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 test_parse_manifest_raises_runtime_error_if_no_filename(self):
# Create manifest.json file without fpath.
manifest_fp = os.path.join(TMP_DIR, 'manifest.json')
with open(manifest_fp, 'w') as fh:
json.dump({"nofpath": "/tmp"}, fh)
from jicbioimage.core.image import ImageCollection
image_collection = ImageCollection()
with self.assertRaises(RuntimeError):
image_collection.parse_manifest(manifest_fp)
def test_parse_manifest_raises_runtime_error_if_no_filename(self):
# Create manifest.json file without fpath.
manifest_fp = os.path.join(TMP_DIR, 'manifest.json')
with open(manifest_fp, 'w') as fh:
json.dump({"nofpath": "/tmp"}, fh)
from jicbioimage.core.image import ImageCollection
image_collection = ImageCollection()
with self.assertRaises(RuntimeError):
image_collection.parse_manifest(manifest_fp)
def test_parse_manifest_raises_backwards_compatible_with_abs_paths(self):
# Create manifest.json file without fpath.
manifest_fp = os.path.join(TMP_DIR, 'manifest.json')
shutil.copy(os.path.join(DATA_DIR, "tjelvar.png"), TMP_DIR)
abs_im_fpath = os.path.join(TMP_DIR, 'tjelvar.png')
entry = dict(filename=abs_im_fpath, series=0, channel=0, zslice=0,
timepoint=0)
with open(manifest_fp, 'w') as fh:
json.dump([entry], fh)
from jicbioimage.core.image import ImageCollection, Image
image_collection = ImageCollection()
image_collection.parse_manifest(manifest_fp)
im = image_collection[0].image
expected_im = Image.from_file(abs_im_fpath)
import numpy as np
self.assertTrue(np.array_equal(im, expected_im))
def test_parse_manifest_raises_backwards_compatible_with_abs_paths(self):
# Create manifest.json file without fpath.
manifest_fp = os.path.join(TMP_DIR, 'manifest.json')
shutil.copy(os.path.join(DATA_DIR, "tjelvar.png"), TMP_DIR)
abs_im_fpath = os.path.join(TMP_DIR, 'tjelvar.png')
entry = dict(filename=abs_im_fpath,
series=0,
channel=0,
zslice=0,
timepoint=0)
with open(manifest_fp, 'w') as fh:
json.dump([entry], fh)
from jicbioimage.core.image import ImageCollection, Image
image_collection = ImageCollection()
image_collection.parse_manifest(manifest_fp)
im = image_collection[0].image
expected_im = Image.from_file(abs_im_fpath)
import numpy as np
self.assertTrue(np.array_equal(im, expected_im))