watersheds

from gala import morpho
from gala import imio
import skimage.io as io
import multiprocessing

fn = '/data/hanslovskyp/cremi/gala-from-juan/sample_B_20160630_frags.hdf'
# fn = '/data/hanslovskyp/cremi/gala/sample_B_20160708_frags_46_55.hdf'
# fn = '/data/hanslovskyp/cremi/gala-from-juan/sample_B_20160501.hdf'
# fn = '/data/hanslovskyp/cremi/gala-from-juan/sample_B_20160630_frags.hdf'
# fn = '/data/hanslovskyp/cremi/gala-from-juan/sample_B_20160708_frags_46_55.hdf'

membrane = imio.read_cremi(fn, ['/volumes/membrane'])[0]
fragments = morpho.pipeline_compact_watershed(membrane, n_jobs=multiprocessing.cpu_count())#, max_nbytes='1000M')
imio.write_h5_stack(fragments, fn, group='/volumes/labels/fragments', compression='gzip')