scores[-1])
def test_gridsearch():
# Check that base trees can be grid-searched.
# AdaBoost classification
boost = AdaBoostClassifier(base_estimator=DecisionTreeClassifier())
parameters = {'n_estimators': (1, 2),
'base_estimator__max_depth': (1, 2),
'algorithm': ('SAMME', 'SAMME.R')}
clf = GridSearchCV(boost, parameters)
clf.fit(iris.data, iris.target)
# AdaBoost regression
boost = AdaBoostRegressor(base_estimator=DecisionTreeRegressor(),
random_state=0)
parameters = {'n_estimators': (1, 2),
'base_estimator__max_depth': (1, 2)}
clf = GridSearchCV(boost, parameters)
clf.fit(boston.data, boston.target)
def test_pickle():
# Check pickability.
import pickle
# Adaboost classifier
for alg in ['SAMME', 'SAMME.R']:
obj = AdaBoostClassifier(algorithm=alg)
obj.fit(iris.data, iris.target)
score = obj.score(iris.data, iris.target)
s = pickle.dumps(obj)
obj2 = pickle.loads(s)
assert_equal(type(obj2), obj.__class__)
score2 = obj2.score(iris.data, iris.target)
assert_equal(score, score2)
# Adaboost regressor
obj = AdaBoostRegressor(random_state=0)
obj.fit(boston.data, boston.target)
score = obj.score(boston.data, boston.target)
s = pickle.dumps(obj)
obj2 = pickle.loads(s)
assert_equal(type(obj2), obj.__class__)
score2 = obj2.score(boston.data, boston.target)
assert_equal(score, score2)
def test_importances():
# Check variable importances.
X, y = datasets.make_classification(n_samples=2000,
n_features=10,
n_informative=3,
n_redundant=0,
n_repeated=0,
shuffle=False,
random_state=1)
for alg in ['SAMME', 'SAMME.R']:
clf = AdaBoostClassifier(algorithm=alg)
clf.fit(X, y)
importances = clf.feature_importances_
assert_equal(importances.shape[0], 10)
assert_equal((importances[:3, np.newaxis] >= importances[3:]).all(),
True)
def test_error():
# Test that it gives proper exception on deficient input.
assert_raises(ValueError,
AdaBoostClassifier(learning_rate=-1).fit,
X, y_class)
assert_raises(ValueError,
AdaBoostClassifier(algorithm="foo").fit,
X, y_class)
assert_raises(ValueError,
AdaBoostClassifier().fit,
X, y_class, sample_weight=np.asarray([-1]))
def test_base_estimator():
# Test different base estimators.
from sklearn.ensemble import RandomForestClassifier
from sklearn.svm import SVC
# XXX doesn't work with y_class because RF doesn't support classes_
# Shouldn't AdaBoost run a LabelBinarizer?
clf = AdaBoostClassifier(RandomForestClassifier())
clf.fit(X, y_regr)
clf = AdaBoostClassifier(SVC(), algorithm="SAMME")
clf.fit(X, y_class)
from sklearn.ensemble import RandomForestRegressor
from sklearn.svm import SVR
clf = AdaBoostRegressor(RandomForestRegressor(), random_state=0)
clf.fit(X, y_regr)
clf = AdaBoostRegressor(SVR(), random_state=0)
clf.fit(X, y_regr)
# Check that an empty discrete ensemble fails in fit, not predict.
X_fail = [[1, 1], [1, 1], [1, 1], [1, 1]]
y_fail = ["foo", "bar", 1, 2]
clf = AdaBoostClassifier(SVC(), algorithm="SAMME")
assert_raises_regexp(ValueError, "worse than random",
clf.fit, X_fail, y_fail)
def test_sample_weight_missing():
from sklearn.linear_model import LinearRegression
from sklearn.cluster import KMeans
clf = AdaBoostClassifier(LinearRegression(), algorithm="SAMME")
assert_raises(ValueError, clf.fit, X, y_regr)
clf = AdaBoostRegressor(LinearRegression())
assert_raises(ValueError, clf.fit, X, y_regr)
clf = AdaBoostClassifier(KMeans(), algorithm="SAMME")
assert_raises(ValueError, clf.fit, X, y_regr)
clf = AdaBoostRegressor(KMeans())
assert_raises(ValueError, clf.fit, X, y_regr)
def test_sparse_classification():
# Check classification with sparse input.
class CustomSVC(SVC):
"""SVC variant that records the nature of the training set."""
def fit(self, X, y, sample_weight=None):
"""Modification on fit caries data type for later verification."""
super(CustomSVC, self).fit(X, y, sample_weight=sample_weight)
self.data_type_ = type(X)
return self
X, y = datasets.make_multilabel_classification(n_classes=1, n_samples=15,
n_features=5,
return_indicator=True,
random_state=42)
# Flatten y to a 1d array
y = np.ravel(y)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
for sparse_format in [csc_matrix, csr_matrix, lil_matrix, coo_matrix,
dok_matrix]:
X_train_sparse = sparse_format(X_train)
X_test_sparse = sparse_format(X_test)
# Trained on sparse format
sparse_classifier = AdaBoostClassifier(
base_estimator=CustomSVC(probability=True),
random_state=1,
algorithm="SAMME"
).fit(X_train_sparse, y_train)
# Trained on dense format
dense_classifier = AdaBoostClassifier(
base_estimator=CustomSVC(probability=True),
random_state=1,
algorithm="SAMME"
).fit(X_train, y_train)
# predict
sparse_results = sparse_classifier.predict(X_test_sparse)
dense_results = dense_classifier.predict(X_test)
assert_array_equal(sparse_results, dense_results)
# decision_function
sparse_results = sparse_classifier.decision_function(X_test_sparse)
dense_results = dense_classifier.decision_function(X_test)
assert_array_equal(sparse_results, dense_results)
# predict_log_proba
sparse_results = sparse_classifier.predict_log_proba(X_test_sparse)
dense_results = dense_classifier.predict_log_proba(X_test)
assert_array_equal(sparse_results, dense_results)
# predict_proba
sparse_results = sparse_classifier.predict_proba(X_test_sparse)
dense_results = dense_classifier.predict_proba(X_test)
assert_array_equal(sparse_results, dense_results)
# score
sparse_results = sparse_classifier.score(X_test_sparse, y_test)
dense_results = dense_classifier.score(X_test, y_test)
assert_array_equal(sparse_results, dense_results)
# staged_decision_function
sparse_results = sparse_classifier.staged_decision_function(
X_test_sparse)
dense_results = dense_classifier.staged_decision_function(X_test)
for sprase_res, dense_res in zip(sparse_results, dense_results):
assert_array_equal(sprase_res, dense_res)
# staged_predict
sparse_results = sparse_classifier.staged_predict(X_test_sparse)
dense_results = dense_classifier.staged_predict(X_test)
for sprase_res, dense_res in zip(sparse_results, dense_results):
assert_array_equal(sprase_res, dense_res)
# staged_predict_proba
sparse_results = sparse_classifier.staged_predict_proba(X_test_sparse)
dense_results = dense_classifier.staged_predict_proba(X_test)
for sprase_res, dense_res in zip(sparse_results, dense_results):
assert_array_equal(sprase_res, dense_res)
# staged_score
sparse_results = sparse_classifier.staged_score(X_test_sparse,
y_test)
dense_results = dense_classifier.staged_score(X_test, y_test)
for sprase_res, dense_res in zip(sparse_results, dense_results):
assert_array_equal(sprase_res, dense_res)
# Verify sparsity of data is maintained during training
types = [i.data_type_ for i in sparse_classifier.estimators_]
assert all([(t == csc_matrix or t == csr_matrix)
for t in types])
def test_sparse_regression():
# Check regression with sparse input.
class CustomSVR(SVR):
"""SVR variant that records the nature of the training set."""
def fit(self, X, y, sample_weight=None):
"""Modification on fit caries data type for later verification."""
super(CustomSVR, self).fit(X, y, sample_weight=sample_weight)
self.data_type_ = type(X)
return self
X, y = datasets.make_regression(n_samples=15, n_features=50, n_targets=1,
random_state=42)
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=0)
for sparse_format in [csc_matrix, csr_matrix, lil_matrix, coo_matrix,
dok_matrix]:
X_train_sparse = sparse_format(X_train)
X_test_sparse = sparse_format(X_test)
# Trained on sparse format
sparse_classifier = AdaBoostRegressor(
base_estimator=CustomSVR(),
random_state=1
).fit(X_train_sparse, y_train)
# Trained on dense format
dense_classifier = dense_results = AdaBoostRegressor(
base_estimator=CustomSVR(),
random_state=1
).fit(X_train, y_train)
# predict
sparse_results = sparse_classifier.predict(X_test_sparse)
dense_results = dense_classifier.predict(X_test)
assert_array_equal(sparse_results, dense_results)
# staged_predict
sparse_results = sparse_classifier.staged_predict(X_test_sparse)
dense_results = dense_classifier.staged_predict(X_test)
for sprase_res, dense_res in zip(sparse_results, dense_results):
assert_array_equal(sprase_res, dense_res)
types = [i.data_type_ for i in sparse_classifier.estimators_]
assert all([(t == csc_matrix or t == csr_matrix)
for t in types])
| apache-2.0 |
vipullakhani/mi-instrument | mi/core/instrument/file_publisher.py | 5 | 4306 | """
@package mi.core.instrument.publisher
@file /mi-instrument/mi/core/instrument/file_publisher.py
@author Peter Cable
@brief Event file publisher
Release notes:
initial release
"""
import cPickle as pickle
import json
import numpy as np
import pandas as pd
import xarray as xr
from mi.core.instrument.publisher import Publisher
from mi.logging import log
class CountPublisher(Publisher):
def __init__(self, allowed):
super(CountPublisher, self).__init__(allowed)
self.total = 0
def _publish(self, events, headers):
for e in events:
try:
json.dumps(e)
except (ValueError, UnicodeDecodeError) as err:
log.exception('Unable to publish event: %r %r', e, err)
count = len(events)
self.total += count
log.info('Publish %d events (%d total)', count, self.total)
class FilePublisher(Publisher):
def __init__(self, *args, **kwargs):
super(FilePublisher, self).__init__(*args, **kwargs)
self.samples = {}
@staticmethod
def _flatten(sample):
values = sample.pop('values')
for each in values:
sample[each['value_id']] = each['value']
return sample
def _publish(self, events, headers):
for event in events:
# file publisher only applicable to particles
if event.get('type') != 'DRIVER_ASYNC_EVENT_SAMPLE':
continue
particle = event.get('value', {})
stream = particle.get('stream_name')
if stream:
particle = self._flatten(particle)
self.samples.setdefault(stream, []).append(particle)
def to_dataframes(self):
data_frames = {}
for particle_type in self.samples:
data_frames[particle_type] = self.fix_arrays(pd.DataFrame(self.samples[particle_type]))
return data_frames
def to_datasets(self):
datasets = {}
for particle_type in self.samples:
datasets[particle_type] = self.fix_arrays(pd.DataFrame(self.samples[particle_type]), return_as_xr=True)
return datasets
@staticmethod
def fix_arrays(data_frame, return_as_xr=False):
# round-trip the dataframe through xray to get the multidimensional indexing correct
new_ds = xr.Dataset()
for each in data_frame:
if data_frame[each].dtype == 'object' and isinstance(data_frame[each].values[0], list):
data = np.array([np.array(x) for x in data_frame[each].values])
new_ds[each] = xr.DataArray(data)
else:
new_ds[each] = data_frame[each]
if return_as_xr:
return new_ds
return new_ds.to_dataframe()
def write(self):
log.info('Writing output files...')
self._write()
log.info('Done writing output files...')
def _write(self):
raise NotImplemented
class CsvPublisher(FilePublisher):
def _write(self):
dataframes = self.to_dataframes()
for particle_type in dataframes:
file_path = '%s.csv' % particle_type
dataframes[particle_type].to_csv(file_path)
class PandasPublisher(FilePublisher):
def _write(self):
dataframes = self.to_dataframes()
for particle_type in dataframes:
# very large dataframes don't work with pickle
# split if too large
df = dataframes[particle_type]
max_size = 5000000
if len(df) > max_size:
num_slices = len(df) / max_size
slices = np.array_split(df, num_slices)
for index, df_slice in enumerate(slices):
file_path = '%s_%d.pd' % (particle_type, index)
df_slice.to_pickle(file_path)
else:
log.info('length of dataframe: %d', len(df))
file_path = '%s.pd' % particle_type
dataframes[particle_type].to_pickle(file_path)
class XarrayPublisher(FilePublisher):
def _write(self):
datasets = self.to_datasets()
for particle_type in datasets:
file_path = '%s.xr' % particle_type
with open(file_path, 'w') as fh:
pickle.dump(datasets[particle_type], fh, protocol=-1)
| bsd-2-clause |
18padx08/PPTex | PPTexEnv_x86_64/lib/python2.7/site-packages/matplotlib/backend_bases.py | 10 | 106046 | """
Abstract base classes define the primitives that renderers and
graphics contexts must implement to serve as a matplotlib backend
:class:`RendererBase`
An abstract base class to handle drawing/rendering operations.
:class:`FigureCanvasBase`
The abstraction layer that separates the
:class:`matplotlib.figure.Figure` from the backend specific
details like a user interface drawing area
:class:`GraphicsContextBase`
An abstract base class that provides color, line styles, etc...
:class:`Event`
The base class for all of the matplotlib event
handling. Derived classes suh as :class:`KeyEvent` and
:class:`MouseEvent` store the meta data like keys and buttons
pressed, x and y locations in pixel and
:class:`~matplotlib.axes.Axes` coordinates.
:class:`ShowBase`
The base class for the Show class of each interactive backend;
the 'show' callable is then set to Show.__call__, inherited from
ShowBase.
"""
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import six
from six.moves import xrange
import os
import sys
import warnings
import time
import io
import numpy as np
import matplotlib.cbook as cbook
import matplotlib.colors as colors
import matplotlib.transforms as transforms
import matplotlib.widgets as widgets
#import matplotlib.path as path
from matplotlib import rcParams
from matplotlib import is_interactive
from matplotlib import get_backend
from matplotlib._pylab_helpers import Gcf
from matplotlib.transforms import Bbox, TransformedBbox, Affine2D
import matplotlib.tight_bbox as tight_bbox
import matplotlib.textpath as textpath
from matplotlib.path import Path
from matplotlib.cbook import mplDeprecation
try:
from importlib import import_module
except:
# simple python 2.6 implementation (no relative imports)
def import_module(name):
__import__(name)
return sys.modules[name]
try:
from PIL import Image
_has_pil = True
except ImportError:
_has_pil = False
_default_filetypes = {
'ps': 'Postscript',
'eps': 'Encapsulated Postscript',
'pdf': 'Portable Document Format',
'pgf': 'PGF code for LaTeX',
'png': 'Portable Network Graphics',
'raw': 'Raw RGBA bitmap',
'rgba': 'Raw RGBA bitmap',
'svg': 'Scalable Vector Graphics',
'svgz': 'Scalable Vector Graphics'
}
_default_backends = {
'ps': 'matplotlib.backends.backend_ps',
'eps': 'matplotlib.backends.backend_ps',
'pdf': 'matplotlib.backends.backend_pdf',
'pgf': 'matplotlib.backends.backend_pgf',
'png': 'matplotlib.backends.backend_agg',
'raw': 'matplotlib.backends.backend_agg',
'rgba': 'matplotlib.backends.backend_agg',
'svg': 'matplotlib.backends.backend_svg',
'svgz': 'matplotlib.backends.backend_svg',
}
def register_backend(format, backend, description=None):
"""
Register a backend for saving to a given file format.
format : str
File extention
backend : module string or canvas class
Backend for handling file output
description : str, optional
Description of the file type. Defaults to an empty string
"""
if description is None:
description = ''
_default_backends[format] = backend
_default_filetypes[format] = description
def get_registered_canvas_class(format):
"""
Return the registered default canvas for given file format.
Handles deferred import of required backend.
"""
if format not in _default_backends:
return None
backend_class = _default_backends[format]
if cbook.is_string_like(backend_class):
backend_class = import_module(backend_class).FigureCanvas
_default_backends[format] = backend_class
return backend_class
class ShowBase(object):
"""
Simple base class to generate a show() callable in backends.
Subclass must override mainloop() method.
"""
def __call__(self, block=None):
"""
Show all figures. If *block* is not None, then
it is a boolean that overrides all other factors
determining whether show blocks by calling mainloop().
The other factors are:
it does not block if run inside ipython's "%pylab" mode
it does not block in interactive mode.
"""
managers = Gcf.get_all_fig_managers()
if not managers:
return
for manager in managers:
manager.show()
if block is not None:
if block:
self.mainloop()
return
else:
return
# Hack: determine at runtime whether we are
# inside ipython in pylab mode.
from matplotlib import pyplot
try:
ipython_pylab = not pyplot.show._needmain
# IPython versions >= 0.10 tack the _needmain
# attribute onto pyplot.show, and always set
# it to False, when in %pylab mode.
ipython_pylab = ipython_pylab and get_backend() != 'WebAgg'
# TODO: The above is a hack to get the WebAgg backend
# working with ipython's `%pylab` mode until proper
# integration is implemented.
except AttributeError:
ipython_pylab = False
# Leave the following as a separate step in case we
# want to control this behavior with an rcParam.
if ipython_pylab:
return
if not is_interactive() or get_backend() == 'WebAgg':
self.mainloop()
def mainloop(self):
pass
class RendererBase(object):
"""An abstract base class to handle drawing/rendering operations.
The following methods must be implemented in the backend for full
functionality (though just implementing :meth:`draw_path` alone would
give a highly capable backend):
* :meth:`draw_path`
* :meth:`draw_image`
* :meth:`draw_gouraud_triangle`
The following methods *should* be implemented in the backend for
optimization reasons:
* :meth:`draw_text`
* :meth:`draw_markers`
* :meth:`draw_path_collection`
* :meth:`draw_quad_mesh`
"""
def __init__(self):
self._texmanager = None
self._text2path = textpath.TextToPath()
def open_group(self, s, gid=None):
"""
Open a grouping element with label *s*. If *gid* is given, use
*gid* as the id of the group. Is only currently used by
:mod:`~matplotlib.backends.backend_svg`.
"""
pass
def close_group(self, s):
"""
Close a grouping element with label *s*
Is only currently used by :mod:`~matplotlib.backends.backend_svg`
"""
pass
def draw_path(self, gc, path, transform, rgbFace=None):
"""
Draws a :class:`~matplotlib.path.Path` instance using the
given affine transform.
"""
raise NotImplementedError
def draw_markers(self, gc, marker_path, marker_trans, path,
trans, rgbFace=None):
"""
Draws a marker at each of the vertices in path. This includes
all vertices, including control points on curves. To avoid
that behavior, those vertices should be removed before calling
this function.
*gc*
the :class:`GraphicsContextBase` instance
*marker_trans*
is an affine transform applied to the marker.
*trans*
is an affine transform applied to the path.
This provides a fallback implementation of draw_markers that
makes multiple calls to :meth:`draw_path`. Some backends may
want to override this method in order to draw the marker only
once and reuse it multiple times.
"""
for vertices, codes in path.iter_segments(trans, simplify=False):
if len(vertices):
x, y = vertices[-2:]
self.draw_path(gc, marker_path,
marker_trans +
transforms.Affine2D().translate(x, y),
rgbFace)
def draw_path_collection(self, gc, master_transform, paths, all_transforms,
offsets, offsetTrans, facecolors, edgecolors,
linewidths, linestyles, antialiaseds, urls,
offset_position):
"""
Draws a collection of paths selecting drawing properties from
the lists *facecolors*, *edgecolors*, *linewidths*,
*linestyles* and *antialiaseds*. *offsets* is a list of
offsets to apply to each of the paths. The offsets in
*offsets* are first transformed by *offsetTrans* before being
applied. *offset_position* may be either "screen" or "data"
depending on the space that the offsets are in.
This provides a fallback implementation of
:meth:`draw_path_collection` that makes multiple calls to
:meth:`draw_path`. Some backends may want to override this in
order to render each set of path data only once, and then
reference that path multiple times with the different offsets,
colors, styles etc. The generator methods
:meth:`_iter_collection_raw_paths` and
:meth:`_iter_collection` are provided to help with (and
standardize) the implementation across backends. It is highly
recommended to use those generators, so that changes to the
behavior of :meth:`draw_path_collection` can be made globally.
"""
path_ids = []
for path, transform in self._iter_collection_raw_paths(
master_transform, paths, all_transforms):
path_ids.append((path, transforms.Affine2D(transform)))
for xo, yo, path_id, gc0, rgbFace in self._iter_collection(
gc, master_transform, all_transforms, path_ids, offsets,
offsetTrans, facecolors, edgecolors, linewidths, linestyles,
antialiaseds, urls, offset_position):
path, transform = path_id
transform = transforms.Affine2D(
transform.get_matrix()).translate(xo, yo)
self.draw_path(gc0, path, transform, rgbFace)
def draw_quad_mesh(self, gc, master_transform, meshWidth, meshHeight,
coordinates, offsets, offsetTrans, facecolors,
antialiased, edgecolors):
"""
This provides a fallback implementation of
:meth:`draw_quad_mesh` that generates paths and then calls
:meth:`draw_path_collection`.
"""
from matplotlib.collections import QuadMesh
paths = QuadMesh.convert_mesh_to_paths(
meshWidth, meshHeight, coordinates)
if edgecolors is None:
edgecolors = facecolors
linewidths = np.array([gc.get_linewidth()], np.float_)
return self.draw_path_collection(
gc, master_transform, paths, [], offsets, offsetTrans, facecolors,
edgecolors, linewidths, [], [antialiased], [None], 'screen')
def draw_gouraud_triangle(self, gc, points, colors, transform):
"""
Draw a Gouraud-shaded triangle.
*points* is a 3x2 array of (x, y) points for the triangle.
*colors* is a 3x4 array of RGBA colors for each point of the
triangle.
*transform* is an affine transform to apply to the points.
"""
raise NotImplementedError
def draw_gouraud_triangles(self, gc, triangles_array, colors_array,
transform):
"""
Draws a series of Gouraud triangles.
*points* is a Nx3x2 array of (x, y) points for the trianglex.
*colors* is a Nx3x4 array of RGBA colors for each point of the
triangles.
*transform* is an affine transform to apply to the points.
"""
transform = transform.frozen()
for tri, col in zip(triangles_array, colors_array):
self.draw_gouraud_triangle(gc, tri, col, transform)
def _iter_collection_raw_paths(self, master_transform, paths,
all_transforms):
"""
This is a helper method (along with :meth:`_iter_collection`) to make
it easier to write a space-efficent :meth:`draw_path_collection`
implementation in a backend.
This method yields all of the base path/transform
combinations, given a master transform, a list of paths and
list of transforms.
The arguments should be exactly what is passed in to
:meth:`draw_path_collection`.
The backend should take each yielded path and transform and
create an object that can be referenced (reused) later.
"""
Npaths = len(paths)
Ntransforms = len(all_transforms)
N = max(Npaths, Ntransforms)
if Npaths == 0:
return
transform = transforms.IdentityTransform()
for i in xrange(N):
path = paths[i % Npaths]
if Ntransforms:
transform = Affine2D(all_transforms[i % Ntransforms])
yield path, transform + master_transform
def _iter_collection_uses_per_path(self, paths, all_transforms,
offsets, facecolors, edgecolors):
"""
Compute how many times each raw path object returned by
_iter_collection_raw_paths would be used when calling
_iter_collection. This is intended for the backend to decide
on the tradeoff between using the paths in-line and storing
them once and reusing. Rounds up in case the number of uses
is not the same for every path.
"""
Npaths = len(paths)
if Npaths == 0 or (len(facecolors) == 0 and len(edgecolors) == 0):
return 0
Npath_ids = max(Npaths, len(all_transforms))
N = max(Npath_ids, len(offsets))
return (N + Npath_ids - 1) // Npath_ids
def _iter_collection(self, gc, master_transform, all_transforms,
path_ids, offsets, offsetTrans, facecolors,
edgecolors, linewidths, linestyles,
antialiaseds, urls, offset_position):
"""
This is a helper method (along with
:meth:`_iter_collection_raw_paths`) to make it easier to write
a space-efficent :meth:`draw_path_collection` implementation in a
backend.
This method yields all of the path, offset and graphics
context combinations to draw the path collection. The caller
should already have looped over the results of
:meth:`_iter_collection_raw_paths` to draw this collection.
The arguments should be the same as that passed into
:meth:`draw_path_collection`, with the exception of
*path_ids*, which is a list of arbitrary objects that the
backend will use to reference one of the paths created in the
:meth:`_iter_collection_raw_paths` stage.
Each yielded result is of the form::
xo, yo, path_id, gc, rgbFace
where *xo*, *yo* is an offset; *path_id* is one of the elements of
*path_ids*; *gc* is a graphics context and *rgbFace* is a color to
use for filling the path.
"""
Ntransforms = len(all_transforms)
Npaths = len(path_ids)
Noffsets = len(offsets)
N = max(Npaths, Noffsets)
Nfacecolors = len(facecolors)
Nedgecolors = len(edgecolors)
Nlinewidths = len(linewidths)
Nlinestyles = len(linestyles)
Naa = len(antialiaseds)
Nurls = len(urls)
if (Nfacecolors == 0 and Nedgecolors == 0) or Npaths == 0:
return
if Noffsets:
toffsets = offsetTrans.transform(offsets)
gc0 = self.new_gc()
gc0.copy_properties(gc)
if Nfacecolors == 0:
rgbFace = None
if Nedgecolors == 0:
gc0.set_linewidth(0.0)
xo, yo = 0, 0
for i in xrange(N):
path_id = path_ids[i % Npaths]
if Noffsets:
xo, yo = toffsets[i % Noffsets]
if offset_position == 'data':
if Ntransforms:
transform = (
Affine2D(all_transforms[i % Ntransforms]) +
master_transform)
else:
transform = master_transform
xo, yo = transform.transform_point((xo, yo))
xp, yp = transform.transform_point((0, 0))
xo = -(xp - xo)
yo = -(yp - yo)
if not (np.isfinite(xo) and np.isfinite(yo)):
continue
if Nfacecolors:
rgbFace = facecolors[i % Nfacecolors]
if Nedgecolors:
if Nlinewidths:
gc0.set_linewidth(linewidths[i % Nlinewidths])
if Nlinestyles:
gc0.set_dashes(*linestyles[i % Nlinestyles])
fg = edgecolors[i % Nedgecolors]
if len(fg) == 4:
if fg[3] == 0.0:
gc0.set_linewidth(0)
else:
gc0.set_foreground(fg)
else:
gc0.set_foreground(fg)
if rgbFace is not None and len(rgbFace) == 4:
if rgbFace[3] == 0:
rgbFace = None
gc0.set_antialiased(antialiaseds[i % Naa])
if Nurls:
gc0.set_url(urls[i % Nurls])
yield xo, yo, path_id, gc0, rgbFace
gc0.restore()
def get_image_magnification(self):
"""
Get the factor by which to magnify images passed to :meth:`draw_image`.
Allows a backend to have images at a different resolution to other
artists.
"""
return 1.0
def draw_image(self, gc, x, y, im):
"""
Draw the image instance into the current axes;
*gc*
a GraphicsContext containing clipping information
*x*
is the distance in pixels from the left hand side of the canvas.
*y*
the distance from the origin. That is, if origin is
upper, y is the distance from top. If origin is lower, y
is the distance from bottom
*im*
the :class:`matplotlib._image.Image` instance
"""
raise NotImplementedError
def option_image_nocomposite(self):
"""
override this method for renderers that do not necessarily
want to rescale and composite raster images. (like SVG)
"""
return False
def option_scale_image(self):
"""
override this method for renderers that support arbitrary
scaling of image (most of the vector backend).
"""
return False
def draw_tex(self, gc, x, y, s, prop, angle, ismath='TeX!', mtext=None):
"""
"""
self._draw_text_as_path(gc, x, y, s, prop, angle, ismath="TeX")
def draw_text(self, gc, x, y, s, prop, angle, ismath=False, mtext=None):
"""
Draw the text instance
*gc*
the :class:`GraphicsContextBase` instance
*x*
the x location of the text in display coords
*y*
the y location of the text baseline in display coords
*s*
the text string
*prop*
a :class:`matplotlib.font_manager.FontProperties` instance
*angle*
the rotation angle in degrees
*mtext*
a :class:`matplotlib.text.Text` instance
**backend implementers note**
When you are trying to determine if you have gotten your bounding box
right (which is what enables the text layout/alignment to work
properly), it helps to change the line in text.py::
if 0: bbox_artist(self, renderer)
to if 1, and then the actual bounding box will be plotted along with
your text.
"""
self._draw_text_as_path(gc, x, y, s, prop, angle, ismath)
def _get_text_path_transform(self, x, y, s, prop, angle, ismath):
"""
return the text path and transform
*prop*
font property
*s*
text to be converted
*usetex*
If True, use matplotlib usetex mode.
*ismath*
If True, use mathtext parser. If "TeX", use *usetex* mode.
"""
text2path = self._text2path
fontsize = self.points_to_pixels(prop.get_size_in_points())
if ismath == "TeX":
verts, codes = text2path.get_text_path(prop, s, ismath=False,
usetex=True)
else:
verts, codes = text2path.get_text_path(prop, s, ismath=ismath,
usetex=False)
path = Path(verts, codes)
angle = angle / 180. * 3.141592
if self.flipy():
transform = Affine2D().scale(fontsize / text2path.FONT_SCALE,
fontsize / text2path.FONT_SCALE)
transform = transform.rotate(angle).translate(x, self.height - y)
else:
transform = Affine2D().scale(fontsize / text2path.FONT_SCALE,
fontsize / text2path.FONT_SCALE)
transform = transform.rotate(angle).translate(x, y)
return path, transform
def _draw_text_as_path(self, gc, x, y, s, prop, angle, ismath):
"""
draw the text by converting them to paths using textpath module.
*prop*
font property
*s*
text to be converted
*usetex*
If True, use matplotlib usetex mode.
*ismath*
If True, use mathtext parser. If "TeX", use *usetex* mode.
"""
path, transform = self._get_text_path_transform(
x, y, s, prop, angle, ismath)
color = gc.get_rgb()
gc.set_linewidth(0.0)
self.draw_path(gc, path, transform, rgbFace=color)
def get_text_width_height_descent(self, s, prop, ismath):
"""
get the width and height, and the offset from the bottom to the
baseline (descent), in display coords of the string s with
:class:`~matplotlib.font_manager.FontProperties` prop
"""
if ismath == 'TeX':
# todo: handle props
size = prop.get_size_in_points()
texmanager = self._text2path.get_texmanager()
fontsize = prop.get_size_in_points()
w, h, d = texmanager.get_text_width_height_descent(s, fontsize,
renderer=self)
return w, h, d
dpi = self.points_to_pixels(72)
if ismath:
dims = self._text2path.mathtext_parser.parse(s, dpi, prop)
return dims[0:3] # return width, height, descent
flags = self._text2path._get_hinting_flag()
font = self._text2path._get_font(prop)
size = prop.get_size_in_points()
font.set_size(size, dpi)
# the width and height of unrotated string
font.set_text(s, 0.0, flags=flags)
w, h = font.get_width_height()
d = font.get_descent()
w /= 64.0 # convert from subpixels
h /= 64.0
d /= 64.0
return w, h, d
def flipy(self):
"""
Return true if y small numbers are top for renderer Is used
for drawing text (:mod:`matplotlib.text`) and images
(:mod:`matplotlib.image`) only
"""
return True
def get_canvas_width_height(self):
'return the canvas width and height in display coords'
return 1, 1
def get_texmanager(self):
"""
return the :class:`matplotlib.texmanager.TexManager` instance
"""
if self._texmanager is None:
from matplotlib.texmanager import TexManager
self._texmanager = TexManager()
return self._texmanager
def new_gc(self):
"""
Return an instance of a :class:`GraphicsContextBase`
"""
return GraphicsContextBase()
def points_to_pixels(self, points):
"""
Convert points to display units
*points*
a float or a numpy array of float
return points converted to pixels
You need to override this function (unless your backend
doesn't have a dpi, e.g., postscript or svg). Some imaging
systems assume some value for pixels per inch::
points to pixels = points * pixels_per_inch/72.0 * dpi/72.0
"""
return points
def strip_math(self, s):
return cbook.strip_math(s)
def start_rasterizing(self):
"""
Used in MixedModeRenderer. Switch to the raster renderer.
"""
pass
def stop_rasterizing(self):
"""
Used in MixedModeRenderer. Switch back to the vector renderer
and draw the contents of the raster renderer as an image on
the vector renderer.
"""
pass
def start_filter(self):
"""
Used in AggRenderer. Switch to a temporary renderer for image
filtering effects.
"""
pass
def stop_filter(self, filter_func):
"""
Used in AggRenderer. Switch back to the original renderer.
The contents of the temporary renderer is processed with the
*filter_func* and is drawn on the original renderer as an
image.
"""
pass
class GraphicsContextBase:
"""
An abstract base class that provides color, line styles, etc...
"""
# a mapping from dash styles to suggested offset, dash pairs
dashd = {
'solid': (None, None),
'dashed': (0, (6.0, 6.0)),
'dashdot': (0, (3.0, 5.0, 1.0, 5.0)),
'dotted': (0, (1.0, 3.0)),
}
def __init__(self):
self._alpha = 1.0
self._forced_alpha = False # if True, _alpha overrides A from RGBA
self._antialiased = 1 # use 0,1 not True, False for extension code
self._capstyle = 'butt'
self._cliprect = None
self._clippath = None
self._dashes = None, None
self._joinstyle = 'round'
self._linestyle = 'solid'
self._linewidth = 1
self._rgb = (0.0, 0.0, 0.0, 1.0)
self._orig_color = (0.0, 0.0, 0.0, 1.0)
self._hatch = None
self._url = None
self._gid = None
self._snap = None
self._sketch = None
def copy_properties(self, gc):
'Copy properties from gc to self'
self._alpha = gc._alpha
self._forced_alpha = gc._forced_alpha
self._antialiased = gc._antialiased
self._capstyle = gc._capstyle
self._cliprect = gc._cliprect
self._clippath = gc._clippath
self._dashes = gc._dashes
self._joinstyle = gc._joinstyle
self._linestyle = gc._linestyle
self._linewidth = gc._linewidth
self._rgb = gc._rgb
self._orig_color = gc._orig_color
self._hatch = gc._hatch
self._url = gc._url
self._gid = gc._gid
self._snap = gc._snap
self._sketch = gc._sketch
def restore(self):
"""
Restore the graphics context from the stack - needed only
for backends that save graphics contexts on a stack
"""
pass
def get_alpha(self):
"""
Return the alpha value used for blending - not supported on
all backends
"""
return self._alpha
def get_antialiased(self):
"Return true if the object should try to do antialiased rendering"
return self._antialiased
def get_capstyle(self):
"""
Return the capstyle as a string in ('butt', 'round', 'projecting')
"""
return self._capstyle
def get_clip_rectangle(self):
"""
Return the clip rectangle as a :class:`~matplotlib.transforms.Bbox`
instance
"""
return self._cliprect
def get_clip_path(self):
"""
Return the clip path in the form (path, transform), where path
is a :class:`~matplotlib.path.Path` instance, and transform is
an affine transform to apply to the path before clipping.
"""
if self._clippath is not None:
return self._clippath.get_transformed_path_and_affine()
return None, None
def get_dashes(self):
"""
Return the dash information as an offset dashlist tuple.
The dash list is a even size list that gives the ink on, ink
off in pixels.
See p107 of to PostScript `BLUEBOOK
<http://www-cdf.fnal.gov/offline/PostScript/BLUEBOOK.PDF>`_
for more info.
Default value is None
"""
return self._dashes
def get_forced_alpha(self):
"""
Return whether the value given by get_alpha() should be used to
override any other alpha-channel values.
"""
return self._forced_alpha
def get_joinstyle(self):
"""
Return the line join style as one of ('miter', 'round', 'bevel')
"""
return self._joinstyle
def get_linestyle(self, style):
"""
Return the linestyle: one of ('solid', 'dashed', 'dashdot',
'dotted').
"""
return self._linestyle
def get_linewidth(self):
"""
Return the line width in points as a scalar
"""
return self._linewidth
def get_rgb(self):
"""
returns a tuple of three or four floats from 0-1.
"""
return self._rgb
def get_url(self):
"""
returns a url if one is set, None otherwise
"""
return self._url
def get_gid(self):
"""
Return the object identifier if one is set, None otherwise.
"""
return self._gid
def get_snap(self):
"""
returns the snap setting which may be:
* True: snap vertices to the nearest pixel center
* False: leave vertices as-is
* None: (auto) If the path contains only rectilinear line
segments, round to the nearest pixel center
"""
return self._snap
def set_alpha(self, alpha):
"""
Set the alpha value used for blending - not supported on all backends.
If ``alpha=None`` (the default), the alpha components of the
foreground and fill colors will be used to set their respective
transparencies (where applicable); otherwise, ``alpha`` will override
them.
"""
if alpha is not None:
self._alpha = alpha
self._forced_alpha = True
else:
self._alpha = 1.0
self._forced_alpha = False
self.set_foreground(self._orig_color)
def set_antialiased(self, b):
"""
True if object should be drawn with antialiased rendering
"""
# use 0, 1 to make life easier on extension code trying to read the gc
if b:
self._antialiased = 1
else:
self._antialiased = 0
def set_capstyle(self, cs):
"""
Set the capstyle as a string in ('butt', 'round', 'projecting')
"""
if cs in ('butt', 'round', 'projecting'):
self._capstyle = cs
else:
raise ValueError('Unrecognized cap style. Found %s' % cs)
def set_clip_rectangle(self, rectangle):
"""
Set the clip rectangle with sequence (left, bottom, width, height)
"""
self._cliprect = rectangle
def set_clip_path(self, path):
"""
Set the clip path and transformation. Path should be a
:class:`~matplotlib.transforms.TransformedPath` instance.
"""
assert path is None or isinstance(path, transforms.TransformedPath)
self._clippath = path
def set_dashes(self, dash_offset, dash_list):
"""
Set the dash style for the gc.
*dash_offset*
is the offset (usually 0).
*dash_list*
specifies the on-off sequence as points.
``(None, None)`` specifies a solid line
"""
if dash_list is not None:
dl = np.asarray(dash_list)
if np.any(dl <= 0.0):
raise ValueError("All values in the dash list must be positive")
self._dashes = dash_offset, dash_list
def set_foreground(self, fg, isRGBA=False):
"""
Set the foreground color. fg can be a MATLAB format string, a
html hex color string, an rgb or rgba unit tuple, or a float between 0
and 1. In the latter case, grayscale is used.
If you know fg is rgba, set ``isRGBA=True`` for efficiency.
"""
self._orig_color = fg
if self._forced_alpha:
self._rgb = colors.colorConverter.to_rgba(fg, self._alpha)
elif isRGBA:
self._rgb = fg
else:
self._rgb = colors.colorConverter.to_rgba(fg)
def set_graylevel(self, frac):
"""
Set the foreground color to be a gray level with *frac*
"""
self._orig_color = frac
self._rgb = (frac, frac, frac, self._alpha)
def set_joinstyle(self, js):
"""
Set the join style to be one of ('miter', 'round', 'bevel')
"""
if js in ('miter', 'round', 'bevel'):
self._joinstyle = js
else:
raise ValueError('Unrecognized join style. Found %s' % js)
def set_linewidth(self, w):
"""
Set the linewidth in points
"""
self._linewidth = w
def set_linestyle(self, style):
"""
Set the linestyle to be one of ('solid', 'dashed', 'dashdot',
'dotted'). One may specify customized dash styles by providing
a tuple of (offset, dash pairs). For example, the predefiend
linestyles have following values.:
'dashed' : (0, (6.0, 6.0)),
'dashdot' : (0, (3.0, 5.0, 1.0, 5.0)),
'dotted' : (0, (1.0, 3.0)),
"""
if style in self.dashd:
offset, dashes = self.dashd[style]
elif isinstance(style, tuple):
offset, dashes = style
else:
raise ValueError('Unrecognized linestyle: %s' % str(style))
self._linestyle = style
self.set_dashes(offset, dashes)
def set_url(self, url):
"""
Sets the url for links in compatible backends
"""
self._url = url
def set_gid(self, id):
"""
Sets the id.
"""
self._gid = id
def set_snap(self, snap):
"""
Sets the snap setting which may be:
* True: snap vertices to the nearest pixel center
* False: leave vertices as-is
* None: (auto) If the path contains only rectilinear line
segments, round to the nearest pixel center
"""
self._snap = snap
def set_hatch(self, hatch):
"""
Sets the hatch style for filling
"""
self._hatch = hatch
def get_hatch(self):
"""
Gets the current hatch style
"""
return self._hatch
def get_hatch_path(self, density=6.0):
"""
Returns a Path for the current hatch.
"""
if self._hatch is None:
return None
return Path.hatch(self._hatch, density)
def get_sketch_params(self):
"""
Returns the sketch parameters for the artist.
Returns
-------
sketch_params : tuple or `None`
A 3-tuple with the following elements:
* `scale`: The amplitude of the wiggle perpendicular to the
source line.
* `length`: The length of the wiggle along the line.
* `randomness`: The scale factor by which the length is
shrunken or expanded.
May return `None` if no sketch parameters were set.
"""
return self._sketch
def set_sketch_params(self, scale=None, length=None, randomness=None):
"""
Sets the the sketch parameters.
Parameters
----------
scale : float, optional
The amplitude of the wiggle perpendicular to the source
line, in pixels. If scale is `None`, or not provided, no
sketch filter will be provided.
length : float, optional
The length of the wiggle along the line, in pixels
(default 128.0)
randomness : float, optional
The scale factor by which the length is shrunken or
expanded (default 16.0)
"""
if scale is None:
self._sketch = None
else:
self._sketch = (scale, length or 128.0, randomness or 16.0)
class TimerBase(object):
'''
A base class for providing timer events, useful for things animations.
Backends need to implement a few specific methods in order to use their
own timing mechanisms so that the timer events are integrated into their
event loops.
Mandatory functions that must be implemented:
* `_timer_start`: Contains backend-specific code for starting
the timer
* `_timer_stop`: Contains backend-specific code for stopping
the timer
Optional overrides:
* `_timer_set_single_shot`: Code for setting the timer to
single shot operating mode, if supported by the timer
object. If not, the `Timer` class itself will store the flag
and the `_on_timer` method should be overridden to support
such behavior.
* `_timer_set_interval`: Code for setting the interval on the
timer, if there is a method for doing so on the timer
object.
* `_on_timer`: This is the internal function that any timer
object should call, which will handle the task of running
all callbacks that have been set.
Attributes:
* `interval`: The time between timer events in
milliseconds. Default is 1000 ms.
* `single_shot`: Boolean flag indicating whether this timer
should operate as single shot (run once and then
stop). Defaults to `False`.
* `callbacks`: Stores list of (func, args) tuples that will be
called upon timer events. This list can be manipulated
directly, or the functions `add_callback` and
`remove_callback` can be used.
'''
def __init__(self, interval=None, callbacks=None):
#Initialize empty callbacks list and setup default settings if necssary
if callbacks is None:
self.callbacks = []
else:
self.callbacks = callbacks[:] # Create a copy
if interval is None:
self._interval = 1000
else:
self._interval = interval
self._single = False
# Default attribute for holding the GUI-specific timer object
self._timer = None
def __del__(self):
'Need to stop timer and possibly disconnect timer.'
self._timer_stop()
def start(self, interval=None):
'''
Start the timer object. `interval` is optional and will be used
to reset the timer interval first if provided.
'''
if interval is not None:
self._set_interval(interval)
self._timer_start()
def stop(self):
'''
Stop the timer.
'''
self._timer_stop()
def _timer_start(self):
pass
def _timer_stop(self):
pass
def _get_interval(self):
return self._interval
def _set_interval(self, interval):
# Force to int since none of the backends actually support fractional
# milliseconds, and some error or give warnings.
interval = int(interval)
self._interval = interval
self._timer_set_interval()
interval = property(_get_interval, _set_interval)
def _get_single_shot(self):
return self._single
def _set_single_shot(self, ss=True):
self._single = ss
self._timer_set_single_shot()
single_shot = property(_get_single_shot, _set_single_shot)
def add_callback(self, func, *args, **kwargs):
'''
Register `func` to be called by timer when the event fires. Any
additional arguments provided will be passed to `func`.
'''
self.callbacks.append((func, args, kwargs))
def remove_callback(self, func, *args, **kwargs):
'''
Remove `func` from list of callbacks. `args` and `kwargs` are optional
and used to distinguish between copies of the same function registered
to be called with different arguments.
'''
if args or kwargs:
self.callbacks.remove((func, args, kwargs))
else:
funcs = [c[0] for c in self.callbacks]
if func in funcs:
self.callbacks.pop(funcs.index(func))
def _timer_set_interval(self):
'Used to set interval on underlying timer object.'
pass
def _timer_set_single_shot(self):
'Used to set single shot on underlying timer object.'
pass
def _on_timer(self):
'''
Runs all function that have been registered as callbacks. Functions
can return False (or 0) if they should not be called any more. If there
are no callbacks, the timer is automatically stopped.
'''
for func, args, kwargs in self.callbacks:
ret = func(*args, **kwargs)
# docstring above explains why we use `if ret == False` here,
# instead of `if not ret`.
if ret == False:
self.callbacks.remove((func, args, kwargs))
if len(self.callbacks) == 0:
self.stop()
class Event:
"""
A matplotlib event. Attach additional attributes as defined in
:meth:`FigureCanvasBase.mpl_connect`. The following attributes
are defined and shown with their default values
*name*
the event name
*canvas*
the FigureCanvas instance generating the event
*guiEvent*
the GUI event that triggered the matplotlib event
"""
def __init__(self, name, canvas, guiEvent=None):
self.name = name
self.canvas = canvas
self.guiEvent = guiEvent
class IdleEvent(Event):
"""
An event triggered by the GUI backend when it is idle -- useful
for passive animation
"""
pass
class DrawEvent(Event):
"""
An event triggered by a draw operation on the canvas
In addition to the :class:`Event` attributes, the following event
attributes are defined:
*renderer*
the :class:`RendererBase` instance for the draw event
"""
def __init__(self, name, canvas, renderer):
Event.__init__(self, name, canvas)
self.renderer = renderer
class ResizeEvent(Event):
"""
An event triggered by a canvas resize
In addition to the :class:`Event` attributes, the following event
attributes are defined:
*width*
width of the canvas in pixels
*height*
height of the canvas in pixels
"""
def __init__(self, name, canvas):
Event.__init__(self, name, canvas)
self.width, self.height = canvas.get_width_height()
class CloseEvent(Event):
"""
An event triggered by a figure being closed
In addition to the :class:`Event` attributes, the following event
attributes are defined:
"""
def __init__(self, name, canvas, guiEvent=None):
Event.__init__(self, name, canvas, guiEvent)
class LocationEvent(Event):
"""
An event that has a screen location
The following additional attributes are defined and shown with
their default values.
In addition to the :class:`Event` attributes, the following
event attributes are defined:
*x*
x position - pixels from left of canvas
*y*
y position - pixels from bottom of canvas
*inaxes*
the :class:`~matplotlib.axes.Axes` instance if mouse is over axes
*xdata*
x coord of mouse in data coords
*ydata*
y coord of mouse in data coords
"""
x = None # x position - pixels from left of canvas
y = None # y position - pixels from right of canvas
inaxes = None # the Axes instance if mouse us over axes
xdata = None # x coord of mouse in data coords
ydata = None # y coord of mouse in data coords
# the last event that was triggered before this one
lastevent = None
def __init__(self, name, canvas, x, y, guiEvent=None):
"""
*x*, *y* in figure coords, 0,0 = bottom, left
"""
Event.__init__(self, name, canvas, guiEvent=guiEvent)
self.x = x
self.y = y
if x is None or y is None:
# cannot check if event was in axes if no x,y info
self.inaxes = None
self._update_enter_leave()
return
# Find all axes containing the mouse
if self.canvas.mouse_grabber is None:
axes_list = [a for a in self.canvas.figure.get_axes()
if a.in_axes(self)]
else:
axes_list = [self.canvas.mouse_grabber]
if len(axes_list) == 0: # None found
self.inaxes = None
self._update_enter_leave()
return
elif (len(axes_list) > 1): # Overlap, get the highest zorder
axes_list.sort(key=lambda x: x.zorder)
self.inaxes = axes_list[-1] # Use the highest zorder
else: # Just found one hit
self.inaxes = axes_list[0]
try:
trans = self.inaxes.transData.inverted()
xdata, ydata = trans.transform_point((x, y))
except ValueError:
self.xdata = None
self.ydata = None
else:
self.xdata = xdata
self.ydata = ydata
self._update_enter_leave()
def _update_enter_leave(self):
'process the figure/axes enter leave events'
if LocationEvent.lastevent is not None:
last = LocationEvent.lastevent
if last.inaxes != self.inaxes:
# process axes enter/leave events
try:
if last.inaxes is not None:
last.canvas.callbacks.process('axes_leave_event', last)
except:
pass
# See ticket 2901582.
# I think this is a valid exception to the rule
# against catching all exceptions; if anything goes
# wrong, we simply want to move on and process the
# current event.
if self.inaxes is not None:
self.canvas.callbacks.process('axes_enter_event', self)
else:
# process a figure enter event
if self.inaxes is not None:
self.canvas.callbacks.process('axes_enter_event', self)
LocationEvent.lastevent = self
class MouseEvent(LocationEvent):
"""
A mouse event ('button_press_event',
'button_release_event',
'scroll_event',
'motion_notify_event').
In addition to the :class:`Event` and :class:`LocationEvent`
attributes, the following attributes are defined:
*button*
button pressed None, 1, 2, 3, 'up', 'down' (up and down are used
for scroll events)
*key*
the key depressed when the mouse event triggered (see
:class:`KeyEvent`)
*step*
number of scroll steps (positive for 'up', negative for 'down')
Example usage::
def on_press(event):
print('you pressed', event.button, event.xdata, event.ydata)
cid = fig.canvas.mpl_connect('button_press_event', on_press)
"""
x = None # x position - pixels from left of canvas
y = None # y position - pixels from right of canvas
button = None # button pressed None, 1, 2, 3
dblclick = None # whether or not the event is the result of a double click
inaxes = None # the Axes instance if mouse us over axes
xdata = None # x coord of mouse in data coords
ydata = None # y coord of mouse in data coords
step = None # scroll steps for scroll events
def __init__(self, name, canvas, x, y, button=None, key=None,
step=0, dblclick=False, guiEvent=None):
"""
x, y in figure coords, 0,0 = bottom, left
button pressed None, 1, 2, 3, 'up', 'down'
"""
LocationEvent.__init__(self, name, canvas, x, y, guiEvent=guiEvent)
self.button = button
self.key = key
self.step = step
self.dblclick = dblclick
def __str__(self):
return ("MPL MouseEvent: xy=(%d,%d) xydata=(%s,%s) button=%s " +
"dblclick=%s inaxes=%s") % (self.x, self.y, self.xdata,
self.ydata, self.button,
self.dblclick, self.inaxes)
class PickEvent(Event):
"""
a pick event, fired when the user picks a location on the canvas
sufficiently close to an artist.
Attrs: all the :class:`Event` attributes plus
*mouseevent*
the :class:`MouseEvent` that generated the pick
*artist*
the :class:`~matplotlib.artist.Artist` picked
other
extra class dependent attrs -- e.g., a
:class:`~matplotlib.lines.Line2D` pick may define different
extra attributes than a
:class:`~matplotlib.collections.PatchCollection` pick event
Example usage::
line, = ax.plot(rand(100), 'o', picker=5) # 5 points tolerance
def on_pick(event):
thisline = event.artist
xdata, ydata = thisline.get_data()
ind = event.ind
print('on pick line:', zip(xdata[ind], ydata[ind]))
cid = fig.canvas.mpl_connect('pick_event', on_pick)
"""
def __init__(self, name, canvas, mouseevent, artist,
guiEvent=None, **kwargs):
Event.__init__(self, name, canvas, guiEvent)
self.mouseevent = mouseevent
self.artist = artist
self.__dict__.update(kwargs)
class KeyEvent(LocationEvent):
"""
A key event (key press, key release).
Attach additional attributes as defined in
:meth:`FigureCanvasBase.mpl_connect`.
In addition to the :class:`Event` and :class:`LocationEvent`
attributes, the following attributes are defined:
*key*
the key(s) pressed. Could be **None**, a single case sensitive ascii
character ("g", "G", "#", etc.), a special key
("control", "shift", "f1", "up", etc.) or a
combination of the above (e.g., "ctrl+alt+g", "ctrl+alt+G").
.. note::
Modifier keys will be prefixed to the pressed key and will be in the
order "ctrl", "alt", "super". The exception to this rule is when the
pressed key is itself a modifier key, therefore "ctrl+alt" and
"alt+control" can both be valid key values.
Example usage::
def on_key(event):
print('you pressed', event.key, event.xdata, event.ydata)
cid = fig.canvas.mpl_connect('key_press_event', on_key)
"""
def __init__(self, name, canvas, key, x=0, y=0, guiEvent=None):
LocationEvent.__init__(self, name, canvas, x, y, guiEvent=guiEvent)
self.key = key
class FigureCanvasBase(object):
"""
The canvas the figure renders into.
Public attributes
*figure*
A :class:`matplotlib.figure.Figure` instance
"""
events = [
'resize_event',
'draw_event',
'key_press_event',
'key_release_event',
'button_press_event',
'button_release_event',
'scroll_event',
'motion_notify_event',
'pick_event',
'idle_event',
'figure_enter_event',
'figure_leave_event',
'axes_enter_event',
'axes_leave_event',
'close_event'
]
supports_blit = True
fixed_dpi = None
filetypes = _default_filetypes
if _has_pil:
# JPEG support
register_backend('jpg', 'matplotlib.backends.backend_agg',
'Joint Photographic Experts Group')
register_backend('jpeg', 'matplotlib.backends.backend_agg',
'Joint Photographic Experts Group')
# TIFF support
register_backend('tif', 'matplotlib.backends.backend_agg',
'Tagged Image File Format')
register_backend('tiff', 'matplotlib.backends.backend_agg',
'Tagged Image File Format')
def __init__(self, figure):
figure.set_canvas(self)
self.figure = figure
# a dictionary from event name to a dictionary that maps cid->func
self.callbacks = cbook.CallbackRegistry()
self.widgetlock = widgets.LockDraw()
self._button = None # the button pressed
self._key = None # the key pressed
self._lastx, self._lasty = None, None
self.button_pick_id = self.mpl_connect('button_press_event', self.pick)
self.scroll_pick_id = self.mpl_connect('scroll_event', self.pick)
self.mouse_grabber = None # the axes currently grabbing mouse
self.toolbar = None # NavigationToolbar2 will set me
self._is_saving = False
if False:
## highlight the artists that are hit
self.mpl_connect('motion_notify_event', self.onHilite)
## delete the artists that are clicked on
#self.mpl_disconnect(self.button_pick_id)
#self.mpl_connect('button_press_event',self.onRemove)
def is_saving(self):
"""
Returns `True` when the renderer is in the process of saving
to a file, rather than rendering for an on-screen buffer.
"""
return self._is_saving
def onRemove(self, ev):
"""
Mouse event processor which removes the top artist
under the cursor. Connect this to the 'mouse_press_event'
using::
canvas.mpl_connect('mouse_press_event',canvas.onRemove)
"""
def sort_artists(artists):
# This depends on stable sort and artists returned
# from get_children in z order.
L = [(h.zorder, h) for h in artists]
L.sort()
return [h for zorder, h in L]
# Find the top artist under the cursor
under = sort_artists(self.figure.hitlist(ev))
h = None
if under:
h = under[-1]
# Try deleting that artist, or its parent if you
# can't delete the artist
while h:
if h.remove():
self.draw_idle()
break
parent = None
for p in under:
if h in p.get_children():
parent = p
break
h = parent
def onHilite(self, ev):
"""
Mouse event processor which highlights the artists
under the cursor. Connect this to the 'motion_notify_event'
using::
canvas.mpl_connect('motion_notify_event',canvas.onHilite)
"""
if not hasattr(self, '_active'):
self._active = dict()
under = self.figure.hitlist(ev)
enter = [a for a in under if a not in self._active]
leave = [a for a in self._active if a not in under]
#print "within:"," ".join([str(x) for x in under])
#print "entering:",[str(a) for a in enter]
#print "leaving:",[str(a) for a in leave]
# On leave restore the captured colour
for a in leave:
if hasattr(a, 'get_color'):
a.set_color(self._active[a])
elif hasattr(a, 'get_edgecolor'):
a.set_edgecolor(self._active[a][0])
a.set_facecolor(self._active[a][1])
del self._active[a]
# On enter, capture the color and repaint the artist
# with the highlight colour. Capturing colour has to
# be done first in case the parent recolouring affects
# the child.
for a in enter:
if hasattr(a, 'get_color'):
self._active[a] = a.get_color()
elif hasattr(a, 'get_edgecolor'):
self._active[a] = (a.get_edgecolor(), a.get_facecolor())
else:
self._active[a] = None
for a in enter:
if hasattr(a, 'get_color'):
a.set_color('red')
elif hasattr(a, 'get_edgecolor'):
a.set_edgecolor('red')
a.set_facecolor('lightblue')
else:
self._active[a] = None
self.draw_idle()
def pick(self, mouseevent):
if not self.widgetlock.locked():
self.figure.pick(mouseevent)
def blit(self, bbox=None):
"""
blit the canvas in bbox (default entire canvas)
"""
pass
def resize(self, w, h):
"""
set the canvas size in pixels
"""
pass
def draw_event(self, renderer):
"""
This method will be call all functions connected to the
'draw_event' with a :class:`DrawEvent`
"""
s = 'draw_event'
event = DrawEvent(s, self, renderer)
self.callbacks.process(s, event)
def resize_event(self):
"""
This method will be call all functions connected to the
'resize_event' with a :class:`ResizeEvent`
"""
s = 'resize_event'
event = ResizeEvent(s, self)
self.callbacks.process(s, event)
def close_event(self, guiEvent=None):
"""
This method will be called by all functions connected to the
'close_event' with a :class:`CloseEvent`
"""
s = 'close_event'
try:
event = CloseEvent(s, self, guiEvent=guiEvent)
self.callbacks.process(s, event)
except (TypeError, AttributeError):
pass
# Suppress the TypeError when the python session is being killed.
# It may be that a better solution would be a mechanism to
# disconnect all callbacks upon shutdown.
# AttributeError occurs on OSX with qt4agg upon exiting
# with an open window; 'callbacks' attribute no longer exists.
def key_press_event(self, key, guiEvent=None):
"""
This method will be call all functions connected to the
'key_press_event' with a :class:`KeyEvent`
"""
self._key = key
s = 'key_press_event'
event = KeyEvent(
s, self, key, self._lastx, self._lasty, guiEvent=guiEvent)
self.callbacks.process(s, event)
def key_release_event(self, key, guiEvent=None):
"""
This method will be call all functions connected to the
'key_release_event' with a :class:`KeyEvent`
"""
s = 'key_release_event'
event = KeyEvent(
s, self, key, self._lastx, self._lasty, guiEvent=guiEvent)
self.callbacks.process(s, event)
self._key = None
def pick_event(self, mouseevent, artist, **kwargs):
"""
This method will be called by artists who are picked and will
fire off :class:`PickEvent` callbacks registered listeners
"""
s = 'pick_event'
event = PickEvent(s, self, mouseevent, artist, **kwargs)
self.callbacks.process(s, event)
def scroll_event(self, x, y, step, guiEvent=None):
"""
Backend derived classes should call this function on any
scroll wheel event. x,y are the canvas coords: 0,0 is lower,
left. button and key are as defined in MouseEvent.
This method will be call all functions connected to the
'scroll_event' with a :class:`MouseEvent` instance.
"""
if step >= 0:
self._button = 'up'
else:
self._button = 'down'
s = 'scroll_event'
mouseevent = MouseEvent(s, self, x, y, self._button, self._key,
step=step, guiEvent=guiEvent)
self.callbacks.process(s, mouseevent)
def button_press_event(self, x, y, button, dblclick=False, guiEvent=None):
"""
Backend derived classes should call this function on any mouse
button press. x,y are the canvas coords: 0,0 is lower, left.
button and key are as defined in :class:`MouseEvent`.
This method will be call all functions connected to the
'button_press_event' with a :class:`MouseEvent` instance.
"""
self._button = button
s = 'button_press_event'
mouseevent = MouseEvent(s, self, x, y, button, self._key,
dblclick=dblclick, guiEvent=guiEvent)
self.callbacks.process(s, mouseevent)
def button_release_event(self, x, y, button, guiEvent=None):
"""
Backend derived classes should call this function on any mouse
button release.
*x*
the canvas coordinates where 0=left
*y*
the canvas coordinates where 0=bottom
*guiEvent*
the native UI event that generated the mpl event
This method will be call all functions connected to the
'button_release_event' with a :class:`MouseEvent` instance.
"""
s = 'button_release_event'
event = MouseEvent(s, self, x, y, button, self._key, guiEvent=guiEvent)
self.callbacks.process(s, event)
self._button = None
def motion_notify_event(self, x, y, guiEvent=None):
"""
Backend derived classes should call this function on any
motion-notify-event.
*x*
the canvas coordinates where 0=left
*y*
the canvas coordinates where 0=bottom
*guiEvent*
the native UI event that generated the mpl event
This method will be call all functions connected to the
'motion_notify_event' with a :class:`MouseEvent` instance.
"""
self._lastx, self._lasty = x, y
s = 'motion_notify_event'
event = MouseEvent(s, self, x, y, self._button, self._key,
guiEvent=guiEvent)
self.callbacks.process(s, event)
def leave_notify_event(self, guiEvent=None):
"""
Backend derived classes should call this function when leaving
canvas
*guiEvent*
the native UI event that generated the mpl event
"""
self.callbacks.process('figure_leave_event', LocationEvent.lastevent)
LocationEvent.lastevent = None
self._lastx, self._lasty = None, None
def enter_notify_event(self, guiEvent=None, xy=None):
"""
Backend derived classes should call this function when entering
canvas
*guiEvent*
the native UI event that generated the mpl event
*xy*
the coordinate location of the pointer when the canvas is
entered
"""
if xy is not None:
x, y = xy
self._lastx, self._lasty = x, y
event = Event('figure_enter_event', self, guiEvent)
self.callbacks.process('figure_enter_event', event)
def idle_event(self, guiEvent=None):
"""Called when GUI is idle."""
s = 'idle_event'
event = IdleEvent(s, self, guiEvent=guiEvent)
self.callbacks.process(s, event)
def grab_mouse(self, ax):
"""
Set the child axes which are currently grabbing the mouse events.
Usually called by the widgets themselves.
It is an error to call this if the mouse is already grabbed by
another axes.
"""
if self.mouse_grabber not in (None, ax):
raise RuntimeError('two different attempted to grab mouse input')
self.mouse_grabber = ax
def release_mouse(self, ax):
"""
Release the mouse grab held by the axes, ax.
Usually called by the widgets.
It is ok to call this even if you ax doesn't have the mouse
grab currently.
"""
if self.mouse_grabber is ax:
self.mouse_grabber = None
def draw(self, *args, **kwargs):
"""
Render the :class:`~matplotlib.figure.Figure`
"""
pass
def draw_idle(self, *args, **kwargs):
"""
:meth:`draw` only if idle; defaults to draw but backends can overrride
"""
self.draw(*args, **kwargs)
def draw_cursor(self, event):
"""
Draw a cursor in the event.axes if inaxes is not None. Use
native GUI drawing for efficiency if possible
"""
pass
def get_width_height(self):
"""
Return the figure width and height in points or pixels
(depending on the backend), truncated to integers
"""
return int(self.figure.bbox.width), int(self.figure.bbox.height)
@classmethod
def get_supported_filetypes(cls):
"""Return dict of savefig file formats supported by this backend"""
return cls.filetypes
@classmethod
def get_supported_filetypes_grouped(cls):
"""Return a dict of savefig file formats supported by this backend,
where the keys are a file type name, such as 'Joint Photographic
Experts Group', and the values are a list of filename extensions used
for that filetype, such as ['jpg', 'jpeg']."""
groupings = {}
for ext, name in six.iteritems(cls.filetypes):
groupings.setdefault(name, []).append(ext)
groupings[name].sort()
return groupings
def _get_output_canvas(self, format):
"""Return a canvas that is suitable for saving figures to a specified
file format. If necessary, this function will switch to a registered
backend that supports the format.
"""
method_name = 'print_%s' % format
# check if this canvas supports the requested format
if hasattr(self, method_name):
return self
# check if there is a default canvas for the requested format
canvas_class = get_registered_canvas_class(format)
if canvas_class:
return self.switch_backends(canvas_class)
# else report error for unsupported format
formats = sorted(self.get_supported_filetypes())
raise ValueError('Format "%s" is not supported.\n'
'Supported formats: '
'%s.' % (format, ', '.join(formats)))
def print_figure(self, filename, dpi=None, facecolor='w', edgecolor='w',
orientation='portrait', format=None, **kwargs):
"""
Render the figure to hardcopy. Set the figure patch face and edge
colors. This is useful because some of the GUIs have a gray figure
face color background and you'll probably want to override this on
hardcopy.
Arguments are:
*filename*
can also be a file object on image backends
*orientation*
only currently applies to PostScript printing.
*dpi*
the dots per inch to save the figure in; if None, use savefig.dpi
*facecolor*
the facecolor of the figure
*edgecolor*
the edgecolor of the figure
*orientation*
landscape' | 'portrait' (not supported on all backends)
*format*
when set, forcibly set the file format to save to
*bbox_inches*
Bbox in inches. Only the given portion of the figure is
saved. If 'tight', try to figure out the tight bbox of
the figure. If None, use savefig.bbox
*pad_inches*
Amount of padding around the figure when bbox_inches is
'tight'. If None, use savefig.pad_inches
*bbox_extra_artists*
A list of extra artists that will be considered when the
tight bbox is calculated.
"""
if format is None:
# get format from filename, or from backend's default filetype
if cbook.is_string_like(filename):
format = os.path.splitext(filename)[1][1:]
if format is None or format == '':
format = self.get_default_filetype()
if cbook.is_string_like(filename):
filename = filename.rstrip('.') + '.' + format
format = format.lower()
# get canvas object and print method for format
canvas = self._get_output_canvas(format)
print_method = getattr(canvas, 'print_%s' % format)
if dpi is None:
dpi = rcParams['savefig.dpi']
origDPI = self.figure.dpi
origfacecolor = self.figure.get_facecolor()
origedgecolor = self.figure.get_edgecolor()
self.figure.dpi = dpi
self.figure.set_facecolor(facecolor)
self.figure.set_edgecolor(edgecolor)
bbox_inches = kwargs.pop("bbox_inches", None)
if bbox_inches is None:
bbox_inches = rcParams['savefig.bbox']
if bbox_inches:
# call adjust_bbox to save only the given area
if bbox_inches == "tight":
# when bbox_inches == "tight", it saves the figure
# twice. The first save command is just to estimate
# the bounding box of the figure. A stringIO object is
# used as a temporary file object, but it causes a
# problem for some backends (ps backend with
# usetex=True) if they expect a filename, not a
# file-like object. As I think it is best to change
# the backend to support file-like object, i'm going
# to leave it as it is. However, a better solution
# than stringIO seems to be needed. -JJL
#result = getattr(self, method_name)
result = print_method(
io.BytesIO(),
dpi=dpi,
facecolor=facecolor,
edgecolor=edgecolor,
orientation=orientation,
dryrun=True,
**kwargs)
renderer = self.figure._cachedRenderer
bbox_inches = self.figure.get_tightbbox(renderer)
bbox_artists = kwargs.pop("bbox_extra_artists", None)
if bbox_artists is None:
bbox_artists = self.figure.get_default_bbox_extra_artists()
bbox_filtered = []
for a in bbox_artists:
bbox = a.get_window_extent(renderer)
if a.get_clip_on():
clip_box = a.get_clip_box()
if clip_box is not None:
bbox = Bbox.intersection(bbox, clip_box)
clip_path = a.get_clip_path()
if clip_path is not None and bbox is not None:
clip_path = clip_path.get_fully_transformed_path()
bbox = Bbox.intersection(bbox,
clip_path.get_extents())
if bbox is not None and (bbox.width != 0 or
bbox.height != 0):
bbox_filtered.append(bbox)
if bbox_filtered:
_bbox = Bbox.union(bbox_filtered)
trans = Affine2D().scale(1.0 / self.figure.dpi)
bbox_extra = TransformedBbox(_bbox, trans)
bbox_inches = Bbox.union([bbox_inches, bbox_extra])
pad = kwargs.pop("pad_inches", None)
if pad is None:
pad = rcParams['savefig.pad_inches']
bbox_inches = bbox_inches.padded(pad)
restore_bbox = tight_bbox.adjust_bbox(self.figure, bbox_inches,
canvas.fixed_dpi)
_bbox_inches_restore = (bbox_inches, restore_bbox)
else:
_bbox_inches_restore = None
self._is_saving = True
try:
#result = getattr(self, method_name)(
result = print_method(
filename,
dpi=dpi,
facecolor=facecolor,
edgecolor=edgecolor,
orientation=orientation,
bbox_inches_restore=_bbox_inches_restore,
**kwargs)
finally:
if bbox_inches and restore_bbox:
restore_bbox()
self.figure.dpi = origDPI
self.figure.set_facecolor(origfacecolor)
self.figure.set_edgecolor(origedgecolor)
self.figure.set_canvas(self)
self._is_saving = False
#self.figure.canvas.draw() ## seems superfluous
return result
@classmethod
def get_default_filetype(cls):
"""
Get the default savefig file format as specified in rcParam
``savefig.format``. Returned string excludes period. Overridden
in backends that only support a single file type.
"""
return rcParams['savefig.format']
def get_window_title(self):
"""
Get the title text of the window containing the figure.
Return None if there is no window (e.g., a PS backend).
"""
if hasattr(self, "manager"):
return self.manager.get_window_title()
def set_window_title(self, title):
"""
Set the title text of the window containing the figure. Note that
this has no effect if there is no window (e.g., a PS backend).
"""
if hasattr(self, "manager"):
self.manager.set_window_title(title)
def get_default_filename(self):
"""
Return a string, which includes extension, suitable for use as
a default filename.
"""
default_filename = self.get_window_title() or 'image'
default_filename = default_filename.lower().replace(' ', '_')
return default_filename + '.' + self.get_default_filetype()
def switch_backends(self, FigureCanvasClass):
"""
Instantiate an instance of FigureCanvasClass
This is used for backend switching, e.g., to instantiate a
FigureCanvasPS from a FigureCanvasGTK. Note, deep copying is
not done, so any changes to one of the instances (e.g., setting
figure size or line props), will be reflected in the other
"""
newCanvas = FigureCanvasClass(self.figure)
newCanvas._is_saving = self._is_saving
return newCanvas
def mpl_connect(self, s, func):
"""
Connect event with string *s* to *func*. The signature of *func* is::
def func(event)
where event is a :class:`matplotlib.backend_bases.Event`. The
following events are recognized
- 'button_press_event'
- 'button_release_event'
- 'draw_event'
- 'key_press_event'
- 'key_release_event'
- 'motion_notify_event'
- 'pick_event'
- 'resize_event'
- 'scroll_event'
- 'figure_enter_event',
- 'figure_leave_event',
- 'axes_enter_event',
- 'axes_leave_event'
- 'close_event'
For the location events (button and key press/release), if the
mouse is over the axes, the variable ``event.inaxes`` will be
set to the :class:`~matplotlib.axes.Axes` the event occurs is
over, and additionally, the variables ``event.xdata`` and
``event.ydata`` will be defined. This is the mouse location
in data coords. See
:class:`~matplotlib.backend_bases.KeyEvent` and
:class:`~matplotlib.backend_bases.MouseEvent` for more info.
Return value is a connection id that can be used with
:meth:`~matplotlib.backend_bases.Event.mpl_disconnect`.
Example usage::
def on_press(event):
print('you pressed', event.button, event.xdata, event.ydata)
cid = canvas.mpl_connect('button_press_event', on_press)
"""
return self.callbacks.connect(s, func)
def mpl_disconnect(self, cid):
"""
Disconnect callback id cid
Example usage::
cid = canvas.mpl_connect('button_press_event', on_press)
#...later
canvas.mpl_disconnect(cid)
"""
return self.callbacks.disconnect(cid)
def new_timer(self, *args, **kwargs):
"""
Creates a new backend-specific subclass of
:class:`backend_bases.Timer`. This is useful for getting periodic
events through the backend's native event loop. Implemented only for
backends with GUIs.
optional arguments:
*interval*
Timer interval in milliseconds
*callbacks*
Sequence of (func, args, kwargs) where func(*args, **kwargs) will
be executed by the timer every *interval*.
"""
return TimerBase(*args, **kwargs)
def flush_events(self):
"""
Flush the GUI events for the figure. Implemented only for
backends with GUIs.
"""
raise NotImplementedError
def start_event_loop(self, timeout):
"""
Start an event loop. This is used to start a blocking event
loop so that interactive functions, such as ginput and
waitforbuttonpress, can wait for events. This should not be
confused with the main GUI event loop, which is always running
and has nothing to do with this.
This is implemented only for backends with GUIs.
"""
raise NotImplementedError
def stop_event_loop(self):
"""
Stop an event loop. This is used to stop a blocking event
loop so that interactive functions, such as ginput and
waitforbuttonpress, can wait for events.
This is implemented only for backends with GUIs.
"""
raise NotImplementedError
def start_event_loop_default(self, timeout=0):
"""
Start an event loop. This is used to start a blocking event
loop so that interactive functions, such as ginput and
waitforbuttonpress, can wait for events. This should not be
confused with the main GUI event loop, which is always running
and has nothing to do with this.
This function provides default event loop functionality based
on time.sleep that is meant to be used until event loop
functions for each of the GUI backends can be written. As
such, it throws a deprecated warning.
Call signature::
start_event_loop_default(self,timeout=0)
This call blocks until a callback function triggers
stop_event_loop() or *timeout* is reached. If *timeout* is
<=0, never timeout.
"""
str = "Using default event loop until function specific"
str += " to this GUI is implemented"
warnings.warn(str, mplDeprecation)
if timeout <= 0:
timeout = np.inf
timestep = 0.01
counter = 0
self._looping = True
while self._looping and counter * timestep < timeout:
self.flush_events()
time.sleep(timestep)
counter += 1
def stop_event_loop_default(self):
"""
Stop an event loop. This is used to stop a blocking event
loop so that interactive functions, such as ginput and
waitforbuttonpress, can wait for events.
Call signature::
stop_event_loop_default(self)
"""
self._looping = False
def key_press_handler(event, canvas, toolbar=None):
"""
Implement the default mpl key bindings for the canvas and toolbar
described at :ref:`key-event-handling`
*event*
a :class:`KeyEvent` instance
*canvas*
a :class:`FigureCanvasBase` instance
*toolbar*
a :class:`NavigationToolbar2` instance
"""
# these bindings happen whether you are over an axes or not
if event.key is None:
return
# Load key-mappings from your matplotlibrc file.
fullscreen_keys = rcParams['keymap.fullscreen']
home_keys = rcParams['keymap.home']
back_keys = rcParams['keymap.back']
forward_keys = rcParams['keymap.forward']
pan_keys = rcParams['keymap.pan']
zoom_keys = rcParams['keymap.zoom']
save_keys = rcParams['keymap.save']
quit_keys = rcParams['keymap.quit']
grid_keys = rcParams['keymap.grid']
toggle_yscale_keys = rcParams['keymap.yscale']
toggle_xscale_keys = rcParams['keymap.xscale']
all = rcParams['keymap.all_axes']
# toggle fullscreen mode (default key 'f')
if event.key in fullscreen_keys:
canvas.manager.full_screen_toggle()
# quit the figure (defaut key 'ctrl+w')
if event.key in quit_keys:
Gcf.destroy_fig(canvas.figure)
if toolbar is not None:
# home or reset mnemonic (default key 'h', 'home' and 'r')
if event.key in home_keys:
toolbar.home()
# forward / backward keys to enable left handed quick navigation
# (default key for backward: 'left', 'backspace' and 'c')
elif event.key in back_keys:
toolbar.back()
# (default key for forward: 'right' and 'v')
elif event.key in forward_keys:
toolbar.forward()
# pan mnemonic (default key 'p')
elif event.key in pan_keys:
toolbar.pan()
toolbar._set_cursor(event)
# zoom mnemonic (default key 'o')
elif event.key in zoom_keys:
toolbar.zoom()
toolbar._set_cursor(event)
# saving current figure (default key 's')
elif event.key in save_keys:
toolbar.save_figure()
if event.inaxes is None:
return
# these bindings require the mouse to be over an axes to trigger
# switching on/off a grid in current axes (default key 'g')
if event.key in grid_keys:
event.inaxes.grid()
canvas.draw()
# toggle scaling of y-axes between 'log and 'linear' (default key 'l')
elif event.key in toggle_yscale_keys:
ax = event.inaxes
scale = ax.get_yscale()
if scale == 'log':
ax.set_yscale('linear')
ax.figure.canvas.draw()
elif scale == 'linear':
ax.set_yscale('log')
ax.figure.canvas.draw()
# toggle scaling of x-axes between 'log and 'linear' (default key 'k')
elif event.key in toggle_xscale_keys:
ax = event.inaxes
scalex = ax.get_xscale()
if scalex == 'log':
ax.set_xscale('linear')
ax.figure.canvas.draw()
elif scalex == 'linear':
ax.set_xscale('log')
ax.figure.canvas.draw()
elif (event.key.isdigit() and event.key != '0') or event.key in all:
# keys in list 'all' enables all axes (default key 'a'),
# otherwise if key is a number only enable this particular axes
# if it was the axes, where the event was raised
if not (event.key in all):
n = int(event.key) - 1
for i, a in enumerate(canvas.figure.get_axes()):
# consider axes, in which the event was raised
# FIXME: Why only this axes?
if event.x is not None and event.y is not None \
and a.in_axes(event):
if event.key in all:
a.set_navigate(True)
else:
a.set_navigate(i == n)
class NonGuiException(Exception):
pass
class FigureManagerBase(object):
"""
Helper class for pyplot mode, wraps everything up into a neat bundle
Public attibutes:
*canvas*
A :class:`FigureCanvasBase` instance
*num*
The figure number
"""
def __init__(self, canvas, num):
self.canvas = canvas
canvas.manager = self # store a pointer to parent
self.num = num
self.key_press_handler_id = self.canvas.mpl_connect('key_press_event',
self.key_press)
"""
The returned id from connecting the default key handler via
:meth:`FigureCanvasBase.mpl_connnect`.
To disable default key press handling::
manager, canvas = figure.canvas.manager, figure.canvas
canvas.mpl_disconnect(manager.key_press_handler_id)
"""
def show(self):
"""
For GUI backends, show the figure window and redraw.
For non-GUI backends, raise an exception to be caught
by :meth:`~matplotlib.figure.Figure.show`, for an
optional warning.
"""
raise NonGuiException()
def destroy(self):
pass
def full_screen_toggle(self):
pass
def resize(self, w, h):
""""For gui backends, resize the window (in pixels)."""
pass
def key_press(self, event):
"""
Implement the default mpl key bindings defined at
:ref:`key-event-handling`
"""
key_press_handler(event, self.canvas, self.canvas.toolbar)
def show_popup(self, msg):
"""
Display message in a popup -- GUI only
"""
pass
def get_window_title(self):
"""
Get the title text of the window containing the figure.
Return None for non-GUI backends (e.g., a PS backend).
"""
return 'image'
def set_window_title(self, title):
"""
Set the title text of the window containing the figure. Note that
this has no effect for non-GUI backends (e.g., a PS backend).
"""
pass
class Cursors:
# this class is only used as a simple namespace
HAND, POINTER, SELECT_REGION, MOVE = list(range(4))
cursors = Cursors()
class NavigationToolbar2(object):
"""
Base class for the navigation cursor, version 2
backends must implement a canvas that handles connections for
'button_press_event' and 'button_release_event'. See
:meth:`FigureCanvasBase.mpl_connect` for more information
They must also define
:meth:`save_figure`
save the current figure
:meth:`set_cursor`
if you want the pointer icon to change
:meth:`_init_toolbar`
create your toolbar widget
:meth:`draw_rubberband` (optional)
draw the zoom to rect "rubberband" rectangle
:meth:`press` (optional)
whenever a mouse button is pressed, you'll be notified with
the event
:meth:`release` (optional)
whenever a mouse button is released, you'll be notified with
the event
:meth:`dynamic_update` (optional)
dynamically update the window while navigating
:meth:`set_message` (optional)
display message
:meth:`set_history_buttons` (optional)
you can change the history back / forward buttons to
indicate disabled / enabled state.
That's it, we'll do the rest!
"""
# list of toolitems to add to the toolbar, format is:
# (
# text, # the text of the button (often not visible to users)
# tooltip_text, # the tooltip shown on hover (where possible)
# image_file, # name of the image for the button (without the extension)
# name_of_method, # name of the method in NavigationToolbar2 to call
# )
toolitems = (
('Home', 'Reset original view', 'home', 'home'),
('Back', 'Back to previous view', 'back', 'back'),
('Forward', 'Forward to next view', 'forward', 'forward'),
(None, None, None, None),
('Pan', 'Pan axes with left mouse, zoom with right', 'move', 'pan'),
('Zoom', 'Zoom to rectangle', 'zoom_to_rect', 'zoom'),
(None, None, None, None),
('Subplots', 'Configure subplots', 'subplots', 'configure_subplots'),
('Save', 'Save the figure', 'filesave', 'save_figure'),
)
def __init__(self, canvas):
self.canvas = canvas
canvas.toolbar = self
# a dict from axes index to a list of view limits
self._views = cbook.Stack()
self._positions = cbook.Stack() # stack of subplot positions
self._xypress = None # the location and axis info at the time
# of the press
self._idPress = None
self._idRelease = None
self._active = None
self._lastCursor = None
self._init_toolbar()
self._idDrag = self.canvas.mpl_connect(
'motion_notify_event', self.mouse_move)
self._ids_zoom = []
self._zoom_mode = None
self._button_pressed = None # determined by the button pressed
# at start
self.mode = '' # a mode string for the status bar
self.set_history_buttons()
def set_message(self, s):
"""Display a message on toolbar or in status bar"""
pass
def back(self, *args):
"""move back up the view lim stack"""
self._views.back()
self._positions.back()
self.set_history_buttons()
self._update_view()
def dynamic_update(self):
pass
def draw_rubberband(self, event, x0, y0, x1, y1):
"""Draw a rectangle rubberband to indicate zoom limits"""
pass
def forward(self, *args):
"""Move forward in the view lim stack"""
self._views.forward()
self._positions.forward()
self.set_history_buttons()
self._update_view()
def home(self, *args):
"""Restore the original view"""
self._views.home()
self._positions.home()
self.set_history_buttons()
self._update_view()
def _init_toolbar(self):
"""
This is where you actually build the GUI widgets (called by
__init__). The icons ``home.xpm``, ``back.xpm``, ``forward.xpm``,
``hand.xpm``, ``zoom_to_rect.xpm`` and ``filesave.xpm`` are standard
across backends (there are ppm versions in CVS also).
You just need to set the callbacks
home : self.home
back : self.back
forward : self.forward
hand : self.pan
zoom_to_rect : self.zoom
filesave : self.save_figure
You only need to define the last one - the others are in the base
class implementation.
"""
raise NotImplementedError
def _set_cursor(self, event):
if not event.inaxes or not self._active:
if self._lastCursor != cursors.POINTER:
self.set_cursor(cursors.POINTER)
self._lastCursor = cursors.POINTER
else:
if self._active == 'ZOOM':
if self._lastCursor != cursors.SELECT_REGION:
self.set_cursor(cursors.SELECT_REGION)
self._lastCursor = cursors.SELECT_REGION
elif (self._active == 'PAN' and
self._lastCursor != cursors.MOVE):
self.set_cursor(cursors.MOVE)
self._lastCursor = cursors.MOVE
def mouse_move(self, event):
self._set_cursor(event)
if event.inaxes and event.inaxes.get_navigate():
try:
s = event.inaxes.format_coord(event.xdata, event.ydata)
except (ValueError, OverflowError):
pass
else:
if len(self.mode):
self.set_message('%s, %s' % (self.mode, s))
else:
self.set_message(s)
else:
self.set_message(self.mode)
def pan(self, *args):
"""Activate the pan/zoom tool. pan with left button, zoom with right"""
# set the pointer icon and button press funcs to the
# appropriate callbacks
if self._active == 'PAN':
self._active = None
else:
self._active = 'PAN'
if self._idPress is not None:
self._idPress = self.canvas.mpl_disconnect(self._idPress)
self.mode = ''
if self._idRelease is not None:
self._idRelease = self.canvas.mpl_disconnect(self._idRelease)
self.mode = ''
if self._active:
self._idPress = self.canvas.mpl_connect(
'button_press_event', self.press_pan)
self._idRelease = self.canvas.mpl_connect(
'button_release_event', self.release_pan)
self.mode = 'pan/zoom'
self.canvas.widgetlock(self)
else:
self.canvas.widgetlock.release(self)
for a in self.canvas.figure.get_axes():
a.set_navigate_mode(self._active)
self.set_message(self.mode)
def press(self, event):
"""Called whenver a mouse button is pressed."""
pass
def press_pan(self, event):
"""the press mouse button in pan/zoom mode callback"""
if event.button == 1:
self._button_pressed = 1
elif event.button == 3:
self._button_pressed = 3
else:
self._button_pressed = None
return
x, y = event.x, event.y
# push the current view to define home if stack is empty
if self._views.empty():
self.push_current()
self._xypress = []
for i, a in enumerate(self.canvas.figure.get_axes()):
if (x is not None and y is not None and a.in_axes(event) and
a.get_navigate() and a.can_pan()):
a.start_pan(x, y, event.button)
self._xypress.append((a, i))
self.canvas.mpl_disconnect(self._idDrag)
self._idDrag = self.canvas.mpl_connect('motion_notify_event',
self.drag_pan)
self.press(event)
def press_zoom(self, event):
"""the press mouse button in zoom to rect mode callback"""
# If we're already in the middle of a zoom, pressing another
# button works to "cancel"
if self._ids_zoom != []:
for zoom_id in self._ids_zoom:
self.canvas.mpl_disconnect(zoom_id)
self.release(event)
self.draw()
self._xypress = None
self._button_pressed = None
self._ids_zoom = []
return
if event.button == 1:
self._button_pressed = 1
elif event.button == 3:
self._button_pressed = 3
else:
self._button_pressed = None
return
x, y = event.x, event.y
# push the current view to define home if stack is empty
if self._views.empty():
self.push_current()
self._xypress = []
for i, a in enumerate(self.canvas.figure.get_axes()):
if (x is not None and y is not None and a.in_axes(event) and
a.get_navigate() and a.can_zoom()):
self._xypress.append((x, y, a, i, a.viewLim.frozen(),
a.transData.frozen()))
id1 = self.canvas.mpl_connect('motion_notify_event', self.drag_zoom)
id2 = self.canvas.mpl_connect('key_press_event',
self._switch_on_zoom_mode)
id3 = self.canvas.mpl_connect('key_release_event',
self._switch_off_zoom_mode)
self._ids_zoom = id1, id2, id3
self._zoom_mode = event.key
self.press(event)
def _switch_on_zoom_mode(self, event):
self._zoom_mode = event.key
self.mouse_move(event)
def _switch_off_zoom_mode(self, event):
self._zoom_mode = None
self.mouse_move(event)
def push_current(self):
"""push the current view limits and position onto the stack"""
lims = []
pos = []
for a in self.canvas.figure.get_axes():
xmin, xmax = a.get_xlim()
ymin, ymax = a.get_ylim()
lims.append((xmin, xmax, ymin, ymax))
# Store both the original and modified positions
pos.append((
a.get_position(True).frozen(),
a.get_position().frozen()))
self._views.push(lims)
self._positions.push(pos)
self.set_history_buttons()
def release(self, event):
"""this will be called whenever mouse button is released"""
pass
def release_pan(self, event):
"""the release mouse button callback in pan/zoom mode"""
if self._button_pressed is None:
return
self.canvas.mpl_disconnect(self._idDrag)
self._idDrag = self.canvas.mpl_connect(
'motion_notify_event', self.mouse_move)
for a, ind in self._xypress:
a.end_pan()
if not self._xypress:
return
self._xypress = []
self._button_pressed = None
self.push_current()
self.release(event)
self.draw()
def drag_pan(self, event):
"""the drag callback in pan/zoom mode"""
for a, ind in self._xypress:
#safer to use the recorded button at the press than current button:
#multiple button can get pressed during motion...
a.drag_pan(self._button_pressed, event.key, event.x, event.y)
self.dynamic_update()
def drag_zoom(self, event):
"""the drag callback in zoom mode"""
if self._xypress:
x, y = event.x, event.y
lastx, lasty, a, ind, lim, trans = self._xypress[0]
# adjust x, last, y, last
x1, y1, x2, y2 = a.bbox.extents
x, lastx = max(min(x, lastx), x1), min(max(x, lastx), x2)
y, lasty = max(min(y, lasty), y1), min(max(y, lasty), y2)
if self._zoom_mode == "x":
x1, y1, x2, y2 = a.bbox.extents
y, lasty = y1, y2
elif self._zoom_mode == "y":
x1, y1, x2, y2 = a.bbox.extents
x, lastx = x1, x2
self.draw_rubberband(event, x, y, lastx, lasty)
def release_zoom(self, event):
"""the release mouse button callback in zoom to rect mode"""
for zoom_id in self._ids_zoom:
self.canvas.mpl_disconnect(zoom_id)
self._ids_zoom = []
if not self._xypress:
return
last_a = []
for cur_xypress in self._xypress:
x, y = event.x, event.y
lastx, lasty, a, ind, lim, trans = cur_xypress
# ignore singular clicks - 5 pixels is a threshold
if abs(x - lastx) < 5 or abs(y - lasty) < 5:
self._xypress = None
self.release(event)
self.draw()
return
x0, y0, x1, y1 = lim.extents
# zoom to rect
inverse = a.transData.inverted()
lastx, lasty = inverse.transform_point((lastx, lasty))
x, y = inverse.transform_point((x, y))
Xmin, Xmax = a.get_xlim()
Ymin, Ymax = a.get_ylim()
# detect twinx,y axes and avoid double zooming
twinx, twiny = False, False
if last_a:
for la in last_a:
if a.get_shared_x_axes().joined(a, la):
twinx = True
if a.get_shared_y_axes().joined(a, la):
twiny = True
last_a.append(a)
if twinx:
x0, x1 = Xmin, Xmax
else:
if Xmin < Xmax:
if x < lastx:
x0, x1 = x, lastx
else:
x0, x1 = lastx, x
if x0 < Xmin:
x0 = Xmin
if x1 > Xmax:
x1 = Xmax
else:
if x > lastx:
x0, x1 = x, lastx
else:
x0, x1 = lastx, x
if x0 > Xmin:
x0 = Xmin
if x1 < Xmax:
x1 = Xmax
if twiny:
y0, y1 = Ymin, Ymax
else:
if Ymin < Ymax:
if y < lasty:
y0, y1 = y, lasty
else:
y0, y1 = lasty, y
if y0 < Ymin:
y0 = Ymin
if y1 > Ymax:
y1 = Ymax
else:
if y > lasty:
y0, y1 = y, lasty
else:
y0, y1 = lasty, y
if y0 > Ymin:
y0 = Ymin
if y1 < Ymax:
y1 = Ymax
if self._button_pressed == 1:
if self._zoom_mode == "x":
a.set_xlim((x0, x1))
elif self._zoom_mode == "y":
a.set_ylim((y0, y1))
else:
a.set_xlim((x0, x1))
a.set_ylim((y0, y1))
elif self._button_pressed == 3:
if a.get_xscale() == 'log':
alpha = np.log(Xmax / Xmin) / np.log(x1 / x0)
rx1 = pow(Xmin / x0, alpha) * Xmin
rx2 = pow(Xmax / x0, alpha) * Xmin
else:
alpha = (Xmax - Xmin) / (x1 - x0)
rx1 = alpha * (Xmin - x0) + Xmin
rx2 = alpha * (Xmax - x0) + Xmin
if a.get_yscale() == 'log':
alpha = np.log(Ymax / Ymin) / np.log(y1 / y0)
ry1 = pow(Ymin / y0, alpha) * Ymin
ry2 = pow(Ymax / y0, alpha) * Ymin
else:
alpha = (Ymax - Ymin) / (y1 - y0)
ry1 = alpha * (Ymin - y0) + Ymin
ry2 = alpha * (Ymax - y0) + Ymin
if self._zoom_mode == "x":
a.set_xlim((rx1, rx2))
elif self._zoom_mode == "y":
a.set_ylim((ry1, ry2))
else:
a.set_xlim((rx1, rx2))
a.set_ylim((ry1, ry2))
self.draw()
self._xypress = None
self._button_pressed = None
self._zoom_mode = None
self.push_current()
self.release(event)
def draw(self):
"""Redraw the canvases, update the locators"""
for a in self.canvas.figure.get_axes():
xaxis = getattr(a, 'xaxis', None)
yaxis = getattr(a, 'yaxis', None)
locators = []
if xaxis is not None:
locators.append(xaxis.get_major_locator())
locators.append(xaxis.get_minor_locator())
if yaxis is not None:
locators.append(yaxis.get_major_locator())
locators.append(yaxis.get_minor_locator())
for loc in locators:
loc.refresh()
self.canvas.draw_idle()
def _update_view(self):
"""Update the viewlim and position from the view and
position stack for each axes
"""
lims = self._views()
if lims is None:
return
pos = self._positions()
if pos is None:
return
for i, a in enumerate(self.canvas.figure.get_axes()):
xmin, xmax, ymin, ymax = lims[i]
a.set_xlim((xmin, xmax))
a.set_ylim((ymin, ymax))
# Restore both the original and modified positions
a.set_position(pos[i][0], 'original')
a.set_position(pos[i][1], 'active')
self.canvas.draw_idle()
def save_figure(self, *args):
"""Save the current figure"""
raise NotImplementedError
def set_cursor(self, cursor):
"""
Set the current cursor to one of the :class:`Cursors`
enums values
"""
pass
def update(self):
"""Reset the axes stack"""
self._views.clear()
self._positions.clear()
self.set_history_buttons()
def zoom(self, *args):
"""Activate zoom to rect mode"""
if self._active == 'ZOOM':
self._active = None
else:
self._active = 'ZOOM'
if self._idPress is not None:
self._idPress = self.canvas.mpl_disconnect(self._idPress)
self.mode = ''
if self._idRelease is not None:
self._idRelease = self.canvas.mpl_disconnect(self._idRelease)
self.mode = ''
if self._active:
self._idPress = self.canvas.mpl_connect('button_press_event',
self.press_zoom)
self._idRelease = self.canvas.mpl_connect('button_release_event',
self.release_zoom)
self.mode = 'zoom rect'
self.canvas.widgetlock(self)
else:
self.canvas.widgetlock.release(self)
for a in self.canvas.figure.get_axes():
a.set_navigate_mode(self._active)
self.set_message(self.mode)
def set_history_buttons(self):
"""Enable or disable back/forward button"""
pass
| mit |
costypetrisor/scikit-learn | examples/mixture/plot_gmm_sin.py | 248 | 2747 | """
=================================
Gaussian Mixture Model Sine Curve
=================================
This example highlights the advantages of the Dirichlet Process:
complexity control and dealing with sparse data. The dataset is formed
by 100 points loosely spaced following a noisy sine curve. The fit by
the GMM class, using the expectation-maximization algorithm to fit a
mixture of 10 Gaussian components, finds too-small components and very
little structure. The fits by the Dirichlet process, however, show
that the model can either learn a global structure for the data (small
alpha) or easily interpolate to finding relevant local structure
(large alpha), never falling into the problems shown by the GMM class.
"""
import itertools
import numpy as np
from scipy import linalg
import matplotlib.pyplot as plt
import matplotlib as mpl
from sklearn import mixture
from sklearn.externals.six.moves import xrange
# Number of samples per component
n_samples = 100
# Generate random sample following a sine curve
np.random.seed(0)
X = np.zeros((n_samples, 2))
step = 4 * np.pi / n_samples
for i in xrange(X.shape[0]):
x = i * step - 6
X[i, 0] = x + np.random.normal(0, 0.1)
X[i, 1] = 3 * (np.sin(x) + np.random.normal(0, .2))
color_iter = itertools.cycle(['r', 'g', 'b', 'c', 'm'])
for i, (clf, title) in enumerate([
(mixture.GMM(n_components=10, covariance_type='full', n_iter=100),
"Expectation-maximization"),
(mixture.DPGMM(n_components=10, covariance_type='full', alpha=0.01,
n_iter=100),
"Dirichlet Process,alpha=0.01"),
(mixture.DPGMM(n_components=10, covariance_type='diag', alpha=100.,
n_iter=100),
"Dirichlet Process,alpha=100.")]):
clf.fit(X)
splot = plt.subplot(3, 1, 1 + i)
Y_ = clf.predict(X)
for i, (mean, covar, color) in enumerate(zip(
clf.means_, clf._get_covars(), color_iter)):
v, w = linalg.eigh(covar)
u = w[0] / linalg.norm(w[0])
# as the DP will not use every component it has access to
# unless it needs it, we shouldn't plot the redundant
# components.
if not np.any(Y_ == i):
continue
plt.scatter(X[Y_ == i, 0], X[Y_ == i, 1], .8, color=color)
# Plot an ellipse to show the Gaussian component
angle = np.arctan(u[1] / u[0])
angle = 180 * angle / np.pi # convert to degrees
ell = mpl.patches.Ellipse(mean, v[0], v[1], 180 + angle, color=color)
ell.set_clip_box(splot.bbox)
ell.set_alpha(0.5)
splot.add_artist(ell)
plt.xlim(-6, 4 * np.pi - 6)
plt.ylim(-5, 5)
plt.title(title)
plt.xticks(())
plt.yticks(())
plt.show()
| bsd-3-clause |
cpcloud/ibis | ibis/expr/window.py | 1 | 15482 | """Encapsulation of SQL window clauses."""
import functools
from typing import NamedTuple, Union
import numpy as np
import pandas as pd
import ibis.common.exceptions as com
import ibis.expr.operations as ops
import ibis.expr.types as ir
import ibis.util as util
def _sequence_to_tuple(x):
return tuple(x) if util.is_iterable(x) else x
RowsWithMaxLookback = NamedTuple('RowsWithMaxLookback',
[('rows', Union[int, np.integer]),
('max_lookback', ir.IntervalValue)]
)
def _choose_non_empty_val(first, second):
if isinstance(first, (int, np.integer)) and first:
non_empty_value = first
elif not isinstance(first, (int, np.integer)) and first is not None:
non_empty_value = first
else:
non_empty_value = second
return non_empty_value
def _determine_how(preceding):
offset_type = type(_get_preceding_value(preceding))
if issubclass(offset_type, (int, np.integer)):
how = 'rows'
elif issubclass(offset_type, ir.IntervalScalar):
how = 'range'
else:
raise TypeError(
'Type {} is not supported for row- or range- based trailing '
'window operations'.format(offset_type)
)
return how
@functools.singledispatch
def _get_preceding_value(preceding):
raise TypeError(
"Type {} is not a valid type for 'preceding' "
"parameter".format(type(preceding))
)
@_get_preceding_value.register(tuple)
def _get_preceding_value_tuple(preceding):
start, end = preceding
if start is None:
preceding_value = end
else:
preceding_value = start
return preceding_value
@_get_preceding_value.register(int)
@_get_preceding_value.register(np.integer)
@_get_preceding_value.register(ir.IntervalScalar)
def _get_preceding_value_simple(preceding):
return preceding
@_get_preceding_value.register(RowsWithMaxLookback)
def _get_preceding_value_mlb(preceding):
preceding_value = preceding.rows
if not isinstance(preceding_value, (int, np.integer)):
raise TypeError("'Rows with max look-back' only supports integer "
"row-based indexing.")
return preceding_value
class Window:
"""Class to encapsulate the details of a window frame.
Notes
-----
This class is patterned after SQL window clauses.
Using None for preceding or following currently indicates unbounded. Use 0
for ``CURRENT ROW``.
"""
def __init__(
self,
group_by=None,
order_by=None,
preceding=None,
following=None,
max_lookback=None,
how='rows',
):
if group_by is None:
group_by = []
if order_by is None:
order_by = []
self._group_by = util.promote_list(group_by)
self._order_by = []
for x in util.promote_list(order_by):
if isinstance(x, ir.SortExpr):
pass
elif isinstance(x, ir.Expr):
x = ops.SortKey(x).to_expr()
self._order_by.append(x)
if isinstance(preceding, RowsWithMaxLookback):
# the offset interval is used as the 'preceding' value of a window
# while 'rows' is used to adjust the window created using offset
self.preceding = preceding.max_lookback
self.max_lookback = preceding.rows
else:
self.preceding = _sequence_to_tuple(preceding)
self.max_lookback = max_lookback
self.following = _sequence_to_tuple(following)
self.how = how
self._validate_frame()
def __hash__(self) -> int:
return hash(
(
tuple(gb.op() for gb in self._group_by),
tuple(ob.op() for ob in self._order_by),
self.preceding,
self.following,
self.how,
)
)
def _validate_frame(self):
preceding_tuple = has_preceding = False
following_tuple = has_following = False
if self.preceding is not None:
preceding_tuple = isinstance(self.preceding, tuple)
has_preceding = True
if self.following is not None:
following_tuple = isinstance(self.following, tuple)
has_following = True
if (preceding_tuple and has_following) or (
following_tuple and has_preceding
):
raise com.IbisInputError(
'Can only specify one window side when you want an '
'off-center window'
)
elif preceding_tuple:
start, end = self.preceding
if end is None:
raise com.IbisInputError("preceding end point cannot be None")
if end < 0:
raise com.IbisInputError(
"preceding end point must be non-negative"
)
if start is not None:
if start < 0:
raise com.IbisInputError(
"preceding start point must be non-negative"
)
if start <= end:
raise com.IbisInputError(
"preceding start must be greater than preceding end"
)
elif following_tuple:
start, end = self.following
if start is None:
raise com.IbisInputError(
"following start point cannot be None"
)
if start < 0:
raise com.IbisInputError(
"following start point must be non-negative"
)
if end is not None:
if end < 0:
raise com.IbisInputError(
"following end point must be non-negative"
)
if start >= end:
raise com.IbisInputError(
"following start must be less than following end"
)
else:
if not isinstance(self.preceding, ir.Expr):
if has_preceding and self.preceding < 0:
raise com.IbisInputError(
"'preceding' must be positive, got {}".format(
self.preceding
)
)
if not isinstance(self.following, ir.Expr):
if has_following and self.following < 0:
raise com.IbisInputError(
"'following' must be positive, got {}".format(
self.following
)
)
if self.how not in {'rows', 'range'}:
raise com.IbisInputError(
"'how' must be 'rows' or 'range', got {}".format(self.how)
)
if self.max_lookback is not None:
if not isinstance(
self.preceding, (ir.IntervalValue, pd.Timedelta)):
raise com.IbisInputError(
"'max_lookback' must be specified as an interval "
"or pandas.Timedelta object"
)
def bind(self, table):
# Internal API, ensure that any unresolved expr references (as strings,
# say) are bound to the table being windowed
groups = table._resolve(self._group_by)
sorts = [ops.to_sort_key(table, k) for k in self._order_by]
return self._replace(group_by=groups, order_by=sorts)
def combine(self, window):
if self.how != window.how:
raise com.IbisInputError(
(
"Window types must match. "
"Expecting '{}' Window, got '{}'"
).format(self.how.upper(), window.how.upper())
)
kwds = dict(
preceding=_choose_non_empty_val(self.preceding, window.preceding),
following=_choose_non_empty_val(self.following, window.following),
max_lookback=self.max_lookback or window.max_lookback,
group_by=self._group_by + window._group_by,
order_by=self._order_by + window._order_by,
)
return Window(**kwds)
def group_by(self, expr):
new_groups = self._group_by + util.promote_list(expr)
return self._replace(group_by=new_groups)
def _replace(self, **kwds):
new_kwds = dict(
group_by=kwds.get('group_by', self._group_by),
order_by=kwds.get('order_by', self._order_by),
preceding=kwds.get('preceding', self.preceding),
following=kwds.get('following', self.following),
max_lookback=kwds.get('max_lookback', self.max_lookback),
how=kwds.get('how', self.how),
)
return Window(**new_kwds)
def order_by(self, expr):
new_sorts = self._order_by + util.promote_list(expr)
return self._replace(order_by=new_sorts)
def equals(self, other, cache=None):
if cache is None:
cache = {}
if self is other:
cache[self, other] = True
return True
if not isinstance(other, Window):
cache[self, other] = False
return False
try:
return cache[self, other]
except KeyError:
pass
if len(self._group_by) != len(other._group_by) or not ops.all_equal(
self._group_by, other._group_by, cache=cache
):
cache[self, other] = False
return False
if len(self._order_by) != len(other._order_by) or not ops.all_equal(
self._order_by, other._order_by, cache=cache
):
cache[self, other] = False
return False
equal = ops.all_equal(
self.preceding, other.preceding, cache=cache
) and ops.all_equal(
self.following, other.following, cache=cache
) and ops.all_equal(
self.max_lookback, other.max_lookback, cache=cache
)
cache[self, other] = equal
return equal
def rows_with_max_lookback(rows, max_lookback):
"""Create a bound preceding value for use with trailing window functions"""
return RowsWithMaxLookback(rows, max_lookback)
def window(preceding=None, following=None, group_by=None, order_by=None):
"""Create a window clause for use with window functions.
This ROW window clause aggregates adjacent rows based on differences in row
number.
All window frames / ranges are inclusive.
Parameters
----------
preceding : int, tuple, or None, default None
Specify None for unbounded, 0 to include current row tuple for
off-center window
following : int, tuple, or None, default None
Specify None for unbounded, 0 to include current row tuple for
off-center window
group_by : expressions, default None
Either specify here or with TableExpr.group_by
order_by : expressions, default None
For analytic functions requiring an ordering, specify here, or let Ibis
determine the default ordering (for functions like rank)
Returns
-------
Window
"""
return Window(
preceding=preceding,
following=following,
group_by=group_by,
order_by=order_by,
how='rows',
)
def range_window(preceding=None, following=None, group_by=None, order_by=None):
"""Create a range-based window clause for use with window functions.
This RANGE window clause aggregates rows based upon differences in the
value of the order-by expression.
All window frames / ranges are inclusive.
Parameters
----------
preceding : int, tuple, or None, default None
Specify None for unbounded, 0 to include current row tuple for
off-center window
following : int, tuple, or None, default None
Specify None for unbounded, 0 to include current row tuple for
off-center window
group_by : expressions, default None
Either specify here or with TableExpr.group_by
order_by : expressions, default None
For analytic functions requiring an ordering, specify here, or let Ibis
determine the default ordering (for functions like rank)
Returns
-------
Window
"""
return Window(
preceding=preceding,
following=following,
group_by=group_by,
order_by=order_by,
how='range',
)
def cumulative_window(group_by=None, order_by=None):
"""Create a cumulative window for use with aggregate window functions.
All window frames / ranges are inclusive.
Parameters
----------
group_by : expressions, default None
Either specify here or with TableExpr.group_by
order_by : expressions, default None
For analytic functions requiring an ordering, specify here, or let Ibis
determine the default ordering (for functions like rank)
Returns
-------
Window
"""
return Window(
preceding=None, following=0, group_by=group_by, order_by=order_by
)
def trailing_window(preceding, group_by=None, order_by=None):
"""Create a trailing window for use with aggregate window functions.
Parameters
----------
preceding : int, float or expression of intervals, i.e.
ibis.interval(days=1) + ibis.interval(hours=5)
Int indicates number of trailing rows to include;
0 includes only the current row.
Interval indicates a trailing range window.
group_by : expressions, default None
Either specify here or with TableExpr.group_by
order_by : expressions, default None
For analytic functions requiring an ordering, specify here, or let Ibis
determine the default ordering (for functions like rank)
Returns
-------
Window
"""
how = _determine_how(preceding)
return Window(
preceding=preceding,
following=0,
group_by=group_by,
order_by=order_by,
how=how
)
def trailing_range_window(preceding, order_by, group_by=None):
"""Create a trailing time window for use with aggregate window functions.
Parameters
----------
preceding : float or expression of intervals, i.e.
ibis.interval(days=1) + ibis.interval(hours=5)
order_by : expressions, default None
For analytic functions requiring an ordering, specify here, or let Ibis
determine the default ordering (for functions like rank)
group_by : expressions, default None
Either specify here or with TableExpr.group_by
Returns
-------
Window
"""
return Window(
preceding=preceding,
following=0,
group_by=group_by,
order_by=order_by,
how='range',
)
def propagate_down_window(expr, window):
op = expr.op()
clean_args = []
unchanged = True
for arg in op.args:
if isinstance(arg, ir.Expr) and not isinstance(op, ops.WindowOp):
new_arg = propagate_down_window(arg, window)
if isinstance(new_arg.op(), ops.AnalyticOp):
new_arg = ops.WindowOp(new_arg, window).to_expr()
if arg is not new_arg:
unchanged = False
arg = new_arg
clean_args.append(arg)
if unchanged:
return expr
else:
return type(op)(*clean_args).to_expr()
| apache-2.0 |
econpy/google-ngrams | getngrams.py | 2 | 6725 | #!/usr/bin/env python
# -*- coding: utf-8 -*
from ast import literal_eval
from pandas import DataFrame # http://github.com/pydata/pandas
import re
import requests # http://github.com/kennethreitz/requests
import subprocess
import sys
corpora = dict(eng_us_2012=17, eng_us_2009=5, eng_gb_2012=18, eng_gb_2009=6,
chi_sim_2012=23, chi_sim_2009=11, eng_2012=15, eng_2009=0,
eng_fiction_2012=16, eng_fiction_2009=4, eng_1m_2009=1,
fre_2012=19, fre_2009=7, ger_2012=20, ger_2009=8, heb_2012=24,
heb_2009=9, spa_2012=21, spa_2009=10, rus_2012=25, rus_2009=12,
ita_2012=22)
def getNgrams(query, corpus, startYear, endYear, smoothing, caseInsensitive):
params = dict(content=query, year_start=startYear, year_end=endYear,
corpus=corpora[corpus], smoothing=smoothing,
case_insensitive=caseInsensitive)
if params['case_insensitive'] is False:
params.pop('case_insensitive')
if '?' in params['content']:
params['content'] = params['content'].replace('?', '*')
if '@' in params['content']:
params['content'] = params['content'].replace('@', '=>')
req = requests.get('http://books.google.com/ngrams/graph', params=params)
res = re.findall('var data = (.*?);\\n', req.text)
if res:
data = {qry['ngram']: qry['timeseries']
for qry in literal_eval(res[0])}
df = DataFrame(data)
df.insert(0, 'year', list(range(startYear, endYear + 1)))
else:
df = DataFrame()
return req.url, params['content'], df
def runQuery(argumentString):
arguments = argumentString.split()
query = ' '.join([arg for arg in arguments if not arg.startswith('-')])
if '?' in query:
query = query.replace('?', '*')
if '@' in query:
query = query.replace('@', '=>')
params = [arg for arg in arguments if arg.startswith('-')]
corpus, startYear, endYear, smoothing = 'eng_2012', 1800, 2000, 3
printHelp, caseInsensitive, allData = False, False, False
toSave, toPrint, toPlot = True, True, False
# parsing the query parameters
for param in params:
if '-nosave' in param:
toSave = False
elif '-noprint' in param:
toPrint = False
elif '-plot' in param:
toPlot = True
elif '-corpus' in param:
corpus = param.split('=')[1].strip()
elif '-startYear' in param:
startYear = int(param.split('=')[1])
elif '-endYear' in param:
endYear = int(param.split('=')[1])
elif '-smoothing' in param:
smoothing = int(param.split('=')[1])
elif '-caseInsensitive' in param:
caseInsensitive = True
elif '-alldata' in param:
allData = True
elif '-help' in param:
printHelp = True
else:
print(('Did not recognize the following argument: %s' % param))
if printHelp:
print('See README file.')
else:
if '*' in query and caseInsensitive is True:
caseInsensitive = False
notifyUser = True
warningMessage = "*NOTE: Wildcard and case-insensitive " + \
"searches can't be combined, so the " + \
"case-insensitive option was ignored."
elif '_INF' in query and caseInsensitive is True:
caseInsensitive = False
notifyUser = True
warningMessage = "*NOTE: Inflected form and case-insensitive " + \
"searches can't be combined, so the " + \
"case-insensitive option was ignored."
else:
notifyUser = False
url, urlquery, df = getNgrams(query, corpus, startYear, endYear,
smoothing, caseInsensitive)
if not allData:
if caseInsensitive is True:
for col in df.columns:
if col.count('(All)') == 1:
df[col.replace(' (All)', '')] = df.pop(col)
elif col.count(':chi_') == 1 or corpus.startswith('chi_'):
pass
elif col.count(':ger_') == 1 or corpus.startswith('ger_'):
pass
elif col.count(':heb_') == 1 or corpus.startswith('heb_'):
pass
elif col.count('(All)') == 0 and col != 'year':
if col not in urlquery.split(','):
df.pop(col)
if '_INF' in query:
for col in df.columns:
if '_INF' in col:
df.pop(col)
if '*' in query:
for col in df.columns:
if '*' in col:
df.pop(col)
if toPrint:
print((','.join(df.columns.tolist())))
for row in df.iterrows():
try:
print(('%d,' % int(row[1].values[0]) +
','.join(['%.12f' % s for s in row[1].values[1:]])))
except:
print((','.join([str(s) for s in row[1].values])))
queries = ''.join(urlquery.replace(',', '_').split())
if '*' in queries:
queries = queries.replace('*', 'WILDCARD')
if caseInsensitive is True:
word_case = 'caseInsensitive'
else:
word_case = 'caseSensitive'
filename = '%s-%s-%d-%d-%d-%s.csv' % (queries, corpus, startYear,
endYear, smoothing, word_case)
if toSave:
for col in df.columns:
if '>' in col:
df[col.replace('>', '>')] = df.pop(col)
df.to_csv(filename, index=False)
print(('Data saved to %s' % filename))
if toPlot:
try:
subprocess.call(['python', 'xkcd.py', filename])
except:
if not toSave:
print(('Currently, if you want to create a plot you ' +
'must also save the data. Rerun your query, ' +
'removing the -nosave option.'))
else:
print(('Plotting Failed: %s' % filename))
if notifyUser:
print(warningMessage)
if __name__ == '__main__':
argumentString = ' '.join(sys.argv[1:])
if argumentString == '':
argumentString = eval(input('Enter query (or -help):'))
else:
try:
runQuery(argumentString)
except:
print('An error occurred.')
| mit |
gregreen/legacypipe | py/legacypipe/write_initial_catalog.py | 1 | 3639 | from __future__ import print_function
if __name__ == '__main__':
import matplotlib
matplotlib.use('Agg')
import numpy as np
from common import *
from tractor import *
if __name__ == '__main__':
import optparse
parser = optparse.OptionParser()
parser.add_option('-b', '--brick', type=int, help='Brick ID to run: default %default',
default=377306)
parser.add_option('-s', '--sed-matched', action='store_true', default=False,
help='Run SED-matched filter?')
parser.add_option('--bands', default='grz', help='Bands to retrieve')
parser.add_option('-o', '--output', help='Output filename for catalog',
default='initial-cat.fits')
parser.add_option('--threads', type=int, help='Run multi-threaded')
parser.add_option('-W', type=int, default=3600, help='Target image width (default %default)')
parser.add_option('-H', type=int, default=3600, help='Target image height (default %default)')
if not (('BOSS_PHOTOOBJ' in os.environ) and ('PHOTO_RESOLVE' in os.environ)):
print('''$BOSS_PHOTOOBJ and $PHOTO_RESOLVE not set -- on NERSC, you can do:
export BOSS_PHOTOOBJ=/project/projectdirs/cosmo/data/sdss/pre13/eboss/photoObj.v5b
export PHOTO_RESOLVE=/project/projectdirs/cosmo/data/sdss/pre13/eboss/resolve/2013-07-29
To read SDSS files from the local filesystem rather than downloading them.
''')
opt,args = parser.parse_args()
brickid = opt.brick
bands = opt.bands
if opt.threads and opt.threads > 1:
from astrometry.util.multiproc import multiproc
mp = multiproc(opt.threads)
else:
mp = multiproc()
ps = None
plots = False
decals = Decals()
brick = decals.get_brick(brickid)
print('Chosen brick:')
brick.about()
targetwcs = wcs_for_brick(brick, W=opt.W, H=opt.H)
W,H = targetwcs.get_width(), targetwcs.get_height()
# Read SDSS sources
cat,T = get_sdss_sources(bands, targetwcs)
if opt.sed_matched:
# Read images
tims = decals.tims_touching_wcs(targetwcs, mp, mock_psf=True, bands=bands)
print('Rendering detection maps...')
detmaps, detivs = detection_maps(tims, targetwcs, bands, mp)
SEDs = sed_matched_filters(bands)
Tnew,newcat,nil = run_sed_matched_filters(SEDs, bands, detmaps, detivs,
(T.itx,T.ity), targetwcs)
T = merge_tables([T,Tnew], columns='fillzero')
cat.extend(newcat)
from desi_common import prepare_fits_catalog
TT = T.copy()
for k in ['itx','ity','index']:
TT.delete_column(k)
for col in TT.get_columns():
if not col in ['tx', 'ty', 'blob']:
TT.rename(col, 'sdss_%s' % col)
TT.brickid = np.zeros(len(TT), np.int32) + brickid
TT.objid = np.arange(len(TT)).astype(np.int32)
invvars = None
hdr = None
fs = None
cat.thawAllRecursive()
T2,hdr = prepare_fits_catalog(cat, invvars, TT, hdr, bands, fs)
# Unpack shape columns
T2.shapeExp_r = T2.shapeExp[:,0]
T2.shapeExp_e1 = T2.shapeExp[:,1]
T2.shapeExp_e2 = T2.shapeExp[:,2]
T2.shapeDev_r = T2.shapeExp[:,0]
T2.shapeDev_e1 = T2.shapeExp[:,1]
T2.shapeDev_e2 = T2.shapeExp[:,2]
T2.shapeExp_r_ivar = T2.shapeExp_ivar[:,0]
T2.shapeExp_e1_ivar = T2.shapeExp_ivar[:,1]
T2.shapeExp_e2_ivar = T2.shapeExp_ivar[:,2]
T2.shapeDev_r_ivar = T2.shapeExp_ivar[:,0]
T2.shapeDev_e1_ivar = T2.shapeExp_ivar[:,1]
T2.shapeDev_e2_ivar = T2.shapeExp_ivar[:,2]
T2.writeto(opt.output)
print('Wrote', opt.output)
| gpl-2.0 |
SuLab/scheduled-bots | scheduled_bots/phenotypes/mitodb_bot.py | 1 | 6364 | import argparse
import json
import os
from datetime import datetime
from itertools import groupby
from time import gmtime, strftime, strptime
import pandas as pd
from tqdm import tqdm
from scheduled_bots import PROPS, ITEMS
from wikidataintegrator import wdi_core, wdi_helpers, wdi_login
from wikidataintegrator.ref_handlers import update_retrieved_if_new_multiple_refs
from wikidataintegrator.wdi_helpers import PublicationHelper
from wikidataintegrator.wdi_helpers import try_write
__metadata__ = {
'name': 'MitoBot',
'maintainer': 'GSS',
'tags': ['disease', 'phenotype'],
'properties': [PROPS['symptoms']]
}
try:
from scheduled_bots.local import WDUSER, WDPASS
except ImportError:
if "WDUSER" in os.environ and "WDPASS" in os.environ:
WDUSER = os.environ['WDUSER']
WDPASS = os.environ['WDPASS']
else:
raise ValueError("WDUSER and WDPASS must be specified in local.py or as environment variables")
class MitoBot:
def __init__(self, records, login, write=True, run_one=False):
"""
# records is a list of dicts that look like:
{'Added on(yyyy-mm-dd)': '2011-10-27',
'Organ system': 'nervous',
'Percent affected': '100 %',
'Pubmed id': 19696032,
'Symptom/sign': 'ataxia',
'disease': 606002,
'hpo': 'HP:0001251'}
"""
self.records = records
self.login = login
self.write = write
self.run_one = run_one
self.core_props = set()
self.append_props = [PROPS['symptoms']]
self.item_engine = self.make_item_engine()
def make_item_engine(self):
append_props = self.append_props
core_props = self.core_props
class SubCls(wdi_core.WDItemEngine):
def __init__(self, *args, **kwargs):
kwargs['fast_run'] = False
kwargs['ref_handler'] = update_retrieved_if_new_multiple_refs
kwargs['core_props'] = core_props
kwargs['append_value'] = append_props
super(SubCls, self).__init__(*args, **kwargs)
return SubCls
@staticmethod
def create_reference(omim, pmid, login=None):
"""
Reference is:
retrieved: date
stated in: links to pmid items
optional reference URL
"""
#
ref = [wdi_core.WDItemID(ITEMS['MitoDB'], PROPS['curator'], is_reference=True)]
t = strftime("+%Y-%m-%dT00:00:00Z", gmtime())
ref.append(wdi_core.WDTime(t, prop_nr=PROPS['retrieved'], is_reference=True))
pmid_qid, _, success = PublicationHelper(ext_id=pmid, id_type='pmid', source="europepmc").get_or_create(login)
if success is True:
ref.append(wdi_core.WDItemID(pmid_qid, PROPS['stated in'], is_reference=True))
ref_url = "http://mitodb.com/symptoms.php?oid={}&symptoms=Show"
ref.append(wdi_core.WDUrl(ref_url.format(omim), PROPS['reference URL'], is_reference=True))
return ref
@staticmethod
def create_qualifier(incidence):
q = []
if incidence:
q.append(wdi_core.WDQuantity(incidence, PROPS['incidence'], is_qualifier=True,
unit="http://www.wikidata.org/entity/" + ITEMS['percentage']))
pass
return q
def run_one_disease(self, disease_qid, records):
ss = []
for record in records:
incidence = float(record['Percent affected'][:-2])
pmid = record['Pubmed id']
phenotype_qid = record['phenotype_qid']
omim_id = record['disease']
refs = [self.create_reference(omim_id, pmid=pmid, login=self.login)]
qual = self.create_qualifier(incidence)
s = wdi_core.WDItemID(phenotype_qid, PROPS['symptoms'], references=refs, qualifiers=qual)
ss.append(s)
item = self.item_engine(wd_item_id=disease_qid, data=ss)
assert not item.create_new_item
try_write(item, record_id=disease_qid, record_prop=PROPS['symptoms'],
edit_summary="Add phenotype from mitodb", login=self.login, write=self.write)
def run(self):
if self.run_one:
d = [x for x in self.records if x['disease_qid'] == self.run_one]
if d:
print(d[0])
self.run_one_disease(d[0]['disease_qid'], d)
else:
raise ValueError("{} not found".format(self.run_one))
return None
self.records = sorted(self.records, key=lambda x: x['disease_qid'])
record_group = groupby(self.records, key=lambda x: x['disease_qid'])
for disease_qid, sub_records in tqdm(record_group):
self.run_one_disease(disease_qid, sub_records)
def main(write=True, run_one=None):
omim_qid = wdi_helpers.id_mapper(PROPS['OMIM ID'], prefer_exact_match=True, return_as_set=True)
omim_qid = {k: list(v)[0] for k, v in omim_qid.items() if len(v) == 1}
hpo_qid = wdi_helpers.id_mapper(PROPS['Human Phenotype Ontology ID'], prefer_exact_match=True, return_as_set=True)
hpo_qid = {k: list(v)[0] for k, v in hpo_qid.items() if len(v) == 1}
df = pd.read_csv("mitodb.csv", dtype=str)
df['disease_qid'] = df.disease.map(omim_qid.get)
df['phenotype_qid'] = df.hpo.map(hpo_qid.get)
df.dropna(subset=['disease_qid', 'phenotype_qid'], inplace=True)
records = df.to_dict("records")
login = wdi_login.WDLogin(user=WDUSER, pwd=WDPASS)
bot = MitoBot(records, login, write=write, run_one=run_one)
bot.run()
if __name__ == "__main__":
parser = argparse.ArgumentParser(description='run mitodb phenotype bot')
parser.add_argument('--dummy', help='do not actually do write', action='store_true')
parser.add_argument('--run-one', help='run one disease, by qid')
args = parser.parse_args()
log_dir = "./logs"
run_id = datetime.now().strftime('%Y%m%d_%H:%M')
__metadata__['run_id'] = run_id
log_name = '{}-{}.log'.format(__metadata__['name'], run_id)
if wdi_core.WDItemEngine.logger is not None:
wdi_core.WDItemEngine.logger.handles = []
wdi_core.WDItemEngine.setup_logging(log_dir=log_dir, log_name=log_name, header=json.dumps(__metadata__),
logger_name='mitodb')
main(write=not args.dummy, run_one=args.run_one)
| mit |
pbreach/pysd | tests/unit_test_utils.py | 2 | 7923 | from unittest import TestCase
import xarray as xr
import pandas as pd
from . import test_utils
import doctest
class TestUtils(TestCase):
def test_get_return_elements_subscirpts(self):
from pysd.utils import get_return_elements
self.assertEqual(
get_return_elements(["Inflow A[Entry 1,Column 1]",
"Inflow A[Entry 1,Column 2]"],
{'Inflow A': 'inflow_a'},
{'Dim1': ['Entry 1', 'Entry 2'],
'Dim2': ['Column 1', 'Column 2']}),
(['inflow_a'],
{'Inflow A[Entry 1,Column 1]': ('inflow_a', {'Dim1': ['Entry 1'],
'Dim2': ['Column 1']}),
'Inflow A[Entry 1,Column 2]': ('inflow_a', {'Dim1': ['Entry 1'],
'Dim2': ['Column 2']})}
)
)
def test_get_return_elements_realnames(self):
from pysd.utils import get_return_elements
self.assertEqual(
get_return_elements(["Inflow A",
"Inflow B"],
subscript_dict={'Dim1': ['Entry 1', 'Entry 2'],
'Dim2': ['Column 1', 'Column 2']},
namespace={'Inflow A': 'inflow_a',
'Inflow B': 'inflow_b'}),
(['inflow_a', 'inflow_b'],
{'Inflow A': ('inflow_a', {}),
'Inflow B': ('inflow_b', {})}
)
)
def test_get_return_elements_pysafe_names(self):
from pysd.utils import get_return_elements
self.assertEqual(
get_return_elements(["inflow_a",
"inflow_b"],
subscript_dict={'Dim1': ['Entry 1', 'Entry 2'],
'Dim2': ['Column 1', 'Column 2']},
namespace={'Inflow A': 'inflow_a',
'Inflow B': 'inflow_b'}),
(['inflow_a', 'inflow_b'],
{'inflow_a': ('inflow_a', {}),
'inflow_b': ('inflow_b', {})}
)
)
def test_make_flat_df(self):
from pysd.utils import make_flat_df
frames = [{'elem1': xr.DataArray([[1, 2, 3], [4, 5, 6], [7, 8, 9]],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
dims=['Dim1', 'Dim2']),
'elem2': xr.DataArray([[1, 2, 3], [4, 5, 6], [7, 8, 9]],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
dims=['Dim1', 'Dim2'])},
{'elem1': xr.DataArray([[2, 4, 6], [8, 10, 12], [14, 16, 19]],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
dims=['Dim1', 'Dim2']),
'elem2': xr.DataArray([[1, 2, 3], [4, 5, 6], [7, 8, 9]],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
dims=['Dim1', 'Dim2'])}]
return_addresses = {'Elem1[B,F]': ('elem1', {'Dim1': ['B'], 'Dim2': ['F']})}
df = pd.DataFrame([{'Elem1[B,F]': 6}, {'Elem1[B,F]': 12}])
resultdf = make_flat_df(frames, return_addresses)
test_utils.assert_frames_close(resultdf, df, rtol=.01)
def test_visit_addresses(self):
from pysd.utils import visit_addresses
frame = {'elem1': xr.DataArray([[1, 2, 3], [4, 5, 6], [7, 8, 9]],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
dims=['Dim1', 'Dim2']),
'elem2': xr.DataArray([[1, 2, 3], [4, 5, 6], [7, 8, 9]],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
dims=['Dim1', 'Dim2'])}
return_addresses = {'Elem1[B,F]': ('elem1', {'Dim1': ['B'], 'Dim2': ['F']})}
self.assertEqual(visit_addresses(frame, return_addresses),
{'Elem1[B,F]': 6})
def test_visit_addresses_nosubs(self):
from pysd.utils import visit_addresses
frame = {'elem1': 25, 'elem2': 13}
return_addresses = {'Elem1': ('elem1', {}),
'Elem2': ('elem2', {})}
self.assertEqual(visit_addresses(frame, return_addresses),
{'Elem1': 25, 'Elem2': 13})
def test_visit_addresses_return_array(self):
""" There could be cases where we want to
return a whole section of an array - ie, by passing in only part of
the simulation dictionary. in this case, we can't force to float..."""
from pysd.utils import visit_addresses
frame = {'elem1': xr.DataArray([[1, 2, 3], [4, 5, 6], [7, 8, 9]],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
dims=['Dim1', 'Dim2']),
'elem2': xr.DataArray([[1, 2, 3], [4, 5, 6], [7, 8, 9]],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
dims=['Dim1', 'Dim2'])}
return_addresses = {'Elem1[A, Dim2]': ('elem1', {'Dim1': ['A'], 'Dim2': ['D', 'E', 'F']})}
actual = visit_addresses(frame, return_addresses)
expected = {'Elem1[A, Dim2]':
xr.DataArray([[1, 2, 3]],
{'Dim1': ['A'],
'Dim2': ['D', 'E', 'F']},
dims=['Dim1', 'Dim2']),
}
self.assertIsInstance(list(actual.values())[0], xr.DataArray)
self.assertEqual(actual['Elem1[A, Dim2]'].shape,
expected['Elem1[A, Dim2]'].shape)
# Todo: test that the values are equal
def test_make_coord_dict(self):
from pysd.utils import make_coord_dict
self.assertEqual(make_coord_dict(['Dim1', 'D'],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
terse=True),
{'Dim2': ['D']})
self.assertEqual(make_coord_dict(['Dim1', 'D'],
{'Dim1': ['A', 'B', 'C'],
'Dim2': ['D', 'E', 'F']},
terse=False),
{'Dim1': ['A', 'B', 'C'], 'Dim2': ['D']})
def test_find_subscript_name(self):
from pysd.utils import find_subscript_name
self.assertEqual(find_subscript_name({'Dim1': ['A', 'B'],
'Dim2': ['C', 'D', 'E'],
'Dim3': ['F', 'G', 'H', 'I']},
'D'),
'Dim2')
self.assertEqual(find_subscript_name({'Dim1': ['A', 'B'],
'Dim2': ['C', 'D', 'E'],
'Dim3': ['F', 'G', 'H', 'I']},
'Dim3'),
'Dim3')
def test_doctests(self):
import pysd.utils
doctest.DocTestSuite(pysd.utils)
| mit |
mayblue9/scikit-learn | sklearn/datasets/mlcomp.py | 289 | 3855 | # Copyright (c) 2010 Olivier Grisel <[email protected]>
# License: BSD 3 clause
"""Glue code to load http://mlcomp.org data as a scikit.learn dataset"""
import os
import numbers
from sklearn.datasets.base import load_files
def _load_document_classification(dataset_path, metadata, set_=None, **kwargs):
if set_ is not None:
dataset_path = os.path.join(dataset_path, set_)
return load_files(dataset_path, metadata.get('description'), **kwargs)
LOADERS = {
'DocumentClassification': _load_document_classification,
# TODO: implement the remaining domain formats
}
def load_mlcomp(name_or_id, set_="raw", mlcomp_root=None, **kwargs):
"""Load a datasets as downloaded from http://mlcomp.org
Parameters
----------
name_or_id : the integer id or the string name metadata of the MLComp
dataset to load
set_ : select the portion to load: 'train', 'test' or 'raw'
mlcomp_root : the filesystem path to the root folder where MLComp datasets
are stored, if mlcomp_root is None, the MLCOMP_DATASETS_HOME
environment variable is looked up instead.
**kwargs : domain specific kwargs to be passed to the dataset loader.
Read more in the :ref:`User Guide <datasets>`.
Returns
-------
data : Bunch
Dictionary-like object, the interesting attributes are:
'filenames', the files holding the raw to learn, 'target', the
classification labels (integer index), 'target_names',
the meaning of the labels, and 'DESCR', the full description of the
dataset.
Note on the lookup process: depending on the type of name_or_id,
will choose between integer id lookup or metadata name lookup by
looking at the unzipped archives and metadata file.
TODO: implement zip dataset loading too
"""
if mlcomp_root is None:
try:
mlcomp_root = os.environ['MLCOMP_DATASETS_HOME']
except KeyError:
raise ValueError("MLCOMP_DATASETS_HOME env variable is undefined")
mlcomp_root = os.path.expanduser(mlcomp_root)
mlcomp_root = os.path.abspath(mlcomp_root)
mlcomp_root = os.path.normpath(mlcomp_root)
if not os.path.exists(mlcomp_root):
raise ValueError("Could not find folder: " + mlcomp_root)
# dataset lookup
if isinstance(name_or_id, numbers.Integral):
# id lookup
dataset_path = os.path.join(mlcomp_root, str(name_or_id))
else:
# assume name based lookup
dataset_path = None
expected_name_line = "name: " + name_or_id
for dataset in os.listdir(mlcomp_root):
metadata_file = os.path.join(mlcomp_root, dataset, 'metadata')
if not os.path.exists(metadata_file):
continue
with open(metadata_file) as f:
for line in f:
if line.strip() == expected_name_line:
dataset_path = os.path.join(mlcomp_root, dataset)
break
if dataset_path is None:
raise ValueError("Could not find dataset with metadata line: " +
expected_name_line)
# loading the dataset metadata
metadata = dict()
metadata_file = os.path.join(dataset_path, 'metadata')
if not os.path.exists(metadata_file):
raise ValueError(dataset_path + ' is not a valid MLComp dataset')
with open(metadata_file) as f:
for line in f:
if ":" in line:
key, value = line.split(":", 1)
metadata[key.strip()] = value.strip()
format = metadata.get('format', 'unknow')
loader = LOADERS.get(format)
if loader is None:
raise ValueError("No loader implemented for format: " + format)
return loader(dataset_path, metadata, set_=set_, **kwargs)
| bsd-3-clause |
dpshelio/sunpy | examples/plotting/simple_differential_rotation.py | 1 | 3061 | """
============================
Simple Differential Rotation
============================
The Sun is known to rotate differentially, meaning that the rotation rate
near the poles (rotation period of approximately 35 days) is not the same as
the rotation rate near the equator (rotation period of approximately 25 days).
This is possible because the Sun is not a solid body. Though it is still poorly
understood, it is fairly well measured and must be taken into account
when comparing observations of features on the Sun over time.
A good review can be found in Beck 1999 Solar Physics 191, 47–70.
This example illustrates solar differential rotation.
"""
# sphinx_gallery_thumbnail_number = 2
import numpy as np
import matplotlib.pyplot as plt
import astropy.units as u
from astropy.coordinates import SkyCoord
from astropy.time import TimeDelta
import sunpy.map
import sunpy.data.sample
from sunpy.physics.differential_rotation import diff_rot, solar_rotate_coordinate
##############################################################################
# Next lets explore solar differential rotation by replicating Figure 1
# in Beck 1999
latitudes = u.Quantity(np.arange(0, 90, 1), 'deg')
dt = 1 * u.day
rotation_rate = [diff_rot(dt, this_lat) / dt for this_lat in latitudes]
rotation_period = [360 * u.deg / this_rate for this_rate in rotation_rate]
fig = plt.figure()
plt.plot(np.sin(latitudes), [this_period.value for this_period in rotation_period])
plt.ylim(38, 24)
plt.ylabel('Rotation Period [{0}]'.format(rotation_period[0].unit))
plt.xlabel('Sin(Latitude)')
plt.title('Solar Differential Rotation Rate')
##############################################################################
# Next let's show how to this looks like on the Sun.
# Load in an AIA map:
aia_map = sunpy.map.Map(sunpy.data.sample.AIA_171_IMAGE)
##############################################################################
# Let's define our starting coordinates
hpc_y = u.Quantity(np.arange(-700, 800, 100), u.arcsec)
hpc_x = np.zeros_like(hpc_y)
##############################################################################
# Let's define how many days in the future we want to rotate to
dt = TimeDelta(4*u.day)
future_date = aia_map.date + dt
##############################################################################
# Now let's plot the original and rotated positions on the AIA map.
fig = plt.figure()
ax = plt.subplot(projection=aia_map)
aia_map.plot()
ax.set_title('The effect of {0} days of differential rotation'.format(dt.to(u.day).value))
aia_map.draw_grid()
for this_hpc_x, this_hpc_y in zip(hpc_x, hpc_y):
start_coord = SkyCoord(this_hpc_x, this_hpc_y, frame=aia_map.coordinate_frame)
rotated_coord = solar_rotate_coordinate(start_coord, time=future_date)
coord = SkyCoord([start_coord.Tx, rotated_coord.Tx],
[start_coord.Ty, rotated_coord.Ty],
frame=aia_map.coordinate_frame)
ax.plot_coord(coord, 'o-')
plt.ylim(0, aia_map.data.shape[1])
plt.xlim(0, aia_map.data.shape[0])
plt.show()
| bsd-2-clause |
karstenw/nodebox-pyobjc | examples/Extended Application/matplotlib/examples/api/histogram_path.py | 1 | 2441 | """
========================================================
Building histograms using Rectangles and PolyCollections
========================================================
This example shows how to use a path patch to draw a bunch of
rectangles. The technique of using lots of Rectangle instances, or
the faster method of using PolyCollections, were implemented before we
had proper paths with moveto/lineto, closepoly etc in mpl. Now that
we have them, we can draw collections of regularly shaped objects with
homogeneous properties more efficiently with a PathCollection. This
example makes a histogram -- its more work to set up the vertex arrays
at the outset, but it should be much faster for large numbers of
objects
"""
import numpy as np
import matplotlib.pyplot as plt
import matplotlib.patches as patches
import matplotlib.path as path
# nodebox section
if __name__ == '__builtin__':
# were in nodebox
import os
import tempfile
W = 800
inset = 20
size(W, 600)
plt.cla()
plt.clf()
plt.close('all')
def tempimage():
fob = tempfile.NamedTemporaryFile(mode='w+b', suffix='.png', delete=False)
fname = fob.name
fob.close()
return fname
imgx = 20
imgy = 0
def pltshow(plt, dpi=150):
global imgx, imgy
temppath = tempimage()
plt.savefig(temppath, dpi=dpi)
dx,dy = imagesize(temppath)
w = min(W,dx)
image(temppath,imgx,imgy,width=w)
imgy = imgy + dy + 20
os.remove(temppath)
size(W, HEIGHT+dy+40)
else:
def pltshow(mplpyplot):
mplpyplot.show()
# nodebox section end
fig, ax = plt.subplots()
# Fixing random state for reproducibility
np.random.seed(19680801)
# histogram our data with numpy
data = np.random.randn(1000)
n, bins = np.histogram(data, 50)
# get the corners of the rectangles for the histogram
left = np.array(bins[:-1])
right = np.array(bins[1:])
bottom = np.zeros(len(left))
top = bottom + n
# we need a (numrects x numsides x 2) numpy array for the path helper
# function to build a compound path
XY = np.array([[left, left, right, right], [bottom, top, top, bottom]]).T
# get the Path object
barpath = path.Path.make_compound_path_from_polys(XY)
# make a patch out of it
patch = patches.PathPatch(barpath)
ax.add_patch(patch)
# update the view limits
ax.set_xlim(left[0], right[-1])
ax.set_ylim(bottom.min(), top.max())
pltshow(plt)
| mit |
eustislab/horton | scripts/horton-entanglement.py | 1 | 7461 | #!/usr/bin/env python
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2015 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
#
# HORTON is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, see <http://www.gnu.org/licenses/>
#
#--
import numpy as np, argparse
from horton import __version__
def plot(i12ind1, i12ind2, i12val, orbinit, orbfinal, thresh, s1index, s1value):
try:
import matplotlib.pyplot as plt
import matplotlib.lines as mlines
from matplotlib.ticker import NullFormatter
except ImportError:
if log.do_warning:
log.warn('Skipping plots because matplotlib was not found.')
return
norb = orbfinal-orbinit
orbitals = np.arange(orbinit, orbfinal)
theta = 2 * np.pi * (orbitals-orbinit)/(norb)
r = 22*np.ones(norb,int)-3.00*((orbitals-orbinit)%3)
plt.figure(figsize=(10,5))
ax = plt.subplot(121, polar=True)
ax.grid(False)
ax.set_theta_zero_location("N")
ax.set_theta_direction(-1)
plt.plot(theta, r, 'o', markersize=12, alpha=0.2)
for i in range(len(orbitals)):
plt.annotate(
i+1+orbinit,
xy = (theta[i], r[i]), xytext = (0, 0),
textcoords = 'offset points', ha = 'center', va = 'bottom',
fontsize=8, fontweight='bold',
)
ax.yaxis.set_data_interval(0,22.5)
ax.xaxis.set_major_formatter(NullFormatter())
ax.yaxis.set_major_formatter(NullFormatter())
legend = []
for ind in range(len(i12val)):
if i12val[ind] >= thresh:
if i12val[ind] >= 0.0001 and i12val[ind] < 0.001:
plt.plot([theta[i12ind1[ind]-orbinit], theta[i12ind2[ind]-orbinit]],
[r[i12ind1[ind]-orbinit], r[i12ind2[ind]-orbinit]],
':', lw=2, color='orange')
if i12val[ind] >= 0.001 and i12val[ind] < 0.01:
plt.plot([theta[i12ind1[ind]-orbinit], theta[i12ind2[ind]-orbinit]],
[r[i12ind1[ind]-orbinit], r[i12ind2[ind]-orbinit]],
'-.', lw=2, color='g')
if i12val[ind] >= 0.01 and i12val[ind] < 0.1:
plt.plot([theta[i12ind1[ind]-orbinit], theta[i12ind2[ind]-orbinit]],
[r[i12ind1[ind]-orbinit], r[i12ind2[ind]-orbinit]],
'--', lw=2, color='r')
if i12val[ind] >= 0.1:
plt.plot([theta[i12ind1[ind]-orbinit], theta[i12ind2[ind]-orbinit]],
[r[i12ind1[ind]-orbinit], r[i12ind2[ind]-orbinit]],
'-', lw=3, color='b')
blue_line = mlines.Line2D([], [], color='blue', marker='', lw=3, ls='-', label='0.1')
red_line = mlines.Line2D([], [], color='red', marker='', lw=2, ls='--', label='0.01')
green_line = mlines.Line2D([], [], color='green', marker='', ls='-.', lw=2, label='0.001')
orange_line = mlines.Line2D([], [], color='orange', marker='', ls=':', lw=2, label='0.0001')
if thresh >= 0.0001 and thresh < 0.001:
legend.append(blue_line)
legend.append(red_line)
legend.append(green_line)
legend.append(orange_line)
if thresh >= 0.001 and thresh < 0.01:
legend.append(blue_line)
legend.append(red_line)
legend.append(green_line)
if thresh >= 0.01 and thresh < 0.1:
legend.append(blue_line)
legend.append(red_line)
if thresh >= 0.1:
legend.append(blue_line)
plt.legend(handles=legend, loc='center', fancybox=True, fontsize=10)
plt.title('Mutual information')
ax2 = plt.subplot(122)
ax2.axis([orbinit, orbfinal, 0, 0.71])
ax2.vlines(s1index, [0], s1value, color='r', linewidth=2, linestyle='-')
plt.ylabel('single-orbital entropy')
plt.xlabel('Orbital index')
plt.plot(s1index, s1value, 'ro', markersize=8)
plt.savefig('orbital_entanglement.png', dpi=300)
def read_i12_data(orbinit, orbfinal, thresh):
index1 = np.array([])
index2 = np.array([])
value = np.array([])
with open("i12.dat") as f:
counter = 1
for line in f:
words = line.split()
if len(words) != 3:
raise IOError('Expecting 3 fields on each data line in i12.dat')
if float(words[2]) >= thresh and int(words[0]) >= orbinit and \
int(words[1]) >= orbinit and int(words[0]) <= orbfinal and \
int(words[1]) <= orbfinal:
index1 = np.append(index1, int(words[0])-1)
index2 = np.append(index2, int(words[1])-1)
value = np.append(value, float(words[2]))
return index1, index2, value
def read_s1_data(orbinit, orbfinal):
index = np.array([])
value = np.array([])
with open("s1.dat") as f:
for line in f:
words = line.split()
if len(words) != 2:
raise IOError('Expecting 2 fields on each data line in s1.dat')
index = np.append(index, int(words[0]))
value = np.append(value, float(words[1]))
if orbfinal:
newind = np.where(index>=(orbinit+1))
index = index[newind]
value = value[newind]
newind2 = np.where(index<=orbfinal)
index = index[newind2]
value = value[newind2]
return index, value
def parse_args():
parser = argparse.ArgumentParser(prog='horton-entanglement.py',
description='This script makes an orbital entanglement plot. It '
'assumes that the files s1.dat and i12.dat are present in '
'the current directory. These two files will be used to '
'create the figure orbital_entanglement.png.')
parser.add_argument('-V', '--version', action='version',
version="%%(prog)s (HORTON version %s)" % __version__)
parser.add_argument('threshold', type=float,
help='Orbitals with a mutual information below this threshold will not '
'be connected by a line.')
parser.add_argument('init_index', default=1, type=int, nargs='?',
help='The first orbital to be used for the plot. [default=%(default)s]')
parser.add_argument('final_index', default=None, type=int, nargs='?',
help='The last orbital to be used for the plot (inclusive). '
'[default=last orbital]')
return parser.parse_args()
def main():
args = parse_args()
orbinit = args.init_index - 1
orbfinal = args.final_index
# Read s1.dat and store data
s1index, s1value = read_s1_data(orbinit, orbfinal)
if orbfinal is None:
orbfinal = len(s1index)
# Read i12.dat and store data
i12index1, i12index2, i12value = read_i12_data(orbinit, orbfinal, args.threshold)
# Plot i12 graph
plt1 = plot(i12index1, i12index2, i12value, orbinit, orbfinal, args.threshold, s1index, s1value)
if __name__ == '__main__':
main()
| gpl-3.0 |
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