def setImageMasked(self, image, mask=None, lo=None, hi=None):
"""Set the image to be iterated over. This should be an RGB image,
ndim==3, dtype=='B'. This picks a subset of the segmentation to iterate
over, using a mask and lo and hi values.
"""
# print("$$ setImageMasked: image=%s mask=%s lo=%s hi=%s" % (
# desc(image), hexs(mask), hexs(lo), hexs(hi)))
assert image.dtype == dtype('B') or image.dtype == dtype(
'i'), "image must be type B or i"
if image.ndim == 3:
image = rgb2int(image)
imageDescribe("image", image)
assert image.ndim == 2, "wrong number of dimensions"
self.image = image
labels = image
if lo is not None:
labels[labels < lo] = 0
if hi is not None:
labels[labels > hi] = 0
if mask is not None:
labels = bitwise_and(labels, mask)
imageDescribe("labels", labels)
labels, correspondence = morph.renumber_labels_ordered(
labels, correspondence=1)
self.labels = labels
self.correspondence = correspondence
self.objects = [None] + morph.find_objects(labels)
# print("$$ setImageMasked: objects=%d" % len(self.objects))
sizes = [o for o in self.objects]
sizes.sort(key=lambda u: -sliceSize(u))
for i, o in enumerate(sizes[:20]):
print("%5d: %s %s %d" % (i, o, sliceDims(o), sliceSize(o)))
def setImageMasked(self,image,mask=None,lo=None,hi=None):
"""Set the image to be iterated over. This should be an RGB image,
ndim==3, dtype=='B'. This picks a subset of the segmentation to iterate
over, using a mask and lo and hi values.."""
assert image.dtype==dtype('B') or image.dtype==dtype('i'),"image must be type B or i"
if image.ndim==3: image = rgb2int(image)
assert image.ndim==2,"wrong number of dimensions"
self.image = image
labels = image
if lo is not None: labels[labels<lo] = 0
if hi is not None: labels[labels>hi] = 0
if mask is not None: labels = bitwise_and(labels,mask)
labels,correspondence = morph.renumber_labels_ordered(labels,correspondence=1)
self.labels = labels
self.correspondence = correspondence
self.objects = [None]+morph.find_objects(labels)
