Experiment¶

class starfish.core.experiment.experiment.Experiment(fovs, codebook, extras, *, src_doc=None)[source]¶

Encapsulates an experiment, with one or more fields of view and a Codebook. An individual FieldOfView can be retrieved using a key, i.e., experiment[fov_name].

Attributes

codebookCodebook: The codebook associated with this experiment.
extrasDict: Returns the extras dictionary associated with this experiment.

Methods

`fov`([filter_fn, key_fn])	Given a callable filter_fn, apply it to all the FOVs in this experiment.
`fovs`([filter_fn, key_fn])	Given a callable filter_fn, apply it to all the FOVs in this experiment.
`fovs_by_name`(*names)	Given a name or set of names, return all fovs that match.
`from_json`(json_url)	Construct an Experiment from an experiment.json file format specifier.
`items`()	Return all names and fovs in the experiment
`keys`()	Return all fov names in the experiment
`values`()	Return all FieldOfViews in the experiment
`verify_version`(semantic_version_str)	Verifies the compatibility of the current starfish version with the experiment version

fov(filter_fn=<function Experiment.<lambda>>, key_fn=<function Experiment.<lambda>>)[source]¶

Given a callable filter_fn, apply it to all the FOVs in this experiment.

Parameters

filter_fnCallable: Filter to apply to the list of FOVs
key_fnCallable: The key that determines the order of filtered FOVs, default fov.name

Returns

FieldOfView: The first FOV that fulfills the filter parameters.

Raises

LookupError :: If no FOV matches

Return type: FieldOfView

fovs(filter_fn=<function Experiment.<lambda>>, key_fn=<function Experiment.<lambda>>)[source]¶

Given a callable filter_fn, apply it to all the FOVs in this experiment.

Parameters

filter_fnCallable: Filter to apply to the list of FOVs
key_fnCallable: The key that determines the order of filtered FOVs, default fov.name

Returns

Sequence[FieldOfView]: All fovs that pass the filter function.

Return type: Sequence[FieldOfView]

fovs_by_name(*names)[source]¶

Given a name or set of names, return all fovs that match.

Parameters

namesstr: The fov names to search for.

Returns

Sequence[FieldOfView]: All fovs that match the given names.

Return type: Sequence[FieldOfView]

classmethod from_json(json_url)[source]¶

Construct an Experiment from an experiment.json file format specifier. Loads configuration from StarfishConfig.

Parameters

json_urlstr: file path or web link to an experiment.json file

Returns

Experiment :: Experiment object serving the requested experiment data

Return type: Experiment

items()[source]¶: Return all names and fovs in the experiment

keys()[source]¶: Return all fov names in the experiment

values()[source]¶: Return all FieldOfViews in the experiment

classmethod verify_version(semantic_version_str)[source]¶

Verifies the compatibility of the current starfish version with the experiment version

Return type: Version