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import numpy as np
from nose.tools import assert_equal
from umap import UMAP
# ===================================================
# Spatial Data Test cases
# ===================================================
# Use force_approximation_algorithm in order to test
# the region of the code that is called for n>4096
# ---------------------------------------------------
def test_repeated_points_large_sparse_spatial(sparse_spatial_data_repeats):
model = UMAP(n_neighbors=3, unique=True, force_approximation_algorithm=True).fit(
sparse_spatial_data_repeats
)
assert_equal(np.unique(model.embedding_[0:2], axis=0).shape[0], 1)
def test_repeated_points_small_sparse_spatial(sparse_spatial_data_repeats):
model = UMAP(n_neighbors=3, unique=True).fit(sparse_spatial_data_repeats)
assert_equal(np.unique(model.embedding_[0:2], axis=0).shape[0], 1)
# Use force_approximation_algorithm in order to test the region
# of the code that is called for n>4096
def test_repeated_points_large_dense_spatial(spatial_repeats):
model = UMAP(n_neighbors=3, unique=True, force_approximation_algorithm=True).fit(
spatial_repeats
)
assert_equal(np.unique(model.embedding_[0:2], axis=0).shape[0], 1)
def test_repeated_points_small_dense_spatial(spatial_repeats):
model = UMAP(n_neighbors=3, unique=True).fit(spatial_repeats)
assert_equal(np.unique(model.embedding_[0:2], axis=0).shape[0], 1)
# ===================================================
# Binary Data Test cases
# ===================================================
# Use force_approximation_algorithm in order to test
# the region of the code that is called for n>4096
# ---------------------------------------------------
def test_repeated_points_large_sparse_binary(sparse_binary_data_repeats):
model = UMAP(n_neighbors=3, unique=True, force_approximation_algorithm=True).fit(
sparse_binary_data_repeats
)
assert_equal(np.unique(model.embedding_[0:2], axis=0).shape[0], 1)
def test_repeated_points_small_sparse_binary(sparse_binary_data_repeats):
model = UMAP(n_neighbors=3, unique=True).fit(sparse_binary_data_repeats)
assert_equal(np.unique(model.embedding_[0:2], axis=0).shape[0], 1)
# Use force_approximation_algorithm in order to test
# the region of the code that is called for n>4096
def test_repeated_points_large_dense_binary(binary_repeats):
model = UMAP(n_neighbors=3, unique=True, force_approximation_algorithm=True).fit(
binary_repeats
)
assert_equal(np.unique(model.embedding_[0:2], axis=0).shape[0], 1)
def test_repeated_points_small_dense_binary(binary_repeats):
model = UMAP(n_neighbors=3, unique=True).fit(binary_repeats)
assert_equal(np.unique(binary_repeats[0:2], axis=0).shape[0], 1)
assert_equal(np.unique(model.embedding_[0:2], axis=0).shape[0], 1)
# ===================================================
# Repeated Data Test cases
# ===================================================
# ----------------------------------------------------
# This should test whether the n_neighbours are being
# reduced properly when your n_neighbours is larger
# than the unique data set size
# ----------------------------------------------------
def test_repeated_points_large_n(repetition_dense):
model = UMAP(n_neighbors=5, unique=True).fit(repetition_dense)
assert_equal(model._n_neighbors, 3)
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