Source code for cytoflowgui.op_plugins.bleedthrough_linear

#!/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
# 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 <>.

Linear Bleedthrough Compensation

Apply matrix-based bleedthrough correction to a set of fluorescence channels.

This is a traditional matrix-based compensation for bleedthrough.  For each
pair of channels, the module estimates the proportion of the first channel
that bleeds through into the second, then performs a matrix multiplication to 
compensate the raw data.

This works best on data that has had autofluorescence removed first;
if that is the case, then the autofluorescence will be subtracted from
the single-color controls too.

To use, specify the single-color control files and which channels they should
be measured in, then click **Estimate**.  Check the diagnostic plot to make sure
the estimation looks good.  There must be at least two channels corrected.

.. object:: Add Control, Remove Control

    Add or remove single-color controls.
.. object: Subset

    If you specify a subset here, only that data will be used to calculate the
    bleedthrough matrix.  For example, if you applied a gate to the morphological
    channels, that gate can be specified here to restrict the estimation to
    only events that are in that gate.
.. note::

    You cannot have any operations before this one which estimate model
    parameters based on experimental conditions.  (Eg, you can't use a
    **Density Gate** to choose morphological parameters and set *by* to an
    experimental condition.)  If you need this functionality, you can access it 
    using the Python module interface.
.. plot:: 
   :include-source: False

    import cytoflow as flow
    import_op = flow.ImportOp()
    import_op.tubes = [flow.Tube(file = "tasbe/rby.fcs")]
    ex = import_op.apply()
    af_op = flow.AutofluorescenceOp()
    af_op.channels = ["Pacific Blue-A", "FITC-A", "PE-Tx-Red-YG-A"]
    af_op.blank_file = "tasbe/blank.fcs"

    ex2 = af_op.apply(ex)

    bl_op = flow.BleedthroughLinearOp()
    bl_op.controls = {'Pacific Blue-A' : 'tasbe/ebfp.fcs',
                      'FITC-A' : 'tasbe/eyfp.fcs',
                      'PE-Tx-Red-YG-A' : 'tasbe/mkate.fcs'}    


    ex2 = bl_op.apply(ex2)  
from natsort import natsorted

from traits.api import provides, Event, Property, List, Str
from traitsui.api import View, Item, VGroup, ButtonEditor, FileEditor, HGroup, EnumEditor, Controller
from envisage.api import Plugin
from pyface.api import ImageResource

from ..view_plugins import ViewHandler
from ..editors import ColorTextEditor, InstanceHandlerEditor, VerticalListEditor, SubsetListEditor
from ..workflow.operations import BleedthroughLinearWorkflowOp, BleedthroughLinearWorkflowView, BleedthroughControl
from ..subset_controllers import subset_handler_factory

from .i_op_plugin import IOperationPlugin, OP_PLUGIN_EXT
from .op_plugin_base import OpHandler, shared_op_traits_view, PluginHelpMixin

[docs]class ControlHandler(Controller): control_view = View(HGroup(Item('channel', editor = EnumEditor(name = 'context_handler.channels')), Item('file', editor = FileEditor(dialog_style = 'open'), show_label = False)))
[docs]class BleedthroughLinearHandler(OpHandler): add_control = Event remove_control = Event channels = Property(List(Str), observe = 'context.channels') operation_traits_view = \ View(VGroup( Item('controls_list', editor = VerticalListEditor(editor = InstanceHandlerEditor(view = 'control_view', handler_factory = ControlHandler), style = 'custom', mutable = False)), Item('handler.add_control', editor = ButtonEditor(value = True, label = "Add a control")), Item('handler.remove_control', editor = ButtonEditor(value = True, label = "Remove a control")), label = "Controls", show_labels = False), VGroup(Item('subset_list', show_label = False, editor = SubsetListEditor(conditions = "context_handler.previous_conditions", editor = InstanceHandlerEditor(view = 'subset_view', handler_factory = subset_handler_factory))), label = "Subset", show_border = False, show_labels = False), Item('do_estimate', editor = ButtonEditor(value = True, label = "Estimate!"), show_label = False), shared_op_traits_view) # MAGIC: called when add_control is set def _add_control_fired(self): self.model.controls_list.append(BleedthroughControl()) # MAGIC: called when remove_control is set def _remove_control_fired(self): if self.model.controls_list: self.model.controls_list.pop() # MAGIC: returns the value of the 'channels' property def _get_channels(self): if self.context and self.context.channels: return natsorted(self.context.channels) else: return []
[docs]class BleedthroughLinearViewHandler(ViewHandler): view_traits_view = \ View(Item('context.view_warning', resizable = True, visible_when = 'context.view_warning', editor = ColorTextEditor(foreground_color = "#000000", background_color = "#ffff99")), Item('context.view_error', resizable = True, visible_when = 'context.view_error', editor = ColorTextEditor(foreground_color = "#000000", background_color = "#ff9191"))) view_params_view = View()
[docs]@provides(IOperationPlugin) class BleedthroughLinearPlugin(Plugin, PluginHelpMixin): id = '' operation_id = '' view_id = '' short_name = "Linear Compensation" menu_group = "Gates"
[docs] def get_operation(self): return BleedthroughLinearWorkflowOp()
[docs] def get_handler(self, model, context): if isinstance(model, BleedthroughLinearWorkflowOp): return BleedthroughLinearHandler(model = model, context = context) elif isinstance(model, BleedthroughLinearWorkflowView): return BleedthroughLinearViewHandler(model = model, context = context)
[docs] def get_icon(self): return ImageResource('bleedthrough_linear')
plugin = List(contributes_to = OP_PLUGIN_EXT) def _plugin_default(self): return [self]