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[FIX] Outliers widget no longer checks classes and doesn't crash on singular covariances matrices #2677

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Merged
jerneju merged 3 commits into from
Oct 20, 2017
Merged

[FIX] Outliers widget no longer checks classes and doesn't crash on singular covariances matrices #2677

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8c1f339
OWOutliers: Fix crash for singular covariance matrix
janezd Oct 13, 2017
102916c
OWOutliers: Ignore classes to allow no or multiple classes
janezd Oct 13, 2017
aa5fcef
EllipticEnvelopeClassifier: Don't check for classes
janezd Oct 13, 2017
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2 changes: 2 additions & 0 deletions Orange/classification/elliptic_envelope.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

from Orange.base import SklLearner, SklModel
from Orange.data import Table
from Orange.preprocess import Continuize, RemoveNaNColumns, SklImpute

__all__ = ["EllipticEnvelopeLearner"]

Expand All @@ -27,6 +28,7 @@ def mahalanobis(self, observations):
class EllipticEnvelopeLearner(SklLearner):
__wraps__ = skl_covariance.EllipticEnvelope
__returns__ = EllipticEnvelopeClassifier
preprocessors = [Continuize(), RemoveNaNColumns(), SklImpute()]
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@jerneju jerneju Oct 18, 2017

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Where are these preprocessors used?

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@kernc kernc Oct 18, 2017 •
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orange3/Orange/base.py

Lines 132 to 143 in 8ee65c0

def preprocess(self, data):
"""Apply the `preprocessors` to the data"""
for pp in self.active_preprocessors:
data = pp(data)
return data
@property
def active_preprocessors(self):
yield from self.preprocessors
if (self.use_default_preprocessors and
self.preprocessors is not type(self).preprocessors):
yield from type(self).preprocessors


def __init__(self, store_precision=True, assume_centered=False,
support_fraction=None, contamination=0.1,
Expand Down
12 changes: 5 additions & 7 deletions Orange/widgets/data/owoutliers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,6 @@ class Outputs:

class Error(widget.OWWidget.Error):
singular_cov = Msg("Singular covariance matrix.")
multiclass_error = Msg("Multiple class data is not supported")
memory_error = Msg("Not enough memory")

def __init__(self):
Expand Down Expand Up @@ -149,6 +148,7 @@ def _get_outliers(self):
except ValueError:
self.Error.singular_cov()
self.in_out_info_label.setText(self.in_out_info_default)
return None, None
except MemoryError:
self.Error.memory_error()
return None, None
Expand All @@ -170,10 +170,7 @@ def commit(self):
inliers = outliers = None
self.n_inliers = self.n_outliers = None
if self.data is not None and len(self.data) > 0:
if self.data.Y.ndim > 1 and self.data.Y.shape[1] > 1:
self.Error.multiclass_error()
else:
inliers, outliers = self._get_outliers()
inliers, outliers = self._get_outliers()

self.Outputs.inliers.send(inliers)
self.Outputs.outliers.send(outliers)
Expand All @@ -188,8 +185,9 @@ def detect_outliers(self):
support_fraction=self.support_fraction
if self.empirical_covariance else None,
contamination=self.cont / 100.)
model = learner(self.data)
y_pred = model(self.data)
data = self.data.transform(Domain(self.data.domain.attributes))
model = learner(data)
y_pred = model(data)
self.add_metas(model)
return np.array(y_pred)

Expand Down
24 changes: 9 additions & 15 deletions Orange/widgets/data/tests/test_owoutliers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@

import numpy as np

from Orange.data import Table, Domain, ContinuousVariable, DiscreteVariable
from Orange.data import Table
from Orange.widgets.data.owoutliers import OWOutliers
from Orange.widgets.tests.base import WidgetTest

Expand All @@ -25,20 +25,6 @@ def test_data(self):
self.assertEqual(self.widget.data, None)
self.assertIsNone(self.get_output("Data"))

def test_multiclass(self):
"""Check widget for multiclass dataset"""
attrs = [ContinuousVariable("c1"), ContinuousVariable("c2")]
class_vars = [DiscreteVariable("cls", ["a", "b", "c"]),
DiscreteVariable("cls", ["aa", "bb", "cc"])]
domain = Domain(attrs, class_vars)
X = np.arange(12).reshape(6, 2)
Y = np.array([[0, 1], [2, 1], [0, 2], [1, 1], [1, 2], [2, 0]])
data = Table(domain, X, Y)
self.send_signal(self.widget.Inputs.data, data)
self.assertTrue(self.widget.Error.multiclass_error.is_shown())
self.send_signal(self.widget.Inputs.data, None)
self.assertFalse(self.widget.Error.multiclass_error.is_shown())

def test_memory_error(self):
"""
Handling memory error.
Expand All @@ -51,3 +37,11 @@ def test_memory_error(self):
side_effect=MemoryError):
self.send_signal("Data", data)
self.assertTrue(self.widget.Error.memory_error.is_shown())

def test_nans(self):
"""Widget does not crash with nans"""
a = np.arange(20, dtype=float).reshape(4, 5)
a[0, 0] = np.nan
data = Table(a)
self.send_signal(self.widget.Inputs.data, data)
self.assertIsNot(self.get_output(self.widget.Outputs.inliers), None)