Source code for cytoflowgui.op_plugins.threshold

#!/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/>.


'''
Threshold Gate
--------------

Draw a threshold gate.  To set a new threshold, click on the plot.

.. object:: Name

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

    The name of the channel to apply the gate to.

.. object:: Threshold

    The threshold of the gate.
    
.. object:: Scale

    The scale of the 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()

    thresh_op = flow.ThresholdOp(name = 'Threshold',
                                 channel = 'Y2-A',
                                 threshold = 2000)

    thresh_op.default_view(scale = 'log').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.histogram import HistogramParamsHandler
from ..editors import SubsetListEditor, ColorTextEditor, ExtendableEnumEditor, InstanceHandlerEditor
from ..workflow.operations import ThresholdWorkflowOp, ThresholdSelectionView
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 ThresholdHandler(OpHandler): operation_traits_view = \ View(Item('name', editor = TextEditor(auto_set = False, placeholder = "None")), Item('channel', editor=EnumEditor(name='context_handler.previous_channels'), label = "Channel"), Item('threshold', editor = TextEditor(auto_set = False, evaluate = float, format_func = lambda x: "" if x is None else str(x), placeholder = "None")), shared_op_traits_view)
[docs]class ThresholdViewHandler(ViewHandler): view_traits_view = \ View(VGroup( VGroup(Item('channel', label = "Channel", style = "readonly"), Item('threshold', label = "Threshold", style = "readonly"), Item('scale'), Item('huefacet', editor=ExtendableEnumEditor(name='context_handler.previous_conditions_names', extra_items = {"None" : ""}), label="Color\nFacet"), label = "Threshold 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 = HistogramParamsHandler), style = 'custom', show_label = False))
[docs]@provides(IOperationPlugin) class ThresholdPlugin(Plugin, PluginHelpMixin): id = 'edu.mit.synbio.cytoflowgui.op_plugins.threshold' operation_id = 'edu.mit.synbio.cytoflow.operations.threshold' view_id = 'edu.mit.synbio.cytoflow.views.threshold' short_name = "Threshold" menu_group = "Gates"
[docs] def get_operation(self): return ThresholdWorkflowOp()
[docs] def get_handler(self, model, context): if isinstance(model, ThresholdWorkflowOp): return ThresholdHandler(model = model, context = context) elif isinstance(model, ThresholdSelectionView): return ThresholdViewHandler(model = model, context = context)
[docs] def get_icon(self): return ImageResource('threshold')
plugin = List(contributes_to = OP_PLUGIN_EXT) def _plugin_default(self): return [self]