#!/usr/bin/env python3.8
# coding: latin-1
# (c) Massachusetts Institute of Technology 2015-2018
# (c) Brian Teague 2018-2022
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
"""
cytoflow.operations.i_operation
-------------------------------
`i_operation` contains just one class:
`IOperation` -- an `traits.has_traits.Interface` that all operation classes must implement.
"""
from traits.api import Interface, Constant
[docs]class IOperation(Interface):
"""
The basic interface for an operation on cytometry data.
Attributes
----------
id : Str
a unique identifier for this class. prefix: ``edu.mit.synbio.cytoflow.operations``
friendly_id : Str
The operation's human-readable id (like ``Threshold`` or ``K-means``).
Used for UI implementations.
name : Str
The name of this IOperation instance (like ``Debris_Filter``). Useful
for UI implementations; sometimes used for naming gates' metadata
"""
# interface traits
id = Constant('FIXME')
friendly_id = Constant('FIXME')
[docs] def estimate(self, 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.
"""
[docs] def apply(self, experiment):
"""
Apply an operation to an experiment.
Parameters
----------
experiment : `Experiment`
the `Experiment` to apply this op to
Returns
-------
`Experiment`
the old `Experiment` with this operation applied
Raises
------
`CytoflowOpException`
If the operation can't be be completed because of bad op
parameters.
"""
[docs] def default_view(self, **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
-------
`IView`
the `IView` instance
"""