def test_jaccard_rows(self):
assert_almost_equal = np.testing.assert_almost_equal
model = distance.Jaccard().fit(self.data)
assert_almost_equal(model.ps, [0.75, 0.5, 0.75])
assert_almost_equal(
model(self.data),
1 - np.array([[1, 2/3, 1/3, 0],
[2/3, 1, 2/3, 1/3],
[1/3, 2/3, 1, 1/2],
[0, 1/3, 1/2, 1]]))
X = self.data.X
with self.data.unlocked():
X[1, 0] = X[2, 0] = X[3, 1] = np.nan
model = distance.Jaccard().fit(self.data)
assert_almost_equal(model.ps, np.array([0.5, 2/3, 0.75]))
# pylint: disable=bad-whitespace
assert_almost_equal(
model(self.data),
1 - np.array([[ 1, 2 / 2.5, 1 / 2.5, 2/3 / 3],
[2 / 2.5, 1, 1.25 / 2.75, (1/2+2/3) / 3],
[1 / 2.5, 1.25 / 2.75, 1, 0.5 / (2+2/3)],
[2/3 / 3, (1/2+2/3) / 3, 0.5 / (2+2/3), 1]]))
def test_jaccard_cols(self):
assert_almost_equal = np.testing.assert_almost_equal
model = distance.Jaccard(axis=0).fit(self.data)
assert_almost_equal(model.ps, [0.75, 0.5, 0.75])
assert_almost_equal(
model(self.data),
1 - np.array([[1, 1 / 4, 1 / 2], [1 / 4, 1, 2 / 3],
[1 / 2, 2 / 3, 1]]))
self.data.X = np.array([[0, 1, 1], [np.nan, np.nan, 1], [np.nan, 0, 1],
[1, 1, 0]])
model = distance.Jaccard(axis=0).fit(self.data)
assert_almost_equal(model.ps, [0.5, 2 / 3, 0.75])
assert_almost_equal(
model(self.data), 1 -
np.array([[1, 0.4, 0.25], [0.4, 1, 5 / 12], [0.25, 5 / 12, 1]]))
import Orange.data
import Orange.misc
from Orange.widgets import widget, gui, settings
from Orange import distance
_METRICS = [
("Euclidean", distance.Euclidean()),
("Manhattan", distance.Manhattan()),
("Cosine", distance.Cosine()),
("Jaccard", distance.Jaccard()),
("Mahalanobis", distance.Mahalanobis()),
("Spearman", distance.SpearmanR()),
("Spearman absolute", distance.SpearmanRAbsolute()),
("Pearson", distance.PearsonR()),
("Pearson absolute", distance.PearsonRAbsolute()),
]
class OWDistances(widget.OWWidget):
name = "Distances"
description = "Compute a matrix of pairwise distances."
icon = "icons/Distance.svg"
inputs = [("Data", Orange.data.Table, "set_data")]
outputs = [("Distances", Orange.misc.DistMatrix)]
axis = settings.Setting(0)
metric_idx = settings.Setting(0)
autocommit = settings.Setting(False)
want_main_area = False
