def label_objects(I,
min_object_size,
threshold=220,
connectivity=8,
kernel=8,
apply_watershed=False):
# try:
BW = (cv2.cvtColor(I, cv2.COLOR_BGR2GRAY) < threshold).astype(bool)
# if apply_watershed:
# BW = morph.binary_opening(BW, np.ones((connectivity,connectivity)).astype(int))
labels = scilabel(BW)[0]
BW = fill_holes(
morph.remove_small_objects(labels,
min_size=min_object_size,
connectivity=connectivity,
in_place=True))
if apply_watershed:
distance = distance_transform_edt(BW)
local_maxi = peak_local_max(distance,
indices=False,
footprint=np.ones((kernel, kernel)),
labels=BW)
markers = scilabel(local_maxi)[0]
labels = watershed(-distance, markers, mask=BW)
else:
labels = scilabel(BW)[0]
return (BW != 0), labels
def label_objects(img,
otsu=True,
min_object_size=100000,
threshold=240,
connectivity=8,
kernel=61,
keep_holes=False,
max_hole_size=0,
gray_before_close=False,
blur_size=0):
I=cv2.cvtColor(img,cv2.COLOR_RGB2GRAY)
gray_mask=filter_grays(img, output_type="bool")
if otsu: threshold = threshold_otsu(I)
BW = (I<threshold).astype(bool)
if gray_before_close: BW=BW&gray_mask
if kernel>0: BW = morph.binary_closing(BW, morph.disk(kernel))#square
if not gray_before_close: BW=BW&gray_mask
if blur_size: BW=(cv2.blur(BW.astype(np.uint8), (blur_size,blur_size))==1)
labels = scilabel(BW)[0]
labels=morph.remove_small_objects(labels, min_size=min_object_size, connectivity = connectivity, in_place=True)
if not keep_holes and max_hole_size:
BW=morph.remove_small_objects(labels==0, min_size=max_hole_size, connectivity = connectivity, in_place=True)==False#remove_small_holes(labels,area_threshold=max_hole_size, connectivity = connectivity, in_place=True)>0
elif keep_holes:
BW=labels>0
else:
BW=fill_holes(labels)
labels = scilabel(BW)[0]
return(BW!=0),labels
def label_objects(I,
min_object_size,
threshold=220,
connected_components=False,
connectivity=8,
kernel=8,
apply_watershed=False):
#try:
BW = (cv2.cvtColor(I, cv2.COLOR_RGB2GRAY) < threshold).astype(bool)
# if apply_watershed:
# BW = morph.binary_opening(BW, np.ones((connectivity,connectivity)).astype(int))
labels = scilabel(BW)[0]
if connected_components:
BW = fill_holes(
morph.remove_small_objects(labels,
min_size=min_object_size,
connectivity=connectivity,
in_place=True))
labels = scilabel(BW)[0]
return (BW != 0), labels