Source code for cytoflowgui.op_plugins.quad

#!/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/>.

"""
Quadrant Gate
-------------

Draw a "quadrant" gate.  To create a new gate, just click where you'd like the
intersection to be. Creates a new metadata column named `name`, with values 
``name_1`` (upper-left quadrant), ``name_2`` (upper-right), 
``name_3`` (lower-left), and ``name_4`` (lower-right).

.. note::

    This matches the order of FACSDiva quad gates.
    

.. object:: Name

    The operation name.  Used to name the new metadata field that's created by 
    this operation.
        
.. object:: X channel

    The name of the channel on the X axis.
        
.. object:: X threshold

    The threshold in the X channel.

.. object:: Y channel

    The name of the channel on the Y axis.
        
.. object:: Y threshold

    The threshold in the Y channel.

.. object:: X Scale

    The scale of the X axis for the interactive plot.
    
.. object:: Y Scale

    The scale of the Y axis for the interactive plot
    
.. object:: Hue facet

    Show different experimental conditions in different colors.
    
.. object:: Subset

    Show only a subset of the data.
        
.. plot::
   :include-source: False

    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()

    quad = flow.QuadOp(name = "Quad",
                       xchannel = "V2-A",
                       xthreshold = 100,
                       ychannel = "Y2-A",
                       ythreshold = 1000)

    qv = quad.default_view(xscale = 'log', yscale = 'log')
    qv.plot(ex)
"""


from traits.api import provides, List
from traitsui.api import View, Item, EnumEditor, VGroup, TextEditor
from envisage.api import Plugin
from pyface.api import ImageResource

from ..view_plugins import ViewHandler
from ..view_plugins.scatterplot import ScatterplotParamsHandler
from ..editors import SubsetListEditor, ColorTextEditor, ExtendableEnumEditor, InstanceHandlerEditor
from ..workflow.operations import QuadWorkflowOp, QuadSelectionView
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 QuadHandler(OpHandler): operation_traits_view = \ View(Item('name', editor = TextEditor(auto_set = False, placeholder = "None")), Item('xchannel', editor=EnumEditor(name='context_handler.previous_channels'), label = "X Channel"), Item('xthreshold', editor = TextEditor(auto_set = False, evaluate = float, format_func = lambda x: "" if x is None else str(x), placeholder = "None"), label = "X Threshold"), Item('ychannel', editor=EnumEditor(name='context_handler.previous_channels'), label = "Y Channel"), Item('ythreshold', editor = TextEditor(auto_set = False, evaluate = float, format_func = lambda x: "" if x is None else str(x), placeholder = "None"), label = "Y Threshold"), shared_op_traits_view)
[docs]class QuadViewHandler(ViewHandler): view_traits_view = \ View(VGroup( VGroup(Item('xchannel', label = "X Channel", style = "readonly"), Item('xthreshold', label = "X Threshold", style = "readonly"), Item('xscale', label = "X scale"), Item('ychannel', label = "Y Channel", style = "readonly"), Item('ythreshold', label = "Y Threshold", style = "readonly"), Item('yscale', label = "Y Scale"), Item('huefacet', editor=ExtendableEnumEditor(name='context_handler.previous_conditions_names', extra_items = {"None" : ""}), label="Color\nFacet"), label = "Quad Setup View", show_border = 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), mutable = False)), label = "Subset", show_border = False, show_labels = False), 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(Item('plot_params', editor = InstanceHandlerEditor(view = 'view_params_view', handler_factory = ScatterplotParamsHandler), style = 'custom', show_label = False))
[docs]@provides(IOperationPlugin) class QuadPlugin(Plugin, PluginHelpMixin): id = 'edu.mit.synbio.cytoflowgui.op_plugins.quad' operation_id = 'edu.mit.synbio.cytoflow.operations.quad' view_id = 'edu.mit.synbio.cytoflow.views.quad' short_name = "Quad" menu_group = "Gates"
[docs] def get_operation(self): return QuadWorkflowOp()
[docs] def get_handler(self, model, context): if isinstance(model, QuadWorkflowOp): return QuadHandler(model = model, context = context) elif isinstance(model, QuadSelectionView): return QuadViewHandler(model = model, context = context)
[docs] def get_icon(self): return ImageResource('quad')
plugin = List(contributes_to = OP_PLUGIN_EXT) def _plugin_default(self): return [self]