def test_bbox_search(img):
prob = edt_prob(img)
dist = star_dist(img, n_rays=32, mode="cpp")
coord = dist_to_coord(dist)
nms_a = non_maximum_suppression(
coord, prob, prob_thresh=0.4, verbose=False, max_bbox_search=False)
nms_b = non_maximum_suppression(
coord, prob, prob_thresh=0.4, verbose=False, max_bbox_search=True)
check_similar(nms_a, nms_b)
def test_types(img, n_rays):
mode = "cpp"
gt = star_dist(img, n_rays=n_rays, mode=mode)
for dtype in (np.int8, np.int16, np.int32, np.uint8, np.uint16, np.uint32):
x = star_dist(img.astype(dtype), n_rays=n_rays, mode=mode)
print(
"test_stardist2D (mode {mode}) for shape {img.shape} and type {dtype}"
.format(mode=mode, img=img, dtype=dtype))
check_similar(gt, x)
def test_cpu_gpu(img, n_rays, grid):
print(tuple(s//g for s, g in zip(img.shape, grid)))
rays = Rays_GoldenSpiral(n_rays)
with Timer(f"stardist {img.shape} {n_rays} rays - CPU"):
s_cpp = star_dist3D(img, rays=rays, grid=grid, mode="cpp")
with Timer(f"stardist {img.shape} {n_rays} rays - GPU"):
s_ocl = star_dist3D(img, rays=rays, grid=grid, mode="opencl")
check_similar(s_cpp, s_ocl)
return s_cpp, s_ocl
def test_types(img, n_rays, grid):
mode = "cpp"
rays = Rays_GoldenSpiral(n_rays)
gt = star_dist3D(img, rays=rays, grid=grid, mode=mode)
for dtype in (np.int8, np.int16, np.int32,
np.uint8, np.uint16, np.uint32):
x = star_dist3D(img.astype(dtype), rays=rays, grid=grid, mode=mode)
print("test_stardist3D (mode {mode}) for shape {img.shape} and type {dtype}".format(mode =mode, img = img, dtype = dtype))
check_similar(gt, x)
def test_bbox_search_old(img):
from stardist.geometry.geom2d import _polygons_to_label_old, _dist_to_coord_old
from stardist.nms import _non_maximum_suppression_old
prob = edt_prob(img)
dist = star_dist(img, n_rays=32, mode="cpp")
coord = _dist_to_coord_old(dist)
points_a = _non_maximum_suppression_old(coord, prob, prob_thresh=0.4, verbose=False, max_bbox_search=False)
points_b = _non_maximum_suppression_old(coord, prob, prob_thresh=0.4, verbose=False, max_bbox_search=True)
img2_a = _polygons_to_label_old(coord, prob, points_a, shape=img.shape)
img2_b = _polygons_to_label_old(coord, prob, points_b, shape=img.shape)
check_similar(points_a, points_b)
check_similar(img2_a, img2_b)
def test_cpu_gpu(img, n_rays, grid):
rays = Rays_GoldenSpiral(n_rays)
s_cpp = star_dist3D(img, rays=rays, grid=grid, mode="cpp")
s_ocl = star_dist3D(img, rays=rays, grid=grid, mode="opencl")
check_similar(s_cpp, s_ocl)
def test_cpu_gpu(img, n_rays):
s_cpp = star_dist(img, n_rays=n_rays, mode="cpp")
s_ocl = star_dist(img, n_rays=n_rays, mode="opencl")
check_similar(s_cpp, s_ocl)
