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 fix_tifs(animal, channel):
sqlController = SqlController(animal)
fileLocationManager = FileLocationManager(animal)
dir = fileLocationManager.tif
db_files = sqlController.get_sections(animal, channel)
source_files = []
source_keys = []
for tif in db_files:
source_files.append(tif.file_name)
source_keys.append(tif.id)
files = os.listdir(dir)
files = [file for file in files if 'C{}.tif'.format(channel) in file]
missing_files = list(set(source_files) - set(files))
for i, missing in enumerate(missing_files):
#pass
file_id = source_keys[source_files.index(missing)]
section = sqlController.get_section(file_id)
print(i, missing, file_id, section.id, section.file_name)
make_tif(animal, section.tif_id, file_id, testing=False)
