def oversegment(oversegmenter, lim=0, infile=None, outfile=None):
module = importer.get_module('oversegmenters', oversegmenter)
use_bm = hasattr(module, 'oversegment_bm')
use_aff = hasattr(module, 'oversegment_aff')
if use_bm and use_aff:
raise ImportError("Bad module: '%s'" % module.__name__)
if use_bm:
if not infile:
infile = config.fn_bm
bm_3d = formats.read_bm(infile)
if lim:
bm_3d = bm_3d[:lim]
labels_3d, n_labels = module.oversegment_bm(bm_3d)
elif use_aff:
if not infile:
infile = config.fn_aff
aff_3d = formats.read_aff(infile)
if lim:
aff_3d = aff_3d[:lim]
# Need edges going out-of-bounds to be 0, to prevent the exploring
# of out-of-bounds vertices
formats.clean_aff(aff_3d)
labels_3d, n_labels = module.oversegment_aff(aff_3d)
else:
raise ImportError("Bad module: '%s'" % module.__name__)
logging.info("Found %d labels" % n_labels)
# Write labels to disk
if not outfile:
outfile = io.get_filename(config.dn_data, "oversegment-%s" % oversegmenter, "tif")
formats.save_labels(outfile, labels_3d)
"""
Wrapper for formats.save_aff_tiff.
"""
from jpyutils.jlogging import logging_setup
import sys
from structs import formats
logging_setup('debug')
in_fn, out_fn = sys.argv[1:3]
if len(sys.argv) > 3:
dim = int(sys.argv[3])
else:
# Default to taking min of all affinities
dim = 3
formats.save_aff_tiff(out_fn, formats.read_aff(in_fn), dim)
"""
Convert edge affinities file from .aff (snemi3d) to .raw (aleks).
"""
from jpyutils.jlogging import logging_setup
import sys
from structs import formats
logging_setup('debug')
in_fn, out_fn = sys.argv[1:3]
if len(sys.argv) > 3:
lim = int(sys.argv[3])
else:
lim = 0
aff_3d = formats.read_aff(in_fn)
if lim:
aff_3d = aff_3d[:lim]
aff_3d = formats.WEIGHT_DTYPE_FLOAT(aff_3d) / formats.WEIGHT_MAX_UINT
formats.save_aff(out_fn, aff_3d)
