def batch(recon_root, proc_recon_root, csv_path):
"""
Script to automatically generate crops, scled images and compressed files
:param recon_list:
:param mount:
:return:
"""
with open(csv_path, 'r') as fh:
recon_list = [row[0] for row in csv.reader(fh)]
app = AppData()
auto = Autofill(None)
update = FakeUpdate()
for recon_id in recon_list:
stage = get_stage(recon_id)
proc_recon_path = join(proc_recon_root, recon_id)
cropped_dir = join(proc_recon_path, 'cropped')
if not isdir(cropped_dir):
mkdir(cropped_dir)
scaled_dir = join(proc_recon_path, 'scaled_stacks')
metadata_dir = join(proc_recon_path, 'Metadata')
recon_id = get_input_id(join(metadata_dir, 'config4user.log'))
recon_path = join(recon_root, recon_id)
# Performing cropping if directory does not exist or is empty
if len(listdir(cropped_dir)) == 0:
fake_config = lambda: None
fake_config.meta_path = metadata_dir
fake_config.value = 0
cropper = Crop(recon_path,
cropped_dir,
update.emit,
fake_config,
fake_config,
app,
def_crop=None,
repeat_crop=None)
img_list = cropper.run(auto=True)
else:
img_list = app.getfilelist(cropped_dir)
# Get recon log and pixel size
log_paths = [f for f in listdir(cropped_dir) if f.endswith("_rec.log")]
if len(log_paths) < 1:
print('Cannot find log in cropped directory')
continue
log = join(cropped_dir, log_paths[0])
with open(log, 'rb') as log_file:
original_pixel_size = float(auto.get_pixel(stage, log_file))
# Scaling
if not isdir(scaled_dir):
mkdir(scaled_dir)
for scale in SCALING[stage]:
scale_by_int = False
if type(scale) is int:
sf = scale
new_pixel_size = original_pixel_size * float(scale)
scale_by_int = True
else:
sf = float(scale) / float(original_pixel_size)
new_pixel_size = sf * original_pixel_size
out_name = join(
scaled_dir, '{}_scaled_{:.4f}_pixel_{:.2f}.{}'.format(
recon_id, sf, new_pixel_size, ext))
if scaled_stack_exists(scaled_dir, sf, new_pixel_size):
continue
resample(img_list, sf, out_name, scale_by_int, update)
# Compression
bz2_file = join(proc_recon_path,
'IMPC_cropped_{}.nrrd'.format(recon_id))
if not isfile(bz2_file + '.bz2'):
print "Generating missing bz2 file for '{}'".format(recon_id)
try:
bz2_nnrd(img_list, bz2_file, 'Compressing cropped recon',
update)
except IOError as e:
print(
'Failed to write the compressed bzp2 file. Network issues?\n{}'
.format(e))
