#!/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/>.
'''
TASBE Calibrated Flow Cytometry
-------------------------------
This module combines all of the other calibrated flow cytometry modules
(autofluorescence, bleedthrough compensation, bead calibration, and channel
translation) into one easy-use-interface.
.. object:: Channels
Which channels are you calibrating?
.. object:: Autofluorescence
.. object:: Blank File
The FCS file with the blank (unstained or untransformed) cells, for
autofluorescence correction.
.. plot::
:context: close-figs
:include-source: False
import cytoflow as flow
import_op = flow.ImportOp()
import_op.tubes = [flow.Tube(file = "tasbe/rby.fcs")]
ex = import_op.apply()
af_op = flow.AutofluorescenceOp()
af_op.channels = ["Pacific Blue-A", "FITC-A", "PE-Tx-Red-YG-A"]
af_op.blank_file = "tasbe/blank.fcs"
af_op.estimate(ex)
af_op.default_view().plot(ex)
ex2 = af_op.apply(ex)
.. object:: Bleedthrough Correction
A list of single-color controls to use in bleedthrough compensation.
There's one entry per channel to compensate.
.. object:: Channel
The channel that this file is the single-color control for.
.. object:: File
The FCS file containing the single-color control data.
.. plot::
:context: close-figs
:include-source: False
bl_op = flow.BleedthroughLinearOp()
bl_op.controls = {'Pacific Blue-A' : 'tasbe/ebfp.fcs',
'FITC-A' : 'tasbe/eyfp.fcs',
'PE-Tx-Red-YG-A' : 'tasbe/mkate.fcs'}
bl_op.estimate(ex2)
bl_op.default_view().plot(ex2)
ex3 = bl_op.apply(ex2)
.. object:: Bead Calibration
.. object: Beads
The beads that you used for calibration. Make sure to check the lot
number as well!
.. object: Beads File
The FCS file containing the bead data.
.. object: Beads Unit
The unit (such as *MEFL*) to calibrate to.
.. object:: Peak Quantile
The minimum quantile required to call a peak in the bead data. Check
the diagnostic plot: if you have peaks that aren't getting called, decrease
this. If you have "noise" peaks that are getting called incorrectly,
increase this.
.. object:: Peak Threshold
The minumum brightness where the module will call a peak.
.. object:: Peak Cutoff
The maximum brightness where the module will call a peak. Use this to
remove peaks that are saturating the detector.
.. plot::
:context: close-figs
:include-source: False
bead_op = flow.BeadCalibrationOp()
beads = "RCP-30-5A Lot AA01, AA02, AA03, AA04, AB01, AB02, AC01 & GAA01-R"
bead_op.beads = flow.BeadCalibrationOp.BEADS[beads]
bead_op.units = {"Pacific Blue-A" : "MEBFP",
"FITC-A" : "MEFL",
"PE-Tx-Red-YG-A" : "MEPTR"}
bead_op.beads_file = "tasbe/beads.fcs"
bead_op.estimate(ex2)
bead_op.default_view().plot(ex2)
ex3 = bead_op.apply(ex2)
.. object:: Color Translation
.. object:: To Channel
Which channel should we rescale all the other channels to?
.. object:: Use mixture model?
If this is set, the module will try to separate the data using a
mixture-of-Gaussians, then only compute the translation using the higher
population. This is the kind of behavior that you see in a transient
transfection in mammalian cells, for example.
.. object:: Translation list
Each pair of channels must have a multi-color control from which to
compute the scaling factor.
.. plot::
:context: close-figs
:include-source: False
color_op = flow.ColorTranslationOp()
color_op.controls = {("Pacific Blue-A", "FITC-A") : "tasbe/rby.fcs",
("PE-Tx-Red-YG-A", "FITC-A") : "tasbe/rby.fcs"}
color_op.mixture_model = True
color_op.estimate(ex3)
color_op.default_view().plot(ex3)
ex4 = color_op.apply(ex3)
'''
from traits.api import provides, Property, List
from traitsui.api import View, Item, VGroup, ButtonEditor, FileEditor, HGroup, EnumEditor, Controller, CheckListEditor, TextEditor
from envisage.api import Plugin
from pyface.api import ImageResource
from cytoflow.operations.bead_calibration import BeadCalibrationOp
from ..view_plugins import ViewHandler
from ..editors import ColorTextEditor, InstanceHandlerEditor, VerticalListEditor, SubsetListEditor
from ..subset_controllers import subset_handler_factory
from ..workflow.operations import TasbeWorkflowOp, TasbeWorkflowView
from .i_op_plugin import IOperationPlugin, OP_PLUGIN_EXT
from .op_plugin_base import OpHandler, shared_op_traits_view, PluginHelpMixin
[docs]class BleedthroughControlHandler(Controller):
control_view = View(HGroup(Item('channel', style = 'readonly'),
Item('file',
editor = FileEditor(dialog_style = 'open'),
show_label = False),
show_labels = False))
[docs]class TranslationControlHandler(Controller):
control_view = View(HGroup(Item('from_channel', style = 'readonly', show_label = False),
Item('', label = '->'),
Item('to_channel', style = 'readonly', show_label = False),
Item('file',
editor = FileEditor(dialog_style = 'open'),
show_label = False),
show_labels = False))
[docs]class UnitHandler(Controller):
unit_view = View(HGroup(Item('channel', style = 'readonly', show_label = False),
Item('unit',
editor = EnumEditor(name = 'context_handler.beads_units'),
show_label = False)))
[docs]class TasbeHandler(OpHandler):
beads_name_choices = Property(transient = True)
beads_units = Property(observe = 'model.beads_name')
def _get_beads_name_choices(self):
return list(BeadCalibrationOp.BEADS.keys())
def _get_beads_units(self):
if self.model.beads_name:
return list(BeadCalibrationOp.BEADS[self.model.beads_name].keys())
else:
return []
operation_traits_view = \
View(Item("channels",
editor = CheckListEditor(cols = 2,
name = 'context_handler.previous_channels'),
style = 'custom'),
VGroup(
Item('blank_file',
editor = FileEditor(dialog_style = 'open')),
label = "Autofluorescence"),
VGroup(
Item('bleedthrough_list',
editor = VerticalListEditor(editor = InstanceHandlerEditor(view = 'control_view',
handler_factory = BleedthroughControlHandler),
style = 'custom',
mutable = False)),
label = "Bleedthrough Correction",
show_border = False,
show_labels = False),
VGroup(
Item('beads_name',
editor = EnumEditor(name = 'handler.beads_name_choices'),
label = "Beads",
width = -125),
Item('beads_file',
editor = FileEditor(dialog_style = 'open')),
Item('beads_unit',
editor = EnumEditor(name = 'handler.beads_units'),
visible_when = 'do_color_translation == True'),
Item('units_list',
editor = VerticalListEditor(editor = InstanceHandlerEditor(view = 'unit_view',
handler_factory = UnitHandler),
style = 'custom',
mutable = False),
label = "Bead\nunits",
visible_when = 'do_color_translation == False'),
Item('bead_peak_quantile',
editor = TextEditor(auto_set = False,
evaluate = int,
format_func = lambda x: "" if x is None else str(x),
placeholder = "None"),
label = "Peak\nQuantile"),
Item('bead_brightness_threshold',
editor = TextEditor(auto_set = False,
evaluate = float,
format_func = lambda x: "" if x is None else str(x),
placeholder = "None"),
label = "Peak\nThreshold "),
Item('bead_brightness_cutoff',
editor = TextEditor(auto_set = False,
evaluate = float,
format_func = lambda x: "" if x is None else str(x),
placeholder = "None"),
label = "Peak\nCutoff"),
label = "Bead Calibration",
show_border = False),
VGroup(
Item('do_color_translation', label = 'Do color translation?'),
Item('to_channel',
editor = EnumEditor(name = 'channels'),
visible_when = 'do_color_translation == True'),
Item('mixture_model',
label = "Use mixture\nmodel?",
visible_when = 'do_color_translation == True'),
label = "Color Translation"),
VGroup(
Item('translation_list',
editor = VerticalListEditor(editor = InstanceHandlerEditor(view = 'control_view',
handler_factory = TranslationControlHandler),
style = 'custom',
mutable = False),
visible_when = 'do_color_translation == True'),
show_labels = 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))),
label = "Subset",
show_border = False,
show_labels = False),
Item('estimate_progress', style = 'readonly'),
Item('do_estimate',
editor = ButtonEditor(value = True,
label = "Estimate!"),
show_label = False),
shared_op_traits_view)
[docs]class TasbeViewHandler(ViewHandler):
view_traits_view = \
View(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()
[docs]@provides(IOperationPlugin)
class TasbePlugin(Plugin, PluginHelpMixin):
id = 'edu.mit.synbio.cytoflowgui.op_plugins.tasbe'
operation_id = 'edu.mit.synbio.cytoflowgui.workflow.operations.tasbe'
view_id = 'edu.mit.synbio.cytoflowgui.workflow.operations.tasbeview'
short_name = "TASBE Calibration"
menu_group = "Gates"
[docs] def get_operation(self):
return TasbeWorkflowOp()
[docs] def get_handler(self, model, context):
if isinstance(model, TasbeWorkflowOp):
return TasbeHandler(model = model, context = context)
elif isinstance(model, TasbeWorkflowView):
return TasbeViewHandler(model = model, context = context)
[docs] def get_icon(self):
return ImageResource('tasbe')
plugin = List(contributes_to = OP_PLUGIN_EXT)
def _plugin_default(self):
return [self]