def resample(original_dir,preprocessed_dir): if not os.path.exists(preprocessed_dir): os.mkdir(preprocessed_dir) for input_swc_path in glob.glob(original_dir + "/*.swc"): print input_swc_path swc_fn = input_swc_path.split('/')[-1] preprocessed_swc_fn = preprocessed_dir+'/' + swc_fn bn.resample(input_swc_path, preprocessed_swc_fn) ## due to the pw alignment, no alignment are necessary ##bn.pre_processing(input_swc_path, preprocessed_swc_fn) return
def resample_and_sort(data_dir, resampled_dir, sorted_dir, GEN_QSUB=0, overwrite_sorted=1, filelist=None): failure_file = open(data_dir + "/failurecases_via_size.txt", "w") i = 0 subfolder = 1 if filelist == None: filelist = glob.glob(data_dir + "/*/*.swc") if len(filelist) < 1: filelist = glob.glob(data_dir + "/*.swc") subfolder = 0 for input_swc_path in filelist: i = i + 1 print "\n\n " print i #if( os.path.getsize(input_swc_path) < 1024*1024)): if not "tmp_cache_img" in input_swc_path: # skip the tmp files if subfolder > 0: swc_fn = "/".join(input_swc_path.split("/") [-2:]) # to keep the subfolder structure else: swc_fn = "/".join(input_swc_path.split("/")[-1:]) sorted_swc_path = sorted_dir + '/' + swc_fn resampled_swc_path = resampled_dir + '/' + swc_fn if not os.path.isfile( resampled_swc_path ) or overwrite_sorted: # if already generated # resample resampled_swc_path = resampled_dir + '/' + swc_fn print "resample : " + input_swc_path bn.resample(input_swc_path, resampled_swc_path, 3, GEN_QSUB, data_dir + '/qsub/resample') # generate QSUB scripts # sort sorted_swc_path = sorted_dir + '/' + swc_fn #bn.sort_swc(preprocessed_swc_path, sorted_swc_path,GEN_QSUB,data_dir+'/qsub/sort') #else: # failure_file.write(input_swc_path+" "+str(os.path.getsize(input_swc_path))+"\n ") #failure_file.close() #print "failure cases with file sizes that are too big or too small are logged at:"+ data_dir+"/failurecases_via_size.txt" print "done resampling " #and sorting" return
def resample(original_dir, preprocessed_dir): if not os.path.exists(preprocessed_dir): os.mkdir(preprocessed_dir) for input_swc_path in glob.glob(original_dir + "/*.swc"): print input_swc_path swc_fn = input_swc_path.split('/')[-1] preprocessed_swc_fn = preprocessed_dir + '/' + swc_fn bn.resample(input_swc_path, preprocessed_swc_fn ) ## due to the pw alignment, no alignment are necessary ##bn.pre_processing(input_swc_path, preprocessed_swc_fn) return
def resample_and_sort(data_dir,resampled_dir,sorted_dir, GEN_QSUB = 0,overwrite_sorted = 1,filelist=None): failure_file = open(data_dir +"/failurecases_via_size.txt","w") i = 0 subfolder = 1 if filelist == None: filelist= glob.glob(data_dir+"/*/*.swc") if len(filelist)<1 : filelist= glob.glob(data_dir+"/*.swc") subfolder = 0 for input_swc_path in filelist: i = i+1 print "\n\n " print i #if( os.path.getsize(input_swc_path) < 1024*1024)): if not "tmp_cache_img" in input_swc_path: # skip the tmp files if subfolder >0: swc_fn = "/".join (input_swc_path.split("/")[-2:]) # to keep the subfolder structure else: swc_fn = "/".join (input_swc_path.split("/")[-1:]) sorted_swc_path = sorted_dir+ '/'+swc_fn resampled_swc_path = resampled_dir+ '/'+swc_fn if not os.path.isfile(resampled_swc_path) or overwrite_sorted: # if already generated # resample resampled_swc_path = resampled_dir+ '/'+swc_fn print "resample : "+ input_swc_path bn.resample(input_swc_path, resampled_swc_path,3,GEN_QSUB,data_dir+'/qsub/resample') # generate QSUB scripts # sort sorted_swc_path = sorted_dir+ '/'+swc_fn #bn.sort_swc(preprocessed_swc_path, sorted_swc_path,GEN_QSUB,data_dir+'/qsub/sort') #else: # failure_file.write(input_swc_path+" "+str(os.path.getsize(input_swc_path))+"\n ") #failure_file.close() #print "failure cases with file sizes that are too big or too small are logged at:"+ data_dir+"/failurecases_via_size.txt" print "done resampling "#and sorting" return