#!/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/>.
"""
Table
-----
Make a table out of a statistic. The table can then be exported.
.. object:: Statistic
Which statistic to view.
.. object:: Feature
The column in the statistic to view (often a channel name.)
.. object:: Rows
Which variable to use for the rows
.. object:: Subrows
Which variable to use for subrows.
.. object:: Columns
Which variable to use for the columns.
.. object:: Subcolumns
Which variable to use for the subcolumns.
.. object:: Export
Export the table to a CSV file.
.. 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()
ex2 = flow.ThresholdOp(name = 'Threshold',
channel = 'Y2-A',
threshold = 2000).apply(ex)
ex3 = flow.ChannelStatisticOp(name = "ByDox",
channel = "Y2-A",
by = ['Dox', 'Threshold'],
function = len).apply(ex2)
flow.TableView(statistic = "ByDox",
feature = "Y2-A",
row_facet = "Dox",
column_facet = "Threshold").plot(ex3)
"""
import pandas as pd
from traits.api import provides, Property, Event, observe, List
from traitsui.api import View, Item, EnumEditor, VGroup, ButtonEditor
from envisage.api import Plugin
from pyface.api import ImageResource, FileDialog, OK # @UnresolvedImport
from ..workflow.views import TableWorkflowView
from ..util import DefaultFileDialog
from ..editors import SubsetListEditor, ColorTextEditor, ExtendableEnumEditor, InstanceHandlerEditor
from ..subset_controllers import subset_handler_factory
from .i_view_plugin import IViewPlugin, VIEW_PLUGIN_EXT
from .view_plugin_base import ViewHandler, PluginHelpMixin
[docs]
class TableHandler(ViewHandler):
indices = Property(depends_on = "context.statistics, model.statistic, model.subset")
levels = Property(depends_on = "context.statistics, model.statistic")
features = Property(depends_on = "context.statistics, model.statistic")
export = Event()
view_traits_view = \
View(VGroup(
VGroup(Item('statistic',
editor = EnumEditor(name='context_handler.statistics_names'),
label = "Statistic"),
Item('feature',
editor = EnumEditor(name = 'handler.features'),
label = "Feature"),
Item('row_facet',
editor = ExtendableEnumEditor(name='handler.indices',
extra_items = {"None" : ""}),
label = "Rows"),
Item('subrow_facet',
editor = ExtendableEnumEditor(name='handler.indices',
extra_items = {"None" : ""}),
label = "Subrows"),
Item('column_facet',
editor = ExtendableEnumEditor(name='handler.indices',
extra_items = {"None" : ""}),
label = "Columns"),
Item('subcolumn_facet',
editor = ExtendableEnumEditor(name='handler.indices',
extra_items = {"None" : ""}),
label = "Subcolumn"),
Item('handler.export',
editor = ButtonEditor(label = "Export..."),
enabled_when = 'result is not None',
show_label = False),
label = "Table View",
show_border = False),
VGroup(Item('subset_list',
show_label = False,
editor = SubsetListEditor(conditions = "handler.levels",
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() # empty view -- no parameters for a table view
# MAGIC: gets the value for the property indices
def _get_indices(self):
if not (self.context and self.context.statistics
and self.model.statistic in self.context.statistics):
return []
stat = self.context.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.statistics
and self.model.statistic in self.context.statistics):
return {}
stat = self.context.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(index.get_level_values(name)).sort_values()
ret[name] = pd.Series(ret[name].unique())
return ret
# MAGIC: gets the value for the property "features"
def _get_features(self):
if not (self.context and self.context.statistics
and self.model.statistic in self.context.statistics):
return []
stat = self.context.statistics[self.model.statistic]
return stat.columns.to_list()
@observe('export')
def _on_export(self, _):
dialog = DefaultFileDialog(parent = None,
action = 'save as',
default_suffix = "csv",
wildcard = (FileDialog.create_wildcard("CSV", "*.csv") + ';' + #@UndefinedVariable
FileDialog.create_wildcard("All files", "*"))) #@UndefinedVariable
if dialog.open() != OK:
return
self.model._export_data(self.model.result, self.model.feature, dialog.path)
[docs]
@provides(IViewPlugin)
class TablePlugin(Plugin, PluginHelpMixin):
id = 'cytoflowgui.view.table'
view_id = 'cytoflow.view.table'
name = "Table View"
short_name = "Table"
[docs]
def get_view(self):
return TableWorkflowView()
[docs]
def get_handler(self, model, context):
if isinstance(model, TableWorkflowView):
return TableHandler(model = model, context = context)
else:
return None
[docs]
def get_icon(self):
return ImageResource('table')
plugin = List(contributes_to = VIEW_PLUGIN_EXT)
def _plugin_default(self):
return [self]