def from_json(cls, json_url: str) -> "Experiment":
"""
Construct an Experiment from an experiment.json file format specifier.
Loads configuration from StarfishConfig.
Parameters
----------
json_url : str
file path or web link to an experiment.json file
Returns
-------
Experiment :
Experiment object serving the requested experiment data
"""
config = StarfishConfig()
if config.strict:
valid = validate_sptx.validate(json_url)
if not valid:
raise Exception("validation failed")
backend, name, baseurl = resolve_path_or_url(json_url, config.slicedimage)
with backend.read_contextmanager(name) as fh:
experiment_document = json.load(fh)
version = cls.verify_version(experiment_document['version'])
_, codebook_name, codebook_baseurl = resolve_url(experiment_document['codebook'],
baseurl, config.slicedimage)
codebook_absolute_url = pathjoin(codebook_baseurl, codebook_name)
codebook = Codebook.open_json(codebook_absolute_url)
extras = experiment_document['extras']
fovs: MutableSequence[FieldOfView] = list()
fov_tilesets: MutableMapping[str, TileSet]
if version < Version("5.0.0"):
primary_image: Collection = Reader.parse_doc(experiment_document['primary_images'],
baseurl, config.slicedimage)
auxiliary_images: MutableMapping[str, Collection] = dict()
for aux_image_type, aux_image_url in experiment_document['auxiliary_images'].items():
auxiliary_images[aux_image_type] = Reader.parse_doc(
aux_image_url, baseurl, config.slicedimage)
for fov_name, primary_tileset in primary_image.all_tilesets():
fov_tilesets = dict()
fov_tilesets[FieldOfView.PRIMARY_IMAGES] = primary_tileset
for aux_image_type, aux_image_collection in auxiliary_images.items():
aux_image_tileset = aux_image_collection.find_tileset(fov_name)
if aux_image_tileset is not None:
fov_tilesets[aux_image_type] = aux_image_tileset
fov = FieldOfView(fov_name, image_tilesets=fov_tilesets)
fovs.append(fov)
else:
images: MutableMapping[str, Collection] = dict()
all_fov_names: MutableSet[str] = set()
for image_type, image_url in experiment_document['images'].items():
image = Reader.parse_doc(image_url, baseurl, config.slicedimage)
images[image_type] = image
for fov_name, _ in image.all_tilesets():
all_fov_names.add(fov_name)
for fov_name in all_fov_names:
fov_tilesets = dict()
for image_type, image_collection in images.items():
image_tileset = image_collection.find_tileset(fov_name)
if image_tileset is not None:
fov_tilesets[image_type] = image_tileset
fov = FieldOfView(fov_name, image_tilesets=fov_tilesets)
fovs.append(fov)
return Experiment(fovs, codebook, extras, src_doc=experiment_document)
def load(self, input_parameter: str) -> Codebook:
return Codebook.open_json(input_parameter)