def extractWithMask(self,
source,
i,
grow=0,
bg=0,
margin=None,
dtype=None):
"""Extract the image and mask corresponding to group i"""
if dtype is None: dtype = source.dtype
if self.isEmpty(i): return None
if margin is None: margin = grow
box, labels = self.groups[i]
image = sl.cut(source, box, margin=margin, bg=bg, dtype=dtype)
mask = sl.cut(self.segmentation, box, margin=grow, bg=0)
mask = in1d(mask, array(labels, 'i')).reshape(image.shape)
mask = morphology.binary_dilation(mask, iterations=grow)
return where(mask, image, bg), mask
def getMask(self, i, margin=0):
"""Get the mask image for group i."""
box, labels = self.groups[i]
if sl.empty(box): return None
mask = sl.cut(self.segmentation, box, margin=margin)
shape = mask.shape
mask = in1d(mask, array(labels, 'i'))
mask.shape = shape
return mask
def cut(image, box, margin=0, bg=0, dtype=None):
"""Cuts out subimages with margins and background. The box
is given as (row0,column0,row1,column1). This uses
sl.cut (but with different conventions for the box)."""
(r0, c0, r1, c1) = box
return sl.cut(image,
sl.box(r0, r1, c0, c1),
margin=margin,
bg=bg,
dtype=dtype)
def extractWithBackground(self, source, dflt, i, grow=0, dtype=None):
"""Extract the image corresponding to group i. Background pixels are
filled in with dflt."""
if dtype is None: dtype = source.dtype
if self.isEmpty(i): return None
image = sl.cut(source,
self.boundingBox(i),
margin=grow,
bg=dflt,
dtype=dtype)
return image
def extractMasked(self,image,index,grow=0,bg=None,margin=0,dtype=None):
"""Return the masked subimage for component index, elsewhere the bg value."""
if bg is None: bg = amax(image)
h,w = image.shape[:2]
mask = self.mask(index,margin=margin)
# FIXME ... not circular
if grow>0: mask = morphology.binary_dilation(mask,iterations=grow)
mh,mw = mask.shape
box = self.bbox(index)
r0,c0,r1,c1 = box
subimage = sl.cut(image,(r0,c0,r0+mh-2*margin,c0+mw-2*margin),margin,bg=bg)
return where(mask,subimage,bg)
def extractMasked(self,image,index,grow=0,bg=None,margin=0,dtype=None):
"""Return the masked subimage for component index, elsewhere the bg value."""
if bg is None: bg = amax(image)
h,w = image.shape[:2]
mask = self.mask(index,margin=margin)
# FIXME ... not circular
if grow>0: mask = morphology.binary_dilation(mask,iterations=grow)
mh,mw = mask.shape
box = self.bbox(index)
r0,c0,r1,c1 = box
subimage = sl.cut(image,(r0,c0,r0+mh-2*margin,c0+mw-2*margin),margin,bg=bg)
return where(mask,subimage,bg)
def cut(image,box,margin=0,bg=0,dtype=None):
"""Cuts out subimages with margins and background. The box
is given as (row0,column0,row1,column1). This uses
sl.cut (but with different conventions for the box)."""
(r0,c0,r1,c1) = box
return sl.cut(image,sl.box(r0,r1,c0,c1),margin=margin,bg=bg,dtype=dtype)