def clear_estimate(self):
self._af_op = AutofluorescenceOp()
self._bleedthrough_op = BleedthroughPiecewiseOp()
self._bead_calibration_op = BeadCalibrationOp()
self._color_translation_op = ColorTranslationOp()
self.changed = "estimate_result"
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)
try:
ColorTranslationOp.estimate(self, experiment, subset = self.subset)
except:
raise
finally:
self.changed = (Changed.ESTIMATE_RESULT, self)
def clear_estimate(self):
self._af_op = AutofluorescenceOp()
self._bleedthrough_op = BleedthroughLinearOp()
self._bead_calibration_op = BeadCalibrationOp()
self._color_translation_op = ColorTranslationOp()
self.changed = (Changed.ESTIMATE_RESULT, self)
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 ""))
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))
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)
ColorTranslationOp.estimate(self, experiment, subset=self.subset)
self.changed = "estimate_result"
class TasbePluginOp(PluginOpMixin):
handler_factory = Callable(TasbeHandler)
id = Constant(
'edu.mit.synbio.cytoflowgui.op_plugins.bleedthrough_piecewise')
friendly_id = Constant("Quantitative Pipeline")
name = Constant("TASBE")
channels = List(Str, estimate=True)
blank_file = File(filter=["*.fcs"], estimate=True)
bleedthrough_list = List(_BleedthroughControl, estimate=True)
beads_name = Str(estimate=True)
beads_file = File(filter=["*.fcs"], estimate=True)
beads_unit = Str(estimate=True)
bead_peak_quantile = Int(80, estimate=True)
bead_brightness_threshold = Float(100, estimate=True)
bead_brightness_cutoff = Float(Undefined, estimate=True)
to_channel = Str(estimate=True)
translation_list = List(_TranslationControl, estimate=True)
mixture_model = Bool(False, estimate=True)
_af_op = Instance(AutofluorescenceOp, (), transient=True)
_bleedthrough_op = Instance(BleedthroughLinearOp, (), transient=True)
_bead_calibration_op = Instance(BeadCalibrationOp, (), transient=True)
_color_translation_op = Instance(ColorTranslationOp, (), transient=True)
subset_list = List(ISubset, estimate=True)
subset = Property(Str, depends_on="subset_list.str")
# 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])
@on_trait_change("subset_list.str", post_init=True)
def _subset_changed(self, obj, name, old, new):
self.changed = (Changed.ESTIMATE, ('subset_list', self.subset_list))
@on_trait_change('channels[]', post_init=True)
def _channels_changed(self, obj, name, old, new):
self.bleedthrough_list = []
for c in self.channels:
self.bleedthrough_list.append(_BleedthroughControl(channel=c))
self.changed = (Changed.ESTIMATE, ('bleedthrough_list',
self.bleedthrough_list))
self.translation_list = []
if self.to_channel:
for c in self.channels:
if c == self.to_channel:
continue
self.translation_list.append(
_TranslationControl(from_channel=c,
to_channel=self.to_channel))
self.changed = (Changed.ESTIMATE, ('translation_list',
self.translation_list))
@on_trait_change('to_channel', post_init=True)
def _to_channel_changed(self, obj, name, old, new):
self.translation_list = []
if self.to_channel:
for c in self.channels:
if c == self.to_channel:
continue
self.translation_list.append(
_TranslationControl(from_channel=c,
to_channel=self.to_channel))
self.changed = (Changed.ESTIMATE, ('translation_list',
self.translation_list))
@on_trait_change("bleedthrough_list_items, bleedthrough_list.+",
post_init=True)
def _bleedthrough_controls_changed(self, obj, name, old, new):
self.changed = (Changed.ESTIMATE, ('bleedthrough_list',
self.bleedthrough_list))
@on_trait_change("translation_list_items, translation_list.+",
post_init=True)
def _translation_controls_changed(self, obj, name, old, new):
self.changed = (Changed.ESTIMATE, ('translation_list',
self.translation_list))
def estimate(self, experiment, subset=None):
if not self.subset:
warnings.warn(
"Are you sure you don't want to specify a subset "
"used to estimate the model?", util.CytoflowOpWarning)
if experiment is None:
raise util.CytoflowOpError("No valid result to estimate with")
experiment = experiment.clone()
self._af_op.channels = self.channels
self._af_op.blank_file = self.blank_file
self._af_op.estimate(experiment, subset=self.subset)
self.changed = (Changed.ESTIMATE_RESULT, self)
experiment = self._af_op.apply(experiment)
self._bleedthrough_op.controls.clear()
for control in self.bleedthrough_list:
self._bleedthrough_op.controls[control.channel] = control.file
self._bleedthrough_op.estimate(experiment, subset=self.subset)
self.changed = (Changed.ESTIMATE_RESULT, self)
experiment = self._bleedthrough_op.apply(experiment)
self._bead_calibration_op.beads = BeadCalibrationOp.BEADS[
self.beads_name]
self._bead_calibration_op.beads_file = self.beads_file
self._bead_calibration_op.bead_peak_quantile = self.bead_peak_quantile
self._bead_calibration_op.bead_brightness_threshold = self.bead_brightness_threshold
self._bead_calibration_op.bead_brightness_cutoff = self.bead_brightness_cutoff
self._bead_calibration_op.units.clear()
# this is the old way
# for channel in self.channels:
# self._bead_calibration_op.units[channel] = self.beads_unit
# this way matches TASBE better
self._bead_calibration_op.units[self.to_channel] = self.beads_unit
self._bead_calibration_op.estimate(experiment)
self.changed = (Changed.ESTIMATE_RESULT, self)
experiment = self._bead_calibration_op.apply(experiment)
self._color_translation_op.mixture_model = self.mixture_model
self._color_translation_op.controls.clear()
for control in self.translation_list:
self._color_translation_op.controls[(
control.from_channel, control.to_channel)] = control.file
self._color_translation_op.estimate(experiment, subset=self.subset)
self.changed = (Changed.ESTIMATE_RESULT, self)
def should_clear_estimate(self, changed):
if changed == Changed.ESTIMATE:
return True
return False
def clear_estimate(self):
self._af_op = AutofluorescenceOp()
self._bleedthrough_op = BleedthroughLinearOp()
self._bead_calibration_op = BeadCalibrationOp()
self._color_translation_op = ColorTranslationOp()
self.changed = (Changed.ESTIMATE_RESULT, self)
def apply(self, experiment):
if experiment is None:
raise util.CytoflowOpError("No experiment was specified")
experiment = self._af_op.apply(experiment)
experiment = self._bleedthrough_op.apply(experiment)
experiment = self._bead_calibration_op.apply(experiment)
experiment = self._color_translation_op.apply(experiment)
return experiment
def default_view(self, **kwargs):
return TasbePluginView(op=self, **kwargs)
class TasbePluginOp(PluginOpMixin):
handler_factory = Callable(TasbeHandler)
id = Constant('edu.mit.synbio.cytoflowgui.op_plugins.bleedthrough_piecewise')
friendly_id = Constant("Quantitative Pipeline")
name = Constant("TASBE")
channels = List(Str, estimate = True)
blank_file = File(filter = ["*.fcs"], estimate = True)
bleedthrough_list = List(_BleedthroughControl, estimate = True)
beads_name = Str(estimate = True)
beads_file = File(filter = ["*.fcs"], estimate = True)
beads_unit = Str(estimate = True)
bead_peak_quantile = CInt(80, estimate = True)
bead_brightness_threshold = CFloat(100.0, estimate = True)
bead_brightness_cutoff = util.CFloatOrNone(None, estimate = True)
to_channel = Str(estimate = True)
translation_list = List(_TranslationControl, estimate = True)
mixture_model = Bool(False, estimate = True)
_af_op = Instance(AutofluorescenceOp, (), transient = True)
_bleedthrough_op = Instance(BleedthroughLinearOp, (), transient = True)
_bead_calibration_op = Instance(BeadCalibrationOp, (), transient = True)
_color_translation_op = Instance(ColorTranslationOp, (), transient = True)
subset_list = List(ISubset, estimate = True)
subset = Property(Str, depends_on = "subset_list.str")
# 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])
@on_trait_change("subset_list.str")
def _subset_changed(self, obj, name, old, new):
self.changed = (Changed.ESTIMATE, ('subset_list', self.subset_list))
@on_trait_change('channels[]', post_init = True)
def _channels_changed(self, obj, name, old, new):
for channel in self.channels:
if channel not in [control.channel for control in self.bleedthrough_list]:
self.bleedthrough_list.append(_BleedthroughControl(channel = channel))
to_remove = []
for control in self.bleedthrough_list:
if control.channel not in self.channels:
to_remove.append(control)
for control in to_remove:
self.bleedthrough_list.remove(control)
for c in self.channels:
if c == self.to_channel:
continue
if channel not in [control.from_channel for control in self.translation_list]:
self.translation_list.append(_TranslationControl(from_channel = c,
to_channel = self.to_channel))
to_remove = []
for control in self.translation_list:
if control.from_channel not in self.channels:
to_remove.append(control)
for control in to_remove:
self.translation_list.remove(control)
self.changed = (Changed.ESTIMATE, ('translation_list', self.translation_list))
self.changed = (Changed.ESTIMATE, ('bleedthrough_list', self.bleedthrough_list))
@on_trait_change('to_channel', post_init = True)
def _to_channel_changed(self, obj, name, old, new):
self.translation_list = []
if self.to_channel:
for c in self.channels:
if c == self.to_channel:
continue
self.translation_list.append(_TranslationControl(from_channel = c,
to_channel = self.to_channel))
self.changed = (Changed.ESTIMATE, ('translation_list', self.translation_list))
@on_trait_change("bleedthrough_list_items, bleedthrough_list.+", post_init = True)
def _bleedthrough_controls_changed(self, obj, name, old, new):
self.changed = (Changed.ESTIMATE, ('bleedthrough_list', self.bleedthrough_list))
@on_trait_change("translation_list_items, translation_list.+", post_init = True)
def _translation_controls_changed(self, obj, name, old, new):
self.changed = (Changed.ESTIMATE, ('translation_list', self.translation_list))
def estimate(self, experiment, subset = None):
if not self.subset:
warnings.warn("Are you sure you don't want to specify a subset "
"used to estimate the model?",
util.CytoflowOpWarning)
if experiment is None:
raise util.CytoflowOpError("No valid result to estimate with")
# TODO - don't actually need to apply these operations to data in estimate
experiment = experiment.clone()
self._af_op.channels = self.channels
self._af_op.blank_file = self.blank_file
try:
self._af_op.estimate(experiment, subset = self.subset)
except:
raise
finally:
self.changed = (Changed.ESTIMATE_RESULT, self)
experiment = self._af_op.apply(experiment)
self._bleedthrough_op.controls.clear()
for control in self.bleedthrough_list:
self._bleedthrough_op.controls[control.channel] = control.file
try:
self._bleedthrough_op.estimate(experiment, subset = self.subset)
except:
raise
finally:
self.changed = (Changed.ESTIMATE_RESULT, self)
experiment = self._bleedthrough_op.apply(experiment)
self._bead_calibration_op.beads = BeadCalibrationOp.BEADS[self.beads_name]
self._bead_calibration_op.beads_file = self.beads_file
self._bead_calibration_op.bead_peak_quantile = self.bead_peak_quantile
self._bead_calibration_op.bead_brightness_threshold = self.bead_brightness_threshold
self._bead_calibration_op.bead_brightness_cutoff = self.bead_brightness_cutoff
self._bead_calibration_op.units.clear()
# this is the old way
# for channel in self.channels:
# self._bead_calibration_op.units[channel] = self.beads_unit
# this way matches TASBE better
self._bead_calibration_op.units[self.to_channel] = self.beads_unit
try:
self._bead_calibration_op.estimate(experiment)
except:
raise
finally:
self.changed = (Changed.ESTIMATE_RESULT, self)
experiment = self._bead_calibration_op.apply(experiment)
self._color_translation_op.mixture_model = self.mixture_model
self._color_translation_op.controls.clear()
for control in self.translation_list:
self._color_translation_op.controls[(control.from_channel,
control.to_channel)] = control.file
try:
self._color_translation_op.estimate(experiment, subset = self.subset)
except:
raise
finally:
self.changed = (Changed.ESTIMATE_RESULT, self)
def should_clear_estimate(self, changed, payload):
if changed == Changed.ESTIMATE:
return True
return False
def clear_estimate(self):
self._af_op = AutofluorescenceOp()
self._bleedthrough_op = BleedthroughLinearOp()
self._bead_calibration_op = BeadCalibrationOp()
self._color_translation_op = ColorTranslationOp()
self.changed = (Changed.ESTIMATE_RESULT, self)
def apply(self, experiment):
if experiment is None:
raise util.CytoflowOpError("No experiment was specified")
experiment = self._af_op.apply(experiment)
experiment = self._bleedthrough_op.apply(experiment)
experiment = self._bead_calibration_op.apply(experiment)
experiment = self._color_translation_op.apply(experiment)
return experiment
def default_view(self, **kwargs):
return TasbePluginView(op = self, **kwargs)
def get_notebook_code(self, idx):
self._af_op.channels = self.channels
self._af_op.blank_file = self.blank_file
self._bleedthrough_op.controls.clear()
for control in self.bleedthrough_list:
self._bleedthrough_op.controls[control.channel] = control.file
self._bead_calibration_op.beads = BeadCalibrationOp.BEADS[self.beads_name]
self._bead_calibration_op.beads_file = self.beads_file
self._bead_calibration_op.bead_peak_quantile = self.bead_peak_quantile
self._bead_calibration_op.bead_brightness_threshold = self.bead_brightness_threshold
self._bead_calibration_op.bead_brightness_cutoff = self.bead_brightness_cutoff
self._bead_calibration_op.units.clear()
self._bead_calibration_op.units[self.to_channel] = self.beads_unit
self._color_translation_op.mixture_model = self.mixture_model
self._color_translation_op.controls.clear()
for control in self.translation_list:
self._color_translation_op.controls[(control.from_channel,
control.to_channel)] = control.file
return dedent("""
# the TASBE-style calibration is not a single Cytoflow module. Instead, it
# is a specific sequence of four calibrations: autofluorescence correction,
# bleedthrough, bead calibration and color translation.
# autofluorescence
op_{idx}_af = {af_repr}
op_{idx}_af.estimate(ex_{prev_idx}{subset})
ex_{idx}_af = op_{idx}_af.apply(ex_{prev_idx})
# bleedthrough
op_{idx}_bleedthrough = {bleedthrough_repr}
op_{idx}_bleedthrough.estimate(ex_{idx}_af{subset})
ex_{idx}_bleedthrough = op_{idx}_bleedthrough.apply(ex_{idx}_af)
# bead calibration
# beads: {beads}
op_{idx}_beads = {beads_repr}
op_{idx}_beads.estimate(ex_{idx}_bleedthrough)
ex_{idx}_beads = op_{idx}_beads.apply(ex_{idx}_bleedthrough)
# color translation
op_{idx}_color = {color_repr}
op_{idx}_color.estimate(ex_{idx}_beads{subset})
ex_{idx} = op_{idx}_color.apply(ex_{idx}_beads)
"""
.format(idx = idx,
prev_idx = idx - 1,
af_repr = repr(self._af_op),
bleedthrough_repr = repr(self._bleedthrough_op),
color_repr = repr(self._color_translation_op),
beads = self.beads_name,
beads_repr = repr(self._bead_calibration_op),
subset = ", subset = " + repr(self.subset) if self.subset else ""))
class TasbePluginOp(PluginOpMixin):
handler_factory = Callable(TasbeHandler)
id = Constant('edu.mit.synbio.cytoflowgui.op_plugins.bleedthrough_piecewise')
friendly_id = Constant("Quantitative Pipeline")
name = Constant("TASBE")
channels = List(Str, estimate = True)
blank_file = File(filter = ["*.fcs"], estimate = True)
bleedthrough_list = List(_BleedthroughControl, estimate = True)
beads_name = Str(estimate = True)
beads_file = File(filter = ["*.fcs"], estimate = True)
beads_unit = Str(estimate = True)
bead_peak_quantile = Int(80, estimate = True)
bead_brightness_threshold = Float(100, estimate = True)
bead_brightness_cutoff = Float(Undefined, estimate = True)
to_channel = Str(estimate = True)
translation_list = List(_TranslationControl, estimate = True)
mixture_model = Bool(False, estimate = True)
_af_op = Instance(AutofluorescenceOp, (), transient = True)
_bleedthrough_op = Instance(BleedthroughPiecewiseOp, (), transient = True)
_bead_calibration_op = Instance(BeadCalibrationOp, (), transient = True)
_color_translation_op = Instance(ColorTranslationOp, (), transient = True)
@on_trait_change('channels[]', post_init = True)
def _channels_changed(self, obj, name, old, new):
self.bleedthrough_list = []
for c in self.channels:
self.bleedthrough_list.append(_BleedthroughControl(channel = c))
self.translation_list = []
if self.to_channel:
for c in self.channels:
if c == self.to_channel:
continue
self.translation_list.append(_TranslationControl(from_channel = c,
to_channel = self.to_channel))
self.changed = "estimate"
@on_trait_change('to_channel', post_init = True)
def _to_channel_changed(self, obj, name, old, new):
self.translation_list = []
if self.to_channel:
for c in self.channels:
if c == self.to_channel:
continue
self.translation_list.append(_TranslationControl(from_channel = c,
to_channel = self.to_channel))
def estimate(self, experiment, subset = None):
if not self.subset:
warnings.warn("Are you sure you don't want to specify a subset "
"used to estimate the model?",
util.CytoflowOpWarning)
experiment = experiment.clone()
self._af_op.channels = self.channels
self._af_op.blank_file = self.blank_file
self._af_op.estimate(experiment, subset = self.subset)
self.changed = "estimate_result"
experiment = self._af_op.apply(experiment)
self._bleedthrough_op.controls.clear()
for control in self.bleedthrough_list:
self._bleedthrough_op.controls[control.channel] = control.file
self._bleedthrough_op.estimate(experiment, subset = self.subset)
self.changed = "estimate_result"
experiment = self._bleedthrough_op.apply(experiment)
self._bead_calibration_op.beads = BeadCalibrationOp.BEADS[self.beads_name]
self._bead_calibration_op.beads_file = self.beads_file
self._bead_calibration_op.bead_peak_quantile = self.bead_peak_quantile
self._bead_calibration_op.bead_brightness_threshold = self.bead_brightness_threshold
self._bead_calibration_op.bead_brightness_cutoff = self.bead_brightness_cutoff
self._bead_calibration_op.units.clear()
for channel in self.channels:
self._bead_calibration_op.units[channel] = self.beads_unit
self._bead_calibration_op.estimate(experiment)
self.changed = "estimate_result"
experiment = self._bead_calibration_op.apply(experiment)
self._color_translation_op.mixture_model = self.mixture_model
self._color_translation_op.controls.clear()
for control in self.translation_list:
self._color_translation_op.controls[(control.from_channel,
control.to_channel)] = control.file
self._color_translation_op.estimate(experiment, subset = self.subset)
self.changed = "estimate_result"
def should_clear_estimate(self, changed):
"""
Should the owning WorkflowItem clear the estimated model by calling
op.clear_estimate()? `changed` can be:
- "estimate" -- the parameters required to call 'estimate()' (ie
traits with estimate = True metadata) have changed
- "prev_result" -- the previous WorkflowItem's result changed
"""
if changed == "prev_result":
return False
return True
def clear_estimate(self):
self._af_op = AutofluorescenceOp()
self._bleedthrough_op = BleedthroughPiecewiseOp()
self._bead_calibration_op = BeadCalibrationOp()
self._color_translation_op = ColorTranslationOp()
self.changed = "estimate_result"
def apply(self, experiment):
experiment = self._af_op.apply(experiment)
experiment = self._bleedthrough_op.apply(experiment)
experiment = self._bead_calibration_op.apply(experiment)
experiment = self._color_translation_op.apply(experiment)
return experiment
def default_view(self, **kwargs):
return TasbePluginView(op = self, **kwargs)
class TasbeWorkflowOp(WorkflowOperation):
id = Constant('edu.mit.synbio.cytoflowgui.workflow.operations.tasbe')
friendly_id = Constant("Quantitative Pipeline")
name = Constant("TASBE")
channels = List(Str, estimate=True)
blank_file = File(filter=["*.fcs"], estimate=True)
bleedthrough_list = List(BleedthroughControl, estimate=True)
beads_name = Str(estimate=True)
beads_file = File(filter=["*.fcs"], estimate=True)
beads_unit = Str(estimate=True) # used if do_color_translation is True
units_list = List(BeadUnit,
estimate=True) # used if do_color_translation is False
bead_peak_quantile = Int(80, estimate=True)
bead_brightness_threshold = Float(100.0, estimate=True)
bead_brightness_cutoff = util.FloatOrNone(None, estimate=True)
do_color_translation = Bool(False, estimate=True)
to_channel = Str(estimate=True)
translation_list = List(TranslationControl, estimate=True)
mixture_model = Bool(False, estimate=True)
_af_op = Instance(AutofluorescenceOp, (), transient=True)
_bleedthrough_op = Instance(BleedthroughLinearOp, (), transient=True)
_bead_calibration_op = Instance(BeadCalibrationOp, (), transient=True)
_color_translation_op = Instance(ColorTranslationOp, (), transient=True)
estimate_progress = Str(Progress.NO_MODEL,
transient=True,
estimate_result=True,
status=True)
# 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])
@observe('channels.items,to_channel,do_color_translation', post_init=True)
def _on_channels_changed(self, _):
# bleedthrough
for channel in self.channels:
if channel not in [
control.channel for control in self.bleedthrough_list
]:
self.bleedthrough_list.append(
BleedthroughControl(channel=channel))
to_remove = []
for control in self.bleedthrough_list:
if control.channel not in self.channels:
to_remove.append(control)
for control in to_remove:
self.bleedthrough_list.remove(control)
# bead calibration
for channel in self.channels:
if channel not in [unit.channel for unit in self.units_list]:
self.units_list.append(BeadUnit(channel=channel))
to_remove = []
for unit in self.units_list:
if unit.channel not in self.channels:
to_remove.append(unit)
for unit in to_remove:
self.units_list.remove(unit)
# color translation
if self.to_channel not in self.channels:
self.translation_list = []
self.to_channel = ''
return
for channel in self.channels:
if channel != self.to_channel:
if channel not in [
control.from_channel
for control in self.translation_list
]:
self.translation_list.append(
TranslationControl(from_channel=channel,
to_channel=self.to_channel))
to_remove = []
for control in self.translation_list:
if control.from_channel not in self.channels or \
control.to_channel not in self.channels:
to_remove.append(control)
for control in to_remove:
self.translation_list.remove(control)
@observe('to_channel', post_init=True)
def _on_to_channel_changed(self, _):
self.translation_list = []
if self.to_channel:
for c in self.channels:
if c == self.to_channel:
continue
self.translation_list.append(
TranslationControl(from_channel=c,
to_channel=self.to_channel))
@observe("bleedthrough_list:items:file", post_init=True)
def _bleedthrough_controls_changed(self, _):
self.changed = 'bleedthrough_list'
@observe("translation_list:items:file", post_init=True)
def _translation_controls_changed(self, _):
self.changed = 'translation_list'
@observe('units_list:items:unit', post_init=True)
def _on_units_changed(self, _):
self.changed = 'units_list'
def estimate(self, experiment, subset=None):
if not self.subset:
warnings.warn(
"Are you sure you don't want to specify a subset "
"used to estimate the model?", util.CytoflowOpWarning)
if experiment is None:
raise util.CytoflowOpError("No valid result to estimate with")
# TODO - don't actually need to apply these operations to data in estimate
experiment = experiment.clone()
self.estimate_progress = Progress.AUTOFLUORESCENCE
self._af_op.channels = self.channels
self._af_op.blank_file = self.blank_file
self._af_op.estimate(experiment, subset=self.subset)
experiment = self._af_op.apply(experiment)
self.estimate_progress = Progress.BLEEDTHROUGH
self._bleedthrough_op.controls.clear()
for control in self.bleedthrough_list:
self._bleedthrough_op.controls[control.channel] = control.file
self._bleedthrough_op.estimate(experiment, subset=self.subset)
experiment = self._bleedthrough_op.apply(experiment)
self.estimate_progress = Progress.BEAD_CALIBRATION
self._bead_calibration_op.beads = BeadCalibrationOp.BEADS[
self.beads_name]
self._bead_calibration_op.beads_file = self.beads_file
self._bead_calibration_op.bead_peak_quantile = self.bead_peak_quantile
self._bead_calibration_op.bead_brightness_threshold = self.bead_brightness_threshold
self._bead_calibration_op.bead_brightness_cutoff = self.bead_brightness_cutoff
if self.do_color_translation:
# this way matches TASBE better
self._bead_calibration_op.units.clear()
self._bead_calibration_op.units[self.to_channel] = self.beads_unit
self._bead_calibration_op.estimate(experiment)
experiment = self._bead_calibration_op.apply(experiment)
self.estimate_progress = Progress.COLOR_TRANSLATION
self._color_translation_op.mixture_model = self.mixture_model
self._color_translation_op.controls.clear()
for control in self.translation_list:
self._color_translation_op.controls[(
control.from_channel, control.to_channel)] = control.file
self._color_translation_op.estimate(experiment, subset=self.subset)
else:
self._bead_calibration_op.units.clear()
for unit in self.units_list:
self._bead_calibration_op.units[unit.channel] = unit.unit
self._bead_calibration_op.estimate(experiment)
experiment = self._bead_calibration_op.apply(experiment)
self.estimate_progress = Progress.VALID
def should_clear_estimate(self, changed, payload):
if changed == Changed.ESTIMATE:
return True
return False
def clear_estimate(self):
self._af_op = AutofluorescenceOp()
self._bleedthrough_op = BleedthroughLinearOp()
self._bead_calibration_op = BeadCalibrationOp()
self._color_translation_op = ColorTranslationOp()
self.estimate_progress = Progress.NO_MODEL
def apply(self, experiment):
if self.estimate_progress == Progress.NO_MODEL:
raise util.CytoflowOpError(None, 'Click "Estimate"!')
elif self.estimate_progress != Progress.VALID:
raise util.CytoflowOpError(None, 'No valid model')
experiment = self._af_op.apply(experiment)
experiment = self._bleedthrough_op.apply(experiment)
experiment = self._bead_calibration_op.apply(experiment)
if self.do_color_translation:
experiment = self._color_translation_op.apply(experiment)
return experiment
def default_view(self, **kwargs):
return TasbeWorkflowView(op=self, **kwargs)
def get_notebook_code(self, idx):
self._af_op.channels = self.channels
self._af_op.blank_file = self.blank_file
self._bleedthrough_op.controls.clear()
for control in self.bleedthrough_list:
self._bleedthrough_op.controls[control.channel] = control.file
self._bead_calibration_op.beads = BeadCalibrationOp.BEADS[
self.beads_name]
self._bead_calibration_op.beads_file = self.beads_file
self._bead_calibration_op.bead_peak_quantile = self.bead_peak_quantile
self._bead_calibration_op.bead_brightness_threshold = self.bead_brightness_threshold
self._bead_calibration_op.bead_brightness_cutoff = self.bead_brightness_cutoff
self._bead_calibration_op.units.clear()
self._bead_calibration_op.units[self.to_channel] = self.beads_unit
self._color_translation_op.mixture_model = self.mixture_model
self._color_translation_op.controls.clear()
for control in self.translation_list:
self._color_translation_op.controls[(
control.from_channel, control.to_channel)] = control.file
return dedent("""
# the TASBE-style calibration is not a single Cytoflow module. Instead, it
# is a specific sequence of four calibrations: autofluorescence correction,
# bleedthrough, bead calibration and color translation.
# autofluorescence
op_{idx}_af = {af_repr}
op_{idx}_af.estimate(ex_{prev_idx}{subset})
ex_{idx}_af = op_{idx}_af.apply(ex_{prev_idx})
# bleedthrough
op_{idx}_bleedthrough = {bleedthrough_repr}
op_{idx}_bleedthrough.estimate(ex_{idx}_af{subset})
ex_{idx}_bleedthrough = op_{idx}_bleedthrough.apply(ex_{idx}_af)
# bead calibration
# beads: {beads}
op_{idx}_beads = {beads_repr}
op_{idx}_beads.estimate(ex_{idx}_bleedthrough)
ex_{idx}_beads = op_{idx}_beads.apply(ex_{idx}_bleedthrough)
# color translation
op_{idx}_color = {color_repr}
op_{idx}_color.estimate(ex_{idx}_beads{subset})
ex_{idx} = op_{idx}_color.apply(ex_{idx}_beads)
""".format(idx=idx,
prev_idx=idx - 1,
af_repr=repr(self._af_op),
bleedthrough_repr=repr(self._bleedthrough_op),
color_repr=repr(self._color_translation_op),
beads=self.beads_name,
beads_repr=repr(self._bead_calibration_op),
subset=", subset = " +
repr(self.subset) if self.subset else ""))
def clear_estimate(self):
self._af_op = AutofluorescenceOp()
self._bleedthrough_op = BleedthroughLinearOp()
self._bead_calibration_op = BeadCalibrationOp()
self._color_translation_op = ColorTranslationOp()
self.estimate_progress = Progress.NO_MODEL
