def testAddLevel(self):
"""
Tests addLevel()
"""
# one level data
hi_data = numpy.array([[1, 0, 2],
[1, 2, 2]])
hi = Hierarchy(data=hi_data)
hi.inset = [slice(3,5), slice(2,5)]
hi.setIds(ids=[1,2])
hi.levelIds = [[], [1,2]]
# segment (different inset)
seg_data = numpy.array([[2, 1],
[1, 1]])
seg = Segment(data=seg_data)
seg.inset = [slice(3,5), slice(1,3)]
# add
hi.addLevel(segment=seg, level=2, check=False, shift=10)
desired_data = numpy.array([[12, 1, 0, 2],
[11, 1, 2, 2]])
desired_inset = [slice(3,5), slice(1,5)]
np_test.assert_equal(hi.data, desired_data)
np_test.assert_equal(hi.inset, desired_inset)
np_test.assert_equal(hi.levelIds, [[], [1,2], [11,12]])
np_test.assert_equal(hi._higherIds, {1:11, 2:0})
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])
image_1in2 = Grey(image_ar_1[1:7, 1:9])
image_1in2.inset = [slice(1, 7), slice(1, 9)]
# boundaries 1
bound_ar_inset_1 = numpy.array(\
[[3, 3, 3, 3, 3, 3, 3, 3],
[5, 5, 5, 5, 5, 5, 5, 5],
[5, 5, 5, 5, 5, 5, 5, 5],
[5, 5, 5, 5, 5, 5, 5, 5],
[5, 5, 5, 5, 5, 5, 5, 5],
[4, 4, 4, 4, 4, 4, 4, 4]])
bound_ar_1 = numpy.zeros((10, 10), dtype=int)
bound_ar_1[1:7, 1:9] = bound_ar_inset_1
bound_1 = Segment(bound_ar_1)
bound_1in = Segment(bound_ar_inset_1)
bound_1in.inset = [slice(1, 7), slice(1, 9)]
# expected segmentation
threshold_1 = list(range(8))
ids_1 = list(range(1, 15))
levelIds_1 = [[], [1, 2], [3, 4, 5], [6, 7, 8, 9], [10, 11], [12], [13], [14]]
thresh_1 = [0, 1, 1, 2, 2, 2, 3, 3, 3, 3, 4, 4, 5, 6, 7]
data_1 = numpy.zeros((8, 4, 8), dtype='int')
data_1[0] = numpy.zeros((4, 8), dtype='int')
data_1[1] = numpy.array([[0, 1, 0, 0, 0, 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]])
data_1[2] = numpy.array([[0, 3, 0, 0, 0, 4, 4, 0], [0, 3, 0, 0, 0, 0, 4, 0],
[0, 0, 0, 0, 0, 0, 4, 0], [5, 0, 0, 0, 0, 0, 4, 0]])
data_1[3] = numpy.array([[0, 6, 0, 0, 0, 7, 7, 0], [0, 6, 0, 0, 0, 0, 7, 0],
[6, 6, 0, 0, 0, 0, 7, 0], [6, 0, 8, 0, 9, 0, 7, 0]])
data_1[4] = numpy.array([[0, 10, 0, 0, 11, 11, 11, 0],