cytoflow.operations.i_operation

class cytoflow.operations.i_operation.IOperation

Bases: traits.has_traits.Interface

The basic interface for an operation on cytometry data.

id

a unique identifier for this class. prefix: edu.mit.synbio.cytoflow.operations

Type:Str

friendly_id

The operation’s human-readable id (like Threshold or K-means). Used for UI implementations.

Type:Str

name

The name of this IOperation instance (like Debris_Filter). Useful for UI implementations; sometimes used for naming gates’ metadata

Type:Str

estimate(experiment, subset=None)

Estimate this operation’s parameters from some data.

For operations that are data-driven (for example, a mixture model), estimate the operation’s parameters from an experiment.

Parameters:

• experiment (Experiment) – the Experiment to use in the estimation.
• subset (Str (optional)) – a string passed to pandas.DataFrame.query() to select the subset of data on which to run the parameter estimation.

Raises:

CytoflowOpException – If the operation can’t be be completed because of bad op parameters.

apply(experiment)

Apply an operation to an experiment.

Parameters:experiment (Experiment) – the Experiment to apply this op to Returns:the old Experiment with this operation applied Return type:Experiment Raises:CytoflowOpException – If the operation can’t be be completed because of bad op parameters.

default_view(**kwargs)

Many operations have a “default” view. This can either be a diagnostic for the operation’s estimate() method, an interactive for setting gates, etc. Frequently it makes sense to link the properties of the view to the properties of the IOperation; sometimes, default_view() is the only way to get the view (ie, it’s not useful when it doesn’t reference an IOperation instance.)

Parameters:**kwargs (Dict) – The keyword args passed to the view’s constructor Returns:the IView instance Return type:IView