def test_manual_addition_of_ImageCollection_to_DataManager(self):
# We start off by creating a :class:`jicbioimage.core.io.DataManager`.
# This takes a backend argument. The backend provides a means to store
# unpacked image files.
from jicbioimage.core.io import DataManager, FileBackend
backend = FileBackend(directory=TMP_DIR)
data_manager = DataManager(backend=backend)
# The :func:`jicbioimage.core.image.DataManager.conver` function is be
# default an instance of the callable
# :class:`jicbioimage.core.io.BFConvertWrapper` class.
from jicbioimage.core.io import BFConvertWrapper, _md5_hexdigest_from_file
self.assertTrue(isinstance(data_manager.convert, BFConvertWrapper))
# We also need to import an ImageCollection
from jicbioimage.core.image import ImageCollection
# If the input file has not already been converted with do so.
fpath = os.path.join(DATA_DIR, 'z-series.ome.tif')
self.assertFalse(data_manager.convert.already_converted(fpath))
if not data_manager.convert.already_converted(fpath):
path_to_manifest = data_manager.convert(fpath) # unpacks and creates manifests
self.assertEqual(path_to_manifest, os.path.join(TMP_DIR,
_md5_hexdigest_from_file(fpath),
'manifest.json'))
image_collection = ImageCollection()
image_collection.parse_manifest(path_to_manifest)
self.assertEqual(len(image_collection), 5)
data_manager.append(image_collection)
self.assertEqual(len(data_manager), 1)
self.assertTrue(data_manager.convert.already_converted(fpath))
def get_microscopy_collection_from_tiff(input_file):
"""Return microscopy collection from tiff file."""
data_manager, backend_dir = get_data_manager()
data_manager.load(input_file)
md5_hex = _md5_hexdigest_from_file(input_file)
manifest_path = os.path.join(backend_dir, md5_hex, "manifest.json")
microscopy_collection = MicroscopyCollection()
microscopy_collection.parse_manifest(manifest_path)
return microscopy_collection
def get_microscopy_collection_from_tiff(input_file):
"""Return microscopy collection from tiff file."""
data_manager, backend_dir = get_data_manager()
data_manager.load(input_file)
md5_hex = _md5_hexdigest_from_file(input_file)
manifest_path = os.path.join(backend_dir, md5_hex, "manifest.json")
microscopy_collection = MicroscopyCollection()
microscopy_collection.parse_manifest(manifest_path)
return microscopy_collection
def test_md5_from_file_with_smaller_blocksize(self):
from jicbioimage.core.io import _md5_hexdigest_from_file
input_file = os.path.join(DATA_DIR, "tjelvar.png")
self.assertEqual(_md5_hexdigest_from_file(input_file, 4096),
"894c9860e11667d29cdbf034e58ee75f")
def test_md5_from_file_with_smaller_blocksize(self):
from jicbioimage.core.io import _md5_hexdigest_from_file
input_file = os.path.join(DATA_DIR, "tjelvar.png")
self.assertEqual(_md5_hexdigest_from_file(input_file, 4096),
"894c9860e11667d29cdbf034e58ee75f")
