#!/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/>.
'''
Binning
-------
Bin data along an axis.
This operation creates equally spaced bins (in linear or log space)
along an axis and adds a condition assigning each event to a bin. The
value of the event's condition is the left end of the bin's interval in
which the event is located.
.. object:: Name
The name of the new condition created by this operation.
.. object:: Channel
The channel to apply the binning to.
.. object:: Scale
The scale to apply to the channel before binning.
.. object:: Bin Width
How wide should each bin be? Can only set if **Scale** is *linear* or
*log* (in which case, **Bin Width** is in log10-units.)
.. plot::
:include-source: False
import cytoflow as flow
import_op = flow.ImportOp()
import_op.tubes = [flow.Tube(file = "tasbe/rby.fcs")]
ex = import_op.apply()
bin_op = flow.BinningOp()
bin_op.name = "Bin"
bin_op.channel = "FITC-A"
bin_op.scale = "log"
bin_op.bin_width = 0.2
ex2 = bin_op.apply(ex)
bin_op.default_view().plot(ex2)
'''
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, InstanceHandlerEditor
from ..workflow.operations import BinningWorkflowOp, BinningWorkflowView
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 BinningHandler(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('scale',
editor = EnumEditor(values = ['linear', 'log'])),
Item('bin_width',
editor = TextEditor(auto_set = False,
evaluate = float,
format_func = lambda x: "" if x is None else str(x),
placeholder = "None"),
label = "Bin Width"),
shared_op_traits_view)
[docs]class BinningViewHandler(ViewHandler):
view_traits_view = \
View(VGroup(
VGroup(Item('channel',
style = 'readonly'),
label = "Binning Default Plot",
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 BinningPlugin(Plugin, PluginHelpMixin):
id = 'edu.mit.synbio.cytoflowgui.op_plugins.binning'
operation_id = 'edu.mit.synbio.cytoflow.operations.binning'
view_id = 'edu.mit.synbio.cytoflow.views.binning'
short_name = "Binning"
menu_group = "Gates"
[docs] def get_operation(self):
return BinningWorkflowOp()
[docs] def get_handler(self, model, context):
if isinstance(model, BinningWorkflowOp):
return BinningHandler(model = model, context = context)
elif isinstance(model, BinningWorkflowView):
return BinningViewHandler(model = model, context = context)
[docs] def get_icon(self):
return ImageResource('binning')
plugin = List(contributes_to = OP_PLUGIN_EXT)
def _plugin_default(self):
return [self]