Source code for cytoflowgui.workflow.operations.bead_calibration

#!/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)