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