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)