def ring_dilation_above_offset_buffer(labels, img, MARGIN=0, RINGWIDTH=2, BUFFER=2,
OFFSET=100, FILSIZE=50):
"""Dilate from label to make a ring.
Calculate the local minimum as a background, and if image is less brighter
than background + offset, remove the region from the ring.
"""
sub_label = dilate_to_cytoring_buffer(labels, RINGWIDTH, MARGIN, BUFFER)
minimg = minimum_filter(img, size=FILSIZE)
sub_label[img < (minimg + OFFSET)] = 0
return sub_label
def ring_dilation_above_adaptive(labels,
img,
MARGIN=0,
RINGWIDTH=4,
BUFFER=2,
RATIO=1.05,
FILSIZE=10):
sub_labels = dilate_to_cytoring_buffer(labels, RINGWIDTH, MARGIN, BUFFER)
bw = adaptive_thresh(img, R=RATIO, FILTERINGSIZE=FILSIZE)
sub_labels[-bw] = 0
return sub_labels
def ring_dilation(labels, MARGIN=0, RINGWIDTH=4, BUFFER=0):
"""Create a ring around label.
:param RINGWIDTH (int): Width of rings
:param MARGIN (int): A region of rings is ignored if they are within MARGIN pixels away from label.
Examples:
>>> arr = np.zeros((5, 5));arr[2, 2] = 10
>>> ring_dilation(None, arr, None, MARGIN=1, RINGWIDTH=2)
array([[ 0, 10, 10, 10, 0],
[10, 0, 0, 0, 10],
[10, 0, 0, 0, 10],
[10, 0, 0, 0, 10],
[ 0, 10, 10, 10, 0]], dtype=uint16)
"""
if BUFFER == 0:
return dilate_to_cytoring(labels, RINGWIDTH, MARGIN)
else:
return dilate_to_cytoring_buffer(labels, RINGWIDTH, MARGIN, BUFFER)
def ring_dilation_buffer(labels, MARGIN=0, RINGWIDTH=4, BUFFER=2):
return dilate_to_cytoring_buffer(labels, RINGWIDTH, MARGIN, BUFFER)
