def process_czi_dir(self):
"""
After the CZI files are placed on birdstore, they need to be scanned to get the metadata for
the tif files. Set the progress status here.
"""
lookup_ids = [1, 2, 3]
scan_id = max(self.scan_ids)
self.session.query(AlcSlide).filter(
AlcSlide.scan_run_id.in_(
self.scan_ids)).delete(synchronize_session=False)
self.session.query(Task).filter(Task.lookup_id.in_(lookup_ids))\
.filter(Task.prep_id == self.animal.prep_id)\
.delete(synchronize_session=False)
for i in lookup_ids:
task = Task(self.animal.prep_id, i, True)
self.session.add(task)
self.session.commit()
try:
czi_files = sorted(os.listdir(self.CZI_FOLDER))
except OSError as e:
print(e)
sys.exit()
section_number = 1
#czi_files = ['DK43_slide060_2020_01_23__8024.czi']
for i, czi_file in enumerate(czi_files):
slide = AlcSlide()
slide.scan_run_id = scan_id
slide.slide_physical_id = int(re.findall(r'\d+', czi_file)[1])
slide.rescan_number = "1"
slide.slide_status = 'Good'
slide.processed = False
slide.file_size = os.path.getsize(
os.path.join(self.CZI_FOLDER, czi_file))
slide.file_name = czi_file
slide.created = datetime.fromtimestamp(
os.path.getmtime(os.path.join(self.CZI_FOLDER, czi_file)))
self.session.add(slide)
self.session.flush()
# Get metadata from the czi file
czi_file_path = os.path.join(self.CZI_FOLDER, czi_file)
metadata_dict = get_czi_metadata(czi_file_path)
series = get_fullres_series_indices(metadata_dict)
scene_counter = 0
for j, series_index in enumerate(series):
scene_counter += 1
channels = range(metadata_dict[series_index]['channels'])
channel_counter = 0
width = metadata_dict[series_index]['width']
height = metadata_dict[series_index]['height']
for channel in channels:
channel_counter += 1
newtif = os.path.splitext(czi_file)[0]
newtif = '{}_S{}_C{}.tif'.format(czi_file, scene_counter,
channel_counter)
newtif = newtif.replace('.czi', '')
tif = AlcSlideCziTif()
tif.slide_id = slide.id
tif.section_number = section_number
tif.scene_number = scene_counter
tif.channel = channel_counter
tif.file_name = newtif
tif.file_size = 0
tif.active = 1
tif.width = width
tif.height = height
tif.channel_index = channel
tif.scene_index = series_index
tif.processing_duration = 0
tif.created = time.strftime('%Y-%m-%d %H:%M:%S')
print('{}\t{}\t{}\t{}\t{}\t{}'.format(
newtif, tif.slide_id, tif.scene_number, tif.channel,
width, height))
self.session.add(tif)
section_number += 1
# lookup_id=3 is for the scanning CZI
task = self.session.query(Task).filter(Task.lookup_id == 3)\
.filter(Task.prep_id == self.animal.prep_id).one()
task.end_date = datetime.now()
self.session.merge(task)
self.session.commit()
