def __init__(self):
self.CHANNEL_NAMES = pd.read_csv(
self.CHANNEL_PATH, sep='\t', header=None).values[:, 0]
VALID_IMAGE_EXTENSIONS = ('tif', 'jpg', 'png')
self.FILENAMES = [f for f in os.listdir(self.DIRECTORY_PATH) if f.endswith(
VALID_IMAGE_EXTENSIONS) and not f.startswith('.') and not f.endswith(self.FILENAME_ENDS_TO_EXCLUDE)]
if len(self.FILENAMES) < 1:
raise NameError(
'No image files found. Make sure you are pointing to the right directory')
reference_image_path = os.path.join(self.DIRECTORY_PATH, self.FILENAMES[0])
if self.AUTOBOOST_REFERENCE_IMAGE != '' and self.BOOST == 'auto':
if self.AUTOBOOST_REFERENCE_IMAGE in self.FILENAMES:
self.FILENAMES.remove(self.AUTOBOOST_REFERENCE_IMAGE)
self.FILENAMES.insert(0, self.AUTOBOOST_REFERENCE_IMAGE)
print('Using autoboost reference image with filename', self.AUTOBOOST_REFERENCE_IMAGE)
else:
print('AUTOBOOST_REFERENCE_IMAGE does not exist. Check your config file - image filename must match exactly.')
print('Defaulting to first image reference...')
self.N_DIMS, self.EXT, self.DTYPE, self.SHAPE, self.READ_METHOD = cvutils.meta_from_image(reference_image_path)
self.PROGRESS_TABLE = []
if(os.path.exists(self.PROGRESS_TABLE_PATH)):
self.PROGRESS_TABLE = [line.rstrip('\n') for line in open(self.PROGRESS_TABLE_PATH)]
def __init__(self):
if self.IS_CODEX_OUTPUT:
self.CHANNEL_NAMES = pd.read_csv(self.CHANNEL_PATH,
sep='\t',
header=None).values[:, 0]
VALID_IMAGE_EXTENSIONS = ('tif', 'jpg', 'png')
self.FILENAMES = [
f for f in os.listdir(self.DIRECTORY_PATH)
if f.endswith(VALID_IMAGE_EXTENSIONS) and not f.startswith('.')
]
if len(self.FILENAMES) < 1:
raise NameError(
'No image files found. Make sure you are pointing to the right directory'
)
self.N_DIMS, self.EXT, self.DTYPE, self.SHAPE, self.READ_METHOD = cvutils.meta_from_image(
os.path.join(self.DIRECTORY_PATH, self.FILENAMES[0]))