def write_output(outpath, out, props, imtype='Label'):
"""Write data to an image on disk."""
props['dtype'] = out.dtype
if imtype == 'Label':
mo = LabelImage(outpath, **props)
elif imtype == 'Mask':
mo = MaskImage(outpath, **props)
else:
mo = Image(outpath, **props)
mo.create()
mo.write(out)
return mo
def split_nucl_and_memb(labels, outpat, nuclearmask=None):
labeldata = labels.slice_dataset()
labeldata, labeldata_nucl = split_nucl_and_memb_data(
labeldata, nuclearmask)
pf = '_memb'
outpath = outpat.format(pf)
im_memb = LabelImage(outpath, **props)
im_memb.create()
im_memb.write(labeldata)
pf = '_nucl'
outpath = outpat.format(pf)
im_nucl = LabelImage(outpath, **props)
im_nucl.create()
im_nucl.write(labeldata_nucl)
return im_memb, im_nucl
def write(out, outstem, postfix, ref_im, imtype='Image'):
"""Write an image to disk."""
outstem = outstem or gen_outpath(ref_im, '')
outpath = '{}{}'.format(outstem, postfix)
props = ref_im.get_props()
props['dtype'] = out.dtype
if imtype == 'Label':
mo = LabelImage(outpath, **props)
elif imtype == 'Mask':
mo = MaskImage(outpath, **props)
else:
mo = Image(outpath, **props)
mo.create()
mo.write(out)
if imtype == 'Label':
mo.set_maxlabel()
mo.ds.attrs.create('maxlabel', mo.maxlabel, dtype='uint32')
return mo
def mergeblocks(
images_in,
dataslices=None,
blocksize=[],
blockmargin=[],
blockrange=[],
blockoffset=[0, 0, 0],
fullsize=[],
is_labelimage=False,
relabel=False,
neighbourmerge=False,
save_fwmap=False,
blockreduce=[],
func='np.amax',
datatype='',
usempi=False,
outputpath='',
save_steps=False,
protective=False,
):
"""Merge blocks of data into a single hdf5 file."""
if blockrange:
images_in = images_in[blockrange[0]:blockrange[1]]
mpi = wmeMPI(usempi)
im = Image(images_in[0], permission='r')
im.load(mpi.comm, load_data=False)
props = im.get_props(protective=protective, squeeze=True)
ndim = im.get_ndim()
props['dtype'] = datatype or props['dtype']
props['chunks'] = props['chunks'] or None
# get the size of the outputfile
# TODO: option to derive fullsize from dset_names?
if blockreduce:
datasize = np.subtract(fullsize, blockoffset)
outsize = [
int(np.ceil(d / np.float(b)))
for d, b in zip(datasize, blockreduce)
]
props['elsize'] = [e * b for e, b in zip(im.elsize, blockreduce)]
else: # FIXME: 'zyx(c)' stack assumed
outsize = np.subtract(fullsize, blockoffset)
if ndim == 4:
outsize = list(outsize) + [im.ds.shape[3]] # TODO: flexible insert
if outputpath.endswith('.ims'):
mo = LabelImage(outputpath)
mo.create(comm=mpi.comm)
else:
props['shape'] = outsize
mo = LabelImage(outputpath, **props)
mo.create(comm=mpi.comm)
mpi.blocks = [{'path': image_in} for image_in in images_in]
mpi.nblocks = len(images_in)
mpi.scatter_series()
# merge the datasets
maxlabel = 0
for i in mpi.series:
block = mpi.blocks[i]
# try:
maxlabel = process_block(block['path'], ndim, blockreduce, func,
blockoffset, blocksize, blockmargin, fullsize,
mo, is_labelimage, relabel, neighbourmerge,
save_fwmap, maxlabel, mpi)
print('processed block {:03d}: {}'.format(i, block['path']))
# except Exception as e:
# print('failed block {:03d}: {}'.format(i, block['path']))
# print(e)
im.close()
mo.close()
return mo