def make_tif(animal, tif_id, file_id, testing=False):
fileLocationManager = FileLocationManager(animal)
sqlController = SqlController(animal)
INPUT = fileLocationManager.czi
OUTPUT = fileLocationManager.tif
start = time.time()
tif = sqlController.get_tif(tif_id)
slide = sqlController.get_slide(tif.slide_id)
czi_file = os.path.join(INPUT, slide.file_name)
section = sqlController.get_section(file_id)
tif_file = os.path.join(OUTPUT, section.file_name)
if not os.path.exists(czi_file) and not testing:
return 0
if os.path.exists(tif_file):
return 1
if testing:
command = ['touch', tif_file]
else:
command = ['/usr/local/share/bftools/bfconvert', '-bigtiff', '-separate',
'-series', str(tif.scene_index), '-channel', str(tif.channel-1), '-nooverwrite', czi_file, tif_file]
run(command)
end = time.time()
if os.path.exists(tif_file):
tif.file_size = os.path.getsize(tif_file)
tif.processing_duration = end - start
sqlController.update_row(tif)
return 1
def update_tifs(animal, channel):
"""
Args:
animal: the prep id of the animal
channel: the channel of the stack to process
njobs: number of jobs for parallel computing
Returns:
nothing
"""
fileLocationManager = FileLocationManager(animal)
sqlController = SqlController(animal)
tifs = sqlController.get_distinct_section_filenames(animal, channel)
INPUT = os.path.join(fileLocationManager.prep, 'CH1', 'full')
# Update TIFs' size
try:
os.listdir(INPUT)
except OSError as e:
print(e)
sys.exit()
for i, tif in enumerate(tqdm(tifs)):
print(tif.file_name)
input_path = os.path.join(INPUT, str(i).zfill(3) + '.tif')
if os.path.exists(input_path):
print(input_path)
tif.file_size = os.path.getsize(input_path)
sqlController.update_row(tif)
