def save_id_tract_plus_sff(tracks_filename, id_file, num_proto, distance, out_fname):
if (tracks_filename[-3:]=='dpy'):
dpr_tracks = Dpy(tracks_filename, 'r')
all_tracks=dpr_tracks.read_tracks()
dpr_tracks.close()
else:
all_tracks = load_whole_tract_trk(tracks_filename)
tracks_id = load_pickle(id_file)
tract = [all_tracks[i] for i in tracks_id]
not_tract_fil = []
id_not_tract_fil = []
min_len = min(len(i) for i in tract)
#print 'min_len of cst', min_len
min_len = min_len*2.2/3#2./3.2# - 20
for i in np.arange(len(all_tracks)):
if (i not in tracks_id) and (length(all_tracks[i]) > min_len):
not_tract_fil.append(all_tracks[i])
id_not_tract_fil.append(i)
not_tract_fil = np.array(not_tract_fil,dtype=np.object)
sff_pro_id = sff(not_tract_fil, num_proto, distance)
tract_sff_id = []
for i in tracks_id:
tract_sff_id.append(i)
for idx in sff_pro_id:
tract_sff_id.append(id_not_tract_fil[idx])
#tract_sff_id.append(id_not_tract_fil[i] for i in sff_pro_id)
print len(tract), len(tract_sff_id)
save_pickle(out_fname, tract_sff_id)
return tract_sff_id
def save_id_tract_plus_sff_in_ext(tracks_filename, id_file, num_proto, distance, out_fname_ext , out_fname_sff_in_ext, thres_len= 2.2/3., thres_vol = 1.4 , thres_dis = 3./2.):
tract_ext_id = save_id_tract_ext1(tracks_filename,id_file, distance, out_fname_ext, thres_len, thres_vol , thres_dis)
if (tracks_filename[-3:]=='dpy'):
dpr_tracks = Dpy(tracks_filename, 'r')
all_tracks=dpr_tracks.read_tracks()
dpr_tracks.close()
else:
all_tracks = load_whole_tract_trk(tracks_filename)
tracks_id = load_pickle(id_file)
ext_not_tract_id = []
ext_not_tract = []
for idx in tract_ext_id:
if idx not in tracks_id:
ext_not_tract.append(all_tracks[idx])
ext_not_tract_id.append(idx)
ext_not_tract = np.array(ext_not_tract,dtype=np.object)
sff_pro_id = sff(ext_not_tract, num_proto, distance)
tract_sff_in_ext_id = []
for i in tracks_id:
tract_sff_in_ext_id.append(i)
for k in sff_pro_id:
tract_sff_in_ext_id.append(ext_not_tract_id[k])
#tract_sff_id.append(id_not_tract_fil[i] for i in sff_pro_id)
print len(tracks_id), len(tract_sff_in_ext_id), len(tract_ext_id)
save_pickle( out_fname_sff_in_ext, tract_sff_in_ext_id)
return tract_sff_in_ext_id