def test_background(self):
x = cp.zeros((2, 3, 3), int)
# fmt: off
x[0] = cp.array([[1, 0, 0],
[1, 0, 0],
[0, 0, 0]])
x[1] = cp.array([[0, 0, 0],
[0, 1, 5],
[0, 0, 0]])
lnb = x.copy()
lnb[0] = cp.array([[1, 2, 2],
[1, 2, 2],
[2, 2, 2]])
lnb[1] = cp.array([[2, 2, 2],
[2, 1, 3],
[2, 2, 2]])
lb = x.copy()
lb[0] = cp.array([[1, BG, BG], # noqa
[1, BG, BG], # noqa
[BG, BG, BG]])
lb[1] = cp.array([[BG, BG, BG],
[BG, 1, 2], # noqa
[BG, BG, BG]])
# fmt: on
assert_array_equal(label(x), lb)
assert_array_equal(label(x, background=-1), lnb)
def test_return_num(self):
# fmt: off
x = cp.array([[1, 0, 6],
[0, 0, 6],
[5, 5, 5]])
# fmt: on
assert_array_equal(label(x, return_num=True)[1], 3)
assert_array_equal(label(x, background=-1, return_num=True)[1], 4)
def test_connectivity_1_vs_2(self):
x = cp.zeros((2, 2, 2), int)
x[0, 1, 1] = 1
x[1, 0, 0] = 1
label1 = x.copy()
label1[1, 0, 0] = 2
assert_array_equal(label(x, connectivity=1), label1)
assert_array_equal(label(x, connectivity=3), x)
def test_basic(self):
assert_array_equal(label(self.x), self.labels)
# Make sure data wasn't modified
assert self.x[0, 2] == 3
# Check that everything works if there is no background
assert_array_equal(label(self.x, background=99), self.labels_nobg)
# Check that everything works if background value != 0
assert_array_equal(label(self.x, background=9), self.labels_bg_9)
def test_4_vs_8(self):
# fmt: off
x = cp.array([[0, 1],
[1, 0]], dtype=int)
assert_array_equal(label(x, connectivity=1),
[[0, 1],
[2, 0]])
assert_array_equal(label(x, connectivity=2),
[[0, 1],
[1, 0]])
def test_background(self):
# fmt: off
x = cp.array([[1, 0, 0],
[1, 1, 5],
[0, 0, 0]])
assert_array_equal(label(x), [[1, 0, 0],
[1, 1, 2],
[0, 0, 0]])
assert_array_equal(label(x, background=0),
[[1, 0, 0],
[1, 1, 2],
[0, 0, 0]])
def test_random(self):
x = (cp.random.rand(20, 30) * 5).astype(cp.int)
labels = label(x)
n = int(labels.max())
for i in range(n):
values = x[labels == i]
assert cp.all(values == values[0])
def test_background_one_region_center(self):
x = cp.zeros((3, 3, 3), int)
x[1, 1, 1] = 1
lb = cp.ones_like(x) * BG
lb[1, 1, 1] = 1
assert_array_equal(label(x, connectivity=1, background=0), lb)
def test_background_one_region_center(self):
# fmt: off
x = cp.array([[0, 0, 0],
[0, 1, 0],
[0, 0, 0]])
assert_array_equal(label(x, connectivity=1, background=0),
[[0, 0, 0],
[0, 1, 0],
[0, 0, 0]])
def test_1D(self):
x = cp.array((0, 1, 2, 2, 1, 1, 0, 0))
xlen = len(x)
y = cp.array((0, 1, 2, 2, 3, 3, 0, 0))
reshapes = ((xlen,),
(1, xlen), (xlen, 1),
(1, xlen, 1), (xlen, 1, 1), (1, 1, xlen))
for reshape in reshapes:
x2 = x.reshape(reshape)
labelled = label(x2)
assert_array_equal(y, labelled.flatten())
def test_background_two_regions(self):
# fmt: off
x = cp.array([[0, 0, 6],
[0, 0, 6],
[5, 5, 5]])
res = label(x, background=0)
assert_array_equal(res,
[[0, 0, 1],
[0, 0, 1],
[2, 2, 2]])
def test_background_two_regions(self):
x = cp.zeros((2, 3, 3), int)
# fmt: off
x[0] = cp.array([[0, 0, 6],
[0, 0, 6],
[5, 5, 5]])
x[1] = cp.array([[6, 6, 0],
[5, 0, 0],
[0, 0, 0]])
lb = x.copy()
lb[0] = cp.array([[BG, BG, 1],
[BG, BG, 1],
[2, 2, 2]]) # noqa
lb[1] = cp.array([[1, 1, BG], # noqa
[2, BG, BG], # noqa
[BG, BG, BG]])
# fmt: on
res = label(x, background=0)
assert_array_equal(res, lb)
def test_diag(self):
# fmt: off
x = cp.array([[0, 0, 1],
[0, 1, 0],
[1, 0, 0]])
assert_array_equal(label(x), x)
def test_diag(self):
x = cp.zeros((3, 3, 3), int)
x[0, 2, 2] = 1
x[1, 1, 1] = 1
x[2, 0, 0] = 1
assert_array_equal(label(x), x)
def test_basic(self):
labels = label(self.x)
assert_array_equal(labels, self.labels)
assert self.x[0, 0, 2] == 2, "Data was modified!"
def _prominent_peaks(image, min_xdistance=1, min_ydistance=1,
threshold=None, num_peaks=np.inf):
"""Return peaks with non-maximum suppression.
Identifies most prominent features separated by certain distances.
Non-maximum suppression with different sizes is applied separately
in the first and second dimension of the image to identify peaks.
Parameters
----------
image : (M, N) ndarray
Input image.
min_xdistance : int
Minimum distance separating features in the x dimension.
min_ydistance : int
Minimum distance separating features in the y dimension.
threshold : float
Minimum intensity of peaks. Default is `0.5 * max(image)`.
num_peaks : int
Maximum number of peaks. When the number of peaks exceeds `num_peaks`,
return `num_peaks` coordinates based on peak intensity.
Returns
-------
intensity, xcoords, ycoords : tuple of array
Peak intensity values, x and y indices.
"""
img = image.copy()
rows, cols = img.shape
if threshold is None:
threshold = 0.5 * np.max(img)
ycoords_size = 2 * min_ydistance + 1
xcoords_size = 2 * min_xdistance + 1
img_max = ndi.maximum_filter1d(img, size=ycoords_size, axis=0,
mode='constant', cval=0)
img_max = ndi.maximum_filter1d(img_max, size=xcoords_size, axis=1,
mode='constant', cval=0)
mask = (img == img_max)
img *= mask
img_t = img > threshold
label_img = measure.label(img_t)
props = measure.regionprops(label_img, img_max)
# Sort the list of peaks by intensity, not left-right, so larger peaks
# in Hough space cannot be arbitrarily suppressed by smaller neighbors
props = sorted(props, key=lambda x: x.max_intensity)[::-1]
coords = cp.asarray([np.round(p.centroid) for p in props], dtype=int)
img_peaks = []
ycoords_peaks = []
xcoords_peaks = []
# relative coordinate grid for local neighbourhood suppression
ycoords_ext, xcoords_ext = cp.mgrid[-min_ydistance:min_ydistance + 1,
-min_xdistance:min_xdistance + 1]
for ycoords_idx, xcoords_idx in coords:
accum = img_max[ycoords_idx, xcoords_idx]
if accum > threshold:
# absolute coordinate grid for local neighbourhood suppression
ycoords_nh = ycoords_idx + ycoords_ext
xcoords_nh = xcoords_idx + xcoords_ext
# no reflection for distance neighbourhood
ycoords_in = cp.logical_and(ycoords_nh > 0, ycoords_nh < rows)
ycoords_nh = ycoords_nh[ycoords_in]
xcoords_nh = xcoords_nh[ycoords_in]
# reflect xcoords and assume xcoords are continuous,
# e.g. for angles:
# (..., 88, 89, -90, -89, ..., 89, -90, -89, ...)
xcoords_low = xcoords_nh < 0
ycoords_nh[xcoords_low] = rows - ycoords_nh[xcoords_low]
xcoords_nh[xcoords_low] += cols
xcoords_high = xcoords_nh >= cols
ycoords_nh[xcoords_high] = rows - ycoords_nh[xcoords_high]
xcoords_nh[xcoords_high] -= cols
# suppress neighbourhood
img_max[ycoords_nh, xcoords_nh] = 0
# add current feature to peaks
img_peaks.append(accum)
ycoords_peaks.append(ycoords_idx)
xcoords_peaks.append(xcoords_idx)
img_peaks = cp.array(img_peaks)
ycoords_peaks = cp.array(ycoords_peaks)
xcoords_peaks = cp.array(xcoords_peaks)
if num_peaks < len(img_peaks):
idx_maxsort = cp.argsort(img_peaks)[::-1][:num_peaks]
img_peaks = img_peaks[idx_maxsort]
ycoords_peaks = ycoords_peaks[idx_maxsort]
xcoords_peaks = xcoords_peaks[idx_maxsort]
return img_peaks, xcoords_peaks, ycoords_peaks
