def test_zero_points_nan_outcome(self):
"""Zero points should return NaN."""
point_cloud = create_point_cloud(np.zeros(0), np.zeros(0), np.zeros(0))
targets = create_point_cloud(np.zeros(1), np.zeros(1), np.zeros(1))
result = BandRatioFeatureExtractor(2,
4).extract(point_cloud, [[]],
targets, 0, Cell(4))
self.assertTrue(np.isnan(result[0]))
def test_cell_grid_origin(self):
_, points = create_points_in_xy_grid(lambda x, y: np.random.rand())
point_cloud = create_point_cloud(points[:, 0], points[:, 1], points[:,
2])
targets = create_point_cloud(np.array([0]), np.array([0]),
np.array([0])) # Center of grid
neighborhoods = list(
compute_neighborhoods(point_cloud, targets, Cell(1.99)))
assert_equal(len(neighborhoods[0]), 1)
def test_cube_grid(self):
_, points = create_points_in_xy_grid(lambda x, y: 10 * (x % 2))
point_cloud = create_point_cloud(points[:, 0], points[:, 1], points[:,
2])
targets = create_point_cloud(np.array([4.5]), np.array([4.5]),
np.array([0])) # Center of grid
neighborhoods = list(
compute_neighborhoods(point_cloud, targets, Cube(2)))
assert_equal(len(neighborhoods[0]), 2)
def assert_std_for_z_function_in_xy_grid(z_checkered, expected):
"""Assert that the standard deviation of z values in a grid of unit x and y"""
n_points, points = create_points_in_xy_grid(z_checkered)
point_cloud = create_point_cloud(points[:, 0], points[:, 1], points[:, 2])
targets = create_point_cloud([0], [0], [0])
compute_features(point_cloud, [range(n_points)], 0, targets, ['sigma_z'],
InfiniteCylinder(10))
np.testing.assert_almost_equal(targets[keys.point]['sigma_z']['data'][0],
expected)
def test_cell_grid(self):
_, points = create_points_in_xy_grid(lambda x, y: np.random.rand())
point_cloud = create_point_cloud(points[:, 0], points[:, 1], points[:,
2])
targets = create_point_cloud(np.array([4.5]), np.array([4.5]),
np.array([4.5])) # Center of grid
neighborhoods = compute_neighborhoods(point_cloud, targets, Cell(2))
neighborhood = next(neighborhoods)
assert_equal(len(neighborhood[0]), 4)
def test_no_lower_bound_correct_outcome(self):
"""No lower bound should return all points below."""
n = 10
point_cloud = create_point_cloud(np.zeros(n), np.zeros(n),
np.hstack([np.zeros(8),
np.ones(2)]))
targets = create_point_cloud(np.zeros(1), np.zeros(1), np.zeros(1))
result = BandRatioFeatureExtractor(None, 0.5).extract(
point_cloud, [range(n)], targets, 0, Cell(4))
np.testing.assert_equal(result[0], 0.8)
def test_cell_grid_larger_sample_size(self):
_, points = create_points_in_xy_grid(lambda x, y: np.random.rand())
point_cloud = create_point_cloud(points[:, 0], points[:, 1], points[:,
2])
targets = create_point_cloud(np.array([4.5]), np.array([4.5]),
np.array([4.5])) # Center of grid
neighborhoods = compute_neighborhoods(
point_cloud, targets, Cell(5),
sample_size=10000) # Result 36 neighbors
_ = next(neighborhoods)
def test_cell(self):
n_included = 123
n_excluded = 456
x = np.append(np.zeros(n_included), np.ones(n_excluded))
environment = create_point_cloud(x, x, x)
target = create_point_cloud(np.zeros(1), np.zeros(1), np.zeros(1))
cube = Cube(1) # volume = 1.0
neighborhoods = compute_neighborhoods(environment, target, cube)
extractor = PointDensityFeatureExtractor()
densities = extractor.extract(environment, neighborhoods, target, [0], cube)
np.testing.assert_allclose(densities, n_included)
def test_cell(self):
n_included = 123
n_excluded = 456
x = np.append(np.zeros(n_included), np.ones(n_excluded))
environment = create_point_cloud(x, x, x)
target = create_point_cloud(np.zeros(1), np.zeros(1), np.zeros(1))
cube = Cube(1) # volume = 1.0
neighbors_index = compute_neighborhoods(environment, target, cube)
extractor = PointDensityFeatureExtractor()
for index in neighbors_index:
d = extractor.extract(environment, index, target, [0], cube)
self.assertEqual(d, n_included)
def test_target_number_matches_neighborhood_number(self):
_, points = create_points_in_xy_grid(lambda x, y: 10 * (x % 2))
environment_point_cloud = create_point_cloud(points[:, 0],
points[:, 1], points[:,
2])
assert_target_number_matches_neighborhood_number(
environment_point_cloud)
def test_cell_no_points(self):
point_cloud = create_emtpy_point_cloud()
targets = create_point_cloud(np.zeros(1), np.zeros(1), np.zeros(1))
neighborhoods = compute_neighborhoods(point_cloud, targets, Cell(1))
neighborhood = next(neighborhoods)
print(neighborhood)
assert_equal(len(neighborhood[0]), 0)
def _create_targets_and_extract_features(feature_names, n):
x = np.ones(n)
y = np.ones(n)
z = np.ones(n)
target = test_tools.create_point_cloud(x, y, z)
_compute_features(target, feature_names)
return target
def assert_target_number_matches_neighborhood_number(environment_point_cloud):
n_targets = 99
targets = create_point_cloud(np.array(range(n_targets)),
np.array(range(n_targets)),
np.array(range(n_targets)))
neighborhoods = list(
compute_neighborhoods(environment_point_cloud, targets, Cube(2)))
assert_equal(len(neighborhoods), n_targets)
def _get_random_targets(self):
"""Get a random target pc."""
num_all_pc_points = len(self.point_cloud[keys.point]["x"]["data"])
rand_indices = [
random.randint(0, num_all_pc_points) for p in range(20)
]
x, y, z = utils.get_point(self.point_cloud, rand_indices)
return create_point_cloud(x, y, z)
def test_normalize_tiny_unequal_point_cloud(self):
point_cloud = create_point_cloud([0, 0, 0], [0, 0, 0], [1, 2, 3])
normalized_point_cloud = normalize(point_cloud)
normalized_values = get_attribute_value(normalized_point_cloud,
range(3), normalized_height)
np.testing.assert_allclose(normalized_values,
np.array([0, 1, 2]),
atol=1e-7)
def test_percentile_z(self):
xyz = np.array([list(p) for p in list(itertools.product(np.linspace(0, 1, 11), repeat=3))])
point_cloud = create_point_cloud(xyz[:, 0], xyz[:, 1], xyz[:, 2])
expected = np.linspace(0.1, 1.0, 10)
extractors = [PercentileFeatureExtractor(p) for p in range(10, 110, 10)]
percentiles = [e.extract(point_cloud, [range(len(xyz))], None, None, None)[0] for e in extractors]
np.testing.assert_allclose(percentiles, expected)
def test_percentile_norm_z(self):
xyz = np.array([list(p) for p in list(itertools.product(np.linspace(0, 1, 11), repeat=3))])
point_cloud = create_point_cloud(xyz[:, 0], xyz[:, 1], np.zeros_like(xyz[:, 2]), normalized_z=xyz[:, 2])
expected = np.linspace(0.1, 1.0, 10)
extractors = [PercentileFeatureExtractor(p, data_key=keys.normalized_height) for p in range(10, 110, 10)]
percentiles = np.hstack([e.extract(point_cloud, [range(len(xyz))], None, None, None)[0] for e in extractors])
np.testing.assert_allclose(percentiles, expected)
def test_normalize_tiny_unequal_point_cloud_multiple_cells(self):
"""Last of the 3 points is not in the neighborhood of the others."""
point_cloud = create_point_cloud([0, 0, 5], [0, 0, 0], [1, 2, 3])
normalized_point_cloud = normalize(point_cloud, cell_size=2)
normalized_values = get_attribute_value(normalized_point_cloud,
range(3), normalized_height)
np.testing.assert_allclose(normalized_values,
np.array([0, 1, 0]),
atol=1e-7)
def test_use_norm_z(self):
x = y = np.array([0, 0, 0])
z = np.array([2, 2, 2])
normalized_z = np.array([3, 4, 5])
point_cloud = create_point_cloud(x, y, z, normalized_z=normalized_z)
neighborhood = [[0, 1, 2]]
kurtosis = self.extractor.extract(point_cloud, neighborhood, None, None, None)[0]
self.assertAlmostEqual(kurtosis, -1.5)
def test_use_norm_z(self):
x = y = np.array([0, 0, 0])
z = np.array([2, 2, 2])
normalized_z = np.array([3, 4, 6])
point_cloud = create_point_cloud(x, y, z, normalized_z=normalized_z)
neighborhood = [[0, 1, 2]]
median = self.extractor.extract(point_cloud, neighborhood, None, None, None)
np.testing.assert_almost_equal(median, 4)
def test_vectorized_chunks():
"""Should not throw error for non requested but provided features."""
feature_map._get_default_extractors = _get_test_extractors
n = 2000000 # enough to be too big for a single chunk
x = np.zeros(n)
y = np.zeros(n)
z = np.zeros(n)
target = test_tools.create_point_cloud(x, y, z)
feature_names = ['vectorized1']
_compute_features(target, feature_names)
def test_use_norm_z(self):
x = y = np.array([0, 0, 0])
z = np.array([2, 2, 2])
normalized_z = np.array([3, 4, 6])
point_cloud = create_point_cloud(x, y, z, normalized_z=normalized_z)
neighborhood = [[0, 1, 2]]
skew = self.extractor.extract(point_cloud, neighborhood, None, None, None)
self.assertGreater(skew, 0.1)
def test_use_optional_data_key(self):
"""Should use data under the given data key (normalized z)."""
n = 10
zeros = np.zeros(n)
point_cloud = create_point_cloud(zeros,
zeros,
zeros,
normalized_z=np.hstack(
[np.zeros(8),
np.ones(2)]))
targets = create_point_cloud(np.zeros(1), np.zeros(1), np.zeros(1))
extractor = BandRatioFeatureExtractor(None,
0.5,
data_key=keys.normalized_height)
result = extractor.extract(point_cloud, [range(n)], targets, 0,
Cell(4))
np.testing.assert_equal(result[0], 0.8)
def test_use_norm_z(self):
x = y = np.array([0, 0, 0])
z = np.array([2, 2, 2])
normalized_z = np.array([3, 4, 5])
point_cloud = create_point_cloud(x, y, z, normalized_z=normalized_z)
neighborhoods = [[0, 1, 2]]
entropy = self.extractor.extract(point_cloud, neighborhoods, None,
None, None)[0]
self.assertNotAlmostEqual(entropy, 0)
def test_height_stats(self):
x = y = np.array([0, 0, 0])
z = np.array([2, 2, 2])
normalized_z = np.array([3, 4, 5])
point_cloud = create_point_cloud(x, y, z, normalized_z=normalized_z)
neighborhood = [[0, 1, 2]]
variance = self.extractor.extract(point_cloud, [neighborhood], None,
None, None)[0]
self.assertAlmostEqual(variance, 2 / 3)
def test_with_neighborhood_generator():
"""Should run for all extractors without error meaning that neighborhood generator is only iterated once.
Using actual feature extractors here because test feature extractors don't use neighborhoods. """
n = 200
feature_names = ['vectorized1', 'test1_a', 'median_z', 'mean_z']
x = np.ones(n)
y = np.ones(n)
z = np.ones(n)
target = test_tools.create_point_cloud(x, y, z)
neighborhoods = ([] for _ in range(len(target["vertex"]["x"]["data"])))
feature_extraction.compute_features({}, neighborhoods, target,
feature_names, Sphere(5))
def test_eigenvalues_of_too_few_points_results_in_0():
"""If there are too few points to calculate the eigen values don't output NaN or inf."""
a = np.array([5])
pc = create_point_cloud(a, a, a)
compute_features(pc, [[0]], pc, ["eigenv_1", "eigenv_2", "eigenv_3"],
InfiniteCylinder(5))
eigen_val_123 = np.array(
[pc[keys.point]['eigenv_{}'.format(i)]['data'] for i in [1, 2, 3]])
assert not np.any(np.isnan(eigen_val_123))
assert not np.any(np.isinf(eigen_val_123))
def assert_expected_ratios(expected_ratios,
n_below_limits,
n_withins,
n_above_limits,
volume=Cell(4)):
n_ratios = len(expected_ratios)
neighborhoods, point_cloud = generate_test_point_cloud_and_neighborhoods(
n_below_limits, n_withins, n_above_limits, n_ratios)
targets = create_point_cloud(np.zeros(n_ratios), np.zeros(n_ratios),
np.zeros(n_ratios))
extractor = BandRatioFeatureExtractor(LOWER_LIMIT, UPPER_LIMIT)
result = extractor.extract(point_cloud, neighborhoods, targets, 0, volume)
np.testing.assert_allclose(result, expected_ratios)
def test_use_norm(self):
x = y = np.array([0, 0, 0])
z = np.array([2, 2, 2])
normalized_z = np.array([3, 4, 5])
point_cloud = create_point_cloud(x, y, z, normalized_z=normalized_z)
neighborhood = [[0, 1, 2]]
extractor = RangeFeatureExtractor(data_key=keys.normalized_height)
_max, _min, _range = extractor.extract(point_cloud, neighborhood, None, None, None)
self.assertAlmostEquals(_max, 5)
self.assertAlmostEquals(_min, 3)
self.assertAlmostEquals(_range, 2)
def test_height_stats(self):
x = y = np.array([0, 0, 0])
z = np.array([2, 2, 2])
normalized_z = np.array([3, 4, 5])
point_cloud = create_point_cloud(x, y, z, normalized_z=normalized_z)
neighborhood = [[0, 1, 2]]
mean, std, coeff = self.extractor.extract(point_cloud, neighborhood,
None, None, None)
self.assertAlmostEquals(mean, 4)
self.assertAlmostEquals(std, np.sqrt(2 / 3))
self.assertAlmostEquals(coeff, np.sqrt(2 / 3) / 4)