#!/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/>.
'''
Polygon Gate
------------
Draw a polygon gate. To add vertices, use a single-click; to close the
polygon, click the first vertex a second time.
.. object:: Name
The operation name. Used to name the new metadata field that's created by
this module.
.. object:: X Channel
The name of the channel on the gate's X axis.
.. object:: Y Channel
The name of the channel on the gate's Y axis.
.. 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()
p = flow.PolygonOp(name = "Polygon",
xchannel = "V2-A",
ychannel = "Y2-A")
p.vertices = [(23.411982294776319, 5158.7027015021222),
(102.22182270573683, 23124.058843387455),
(510.94519955277201, 23124.058843387455),
(1089.5215641232173, 3800.3424832180476),
(340.56382570202402, 801.98947404942271),
(65.42597937575897, 1119.3133482602157)]
p.default_view(huefacet = "Dox",
xscale = 'log',
yscale = 'log').plot(ex)
'''
from traits.api import provides, List
from traitsui.api import View, Item, EnumEditor, VGroup, TextEditor, Controller
from envisage.api import Plugin
from pyface.api import ImageResource # @UnresolvedImport
from ..view_plugins import ViewHandler
from ..view_plugins.view_plugin_base import Data2DPlotParamsView
from ..editors import SubsetListEditor, ColorTextEditor, ExtendableEnumEditor, InstanceHandlerEditor
from ..workflow.operations import PolygonWorkflowOp, PolygonSelectionView
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 PolygonViewParamsHandler(Controller):
view_params_view = \
View(Item('density'),
# density-specific
Item('gridsize',
editor = TextEditor(auto_set = False),
visible_when = 'density',
label = "Grid size"),
Item('smoothed',
visible_when = 'density',
label = "Smooth"),
Item('smoothed_sigma',
editor = TextEditor(auto_set = False),
label = "Smooth\nsigma",
visible_when = "density and smoothed"),
# scatterplot-specific
Item('alpha',
editor = TextEditor(auto_set = False),
visible_when = 'not density'),
Item('s',
editor = TextEditor(auto_set = False),
visible_when = 'not density',
label = "Size"),
Item('marker',
visible_when = 'not density'),
Data2DPlotParamsView.content)
[docs]
class PolygonHandler(OpHandler):
operation_traits_view = \
View(Item('name',
editor = TextEditor(auto_set = False)),
Item('xchannel',
editor=EnumEditor(name='context_handler.previous_channels'),
label = "X Channel"),
Item('ychannel',
editor=EnumEditor(name='context_handler.previous_channels'),
label = "Y Channel"),
shared_op_traits_view)
[docs]
class PolygonViewHandler(ViewHandler):
view_traits_view = \
View(VGroup(
VGroup(Item('xchannel',
label = "X Channel",
style = 'readonly'),
Item('xscale',
label = "X Scale"),
Item('ychannel',
label = "Y Channel",
style = 'readonly'),
Item('yscale',
label = "Y Scale"),
Item('huefacet',
editor=ExtendableEnumEditor(name='context_handler.previous_conditions_names',
extra_items = {"None" : ""}),
visible_when = 'not plot_params.density',
label="Color\nFacet"),
Item('huescale',
visible_when = 'plot_params.density',
label = "Color\nScale"),
label = "Polygon 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 = PolygonViewParamsHandler),
style = 'custom',
show_label = False))
[docs]
@provides(IOperationPlugin)
class PolygonPlugin(Plugin, PluginHelpMixin):
id = 'cytoflowgui.op_plugins.polygon'
operation_id = 'cytoflow.operations.polygon'
view_id = 'cytoflowgui.workflow.operations.polygonview'
name = "Polygon Gate"
short_name = "Polygon"
menu_group = "Gates"
[docs]
def get_operation(self):
return PolygonWorkflowOp()
[docs]
def get_handler(self, model, context):
if isinstance(model, PolygonWorkflowOp):
return PolygonHandler(model = model, context = context)
elif isinstance(model, PolygonSelectionView):
return PolygonViewHandler(model = model, context = context)
[docs]
def get_icon(self):
return ImageResource('polygon')
plugin = List(contributes_to = OP_PLUGIN_EXT)
def _plugin_default(self):
return [self]