def __init__(
self,
syn_file,
cleft_cc_ds,
cleft_ds,
pre_ds,
post_ds,
seg_file,
seg_ds,
tgt_file,
raw_file=None,
raw_ds=None,
offset=(0.0, 0.0, 0.0),
safe_mem=False,
pre_thr=42,
post_thr=42,
dist_thr=600,
size_thr=5,
):
logging.debug("initializing matchmaker")
self.synf = zarr.open(syn_file, mode="r")
self.segf = zarr.open(seg_file, mode="r")
self.cleft_cc = self.synf[cleft_cc_ds]
self.cleft_cc_np = self.synf[cleft_cc_ds][:]
self.seg = self.segf[seg_ds]
self.pre = self.synf[pre_ds]
self.post = self.synf[post_ds]
self.partners = None
logging.debug("finding list of cleftids")
try:
self.list_of_cleftids = list(range(1, self.cleft_cc.attrs["max_id"] + 1))
except Exception:
self.list_of_cleftids = np.unique(self.cleft_cc[:])[1:]
logging.debug(
"list of cleftids from {0:} to {1:}".format(
np.min(self.list_of_cleftids), np.max(self.list_of_cleftids)
)
)
logging.debug("initializing list of clefts")
self.list_of_clefts = [
Cleft(
self,
cid,
safe_mem=safe_mem,
pre_thr=pre_thr,
post_thr=post_thr,
dist_thr=dist_thr,
size_thr=size_thr,
)
for cid in self.list_of_cleftids
]
logging.debug("intitialized clefts")
self.cremi_file = cremi.CremiFile(tgt_file, "w")
self.offset = offset
if raw_file is not None:
self.rawf = zarr.open(raw_file, mode="r")
self.raw = self.rawf[raw_ds]
else:
self.rawf = None
self.raw = None
def __init__(self,
syn_file,
cleft_cc_ds,
cleft_ds,
pre_ds,
post_ds,
seg_file,
seg_ds,
tgt_file,
raw_file=None,
raw_ds=None,
offset=(0., 0., 0.),
num_cores=10,
safe_mem=False,
pre_thr=42,
post_thr=42,
dist_thr=600,
size_thr=5,
ngbrs=True,
mvpts=True,
splitcc=True):
self.synf = z5py.File(syn_file, use_zarr_format=False)
self.segf = z5py.File(seg_file, use_zarr_format=False)
self.cleft = self.synf[cleft_ds]
self.cleft_cc = self.synf[cleft_cc_ds]
self.cleft_cc_np = self.synf[cleft_cc_ds][:]
self.seg = self.segf[seg_ds]
self.pre = self.synf[pre_ds]
self.post = self.synf[post_ds]
self.partners = None
self.num_cores = num_cores
#inputs = np.unique(self.cleft_cc[:])[1:]
#self.list_of_clefts = Parallel(n_jobs=self.num_cores)(delayed(Cleft.__init__)(Cleft.__new__(Cleft), self,
# cid) for cid in inputs)
print("finding all clefts...")
try:
self.list_of_cleftids = range(1, self.cleft_cc.attrs['max_id'] + 1)
except AssertionError:
self.list_of_cleftids = np.unique(self.cleft_cc[:])[1:]
self.list_of_clefts = [
Cleft(self,
cid,
safe_mem=safe_mem,
splitcc=splitcc,
pre_thr=pre_thr,
post_thr=post_thr,
dist_thr=dist_thr,
size_thr=size_thr,
ngbrs=ngbrs,
mvpts=mvpts) for cid in self.list_of_cleftids
]
self.cremi_file = cremi.CremiFile(tgt_file, 'w')
self.offset = offset
if raw_file is not None:
self.rawf = z5py.File(raw_file, use_zarr_format=False)
self.raw = self.rawf[raw_ds]
else:
self.rawf = None
self.raw = None
def __init__(self,
syn_file,
cleft_cc_ds,
cleft_ds,
pre_ds,
post_ds,
seg_file,
seg_ds,
tgt_file,
raw_file=None,
raw_ds=None,
offset=(0., 0., 0.),
safe_mem=False,
pre_thr=42,
post_thr=42,
dist_thr=600,
size_thr=5):
logging.debug('initializing matchmaker')
self.synf = z5py.File(syn_file, use_zarr_format=False)
self.segf = z5py.File(seg_file, use_zarr_format=False)
self.cleft = self.synf[cleft_ds]
self.cleft_cc = self.synf[cleft_cc_ds]
self.cleft_cc_np = self.synf[cleft_cc_ds][:]
self.seg = self.segf[seg_ds]
self.pre = self.synf[pre_ds]
self.post = self.synf[post_ds]
self.partners = None
logging.debug('finding list of cleftids')
try:
self.list_of_cleftids = range(1, self.cleft_cc.attrs['max_id'] + 1)
except Exception:
self.list_of_cleftids = np.unique(self.cleft_cc[:])[1:]
logging.debug('list of cleftids from {0:} to {1:}'.format(
np.min(self.list_of_cleftids), np.max(self.list_of_cleftids)))
logging.debug('initializing list of clefts')
self.list_of_clefts = [
Cleft(self,
cid,
safe_mem=safe_mem,
pre_thr=pre_thr,
post_thr=post_thr,
dist_thr=dist_thr,
size_thr=size_thr) for cid in self.list_of_cleftids
]
logging.debug('intitialized clefts')
self.cremi_file = cremi.CremiFile(tgt_file, 'w')
self.offset = offset
if raw_file is not None:
self.rawf = z5py.File(raw_file, use_zarr_format=False)
self.raw = self.rawf[raw_ds]
else:
self.rawf = None
self.raw = None
def __init__(
self,
syn_file,
cleft_cc_ds,
seg_file,
seg_ds,
tgt_file,
raw_file=None,
raw_ds=None,
offset=(0.0, 0.0, 0.0),
num_cores=10,
safe_mem=False,
):
self.synf = zarr.open(syn_file, mode="r")
self.segf = zarr.open(seg_file, mode="r")
self.cleft_cc = self.synf[cleft_cc_ds]
self.cleft_cc_np = self.synf[cleft_cc_ds][:]
self.seg = self.segf[seg_ds]
self.partners = None
self.num_cores = num_cores
# inputs = np.unique(self.cleft_cc[:])[1:]
# self.list_of_clefts = Parallel(n_jobs=self.num_cores)(delayed(Cleft.__init__)(Cleft.__new__(Cleft), self,
# cid) for cid in inputs)
print("finding all clefts...")
try:
self.list_of_cleftids = list(
range(1, self.cleft_cc.attrs["max_id"] + 1))
except AssertionError:
self.list_of_cleftids = np.unique(self.cleft_cc[:])[1:]
self.list_of_clefts = [
Cleft(self, cid, safe_mem=safe_mem)
for cid in self.list_of_cleftids
]
self.cremi_file = cremi.CremiFile(tgt_file, "w")
self.offset = offset
if raw_file is not None:
self.rawf = zarr.open(raw_file, mode="r")
self.raw = self.rawf[raw_ds]
else:
self.rawf = None
self.raw = None
