def test_custom_dist_func(self):
# Several 2D random walkers
N = 5
length = 5
step_size = 2
search_range = 3
steps = (np.random.random((2, length, N)) - 0.5) * step_size
x, y = np.cumsum(steps, axis=2)
f = DataFrame(dict(x=x.ravel(), y=y.ravel(),
frame=np.repeat(np.arange(length), N)))
# link in normal (2D Euclidean) coordinates
expected = self.link(f, search_range)
# compute radial coordinates
f_radial = f.copy()
f_radial['angle'] = np.arctan2(f_radial['y'], f_radial['x'])
f_radial['r'] = np.sqrt(f_radial['y']**2 + f_radial['x']**2)
# leave x, y for the comparison at the end
def dist_func(a, b):
x1 = a[0] * np.cos(a[1])
y1 = a[0] * np.sin(a[1])
x2 = b[0] * np.cos(b[1])
y2 = b[0] * np.sin(b[1])
return np.sqrt((x1 - x2)**2 + (y1 - y2)**2)
# link using a custom distance function
actual = self.link(f_radial, search_range, pos_columns=['r', 'angle'],
dist_func=dist_func)
assert_traj_equal(actual, expected)
def test_isolated_continuous_random_walks(self):
# Two 2D random walks
np.random.seed(0)
N = 30
Y = 250
M = 20 # margin, because negative values raise OutOfHash
a = DataFrame({'x': M + random_walk(N), 'y': M + random_walk(N), 'frame': np.arange(N)})
b = DataFrame({'x': M + random_walk(N - 1), 'y': M + Y + random_walk(N - 1), 'frame': np.arange(1, N)})
f = pd.concat([a, b])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate([np.zeros(N), np.ones(N - 1)])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
# Many 2D random walks
np.random.seed(0)
initial_positions = [(100, 100), (200, 100), (100, 200), (200, 200)]
import itertools
c = itertools.count()
def walk(x, y):
i = next(c)
return DataFrame({'x': x + random_walk(N - i),
'y': y + random_walk(N - i),
'frame': np.arange(i, N)})
f = pd.concat([walk(*pos) for pos in initial_positions])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate([i*np.ones(N - i) for i in range(len(initial_positions))])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
def test_two_isolated(self):
shape = (32, 32)
expected = DataFrame({'x': [8, 16, 24, 16], 'y': [8, 8, 24, 24],
'frame': [0, 1, 0, 1], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
def test_quadrature_distances(self):
"""A simple test to check whether the subnet linker adds
orthogonal coordinates in quadrature (as in Pythagoras).
We have two possible linking results:
1. A->C and B->D, cost (linear) = 16, cost (quadrature) = 200
2. A->D and B->C, cost (linear) = 28, cost (quadrature) = 200
"""
def subnet_test(epsilon):
"""Returns 2 features in 2 frames, which represent a special
case when the subnet linker adds distances in quadrature. With
epsilon=0, subnet linking is degenerate. Therefore
linking should differ for positive and negative epsilon."""
return pd.DataFrame([(0, 6, 0), #A
(0, 14 + epsilon, 8), #B
(1, 8, 0), #C
(1, 0, 8)], #D
columns=['frame', 'x', 'y'])
trpos = self.link(subnet_test(1), 20)
expected = subnet_test(1)
expected['particle'] = np.array([0, 1, 1, 0])
assert_traj_equal(trpos, expected)
trneg = self.link(subnet_test(-1), 20)
expected = subnet_test(-1)
expected['particle'] = np.array([0, 1, 0, 1])
assert_traj_equal(trneg, expected)
def test_custom_to_eucl(self):
# Several 2D random walkers
N = 5
length = 5
step_size = 2
search_range = 3
steps = (np.random.random((2, length, N)) - 0.5) * step_size
x, y = np.cumsum(steps, axis=2)
f = DataFrame(dict(x=x.ravel(), y=y.ravel(),
frame=np.repeat(np.arange(length), N)))
# link in normal (2D Euclidean) coordinates
expected = self.link(f, search_range)
# compute radial coordinates
f_radial = f.copy()
f_radial['angle'] = np.arctan2(f_radial['y'], f_radial['x'])
f_radial['r'] = np.sqrt(f_radial['y'] ** 2 + f_radial['x'] ** 2)
# leave x, y for the comparison at the end
def to_eucl(arr):
r, angle = arr.T
x = r * np.cos(angle)
y = r * np.sin(angle)
return np.array([x, y]).T
# link using a custom distance function
actual = self.link(f_radial, search_range, pos_columns=['r', 'angle'],
to_eucl=to_eucl)
assert_traj_equal(actual, expected)
def test_one(self):
expected = DataFrame({'x': [8, 16], 'y': [16, 16],
'frame': [0, 1], 'particle': [0, 0]})
actual = self.link(expected, shape=(24, 24), remove=[0])
assert_traj_equal(actual, expected)
actual = self.link(expected, shape=(24, 24), search_range=7, remove=[0])
assert_equal(len(actual), 1)
def test_link_memory(self):
expected = pd.DataFrame(self.coords_link,
columns=self.pos_columns + ['frame'])
expected['frame'] = expected['frame'].astype(np.int)
actual = tp.link(expected, memory=self.memory, **self.link_params)
expected['particle'] = self.expected_link_memory
assert_traj_equal(actual, expected)
def test_one_trivial_stepper(self):
# One 1D stepper
N = 5
f = DataFrame({'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
expected = f.copy()
expected['particle'] = np.zeros(N)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
def test_blank_frame_no_memory(self):
# One 1D stepper
N = 5
f = DataFrame({'x': np.arange(N), 'y': np.ones(N),
'frame': [0, 1, 2, 4, 5],
'particle': [0, 0, 0, 1, 1]})
expected = f.copy()
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
def test_two_full_overlap(self):
shape = (24, 24)
# a --> b
# c --> d # a-c, b-c, b-d, a-d overlap
expected = DataFrame({'x': [8, 15, 8, 15], 'y': [8, 8, 16, 16],
'frame': [0, 1, 0, 1], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
def test_start_at_frame_other_than_zero(self):
# One 1D stepper
N = 5
FIRST_FRAME = 3
f = DataFrame({'x': np.arange(N), 'y': np.ones(N),
'frame': FIRST_FRAME + np.arange(N)})
expected = f.copy()
expected['particle'] = np.zeros(N)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
def test_splitting_subnets(self):
shape = (24, 48)
expected = pd.DataFrame({'x': [8, 12, 16, 20, 32, 28, 40, 36],
'y': [8, 16, 8, 16, 8, 16, 8, 16],
'frame': [1, 0, 1, 0, 1, 0, 1, 0],
'particle': [0, 0, 1, 1, 2, 2, 3, 3]})
for n in range(5):
for remove in itertools.combinations(range(4), n):
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
def test_args_dtype(self):
"""Check whether find_link accepts float typed arguments"""
# One 1D stepper
N = 5
f = DataFrame(
{'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
expected = f.copy()
expected['particle'] = np.zeros(N)
# Should not raise
actual = self.link_df(f, 5.2, separation=9.5, diameter=15.2)
assert_traj_equal(actual, expected)
def test_copy(self):
"""Check inplace/copy behavior of link_df """
# One 1D stepper
N = 5
f = DataFrame({'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
expected = f.copy()
expected['particle'] = np.zeros(N)
# Should copy
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
assert 'particle' not in f.columns
def test_shifting_string(self):
shape = (24, 48)
shift = 5
expected = pd.DataFrame({'x': [8, 8+shift, 16, 16+shift,
24, 24+shift, 32, 32+shift],
'y': [8, 16, 8, 16, 8, 16, 8, 16],
'frame': [0, 1, 0, 1, 0, 1, 0, 1],
'particle': [0, 0, 1, 1, 2, 2, 3, 3]})
for n in range(5):
for remove in itertools.combinations(range(4), n):
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
def test_copy(self):
"""Check inplace/copy behavior of link_df, link_df_iter"""
# One 1D stepper
N = 5
f = DataFrame({'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
f_inplace = f.copy()
expected = f.copy()
expected['particle'] = np.zeros(N)
# Should add particle column in-place
# UNLESS diagnostics are enabled (or input dataframe is not writeable)
actual = self.link_df(f_inplace, 5)
assert_traj_equal(actual, expected)
if self.do_diagnostics:
assert 'particle' not in f_inplace.columns
else:
assert_traj_equal(actual, f_inplace)
# Should copy
actual = self.link_df(f, 5, copy_features=True)
assert_traj_equal(actual, expected)
assert 'particle' not in f.columns
# Should copy
actual_iter = self.link_df_iter(f, 5, hash_size=(10, 2))
assert_traj_equal(actual_iter, expected)
assert 'particle' not in f.columns
def test_multiple_lost_simple(self):
shape = (32, 32)
# b a, b, c, d in frame 0
# a e c e in frame 1, disappears, should be linked to correct one
# d
# left
expected = pd.DataFrame({'x': [8, 16, 24, 16, 15],
'y': [16, 8, 16, 24, 16],
'frame': [0, 0, 0, 0, 1],
'particle': [0, 1, 2, 3, 0]})
actual = self.link(expected, shape=shape, remove=[0])
assert_traj_equal(actual, expected)
# top
expected = pd.DataFrame({'x': [8, 16, 24, 16, 16],
'y': [16, 8, 16, 24, 15],
'frame': [0, 0, 0, 0, 1],
'particle': [0, 1, 2, 3, 1]})
actual = self.link(expected, shape=shape, remove=[0])
assert_traj_equal(actual, expected)
# right
expected = pd.DataFrame({'x': [8, 16, 24, 16, 17],
'y': [16, 8, 16, 24, 16],
'frame': [0, 0, 0, 0, 1],
'particle': [0, 1, 2, 3, 2]})
actual = self.link(expected, shape=shape, remove=[0])
assert_traj_equal(actual, expected)
# bottom
expected = pd.DataFrame({'x': [8, 16, 24, 16, 16],
'y': [16, 8, 16, 24, 17],
'frame': [0, 0, 0, 0, 1],
'particle': [0, 1, 2, 3, 3]})
actual = self.link(expected, shape=shape, remove=[0])
assert_traj_equal(actual, expected)
def test_two_double_overlap(self):
shape = (24, 32)
# (a b) c --> d # a-c and b-c overlap
expected = DataFrame({'x': [8, 8, 16, 24], 'y': [8, 16, 12, 12],
'frame': [0, 1, 0, 1], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
# (a b) d <-- c # a-d and b-d overlap
expected = DataFrame({'x': [8, 8, 16, 24], 'y': [8, 16, 12, 12],
'frame': [0, 1, 1, 0], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
def test_blank_frame_no_memory(self):
N = 5
f = DataFrame({'x': np.arange(N), 'y': np.ones(N),
'frame': [0, 1, 2, 4, 5]})
expected = f.copy()
# Using link_df, the particle will be given a new ID after the gap.
expected['particle'] = np.array([0, 0, 0, 1, 1], dtype=np.float64)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
# link_df_iter will (in this test suite) iterate over only the frames
# present in the dataframe, so the gap will be ignored.
expected['particle'] = 0.0
actual = self.link_df_iter(f, 5, hash_size=(10, 10))
assert_traj_equal(actual, expected)
def test_one_trivial_stepper(self):
# One 1D stepper
N = 5
f = DataFrame({'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
expected = f.copy()
expected['particle'] = np.zeros(N)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(f, 5, hash_size=(10, 2))
assert_traj_equal(actual_iter, expected)
if self.do_diagnostics:
assert 'diag_search_range' in self.diag.columns
# Except for first frame, all particles should have been labeled
# with a search_range
assert not any(self.diag['diag_search_range'][
actual_iter.frame > 0].isnull())
def test_drop_link(self):
# One 1D stepper. A new particle appears in frame 2.
# The resulting subnet causes the trajectory to be broken
# when link_strategy is 'drop' and search_range is large enough.
N = 2
f_1particle = DataFrame({'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
f = f_1particle.append(DataFrame(
{'x': [3], 'y': [1], 'frame': [1]}), ignore_index=True)
f_expected_without_subnet = f.copy()
f_expected_without_subnet['particle'] = [0, 0, 1]
# The linker assigns new particle IDs in arbitrary order. So
# comparing with expected values is tricky.
# We just check for the creation of 2 new trajectories.
without_subnet = self.link_df(f, 1.5, retain_index=True)
assert_traj_equal(without_subnet, f_expected_without_subnet)
with_subnet = self.link_df(f, 5, retain_index=True)
assert set(with_subnet.particle) == set((0, 1, 2))
def test_quadrature_sum(self):
"""A simple test to check whether the subnet linker adds
distances in quadrature (as in Crocker-Grier)."""
def subnet_test(epsilon):
"""Returns 2 features in 2 frames, which represent a special
case when the subnet linker adds distances in quadrature. With
epsilon=0, subnet linking is degenerate. Therefore
linking should differ for positive and negative epsilon."""
return pd.DataFrame([(0, 10, 30), (0, 10, 0),
(1, 0, 20), (1, 30, 20 + epsilon)],
columns=['frame', 'x', 'y'])
trpos = self.link(subnet_test(1), 30)
expected = subnet_test(1)
expected['particle'] = np.array([0, 1, 1, 0])
assert_traj_equal(trpos, expected)
trneg = self.link(subnet_test(-1), 30)
expected = subnet_test(-1)
expected['particle'] = np.array([0, 1, 0, 1])
assert_traj_equal(trneg, expected)
def test_multiple_lost_subnet(self):
shape = (24, 48)
# (subnet 1, a-c) g (subnet 2, d-f)
# left
expected = pd.DataFrame({'x': [8, 10, 16, 32, 40, 38, 23],
'y': [8, 16, 8, 8, 8, 16, 8],
'frame': [0, 1, 0, 0, 0, 1, 1],
'particle': [0, 0, 1, 2, 3, 3, 1]})
for n in range(3):
for remove in itertools.combinations(range(3), n):
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
# right
expected = pd.DataFrame({'x': [8, 10, 16, 32, 40, 38, 25],
'y': [8, 16, 8, 8, 8, 16, 8],
'frame': [0, 1, 0, 0, 0, 1, 1],
'particle': [0, 0, 1, 2, 3, 3, 2]})
for n in range(3):
for remove in itertools.combinations(range(3), n):
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
def test_memory_on_one_gap(self):
N = 5
Y = 2
# Begin second feature one frame later than the first, so the particle labeling (0, 1) is
# established and not arbitrary.
a = DataFrame({'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
b = DataFrame({'x': np.arange(1, N), 'y': Y + np.ones(N - 1), 'frame': np.arange(1, N)})
a = a.drop(3).reset_index(drop=True)
f = pd.concat([a, b])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate([np.array([0, 0, 0, 0]), np.ones(N - 1)])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
expected.reset_index(drop=True, inplace=True)
actual = self.link_df(f, 5, memory=1)
assert_traj_equal(actual, expected)
# Sort rows by frame (normal use)
actual = self.link_df(pandas_sort(f, 'frame'), 5, memory=1)
assert_traj_equal(actual, expected)
# Shuffle rows (crazy!)
np.random.seed(0)
f1 = f.reset_index(drop=True)
f1.reindex(np.random.permutation(f1.index))
actual = self.link_df(f1, 5, memory=1)
assert_traj_equal(actual, expected)
def test_two_isolated_steppers_one_gapped(self):
N = 5
Y = 25
# Begin second feature one frame later than the first,
# so the particle labeling (0, 1) is established and not arbitrary.
a = DataFrame({'x': np.arange(N), 'y': np.ones(N),
'frame': np.arange(N)})
a = a.drop(3).reset_index(drop=True)
b = DataFrame({'x': np.arange(1, N), 'y': Y + np.ones(N - 1),
'frame': np.arange(1, N)})
f = pd.concat([a, b])
expected = f.copy()
expected['particle'] = np.concatenate([np.array([0, 0, 0, 2]), np.ones(N - 1)])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
expected.reset_index(drop=True, inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
# link_df_iter() tests not performed, because hash_size is
# not knowable from the first frame alone.
# Sort rows by frame (normal use)
actual = self.link_df(pandas_sort(f, 'frame'), 5)
assert_traj_equal(actual, expected)
# Shuffle rows (crazy!)
np.random.seed(0)
f1 = f.reset_index(drop=True)
f1.reindex(np.random.permutation(f1.index))
actual = self.link_df(f1, 5)
assert_traj_equal(actual, expected)
def test_two_single_overlap(self):
shape = (16, 40)
# a --> b c --> d : b-c overlap
expected = DataFrame({'x': [8, 16, 24, 32], 'y': [8, 8, 8, 8],
'frame': [0, 1, 0, 1], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
# a --> b d <-- c : b-d overlap
expected = DataFrame({'x': [8, 16, 24, 32], 'y': [8, 8, 8, 8],
'frame': [0, 1, 1, 0], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
# b <-- a d --> c : a-d overlap
expected = DataFrame({'x': [8, 16, 24, 32], 'y': [8, 8, 8, 8],
'frame': [1, 0, 0, 1], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
def test_two_triple_overlap(self):
shape = (24, 32)
# a --> b
# c --> d # a-c, b-c, and b-d overlap
expected = DataFrame({'x': [8, 16, 16, 24], 'y': [8, 8, 16, 16],
'frame': [0, 1, 0, 1], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
# a --> b
# d <-- c # a-d, b-d, and b-c overlap
expected = DataFrame({'x': [8, 16, 16, 24], 'y': [8, 8, 16, 16],
'frame': [0, 1, 1, 0], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
# b <-- a
# c -- > d # b-c, a-c, and a-d overlap
expected = DataFrame({'x': [8, 16, 16, 24], 'y': [8, 8, 16, 16],
'frame': [1, 0, 0, 1], 'particle': [0, 0, 1, 1]})
for remove in [[], [0], [1], [0, 1]]:
actual = self.link(expected, shape=shape, remove=remove)
assert_traj_equal(actual, expected)
def test_nearby_continuous_random_walks(self):
# Two 2D random walks
np.random.seed(0)
N = 30
Y = 250
M = 20 # margin, because negative values raise OutOfHash
a = DataFrame({'x': M + random_walk(N),
'y': M + random_walk(N),
'frame': np.arange(N)})
b = DataFrame({'x': M + random_walk(N - 1),
'y': M + Y + random_walk(N - 1),
'frame': np.arange(1, N)})
f = pandas_concat([a, b])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate([np.zeros(N), np.ones(N - 1)])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
actual = self.link_df_iter(f, 5, hash_size=(2*M, 2*M + Y))
assert_traj_equal(actual, expected)
# Several 2D random walks
np.random.seed(0)
initial_positions = [(10, 11), (10, 18), (14, 15), (20, 21), (13, 13),
(10, 10), (17, 19)]
import itertools
c = itertools.count()
def walk(x, y):
i = next(c)
return DataFrame({'x': x + random_walk(N - i),
'y': y + random_walk(N - i),
'frame': np.arange(i, N)})
f = pandas_concat([walk(*pos) for pos in initial_positions])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate([i*np.ones(N - i) for i in range(len(initial_positions))])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
actual = self.link_df_iter(f, 5, hash_size=(2*M, 2*M))
assert_traj_equal(actual, expected)
# Shuffle rows (crazy!)
np.random.seed(0)
f1 = f.reset_index(drop=True)
f1.reindex(np.random.permutation(f1.index))
actual = self.link_df(f1, 5)
assert_traj_equal(actual, expected)
actual = self.link_df_iter(f1, 5, hash_size=(2*M, 2*M))
assert_traj_equal(actual, expected)
def test_two_nearby_steppers_one_gapped(self):
N = 5
Y = 2
# Begin second feature one frame later than the first, so the particle labeling (0, 1) is
# established and not arbitrary.
a = DataFrame({'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
b = DataFrame({'x': np.arange(1, N), 'y': Y + np.ones(N - 1), 'frame': np.arange(1, N)})
a = a.drop(3).reset_index(drop=True)
f = pandas_concat([a, b])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate([np.array([0, 0, 0, 2]), np.ones(N - 1)])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
expected.reset_index(drop=True, inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(f, 5, hash_size=(50, 50))
assert_traj_equal(actual_iter, expected)
# Sort rows by frame (normal use)
actual = self.link_df(pandas_sort(f, 'frame'), 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(pandas_sort(f, 'frame'), 5, hash_size=(50, 50))
assert_traj_equal(actual_iter, expected)
# Shuffle rows (crazy!)
np.random.seed(0)
f1 = f.reset_index(drop=True)
f1.reindex(np.random.permutation(f1.index))
actual = self.link_df(f1, 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(f1, 5, hash_size=(50, 50))
assert_traj_equal(actual_iter, expected)
def test_two_nearby_steppers(self):
N = 5
Y = 2
# Begin second feature one frame later than the first, so the particle labeling (0, 1) is
# established and not arbitrary.
a = DataFrame({'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
b = DataFrame({'x': np.arange(1, N), 'y': Y + np.ones(N - 1), 'frame': np.arange(1, N)})
f = pandas_concat([a, b])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate([np.zeros(N), np.ones(N - 1)])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(f, 5, hash_size=(50, 50))
assert_traj_equal(actual_iter, expected)
# Sort rows by frame (normal use)
actual = self.link_df(pandas_sort(f, 'frame'), 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(pandas_sort(f, 'frame'), 5, hash_size=(50, 50))
assert_traj_equal(actual_iter, expected)
# Shuffle rows (crazy!)
np.random.seed(0)
f1 = f.reset_index(drop=True)
f1.reindex(np.random.permutation(f1.index))
actual = self.link_df(f1, 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(f1, 5, hash_size=(50, 50))
assert_traj_equal(actual_iter, expected)
if self.do_diagnostics:
assert 'diag_subnet' in self.diag.columns
assert 'diag_subnet_size' in self.diag.columns
# Except for frame in which they appear, all particles should have
# been labeled with a search_range
assert not any(self.diag['diag_search_range'][
actual_iter.frame > 1].isnull())
# The number of loop iterations is reported by the numba linker only
if self.linker_opts['link_strategy'] == 'numba':
assert 'diag_subnet_iterations' in self.diag.columns
def test_two_isolated_steppers(self):
N = 5
Y = 25
# Begin second feature one frame later than the first, so the particle labeling (0, 1) is
# established and not arbitrary.
a = DataFrame({'x': np.arange(N), 'y': np.ones(N), 'frame': np.arange(N)})
b = DataFrame({'x': np.arange(1, N), 'y': Y + np.ones(N - 1), 'frame': np.arange(1, N)})
f = pandas_concat([a, b])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate([np.zeros(N), np.ones(N - 1)])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(f, 5, hash_size=(50, 50))
assert_traj_equal(actual_iter, expected)
# Sort rows by frame (normal use)
actual = self.link_df(pandas_sort(f, 'frame'), 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(pandas_sort(f, 'frame'), 5, hash_size=(50, 50))
assert_traj_equal(actual_iter, expected)
# Shuffle rows (crazy!)
np.random.seed(0)
f1 = f.reset_index(drop=True)
f1.reindex(np.random.permutation(f1.index))
actual = self.link_df(f1, 5)
assert_traj_equal(actual, expected)
actual_iter = self.link_df_iter(f1, 5, hash_size=(50, 50))
assert_traj_equal(actual_iter, expected)
def test_nearby_continuous_random_walks(self):
# Two 2D random walks
np.random.seed(0)
N = 30
Y = 250
M = 20 # margin, because negative values raise OutOfHash
a = DataFrame({
'x': M + random_walk(N),
'y': M + random_walk(N),
'frame': np.arange(N)
})
b = DataFrame({
'x': M + random_walk(N - 1),
'y': M + Y + random_walk(N - 1),
'frame': np.arange(1, N)
})
f = pandas_concat([a, b])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate([np.zeros(N), np.ones(N - 1)])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
actual = self.link_df_iter(f, 5, hash_size=(2 * M, 2 * M + Y))
assert_traj_equal(actual, expected)
# Several 2D random walks
np.random.seed(0)
initial_positions = [(10, 11), (10, 18), (14, 15), (20, 21), (13, 13),
(10, 10), (17, 19)]
import itertools
c = itertools.count()
def walk(x, y):
i = next(c)
return DataFrame({
'x': x + random_walk(N - i),
'y': y + random_walk(N - i),
'frame': np.arange(i, N)
})
f = pandas_concat([walk(*pos) for pos in initial_positions])
expected = f.copy().reset_index(drop=True)
expected['particle'] = np.concatenate(
[i * np.ones(N - i) for i in range(len(initial_positions))])
pandas_sort(expected, ['particle', 'frame'], inplace=True)
actual = self.link_df(f, 5)
assert_traj_equal(actual, expected)
actual = self.link_df_iter(f, 5, hash_size=(2 * M, 2 * M))
assert_traj_equal(actual, expected)
# Shuffle rows (crazy!)
np.random.seed(0)
f1 = f.reset_index(drop=True)
f1.reindex(np.random.permutation(f1.index))
actual = self.link_df(f1, 5)
assert_traj_equal(actual, expected)
actual = self.link_df_iter(f1, 5, hash_size=(2 * M, 2 * M))
assert_traj_equal(actual, expected)