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()