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scikit-image/skimage/morphology/tests/test_watershed.py
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Josh Warner (Mac) b8334e85c8 failUnless -> assertTrue
2014-05-07 23:16:42 -05:00

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"""test_watershed.py - tests the watershed function
Originally part of CellProfiler, code licensed under both GPL and BSD licenses.
Website: http://www.cellprofiler.org
Copyright (c) 2003-2009 Massachusetts Institute of Technology
Copyright (c) 2009-2011 Broad Institute
All rights reserved.
Original author: Lee Kamentsky
"""
#Portions of this test were taken from scipy's watershed test in test_ndimage.py
#
# Copyright (C) 2003-2005 Peter J. Verveer
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
#
# 2. Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
#
# 3. The name of the author may not be used to endorse or promote
# products derived from this software without specific prior
# written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE AUTHOR ``AS IS'' AND ANY EXPRESS
# OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
# DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE
# GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
# WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
# NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import math
import unittest
import numpy as np
import scipy.ndimage
from skimage.morphology.watershed import watershed, _slow_watershed
eps = 1e-12
def diff(a, b):
if not isinstance(a, np.ndarray):
a = np.asarray(a)
if not isinstance(b, np.ndarray):
b = np.asarray(b)
if (0 in a.shape) and (0 in b.shape):
return 0.0
b[a == 0] = 0
if (a.dtype in [np.complex64, np.complex128] or
b.dtype in [np.complex64, np.complex128]):
a = np.asarray(a, np.complex128)
b = np.asarray(b, np.complex128)
t = ((a.real - b.real)**2).sum() + ((a.imag - b.imag)**2).sum()
else:
a = np.asarray(a)
a = a.astype(np.float64)
b = np.asarray(b)
b = b.astype(np.float64)
t = ((a - b)**2).sum()
return math.sqrt(t)
class TestWatershed(unittest.TestCase):
eight = np.ones((3, 3), bool)
def test_watershed01(self):
"watershed 1"
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, 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, 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 = watershed(data, markers, self.eight)
expected = np.array([[-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],
[-1, -1, -1, -1, -1, -1, -1],
[-1, -1, -1, -1, -1, -1, -1]])
error = diff(expected, out)
assert error < eps
out = _slow_watershed(data, markers, 8)
error = diff(expected, out)
assert error < eps
def test_watershed02(self):
"watershed 2"
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, 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, 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 = watershed(data, markers)
error = diff([[-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],
[-1, -1, 1, 1, 1, -1, -1],
[-1, -1, -1, -1, -1, -1, -1],
[-1, -1, -1, -1, -1, -1, -1]], out)
self.assertTrue(error < eps)
def test_watershed03(self):
"watershed 3"
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],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 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, 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 = watershed(data, markers)
error = diff([[-1, -1, -1, -1, -1, -1, -1],
[-1, 0, 2, 0, 3, 0, -1],
[-1, 2, 2, 0, 3, 3, -1],
[-1, 2, 2, 0, 3, 3, -1],
[-1, 2, 2, 0, 3, 3, -1],
[-1, 0, 2, 0, 3, 0, -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]], out)
self.assertTrue(error < eps)
def test_watershed04(self):
"watershed 4"
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],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 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, 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 = watershed(data, markers, self.eight)
error = diff([[-1, -1, -1, -1, -1, -1, -1],
[-1, 2, 2, 0, 3, 3, -1],
[-1, 2, 2, 0, 3, 3, -1],
[-1, 2, 2, 0, 3, 3, -1],
[-1, 2, 2, 0, 3, 3, -1],
[-1, 2, 2, 0, 3, 3, -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]], out)
self.assertTrue(error < eps)
def test_watershed05(self):
"watershed 5"
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],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 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, 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 = watershed(data, markers, self.eight)
error = diff([[-1, -1, -1, -1, -1, -1, -1],
[-1, 3, 3, 0, 2, 2, -1],
[-1, 3, 3, 0, 2, 2, -1],
[-1, 3, 3, 0, 2, 2, -1],
[-1, 3, 3, 0, 2, 2, -1],
[-1, 3, 3, 0, 2, 2, -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]], out)
self.assertTrue(error < eps)
def test_watershed06(self):
"watershed 6"
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],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0]], np.uint8)
markers = np.array([[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],
[0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0],
[-1, 0, 0, 0, 0, 0, 0]], np.int8)
out = watershed(data, markers, self.eight)
error = diff([[-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],
[-1, -1, -1, -1, -1, -1, -1]], out)
self.assertTrue(error < eps)
def test_watershed07(self):
"A regression test of a competitive case that failed"
data = np.array([[255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 204, 204, 204, 204, 204, 204, 255, 255, 255, 255, 255],
[255, 255, 255, 204, 204, 183, 153, 153, 153, 153, 183, 204, 204, 255, 255, 255],
[255, 255, 204, 183, 153, 141, 111, 103, 103, 111, 141, 153, 183, 204, 255, 255],
[255, 255, 204, 153, 111, 94, 72, 52, 52, 72, 94, 111, 153, 204, 255, 255],
[255, 255, 204, 153, 111, 72, 39, 1, 1, 39, 72, 111, 153, 204, 255, 255],
[255, 255, 204, 183, 141, 111, 72, 39, 39, 72, 111, 141, 183, 204, 255, 255],
[255, 255, 255, 204, 183, 141, 111, 72, 72, 111, 141, 183, 204, 255, 255, 255],
[255, 255, 255, 255, 204, 183, 141, 94, 94, 141, 183, 204, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 204, 153, 103, 103, 153, 204, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 204, 183, 141, 94, 94, 141, 183, 204, 255, 255, 255, 255],
[255, 255, 255, 204, 183, 141, 111, 72, 72, 111, 141, 183, 204, 255, 255, 255],
[255, 255, 204, 183, 141, 111, 72, 39, 39, 72, 111, 141, 183, 204, 255, 255],
[255, 255, 204, 153, 111, 72, 39, 1, 1, 39, 72, 111, 153, 204, 255, 255],
[255, 255, 204, 153, 111, 94, 72, 52, 52, 72, 94, 111, 153, 204, 255, 255],
[255, 255, 204, 183, 153, 141, 111, 103, 103, 111, 141, 153, 183, 204, 255, 255],
[255, 255, 255, 204, 204, 183, 153, 153, 153, 153, 183, 204, 204, 255, 255, 255],
[255, 255, 255, 255, 255, 204, 204, 204, 204, 204, 204, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255]])
mask = (data != 255)
markers = np.zeros(data.shape, int)
markers[6, 7] = 1
markers[14, 7] = 2
out = watershed(data, markers, self.eight, mask=mask)
#
# The two objects should be the same size, except possibly for the
# border region
#
size1 = np.sum(out == 1)
size2 = np.sum(out == 2)
self.assertTrue(abs(size1 - size2) <= 6)
def test_watershed08(self):
"The border pixels + an edge are all the same value"
data = np.array([[255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 204, 204, 204, 204, 204, 204, 255, 255, 255, 255, 255],
[255, 255, 255, 204, 204, 183, 153, 153, 153, 153, 183, 204, 204, 255, 255, 255],
[255, 255, 204, 183, 153, 141, 111, 103, 103, 111, 141, 153, 183, 204, 255, 255],
[255, 255, 204, 153, 111, 94, 72, 52, 52, 72, 94, 111, 153, 204, 255, 255],
[255, 255, 204, 153, 111, 72, 39, 1, 1, 39, 72, 111, 153, 204, 255, 255],
[255, 255, 204, 183, 141, 111, 72, 39, 39, 72, 111, 141, 183, 204, 255, 255],
[255, 255, 255, 204, 183, 141, 111, 72, 72, 111, 141, 183, 204, 255, 255, 255],
[255, 255, 255, 255, 204, 183, 141, 94, 94, 141, 183, 204, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 204, 153, 141, 141, 153, 204, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 204, 183, 141, 94, 94, 141, 183, 204, 255, 255, 255, 255],
[255, 255, 255, 204, 183, 141, 111, 72, 72, 111, 141, 183, 204, 255, 255, 255],
[255, 255, 204, 183, 141, 111, 72, 39, 39, 72, 111, 141, 183, 204, 255, 255],
[255, 255, 204, 153, 111, 72, 39, 1, 1, 39, 72, 111, 153, 204, 255, 255],
[255, 255, 204, 153, 111, 94, 72, 52, 52, 72, 94, 111, 153, 204, 255, 255],
[255, 255, 204, 183, 153, 141, 111, 103, 103, 111, 141, 153, 183, 204, 255, 255],
[255, 255, 255, 204, 204, 183, 153, 153, 153, 153, 183, 204, 204, 255, 255, 255],
[255, 255, 255, 255, 255, 204, 204, 204, 204, 204, 204, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255],
[255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255, 255]])
mask = (data != 255)
markers = np.zeros(data.shape, int)
markers[6, 7] = 1
markers[14, 7] = 2
out = watershed(data, markers, self.eight, mask=mask)
#
# The two objects should be the same size, except possibly for the
# border region
#
size1 = np.sum(out == 1)
size2 = np.sum(out == 2)
self.assertTrue(abs(size1 - size2) <= 6)
def test_watershed09(self):
"""Test on an image of reasonable size
This is here both for timing (does it take forever?) and to
ensure that the memory constraints are reasonable
"""
image = np.zeros((1000, 1000))
coords = np.random.uniform(0, 1000, (100, 2)).astype(int)
markers = np.zeros((1000, 1000), int)
idx = 1
for x, y in coords:
image[x, y] = 1
markers[x, y] = idx
idx += 1
image = scipy.ndimage.gaussian_filter(image, 4)
watershed(image, markers, self.eight)
scipy.ndimage.watershed_ift(image.astype(np.uint16), markers,
self.eight)
if __name__ == "__main__":
np.testing.run_module_suite()
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