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