1410 lines
47 KiB
Python
1410 lines
47 KiB
Python
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import os.path
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import numpy as np
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from numpy.testing import (
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assert_,
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assert_allclose,
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assert_almost_equal,
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assert_array_almost_equal,
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assert_array_equal,
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assert_equal,
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suppress_warnings,
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)
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from pytest import raises as assert_raises
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import scipy.ndimage as ndimage
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from . import types
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class Test_measurements_stats:
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"""ndimage._measurements._stats() is a utility used by other functions."""
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def test_a(self):
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x = [0, 1, 2, 6]
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labels = [0, 0, 1, 1]
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index = [0, 1]
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for shp in [(4,), (2, 2)]:
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x = np.array(x).reshape(shp)
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labels = np.array(labels).reshape(shp)
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counts, sums = ndimage._measurements._stats(
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x, labels=labels, index=index)
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assert_array_equal(counts, [2, 2])
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assert_array_equal(sums, [1.0, 8.0])
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def test_b(self):
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# Same data as test_a, but different labels. The label 9 exceeds the
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# length of 'labels', so this test will follow a different code path.
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x = [0, 1, 2, 6]
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labels = [0, 0, 9, 9]
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index = [0, 9]
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for shp in [(4,), (2, 2)]:
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x = np.array(x).reshape(shp)
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labels = np.array(labels).reshape(shp)
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counts, sums = ndimage._measurements._stats(
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x, labels=labels, index=index)
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assert_array_equal(counts, [2, 2])
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assert_array_equal(sums, [1.0, 8.0])
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def test_a_centered(self):
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x = [0, 1, 2, 6]
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labels = [0, 0, 1, 1]
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index = [0, 1]
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for shp in [(4,), (2, 2)]:
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x = np.array(x).reshape(shp)
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labels = np.array(labels).reshape(shp)
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counts, sums, centers = ndimage._measurements._stats(
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x, labels=labels, index=index, centered=True)
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assert_array_equal(counts, [2, 2])
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assert_array_equal(sums, [1.0, 8.0])
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assert_array_equal(centers, [0.5, 8.0])
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def test_b_centered(self):
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x = [0, 1, 2, 6]
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labels = [0, 0, 9, 9]
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index = [0, 9]
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for shp in [(4,), (2, 2)]:
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x = np.array(x).reshape(shp)
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labels = np.array(labels).reshape(shp)
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counts, sums, centers = ndimage._measurements._stats(
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x, labels=labels, index=index, centered=True)
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assert_array_equal(counts, [2, 2])
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assert_array_equal(sums, [1.0, 8.0])
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assert_array_equal(centers, [0.5, 8.0])
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def test_nonint_labels(self):
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x = [0, 1, 2, 6]
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labels = [0.0, 0.0, 9.0, 9.0]
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index = [0.0, 9.0]
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for shp in [(4,), (2, 2)]:
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x = np.array(x).reshape(shp)
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labels = np.array(labels).reshape(shp)
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counts, sums, centers = ndimage._measurements._stats(
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x, labels=labels, index=index, centered=True)
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assert_array_equal(counts, [2, 2])
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assert_array_equal(sums, [1.0, 8.0])
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assert_array_equal(centers, [0.5, 8.0])
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class Test_measurements_select:
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"""ndimage._measurements._select() is a utility used by other functions."""
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def test_basic(self):
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x = [0, 1, 6, 2]
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cases = [
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([0, 0, 1, 1], [0, 1]), # "Small" integer labels
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([0, 0, 9, 9], [0, 9]), # A label larger than len(labels)
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([0.0, 0.0, 7.0, 7.0], [0.0, 7.0]), # Non-integer labels
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]
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for labels, index in cases:
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result = ndimage._measurements._select(
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x, labels=labels, index=index)
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assert_(len(result) == 0)
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result = ndimage._measurements._select(
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x, labels=labels, index=index, find_max=True)
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assert_(len(result) == 1)
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assert_array_equal(result[0], [1, 6])
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result = ndimage._measurements._select(
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x, labels=labels, index=index, find_min=True)
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assert_(len(result) == 1)
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assert_array_equal(result[0], [0, 2])
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result = ndimage._measurements._select(
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x, labels=labels, index=index, find_min=True,
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find_min_positions=True)
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assert_(len(result) == 2)
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assert_array_equal(result[0], [0, 2])
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assert_array_equal(result[1], [0, 3])
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assert_equal(result[1].dtype.kind, 'i')
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result = ndimage._measurements._select(
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x, labels=labels, index=index, find_max=True,
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find_max_positions=True)
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assert_(len(result) == 2)
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assert_array_equal(result[0], [1, 6])
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assert_array_equal(result[1], [1, 2])
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assert_equal(result[1].dtype.kind, 'i')
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def test_label01():
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data = np.ones([])
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out, n = ndimage.label(data)
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assert_array_almost_equal(out, 1)
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assert_equal(n, 1)
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def test_label02():
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data = np.zeros([])
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out, n = ndimage.label(data)
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assert_array_almost_equal(out, 0)
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assert_equal(n, 0)
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def test_label03():
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data = np.ones([1])
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out, n = ndimage.label(data)
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assert_array_almost_equal(out, [1])
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assert_equal(n, 1)
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def test_label04():
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data = np.zeros([1])
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out, n = ndimage.label(data)
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assert_array_almost_equal(out, [0])
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assert_equal(n, 0)
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def test_label05():
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data = np.ones([5])
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out, n = ndimage.label(data)
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assert_array_almost_equal(out, [1, 1, 1, 1, 1])
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assert_equal(n, 1)
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def test_label06():
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data = np.array([1, 0, 1, 1, 0, 1])
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out, n = ndimage.label(data)
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assert_array_almost_equal(out, [1, 0, 2, 2, 0, 3])
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assert_equal(n, 3)
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def test_label07():
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data = np.array([[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0]])
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out, n = ndimage.label(data)
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assert_array_almost_equal(out, [[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0],
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[0, 0, 0, 0, 0, 0]])
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assert_equal(n, 0)
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def test_label08():
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data = np.array([[1, 0, 0, 0, 0, 0],
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[0, 0, 1, 1, 0, 0],
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[0, 0, 1, 1, 1, 0],
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[1, 1, 0, 0, 0, 0],
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[1, 1, 0, 0, 0, 0],
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[0, 0, 0, 1, 1, 0]])
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out, n = ndimage.label(data)
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assert_array_almost_equal(out, [[1, 0, 0, 0, 0, 0],
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[0, 0, 2, 2, 0, 0],
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[0, 0, 2, 2, 2, 0],
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[3, 3, 0, 0, 0, 0],
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[3, 3, 0, 0, 0, 0],
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[0, 0, 0, 4, 4, 0]])
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assert_equal(n, 4)
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def test_label09():
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data = np.array([[1, 0, 0, 0, 0, 0],
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[0, 0, 1, 1, 0, 0],
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[0, 0, 1, 1, 1, 0],
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[1, 1, 0, 0, 0, 0],
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[1, 1, 0, 0, 0, 0],
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[0, 0, 0, 1, 1, 0]])
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struct = ndimage.generate_binary_structure(2, 2)
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out, n = ndimage.label(data, struct)
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assert_array_almost_equal(out, [[1, 0, 0, 0, 0, 0],
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[0, 0, 2, 2, 0, 0],
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[0, 0, 2, 2, 2, 0],
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[2, 2, 0, 0, 0, 0],
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[2, 2, 0, 0, 0, 0],
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[0, 0, 0, 3, 3, 0]])
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assert_equal(n, 3)
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def test_label10():
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data = np.array([[0, 0, 0, 0, 0, 0],
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[0, 1, 1, 0, 1, 0],
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[0, 1, 1, 1, 1, 0],
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[0, 0, 0, 0, 0, 0]])
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struct = ndimage.generate_binary_structure(2, 2)
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out, n = ndimage.label(data, struct)
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assert_array_almost_equal(out, [[0, 0, 0, 0, 0, 0],
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[0, 1, 1, 0, 1, 0],
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[0, 1, 1, 1, 1, 0],
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[0, 0, 0, 0, 0, 0]])
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assert_equal(n, 1)
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def test_label11():
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for type in types:
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data = np.array([[1, 0, 0, 0, 0, 0],
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[0, 0, 1, 1, 0, 0],
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[0, 0, 1, 1, 1, 0],
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[1, 1, 0, 0, 0, 0],
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[1, 1, 0, 0, 0, 0],
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[0, 0, 0, 1, 1, 0]], type)
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out, n = ndimage.label(data)
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expected = [[1, 0, 0, 0, 0, 0],
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[0, 0, 2, 2, 0, 0],
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[0, 0, 2, 2, 2, 0],
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[3, 3, 0, 0, 0, 0],
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[3, 3, 0, 0, 0, 0],
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[0, 0, 0, 4, 4, 0]]
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assert_array_almost_equal(out, expected)
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assert_equal(n, 4)
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def test_label11_inplace():
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for type in types:
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data = np.array([[1, 0, 0, 0, 0, 0],
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[0, 0, 1, 1, 0, 0],
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[0, 0, 1, 1, 1, 0],
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[1, 1, 0, 0, 0, 0],
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[1, 1, 0, 0, 0, 0],
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[0, 0, 0, 1, 1, 0]], type)
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n = ndimage.label(data, output=data)
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expected = [[1, 0, 0, 0, 0, 0],
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[0, 0, 2, 2, 0, 0],
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[0, 0, 2, 2, 2, 0],
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[3, 3, 0, 0, 0, 0],
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[3, 3, 0, 0, 0, 0],
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[0, 0, 0, 4, 4, 0]]
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assert_array_almost_equal(data, expected)
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assert_equal(n, 4)
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def test_label12():
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for type in types:
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data = np.array([[0, 0, 0, 0, 1, 1],
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[0, 0, 0, 0, 0, 1],
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[0, 0, 1, 0, 1, 1],
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[0, 0, 1, 1, 1, 1],
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[0, 0, 0, 1, 1, 0]], type)
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out, n = ndimage.label(data)
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expected = [[0, 0, 0, 0, 1, 1],
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[0, 0, 0, 0, 0, 1],
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[0, 0, 1, 0, 1, 1],
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[0, 0, 1, 1, 1, 1],
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[0, 0, 0, 1, 1, 0]]
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assert_array_almost_equal(out, expected)
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assert_equal(n, 1)
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def test_label13():
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for type in types:
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data = np.array([[1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1],
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[1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1],
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[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
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[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]],
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type)
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out, n = ndimage.label(data)
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expected = [[1, 0, 1, 1, 1, 0, 1, 1, 1, 0, 1],
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[1, 1, 1, 0, 1, 1, 1, 0, 1, 1, 1],
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[1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1],
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[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1]]
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assert_array_almost_equal(out, expected)
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assert_equal(n, 1)
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def test_label_output_typed():
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data = np.ones([5])
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for t in types:
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output = np.zeros([5], dtype=t)
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n = ndimage.label(data, output=output)
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assert_array_almost_equal(output, 1)
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assert_equal(n, 1)
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def test_label_output_dtype():
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data = np.ones([5])
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for t in types:
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output, n = ndimage.label(data, output=t)
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assert_array_almost_equal(output, 1)
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assert output.dtype == t
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def test_label_output_wrong_size():
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data = np.ones([5])
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for t in types:
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output = np.zeros([10], t)
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assert_raises((RuntimeError, ValueError),
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ndimage.label, data, output=output)
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def test_label_structuring_elements():
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data = np.loadtxt(os.path.join(os.path.dirname(
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__file__), "data", "label_inputs.txt"))
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strels = np.loadtxt(os.path.join(
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os.path.dirname(__file__), "data", "label_strels.txt"))
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results = np.loadtxt(os.path.join(
|
||
|
|
os.path.dirname(__file__), "data", "label_results.txt"))
|
||
|
|
data = data.reshape((-1, 7, 7))
|
||
|
|
strels = strels.reshape((-1, 3, 3))
|
||
|
|
results = results.reshape((-1, 7, 7))
|
||
|
|
r = 0
|
||
|
|
for i in range(data.shape[0]):
|
||
|
|
d = data[i, :, :]
|
||
|
|
for j in range(strels.shape[0]):
|
||
|
|
s = strels[j, :, :]
|
||
|
|
assert_equal(ndimage.label(d, s)[0], results[r, :, :])
|
||
|
|
r += 1
|
||
|
|
|
||
|
|
|
||
|
|
def test_ticket_742():
|
||
|
|
def SE(img, thresh=.7, size=4):
|
||
|
|
mask = img > thresh
|
||
|
|
rank = len(mask.shape)
|
||
|
|
la, co = ndimage.label(mask,
|
||
|
|
ndimage.generate_binary_structure(rank, rank))
|
||
|
|
_ = ndimage.find_objects(la)
|
||
|
|
|
||
|
|
if np.dtype(np.intp) != np.dtype('i'):
|
||
|
|
shape = (3, 1240, 1240)
|
||
|
|
a = np.random.rand(np.prod(shape)).reshape(shape)
|
||
|
|
# shouldn't crash
|
||
|
|
SE(a)
|
||
|
|
|
||
|
|
|
||
|
|
def test_gh_issue_3025():
|
||
|
|
"""Github issue #3025 - improper merging of labels"""
|
||
|
|
d = np.zeros((60, 320))
|
||
|
|
d[:, :257] = 1
|
||
|
|
d[:, 260:] = 1
|
||
|
|
d[36, 257] = 1
|
||
|
|
d[35, 258] = 1
|
||
|
|
d[35, 259] = 1
|
||
|
|
assert ndimage.label(d, np.ones((3, 3)))[1] == 1
|
||
|
|
|
||
|
|
|
||
|
|
def test_label_default_dtype():
|
||
|
|
test_array = np.random.rand(10, 10)
|
||
|
|
label, no_features = ndimage.label(test_array > 0.5)
|
||
|
|
assert_(label.dtype in (np.int32, np.int64))
|
||
|
|
# Shouldn't raise an exception
|
||
|
|
ndimage.find_objects(label)
|
||
|
|
|
||
|
|
|
||
|
|
def test_find_objects01():
|
||
|
|
data = np.ones([], dtype=int)
|
||
|
|
out = ndimage.find_objects(data)
|
||
|
|
assert_(out == [()])
|
||
|
|
|
||
|
|
|
||
|
|
def test_find_objects02():
|
||
|
|
data = np.zeros([], dtype=int)
|
||
|
|
out = ndimage.find_objects(data)
|
||
|
|
assert_(out == [])
|
||
|
|
|
||
|
|
|
||
|
|
def test_find_objects03():
|
||
|
|
data = np.ones([1], dtype=int)
|
||
|
|
out = ndimage.find_objects(data)
|
||
|
|
assert_equal(out, [(slice(0, 1, None),)])
|
||
|
|
|
||
|
|
|
||
|
|
def test_find_objects04():
|
||
|
|
data = np.zeros([1], dtype=int)
|
||
|
|
out = ndimage.find_objects(data)
|
||
|
|
assert_equal(out, [])
|
||
|
|
|
||
|
|
|
||
|
|
def test_find_objects05():
|
||
|
|
data = np.ones([5], dtype=int)
|
||
|
|
out = ndimage.find_objects(data)
|
||
|
|
assert_equal(out, [(slice(0, 5, None),)])
|
||
|
|
|
||
|
|
|
||
|
|
def test_find_objects06():
|
||
|
|
data = np.array([1, 0, 2, 2, 0, 3])
|
||
|
|
out = ndimage.find_objects(data)
|
||
|
|
assert_equal(out, [(slice(0, 1, None),),
|
||
|
|
(slice(2, 4, None),),
|
||
|
|
(slice(5, 6, None),)])
|
||
|
|
|
||
|
|
|
||
|
|
def test_find_objects07():
|
||
|
|
data = np.array([[0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0]])
|
||
|
|
out = ndimage.find_objects(data)
|
||
|
|
assert_equal(out, [])
|
||
|
|
|
||
|
|
|
||
|
|
def test_find_objects08():
|
||
|
|
data = np.array([[1, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 2, 2, 0, 0],
|
||
|
|
[0, 0, 2, 2, 2, 0],
|
||
|
|
[3, 3, 0, 0, 0, 0],
|
||
|
|
[3, 3, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 4, 4, 0]])
|
||
|
|
out = ndimage.find_objects(data)
|
||
|
|
assert_equal(out, [(slice(0, 1, None), slice(0, 1, None)),
|
||
|
|
(slice(1, 3, None), slice(2, 5, None)),
|
||
|
|
(slice(3, 5, None), slice(0, 2, None)),
|
||
|
|
(slice(5, 6, None), slice(3, 5, None))])
|
||
|
|
|
||
|
|
|
||
|
|
def test_find_objects09():
|
||
|
|
data = np.array([[1, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 2, 2, 0, 0],
|
||
|
|
[0, 0, 2, 2, 2, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 4, 4, 0]])
|
||
|
|
out = ndimage.find_objects(data)
|
||
|
|
assert_equal(out, [(slice(0, 1, None), slice(0, 1, None)),
|
||
|
|
(slice(1, 3, None), slice(2, 5, None)),
|
||
|
|
None,
|
||
|
|
(slice(5, 6, None), slice(3, 5, None))])
|
||
|
|
|
||
|
|
|
||
|
|
def test_value_indices01():
|
||
|
|
"Test dictionary keys and entries"
|
||
|
|
data = np.array([[1, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 2, 2, 0, 0],
|
||
|
|
[0, 0, 2, 2, 2, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 4, 4, 0]])
|
||
|
|
vi = ndimage.value_indices(data, ignore_value=0)
|
||
|
|
true_keys = [1, 2, 4]
|
||
|
|
assert_equal(list(vi.keys()), true_keys)
|
||
|
|
|
||
|
|
truevi = {}
|
||
|
|
for k in true_keys:
|
||
|
|
truevi[k] = np.where(data == k)
|
||
|
|
|
||
|
|
vi = ndimage.value_indices(data, ignore_value=0)
|
||
|
|
assert_equal(vi, truevi)
|
||
|
|
|
||
|
|
|
||
|
|
def test_value_indices02():
|
||
|
|
"Test input checking"
|
||
|
|
data = np.zeros((5, 4), dtype=np.float32)
|
||
|
|
msg = "Parameter 'arr' must be an integer array"
|
||
|
|
with assert_raises(ValueError, match=msg):
|
||
|
|
ndimage.value_indices(data)
|
||
|
|
|
||
|
|
|
||
|
|
def test_value_indices03():
|
||
|
|
"Test different input array shapes, from 1-D to 4-D"
|
||
|
|
for shape in [(36,), (18, 2), (3, 3, 4), (3, 3, 2, 2)]:
|
||
|
|
a = np.array((12*[1]+12*[2]+12*[3]), dtype=np.int32).reshape(shape)
|
||
|
|
trueKeys = np.unique(a)
|
||
|
|
vi = ndimage.value_indices(a)
|
||
|
|
assert_equal(list(vi.keys()), list(trueKeys))
|
||
|
|
for k in trueKeys:
|
||
|
|
trueNdx = np.where(a == k)
|
||
|
|
assert_equal(vi[k], trueNdx)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum01():
|
||
|
|
for type in types:
|
||
|
|
input = np.array([], type)
|
||
|
|
output = ndimage.sum(input)
|
||
|
|
assert_equal(output, 0.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum02():
|
||
|
|
for type in types:
|
||
|
|
input = np.zeros([0, 4], type)
|
||
|
|
output = ndimage.sum(input)
|
||
|
|
assert_equal(output, 0.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum03():
|
||
|
|
for type in types:
|
||
|
|
input = np.ones([], type)
|
||
|
|
output = ndimage.sum(input)
|
||
|
|
assert_almost_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum04():
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1, 2], type)
|
||
|
|
output = ndimage.sum(input)
|
||
|
|
assert_almost_equal(output, 3.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum05():
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.sum(input)
|
||
|
|
assert_almost_equal(output, 10.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum06():
|
||
|
|
labels = np.array([], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([], type)
|
||
|
|
output = ndimage.sum(input, labels=labels)
|
||
|
|
assert_equal(output, 0.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum07():
|
||
|
|
labels = np.ones([0, 4], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.zeros([0, 4], type)
|
||
|
|
output = ndimage.sum(input, labels=labels)
|
||
|
|
assert_equal(output, 0.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum08():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1, 2], type)
|
||
|
|
output = ndimage.sum(input, labels=labels)
|
||
|
|
assert_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum09():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.sum(input, labels=labels)
|
||
|
|
assert_almost_equal(output, 4.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum10():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
input = np.array([[1, 2], [3, 4]], bool)
|
||
|
|
output = ndimage.sum(input, labels=labels)
|
||
|
|
assert_almost_equal(output, 2.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum11():
|
||
|
|
labels = np.array([1, 2], np.int8)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.sum(input, labels=labels,
|
||
|
|
index=2)
|
||
|
|
assert_almost_equal(output, 6.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum12():
|
||
|
|
labels = np.array([[1, 2], [2, 4]], np.int8)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.sum(input, labels=labels, index=[4, 8, 2])
|
||
|
|
assert_array_almost_equal(output, [4.0, 0.0, 5.0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_sum_labels():
|
||
|
|
labels = np.array([[1, 2], [2, 4]], np.int8)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output_sum = ndimage.sum(input, labels=labels, index=[4, 8, 2])
|
||
|
|
output_labels = ndimage.sum_labels(
|
||
|
|
input, labels=labels, index=[4, 8, 2])
|
||
|
|
|
||
|
|
assert (output_sum == output_labels).all()
|
||
|
|
assert_array_almost_equal(output_labels, [4.0, 0.0, 5.0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_mean01():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.mean(input, labels=labels)
|
||
|
|
assert_almost_equal(output, 2.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_mean02():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
input = np.array([[1, 2], [3, 4]], bool)
|
||
|
|
output = ndimage.mean(input, labels=labels)
|
||
|
|
assert_almost_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_mean03():
|
||
|
|
labels = np.array([1, 2])
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.mean(input, labels=labels,
|
||
|
|
index=2)
|
||
|
|
assert_almost_equal(output, 3.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_mean04():
|
||
|
|
labels = np.array([[1, 2], [2, 4]], np.int8)
|
||
|
|
with np.errstate(all='ignore'):
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.mean(input, labels=labels,
|
||
|
|
index=[4, 8, 2])
|
||
|
|
assert_array_almost_equal(output[[0, 2]], [4.0, 2.5])
|
||
|
|
assert_(np.isnan(output[1]))
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum01():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.minimum(input, labels=labels)
|
||
|
|
assert_almost_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum02():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
input = np.array([[2, 2], [2, 4]], bool)
|
||
|
|
output = ndimage.minimum(input, labels=labels)
|
||
|
|
assert_almost_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum03():
|
||
|
|
labels = np.array([1, 2])
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.minimum(input, labels=labels,
|
||
|
|
index=2)
|
||
|
|
assert_almost_equal(output, 2.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum04():
|
||
|
|
labels = np.array([[1, 2], [2, 3]])
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.minimum(input, labels=labels,
|
||
|
|
index=[2, 3, 8])
|
||
|
|
assert_array_almost_equal(output, [2.0, 4.0, 0.0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum01():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.maximum(input, labels=labels)
|
||
|
|
assert_almost_equal(output, 3.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum02():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
input = np.array([[2, 2], [2, 4]], bool)
|
||
|
|
output = ndimage.maximum(input, labels=labels)
|
||
|
|
assert_almost_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum03():
|
||
|
|
labels = np.array([1, 2])
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.maximum(input, labels=labels,
|
||
|
|
index=2)
|
||
|
|
assert_almost_equal(output, 4.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum04():
|
||
|
|
labels = np.array([[1, 2], [2, 3]])
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.maximum(input, labels=labels,
|
||
|
|
index=[2, 3, 8])
|
||
|
|
assert_array_almost_equal(output, [3.0, 4.0, 0.0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum05():
|
||
|
|
# Regression test for ticket #501 (Trac)
|
||
|
|
x = np.array([-3, -2, -1])
|
||
|
|
assert_equal(ndimage.maximum(x), -1)
|
||
|
|
|
||
|
|
|
||
|
|
def test_median01():
|
||
|
|
a = np.array([[1, 2, 0, 1],
|
||
|
|
[5, 3, 0, 4],
|
||
|
|
[0, 0, 0, 7],
|
||
|
|
[9, 3, 0, 0]])
|
||
|
|
labels = np.array([[1, 1, 0, 2],
|
||
|
|
[1, 1, 0, 2],
|
||
|
|
[0, 0, 0, 2],
|
||
|
|
[3, 3, 0, 0]])
|
||
|
|
output = ndimage.median(a, labels=labels, index=[1, 2, 3])
|
||
|
|
assert_array_almost_equal(output, [2.5, 4.0, 6.0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_median02():
|
||
|
|
a = np.array([[1, 2, 0, 1],
|
||
|
|
[5, 3, 0, 4],
|
||
|
|
[0, 0, 0, 7],
|
||
|
|
[9, 3, 0, 0]])
|
||
|
|
output = ndimage.median(a)
|
||
|
|
assert_almost_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_median03():
|
||
|
|
a = np.array([[1, 2, 0, 1],
|
||
|
|
[5, 3, 0, 4],
|
||
|
|
[0, 0, 0, 7],
|
||
|
|
[9, 3, 0, 0]])
|
||
|
|
labels = np.array([[1, 1, 0, 2],
|
||
|
|
[1, 1, 0, 2],
|
||
|
|
[0, 0, 0, 2],
|
||
|
|
[3, 3, 0, 0]])
|
||
|
|
output = ndimage.median(a, labels=labels)
|
||
|
|
assert_almost_equal(output, 3.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_median_gh12836_bool():
|
||
|
|
# test boolean addition fix on example from gh-12836
|
||
|
|
a = np.asarray([1, 1], dtype=bool)
|
||
|
|
output = ndimage.median(a, labels=np.ones((2,)), index=[1])
|
||
|
|
assert_array_almost_equal(output, [1.0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_median_no_int_overflow():
|
||
|
|
# test integer overflow fix on example from gh-12836
|
||
|
|
a = np.asarray([65, 70], dtype=np.int8)
|
||
|
|
output = ndimage.median(a, labels=np.ones((2,)), index=[1])
|
||
|
|
assert_array_almost_equal(output, [67.5])
|
||
|
|
|
||
|
|
|
||
|
|
def test_variance01():
|
||
|
|
with np.errstate(all='ignore'):
|
||
|
|
for type in types:
|
||
|
|
input = np.array([], type)
|
||
|
|
with suppress_warnings() as sup:
|
||
|
|
sup.filter(RuntimeWarning, "Mean of empty slice")
|
||
|
|
output = ndimage.variance(input)
|
||
|
|
assert_(np.isnan(output))
|
||
|
|
|
||
|
|
|
||
|
|
def test_variance02():
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1], type)
|
||
|
|
output = ndimage.variance(input)
|
||
|
|
assert_almost_equal(output, 0.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_variance03():
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1, 3], type)
|
||
|
|
output = ndimage.variance(input)
|
||
|
|
assert_almost_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_variance04():
|
||
|
|
input = np.array([1, 0], bool)
|
||
|
|
output = ndimage.variance(input)
|
||
|
|
assert_almost_equal(output, 0.25)
|
||
|
|
|
||
|
|
|
||
|
|
def test_variance05():
|
||
|
|
labels = [2, 2, 3]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1, 3, 8], type)
|
||
|
|
output = ndimage.variance(input, labels, 2)
|
||
|
|
assert_almost_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_variance06():
|
||
|
|
labels = [2, 2, 3, 3, 4]
|
||
|
|
with np.errstate(all='ignore'):
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1, 3, 8, 10, 8], type)
|
||
|
|
output = ndimage.variance(input, labels, [2, 3, 4])
|
||
|
|
assert_array_almost_equal(output, [1.0, 1.0, 0.0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_standard_deviation01():
|
||
|
|
with np.errstate(all='ignore'):
|
||
|
|
for type in types:
|
||
|
|
input = np.array([], type)
|
||
|
|
with suppress_warnings() as sup:
|
||
|
|
sup.filter(RuntimeWarning, "Mean of empty slice")
|
||
|
|
output = ndimage.standard_deviation(input)
|
||
|
|
assert_(np.isnan(output))
|
||
|
|
|
||
|
|
|
||
|
|
def test_standard_deviation02():
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1], type)
|
||
|
|
output = ndimage.standard_deviation(input)
|
||
|
|
assert_almost_equal(output, 0.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_standard_deviation03():
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1, 3], type)
|
||
|
|
output = ndimage.standard_deviation(input)
|
||
|
|
assert_almost_equal(output, np.sqrt(1.0))
|
||
|
|
|
||
|
|
|
||
|
|
def test_standard_deviation04():
|
||
|
|
input = np.array([1, 0], bool)
|
||
|
|
output = ndimage.standard_deviation(input)
|
||
|
|
assert_almost_equal(output, 0.5)
|
||
|
|
|
||
|
|
|
||
|
|
def test_standard_deviation05():
|
||
|
|
labels = [2, 2, 3]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1, 3, 8], type)
|
||
|
|
output = ndimage.standard_deviation(input, labels, 2)
|
||
|
|
assert_almost_equal(output, 1.0)
|
||
|
|
|
||
|
|
|
||
|
|
def test_standard_deviation06():
|
||
|
|
labels = [2, 2, 3, 3, 4]
|
||
|
|
with np.errstate(all='ignore'):
|
||
|
|
for type in types:
|
||
|
|
input = np.array([1, 3, 8, 10, 8], type)
|
||
|
|
output = ndimage.standard_deviation(input, labels, [2, 3, 4])
|
||
|
|
assert_array_almost_equal(output, [1.0, 1.0, 0.0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_standard_deviation07():
|
||
|
|
labels = [1]
|
||
|
|
with np.errstate(all='ignore'):
|
||
|
|
for type in types:
|
||
|
|
input = np.array([-0.00619519], type)
|
||
|
|
output = ndimage.standard_deviation(input, labels, [1])
|
||
|
|
assert_array_almost_equal(output, [0])
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum_position01():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.minimum_position(input, labels=labels)
|
||
|
|
assert_equal(output, (0, 0))
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum_position02():
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 0, 2],
|
||
|
|
[1, 5, 1, 1]], type)
|
||
|
|
output = ndimage.minimum_position(input)
|
||
|
|
assert_equal(output, (1, 2))
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum_position03():
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 0, 2],
|
||
|
|
[1, 5, 1, 1]], bool)
|
||
|
|
output = ndimage.minimum_position(input)
|
||
|
|
assert_equal(output, (1, 2))
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum_position04():
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 1, 2],
|
||
|
|
[1, 5, 1, 1]], bool)
|
||
|
|
output = ndimage.minimum_position(input)
|
||
|
|
assert_equal(output, (0, 0))
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum_position05():
|
||
|
|
labels = [1, 2, 0, 4]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 0, 2],
|
||
|
|
[1, 5, 2, 3]], type)
|
||
|
|
output = ndimage.minimum_position(input, labels)
|
||
|
|
assert_equal(output, (2, 0))
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum_position06():
|
||
|
|
labels = [1, 2, 3, 4]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 0, 2],
|
||
|
|
[1, 5, 1, 1]], type)
|
||
|
|
output = ndimage.minimum_position(input, labels, 2)
|
||
|
|
assert_equal(output, (0, 1))
|
||
|
|
|
||
|
|
|
||
|
|
def test_minimum_position07():
|
||
|
|
labels = [1, 2, 3, 4]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 0, 2],
|
||
|
|
[1, 5, 1, 1]], type)
|
||
|
|
output = ndimage.minimum_position(input, labels,
|
||
|
|
[2, 3])
|
||
|
|
assert_equal(output[0], (0, 1))
|
||
|
|
assert_equal(output[1], (1, 2))
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum_position01():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output = ndimage.maximum_position(input,
|
||
|
|
labels=labels)
|
||
|
|
assert_equal(output, (1, 0))
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum_position02():
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 8, 2],
|
||
|
|
[1, 5, 1, 1]], type)
|
||
|
|
output = ndimage.maximum_position(input)
|
||
|
|
assert_equal(output, (1, 2))
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum_position03():
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 8, 2],
|
||
|
|
[1, 5, 1, 1]], bool)
|
||
|
|
output = ndimage.maximum_position(input)
|
||
|
|
assert_equal(output, (0, 0))
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum_position04():
|
||
|
|
labels = [1, 2, 0, 4]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 8, 2],
|
||
|
|
[1, 5, 1, 1]], type)
|
||
|
|
output = ndimage.maximum_position(input, labels)
|
||
|
|
assert_equal(output, (1, 1))
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum_position05():
|
||
|
|
labels = [1, 2, 0, 4]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 8, 2],
|
||
|
|
[1, 5, 1, 1]], type)
|
||
|
|
output = ndimage.maximum_position(input, labels, 1)
|
||
|
|
assert_equal(output, (0, 0))
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum_position06():
|
||
|
|
labels = [1, 2, 0, 4]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 8, 2],
|
||
|
|
[1, 5, 1, 1]], type)
|
||
|
|
output = ndimage.maximum_position(input, labels,
|
||
|
|
[1, 2])
|
||
|
|
assert_equal(output[0], (0, 0))
|
||
|
|
assert_equal(output[1], (1, 1))
|
||
|
|
|
||
|
|
|
||
|
|
def test_maximum_position07():
|
||
|
|
# Test float labels
|
||
|
|
labels = np.array([1.0, 2.5, 0.0, 4.5])
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 8, 2],
|
||
|
|
[1, 5, 1, 1]], type)
|
||
|
|
output = ndimage.maximum_position(input, labels,
|
||
|
|
[1.0, 4.5])
|
||
|
|
assert_equal(output[0], (0, 0))
|
||
|
|
assert_equal(output[1], (0, 3))
|
||
|
|
|
||
|
|
|
||
|
|
def test_extrema01():
|
||
|
|
labels = np.array([1, 0], bool)
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output1 = ndimage.extrema(input, labels=labels)
|
||
|
|
output2 = ndimage.minimum(input, labels=labels)
|
||
|
|
output3 = ndimage.maximum(input, labels=labels)
|
||
|
|
output4 = ndimage.minimum_position(input,
|
||
|
|
labels=labels)
|
||
|
|
output5 = ndimage.maximum_position(input,
|
||
|
|
labels=labels)
|
||
|
|
assert_equal(output1, (output2, output3, output4, output5))
|
||
|
|
|
||
|
|
|
||
|
|
def test_extrema02():
|
||
|
|
labels = np.array([1, 2])
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output1 = ndimage.extrema(input, labels=labels,
|
||
|
|
index=2)
|
||
|
|
output2 = ndimage.minimum(input, labels=labels,
|
||
|
|
index=2)
|
||
|
|
output3 = ndimage.maximum(input, labels=labels,
|
||
|
|
index=2)
|
||
|
|
output4 = ndimage.minimum_position(input,
|
||
|
|
labels=labels, index=2)
|
||
|
|
output5 = ndimage.maximum_position(input,
|
||
|
|
labels=labels, index=2)
|
||
|
|
assert_equal(output1, (output2, output3, output4, output5))
|
||
|
|
|
||
|
|
|
||
|
|
def test_extrema03():
|
||
|
|
labels = np.array([[1, 2], [2, 3]])
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 2], [3, 4]], type)
|
||
|
|
output1 = ndimage.extrema(input, labels=labels,
|
||
|
|
index=[2, 3, 8])
|
||
|
|
output2 = ndimage.minimum(input, labels=labels,
|
||
|
|
index=[2, 3, 8])
|
||
|
|
output3 = ndimage.maximum(input, labels=labels,
|
||
|
|
index=[2, 3, 8])
|
||
|
|
output4 = ndimage.minimum_position(input,
|
||
|
|
labels=labels, index=[2, 3, 8])
|
||
|
|
output5 = ndimage.maximum_position(input,
|
||
|
|
labels=labels, index=[2, 3, 8])
|
||
|
|
assert_array_almost_equal(output1[0], output2)
|
||
|
|
assert_array_almost_equal(output1[1], output3)
|
||
|
|
assert_array_almost_equal(output1[2], output4)
|
||
|
|
assert_array_almost_equal(output1[3], output5)
|
||
|
|
|
||
|
|
|
||
|
|
def test_extrema04():
|
||
|
|
labels = [1, 2, 0, 4]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[5, 4, 2, 5],
|
||
|
|
[3, 7, 8, 2],
|
||
|
|
[1, 5, 1, 1]], type)
|
||
|
|
output1 = ndimage.extrema(input, labels, [1, 2])
|
||
|
|
output2 = ndimage.minimum(input, labels, [1, 2])
|
||
|
|
output3 = ndimage.maximum(input, labels, [1, 2])
|
||
|
|
output4 = ndimage.minimum_position(input, labels,
|
||
|
|
[1, 2])
|
||
|
|
output5 = ndimage.maximum_position(input, labels,
|
||
|
|
[1, 2])
|
||
|
|
assert_array_almost_equal(output1[0], output2)
|
||
|
|
assert_array_almost_equal(output1[1], output3)
|
||
|
|
assert_array_almost_equal(output1[2], output4)
|
||
|
|
assert_array_almost_equal(output1[3], output5)
|
||
|
|
|
||
|
|
|
||
|
|
def test_center_of_mass01():
|
||
|
|
expected = [0.0, 0.0]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 0], [0, 0]], type)
|
||
|
|
output = ndimage.center_of_mass(input)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_center_of_mass02():
|
||
|
|
expected = [1, 0]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[0, 0], [1, 0]], type)
|
||
|
|
output = ndimage.center_of_mass(input)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_center_of_mass03():
|
||
|
|
expected = [0, 1]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[0, 1], [0, 0]], type)
|
||
|
|
output = ndimage.center_of_mass(input)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_center_of_mass04():
|
||
|
|
expected = [1, 1]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[0, 0], [0, 1]], type)
|
||
|
|
output = ndimage.center_of_mass(input)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_center_of_mass05():
|
||
|
|
expected = [0.5, 0.5]
|
||
|
|
for type in types:
|
||
|
|
input = np.array([[1, 1], [1, 1]], type)
|
||
|
|
output = ndimage.center_of_mass(input)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_center_of_mass06():
|
||
|
|
expected = [0.5, 0.5]
|
||
|
|
input = np.array([[1, 2], [3, 1]], bool)
|
||
|
|
output = ndimage.center_of_mass(input)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_center_of_mass07():
|
||
|
|
labels = [1, 0]
|
||
|
|
expected = [0.5, 0.0]
|
||
|
|
input = np.array([[1, 2], [3, 1]], bool)
|
||
|
|
output = ndimage.center_of_mass(input, labels)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_center_of_mass08():
|
||
|
|
labels = [1, 2]
|
||
|
|
expected = [0.5, 1.0]
|
||
|
|
input = np.array([[5, 2], [3, 1]], bool)
|
||
|
|
output = ndimage.center_of_mass(input, labels, 2)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_center_of_mass09():
|
||
|
|
labels = [1, 2]
|
||
|
|
expected = [(0.5, 0.0), (0.5, 1.0)]
|
||
|
|
input = np.array([[1, 2], [1, 1]], bool)
|
||
|
|
output = ndimage.center_of_mass(input, labels, [1, 2])
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_histogram01():
|
||
|
|
expected = np.ones(10)
|
||
|
|
input = np.arange(10)
|
||
|
|
output = ndimage.histogram(input, 0, 10, 10)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_histogram02():
|
||
|
|
labels = [1, 1, 1, 1, 2, 2, 2, 2]
|
||
|
|
expected = [0, 2, 0, 1, 1]
|
||
|
|
input = np.array([1, 1, 3, 4, 3, 3, 3, 3])
|
||
|
|
output = ndimage.histogram(input, 0, 4, 5, labels, 1)
|
||
|
|
assert_array_almost_equal(output, expected)
|
||
|
|
|
||
|
|
|
||
|
|
def test_histogram03():
|
||
|
|
labels = [1, 0, 1, 1, 2, 2, 2, 2]
|
||
|
|
expected1 = [0, 1, 0, 1, 1]
|
||
|
|
expected2 = [0, 0, 0, 3, 0]
|
||
|
|
input = np.array([1, 1, 3, 4, 3, 5, 3, 3])
|
||
|
|
output = ndimage.histogram(input, 0, 4, 5, labels, (1, 2))
|
||
|
|
|
||
|
|
assert_array_almost_equal(output[0], expected1)
|
||
|
|
assert_array_almost_equal(output[1], expected2)
|
||
|
|
|
||
|
|
|
||
|
|
def test_stat_funcs_2d():
|
||
|
|
a = np.array([[5, 6, 0, 0, 0], [8, 9, 0, 0, 0], [0, 0, 0, 3, 5]])
|
||
|
|
lbl = np.array([[1, 1, 0, 0, 0], [1, 1, 0, 0, 0], [0, 0, 0, 2, 2]])
|
||
|
|
|
||
|
|
mean = ndimage.mean(a, labels=lbl, index=[1, 2])
|
||
|
|
assert_array_equal(mean, [7.0, 4.0])
|
||
|
|
|
||
|
|
var = ndimage.variance(a, labels=lbl, index=[1, 2])
|
||
|
|
assert_array_equal(var, [2.5, 1.0])
|
||
|
|
|
||
|
|
std = ndimage.standard_deviation(a, labels=lbl, index=[1, 2])
|
||
|
|
assert_array_almost_equal(std, np.sqrt([2.5, 1.0]))
|
||
|
|
|
||
|
|
med = ndimage.median(a, labels=lbl, index=[1, 2])
|
||
|
|
assert_array_equal(med, [7.0, 4.0])
|
||
|
|
|
||
|
|
min = ndimage.minimum(a, labels=lbl, index=[1, 2])
|
||
|
|
assert_array_equal(min, [5, 3])
|
||
|
|
|
||
|
|
max = ndimage.maximum(a, labels=lbl, index=[1, 2])
|
||
|
|
assert_array_equal(max, [9, 5])
|
||
|
|
|
||
|
|
|
||
|
|
class TestWatershedIft:
|
||
|
|
|
||
|
|
def test_watershed_ift01(self):
|
||
|
|
data = np.array([[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.uint8)
|
||
|
|
markers = np.array([[-1, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 1, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.int8)
|
||
|
|
out = ndimage.watershed_ift(data, markers, structure=[[1, 1, 1],
|
||
|
|
[1, 1, 1],
|
||
|
|
[1, 1, 1]])
|
||
|
|
expected = [[-1, -1, -1, -1, -1, -1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1]]
|
||
|
|
assert_array_almost_equal(out, expected)
|
||
|
|
|
||
|
|
def test_watershed_ift02(self):
|
||
|
|
data = np.array([[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.uint8)
|
||
|
|
markers = np.array([[-1, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 1, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.int8)
|
||
|
|
out = ndimage.watershed_ift(data, markers)
|
||
|
|
expected = [[-1, -1, -1, -1, -1, -1, -1],
|
||
|
|
[-1, -1, 1, 1, 1, -1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, -1, 1, 1, 1, -1, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1]]
|
||
|
|
assert_array_almost_equal(out, expected)
|
||
|
|
|
||
|
|
def test_watershed_ift03(self):
|
||
|
|
data = np.array([[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 1, 0, 1, 0, 1, 0],
|
||
|
|
[0, 1, 0, 1, 0, 1, 0],
|
||
|
|
[0, 1, 0, 1, 0, 1, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.uint8)
|
||
|
|
markers = np.array([[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 2, 0, 3, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, -1]], np.int8)
|
||
|
|
out = ndimage.watershed_ift(data, markers)
|
||
|
|
expected = [[-1, -1, -1, -1, -1, -1, -1],
|
||
|
|
[-1, -1, 2, -1, 3, -1, -1],
|
||
|
|
[-1, 2, 2, 3, 3, 3, -1],
|
||
|
|
[-1, 2, 2, 3, 3, 3, -1],
|
||
|
|
[-1, 2, 2, 3, 3, 3, -1],
|
||
|
|
[-1, -1, 2, -1, 3, -1, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1]]
|
||
|
|
assert_array_almost_equal(out, expected)
|
||
|
|
|
||
|
|
def test_watershed_ift04(self):
|
||
|
|
data = np.array([[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 1, 0, 1, 0, 1, 0],
|
||
|
|
[0, 1, 0, 1, 0, 1, 0],
|
||
|
|
[0, 1, 0, 1, 0, 1, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.uint8)
|
||
|
|
markers = np.array([[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 2, 0, 3, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, -1]],
|
||
|
|
np.int8)
|
||
|
|
out = ndimage.watershed_ift(data, markers,
|
||
|
|
structure=[[1, 1, 1],
|
||
|
|
[1, 1, 1],
|
||
|
|
[1, 1, 1]])
|
||
|
|
expected = [[-1, -1, -1, -1, -1, -1, -1],
|
||
|
|
[-1, 2, 2, 3, 3, 3, -1],
|
||
|
|
[-1, 2, 2, 3, 3, 3, -1],
|
||
|
|
[-1, 2, 2, 3, 3, 3, -1],
|
||
|
|
[-1, 2, 2, 3, 3, 3, -1],
|
||
|
|
[-1, 2, 2, 3, 3, 3, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1]]
|
||
|
|
assert_array_almost_equal(out, expected)
|
||
|
|
|
||
|
|
def test_watershed_ift05(self):
|
||
|
|
data = np.array([[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 1, 0, 1, 0, 1, 0],
|
||
|
|
[0, 1, 0, 1, 0, 1, 0],
|
||
|
|
[0, 1, 0, 1, 0, 1, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.uint8)
|
||
|
|
markers = np.array([[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 3, 0, 2, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, -1]],
|
||
|
|
np.int8)
|
||
|
|
out = ndimage.watershed_ift(data, markers,
|
||
|
|
structure=[[1, 1, 1],
|
||
|
|
[1, 1, 1],
|
||
|
|
[1, 1, 1]])
|
||
|
|
expected = [[-1, -1, -1, -1, -1, -1, -1],
|
||
|
|
[-1, 3, 3, 2, 2, 2, -1],
|
||
|
|
[-1, 3, 3, 2, 2, 2, -1],
|
||
|
|
[-1, 3, 3, 2, 2, 2, -1],
|
||
|
|
[-1, 3, 3, 2, 2, 2, -1],
|
||
|
|
[-1, 3, 3, 2, 2, 2, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1]]
|
||
|
|
assert_array_almost_equal(out, expected)
|
||
|
|
|
||
|
|
def test_watershed_ift06(self):
|
||
|
|
data = np.array([[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.uint8)
|
||
|
|
markers = np.array([[-1, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 1, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.int8)
|
||
|
|
out = ndimage.watershed_ift(data, markers,
|
||
|
|
structure=[[1, 1, 1],
|
||
|
|
[1, 1, 1],
|
||
|
|
[1, 1, 1]])
|
||
|
|
expected = [[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1]]
|
||
|
|
assert_array_almost_equal(out, expected)
|
||
|
|
|
||
|
|
def test_watershed_ift07(self):
|
||
|
|
shape = (7, 6)
|
||
|
|
data = np.zeros(shape, dtype=np.uint8)
|
||
|
|
data = data.transpose()
|
||
|
|
data[...] = np.array([[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 0, 0, 0, 1, 0],
|
||
|
|
[0, 1, 1, 1, 1, 1, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.uint8)
|
||
|
|
markers = np.array([[-1, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 1, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0],
|
||
|
|
[0, 0, 0, 0, 0, 0, 0]], np.int8)
|
||
|
|
out = np.zeros(shape, dtype=np.int16)
|
||
|
|
out = out.transpose()
|
||
|
|
ndimage.watershed_ift(data, markers,
|
||
|
|
structure=[[1, 1, 1],
|
||
|
|
[1, 1, 1],
|
||
|
|
[1, 1, 1]],
|
||
|
|
output=out)
|
||
|
|
expected = [[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, 1, 1, 1, 1, 1, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1],
|
||
|
|
[-1, -1, -1, -1, -1, -1, -1]]
|
||
|
|
assert_array_almost_equal(out, expected)
|
||
|
|
|
||
|
|
def test_watershed_ift08(self):
|
||
|
|
# Test cost larger than uint8. See gh-10069.
|
||
|
|
data = np.array([[256, 0],
|
||
|
|
[0, 0]], np.uint16)
|
||
|
|
markers = np.array([[1, 0],
|
||
|
|
[0, 0]], np.int8)
|
||
|
|
out = ndimage.watershed_ift(data, markers)
|
||
|
|
expected = [[1, 1],
|
||
|
|
[1, 1]]
|
||
|
|
assert_array_almost_equal(out, expected)
|
||
|
|
|
||
|
|
def test_watershed_ift09(self):
|
||
|
|
# Test large cost. See gh-19575
|
||
|
|
data = np.array([[np.iinfo(np.uint16).max, 0],
|
||
|
|
[0, 0]], np.uint16)
|
||
|
|
markers = np.array([[1, 0],
|
||
|
|
[0, 0]], np.int8)
|
||
|
|
out = ndimage.watershed_ift(data, markers)
|
||
|
|
expected = [[1, 1],
|
||
|
|
[1, 1]]
|
||
|
|
assert_allclose(out, expected)
|