def test_euler_number():
en = regionprops(SAMPLE)[0].euler_number
assert en == 0
SAMPLE_mod = SAMPLE.copy()
SAMPLE_mod[7, -3] = 0
en = regionprops(SAMPLE_mod)[0].euler_number
assert en == -1
en = euler_number(SAMPLE, 1)
assert en == 2
en = euler_number(SAMPLE_mod, 1)
assert en == 1
en = euler_number(SAMPLE_3D, 1)
assert en == 1
en = euler_number(SAMPLE_3D, 3)
assert en == 1
# for convex body, Euler number is 1
SAMPLE_3D_2 = cp.zeros((100, 100, 100))
SAMPLE_3D_2[40:60, 40:60, 40:60] = 1
en = euler_number(SAMPLE_3D_2, 3)
assert en == 1
SAMPLE_3D_2[45:55, 45:55, 45:55] = 0
en = euler_number(SAMPLE_3D_2, 3)
assert en == 2
def test_extra_properties_nr_args():
with pytest.raises(AttributeError):
region = regionprops(SAMPLE, extra_properties=(too_few_args, ))[0]
_ = region.too_few_args
with pytest.raises(AttributeError):
region = regionprops(SAMPLE, extra_properties=(too_many_args, ))[0]
_ = region.too_many_args
def test_multichannel():
"""Test that computing multichannel properties works."""
astro = data.astronaut()[::4, ::4]
labels = slic(astro.astype(float), start_label=1)
astro = cp.asarray(astro)
astro_green = astro[..., 1]
labels = cp.asarray(labels)
segment_idx = int(cp.max(labels) // 2)
region = regionprops(labels, astro_green)[segment_idx]
region_multi = regionprops(labels, astro)[segment_idx]
for prop in PROPS:
p = region[prop]
p_multi = region_multi[prop]
if isinstance(p, (list, tuple)):
p = tuple([cp.asnumpy(p_) for p_ in p])
p = np.stack(p)
if isinstance(p_multi, (list, tuple)):
p_multi = tuple([cp.asnumpy(p_) for p_ in p_multi])
p_multi = np.stack(p_multi)
if np.shape(p) == np.shape(p_multi):
# property does not depend on multiple channels
assert_array_equal(p, p_multi)
else:
# property uses multiple channels, returns props stacked along
# final axis
assert_array_equal(p, p_multi[..., 1])
def test_euler_number():
en = regionprops(SAMPLE)[0].euler_number
assert en == 1
SAMPLE_mod = SAMPLE.copy()
SAMPLE_mod[7, -3] = 0
en = regionprops(SAMPLE_mod)[0].euler_number
assert en == 0
def test_filled_area():
area = regionprops(SAMPLE)[0].filled_area
assert area == cp.sum(SAMPLE)
SAMPLE_mod = SAMPLE.copy()
SAMPLE_mod[7, -3] = 0
area = regionprops(SAMPLE_mod)[0].filled_area
assert area == cp.sum(SAMPLE)
def test_eccentricity():
eps = regionprops(SAMPLE)[0].eccentricity
assert_almost_equal(eps, 0.814629313427)
img = cp.zeros((5, 5), dtype=cp.int)
img[2, 2] = 1
eps = regionprops(img)[0].eccentricity
assert_almost_equal(eps, 0)
def test_iterate_all_props():
region = regionprops(SAMPLE)[0]
p0 = {p: region[p] for p in region}
region = regionprops(SAMPLE, intensity_image=INTENSITY_SAMPLE)[0]
p1 = {p: region[p] for p in region}
assert len(p0) < len(p1)
def test_dtype():
regionprops(cp.zeros((10, 10), dtype=cp.int))
regionprops(cp.zeros((10, 10), dtype=cp.uint))
with pytest.raises(TypeError):
regionprops(cp.zeros((10, 10), dtype=cp.float))
with pytest.raises(TypeError):
regionprops(cp.zeros((10, 10), dtype=cp.double))
with pytest.raises(TypeError):
regionprops(cp.zeros((10, 10), dtype=np.bool_))
def test_coordinates():
sample = cp.zeros((10, 10), dtype=cp.int8)
coords = cp.array([[3, 2], [3, 3], [3, 4]])
sample[coords[:, 0], coords[:, 1]] = 1
prop_coords = regionprops(sample)[0].coords
assert_array_equal(prop_coords, coords)
sample = cp.zeros((6, 6, 6), dtype=cp.int8)
coords = cp.array([[1, 1, 1], [1, 2, 1], [1, 3, 1]])
sample[coords[:, 0], coords[:, 1], coords[:, 2]] = 1
prop_coords = regionprops(sample)[0].coords
assert_array_equal(prop_coords, coords)
def test_bbox():
bbox = regionprops(SAMPLE)[0].bbox
assert_array_almost_equal(bbox, (0, 0, SAMPLE.shape[0], SAMPLE.shape[1]))
SAMPLE_mod = SAMPLE.copy()
SAMPLE_mod[:, -1] = 0
bbox = regionprops(SAMPLE_mod)[0].bbox
assert_array_almost_equal(bbox,
(0, 0, SAMPLE.shape[0], SAMPLE.shape[1] - 1))
bbox = regionprops(SAMPLE_3D)[0].bbox
assert_array_almost_equal(bbox, (1, 1, 1, 4, 3, 3))
def test_equals():
arr = cp.zeros((100, 100), dtype=cp.int)
arr[0:25, 0:25] = 1
arr[50:99, 50:99] = 2
regions = regionprops(arr)
r1 = regions[0]
regions = regionprops(arr)
r2 = regions[0]
r3 = regions[1]
assert_equal(r1 == r2, True, "Same regionprops are not equal")
assert_equal(r1 != r3, True, "Different regionprops are equal")
def test_orientation():
orient = regionprops(SAMPLE)[0].orientation
# determined with MATLAB
assert_almost_equal(orient, -1.4663278802756865)
# test diagonal regions
diag = cp.eye(10, dtype=int)
orient_diag = regionprops(diag)[0].orientation
assert_almost_equal(orient_diag, -math.pi / 4)
orient_diag = regionprops(cp.flipud(diag))[0].orientation
assert_almost_equal(orient_diag, math.pi / 4)
orient_diag = regionprops(cp.fliplr(diag))[0].orientation
assert_almost_equal(orient_diag, math.pi / 4)
orient_diag = regionprops(cp.fliplr(cp.flipud(diag)))[0].orientation
assert_almost_equal(orient_diag, -math.pi / 4)
def test_column_dtypes_correct():
msg = "mismatch with expected type,"
region = regionprops(SAMPLE, intensity_image=INTENSITY_SAMPLE)[0]
for col in COL_DTYPES:
r = region[col]
if col in OBJECT_COLUMNS:
assert COL_DTYPES[col] == object
continue
# TODO: grlee77: check desired types for returned.
# e.g. currently inertia_tensor_eigvals returns a list of 0-dim
# arrays
if isinstance(r, (tuple, list)):
r0 = r[0]
if isinstance(r0, cp.ndarray) and r0.ndim == 0:
r0 = r0.item()
t = type(r0)
elif cp.isscalar(r):
t = type(r)
else:
t = type(r.ravel()[0].item())
if cp.issubdtype(t, cp.floating):
assert (COL_DTYPES[col] == float
), f"{col} dtype {t} {msg} {COL_DTYPES[col]}"
elif cp.issubdtype(t, cp.integer):
assert (COL_DTYPES[col] == int
), f"{col} dtype {t} {msg} {COL_DTYPES[col]}"
else:
assert False, f"{col} dtype {t} {msg} {COL_DTYPES[col]}"
def test_extra_properties_intensity():
region = regionprops(
SAMPLE,
intensity_image=INTENSITY_SAMPLE,
extra_properties=(median_intensity, ),
)[0]
assert region.median_intensity == cp.median(INTENSITY_SAMPLE[SAMPLE == 1])
def test_all_props():
region = regionprops(SAMPLE, INTENSITY_SAMPLE)[0]
for prop in PROPS:
try:
assert_array_almost_equal(region[prop],
getattr(region, PROPS[prop]))
except TypeError: # the `slice` property causes this
pass
def test_invalid():
ps = regionprops(SAMPLE)
def get_intensity_image():
ps[0].intensity_image
with pytest.raises(AttributeError):
get_intensity_image()
def test_all_props_3d():
region = regionprops(SAMPLE_3D, INTENSITY_SAMPLE_3D)[0]
for prop in PROPS:
try:
assert_array_almost_equal(region[prop],
getattr(region, PROPS[prop]))
except (NotImplementedError, TypeError):
pass
def test_extra_properties_mixed():
# mixed properties, with and without intensity
region = regionprops(
SAMPLE,
intensity_image=INTENSITY_SAMPLE,
extra_properties=(median_intensity, pixelcount),
)[0]
assert region.median_intensity == cp.median(INTENSITY_SAMPLE[SAMPLE == 1])
assert region.pixelcount == cp.sum(SAMPLE == 1)
def test_weighted_moments():
wm = regionprops(SAMPLE,
intensity_image=INTENSITY_SAMPLE)[0].weighted_moments
ref = cp.asarray([
[7.4000000e01, 6.9900000e02, 7.8630000e03, 9.7317000e04],
[4.1000000e02, 3.7850000e03, 4.4063000e04, 5.7256700e05],
[2.7500000e03, 2.4855000e04, 2.9347700e05, 3.9007170e06],
[1.9778000e04, 1.7500100e05, 2.0810510e06, 2.8078871e07],
])
assert_array_almost_equal(wm, ref)
def test_moments_normalized():
nu = regionprops(SAMPLE)[0].moments_normalized
# determined with OpenCV
assert_almost_equal(nu[0, 2], 0.24301268861454037)
assert_almost_equal(nu[0, 3], -0.017278118992041805)
assert_almost_equal(nu[1, 1], -0.016846707818929982)
assert_almost_equal(nu[1, 2], 0.045473992910668816)
assert_almost_equal(nu[2, 0], 0.08410493827160502)
assert_almost_equal(nu[2, 1], -0.002899800614433943)
def test_moments_central():
mu = regionprops(SAMPLE)[0].moments_central
# determined with OpenCV
assert_almost_equal(mu[2, 0], 436.00000000000045)
# different from OpenCV results, bug in OpenCV
assert_almost_equal(mu[3, 0], -737.333333333333)
assert_almost_equal(mu[1, 1], -87.33333333333303)
assert_almost_equal(mu[2, 1], -127.5555555555593)
assert_almost_equal(mu[0, 2], 1259.7777777777774)
assert_almost_equal(mu[1, 2], 2000.296296296291)
assert_almost_equal(mu[0, 3], -760.0246913580195)
def test_weighted_moments_normalized():
wnu = regionprops(
SAMPLE,
intensity_image=INTENSITY_SAMPLE)[0].weighted_moments_normalized
ref = cp.asarray([
[cp.nan, cp.nan, 0.2301467830, -0.0162529732],
[cp.nan, -0.0160405109, 0.0457932622, -0.0104598869],
[0.0873590903, -0.0031421072, 0.0165315478, -0.0028544152],
[-0.0161217406, -0.0031376984, 0.0043903193, -0.0011057191],
])
assert_array_almost_equal(wnu, ref)
def test_moments_hu():
hu = regionprops(SAMPLE)[0].moments_hu
ref = cp.asarray([
3.27117627e-01,
2.63869194e-02,
2.35390060e-02,
1.23151193e-03,
1.38882330e-06,
-2.72586158e-05,
-6.48350653e-06,
])
# bug in OpenCV caused in Central Moments calculation?
assert_array_almost_equal(hu, ref)
def test_moments():
m = regionprops(SAMPLE)[0].moments
# determined with OpenCV
assert_almost_equal(m[0, 0], 72.0)
assert_almost_equal(m[0, 1], 680.0)
assert_almost_equal(m[0, 2], 7682.0)
assert_almost_equal(m[0, 3], 95588.0)
assert_almost_equal(m[1, 0], 408.0)
assert_almost_equal(m[1, 1], 3766.0)
assert_almost_equal(m[1, 2], 43882.0)
assert_almost_equal(m[2, 0], 2748.0)
assert_almost_equal(m[2, 1], 24836.0)
assert_almost_equal(m[3, 0], 19776.0)
def test_weighted_moments_hu():
whu = regionprops(SAMPLE,
intensity_image=INTENSITY_SAMPLE)[0].weighted_moments_hu
ref = cp.asarray([
3.1750587329e-01,
2.1417517159e-02,
2.3609322038e-02,
1.2565683360e-03,
8.3014209421e-07,
-3.5073773473e-05,
-6.7936409056e-06,
])
assert_array_almost_equal(whu, ref)
def test_props_to_dict():
regions = regionprops(SAMPLE)
out = _props_to_dict(regions)
assert out == {
"label": cp.asarray([1]),
"bbox-0": cp.asarray([0]),
"bbox-1": cp.asarray([0]),
"bbox-2": cp.asarray([10]),
"bbox-3": cp.asarray([18]),
}
regions = regionprops(SAMPLE)
out = _props_to_dict(regions,
properties=("label", "area", "bbox"),
separator="+")
assert out == {
"label": cp.asarray([1]),
"area": cp.asarray([72]),
"bbox+0": cp.asarray([0]),
"bbox+1": cp.asarray([0]),
"bbox+2": cp.asarray([10]),
"bbox+3": cp.asarray([18]),
}
def test_convex_image():
img = regionprops(SAMPLE)[0].convex_image
ref = cp.asarray([
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 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, 1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
], )
assert_array_equal(img, ref)
def test_cache():
SAMPLE_mod = SAMPLE.copy()
region = regionprops(SAMPLE_mod)[0]
f0 = region.filled_image
region._label_image[:10] = 1
f1 = region.filled_image
# Changed underlying image, but cache keeps result the same
assert_array_equal(f0, f1)
# Now invalidate cache
region._cache_active = False
f1 = region.filled_image
assert cp.any(f0 != f1)
def test_convex_image():
img = regionprops(SAMPLE)[0].convex_image
# determined with MATLAB
ref = cp.asarray([
[0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0],
[0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 0],
[0, 0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0],
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
[0, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1],
])
assert_array_equal(img, ref)
def test_docstrings_and_props():
def foo():
"""foo"""
has_docstrings = bool(foo.__doc__)
region = regionprops(SAMPLE)[0]
docs = _parse_docs()
props = [m for m in dir(region) if not m.startswith("_")]
nr_docs_parsed = len(docs)
nr_props = len(props)
if has_docstrings:
assert_equal(nr_docs_parsed, nr_props)
ds = docs["weighted_moments_normalized"]
assert "iteration" not in ds
assert len(ds.split("\n")) > 3
else:
assert_equal(nr_docs_parsed, 0)