#!/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/>.
'''
2D Range Gate
-------------
Draw a 2-dimensional range gate (eg, a rectangle). To set the gate,
click-and-drag on the plot.
.. 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 Low
The low threshold in the X channel.
.. object:: X High
The high threshold in the X channel.
.. object:: Y channel
The name of the channel on the Y axis.
.. object:: Y Low
The low threshold in the Y channel.
.. object:: Y High
The high 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()
r = flow.Range2DOp(name = "Range2D",
xchannel = "V2-A",
xlow = 10,
xhigh = 1000,
ychannel = "Y2-A",
ylow = 1000,
yhigh = 20000)
r.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
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 Range2DWorkflowOp, Range2DSelectionView
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 Range2DHandler(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('xlow',
editor = TextEditor(auto_set = False,
evaluate = float,
format_func = lambda x: "" if x is None else str(x),
placeholder = "None"),
label = "X Low"),
Item('xhigh',
editor = TextEditor(auto_set = False,
evaluate = float,
format_func = lambda x: "" if x is None else str(x),
placeholder = "None"),
label = "X High"),
Item('ychannel',
editor=EnumEditor(name='context_handler.previous_channels'),
label = "Y Channel"),
Item('ylow',
editor = TextEditor(auto_set = False,
evaluate = float,
format_func = lambda x: "" if x is None else str(x),
placeholder = "None"),
label = "Y Low"),
Item('yhigh',
editor = TextEditor(auto_set = False,
evaluate = float,
format_func = lambda x: "" if x is None else str(x),
placeholder = "None"),
label = "Y High"),
shared_op_traits_view)
[docs]class Range2DViewHandler(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" : ""}),
label="Color\nFacet"),
label = "2D Range 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 Range2DPlugin(Plugin, PluginHelpMixin):
"""
class docs
"""
id = 'edu.mit.synbio.cytoflowgui.op_plugins.range2d'
operation_id = 'edu.mit.synbio.cytoflow.operations.range2d'
view_id = 'edu.mit.synbio.cytoflow.views.range2d'
short_name = "Range 2D"
menu_group = "Gates"
[docs] def get_operation(self):
return Range2DWorkflowOp()
[docs] def get_handler(self, model, context):
if isinstance(model, Range2DWorkflowOp):
return Range2DHandler(model = model, context = context)
elif isinstance(model, Range2DSelectionView):
return Range2DViewHandler(model = model, context = context)
[docs] def get_icon(self):
return ImageResource('range2d')
plugin = List(contributes_to = OP_PLUGIN_EXT)
def _plugin_default(self):
return [self]