count = 0
gap_threshold = 1
for recon_dir in subdirs[1:]:
folder_name = recon_dir.split('/')[-1]
if 'auto_recons' in folder_name:
print recon_dir
folder_name = recon_dir.split('/')[-1]
files = glob.glob(recon_dir + '/../00_*.swc')
if len(files) > 0:
gs_swc_file = files[0]
out_gs_file = gs_swc_file.split('.swc')[0] + '.strict.swc'
if not os.path.exists(out_gs_file):
bn.standardize(input_swc_path=gs_swc_file,
ref_swc_file=gs_swc_file,
output_swc_path=out_gs_file,
gap_threshold=1,
new_type=3,
GEN_QSUB=1,
qsub_script_dir=data_DIR + "/qsub",
id=None)
swc_files = glob.glob(recon_dir + '/*.swc')
for i in range(len(swc_files)):
input = swc_files[i]
fn = (input.split('/')[-1]).split('.swc')[0] + '.strict.swc'
out_fn = recon_dir + "/../processed/" + fn
if not os.path.exists(out_fn):
if os.path.getsize(input) < 5 * 1024 * 1024:
bn.standardize(input_swc_path=input,
ref_swc_file=gs_swc_file,
output_swc_path=out_fn,
gap_threshold=1,
os.system("rm "+data_DIR+"/qsub/*.o*")
subdirs = [x[0] for x in os.walk(data_DIR)]
count = 0
gap_threshold =1
for recon_dir in subdirs[1:]:
folder_name = recon_dir.split('/')[-1]
if 'auto_recons' in folder_name:
print recon_dir
folder_name = recon_dir.split('/')[-1]
files = glob.glob(recon_dir+'/../00_*.swc')
if len(files)>0:
gs_swc_file =files[0]
out_gs_file = gs_swc_file.split('.swc')[0]+'.strict.swc'
if not os.path.exists(out_gs_file):
bn.standardize(input_swc_path=gs_swc_file, ref_swc_file=gs_swc_file,output_swc_path=out_gs_file, gap_threshold=1, new_type=3, GEN_QSUB = 1, qsub_script_dir= data_DIR+"/qsub", id=None)
swc_files = glob.glob(recon_dir+'/*.swc')
for i in range(len(swc_files)) :
input = swc_files[i]
fn=(input.split('/')[-1]).split('.swc')[0]+'.strict.swc'
out_fn=recon_dir+"/../processed/"+fn
if not os.path.exists(out_fn):
if os.path.getsize(input) < 5*1024*1024:
bn.standardize(input_swc_path=input, ref_swc_file=gs_swc_file,output_swc_path=out_fn, gap_threshold=1, new_type=3, GEN_QSUB = 1, qsub_script_dir= data_DIR+"/qsub", id=None)
else:
print "swc file size too big, skip:",input
bn.standardize(input_swc_path=recon_dir+'/../consensus3.eswc', ref_swc_file=gs_swc_file,output_swc_path=recon_dir+'/../consensus3.strict.swc', gap_threshold=1, new_type=3, GEN_QSUB = 1, qsub_script_dir= data_DIR+"/qsub", id=None)
if '.v3d' in case_folder_name:
print case_folder_name
else:
continue
image_id = int(case_folder_name.split(".")[0])
image_file_name = df_lookup_table.image_file_name[image_id-1]
gs_swc_file = map_image_to_silver_swc[image_file_name]
out_gs_file = gs_swc_file.split('.swc')[0]+'.strict.swc'
if not os.path.exists(out_gs_file):
bn.standardize(input_swc_path=gs_swc_file, ref_swc_file=gs_swc_file,output_swc_path=out_gs_file, gap_threshold=1, new_type=3, GEN_QSUB = 1, qsub_script_dir= data_DIR+"/qsub", id=None)
swc_files = glob.glob(recon_dir+'/*.swc')
for i in range(len(swc_files)) :
input = swc_files[i]
fn=(input.split('/')[-1]).split('.swc')[0]+'.strict.swc'
out_fn=processed_folder+"/"+case_folder_name+'/'+fn
if not os.path.exists(out_fn):
if os.path.getsize(input) < 5*1024*1024:
bn.standardize(input_swc_path=input, ref_swc_file=gs_swc_file,output_swc_path=out_fn, gap_threshold=1, new_type=3, GEN_QSUB = 1, qsub_script_dir= data_DIR+"/qsub", id=None)
else:
print "swc file size too big, skip:",input
#bn.standardize(input_swc_path=recon_dir+'/../consensus3.eswc', ref_swc_file=gs_swc_file,output_swc_path=recon_dir+'/../consensus3.strict.swc', gap_threshold=1, new_type=3, GEN_QSUB = 1, qsub_script_dir= data_DIR+"/qsub", id=None)
