def multi_mask(img, *names, **kwargs):
""" Return a list/tuple/generator of masks of an image, one for each unique
label found in a colored img. EVERYTHING DOWN-CONVERTED TO UINT: NECESSARY
FOR MORPHOLOGY.LABELS ANYWAY, ALTHOUGH POSSIBLY SHOULD DO RGB2GRAY OR 255
LABELS IS MAX"""
astype = kwargs.pop('astype', tuple)
ignore = kwargs.pop('ignore', 'black')
names = list(names)
# THIS WILL DRASTICALLY REDUCE NUMBER OF UNIQUE LABELS ALLOWED RIGHT?
# SINCE IT ONLY HAS 255 POSSIBLE VALUES?!
if img.ndim == 3:
img = putil.rgb2uint(img, warnmsg=True)
# Labels requires on grayscale; npunique also doesn't play nice w/ rgb
if ignore == 'black' or ignore == (0,0,0):
ignore = 0
elif ignore == 'white' or ignore == (1,1,1):
ignore = 255
unique = ptools.unique(img)
if ignore not in unique:
logger.warn("Ignore set to %s but was not found on image." % ignore)
else:
unique = [v for v in unique if v != ignore]
names = _parse_names(names, unique)
# Make the mask dict as generator
out = ((str(names[idx]), (img==v)) for idx, v in enumerate(unique))
return putil._parse_generator(out, astype)
def from_labeled(cls, img, *names, **pmankwargs):
""" Labels an image and creates multi-canvas, one for each species
in the image. Since labels require gray image, putil.rgb2uint used
internally.
Attributes
----------
mapper : iterable of pairs, ordered dict or dict
Specifies which colors correspond to which labels. Order of labels
is also used as order of multicanvas names, so if using dict,
this will be scrambled.
Examples
--------
mc = MultiCanvas.from_labeled(image, singles, doubles)
mc = MultiCanvas.from_labeled(image,
mapper=(('singles','red'), ('doubles',(1,1,0)) ))
"""
ignore = pmankwargs.pop('ignore', 'black')
neighbors = pmankwargs.pop('neighbors', 4)
maximum = pmankwargs.pop('maximum', MAXDEFAULT)
mapper = pmankwargs.pop('mapper', [])
storecolors = pmankwargs.pop('storecolors', True)
# Retro-support *names positional arg by converting to mapper
# since mapper already works downstream
if names:
if mapper:
raise MultiError("Names must be positional arguments or"
" mapper, but not both.")
mapper = zip(names, putil._get_ccycle(upto=len(names)) )
# BAD PRACTICE TO USE DICT CUZ UNSORTED
if isinstance(mapper, dict):
mapper = mapper.items()
if mapper:
cnames, colors = zip(*mapper)
else:
cnames, colors = [], []
# TEST ON GRAY IMAGE
if img.ndim == 3:
img = putil.any2rgb(img)
unique = [tuple(v) for v in ptools.unique(img)]
threechan = True
else:
# img = putil.any2uint(img)
unique = [float(v) for v in ptools.unique(img)]
threechan=False
# Redundant w/ name masks but oh well
if ignore is None:
color_ignore = []
elif ignore == 'black' or ignore == (0,0,0) or ignore == 0:
color_ignore = [0, (0,0,0)]
elif ignore == 'white' or ignore == (1,1,1) or ignore == 255:
color_ignore = [255, (1,1,1), (255,255,255)]
# A list of values, take besut guess
else:
color_ignore = zip(*putil.guess_colors(ignore, unique,
threechan=threechan))[1]
# Store indicies to ignore
index_ignore = [idx for idx, v in enumerate(unique) if v in color_ignore]
unique = [v for v in unique if v not in color_ignore]
# Sort by gray values; multimask will expect this
color_gray = zip(map(putil.any2rgb, unique), map(putil.any2uint, unique) )
unique, grayunique = zip(*sorted(color_gray, key=operator.itemgetter(1)))
if img.ndim < 3:
unique = grayunique
_colormapper = dict(putil.guess_colors(colors, unique, threechan=threechan))
mout =[(str(c), c) for c in unique]
_tempmap = {}
for k,v in mapper:
_tempmap[k] = _colormapper[v]
_tempmap = dict((str(v),k) for k,v in _tempmap.items())
def _tryeval(val):
def r2(x): return round(x,2)
try:
val = eval(val)
except NameError:
return val
try:
r,g,b = val
except TypeError:
return str(r2(val))
else:
return str(tuple(map(r2, val)))
mapper = []
for k,v in mout:
if k in _tempmap:
kout = _tempmap[k]
else:
kout = k
kout = _tryeval(kout)
mapper.append((kout,v))
name_masks = multi_mask(img, *names, astype=tuple, ignore=None)
if len(name_masks) > maximum:
raise MultiError("%s labels found, exceeding maximum of %s"
" increasing maximum may result in slowdown." %
(len(name_masks), maximum) )
canvii = [] ; names = []
j=0
for idx, (name, mask) in enumerate(name_masks):
if idx not in index_ignore:
labels = morphology.label(mask, neighbors, background=False)
particles = ParticleManager.from_labels(labels,
prefix=name, **pmankwargs)
canvii.append(Canvas(particles=particles, rez=mask.shape) )
names.append(mapper[j][0])
j += 1
mc = cls(canvii=canvii, names=names)
# Map colors
if storecolors:
mc.set_colors(**dict((k,v) for k,v in mapper if k in names))
# Reorder names: user cnames first, then remaining in mapper
neworder = list(cnames)
for idx, (name, v) in enumerate(mapper):
if idx not in index_ignore:
if name not in cnames:
neworder.append(name)
mc.reorder(*neworder, inplace=True)
return mc