#!/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/>.
'''
Bead Calibration
----------------
Calibrate arbitrary channels to molecules-of-fluorophore using fluorescent
beads (eg, the **Spherotech RCP-30-5A** rainbow beads.)
Computes a log-linear calibration function that maps arbitrary fluorescence
units to physical units (ie molecules equivalent fluorophore, or *MEF*).
To use, set **Beads** to the beads you calibrated with (check the lot!) and
**Beads File** to an FCS file containing events collected *using
the same cytometer settings as the data you're calibrating*. Then, click
**Add a channel** to add the channels to calibrate, and set both the channel
name and the units you want calibrate to. Click **Estimate**, and *make sure
you check the diagnostic plot to see that the correct peaks were found.*
If it didn't find all the peaks (or found too many), try tweaking
**Peak Quantile**, **Peak Threshold** and **Peak Cutoff**. If you can't make
the peak finding work by tweaking , please submit a bug report!
.. object:: Beads
The beads you're calibrating with. Make sure to check the lot number!
.. object:: Beads file
A file containing the FCS events from the beads.
.. object:: Channels
A list of the channels you want calibrated and the units you want them
calibrated in.
.. object:: Peak Quantile
Peaks must be at least this quantile high to be considered. Default = 80.
.. object:: Peak Threshold
Don't search for peaks below this brightness. Default = 100.
.. object: Peak Cutoff
Don't search for peaks above this brightness. Default: 70% of detector range.
.. 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()
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(ex)
bead_op.default_view().plot(ex)
ex = bead_op.apply(ex)
'''
from natsort import natsorted
from traits.api import provides, Event, Property, List, Str
from traitsui.api import View, Item, VGroup, TextEditor, ButtonEditor, FileEditor, HGroup, EnumEditor, Controller
from envisage.api import Plugin
from pyface.api import ImageResource
from ..view_plugins import ViewHandler
from ..editors import ColorTextEditor, InstanceHandlerEditor, VerticalListEditor
from ..workflow.operations import BeadCalibrationWorkflowOp, BeadCalibrationWorkflowView, BeadCalibrationUnit
from .i_op_plugin import IOperationPlugin, OP_PLUGIN_EXT
from .op_plugin_base import OpHandler, shared_op_traits_view, PluginHelpMixin
[docs]class UnitHandler(Controller):
unit_view = View(HGroup(Item('channel',
editor = EnumEditor(name = 'context_handler.channels')),
Item('unit',
editor = EnumEditor(name = 'context_handler.beads_units'),
show_label = False)))
[docs]class BeadCalibrationHandler(OpHandler):
add_channel = Event
remove_channel = Event
channels = Property(List(Str), observe = 'context.channels')
beads_name_choices = Property
beads_units = Property(observe = 'model.beads_name')
operation_traits_view = \
View(Item('beads_name',
editor = EnumEditor(name = 'handler.beads_name_choices'),
label = "Beads",
width = -150), # these names are LONG -- constrain the width
Item('beads_file',
editor = FileEditor(dialog_style = 'open')),
VGroup(Item('units_list',
editor = VerticalListEditor(editor = InstanceHandlerEditor(view = 'unit_view',
handler_factory = UnitHandler),
style = 'custom',
mutable = False)),
Item('handler.add_channel',
editor = ButtonEditor(value = True,
label = "Add a channel")),
Item('handler.remove_channel',
editor = ButtonEditor(value = True,
label = "Remove a channel")),
label = "Channels",
show_labels = 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"),
Item('do_estimate',
editor = ButtonEditor(value = True,
label = "Estimate!"),
show_label = False),
shared_op_traits_view)
# MAGIC: called when add_control is set
def _add_channel_fired(self):
self.model.units_list.append(BeadCalibrationUnit())
def _remove_channel_fired(self):
if self.model.units_list:
self.model.units_list.pop()
def _get_channels(self):
if self.context and self.context.channels:
return natsorted(self.context.channels)
else:
return []
def _get_beads_name_choices(self):
return list(self.model.BEADS.keys())
def _get_beads_units(self):
if self.model.beads_name:
return list(self.model.BEADS[self.model.beads_name].keys())
else:
return []
[docs]class BeadCalibrationViewHandler(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 BeadCalibrationPlugin(Plugin, PluginHelpMixin):
id = 'edu.mit.synbio.cytoflowgui.op_plugins.beads_calibrate'
operation_id = 'edu.mit.synbio.cytoflow.operations.beads_calibrate'
view_id = 'edu.mit.synbio.cytoflow.view.beadcalibrationdiagnosticview'
short_name = "Bead Calibration"
menu_group = "Calibration"
[docs] def get_operation(self):
return BeadCalibrationWorkflowOp()
[docs] def get_handler(self, model, context):
if isinstance(model, BeadCalibrationWorkflowOp):
return BeadCalibrationHandler(model = model, context = context)
elif isinstance(model, BeadCalibrationWorkflowView):
return BeadCalibrationViewHandler(model = model, context = context)
[docs] def get_icon(self):
return ImageResource('bead_calibration')
plugin = List(contributes_to = OP_PLUGIN_EXT)
def _plugin_default(self):
return [self]