#!/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/>.
"""
cytoflowgui.workflow.operations.bead_calibration
------------------------------------------------
"""
from traits.api import (HasTraits, provides, Str, observe, Instance,
List, Dict, File, Float, Int, Callable)
from cytoflow.operations.bead_calibration import BeadCalibrationOp, BeadCalibrationDiagnostic
import cytoflow.utility as util
from .. import Changed
from ..views import IWorkflowView, WorkflowView
from ..serialization import camel_registry, traits_str, traits_repr, dedent
from .operation_base import IWorkflowOperation, WorkflowOperation
BeadCalibrationOp.__repr__ = traits_repr
[docs]class Unit(HasTraits):
channel = Str
unit = Str
def __repr__(self):
return traits_repr(self)
[docs]@provides(IWorkflowOperation)
class BeadCalibrationWorkflowOp(WorkflowOperation, BeadCalibrationOp):
# add the 'estimate' metadata
beads_name = Str(estimate = True)
beads_file = File(filter = ["*.fcs"], estimate = True)
units_list = List(Unit, estimate = True)
bead_peak_quantile = Int(80, estimate = True)
bead_brightness_threshold = Float(100.0, estimate = True)
bead_brightness_cutoff = util.FloatOrNone(None, estimate = True)
# add 'estimate_result' metadata
_calibration_functions = Dict(Str, Callable, transient = True, estimate_result = True)
@observe('units_list:items,units_list:items.+type', post_init = True)
def _on_units_changed(self, _):
self.changed = 'units_list'
[docs] def default_view(self, **kwargs):
return BeadCalibrationWorkflowView(op = self, **kwargs)
[docs] def apply(self, experiment):
if not self.beads_name:
raise util.CytoflowOpError("Specify which beads to calibrate with.")
self.beads = self.BEADS[self.beads_name]
for i, unit_i in enumerate(self.units_list):
for j, unit_j in enumerate(self.units_list):
if unit_i.channel == unit_j.channel and i != j:
raise util.CytoflowOpError("Channel {0} is included more than once"
.format(unit_i.channel))
self.units = {u.channel : u.unit for u in self.units_list}
return super().apply(experiment)
[docs] def estimate(self, experiment):
if not self.beads_name:
raise util.CytoflowOpError("Specify which beads to calibrate with.")
self.beads = self.BEADS[self.beads_name]
for i, unit_i in enumerate(self.units_list):
for j, unit_j in enumerate(self.units_list):
if unit_i.channel == unit_j.channel and i != j:
raise util.CytoflowOpError("Channel {0} is included more than once"
.format(unit_i.channel))
self.units = {u.channel : u.unit for u in self.units_list}
super().estimate(experiment)
[docs] def should_clear_estimate(self, changed, payload):
if changed == Changed.ESTIMATE:
return True
return False
[docs] def clear_estimate(self):
self._peaks = {}
self._mefs = {}
self._histograms = {}
self._calibration_functions = {}
[docs] def get_notebook_code(self, idx):
op = BeadCalibrationOp()
op.copy_traits(self, op.copyable_trait_names())
for unit in self.units_list:
op.units[unit.channel] = unit.unit
op.beads = self.BEADS[self.beads_name]
return dedent("""
# Beads: {beads}
op_{idx} = {repr}
op_{idx}.estimate(ex_{prev_idx})
ex_{idx} = op_{idx}.apply(ex_{prev_idx})
"""
.format(beads = self.beads_name,
repr = repr(op),
idx = idx,
prev_idx = idx - 1))
[docs]@provides(IWorkflowView)
class BeadCalibrationWorkflowView(WorkflowView, BeadCalibrationDiagnostic):
plot_params = Instance(HasTraits, ())
[docs] def should_plot(self, changed, payload):
if changed == Changed.ESTIMATE_RESULT:
return True
return False
[docs] def get_notebook_code(self, idx):
view = BeadCalibrationDiagnostic()
view.copy_traits(self, view.copyable_trait_names())
return dedent("""
op_{idx}.default_view({traits}).plot(ex_{prev_idx})
"""
.format(traits = traits_str(view),
idx = idx,
prev_idx = idx - 1))
### Serialization
@camel_registry.dumper(BeadCalibrationWorkflowOp, 'bead-calibration', version = 1)
def _dump(bead_op):
return dict(beads_name = bead_op.beads_name,
beads_file = bead_op.beads_file,
units_list = bead_op.units_list,
bead_peak_quantile = bead_op.bead_peak_quantile,
bead_brightness_threshold = bead_op.bead_brightness_threshold,
bead_brightness_cutoff = bead_op.bead_brightness_cutoff)
@camel_registry.loader('bead-calibration', version = 1)
def _load(data, version):
if data['beads_name'] not in BeadCalibrationOp.BEADS:
import warnings
warnings.warn('The available bead data has changed recently; please re-select your beads.')
data['beads_name'] = ""
return BeadCalibrationWorkflowOp(**data)
@camel_registry.dumper(Unit, 'bead-unit', version = 1)
def _dump_unit(unit):
return dict(channel = unit.channel,
unit = unit.unit)
@camel_registry.loader('bead-unit', version = 1)
def _load_unit(data, version):
return Unit(**data)
@camel_registry.dumper(BeadCalibrationWorkflowView, 'bead-calibration-view', version = 1)
def _dump_view(view):
return dict(op = view.op)
@camel_registry.loader('bead-calibration-view', version = 1)
def _load_view(data, version):
return BeadCalibrationWorkflowView(**data)