class BeadCalibrationPluginOp(PluginOpMixin, BeadCalibrationOp):
handler_factory = Callable(BeadCalibrationHandler)
beads_name = Str(estimate=True)
beads = Dict(Str, List(Float), transient=True)
beads_file = File(filter=["*.fcs"], estimate=True)
units_list = List(_Unit, estimate=True)
units = Dict(Str, Str, transient=True)
bead_peak_quantile = CInt(80, estimate=True)
bead_brightness_threshold = CFloat(100.0, estimate=True)
bead_brightness_cutoff = util.CFloatOrNone(None, estimate=True)
@on_trait_change('units_list_items,units_list.+', post_init=True)
def _controls_changed(self, obj, name, old, new):
self.changed = (Changed.ESTIMATE, ('units_list', self.units_list))
def default_view(self, **kwargs):
return BeadCalibrationPluginView(op=self, **kwargs)
def apply(self, experiment):
if not self.beads_name:
raise util.CytoflowOpError(
"Specify which beads to calibrate with.")
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 = {}
for unit in self.units_list:
self.units[unit.channel] = unit.unit
self.beads = self.BEADS[self.beads_name]
return BeadCalibrationOp.apply(self, experiment)
def estimate(self, experiment):
if not self.beads_name:
raise util.CytoflowOpError(
"Specify which beads to calibrate with.")
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 = {}
for unit in self.units_list:
self.units[unit.channel] = unit.unit
self.beads = self.BEADS[self.beads_name]
BeadCalibrationOp.estimate(self, experiment)
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._calibration_functions.clear()
self._peaks.clear()
self._mefs.clear()
self._histograms.clear()
self.changed = (Changed.ESTIMATE_RESULT, self)
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))
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 ""))
