def segs_to_raveler(sps, bodies, **kwargs):
import morpho
min_sp_size = kwargs.get('min_sp_size', 16)
sps_out = []
sps_per_plane = []
sp_to_segment = []
segment_to_body = [array([[0,0]])]
total_nsegs = 0
for i, (sp_map, body_map) in enumerate(zip(sps, bodies)):
sp_map, nsps = label(
morpho.remove_small_connected_components(sp_map, min_sp_size, True)
)
segment_map, nsegs = label(body_map)
segment_map += total_nsegs
segment_map *= sp_map.astype(bool)
total_nsegs += nsegs
sps_out.append(sp_map[newaxis,...])
sps_per_plane.append(nsps)
valid = (sp_map != 0) + (segment_map == 0)
sp_to_segment.append(unique(
zip(it.repeat(i), sp_map[valid], segment_map[valid])))
valid = segment_map != 0
logging.debug('plane %i done'%i)
segment_to_body.append(unique(
zip(segment_map[valid], body_map[valid])))
logging.info('total superpixels before: ' + str(len(unique(sps))) +
'total superpixels after: ' + str(sum(sps_per_plane)))
sps_out = concatenate(sps_out, axis=0)
sp_to_segment = concatenate(sp_to_segment, axis=0)
segment_to_body = concatenate(segment_to_body, axis=0)
return sps_out, sp_to_segment, segment_to_body
def segs_to_raveler(sps, bodies, **kwargs):
import morpho
min_sp_size = kwargs.get('min_sp_size', 16)
sps_out = []
sps_per_plane = []
sp_to_segment = []
segment_to_body = [array([[0, 0]])]
total_nsegs = 0
for i, (sp_map, body_map) in enumerate(zip(sps, bodies)):
sp_map, nsps = label(
morpho.remove_small_connected_components(sp_map, min_sp_size,
True))
segment_map, nsegs = label(body_map)
segment_map += total_nsegs
segment_map *= sp_map.astype(bool)
total_nsegs += nsegs
sps_out.append(sp_map[newaxis, ...])
sps_per_plane.append(nsps)
valid = (sp_map != 0) + (segment_map == 0)
sp_to_segment.append(
unique(zip(it.repeat(i), sp_map[valid], segment_map[valid])))
valid = segment_map != 0
logging.debug('plane %i done' % i)
segment_to_body.append(unique(zip(segment_map[valid],
body_map[valid])))
logging.info('total superpixels before: ' + str(len(unique(sps))) +
'total superpixels after: ' + str(sum(sps_per_plane)))
sps_out = concatenate(sps_out, axis=0)
sp_to_segment = concatenate(sp_to_segment, axis=0)
segment_to_body = concatenate(segment_to_body, axis=0)
return sps_out, sp_to_segment, segment_to_body
def remove_small(a):
return morpho.remove_small_connected_components(a, min_size, False)
def remove_small(a):
return morpho.remove_small_connected_components(a, min_size, False)