def default_traits_view(self):
return View(Item("channels",
editor = CheckListEditor(cols = 2,
name = 'context.previous_wi.channels'),
style = 'custom'),
VGroup(
Item('blank_file'),
label = "Autofluorescence"),
VGroup(
Item('bleedthrough_list',
editor = VerticalListEditor(editor = InstanceEditor(view = self.bleedthrough_traits_view()),
style = 'custom',
mutable = False),
style = 'custom'),
label = "Bleedthrough Correction",
show_border = False,
show_labels = False),
VGroup(
Item('beads_name',
editor = EnumEditor(name = 'handler.beads_name_choices'),
label = "Beads",
width = -125),
Item('beads_file'),
Item('beads_unit',
editor = EnumEditor(name = 'handler.beads_units')),
Item('bead_peak_quantile',
label = "Peak\nQuantile"),
Item('bead_brightness_threshold',
label = "Peak\nThreshold "),
Item('bead_brightness_cutoff',
label = "Peak\nCutoff"),
label = "Bead Calibration",
show_border = False),
VGroup(
Item('to_channel',
editor = EnumEditor(name = 'channels')),
Item('mixture_model',
label = "Use mixture\nmodel?"),
label = "Color Translation"),
VGroup(
Item('translation_list',
editor = VerticalListEditor(editor = InstanceEditor(view = self.translation_traits_view()),
style = 'custom',
mutable = False),
style = 'custom'),
show_labels = False),
VGroup(Item('subset_list',
show_label = False,
editor = SubsetListEditor(conditions = "context.previous_wi.conditions",
metadata = "context.previous_wi.metadata",
when = "'experiment' not in vars() or not experiment")),
label = "Subset",
show_border = False,
show_labels = False),
Item('do_estimate',
editor = ButtonEditor(value = True,
label = "Estimate!"),
show_label = False),
shared_op_traits)
def default_traits_view(self):
return View(VGroup(Item('controls_list',
editor = VerticalListEditor(editor = InstanceEditor(view = self.control_traits_view()),
style = 'custom',
mutable = False),
style = 'custom'),
Item('handler.add_control',
editor = ButtonEditor(value = True,
label = "Add a control")),
Item('handler.remove_control',
editor = ButtonEditor(value = True,
label = "Remove a control")),
label = "Controls",
show_labels = False),
Item('mixture_model',
label = "Use mixture\nmodel?"),
VGroup(Item('subset_list',
show_label = False,
editor = SubsetListEditor(conditions = "context.previous_wi.conditions",
metadata = "context.previous_wi.metadata",
when = "'experiment' not in vars() or not experiment")),
label = "Subset",
show_border = False,
show_labels = False),
Item('do_estimate',
editor = ButtonEditor(value = True,
label = "Estimate!"),
show_label = False),
shared_op_traits)
def default_traits_view(self):
return View(
VGroup(
Item('beads_name',
editor=EnumEditor(name='handler.beads_name_choices'),
label="Beads",
width=-125), Item('beads_file', width=-125)),
VGroup(Item('units_list',
editor=VerticalListEditor(editor=InstanceEditor(
view=self.unit_traits_view()),
style='custom',
mutable=False),
style='custom'),
Item('handler.add_channel',
editor=ButtonEditor(value=True,
label="Add a channel")),
Item('handler.remove_channel',
editor=ButtonEditor(value=True,
label="Remove a channel")),
label="Controls",
show_labels=False),
Item('bead_peak_quantile', label="Peak\nQuantile"),
Item('bead_brightness_threshold', label="Peak\nThreshold "),
Item('bead_brightness_cutoff', label="Peak\nCutoff"),
Item('do_estimate',
editor=ButtonEditor(value=True, label="Estimate!"),
show_label=False), shared_op_traits)
def default_traits_view(self):
return View(
VGroup(Item('channels_list',
editor=VerticalListEditor(editor=InstanceEditor(
view=self.channel_traits_view()),
style='custom',
mutable=False),
style='custom'),
Item('handler.add_channel',
editor=ButtonEditor(value=True,
label="Add a channel")),
Item('handler.remove_channel',
editor=ButtonEditor(value=True,
label="Remove a channel")),
show_labels=False),
VGroup(Item('xfacet',
editor=ExtendableEnumEditor(
name='handler.conditions_names',
extra_items={"None": ""}),
label="Horizontal\nFacet"),
Item('yfacet',
editor=ExtendableEnumEditor(
name='handler.conditions_names',
extra_items={"None": ""}),
label="Vertical\nFacet"),
Item('huefacet',
editor=ExtendableEnumEditor(
name='handler.conditions_names',
extra_items={"None": ""}),
label="Color\nFacet"),
Item('huescale', label="Color\nScale"),
Item('plotfacet',
editor=ExtendableEnumEditor(
name='handler.conditions_names',
extra_items={"None": ""}),
label="Tab\nFacet"),
label="2D Histogram",
show_border=False),
VGroup(Item(
'subset_list',
show_label=False,
editor=SubsetListEditor(conditions="context.conditions")),
label="Subset",
show_border=False,
show_labels=False),
Item('context.view_warning',
resizable=True,
visible_when='context.view_warning',
editor=ColorTextEditor(foreground_color="#000000",
background_color="#ffff99")),
Item('context.view_error',
resizable=True,
visible_when='context.view_error',
editor=ColorTextEditor(foreground_color="#000000",
background_color="#ff9191")))
def default_traits_view(self):
return View(Item('name',
editor = TextEditor(auto_set = False)),
VGroup(Item('channels_list',
editor = VerticalListEditor(editor = InstanceEditor(view = self.channel_traits_view()),
style = 'custom',
mutable = False),
style = 'custom'),
Item('handler.add_channel',
editor = ButtonEditor(value = True,
label = "Add a channel"),
show_label = False),
Item('handler.remove_channel',
editor = ButtonEditor(value = True,
label = "Remove a channel")),
show_labels = False),
VGroup(Item('num_components',
editor = TextEditor(auto_set = False),
label = "Num\nComponents"),
Item('whiten'),
Item('by',
editor = CheckListEditor(cols = 2,
name = 'handler.previous_conditions_names'),
label = 'Group\nEstimates\nBy',
style = 'custom'),
label = "Estimate parameters"),
VGroup(Item('subset_list',
show_label = False,
editor = SubsetListEditor(conditions = "context.previous_wi.conditions",
metadata = "context.previous_wi.metadata",
when = "'experiment' not in vars() or not experiment")),
label = "Subset",
show_border = False,
show_labels = False),
Item('do_estimate',
editor = ButtonEditor(value = True,
label = "Estimate!"),
show_label = False),
shared_op_traits)
def default_traits_view(self):
return View(
VGroup(Label(label="Channels", visible_when='model.tubes'),
Item('object.channels_list',
editor=VerticalListEditor(editor=InstanceEditor(),
style='custom',
mutable=False,
deletable=True),
show_label=False),
Item('handler.reset_channels', show_label=False),
visible_when='object.channels_list'),
Item('object.events',
editor=TextEditor(auto_set=False,
format_func=lambda x: ""
if x == None else str(x)),
label="Events per\nsample"),
Item('handler.samples', label='Samples', style='readonly'),
Item('ret_events', label='Events', style='readonly'),
Item('handler.setup_event', show_label=False),
Item('do_estimate',
editor=ButtonEditor(value=True, label="Import!"),
show_label=False), shared_op_traits)
def default_traits_view(self):
return View(
VGroup(
Item('blank_file'),
label = "Autofluorescence"),
VGroup(
Item('fsc_channel',
editor = EnumEditor(name = '_blank_exp_channels'),
label = "Forward Scatter Channel"),
Item('ssc_channel',
editor = EnumEditor(name = '_blank_exp_channels'),
label = "Side Scatter Channel"),
label = "Morphology"),
VGroup(
Item("channels",
editor = CheckListEditor(cols = 2,
name = '_blank_exp_channels'),
style = 'custom'),
label = "Channels To Calibrate",
show_labels = False),
VGroup(
Item('bleedthrough_list',
editor = VerticalListEditor(editor = InstanceEditor(view = self.bleedthrough_traits_view()),
style = 'custom',
mutable = False),
style = 'custom'),
label = "Bleedthrough Correction",
show_border = False,
show_labels = False),
VGroup(
Item('beads_name',
editor = EnumEditor(name = 'handler.beads_name_choices'),
label = "Beads",
width = -125),
Item('beads_file'),
Item('units_list',
editor = VerticalListEditor(editor = InstanceEditor(view = self.unit_traits_view()),
style = 'custom',
mutable = False),
style = 'custom',
label = "Bead\nunits"),
Item('bead_peak_quantile',
label = "Peak\nQuantile"),
Item('bead_brightness_threshold',
label = "Peak\nThreshold "),
Item('bead_brightness_cutoff',
label = "Peak\nCutoff"),
label = "Bead Calibration",
show_border = False),
VGroup(
Item('do_color_translation',
label = "Do color translation?",
editor = ToggleButtonEditor(),
show_label = False),
Item('to_channel',
editor = EnumEditor(name = 'channels'),
visible_when = 'do_color_translation == True'),
Item('mixture_model',
label = "Use mixture\nmodel?",
visible_when = 'do_color_translation == True'),
VGroup(
Item('translation_list',
editor = VerticalListEditor(editor = InstanceEditor(view = self.translation_traits_view()),
style = 'custom',
mutable = False),
style = 'custom'),
show_labels = False,
visible_when = 'do_color_translation == True'),
label = "Color Translation",
show_border = False),
VGroup(
Item('status',
style = 'readonly'),
Item('output_directory'),
Item('do_estimate',
editor = ButtonEditor(value = True,
label = "Estimate parameters"),
show_label = False),
Item('handler.do_convert',
editor = ButtonEditor(value = True,
label = "Convert files..."),
enabled_when = "valid_model == True",
show_label = False),
label = "Output",
show_border = False),
Item('do_exit',
editor = ButtonEditor(value = True,
label = "Return to Cytoflow"),
show_label = False),
shared_op_traits)
class ExperimentDialogHandler(Controller):
# bits for model initialization
import_op = Instance('cytoflowgui.op_plugins.import_op.ImportPluginOp')
# events
add_tubes = Event
remove_tubes = Event
add_variable = Event
import_csv = Event
# traits to communicate with the TabularEditor
selected_tubes = List
default_view = View(
HGroup(
VGroup(
Label("Variables"),
Item('tube_traits',
editor = VerticalListEditor(editor = InstanceEditor(),
style = 'custom',
mutable = False,
deletable = True),
show_label = False),
HGroup(
Item('handler.add_variable',
editor = ButtonEditor(label = "Add a variable"),
show_label = False))),
VGroup(
Label("Tubes"),
Item(name = 'tubes',
id = 'table',
editor = TableEditor(editable = True,
sortable = True,
auto_size = True,
configurable = False,
selection_mode = 'rows',
selected = 'handler.selected_tubes',
columns = [ObjectColumn(name = 'index',
read_only_cell_color = 'lightgrey',
editable = False)]),
enabled_when = "object.tubes",
show_label = False),
HGroup(
Item('handler.add_tubes',
editor = ButtonEditor(label = "Add tubes..."),
show_label = False),
Item('handler.remove_tubes',
editor = ButtonEditor(label = "Remove tubes"),
show_label = False,
enabled_when = 'object.tubes'),
Item('handler.import_csv',
editor = ButtonEditor(label = "Import from CSV..."),
show_label = False)))),
title = 'Experiment Setup',
buttons = OKCancelButtons,
resizable = True,
width = 0.3,
height = 0.3
)
# keep a ref to the table editor so we can add columns dynamically
table_editor = Instance(TableEditorQt)
updating = Bool(False)
def init(self, info):
# save a reference to the table editor
self.table_editor = info.ui.get_editors('tubes')[0]
# init the model
self.model.init(self.import_op)
return True
def close(self, info, is_ok):
""" Handles the user attempting to close a dialog-based user interface.
This method is called when the user attempts to close a window, by
clicking an **OK** or **Cancel** button, or clicking a Close control
on the window). It is called before the window is actually destroyed.
Override this method to perform any checks before closing a window.
While Traits UI handles "OK" and "Cancel" events automatically, you
can use the value of the *is_ok* parameter to implement additional
behavior.
Parameters
----------
info : UIInfo object
The UIInfo object associated with the view
is_ok : Boolean
Indicates whether the user confirmed the changes (such as by
clicking **OK**.)
Returns
-------
allow_close : bool
A Boolean, indicating whether the window should be allowed to close.
"""
if is_ok:
if not self.model.valid:
error(None,
"Each tube must have a unique set of experimental conditions",
"Invalid experiment!")
return False
if not is_ok:
# we don't need to "undo" anything, we're throwing this model away
info.ui.history = None
return True
def closed(self, info, is_ok):
for trait in self.model.tube_traits:
if trait.type != 'metadata':
for tube in self.model.tubes:
tube.on_trait_change(self._try_multiedit,
trait.name,
remove = True)
if is_ok:
self.model.update_import_op(self.import_op)
@on_trait_change('add_variable')
def _on_add_variable(self):
self.model.tube_traits.append(TubeTrait(model = self.model))
@on_trait_change('import_csv')
def _on_import(self):
"""
Import format: CSV, first column is filename, path relative to CSV.
others are conditions, type is autodetected. first row is header
with names.
"""
file_dialog = FileDialog()
file_dialog.wildcard = "CSV files (*.csv)|*.csv|"
file_dialog.action = 'open'
file_dialog.open()
if file_dialog.return_code != PyfaceOK:
return
csv = pandas.read_csv(file_dialog.path)
csv_folder = Path(file_dialog.path).parent
if self.model.tubes or self.model.tube_traits:
if confirm(parent = None,
message = "This will clear the current conditions and tubes! "
"Are you sure you want to continue?",
title = "Clear tubes and conditions?") != YES:
return
for col in csv.columns[1:]:
self.model.tube_traits.append(TubeTrait(model = self.model,
name = util.sanitize_identifier(col),
type = 'category'))
for _, row in csv.iterrows():
filename = csv_folder / row[0]
try:
metadata, _ = parse_tube(str(filename), metadata_only = True)
except Exception as e:
warning(None, "Had trouble loading file {}: {}".format(filename, str(e)))
continue
metadata['CF_File'] = Path(filename).stem
new_tube = Tube(file = str(filename), parent = self.model, metadata = sanitize_metadata(metadata))
self.model.tubes.append(new_tube)
for col in csv.columns[1:]:
new_tube.trait_set(**{util.sanitize_identifier(col) : row[col]})
@on_trait_change('add_tubes')
def _on_add_tubes(self):
"""
Handle "Add tubes..." button. Add tubes to the experiment.
"""
file_dialog = FileDialog()
file_dialog.wildcard = "Flow cytometry files (*.fcs *.lmd)|*.fcs *.lmd|"
file_dialog.action = 'open files'
file_dialog.open()
if file_dialog.return_code != PyfaceOK:
return
for path in file_dialog.paths:
try:
metadata, _ = parse_tube(path, metadata_only = True)
except Exception as e:
raise RuntimeError("FCS reader threw an error on tube {0}: {1}"\
.format(path, e.value))
# if we're the first tube loaded, create a dummy experiment
# and setup default metadata columns
if not self.model.dummy_experiment:
self.model.dummy_experiment = \
ImportOp(tubes = [CytoflowTube(file = path)]).apply(metadata_only = True)
# check the next tube against the dummy experiment
try:
check_tube(path, self.model.dummy_experiment)
except util.CytoflowError as e:
error(None, e.__str__(), "Error importing tube")
return
metadata['CF_File'] = Path(path).stem
tube = Tube(file = path, parent = self.model, metadata = sanitize_metadata(metadata))
self.model.tubes.append(tube)
for trait in self.model.tube_traits:
if trait.type != 'metadata' and trait.name:
tube.on_trait_change(self._try_multiedit, trait.name)
@on_trait_change('remove_tubes')
def _on_remove_tubes(self):
conf = confirm(None,
"Are you sure you want to remove the selected tube(s)?",
"Remove tubes?")
if conf == YES:
for tube in self.selected_tubes:
self.model.tubes.remove(tube)
if not self.model.tubes:
self.model.dummy_experiment = None
@on_trait_change('model:tube_traits_items', post_init = True)
def _tube_traits_changed(self, event):
for trait in event.added:
if not trait.name:
continue
if self.table_editor:
self.table_editor.columns.append(ExperimentColumn(name = trait.name,
editable = (trait.type != 'metadata')))
for tube in self.model.tubes:
if trait.type != 'metadata' and trait.name:
tube.on_trait_change(self._try_multiedit, trait.name)
for trait in event.removed:
if not trait.name:
continue
table_column = next((x for x in self.table_editor.columns if x.name == trait.name))
self.table_editor.columns.remove(table_column)
for tube in self.model.tubes:
if trait.type != 'metadata' and trait.name:
tube.on_trait_change(self._try_multiedit, trait.name, remove = True)
@on_trait_change('model:tube_traits:name')
def _tube_trait_name_changed(self, trait, _, old_name, new_name):
if old_name:
old_table_column = next((x for x in self.table_editor.columns if x.name == old_name))
column_idx = self.table_editor.columns.index(old_table_column)
else:
column_idx = len(self.table_editor.columns)
if new_name:
self.table_editor.columns.insert(column_idx,
ExperimentColumn(name = new_name,
editable = (trait.type != 'metadata')))
if old_name:
self.table_editor.columns.remove(old_table_column)
for tube in self.model.tubes:
if trait.type != 'metadata':
if old_name:
tube.on_trait_change(self._try_multiedit, old_name, remove = True)
if new_name:
tube.on_trait_change(self._try_multiedit, new_name)
if old_name:
tube.remove_trait(old_name)
self.model.counter.clear()
for tube in self.model.tubes:
tube_hash = tube.conditions_hash()
if tube_hash in self.model.counter:
self.model.counter[tube_hash] += 1
else:
self.model.counter[tube_hash] = 1
@on_trait_change('model:tube_traits:type')
def _tube_trait_type_changed(self, trait, _, old_type, new_type):
if not trait.name:
return
table_column = next((x for x in self.table_editor.columns if x.name == trait.name))
table_column.editable = (new_type != 'metadata')
for tube in self.model.tubes:
if trait.name:
if old_type != 'metadata':
tube.on_trait_change(self._try_multiedit, trait.name, remove = True)
if new_type != 'metadata':
tube.on_trait_change(self._try_multiedit, trait.name)
def _try_multiedit(self, obj, name, old, new):
"""
See if there are multiple elements selected when a tube's trait changes
and if so, edit the same trait for all the selected tubes.
"""
if self.updating:
return
self.updating = True
for tube in self.selected_tubes:
if tube != obj:
old_hash = tube.conditions_hash()
self.model.counter[old_hash] -= 1
if self.model.counter[old_hash] == 0:
del self.model.counter[old_hash]
# update the underlying traits without notifying the editor
# we do this all here for performance reasons
tube.trait_setq(**{name: new})
tube.conditions[name] = new
new_hash = tube.conditions_hash()
if new_hash not in self.model.counter:
self.model.counter[new_hash] = 1
else:
self.model.counter[new_hash] += 1
# now refresh the editor all at once
self.table_editor.refresh_editor()
self.updating = False
