summaryrefslogtreecommitdiff
path: root/src/python/test/test_knn.py
diff options
context:
space:
mode:
Diffstat (limited to 'src/python/test/test_knn.py')
-rwxr-xr-xsrc/python/test/test_knn.py130
1 files changed, 130 insertions, 0 deletions
diff --git a/src/python/test/test_knn.py b/src/python/test/test_knn.py
new file mode 100755
index 00000000..a87ec212
--- /dev/null
+++ b/src/python/test/test_knn.py
@@ -0,0 +1,130 @@
+""" This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ Author(s): Marc Glisse
+
+ Copyright (C) 2020 Inria
+
+ Modification(s):
+ - YYYY/MM Author: Description of the modification
+"""
+
+from gudhi.point_cloud.knn import KNearestNeighbors
+import numpy as np
+import pytest
+
+
+def test_knn_explicit():
+ base = np.array([[1.0, 1], [1, 2], [4, 2], [4, 3]])
+ query = np.array([[1.0, 1], [2, 2], [4, 4]])
+ knn = KNearestNeighbors(2, metric="manhattan", return_distance=True, return_index=True)
+ knn.fit(base)
+ r = knn.transform(query)
+ assert r[0] == pytest.approx(np.array([[0, 1], [1, 0], [3, 2]]))
+ assert r[1] == pytest.approx(np.array([[0.0, 1], [1, 2], [1, 2]]))
+
+ knn = KNearestNeighbors(2, metric="chebyshev", return_distance=True, return_index=False)
+ knn.fit(base)
+ r = knn.transform(query)
+ assert r == pytest.approx(np.array([[0.0, 1], [1, 1], [1, 2]]))
+ r = (
+ KNearestNeighbors(2, metric="chebyshev", return_distance=True, return_index=False, implementation="keops")
+ .fit(base)
+ .transform(query)
+ )
+ assert r == pytest.approx(np.array([[0.0, 1], [1, 1], [1, 2]]))
+ r = (
+ KNearestNeighbors(2, metric="chebyshev", return_distance=True, return_index=False, implementation="keops", enable_autodiff=True)
+ .fit(base)
+ .transform(query)
+ )
+ assert r == pytest.approx(np.array([[0.0, 1], [1, 1], [1, 2]]))
+
+ knn = KNearestNeighbors(2, metric="minkowski", p=3, return_distance=False, return_index=True)
+ knn.fit(base)
+ r = knn.transform(query)
+ assert np.array_equal(r, [[0, 1], [1, 0], [3, 2]])
+ r = (
+ KNearestNeighbors(2, metric="minkowski", p=3, return_distance=False, return_index=True, implementation="keops")
+ .fit(base)
+ .transform(query)
+ )
+ assert np.array_equal(r, [[0, 1], [1, 0], [3, 2]])
+
+ dist = np.array([[0.0, 3, 8], [1, 0, 5], [1, 2, 0]])
+ knn = KNearestNeighbors(2, metric="precomputed", return_index=True, return_distance=False)
+ r = knn.fit_transform(dist)
+ assert np.array_equal(r, [[0, 1], [1, 0], [2, 0]])
+ knn = KNearestNeighbors(2, metric="precomputed", return_index=True, return_distance=True, sort_results=True)
+ r = knn.fit_transform(dist)
+ assert np.array_equal(r[0], [[0, 1], [1, 0], [2, 0]])
+ assert np.array_equal(r[1], [[0, 3], [0, 1], [0, 1]])
+ # Second time in parallel
+ knn = KNearestNeighbors(2, metric="precomputed", return_index=True, return_distance=False, n_jobs=2, sort_results=True)
+ r = knn.fit_transform(dist)
+ assert np.array_equal(r, [[0, 1], [1, 0], [2, 0]])
+ knn = KNearestNeighbors(2, metric="precomputed", return_index=True, return_distance=True, n_jobs=2)
+ r = knn.fit_transform(dist)
+ assert np.array_equal(r[0], [[0, 1], [1, 0], [2, 0]])
+ assert np.array_equal(r[1], [[0, 3], [0, 1], [0, 1]])
+
+
+def test_knn_compare():
+ base = np.array([[1.0, 1], [1, 2], [4, 2], [4, 3]])
+ query = np.array([[1.0, 1], [2, 2], [4, 4]])
+ r0 = (
+ KNearestNeighbors(2, implementation="ckdtree", return_index=True, return_distance=False)
+ .fit(base)
+ .transform(query)
+ )
+ r1 = (
+ KNearestNeighbors(2, implementation="sklearn", return_index=True, return_distance=False)
+ .fit(base)
+ .transform(query)
+ )
+ r2 = (
+ KNearestNeighbors(2, implementation="hnsw", return_index=True, return_distance=False).fit(base).transform(query)
+ )
+ r3 = (
+ KNearestNeighbors(2, implementation="keops", return_index=True, return_distance=False)
+ .fit(base)
+ .transform(query)
+ )
+ assert np.array_equal(r0, r1) and np.array_equal(r0, r2) and np.array_equal(r0, r3)
+
+ r0 = (
+ KNearestNeighbors(2, implementation="ckdtree", return_index=True, return_distance=True)
+ .fit(base)
+ .transform(query)
+ )
+ r1 = (
+ KNearestNeighbors(2, implementation="sklearn", return_index=True, return_distance=True)
+ .fit(base)
+ .transform(query)
+ )
+ r2 = KNearestNeighbors(2, implementation="hnsw", return_index=True, return_distance=True).fit(base).transform(query)
+ r3 = (
+ KNearestNeighbors(2, implementation="keops", return_index=True, return_distance=True).fit(base).transform(query)
+ )
+ assert np.array_equal(r0[0], r1[0]) and np.array_equal(r0[0], r2[0]) and np.array_equal(r0[0], r3[0])
+ d0 = pytest.approx(r0[1])
+ assert r1[1] == d0 and r2[1] == d0 and r3[1] == d0
+
+
+def test_knn_nop():
+ # This doesn't look super useful...
+ p = np.array([[0.0]])
+ assert None is KNearestNeighbors(
+ k=1, return_index=False, return_distance=False, implementation="sklearn"
+ ).fit_transform(p)
+ assert None is KNearestNeighbors(
+ k=1, return_index=False, return_distance=False, implementation="ckdtree"
+ ).fit_transform(p)
+ assert None is KNearestNeighbors(
+ k=1, return_index=False, return_distance=False, implementation="hnsw", ef=5
+ ).fit_transform(p)
+ assert None is KNearestNeighbors(
+ k=1, return_index=False, return_distance=False, implementation="keops"
+ ).fit_transform(p)
+ assert None is KNearestNeighbors(
+ k=1, return_index=False, return_distance=False, metric="precomputed"
+ ).fit_transform(p)