def testLength(self):
# setup
bound_data = numpy.array([[2, 2, 2, 2, 2, 2, 2, 2, 2, 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],
[4, 4, 4, 4, 4, 4, 4, 4, 4, 4]])
bound = Segment(bound_data)
seg_data = numpy.array([[0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 1, 0, 3, 3, 0, 0, 5, 5, 0],
[0, 1, 3, 0, 0, 0, 0, 5, 0, 0],
[1, 1, 0, 3, 0, 5, 5, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0]])
seg = Segment(seg_data)
con = Contact()
con.findContacts(segment=seg, boundary=bound)
# b2b, straight mode
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='b2b',
line='straight',
position=True)
assert_almost_equal(mor.length[seg.ids], [4, 4, numpy.sqrt(17)])
assert_equal(mor.end1[seg.ids], numpy.array([[0, 1], [0, 3], [0, 7]]))
assert_equal(mor.end2[seg.ids], numpy.array([[4, 1], [4, 3], [4, 6]]))
# check lengths in straight mode
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='c2c',
line='straight',
position=True)
assert_almost_equal(mor.length[seg.ids], [2, 2, numpy.sqrt(5)])
assert_equal(mor.end1[seg.ids], numpy.array([[1, 1], [1, 3], [1, 7]]))
assert_equal(mor.end2[seg.ids], numpy.array([[3, 1], [3, 3], [3, 6]]))
# b2c, straight mode
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='b2c',
line='straight',
position=True)
assert_almost_equal(mor.length[seg.ids], [3, 3, numpy.sqrt(10)])
assert_equal(mor.end1[seg.ids], numpy.array([[0, 1], [0, 3], [0, 7]]))
assert_equal(mor.end2[seg.ids], numpy.array([[3, 1], [3, 3], [3, 6]]))
# c2b, straight mode
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='c2b',
line='straight',
position=True)
assert_almost_equal(mor.length[seg.ids], [3, 3, numpy.sqrt(10)])
assert_equal(mor.end1[seg.ids], numpy.array([[1, 1], [1, 3], [1, 7]]))
assert_equal(mor.end2[seg.ids], numpy.array([[4, 1], [4, 3], [4, 6]]))
# b2b in mid mode
bound.data[1, 0] = 1
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='b2b',
line='mid',
position=True)
assert_almost_equal(mor.length[seg.ids],
[4, 2 * numpy.sqrt(5), 2 + numpy.sqrt(5)])
assert_equal(mor.end1[seg.ids], numpy.array([[0, 1], [0, 3], [0, 7]]))
assert_equal(mor.end2[seg.ids], numpy.array([[4, 1], [4, 3], [4, 6]]))
# c2c in mid mode
bound.data[1, 0] = 1
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='c2c',
line='mid',
position=True)
assert_almost_equal(mor.length[seg.ids],
[2, 2 * numpy.sqrt(2), 1 + numpy.sqrt(2)])
assert_equal(mor.end1[seg.ids], numpy.array([[1, 1], [1, 3], [1, 7]]))
assert_equal(mor.end2[seg.ids], numpy.array([[3, 1], [3, 3], [3, 6]]))
# c2b in mid mode
bound.data[1, 0] = 1
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='c2b',
line='mid',
position=True)
assert_almost_equal(
mor.length[seg.ids],
[3, numpy.sqrt(5) + numpy.sqrt(2), 1 + numpy.sqrt(5)])
assert_equal(mor.end1[seg.ids], numpy.array([[1, 1], [1, 3], [1, 7]]))
assert_equal(mor.end2[seg.ids], numpy.array([[4, 1], [4, 3], [4, 6]]))
# b2c in mid mode
bound.data[1, 0] = 1
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='b2c',
line='mid',
position=True)
assert_almost_equal(
mor.length[seg.ids],
[3, numpy.sqrt(5) + numpy.sqrt(2), 2 + numpy.sqrt(2)])
assert_equal(mor.end1[seg.ids], numpy.array([[0, 1], [0, 3], [0, 7]]))
assert_equal(mor.end2[seg.ids], numpy.array([[3, 1], [3, 3], [3, 6]]))
# check length when segment far from the smallest inter-boundary
# distance
wedge_bound_data = numpy.array([[3, 3, 3, 3, 3, 0], [3, 3, 3, 3, 0, 0],
[3, 3, 3, 0, 0, 0], [3, 3, 0, 0, 0, 0],
[3, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0],
[2, 2, 2, 2, 2, 2]])
wedge_bound = Segment(data=wedge_bound_data)
segment_data = numpy.array([[0, 0, 0, 0, 0, 0], [0, 0, 0, 0, 0, 0],
[0, 0, 0, 5, 5, 5], [0, 0, 0, 0, 0, 5],
[0, 0, 0, 0, 0, 5], [0, 0, 0, 5, 5, 5],
[0, 0, 0, 0, 0, 0]])
seg = Segment(data=segment_data)
con = Contact()
con.findContacts(segment=seg, boundary=wedge_bound)
mor = Morphology()
mor.getLength(segments=seg,
boundaries=wedge_bound,
contacts=con,
distance='c2c',
line='straight',
position=True)
assert_almost_equal(mor.length[seg.ids], [3])
mor = Morphology()
mor.getLength(segments=seg,
boundaries=wedge_bound,
contacts=con,
distance='c2c',
line='mid',
position=True)
assert_almost_equal(mor.length[seg.ids], [2 + numpy.sqrt(5.)])
mor = Morphology()
mor.getLength(segments=seg,
boundaries=wedge_bound,
contacts=con,
distance='c2c',
line='mid-seg',
position=True)
assert_almost_equal(mor.length[seg.ids], [2 + numpy.sqrt(5.)])
# boundary not in the smallest segment inset
bound_data = numpy.array([[1, 1, 1], [0, 0, 0], [2, 2, 2]])
bound = Segment(data=bound_data)
seg_data = numpy.array([[0, 0, 0], [0, 5, 0], [0, 0, 0]])
seg = Segment(data=seg_data)
con = Contact()
con.findContacts(segment=seg, boundary=bound)
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='c2c',
line='straight',
position=False)
assert_almost_equal(mor.length[seg.ids], [0])
# boundary not in the given segment inset
bound_data = numpy.array([[1, 1, 1], [0, 0, 0], [2, 2, 2]])
bound = Segment(data=bound_data)
bound.inset = [slice(1, 4), slice(2, 5)]
seg_data = numpy.array([[0, 0, 0], [0, 5, 0], [0, 0, 0]])
seg = Segment(data=seg_data)
seg.inset = [slice(1, 4), slice(2, 5)]
con = Contact()
con.findContacts(segment=seg, boundary=bound)
seg.useInset(inset=[slice(2, 4), slice(2, 5)], mode='abs')
mor = Morphology()
mor.getLength(segments=seg,
boundaries=bound,
contacts=con,
distance='c2c',
line='straight',
position=False)
assert_almost_equal(mor.length[seg.ids], [0])
def testMake(self):
"""
Tests make()
"""
conn, contacts = \
Connected.make(image=common.image_1, boundary=common.bound_1,
thresh=4, boundaryIds=[3, 4], mask=5,
nBoundary=1, boundCount='ge')
np_test.assert_equal(conn.ids, [1, 2])
i1 = conn.data[2, 2]
i2 = conn.data[2, 5]
desired = numpy.zeros((10, 10), dtype=int)
desired[2:6, 1:9] = numpy.array(\
[[0, 1, 0, 0, 2, 2, 2, 0],
[0, 1, 0, 0, 2, 0, 2, 0],
[1, 1, 1, 0, 2, 0, 2, 2],
[1, 0, 1, 0, 2, 0, 2, 0]])
self.id_correspondence(conn.data, desired)
conn, contacts = \
Connected.make(image=common.image_1, boundary=common.bound_1,
thresh=4, boundaryIds=[3, 4], mask=5,
nBoundary=1, boundCount='exact')
np_test.assert_equal(conn.ids, [])
conn, contacts = \
Connected.make(image=common.image_1, boundary=common.bound_1,
thresh=2, boundaryIds=[3, 4], mask=5,
nBoundary=2, boundCount='eq')
np_test.assert_equal(conn.ids, [1])
conn, contacts = \
Connected.make(image=common.image_1, boundary=common.bound_1,
thresh=2, boundaryIds=[3, 4], mask=5,
nBoundary=1, boundCount='at_most')
np_test.assert_equal(conn.ids, [1, 2])
# test ids and data
conn, contacts = \
Connected.make(image=common.image_1, boundary=common.bound_1,
thresh=2, boundaryIds=[3, 4], mask=5,
nBoundary=1, boundCount='at_least')
np_test.assert_equal(conn.ids, [1, 2, 3])
desired = numpy.zeros((10, 10), dtype=int)
desired[2:6, 1:9] = numpy.array(\
[[0, 1, 0, 0, 0, 3, 3, 0],
[0, 1, 0, 0, 0, 0, 3, 0],
[0, 0, 0, 0, 0, 0, 3, 0],
[2, 0, 0, 0, 0, 0, 3, 0]])
self.id_correspondence(conn.data, desired)
# use insets
conn, contacts = Connected.make(image=common.image_1in2,
boundary=common.bound_1in,
thresh=2,
boundaryIds=[3, 4],
mask=5,
nBoundary=1,
boundCount='at_least')
np_test.assert_equal(conn.ids, [1, 2, 3])
self.id_correspondence(conn.data, desired[1:7, 1:9])
# mask Segment
mask = Segment(data=numpy.where(common.bound_1.data == 5, 1, 0))
image_inset = copy(common.image_1.inset)
bound_inset = copy(common.bound_1.inset)
image_data = common.image_1.data.copy()
bound_data = common.bound_1.data.copy()
conn, contacts = Connected.make(image=common.image_1,
boundary=common.bound_1,
thresh=2.,
boundaryIds=[3, 4],
mask=mask,
nBoundary=1,
boundCount='at_least')
np_test.assert_equal(conn.ids, [1, 2, 3])
desired = numpy.zeros((10, 10), dtype=int)
desired[2:6, 1:9] = numpy.array([[0, 1, 0, 0, 0, 3, 3, 0],
[0, 1, 0, 0, 0, 0, 3, 0],
[0, 0, 0, 0, 0, 0, 3, 0],
[2, 0, 0, 0, 0, 0, 3, 0]])
np_test.assert_equal(conn.data > 0, desired > 0)
np_test.assert_equal(image_inset, common.image_1.inset)
np_test.assert_equal(bound_inset, common.bound_1.inset)
np_test.assert_equal(image_data, common.image_1.data)
np_test.assert_equal(bound_data, common.bound_1.data)
# boundary inset, mask Segment same inset
mask = Segment(data=numpy.where(common.bound_1in.data == 5, 1, 0))
mask.setInset(inset=[slice(1, 7), slice(1, 9)], mode='abs')
conn, contacts = Connected.make(image=common.image_1,
boundary=common.bound_1in,
thresh=2,
boundaryIds=[3, 4],
mask=mask,
nBoundary=1,
boundCount='at_least')
np_test.assert_equal(conn.ids, [1, 2, 3])
np_test.assert_equal(conn.data.shape, (6, 8))
np_test.assert_equal(conn.inset, [slice(1, 7), slice(1, 9)])
desired = numpy.zeros((6, 8), dtype=int)
desired[1:5, 0:8] = numpy.array([[0, 1, 0, 0, 0, 3, 3, 0],
[0, 1, 0, 0, 0, 0, 3, 0],
[0, 0, 0, 0, 0, 0, 3, 0],
[2, 0, 0, 0, 0, 0, 3, 0]])
np_test.assert_equal(conn.data > 0, desired > 0)
# boundary inset, mask Segment smaller inset (inside boundaries)
mask = Segment(data=numpy.where(common.bound_1in.data == 5, 1, 0))
mask.setInset(inset=[slice(1, 7), slice(1, 9)], mode='abs')
mask.useInset([slice(2, 6), slice(1, 9)], mode='abs')
conn, contacts = Connected.make(image=common.image_1,
boundary=common.bound_1in,
thresh=2,
boundaryIds=[3, 4],
mask=mask,
nBoundary=1,
boundCount='at_least')
np_test.assert_equal(conn.ids, [1, 2, 3])
np_test.assert_equal(conn.data.shape, (6, 8))
np_test.assert_equal(conn.inset, [slice(1, 7), slice(1, 9)])
desired = numpy.zeros((6, 8), dtype=int)
desired[1:5, 0:8] = numpy.array([[0, 1, 0, 0, 0, 3, 3, 0],
[0, 1, 0, 0, 0, 0, 3, 0],
[0, 0, 0, 0, 0, 0, 3, 0],
[2, 0, 0, 0, 0, 0, 3, 0]])
np_test.assert_equal(conn.data > 0, desired > 0)
# boundary inset, mask Segment even smaller inset (inside boundaries)
mask = Segment(data=numpy.where(common.bound_1in.data == 5, 1, 0))
mask.setInset(inset=[slice(1, 7), slice(1, 9)], mode='abs')
mask.useInset([slice(2, 6), slice(2, 9)], mode='abs')
image_inset = copy(common.image_1.inset)
bound_inset = copy(common.bound_1in.inset)
image_data = common.image_1.data.copy()
bound_data = common.bound_1in.data.copy()
conn, contacts = Connected.make(image=common.image_1,
boundary=common.bound_1in,
thresh=2,
boundaryIds=[3, 4],
mask=mask,
nBoundary=1,
boundCount='at_least')
np_test.assert_equal(conn.ids, [1, 2])
np_test.assert_equal(conn.data.shape, (6, 8))
np_test.assert_equal(conn.inset, [slice(1, 7), slice(1, 9)])
desired = numpy.zeros((6, 8), dtype=int)
desired[1:5, 1:8] = numpy.array([[1, 0, 0, 0, 2, 2, 0],
[1, 0, 0, 0, 0, 2, 0],
[0, 0, 0, 0, 0, 2, 0],
[0, 0, 0, 0, 0, 2, 0]])
np_test.assert_equal(conn.data, desired)
np_test.assert_equal(image_inset, common.image_1.inset)
np_test.assert_equal(bound_inset, common.bound_1in.inset)
np_test.assert_equal(image_data, common.image_1.data)
np_test.assert_equal(bound_data, common.bound_1in.data)
# image smaller than boundaries
mask = Segment(data=numpy.where(common.bound_1in.data == 5, 1, 0))
mask.setInset(inset=[slice(1, 7), slice(1, 9)], mode='abs')
mask.useInset([slice(2, 6), slice(1, 9)], mode='abs')
image_inset = copy(common.image_1in.inset)
image_data = common.image_1in.data.copy()
bound_inset = copy(common.bound_1in.inset)
bound_data = common.bound_1in.data.copy()
conn, contacts = Connected.make(image=common.image_1in,
boundary=common.bound_1in,
thresh=2,
boundaryIds=[3, 4],
mask=mask,
nBoundary=1,
boundCount='at_least')
np_test.assert_equal(conn.ids, [1, 2, 3])
np_test.assert_equal(conn.data.shape, (6, 8))
np_test.assert_equal(conn.inset, [slice(1, 7), slice(1, 9)])
desired = numpy.zeros((6, 8), dtype=int)
desired[1:5, 0:8] = numpy.array([[0, 1, 0, 0, 0, 3, 3, 0],
[0, 1, 0, 0, 0, 0, 3, 0],
[0, 0, 0, 0, 0, 0, 3, 0],
[2, 0, 0, 0, 0, 0, 3, 0]])
np_test.assert_equal(conn.data > 0, desired > 0)
np_test.assert_equal(image_inset, common.image_1in.inset)
np_test.assert_equal(image_data, common.image_1in.data)
np_test.assert_equal(bound_inset, common.bound_1in.inset)
np_test.assert_equal(bound_data, common.bound_1in.data)
# image smaller than boundaries and intersects with free, boundaries
# intersects with free
image = Grey(data=common.image_1.data.copy())
image.useInset(inset=[slice(2, 6), slice(2, 9)], mode='abs')
image_inset = copy(image.inset)
image_data = image.data.copy()
common.bound_1in.useInset(inset=[slice(1, 7), slice(1, 8)], mode='abs')
bound_1in_inset = copy(common.bound_1in.inset)
bound_data = common.bound_1in.data.copy()
mask = Segment(data=numpy.where(common.bound_1in.data == 5, 1, 0))
mask.setInset(inset=[slice(1, 7), slice(1, 9)], mode='abs')
mask.useInset([slice(2, 6), slice(1, 9)], mode='abs')
conn, contacts = Connected.make(image=image,
boundary=common.bound_1in,
thresh=3,
boundaryIds=[3, 4],
mask=mask,
nBoundary=1,
boundCount='at_least')
np_test.assert_equal(conn.ids, [1, 2, 3, 4])
np_test.assert_equal(conn.data.shape, (6, 7))
np_test.assert_equal(conn.inset, [slice(1, 7), slice(1, 8)])
desired = numpy.zeros((6, 7), dtype=int)
desired[1:5, 0:8] = numpy.array([[0, 1, 0, 0, 0, 3, 3],
[0, 1, 0, 0, 0, 0, 3],
[0, 1, 0, 0, 0, 0, 3],
[0, 0, 4, 0, 2, 0, 3]])
np_test.assert_equal(conn.data > 0, desired > 0)
np_test.assert_equal(image_inset, image.inset)
np_test.assert_equal(bound_1in_inset, common.bound_1in.inset)
np_test.assert_equal(image_data, image.data)
np_test.assert_equal(bound_data, common.bound_1in.data)
common.bound_1in.useInset(inset=[slice(1, 7), slice(1, 9)],
mode='abs',
expand=True)
def testMakeFree(self):
"""
Tests makeFree()
"""
# int mask
free = common.bound_1.makeFree(ids=[3, 4],
size=0,
mask=5,
update=False)
np_test.assert_equal(free.data.shape, (10, 10))
np_test.assert_equal(free.data,
numpy.where(common.bound_1.data == 5, 1, 0))
# ndarray mask
mask = numpy.where(common.bound_1.data == 5, 2, 0)
free = common.bound_1.makeFree(ids=[3, 4],
size=0,
mask=mask,
update=False)
np_test.assert_equal(free.data.shape, (10, 10))
np_test.assert_equal(free.data,
numpy.where(common.bound_1.data == 5, 1, 0))
# Segment mask
mask = Segment(data=numpy.where(common.bound_1.data == 5, 3, 0))
free = common.bound_1.makeFree(ids=[3, 4],
size=0,
mask=mask,
update=False)
np_test.assert_equal(free.data.shape, (10, 10))
np_test.assert_equal(free.data,
numpy.where(common.bound_1.data == 5, 1, 0))
# boundary inset, Segment mask full size
mask = Segment(data=numpy.where(common.bound_1.data == 5, 3, 0))
free = common.bound_1in.makeFree(ids=[3, 4],
size=0,
mask=mask,
update=False)
np_test.assert_equal(free.data.shape, (6, 8))
np_test.assert_equal(free.data,
numpy.where(common.bound_1in.data == 5, 1, 0))
np_test.assert_equal(free.inset, [slice(1, 7), slice(1, 9)])
# boundary inset, mask Segment same inset
mask = Segment(data=numpy.where(common.bound_1.data == 5, 3, 0))
mask.useInset(inset=[slice(1, 7), slice(1, 9)])
free = common.bound_1in.makeFree(ids=[3, 4],
size=0,
mask=mask,
update=False)
np_test.assert_equal(free.data.shape, (6, 8))
np_test.assert_equal(free.data,
numpy.where(common.bound_1in.data == 5, 1, 0))
np_test.assert_equal(free.inset, [slice(1, 7), slice(1, 9)])
# boundary full size, mask Segment inset that includes boundary
mask = Segment(data=numpy.where(common.bound_1.data == 5, 3, 0))
mask.useInset(inset=[slice(1, 7), slice(1, 9)])
free = common.bound_1.makeFree(ids=[3, 4],
size=0,
mask=mask,
update=False)
np_test.assert_equal(free.data.shape, (10, 10))
np_test.assert_equal(free.data[1:7, 1:9],
numpy.where(common.bound_1in.data == 5, 1, 0))
np_test.assert_equal(free.inset, [slice(0, 10), slice(0, 10)])
# boundary full size, mask Segment inset that doesn't include boundary
mask = Segment(data=numpy.where(common.bound_1.data == 5, 3, 0))
mask.useInset(inset=[slice(2, 6), slice(1, 9)])
free = common.bound_1.makeFree(ids=[3, 4],
size=0,
mask=mask,
update=False)
np_test.assert_equal(free.data.shape, (10, 10))
np_test.assert_equal(free.data[1:7, 1:9],
numpy.where(common.bound_1in.data == 5, 1, 0))
np_test.assert_equal(free.inset, [slice(0, 10), slice(0, 10)])
# boundary inset, mask smaller inset that doesn't include boundary
mask = Segment(data=numpy.where(common.bound_1.data == 5, 3, 0))
mask.useInset(inset=[slice(2, 6), slice(1, 9)])
free = common.bound_1in.makeFree(ids=[3, 4],
size=0,
mask=mask,
update=False)
np_test.assert_equal(free.data.shape, (6, 8))
np_test.assert_equal(free.data,
numpy.where(common.bound_1in.data == 5, 1, 0))
np_test.assert_equal(free.inset, [slice(1, 7), slice(1, 9)])
# boundary smaller inset than mask
mask = Segment(data=numpy.where(common.bound_1.data == 5, 3, 0))
mask.useInset(inset=[slice(2, 6), slice(1, 9)])
common.bound_1in.useInset([slice(1, 7), slice(2, 7)], mode='absolute')
free = common.bound_1in.makeFree(ids=[3, 4],
size=0,
mask=mask,
update=False)
np_test.assert_equal(free.data.shape, (6, 5))
np_test.assert_equal(
free.data,
numpy.where(common.bound_1.data == 5, 1, 0)[1:7, 2:7])
np_test.assert_equal(free.inset, [slice(1, 7), slice(2, 7)])