def process_waterz(z0a, z1a, y0a, y1a, x0a, x1a):
out_path = get_waterz(x0a, y0a, z0a, wz_thres[-1])
if not os.path.exists(out_path):
# naive
zstep = min(z1a - z0a, vol_sz[0])
if zstep == vol_sz[0]: # fit at least a chunk
zz = range(z0a, z1a, vol_sz[0])
else:
zz = z0 + vol_sz[0] * ((z0a - z0) // vol_sz[0])
numZ = z1a - z0a
xx = range(x0a, x1a, vol_sz[1])
yy = range(y0a, y1a, vol_sz[2])
print xx, yy, zz
aff = np.zeros((3, numZ, vol_sz[1] * len(yy), vol_sz[2] * len(xx)),
dtype=np.float32)
print 'load aff'
for xi, x in enumerate(xx):
for yi, y in enumerate(yy):
for kid, k in enumerate('zyx'):
if zstep == vol_sz[0]: # fit at least a chunk
for zi, z in enumerate(zz):
aff[kid, zi*vol_sz[1]:(zi+1)*vol_sz[0], yi*vol_sz[1]:(yi+1)*vol_sz[1], xi*vol_sz[2]:(xi+1)*vol_sz[2]] = \
np.array(h5py.File(get_aff(x, y, z)+"/%s_min.h5" % (k))['main']).astype(np.float32)/255.0
else: # fit part of a chunk
aff[kid, :, yi*vol_sz[1]:(yi+1)*vol_sz[1], xi*vol_sz[2]:(xi+1)*vol_sz[2]] = \
np.array(h5py.File(get_aff(x, y, zz)+"/%s_min.h5" % (k))['main'])[z0a-zz:z1a-zz].astype(np.float32)/255.0
print 'load 2d seg'
if zstep == vol_sz[0]: # fit at least a chunk
z2d = np.zeros((numZ, vol_sz[1] * len(yy), vol_sz[2] * len(xx)),
dtype=np.uint64)
for zid in range(len(zz)):
sn = get_zwatershed(x0a, y0a, z0a + zid * vol_sz[0])
z2d[zid * vol_sz[0]:(zid + 1) * vol_sz[0]] = np.array(
h5py.File(sn)['main']).astype(np.uint64)
else:
sn = get_zwatershed(x0a, y0a, zz)
z2d = np.array(h5py.File(sn)['main'])[z0a - zz:z1a - zz].astype(
np.uint64)
# unique and relabel ids
next_id = np.uint64(0)
# change value by reference
for zid in range(numZ):
tile = z2d[zid]
tile[np.where(tile > 0)] += next_id
next_id = tile.max()
print 'do segmentation'
seg = waterz(affs=aff,
thresholds=wz_thres,
fragments=z2d,
merge_function=wz_mf)
for tid, tt in enumerate(wz_thres):
out_path = get_waterz(x0a, y0a, z0a, tt)
writeh5(out_path, 'main', relabel(seg[tid]).astype(np.uint32))
et = time.time()
out = relabel(out)
sn = '%s_%f_%f_%d_%f_%d_%f_%d.h5' % (opt, T_aff[0], T_aff[1], T_thres[0],
T_aff[2], T_dust, T_merge)
elif opt == '1':
# 2D watershed + waterz
import waterz
print 'waterz-0.8'
st = time.time()
low = 0.05
high = 0.995
mf = 'aff85_his256'
T_thres = [0.2]
out = waterz.waterz(aff,
T_thres,
merge_function=mf,
gt_border=0,
aff_threshold=[low, high])[0]
et = time.time()
out = relabel(out)
sn = '%s_%f_%f_%f_%s.h5' % (opt, low, high, T_thres[0], mf)
elif opt == '2':
# 2D zwatershed + waterz
import waterz
import zwatershed
print 'zwatershed + waterz'
st = time.time()
T_thres = [800]
T_aff = [0.05, 0.95, 0.2]
T_dust = 600
T_merge = 0.9
import waterz
import numpy as np
aff = np.random.random((3, 5, 5, 5)).astype(np.float32)
seg_gt = None
aff_thresholds = [0.005, 0.995]
seg_thresholds = [0.1, 0.3, 0.6]
seg = waterz.waterz(aff,
seg_thresholds,
merge_function='aff50_his256',
aff_threshold=aff_thresholds,
gt=seg_gt)
T_merge=0.9
T_aff_rel=1
out = zwatershed.zwatershed(aff, T_thres, T_aff=T_aff, \
T_dust=T_dust, T_merge=T_merge,T_aff_relative=T_aff_rel)[0][0]
et = time.time()
out = relabel(out)
sn = '%s_%f_%f_%d_%f_%d_%f_%d'%(args.mode,T_aff[0],T_aff[1],T_thres[0],T_aff[2],T_dust,T_merge,T_aff_rel)
elif args.mode == 1:
# waterz
import waterz
print('waterz:', waterz.__version__)
st = time.time()
low=0.05; high=0.995
mf = 'aff85_his256'; T_thres = [0.3]
out = waterz.waterz(aff, T_thres, merge_function=mf, gt_border=0,
fragments=None, aff_threshold=[low, high], return_seg=True, gt=seg)[0]
et = time.time()
out = relabel(out)
print(out.shape)
sn = '%s_%f_%f_%f_%s'%(args.mode,low,high,T_thres[0],mf)
elif args.mode == 2:
# 2D zwatershed + waterz
import waterz
import zwatershed
print('waterz:', waterz.__version__)
#print('zwatershed:', zwatershed.__version__)
st = time.time()
T_thres = [150]
T_aff=[0.05,0.8,0.2]
T_dust=150