cytoflowgui.workflow.operations.autofluorescence

class cytoflowgui.workflow.operations.autofluorescence.AutofluorescenceWorkflowOp

Bases: WorkflowOperation, AutofluorescenceOp

default_view(**kwargs)

Returns a diagnostic plot to see if the autofluorescence estimation is working.

Returns:

An diagnostic view, call AutofluorescenceDiagnosticView.plot to see the diagnostic plots

Return type:

IView

estimate(experiment)

Estimate the autofluorescence from blank_file in channels specified in channels.

Parameters:

• experiment (Experiment) – The experiment to which this operation is applied

• subset (Str (default = “”)) – An expression that specifies the events used to compute the autofluorescence

apply(experiment)

Applies the autofluorescence correction to channels in an experiment.

Parameters:

experiment (Experiment) – the experiment to which this op is applied

Returns:

a new experiment with the autofluorescence median subtracted. The corrected channels have the following metadata added to them:

• af_median : Float The median of the non-fluorescent distribution

• af_stdev : Float The standard deviation of the non-fluorescent distribution

Return type:

Experiment

clear_estimate()

should_apply(changed, payload)

should_clear_estimate(changed, payload)

get_notebook_code(idx)

class cytoflowgui.workflow.operations.autofluorescence.AutofluorescenceWorkflowView

Bases: WorkflowView, AutofluorescenceDiagnosticView

should_plot(changed, payload)

Should the owning WorkflowItem refresh the plot when certain things change? changed can be: - Changed.VIEW – the view’s parameters changed - Changed.RESULT – this WorkflowItem’s result changed - Changed.PREV_RESULT – the previous WorkflowItem’s result changed - Changed.ESTIMATE_RESULT – the results of calling “estimate” changed

If should_plot is called from a notification handler, the payload is the handler event parameter.

get_notebook_code(idx)