def _execute_GRAPHCUT(self, roi, result):
data = self.Input(roi.start, roi.stop).wait()
data = vigra.taggedView(data, self.Input.meta.axistags)
data_zyx = data[0, ..., 0]
beta = self.GraphcutBeta.value
ft = self.FinalThreshold.value
# The segmentGC() function will implicitly threshold at 0.5,
# but we want to respect the user's FinalThreshold setting.
# Here, we scale from input pixels --> gc potentials in the following way:
#
# 0.0..FT --> 0.0..0.5
# 0.5..FT --> 0.5..1.0
#
# For instance, input pixels that match the user's FT exactly will map to 0.5,
# and graphcut will place them on the threshold border.
above_threshold_mask = (data_zyx >= ft)
below_threshold_mask = ~above_threshold_mask
data_zyx[below_threshold_mask] *= 0.5 / ft
data_zyx[above_threshold_mask] = 0.5 + (
data_zyx[above_threshold_mask] - ft) / (1 - ft)
binary_seg_zyx = segmentGC(data_zyx, beta).astype(np.uint8)
del data_zyx
vigra.analysis.labelMultiArrayWithBackground(binary_seg_zyx,
out=result[0, ..., 0])
def processSingleObject(i):
logger.debug("processing object {}".format(i))
# maxs are inclusive, so we need to add 1
xmin = max(mins[i][0] - margin[0], 0)
ymin = max(mins[i][1] - margin[1], 0)
zmin = max(mins[i][2] - margin[2], 0)
xmax = min(maxs[i][0] + margin[0] + 1, cc.shape[0])
ymax = min(maxs[i][1] + margin[1] + 1, cc.shape[1])
zmax = min(maxs[i][2] + margin[2] + 1, cc.shape[2])
ccbox = cc[xmin:xmax, ymin:ymax, zmin:zmax]
resbox = resultXYZ[xmin:xmax, ymin:ymax, zmin:zmax]
nVoxels = ccbox.size
if nVoxels > MAXBOXSIZE:
#problem too large to run graph cut, assign to seed
logger.warn("Object {} too large for graph cut.".format(i))
resbox[ccbox == i] = 1
return
probbox = pred[xmin:xmax, ymin:ymax, zmin:zmax]
gcsegm = segmentGC(probbox, beta)
gcsegm = vigra.taggedView(gcsegm, axistags='xyz')
ccsegm = vigra.analysis.labelVolumeWithBackground(
gcsegm.astype(np.uint8))
# Extended bboxes of different objects might overlap.
# To avoid conflicting segmentations, we find all connected
# components in the results and only take the one, which
# overlaps with the object "core" or "seed", defined by the
# pre-thresholding
seed = ccbox == i
filtered = seed * ccsegm
passed = vigra.analysis.unique(filtered)
passed.sort()
assert len(passed.shape) == 1
if passed.size > 2:
logger.warn("ambiguous label assignment for region {}".format(
(xmin, xmax, ymin, ymax, zmin, zmax)))
resbox[ccbox == i] = 1
elif passed.size <= 1:
logger.warn("box {} segmented out with beta {}".format(
i, beta))
else:
# assign to the overlap region
label = passed[1] # 0 is background
resbox[ccsegm == label] = 1
def processSingleObject(i):
logger.debug("processing object {}".format(i))
# maxs are inclusive, so we need to add 1
xmin = max(mins[i][0]-margin[0], 0)
ymin = max(mins[i][1]-margin[1], 0)
zmin = max(mins[i][2]-margin[2], 0)
xmax = min(maxs[i][0]+margin[0]+1, cc.shape[0])
ymax = min(maxs[i][1]+margin[1]+1, cc.shape[1])
zmax = min(maxs[i][2]+margin[2]+1, cc.shape[2])
ccbox = cc[xmin:xmax, ymin:ymax, zmin:zmax]
resbox = resultXYZ[xmin:xmax, ymin:ymax, zmin:zmax]
nVoxels = ccbox.size
if nVoxels > MAXBOXSIZE:
#problem too large to run graph cut, assign to seed
logger.warn("Object {} too large for graph cut.".format(i))
resbox[ccbox == i] = 1
return
probbox = pred[xmin:xmax, ymin:ymax, zmin:zmax]
gcsegm = segmentGC(probbox, beta)
gcsegm = vigra.taggedView(gcsegm, axistags='xyz')
ccsegm = vigra.analysis.labelVolumeWithBackground(
gcsegm.astype(np.uint8))
# Extended bboxes of different objects might overlap.
# To avoid conflicting segmentations, we find all connected
# components in the results and only take the one, which
# overlaps with the object "core" or "seed", defined by the
# pre-thresholding
seed = ccbox == i
filtered = seed*ccsegm
passed = vigra.analysis.unique(filtered.astype(np.uint32))
assert len(passed.shape) == 1
if passed.size > 2:
logger.warn("ambiguous label assignment for region {}".format(
(xmin, xmax, ymin, ymax, zmin, zmax)))
resbox[ccbox == i] = 1
elif passed.size <= 1:
logger.warn(
"box {} segmented out with beta {}".format(i, beta))
else:
# assign to the overlap region
label = passed[1] # 0 is background
resbox[ccsegm == label] = 1