def _cli(ctx, input, output, codebook):
ctx.obj = dict(
component=Decoder,
input=input,
output=output,
intensities=IntensityTable.load(input),
codebook=Codebook.from_json(codebook),
)
def _cli(ctx, input, output, codebook):
"""pixel-wise spot detection and decoding"""
print('Detecting Spots ...')
ctx.obj = dict(
component=PixelSpotDecoder,
image_stack=ImageStack.from_path_or_url(input),
output=output,
codebook=Codebook.from_json(codebook),
)
def _cli(ctx, input, output, blobs_stack,
reference_image_from_max_projection, codebook):
print('Detecting Spots ...')
ctx.obj = dict(
component=SpotFinder,
image_stack=ImageStack.from_path_or_url(input),
output=output,
blobs_stack=blobs_stack,
reference_image_from_max_projection=
reference_image_from_max_projection,
codebook=None,
)
if codebook is not None:
ctx.obj["codebook"] = Codebook.from_json(codebook)
def _cli(cls, args, print_help=False):
"""Runs the decoder component based on parsed arguments."""
if args.decoder_algorithm_class is None or print_help:
cls.decoder_group.print_help()
cls.decoder_group.exit(status=2)
instance = args.decoder_algorithm_class(**vars(args))
# load intensities and codebook
intensities = IntensityTable.load(args.input)
codebook = Codebook.from_json(args.codebook)
# decode and save output
intensities = instance.run(intensities, codebook)
intensities.save(args.output)
def from_json(cls,
json_url: str,
strict: bool = None,
config: Optional[Union[str, Dict]] = None) -> "Experiment":
"""
Construct an `Experiment` from an experiment.json file format specifier
Parameters
----------
json_url : str
file path or web link to an experiment.json file
strict : bool
if true, then all JSON loaded by this method will be
passed to the appropriate validator
config : str or dict
configuration property that will be passed to
starfish.util.config.Config
STARISH_CONFIG :
This parameter is read from the environment to permit setting configuration
values either directly or via a file. Keys read include:
- cache.allow_caching
STARFISH_STRICT_LOADING :
This parameter is read from the environment. If set, then all JSON loaded by this
method will be passed to the appropriate validator. The `strict` parameter to this
method has priority over the environment variable.
Returns
-------
Experiment :
Experiment object serving the requested experiment data
"""
if strict is None:
strict = "STARFISH_STRICT_LOADING" in os.environ
if strict:
valid = validate_sptx.validate(json_url)
if not valid:
raise Exception("validation failed")
config_obj = Config(config) # STARFISH_CONFIG is assumed
allow_caching = config_obj.lookup(["cache", "allow_caching"], True)
backend, name, baseurl = resolve_path_or_url(json_url, allow_caching)
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, allow_caching)
codebook_absolute_url = pathjoin(codebook_baseurl, codebook_name)
codebook = Codebook.from_json(codebook_absolute_url)
extras = experiment_document['extras']
fovs: MutableSequence[FieldOfView] = list()
fov_tilesets: MutableMapping[str, TileSet] = dict()
if version < Version("5.0.0"):
primary_image: Collection = Reader.parse_doc(
experiment_document['primary_images'], baseurl)
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)
for fov_name, primary_tileset in primary_image.all_tilesets():
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)
images[image_type] = image
for fov_name, _ in image.all_tilesets():
all_fov_names.add(fov_name)
for fov_name in all_fov_names:
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 loaded_codebook(simple_codebook_json):
return Codebook.from_json(simple_codebook_json, n_ch=2, n_round=2)
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.from_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.from_json(input_parameter)
def from_json(cls, json_url: str, strict: bool=None) -> "Experiment":
"""
Construct an `Experiment` from an experiment.json file format specifier
Parameters
----------
json_url : str
file path or web link to an experiment.json file
strict : bool
if true, then all JSON loaded by this method will be
passed to the appropriate validator
Returns
-------
Experiment :
Experiment object serving the requested experiment data
Environment variables
---------------------
STARFISH_STRICT_LOADING :
If set, then all JSON loaded by this method will be
passed to the appropriate validator. The `strict`
parameter to this method has priority over the
environment variable.
"""
if strict is None:
strict = "STARFISH_STRICT_LOADING" in os.environ
if strict:
valid = validate_sptx.validate(json_url)
if not valid:
raise Exception("validation failed")
backend, name, baseurl = resolve_path_or_url(json_url)
with backend.read_contextmanager(name) as fh:
experiment_document = json.load(fh)
cls.verify_version(experiment_document['version'])
_, codebook_name, codebook_baseurl = resolve_url(experiment_document['codebook'], baseurl)
codebook_absolute_url = pathjoin(codebook_baseurl, codebook_name)
codebook = Codebook.from_json(codebook_absolute_url)
extras = experiment_document['extras']
primary_image: Collection = Reader.parse_doc(experiment_document['primary_images'], baseurl)
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)
fovs: MutableSequence[FieldOfView] = list()
for fov_name, primary_tileset in primary_image.all_tilesets():
aux_image_tilesets_for_fov: MutableMapping[str, TileSet] = dict()
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:
aux_image_tilesets_for_fov[aux_image_type] = aux_image_tileset
fov = FieldOfView(
fov_name,
primary_image_tileset=primary_tileset,
auxiliary_image_tilesets=aux_image_tilesets_for_fov,
)
fovs.append(fov)
return Experiment(fovs, codebook, extras, src_doc=experiment_document)