Source code for cytoflowgui.op_plugins.xform_stat

#!/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/>.

'''
Transform statistic
-------------------

Apply a function to a statistic, 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 statistic in each group.

.. note:: 

    Statistics are a central part of *Cytoflow*.  More documentation is
    forthcoming.

.. object:: Name

    The operation name.  Becomes the first part of the new statistic's name.
    
.. object:: Statistic

    The statistic to apply the function to.
    
.. object:: Function

    The function to compute on each group.
        
.. object:: Subset

    Only apply the function to a subset of the input statistic.  Useful if the 
    function is very slow.

'''

import numpy as np
import pandas as pd

from traits.api import provides, Property, List
from traitsui.api import (View, Item, TextEditor, VGroup, EnumEditor, CheckListEditor)
from pyface.api import ImageResource
from envisage.api import Plugin
                       
from ..workflow.operations import TransformStatisticWorkflowOp
from ..workflow.operations.xform_stat import transform_functions
from ..editors import SubsetListEditor, InstanceHandlerEditor
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 TransformStatisticHandler(OpHandler): # prev_statistics = Property(depends_on = "info.ui.context") indices = Property(depends_on = "context.previous_wi.statistics, " "model.statistic, " "model.subset") levels = Property(depends_on = "context.previous_wi.statistics, model.statistic") # MAGIC: gets the value for the property indices def _get_indices(self): if not (self.context and self.context.previous_wi and self.context.previous_wi.statistics and self.model and self.model.statistic and self.model.statistic in self.context.previous_wi.statistics): return [] stat = self.context.previous_wi.statistics[self.model.statistic] data = pd.DataFrame(index = stat.index) if self.model.subset: data = data.query(self.model.subset) if len(data) == 0: return [] names = list(data.index.names) for name in names: unique_values = data.index.get_level_values(name).unique() if len(unique_values) == 1: data.index = data.index.droplevel(name) return list(data.index.names) # MAGIC: gets the value for the property 'levels' # returns a Dict(Str, pd.Series) def _get_levels(self): if not (self.context and self.context.previous_wi and self.context.previous_wi.statistics and self.model and self.model.statistic and self.model.statistic in self.context.previous_wi.statistics): return {} stat = self.context.previous_wi.statistics[self.model.statistic] index = stat.index names = list(index.names) for name in names: unique_values = index.get_level_values(name).unique() if len(unique_values) == 1: index = index.droplevel(name) names = list(index.names) ret = {} for name in names: ret[name] = pd.Series(np.unique(index.get_level_values(name))) return ret operation_traits_view = \ View(Item('name', editor = TextEditor(auto_set = False, placeholder = "None")), Item('statistic', editor=EnumEditor(name='context_handler.previous_statistics_names'), label = "Statistic"), Item('statistic_name', editor = EnumEditor(values = sorted(transform_functions.keys())), label = "Function"), Item('by', editor = CheckListEditor(cols = 2, name = 'handler.indices'), label = 'Group\nBy', style = 'custom'), VGroup(Item('subset_list', show_label = False, editor = SubsetListEditor(conditions = "handler.levels", editor = InstanceHandlerEditor(view = 'subset_view', handler_factory = subset_handler_factory))), label = "Subset", show_border = False, show_labels = False), shared_op_traits_view)
[docs]@provides(IOperationPlugin) class TransformStatisticPlugin(Plugin, PluginHelpMixin): id = 'edu.mit.synbio.cytoflowgui.op_plugins.transform_statistic' operation_id = 'edu.mit.synbio.cytoflow.operations.transform_statistic' view_id = None short_name = "Transform Statistic" menu_group = "Gates"
[docs] def get_operation(self): return TransformStatisticWorkflowOp()
[docs] def get_handler(self, model, context): return TransformStatisticHandler(model = model, context = context)
[docs] def get_icon(self): return ImageResource('xform_stat')
plugin = List(contributes_to = OP_PLUGIN_EXT) def _plugin_default(self): return [self]