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)
def make_tifs(animal, channel, njobs):
"""
This method will:
1. Fetch the sections from the database
2. Yank the tif out of the czi file according to the index and channel with the bioformats tool.
3. Then updates the database with updated meta information
Args:
animal: the prep id of the animal
channel: the channel of the stack to process
njobs: number of jobs for parallel computing
compression: default is no compression so we can create jp2 files for CSHL. The files get
compressed using LZW when running create_preps.py
Returns:
nothing
"""
logger = get_logger(animal)
fileLocationManager = FileLocationManager(animal)
sqlController = SqlController(animal)
INPUT = fileLocationManager.czi
OUTPUT = fileLocationManager.tif
os.makedirs(OUTPUT, exist_ok=True)
sections = sqlController.get_distinct_section_filenames(animal, channel)
sqlController.set_task(animal, QC_IS_DONE_ON_SLIDES_IN_WEB_ADMIN)
sqlController.set_task(animal, CZI_FILES_ARE_CONVERTED_INTO_NUMBERED_TIFS_FOR_CHANNEL_1)
commands = []
for section in sections:
input_path = os.path.join(INPUT, section.czi_file)
output_path = os.path.join(OUTPUT, section.file_name)
cmd = ['/usr/local/share/bftools/bfconvert', '-bigtiff', '-separate', '-series', str(section.scene_index),
'-channel', str(section.channel_index), '-nooverwrite', input_path, output_path]
if not os.path.exists(input_path):
continue
if os.path.exists(output_path):
continue
commands.append(cmd)
with Pool(njobs) as p:
p.map(workernoshell, commands)
def test_tif(animal, channel):
sqlController = SqlController(animal)
checks = ['tif']
fileLocationManager = FileLocationManager(animal)
# tifs
for name, dir in zip(checks, [fileLocationManager.tif]):
db_files = sqlController.get_distinct_section_filenames(
animal, channel)
valid_file_length = db_files.count()
dir_exists, lfiles, badsize = directory_filled(dir, channel)
if not dir_exists:
print("{} does not exist.".format(dir))
missings = find_missing(dir, db_files)
if len(missings) > 0:
print("Missing files:")
count = 1
for missing in missings:
print(count, missing)
count += 1
