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2024-10-21 adding version 3.11
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@gatoniel
gatoniel committed Oct 21, 2024
1 parent 82feaba commit 544fe95
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Showing 4 changed files with 73 additions and 106 deletions.
2 changes: 1 addition & 1 deletion noxfile.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@


package = "merge_stardist_masks"
python_versions = ["3.10", "3.9", "3.8"]
python_versions = ["3.11", "3.10", "3.9", "3.8"]
nox.needs_version = ">= 2021.6.6"
nox.options.sessions = (
"pre-commit",
Expand Down
29 changes: 15 additions & 14 deletions poetry.lock
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ classifiers = [
Changelog = "https://github.com/gatoniel/merge-stardist-masks/releases"

[tool.poetry.dependencies]
python = ">=3.8,<3.11"
python = ">=3.8,<3.12"
stardist = ">=0.7.3,<0.9.0"
numpy = ">=1.21.0"
edt = "^2.3.0"
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146 changes: 56 additions & 90 deletions tests/test_naive_fusion.py
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Original file line number Diff line number Diff line change
Expand Up @@ -96,9 +96,7 @@ def test_values_of_points_from_grid(shape: IntTuple, grid: IntTuple) -> None:
points = nf.points_from_grid(shape, grid)
mesh = nf.mesh_from_shape(shape)

np.testing.assert_array_equal( # type: ignore [no-untyped-call]
mesh * np.array(grid), points
)
np.testing.assert_array_equal(mesh * np.array(grid), points)


def test_value_error_of_points_from_grid() -> None:
Expand Down Expand Up @@ -137,16 +135,12 @@ def test_values_of_inflate_array(
slices_list.append(slice(None))
slices = tuple(slices_list)
# first test if values at grid points are correct
np.testing.assert_array_equal( # type: ignore [no-untyped-call]
inflated_array[slices], x
)
np.testing.assert_array_equal(inflated_array[slices], x)

# then test if default values are correct
inds = np.ones_like(inflated_array, dtype=bool)
inds[slices] = False
np.testing.assert_equal( # type: ignore [no-untyped-call]
inflated_array[inds], default_value
)
np.testing.assert_equal(inflated_array[inds], default_value)


def test_value_error_of_inflate_array() -> None:
Expand Down Expand Up @@ -213,16 +207,14 @@ def test_my_polyhedron_to_label() -> None:
assert my_label.shape == shape

label = polyhedron_to_label(
np.expand_dims( # type: ignore [no-untyped-call]
np.clip(dists, 1e-3, None), axis=0
),
np.expand_dims(points, axis=0), # type: ignore [no-untyped-call]
np.expand_dims(np.clip(dists, 1e-3, None), axis=0),
np.expand_dims(points, axis=0),
rays,
shape,
verbose=False,
)

np.testing.assert_array_equal(my_label, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(my_label, label)


def test_my_polygons_to_label() -> None:
Expand All @@ -237,14 +229,12 @@ def test_my_polygons_to_label() -> None:
assert my_label.shape == shape

label = polygons_to_label(
np.expand_dims( # type: ignore [no-untyped-call]
np.clip(dists, 1e-3, None), axis=0
),
np.expand_dims(points, axis=0), # type: ignore [no-untyped-call]
np.expand_dims(np.clip(dists, 1e-3, None), axis=0),
np.expand_dims(points, axis=0),
shape,
)

np.testing.assert_array_equal(my_label, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(my_label, label)


@pytest.fixture(params=[True, False])
Expand Down Expand Up @@ -348,9 +338,9 @@ def test_naive_fusion_3d(
label[label == 2] = 2
label[label == 3] = 2

np.testing.assert_array_equal(lbl, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(lbl_iso, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(lbl_aniso, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(lbl, label)
np.testing.assert_array_equal(lbl_iso, label)
np.testing.assert_array_equal(lbl_aniso, label)


@pytest.mark.filterwarnings(
Expand Down Expand Up @@ -427,9 +417,9 @@ def test_naive_fusion_2d(
print(lbl)
print(label)

np.testing.assert_array_equal(lbl, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(lbl_iso, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(lbl_aniso, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(lbl, label)
np.testing.assert_array_equal(lbl_iso, label)
np.testing.assert_array_equal(lbl_aniso, label)


def test_naive_fusion_2d_with_overlaps() -> None:
Expand Down Expand Up @@ -470,7 +460,7 @@ def test_naive_fusion_2d_with_overlaps() -> None:
print(lbl)
print(label)

np.testing.assert_array_equal(lbl, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(lbl, label)


def test_naive_fusion_2d_respect_probs() -> None:
Expand Down Expand Up @@ -510,7 +500,7 @@ def test_naive_fusion_2d_respect_probs() -> None:
print(lbl)
print(label)

np.testing.assert_array_equal(lbl, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(lbl, label)


def test_naive_fusion_2d_anisotropic() -> None:
Expand Down Expand Up @@ -563,7 +553,7 @@ def test_naive_fusion_2d_anisotropic() -> None:
print(lbl)
print(label)

np.testing.assert_array_equal(lbl, label) # type: ignore [no-untyped-call]
np.testing.assert_array_equal(lbl, label)


def test_naive_fusion_2d_winding() -> None:
Expand Down Expand Up @@ -626,17 +616,11 @@ def test_naive_fusion_2d_winding() -> None:
print(label)

# lbl without slicing should not work in this case
np.testing.assert_raises( # type: ignore [no-untyped-call]
AssertionError, np.testing.assert_array_equal, lbl, label
)
np.testing.assert_raises(AssertionError, np.testing.assert_array_equal, lbl, label)
# lbl with slicing should work
np.testing.assert_array_equal( # type: ignore [no-untyped-call]
lbl_no_slicing, label
)
np.testing.assert_array_equal(lbl_no_slicing, label)
# lbl with slicing and anisotropic version should also work
np.testing.assert_array_equal( # type: ignore [no-untyped-call]
lbl_no_slicing_anisotropic, label
)
np.testing.assert_array_equal(lbl_no_slicing_anisotropic, label)


def test_respect_probs_warning_in_naive_fusion() -> None:
Expand Down Expand Up @@ -717,18 +701,14 @@ def test_paint_in_without_overlaps() -> None:
lbl[1:, 1:] = True

x = nf.paint_in_without_overlaps(np.zeros(shape), lbl, 1)
np.testing.assert_equal( # type: ignore [no-untyped-call]
x[1:, 1:], np.ones((2, 2))
)
np.testing.assert_equal(x[:, 0], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[0, :], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[1:, 1:], np.ones((2, 2)))
np.testing.assert_equal(x[:, 0], np.zeros((3,)))
np.testing.assert_equal(x[0, :], np.zeros((3,)))

x = nf.paint_in_without_overlaps(np.ones(shape), lbl, 3)
np.testing.assert_equal( # type: ignore [no-untyped-call]
x[1:, 1:], 3 * np.ones((2, 2))
)
np.testing.assert_equal(x[:, 0], np.ones((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[0, :], np.ones((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[1:, 1:], 3 * np.ones((2, 2)))
np.testing.assert_equal(x[:, 0], np.ones((3,)))
np.testing.assert_equal(x[0, :], np.ones((3,)))


def test_paint_in_with_overlaps() -> None:
Expand All @@ -738,56 +718,46 @@ def test_paint_in_with_overlaps() -> None:
lbl[1:, 1:] = True

x = nf.paint_in_with_overlaps(np.zeros(shape), lbl, 1)
np.testing.assert_equal( # type: ignore [no-untyped-call]
x[1:, 1:], np.ones((2, 2))
)
np.testing.assert_equal(x[:, 0], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[0, :], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[1:, 1:], np.ones((2, 2)))
np.testing.assert_equal(x[:, 0], np.zeros((3,)))
np.testing.assert_equal(x[0, :], np.zeros((3,)))

x = nf.paint_in_with_overlaps(np.ones(shape), lbl, 3)
np.testing.assert_equal( # type: ignore [no-untyped-call]
x[1:, 1:], -np.ones((2, 2))
)
np.testing.assert_equal(x[:, 0], np.ones((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[0, :], np.ones((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[1:, 1:], -np.ones((2, 2)))
np.testing.assert_equal(x[:, 0], np.ones((3,)))
np.testing.assert_equal(x[0, :], np.ones((3,)))

y = np.zeros(shape)
y[1, 1] = 2
x = nf.paint_in_with_overlaps(y, lbl, 3)
assert x[1, 1] == -1
np.testing.assert_equal( # type: ignore [no-untyped-call]
x[1:, 2], 3 * np.ones((2,))
)
np.testing.assert_equal( # type: ignore [no-untyped-call]
x[2, 1:], 3 * np.ones((2,))
)
np.testing.assert_equal(x[:, 0], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[0, :], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[1:, 2], 3 * np.ones((2,)))
np.testing.assert_equal(x[2, 1:], 3 * np.ones((2,)))
np.testing.assert_equal(x[:, 0], np.zeros((3,)))
np.testing.assert_equal(x[0, :], np.zeros((3,)))


def test_paint_in_without_overlaps_check_probs() -> None:
"""Set values of an array and respect their probabilities function."""
shape = (3, 3)
lbl = np.zeros(shape, dtype=bool)
new_probs = np.zeros(shape)
new_probs = np.zeros(shape, dtype=np.float32)
lbl[1:, 1:] = True
new_probs[1:, 1:] = 0.9
new_probs[2, 2] = 0.95

# nothing in paint_in
paint_in = np.zeros(shape)
old_probs = np.zeros(shape)
old_probs = np.zeros(shape, np.float32)
x, p = nf.paint_in_without_overlaps_check_probs(
paint_in, lbl, old_probs, new_probs, 1
)

np.testing.assert_equal( # type: ignore [no-untyped-call]
x[1:, 1:], np.ones((2, 2))
)
np.testing.assert_equal(x[:, 0], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[0, :], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[1:, 1:], np.ones((2, 2)))
np.testing.assert_equal(x[:, 0], np.zeros((3,)))
np.testing.assert_equal(x[0, :], np.zeros((3,)))

np.testing.assert_equal(p, new_probs) # type: ignore [no-untyped-call]
np.testing.assert_equal(p, new_probs)

# too low probability in old_probs
old_probs[1, 1] = 0.8
Expand All @@ -796,13 +766,11 @@ def test_paint_in_without_overlaps_check_probs() -> None:
paint_in, lbl, old_probs, new_probs, 1
)

np.testing.assert_equal( # type: ignore [no-untyped-call]
x[1:, 1:], np.ones((2, 2))
)
np.testing.assert_equal(x[:, 0], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[0, :], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[1:, 1:], np.ones((2, 2)))
np.testing.assert_equal(x[:, 0], np.zeros((3,)))
np.testing.assert_equal(x[0, :], np.zeros((3,)))

np.testing.assert_equal(p, new_probs) # type: ignore [no-untyped-call]
np.testing.assert_equal(p, new_probs)

# too low probability in old_probs
old_probs[2, 2] = 0.93
Expand All @@ -811,13 +779,11 @@ def test_paint_in_without_overlaps_check_probs() -> None:
paint_in, lbl, old_probs, new_probs, 1
)

np.testing.assert_equal( # type: ignore [no-untyped-call]
x[1:, 1:], np.ones((2, 2))
)
np.testing.assert_equal(x[:, 0], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[0, :], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[1:, 1:], np.ones((2, 2)))
np.testing.assert_equal(x[:, 0], np.zeros((3,)))
np.testing.assert_equal(x[0, :], np.zeros((3,)))

np.testing.assert_equal(p, new_probs) # type: ignore [no-untyped-call]
np.testing.assert_equal(p, new_probs)

# too high probability in old_probs
old_probs[1, 1] = 0.93
Expand All @@ -828,15 +794,15 @@ def test_paint_in_without_overlaps_check_probs() -> None:

x_ = np.ones((2, 2))
x_[0, 0] = 3
np.testing.assert_equal(x[1:, 1:], x_) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[:, 0], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[0, :], np.zeros((3,))) # type: ignore [no-untyped-call]
np.testing.assert_equal(x[1:, 1:], x_)
np.testing.assert_equal(x[:, 0], np.zeros((3,)))
np.testing.assert_equal(x[0, :], np.zeros((3,)))

p_ = np.zeros(shape)
p_[1:, 1:] = 0.9
p_[1, 1] = 0.93
p_[2, 2] = 0.95
np.testing.assert_equal(p, p_) # type: ignore [no-untyped-call]
np.testing.assert_equal(p, p_)


def test_polygon_list_with_probs_2d() -> None:
Expand Down Expand Up @@ -879,4 +845,4 @@ def test_polygon_list_with_probs_2d() -> None:
test_array[3:, 5:] = prob1
print(test_array)

np.testing.assert_equal(prob_array, test_array) # type: ignore [no-untyped-call]
np.testing.assert_equal(prob_array, test_array)

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