#!/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/>.
"""
Multi-channel statistic
-----------------------
Apply a function to multiple channels in subsets of a data set, and add it as
a statistic to the experiment.
First, the module groups the data by the unique values of the variables
in **By**, then applies **Function** to the **Channels** in each group.
Multiple channels and functions can be specified
.. object:: Name
The operation name. Becomes the new statistic's name.
.. object:: Channels
For each channel, you must specify:
* The channel to summarize
* The function to apply to it
* The name of the resulting feature
.. object:: Subset
Only apply the function to a subset of the data. Useful if the function
is very slow.
"""
from natsort import natsorted
from traits.api import provides, List, Event, Property, Str
from traitsui.api import (View, Item, TextEditor, VGroup, EnumEditor, CheckListEditor,
Controller, ButtonEditor)
from pyface.api import ImageResource # @UnresolvedImport
from envisage.api import Plugin
from ..workflow.operations import MultiChannelStatisticWorkflowOp, MultiChannelStatisticFunction
from ..workflow.operations.multi_channel_stat import summary_functions
from ..editors import SubsetListEditor, InstanceHandlerEditor, VerticalListEditor
from ..subset_controllers import subset_handler_factory
from .i_op_plugin import IOperationPlugin, OP_PLUGIN_EXT
from .op_plugin_base import OpHandler, PluginHelpMixin, shared_op_traits_view
[docs]
class FunctionHandler(Controller):
function_view = View(VGroup(Item('channel',
editor = EnumEditor(name = 'context_handler.channels')),
Item('function',
editor = EnumEditor(values = sorted(summary_functions.keys()))),
Item('feature'),
Item(name = '_')))
[docs]
class MultiChannelStatisticHandler(OpHandler):
add_function = Event
remove_function = Event
channels = Property(List(Str), observe = 'context.channels')
operation_traits_view = \
View(Item('name',
editor = TextEditor(auto_set = False,
placeholder = "None")),
VGroup(
Item('functions_list',
editor = VerticalListEditor(editor = InstanceHandlerEditor(view = 'function_view',
handler_factory = FunctionHandler),
style = 'custom',
mutable = False)),
Item('handler.add_function',
editor = ButtonEditor(value = True,
label = "Add a function")),
Item('handler.remove_function',
editor = ButtonEditor(value = True,
label = "Remove a function")),
label = "Channels",
show_labels = False),
Item('by',
editor = CheckListEditor(cols = 2,
name = 'context_handler.previous_conditions_names'),
label = 'Group\nBy',
style = 'custom'),
VGroup(Item('subset_list',
show_label = False,
editor = SubsetListEditor(conditions = "context_handler.previous_conditions",
editor = InstanceHandlerEditor(view = 'subset_view',
handler_factory = subset_handler_factory))),
label = "Subset",
show_border = False,
show_labels = False),
shared_op_traits_view)
# MAGIC: called when add_function is set
def _add_function_fired(self):
self.model.functions_list.append(MultiChannelStatisticFunction())
# MAGIC: called when remove_function is set
def _remove_function_fired(self):
if self.model.functions_list:
self.model.functions_list.pop()
# MAGIC: returns the value of the 'channels' property
def _get_channels(self):
if self.context and self.context.channels:
return natsorted(self.context.channels)
else:
return []
[docs]
@provides(IOperationPlugin)
class MultiChannelStatisticPlugin(Plugin, PluginHelpMixin):
id = 'cytoflowgui.op_plugins.multi_channel_statistic'
operation_id = 'cytoflowgui.workflow.operations.multi_channel_stat'
view_id = None
name = "Multi Channel Statistic"
short_name = "Multi\nStatistic"
menu_group = "Statistics"
[docs]
def get_operation(self):
return MultiChannelStatisticWorkflowOp()
[docs]
def get_handler(self, model, context):
return MultiChannelStatisticHandler(model = model, context = context)
[docs]
def get_icon(self):
return ImageResource('multi_channel_stat')
plugin = List(contributes_to = OP_PLUGIN_EXT)
def _plugin_default(self):
return [self]