def main(args):
if args.outdir=='GT':
marker_files = map(string.strip,os.popen('ls '+args.indir+'*-GT.marker').readlines())
substack_ids = [f.split('/')[-1].split('-')[0] for f in marker_files]
else:
marker_files = map(string.strip,os.popen('ls '+args.outdir+'/*/ms.marker').readlines())
substack_ids = [f.split('/')[-2] for f in marker_files]
C_final=set()
plist = None
hue = 0.0
# FIXME: This is way too slow, should use divide & conquer using a binary tree
for marker_file,substack_id in zip(marker_files,substack_ids):
substack=SubStack(args.indir,substack_id, plist)
plist = substack.plist
print('Merging', marker_file, substack_id)
C=substack.load_markers(marker_file,args.outdir=='GT')
# I had forgotten that markers are shifted by 1 in save_markers()
# that was because Vaa3D coordinates starts from 1 rather than 0
# ==> repair original values
for c in C:
c.x -= 1
c.y -= 1
c.z -= 1
hue = hue + 0.31
if hue > 1:
hue = hue -1
merge(C_final, C, substack, hue, args.verbose)
substack.save_markers(args.outfile, C_final)
def main(args):
if args.outdir == 'GT':
marker_files = map(
string.strip,
os.popen('ls ' + args.indir + '*-GT.marker').readlines())
substack_ids = [f.split('/')[-1].split('-')[0] for f in marker_files]
else:
marker_files = map(
string.strip,
os.popen('ls ' + args.outdir + '/*/ms.marker').readlines())
substack_ids = [f.split('/')[-2] for f in marker_files]
C_final = set()
plist = None
hue = 0.0
# FIXME: This is way too slow, should use divide & conquer using a binary tree
for marker_file, substack_id in zip(marker_files, substack_ids):
substack = SubStack(args.indir, substack_id, plist)
plist = substack.plist
print('Merging', marker_file, substack_id)
C = substack.load_markers(marker_file, args.outdir == 'GT')
# I had forgotten that markers are shifted by 1 in save_markers()
# that was because Vaa3D coordinates starts from 1 rather than 0
# ==> repair original values
for c in C:
c.x -= 1
c.y -= 1
c.z -= 1
hue = hue + 0.31
if hue > 1:
hue = hue - 1
merge(C_final, C, substack, hue, args.verbose)
substack.save_markers(args.outfile, C_final)
def merge_views(args):
view_ids=args.view_ids
max_len=0
hue=0.
C_substack=[]
if args.thresholds_dir is None:
print(view_ids)
list_views = get_visible_pairs(args.base_indir,args.substack_id,view_ids)
else:
list_views = get_visible_pairs_from_dir(args.thresholds_dir, args.substack_id, view_ids)
substack = SubStack(args.base_indir+'/'+view_ids[0],args.substack_id)
valid_pairs = filter_valid_pairs(args,substack,list_views)
if len(valid_pairs.keys())==1:
C_substack+=valid_pairs.values()[0]
else:
keys_view_1=[]
keys_view_3=[]
for view_key in valid_pairs.keys():
if view_key[0] == view_ids[2]:
keys_view_3.append(view_key)
elif view_key[0] == view_ids[0]:
keys_view_1.append(view_key)
if len(valid_pairs)==2:
if len(keys_view_1) == 2 or len(keys_view_3) == 2:
total_list=compute_fusion(substack,valid_pairs.values()[0],valid_pairs.values()[1],args.max_distance,match_distance=args.match_distance,verbose=args.verbose)
C_substack+=total_list
elif len(keys_view_1) == 1 and len(keys_view_3) == 1:
C_view_3_t=transform_markers(args,substack,valid_pairs[keys_view_3[0]], view_ids)
total_list=compute_fusion(substack,valid_pairs[keys_view_1[0]],C_view_3_t,args.max_distance,match_distance=args.match_distance,verbose=args.verbose)
C_substack+=total_list
else:
raise Exception('not valid list of views %s'%(str(valid_pairs)))
elif len(valid_pairs)==3:
if len(keys_view_1) == 2:
C_view_1=compute_fusion(substack,valid_pairs[keys_view_1[0]],valid_pairs[keys_view_1[1]],args.max_distance,match_distance=args.match_distance,verbose=args.verbose)
C_view_3_t=transform_markers(args,substack,valid_pairs[keys_view_3[0]], view_ids)
total_list=compute_fusion(substack,C_view_1,C_view_3_t,args.max_distance,match_distance=args.match_distance,verbose=args.verbose)
C_substack+=total_list
elif len(keys_view_3) == 2:
C_view_3=compute_fusion(substack,valid_pairs[keys_view_3[0]],valid_pairs[keys_view_3[1]],args.max_distance,match_distance=args.match_distance,verbose=args.verbose)
C_view_3_t=transform_markers(args,substack,C_view_3, view_ids)
C_view_1=valid_pairs[keys_view_1[0]]
total_list=compute_fusion(substack,C_view_1,C_view_3_t,args.max_distance,match_distance=args.match_distance,verbose=args.verbose)
C_substack+=total_list
else:
raise Exception('not valid list of views %s'%(str(valid_pairs)))
elif len(valid_pairs)==4:
if len(keys_view_1) == 2 and len(keys_view_3) == 2:
C_view_1=compute_fusion(substack,valid_pairs[keys_view_1[0]],valid_pairs[keys_view_1[1]],args.max_distance,match_distance=args.match_distance,verbose=args.verbose)
C_view_3=compute_fusion(substack,valid_pairs[keys_view_3[0]],valid_pairs[keys_view_3[1]],args.max_distance,match_distance=args.match_distance,verbose=args.verbose)
C_view_3_t=transform_markers(args,substack,C_view_3, view_ids)
total_list=compute_fusion(substack,C_view_1,C_view_3_t,args.max_distance,match_distance=args.match_distance,verbose=args.verbose)
C_substack+=total_list
else:
raise Exception('not valid list of views %s'%(str(valid_pairs)))
mkdir_p(args.outdir+'/'+args.substack_id)
if len(C_substack)>0:
C_substack = filter_outside_markers(C_substack,substack)
substack.save_markers(args.outdir+'/'+args.substack_id+'/ms.marker', C_substack, floating_point=True)
def merge_views(args):
view_ids = args.view_ids
max_len = 0
hue = 0.
C_substack = []
if args.thresholds_dir is None:
print(view_ids)
list_views = get_visible_pairs(args.base_indir, args.substack_id,
view_ids)
else:
list_views = get_visible_pairs_from_dir(args.thresholds_dir,
args.substack_id, view_ids)
substack = SubStack(args.base_indir + '/' + view_ids[0], args.substack_id)
valid_pairs = filter_valid_pairs(args, substack, list_views)
if len(valid_pairs.keys()) == 1:
C_substack += valid_pairs.values()[0]
else:
keys_view_1 = []
keys_view_3 = []
for view_key in valid_pairs.keys():
if view_key[0] == view_ids[2]:
keys_view_3.append(view_key)
elif view_key[0] == view_ids[0]:
keys_view_1.append(view_key)
if len(valid_pairs) == 2:
if len(keys_view_1) == 2 or len(keys_view_3) == 2:
total_list = compute_fusion(substack,
valid_pairs.values()[0],
valid_pairs.values()[1],
args.max_distance,
match_distance=args.match_distance,
verbose=args.verbose)
C_substack += total_list
elif len(keys_view_1) == 1 and len(keys_view_3) == 1:
C_view_3_t = transform_markers(args, substack,
valid_pairs[keys_view_3[0]],
view_ids)
total_list = compute_fusion(substack,
valid_pairs[keys_view_1[0]],
C_view_3_t,
args.max_distance,
match_distance=args.match_distance,
verbose=args.verbose)
C_substack += total_list
else:
raise Exception('not valid list of views %s' % (str(valid_pairs)))
elif len(valid_pairs) == 3:
if len(keys_view_1) == 2:
C_view_1 = compute_fusion(substack,
valid_pairs[keys_view_1[0]],
valid_pairs[keys_view_1[1]],
args.max_distance,
match_distance=args.match_distance,
verbose=args.verbose)
C_view_3_t = transform_markers(args, substack,
valid_pairs[keys_view_3[0]],
view_ids)
total_list = compute_fusion(substack,
C_view_1,
C_view_3_t,
args.max_distance,
match_distance=args.match_distance,
verbose=args.verbose)
C_substack += total_list
elif len(keys_view_3) == 2:
C_view_3 = compute_fusion(substack,
valid_pairs[keys_view_3[0]],
valid_pairs[keys_view_3[1]],
args.max_distance,
match_distance=args.match_distance,
verbose=args.verbose)
C_view_3_t = transform_markers(args, substack, C_view_3, view_ids)
C_view_1 = valid_pairs[keys_view_1[0]]
total_list = compute_fusion(substack,
C_view_1,
C_view_3_t,
args.max_distance,
match_distance=args.match_distance,
verbose=args.verbose)
C_substack += total_list
else:
raise Exception('not valid list of views %s' % (str(valid_pairs)))
elif len(valid_pairs) == 4:
if len(keys_view_1) == 2 and len(keys_view_3) == 2:
C_view_1 = compute_fusion(substack,
valid_pairs[keys_view_1[0]],
valid_pairs[keys_view_1[1]],
args.max_distance,
match_distance=args.match_distance,
verbose=args.verbose)
C_view_3 = compute_fusion(substack,
valid_pairs[keys_view_3[0]],
valid_pairs[keys_view_3[1]],
args.max_distance,
match_distance=args.match_distance,
verbose=args.verbose)
C_view_3_t = transform_markers(args, substack, C_view_3, view_ids)
total_list = compute_fusion(substack,
C_view_1,
C_view_3_t,
args.max_distance,
match_distance=args.match_distance,
verbose=args.verbose)
C_substack += total_list
else:
raise Exception('not valid list of views %s' % (str(valid_pairs)))
mkdir_p(args.outdir + '/' + args.substack_id)
if len(C_substack) > 0:
C_substack = filter_outside_markers(C_substack, substack)
substack.save_markers(args.outdir + '/' + args.substack_id +
'/ms.marker',
C_substack,
floating_point=True)
