#!/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.color_translation
-------------------------------------------------
"""
import warnings
from traits.api import (HasTraits, provides, Str, observe, Event, Bool, Instance,
List, Dict, File, Property, Tuple, Constant, Any)
from cytoflow.operations.color_translation import ColorTranslationOp, ColorTranslationDiagnostic
import cytoflow.utility as util
from .. import Changed
from ..views import IWorkflowView, WorkflowView
from ..serialization import camel_registry, traits_str, traits_repr, dedent
from ..subset import ISubset
from .operation_base import IWorkflowOperation, WorkflowOperation
ColorTranslationOp.__repr__ = traits_repr
[docs]class Control(HasTraits):
from_channel = Str
to_channel = Str
file = File
def __repr__(self):
return traits_repr(self)
[docs]@provides(IWorkflowOperation)
class ColorTranslationWorkflowOp(WorkflowOperation, ColorTranslationOp):
add_control = Event
remove_control = Event
# add some metadata
controls = Dict(Tuple(Str, Str), File, transient = True)
controls_list = List(Control, estimate = True)
mixture_model = Bool(False, estimate = True)
translation = Constant(None)
_coefficients = Dict(Tuple(Str, Str), Any, transient = True, estimate_result = True)
@observe('controls_list:items,controls_list:items.+type', post_init = True)
def _on_controls_changed(self, _):
self.changed = 'controls_list'
# override the base class's "subset" with one that is dynamically generated /
# updated from subset_list
subset = Property(Str, observe = "subset_list.items.str")
subset_list = List(ISubset, estimate = True)
# bits to support the subset editor
@observe('subset_list:items.str')
def _on_subset_changed(self, _):
self.changed = 'subset_list'
# MAGIC - returns the value of the "subset" Property, above
def _get_subset(self):
return " and ".join([subset.str for subset in self.subset_list if subset.str])
[docs] def default_view(self, **kwargs):
return ColorTranslationWorkflowView(op = self, **kwargs)
[docs] def estimate(self, experiment):
for i, control_i in enumerate(self.controls_list):
for j, control_j in enumerate(self.controls_list):
if control_i.from_channel == control_j.from_channel and i != j:
raise util.CytoflowOpError("Channel {0} is included more than once"
.format(control_i.from_channel))
# check for experiment metadata used to estimate operations in the
# history, and bail if we find any
for op in experiment.history:
if hasattr(op, 'by'):
for by in op.by:
if 'experiment' in experiment.metadata[by]:
raise util.CytoflowOpError('experiment',
"Prior to applying this operation, "
"you must not apply any operation with 'by' "
"set to an experimental condition.")
self.controls = {}
for control in self.controls_list:
self.controls[(control.from_channel, control.to_channel)] = control.file
if not self.subset:
warnings.warn("Are you sure you don't want to specify a subset "
"used to estimate the model?",
util.CytoflowOpWarning)
super().estimate(experiment, subset = self.subset)
[docs] def apply(self, experiment):
if not self._coefficients:
raise util.CytoflowOpError(None, 'Click "Estimate"!')
return super().apply(experiment)
[docs] def should_clear_estimate(self, changed, payload):
if changed == Changed.ESTIMATE:
return True
return False
[docs] def clear_estimate(self):
self._coefficients = {}
self._trans_fn.clear()
self._sample.clear()
self._means.clear()
[docs] def get_notebook_code(self, idx):
op = ColorTranslationOp()
op.copy_traits(self, op.copyable_trait_names())
for control in self.controls_list:
op.controls[(control.from_channel, control.to_channel)] = control.file
return dedent("""
op_{idx} = {repr}
op_{idx}.estimate(ex_{prev_idx}{subset})
ex_{idx} = op_{idx}.apply(ex_{prev_idx})
"""
.format(repr = repr(op),
idx = idx,
prev_idx = idx - 1,
subset = ", subset = " + repr(self.subset) if self.subset else ""))
[docs]@provides(IWorkflowView)
class ColorTranslationWorkflowView(WorkflowView, ColorTranslationDiagnostic):
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 = ColorTranslationDiagnostic()
view.copy_traits(self, view.copyable_trait_names())
view.subset = self.subset
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(ColorTranslationWorkflowOp, 'color-translation', version = 1)
def _dump(op):
return dict(controls_list = op.controls_list,
mixture_model = op.mixture_model,
subset_list = op.subset_list)
@camel_registry.loader('color-translation', version = 1)
def _load(data, version):
return ColorTranslationWorkflowOp(**data)
@camel_registry.dumper(Control, 'color-translation-control', version = 1)
def _dump_control(c):
return dict(from_channel = c.from_channel,
to_channel = c.to_channel,
file = c.file)
@camel_registry.loader('color-translation-control', version = 1)
def _load_control(data, version):
return Control(**data)
@camel_registry.dumper(ColorTranslationWorkflowView, 'color-translation-view', version = 1)
def _dump_view(view):
return dict(op = view.op)
@camel_registry.loader('color-translation-view', version = 1)
def _load_view(data, ver):
return ColorTranslationWorkflowView(**data)