def overlap_dist(n1,n2,resample=0.,s=1000.,sig=10000.):
if resample != 0.:
ax = catmaid.algorithms.morphology.resample_edges(n1,resample,labels=['axon'])
den = catmaid.algorithms.morphology.resample_edges(n2,resample,labels=['dendrite'])
else:
ax = n1.axons[n1.axons.keys()[0]]['tree']
den = n2.dendrites
sk1 = n1.skeleton['id']
sk2 = n2.skeleton['id']
with open('cylinder_{}_{}.csv'.format(sk1,sk2),'wb') as f_o:
csv_writer = csv.writer(f_o)
for (nron,g) in ((n1,ax),(n2,den)):
for u,v,d in g.edges_iter(data=True):
try:
d['r'],d['n'],d['l'] = edge_to_cylinder(nron.skeleton['vertices'][u],nron.skeleton['vertices'][v])
d['valid'] = True
except EdgeError as e:
logging.error("BADEDGE")
d['valid']=False
total = 0.
for _,_,a in ax.edges_iter(data=True):
if not a['valid']:
continue
max_o = 0.0
sum_o = 0.0
for _,_,d in den.edges_iter(data=True):
if not d['valid']:
continue
o_lap = cylinder_overlap(a,d,sig=sig)
max_o = max(o_lap,max_o)
sum_o += o_lap
total += o_lap
csv_writer.writerow([a['r'][0],a['r'][1],a['r'][2],max_o,sum_o])
return total * 2. * s
def cylinders_csv(nron,resample=0.):
if resample != 0.:
ax = catmaid.algorithms.morphology.resample_edges(nron,resample,labels=['axon'])
den = catmaid.algorithms.morphology.resample_edges(nron,resample,labels=['dendrite'])
else:
ax = nron.axons[nron.axons.keys()[0]]['tree']
den = nron.dendrites
sk1 = nron.skeleton['id']
with open('cylinders_{}_ax.csv'.format(sk1),'wb') as f_ax:
ax_writer = csv.writer(f_ax)
for u,v,d in ax.edges_iter(data=True):
r,n,l = edge_to_cylinder(nron.skeleton['vertices'][u],nron.skeleton['vertices'][v])
ax_writer.writerow(numpy.concatenate((r,n,[l])))
with open('cylinders_{}_den.csv'.format(sk1),'wb') as f_d:
d_writer = csv.writer(f_d)
for u,v,d in den.edges_iter(data=True):
r,n,l = edge_to_cylinder(nron.skeleton['vertices'][u],nron.skeleton['vertices'][v])
d_writer.writerow(numpy.concatenate((r,n,[l])))
def cylinders_csv(nron, resample=0.):
if resample != 0.:
ax = catmaid.algorithms.morphology.resample_edges(nron,
resample,
labels=['axon'])
den = catmaid.algorithms.morphology.resample_edges(nron,
resample,
labels=['dendrite'])
else:
ax = nron.axons[nron.axons.keys()[0]]['tree']
den = nron.dendrites
sk1 = nron.skeleton['id']
with open('cylinders_{}_ax.csv'.format(sk1), 'wb') as f_ax:
ax_writer = csv.writer(f_ax)
for u, v, d in ax.edges_iter(data=True):
r, n, l = edge_to_cylinder(nron.skeleton['vertices'][u],
nron.skeleton['vertices'][v])
ax_writer.writerow(numpy.concatenate((r, n, [l])))
with open('cylinders_{}_den.csv'.format(sk1), 'wb') as f_d:
d_writer = csv.writer(f_d)
for u, v, d in den.edges_iter(data=True):
r, n, l = edge_to_cylinder(nron.skeleton['vertices'][u],
nron.skeleton['vertices'][v])
d_writer.writerow(numpy.concatenate((r, n, [l])))
def overlap_dist(n1, n2, resample=0., s=1000., sig=10000.):
if resample != 0.:
ax = catmaid.algorithms.morphology.resample_edges(n1,
resample,
labels=['axon'])
den = catmaid.algorithms.morphology.resample_edges(n2,
resample,
labels=['dendrite'])
else:
ax = n1.axons[n1.axons.keys()[0]]['tree']
den = n2.dendrites
sk1 = n1.skeleton['id']
sk2 = n2.skeleton['id']
with open('cylinder_{}_{}.csv'.format(sk1, sk2), 'wb') as f_o:
csv_writer = csv.writer(f_o)
for (nron, g) in ((n1, ax), (n2, den)):
for u, v, d in g.edges_iter(data=True):
try:
d['r'], d['n'], d['l'] = edge_to_cylinder(
nron.skeleton['vertices'][u],
nron.skeleton['vertices'][v])
d['valid'] = True
except EdgeError as e:
logging.error("BADEDGE")
d['valid'] = False
total = 0.
for _, _, a in ax.edges_iter(data=True):
if not a['valid']:
continue
max_o = 0.0
sum_o = 0.0
for _, _, d in den.edges_iter(data=True):
if not d['valid']:
continue
o_lap = cylinder_overlap(a, d, sig=sig)
max_o = max(o_lap, max_o)
sum_o += o_lap
total += o_lap
csv_writer.writerow(
[a['r'][0], a['r'][1], a['r'][2], max_o, sum_o])
return total * 2. * s
