#!/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]