cytoflow.views.export_fcs#

A “view” that exports events as FCS files.

ExportFCS – the IView class that does the exporting.

class cytoflow.views.export_fcs.ExportFCS[source]#

Bases: HasStrictTraits

Exports events as FCS files.

This isn’t a traditional view, in that it doesn’t implement plot. Instead, use enum_files to figure out which files will be created from a particular experiment, and export to export the FCS files.

The Cytoflow attributes will be encoded in keywords in the FCS TEXT segment, starting with the characters CF_. Any FCS keywords that are the same across all the input files will also be included.

base#

The prefix of the FCS filenames

Type:: Str

path#

The directory to export to.

Type:: Directory

by#

A list of conditions from Experiment.conditions; each unique combination of conditions will be exported to an FCS file.

Type:: List(Str)

keywords#

If you want to add more keywords to the FCS files’ TEXT segment, specify them here.

Type:: Dict(Str, Str)

subset#

A Python expression used to select a subset of the data

Type:: str

Examples

Make a little data set.

>>> import cytoflow as flow
>>> import_op = flow.ImportOp()
>>> import_op.tubes = [flow.Tube(file = "Plate01/RFP_Well_A3.fcs",
...                              conditions = {'Dox' : 10.0}),
...                    flow.Tube(file = "Plate01/CFP_Well_A4.fcs",
...                              conditions = {'Dox' : 1.0})]
>>> import_op.conditions = {'Dox' : 'float'}
>>> ex = import_op.apply()

Export the data

>>> import tempfile
>>> flow.ExportFCS(path = 'export/',
...                by = ["Dox"],
...                subset = "Dox == 10.0").export(ex)

enum_files(experiment)[source]#

Return an iterator over the file names that this export module will produce from a given experiment.

Parameters:: experiment (Experiment) – The Experiment to export

export(experiment)[source]#

Export FCS files from an experiment.

Parameters:: experiment (Experiment) – The Experiment to export