def make_plots(y_test, y_pred, y_prob, algorithm, timestamp):
def _save_and_close(type):
plt.savefig('static/img/{}/{}-{}.png'.format(type, algorithm,
timestamp),
dpi=200)
plt.close('all')
size = (20, 20)
name = classifier_names[algorithm]
plot_confusion_matrix(y_test,
y_pred,
normalize=True,
figsize=size,
title_fontsize=40,
text_fontsize=30,
title=name)
_save_and_close('cm')
if y_prob is not None:
plot_precision_recall_curve(y_test,
y_prob,
figsize=size,
title_fontsize=40,
text_fontsize=25,
title=name)
_save_and_close('precrec')
plot_roc_curve(y_test,
y_prob,
figsize=size,
title_fontsize=40,
text_fontsize=25,
title=name)
_save_and_close('roc')
def plotRecallPrecision(self, models_results):
for key, values in models_results.items():
fig, axes = plt.subplots(3, 3, figsize=(15, 15))
indexes = [(0, 0), (0, 1), (0, 2), (1, 0), (1, 1), (1, 2), (2, 0),
(2, 1), (2, 2)]
for i, clfr in enumerate(values):
skplt.plot_precision_recall_curve(y_true=clfr.y_test,
y_probas=clfr.probas,
ax=axes[indexes[i]])
plt.sca(axes[indexes[i]])
axes[indexes[i]].set_xlabel("Training/Test ({}/{})".format(
round(clfr.weight_train * 100, 0),
round(clfr.weight_test * 100, 0))) # set x label
axes[indexes[i]].get_xaxis().set_ticks(
[]) # hidden x axis text
axes[indexes[i]].get_yaxis().set_ticks([])
plt.tight_layout()
fig.subplots_adjust(top=0.95)
fig.suptitle(key, fontsize=16)
plt.savefig("plots/precision_recall_curve_{}.pdf".format(key))
def test_array_like(self):
ax = skplt.plot_precision_recall_curve([0, 1],
[[0.8, 0.2], [0.2, 0.8]])
def test_array_like(self):
ax = skplt.plot_precision_recall_curve([0, 1], [[0.8, 0.2], [0.2, 0.8]])
def plot_precision_recall_curve(clf, X, y, title='Precision-Recall Curve', do_cv=True,
cv=None, shuffle=True, random_state=None, ax=None):
"""Generates the Precision-Recall curve for a given classifier and dataset.
Args:
clf: Classifier instance that implements "fit" and "predict_proba" methods.
X (array-like, shape (n_samples, n_features)):
Training vector, where n_samples is the number of samples and
n_features is the number of features.
y (array-like, shape (n_samples) or (n_samples, n_features)):
Target relative to X for classification.
title (string, optional): Title of the generated plot. Defaults to "Precision-Recall Curve".
do_cv (bool, optional): If True, the classifier is cross-validated on the dataset using the
cross-validation strategy in `cv` to generate the confusion matrix. If False, the
confusion matrix is generated without training or cross-validating the classifier.
This assumes that the classifier has already been called with its `fit` method beforehand.
cv (int, cross-validation generator, iterable, optional): Determines the
cross-validation strategy to be used for splitting.
Possible inputs for cv are:
- None, to use the default 3-fold cross-validation,
- integer, to specify the number of folds.
- An object to be used as a cross-validation generator.
- An iterable yielding train/test splits.
For integer/None inputs, if ``y`` is binary or multiclass,
:class:`StratifiedKFold` used. If the estimator is not a classifier
or if ``y`` is neither binary nor multiclass, :class:`KFold` is used.
shuffle (bool, optional): Used when do_cv is set to True. Determines whether to shuffle the
training data before splitting using cross-validation. Default set to True.
random_state (int :class:`RandomState`): Pseudo-random number generator state used
for random sampling.
ax (:class:`matplotlib.axes.Axes`, optional): The axes upon which to plot
the learning curve. If None, the plot is drawn on a new set of axes.
Returns:
ax (:class:`matplotlib.axes.Axes`): The axes on which the plot was drawn.
Example:
>>> nb = classifier_factory(GaussianNB())
>>> nb.plot_precision_recall_curve(X, y, random_state=1)
<matplotlib.axes._subplots.AxesSubplot object at 0x7fe967d64490>
>>> plt.show()
.. image:: _static/examples/plot_precision_recall_curve.png
:align: center
:alt: Precision Recall Curve
"""
y = np.array(y)
if not hasattr(clf, 'predict_proba'):
raise TypeError('"predict_proba" method not in classifier. '
'Cannot calculate Precision-Recall Curve.')
if not do_cv:
probas = clf.predict_proba(X)
y_true = y
else:
if cv is None:
cv = StratifiedKFold(shuffle=shuffle, random_state=random_state)
elif isinstance(cv, int):
cv = StratifiedKFold(n_splits=cv, shuffle=shuffle, random_state=random_state)
else:
pass
clf_clone = clone(clf)
preds_list = []
trues_list = []
for train_index, test_index in cv.split(X, y):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
clf_clone.fit(X_train, y_train)
preds = clf_clone.predict_proba(X_test)
preds_list.append(preds)
trues_list.append(y_test)
probas = np.concatenate(preds_list, axis=0)
y_true = np.concatenate(trues_list)
# Compute Precision-Recall curve and area for each class
ax = plotters.plot_precision_recall_curve(y_true, probas, title=title, ax=ax)
return ax
def plot_precision_recall(self):
skplt.plot_precision_recall_curve(self.y_test, self.y_prob)
plt.show()
"""An example showing the plot_precision_recall method used by a scikit-learn classifier""" from __future__ import absolute_import import matplotlib.pyplot as plt from scikitplot import classifier_factory from sklearn.naive_bayes import GaussianNB from sklearn.datasets import load_digits as load_data X, y = load_data(return_X_y=True) nb = classifier_factory(GaussianNB()) nb.plot_precision_recall_curve(X, y, random_state=1) plt.show() # Using the more flexible functions API from scikitplot import plotters as skplt nb = GaussianNB() nb = nb.fit(X, y) probas = nb.predict_proba(X) skplt.plot_precision_recall_curve(y_true=y, y_probas=probas) plt.show()
generator_test = datagen.flow_from_directory(args.testdir,
target_size=(args.img_width,
args.img_height),
batch_size=1,
class_mode=classmode,
shuffle=False)
probos_finetune = loaded_model.predict_generator(
generator_test, len(generator_test.classes), max_q_size=1)
gnd_truth = generator_test.classes
dics = list(generator_test.class_indices.keys())
dics.extend(["micro-average curve", "macro-average curve"])
skplt.plot_precision_recall_curve(y_true=gnd_truth,
y_probas=probos_finetune)
plt.legend(dics[:5], loc='lower left')
plt.savefig(args.destdir + '/precision_recall_curve.png')
plt.close()
_ = classifier_factory(RandomForestClassifier())
_.plot_confusion_matrix(probos_finetune, gnd_truth, normalize=True)
plt.savefig(args.destdir + '/confusion-matrix.png')
plt.close()
nb = GaussianNB()
classifier_factory(nb)
nb.plot_roc_curve(probos_finetune, gnd_truth, title='roc curves')
plt.legend(dics, loc='lower right')
plt.savefig(args.destdir + '/ROC.png')
plt.close()
from sklearn.model_selection import StratifiedKFold
cv = StratifiedKFold(n_splits=3, shuffle=True)
from sklearn.model_selection import cross_val_score
score = cross_val_score(LogisticRegression(), X_all, y_all, scoring='neg_mean_squared_error', cv=cv).mean()
score = cross_val_score(LogisticRegression(), X_all, y_all, scoring='accuracy', cv=cv).mean()
#### Learning Curve
from scikitplot import plotters as skplt
skplt.plot_learning_curve(LogisticRegression(), X_all, y_all)
plt.show()
skplt.plot_roc_curve(y_true=y_val, y_probas=y_proba)
plt.show()
skplt.plot_precision_recall_curve(y_true=y_val, y_probas=y_proba)
plt.show()
skplt.plot_confusion_matrix(y_true=y_val, y_pred=y_pred, normalize=True)
plt.show()
#### XGBoost
from xgboost import XGBRegressor
import xgboost as xgb
params = {
'objective': 'binary:logistic',
'eval_metric': 'logloss',
}
dtrain = xgb.DMatrix(X_all, label=y_all)
history = xgb.cv(params, dtrain, num_boost_round=1024, early_stopping_rounds=5, verbose_eval=20)
def plot_precision_recall_curve_with_cv(clf, X, y,
title='Precision-Recall Curve',
do_cv=True, cv=None, shuffle=True,
random_state=None,
curves=('micro', 'each_class'),
ax=None, figsize=None,
cmap='nipy_spectral',
title_fontsize="large",
text_fontsize="medium"):
"""Generates the Precision-Recall curve for a given classifier and dataset.
Args:
clf: Classifier instance that implements "fit" and "predict_proba"
methods.
X (array-like, shape (n_samples, n_features)):
Training vector, where n_samples is the number of samples and
n_features is the number of features.
y (array-like, shape (n_samples) or (n_samples, n_features)):
Target relative to X for classification.
title (string, optional): Title of the generated plot. Defaults to
"Precision-Recall Curve".
do_cv (bool, optional): If True, the classifier is cross-validated on
the dataset using the cross-validation strategy in `cv` to generate
the confusion matrix. If False, the confusion matrix is generated
without training or cross-validating the classifier. This assumes
that the classifier has already been called with its `fit` method
beforehand.
cv (int, cross-validation generator, iterable, optional): Determines
the cross-validation strategy to be used for splitting.
Possible inputs for cv are:
- None, to use the default 3-fold cross-validation,
- integer, to specify the number of folds.
- An object to be used as a cross-validation generator.
- An iterable yielding train/test splits.
For integer/None inputs, if ``y`` is binary or multiclass,
:class:`StratifiedKFold` used. If the estimator is not a classifier
or if ``y`` is neither binary nor multiclass, :class:`KFold` is
used.
shuffle (bool, optional): Used when do_cv is set to True. Determines
whether to shuffle the training data before splitting using
cross-validation. Default set to True.
random_state (int :class:`RandomState`): Pseudo-random number generator
state used for random sampling.
curves (array-like): A listing of which curves should be plotted on the
resulting plot. Defaults to `("micro", "each_class")`
i.e. "micro" for micro-averaged curve
ax (:class:`matplotlib.axes.Axes`, optional): The axes upon which to
plot the learning curve. If None, the plot is drawn on a new set of
axes.
figsize (2-tuple, optional): Tuple denoting figure size of the plot
e.g. (6, 6). Defaults to ``None``.
cmap (string or :class:`matplotlib.colors.Colormap` instance, optional):
Colormap used for plotting the projection. View Matplotlib Colormap
documentation for available options.
https://matplotlib.org/users/colormaps.html
title_fontsize (string or int, optional): Matplotlib-style fontsizes.
Use e.g. "small", "medium", "large" or integer-values. Defaults to
"large".
text_fontsize (string or int, optional): Matplotlib-style fontsizes.
Use e.g. "small", "medium", "large" or integer-values. Defaults to
"medium".
Returns:
ax (:class:`matplotlib.axes.Axes`): The axes on which the plot was
drawn.
Example:
>>> nb = classifier_factory(GaussianNB())
>>> nb.plot_precision_recall_curve(X, y, random_state=1)
<matplotlib.axes._subplots.AxesSubplot object at 0x7fe967d64490>
>>> plt.show()
.. image:: _static/examples/plot_precision_recall_curve.png
:align: center
:alt: Precision Recall Curve
"""
y = np.array(y)
if not hasattr(clf, 'predict_proba'):
raise TypeError('"predict_proba" method not in classifier. '
'Cannot calculate Precision-Recall Curve.')
if not do_cv:
probas = clf.predict_proba(X)
y_true = y
else:
if cv is None:
cv = StratifiedKFold(shuffle=shuffle, random_state=random_state)
elif isinstance(cv, int):
cv = StratifiedKFold(n_splits=cv, shuffle=shuffle,
random_state=random_state)
else:
pass
clf_clone = clone(clf)
preds_list = []
trues_list = []
for train_index, test_index in cv.split(X, y):
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
clf_clone.fit(X_train, y_train)
preds = clf_clone.predict_proba(X_test)
preds_list.append(preds)
trues_list.append(y_test)
probas = np.concatenate(preds_list, axis=0)
y_true = np.concatenate(trues_list)
# Compute Precision-Recall curve and area for each class
ax = plotters.plot_precision_recall_curve(y_true, probas, title=title,
curves=curves, ax=ax,
figsize=figsize, cmap=cmap,
title_fontsize=title_fontsize,
text_fontsize=text_fontsize)
return ax
