def constrained_aleks_malis(affs, lbl, threshold=0.5):
"""
adding constraints for malis weight
fill the intracellular space with ground truth when computing merging error
fill the boundary with ground truth when computing spliting error
"""
from cost_fn import constrain_label
mbdm, sbdm = constrain_label(bdm, lbl)
# get the merger weights
mw, mme, mse = aleks_malis(mbdm, lbl)
# get the splitter weights
sw, sme, sse = aleks_malis(sbdm, lbl)
w = mme + sse
return (w, mme, sse)
def constrained_aleks_malis(affs, lbl, threshold=0.5):
"""
adding constraints for malis weight
fill the intracellular space with ground truth when computing merging error
fill the boundary with ground truth when computing spliting error
"""
from cost_fn import constrain_label
mbdm, sbdm = constrain_label(bdm, lbl)
# get the merger weights
mw, mme, mse = aleks_malis(mbdm, lbl)
# get the splitter weights
sw, sme, sse = aleks_malis(sbdm, lbl)
w = mme + sse
return (w, mme, sse)
erosion_size = pars['erosion_size']
if erosion_size > 0:
print "increase boundary width"
erosion_structure = np.ones((erosion_size, erosion_size))
msk = np.copy(lbl > 0)
from scipy.ndimage.morphology import binary_erosion
msk = binary_erosion(msk, structure=erosion_structure)
lbl[msk == False] = 0
print "boundary map: ", bdm
return bdm, lbl
if __name__ == "__main__":
from malis_test import get_params
pars = get_params()
if pars['is_affinity']:
affs, lbl = make_fake_3D_aff(3, 7, 3, 7)
else:
bdm, lbl = read_image(pars)
# normal boundary map and
bdm.astype("float64").tofile("../dataset/malis/bdm.bin")
lbl.astype('float64').tofile("../dataset/malis/lbl.bin")
from cost_fn import constrain_label
mbdm, sbdm = constrain_label(bdm, lbl)
mbdm.astype("float64").tofile("../dataset/malis/bdm_merge.bin")
sbdm.astype("float64").tofile("../dataset/malis/bdm_splite.bin")
# increase boundary width
erosion_size = pars['erosion_size']
if erosion_size>0:
print "increase boundary width"
erosion_structure = np.ones((erosion_size, erosion_size))
msk = np.copy(lbl>0)
from scipy.ndimage.morphology import binary_erosion
msk = binary_erosion(msk, structure=erosion_structure)
lbl[msk==False] = 0
print "boundary map: ", bdm
return bdm, lbl
if __name__ == "__main__":
from malis_test import get_params
pars = get_params()
if pars['is_affinity']:
affs, lbl = make_fake_3D_aff( 3, 7, 3, 7 )
else:
bdm, lbl = read_image(pars)
# normal boundary map and
bdm.astype("float64").tofile("../dataset/malis/bdm.bin")
lbl.astype('float64').tofile("../dataset/malis/lbl.bin")
from cost_fn import constrain_label
mbdm, sbdm = constrain_label(bdm, lbl)
mbdm.astype("float64").tofile("../dataset/malis/bdm_merge.bin")
sbdm.astype("float64").tofile("../dataset/malis/bdm_splite.bin")
