def refconc(brain, ref):
'''
given a reference fibre locates the parallel fibres in brain (tracks)
with threshold_hitdata applied to cut_planes output then follows
with concentration to locate the locus of a neck
'''
hitdata = pf.cut_plane(brain, ref)
reduced_hitdata, heavy_weight_fibres = tl.threshold_hitdata(hitdata, divergence_threshold=0.2, fibre_weight=0.9)
index, centre, conc = concs(reduced_hitdata, ref)
return heavy_weight_fibres, index, centre
def test(bundle_list, divergence_threshold_list=[0.25], fibre_weight_list=[0.8],index_lists=False):
comments = open('/home/ian/tractarian/commentary.txt','w')
#reduced_hits = []
#for b in [1,2,3,4,5,6,7,8]:
for b in bundle_list:
#print 'Starting ...'
refindex = G[b]['indices'].index([R[b]])
ref = G[b]['tracks'][refindex]
#print 'Bundle %d (%s)' % (b,G[b]['label_name'])
print >> comments, 'Bundle %d (%s)' % (b,G[b]['label_name'])
#print 'Removing far tracks ...'
nearbundle,nearbundleindices = tl.rm_far_tracks(ref,tracks)
#print 'Entering cut planes ...'
hitdata = pf.cut_plane(nearbundle,ref)
for divergence_threshold in divergence_threshold_list:
for fibre_weight in fibre_weight_list:
#print 'Reducing hit data ...'
reduced_hitdata,heavy_weight_fibres = \
tl.threshold_hitdata(hitdata,divergence_threshold=divergence_threshold,fibre_weight=fibre_weight)
#print 'Starting ...'
#pbc.show_cut_color(reduced_hitdata,ref,bundle=G[b]['tracks'])
#reduced_hits += [reduced_hitdata]
green = set(G[b]['indices'])
blue = set([nearbundleindices[i] for i in heavy_weight_fibres])
nGB = len(green.intersection(blue))
nG = len(green.difference(blue))
nB = len(blue.difference(green))
#print 'DivThresh %f; FibWt %f' % (divergence_threshold, fibre_weight)
print >> comments, 'DivThresh %f; FibWt %f; Green %d; Blue %d; Green and blue %d; missed Green %d; stray Blue %d' % (divergence_threshold, fibre_weight, len(green),len(blue),nGB,nG,nB)
#print >> comments, 'DivThresh %f; FibWt %f' % (divergence_threshold, fibre_weight)
#print >> comments, 'Green %d; Blue %d; Green and blue %d; missed Green %d; stray Blue %d' \
# % (len(green),len(blue),nGB,nG,nB)
if index_list == True:
return green, blue
comments.close()
