def test_clone_dataset(self):
from mobie.utils import clone_dataset
ds2 = 'test-clone'
clone_dataset(self.root, self.dataset_name, ds2)
validate_project(self.root,
assert_true=self.assertTrue,
assert_in=self.assertIn,
assert_equal=self.assertEqual)
def test_bdv_importer(self):
add_bdv_image(self.xml_path, self.root, self.dataset_name, tmp_folder=self.tmp_folder)
validate_project(self.root)
meta = read_dataset_metadata(f"{self.root}/{self.dataset_name}")
self.assertIn(self.image_name, meta["sources"])
im_path = meta["sources"][self.image_name]["image"]["imageData"]["bdv.n5"]["relativePath"]
im_path = os.path.join(self.root, self.dataset_name, im_path).replace("xml", "n5")
self.assertTrue(os.path.exists(im_path))
with open_file(im_path, "r") as f:
data = f["setup0/timepoint0/s0"][:]
self.assertTrue(np.allclose(data, self.data))
def check_dataset(self, dataset_folder, exp_shape, raw_name, file_format="bdv.n5"):
# validate the full project
validate_project(
self.root, assert_true=self.assertTrue, assert_in=self.assertIn, assert_equal=self.assertEqual
)
# check the raw data
folder_name = file_format.replace(".", "-")
if file_format.startswith("bdv"):
xml_path = os.path.join(dataset_folder, "images", folder_name, f"{raw_name}.xml")
raw_path = get_data_path(xml_path, return_absolute_path=True)
is_h5 = file_format == "bdv.hdf5"
key = get_key(is_h5, 0, 0, 0)
else:
self.assertEqual(file_format, "ome.zarr")
raw_path = os.path.join(dataset_folder, "images", folder_name, f"{raw_name}.ome.zarr")
key = "s0"
with open_file(raw_path, "r") as f:
data = f[key][:]
shape = data.shape
self.assertEqual(shape, exp_shape)
self.assertFalse(np.allclose(data, 0.))
def add_open_organelle_data(
address,
root,
internal_path,
source_name=None,
dataset_name=None,
# region="us-west-2", # we don't seem to need this
anon=True,
view=None,
menu_name=None,
is_default_dataset=False,
overwrite=False):
"""
address [str] -
root [str] -
internal_path [str] -
source_name [str] -
dataset_name [str] -
anon [bool] -
view [dict] - default view settings for this source (default: None)
menu_name [str] - menu name for this source.
If none will be derived from the source name. (default: None)
is_default_dataset [bool] -
overwrite [bool]
"""
if not s3_utils.have_boto():
raise RuntimeError(
"boto3 is required to access open organelle data. Please install it."
)
file_format = 'openOrganelle.s3'
if not metadata.project_exists(root):
metadata.create_project_metadata(root, [file_format])
endpoint, bucket, container = parse_address(address)
dataset_name = bucket if dataset_name is None else dataset_name
ds_exists = metadata.dataset_exists(root, dataset_name)
ds_folder = os.path.join(root, dataset_name)
if ds_exists:
ds_metadata = metadata.read_dataset_metadata(ds_folder)
sources, views = ds_metadata['sources'], ds_metadata['views']
else:
sources, views = {}, {}
client = s3_utils.get_client(endpoint, anon=anon)
name, source, view = get_source(client, bucket, container, internal_path,
endpoint, ds_folder, source_name, view,
menu_name)
if name in sources:
if overwrite:
print("The source", name,
"exists already and will be over-written")
else:
print("The source", name,
"exists already and will not be over-written")
return
sources[name] = source
views[name] = view
if ds_exists:
ds_metadata['sources'] = sources
ds_metadata['views'] = views
metadata.write_dataset_metadata(ds_folder, ds_metadata)
else:
os.makedirs(ds_folder, exist_ok=True)
default_view = views[list(views.keys())[0]]
default_view["sourceDisplays"]["uiSelectionGroup"] = "bookmarks"
views["default"] = default_view
metadata.create_dataset_metadata(ds_folder,
sources=sources,
views=views)
metadata.add_dataset(root, dataset_name, is_default_dataset)
validate_project(root)
def test_validate_project(self):
from mobie.validation import validate_project
validate_project(self.data_folder)