def __init__(self, etype, key, value=None, oldValue=None):
"""
Initialize the event instance
"""
QEvent.__init__(self, etype)
self.__key = key
self.__value = value
self.__oldValue = oldValue
def eventFilter(self, recv: QObject, event: QEvent) -> bool:
if event.type() == QEvent.LayoutRequest \
and recv is self.__centralWidget:
self._layout()
return super().eventFilter(recv, event)
def changeEvent(self, event: QEvent) -> None:
if event.type() == QEvent.StyleChange:
self.styleChange.emit()
super().changeEvent(event)
def eventFilter(self, obj: Union[QSlider, QDoubleSpinBox], event: QEvent) \
-> bool:
if event.type() == QEvent.Wheel:
return True
return super().eventFilter(obj, event)
class OWRadviz(widget.OWWidget):
name = "Radviz"
description = "Radviz"
icon = "icons/Radviz.svg"
priority = 240
class Inputs:
data = Input("Data", Table, default=True)
data_subset = Input("Data Subset", Table)
class Outputs:
selected_data = Output("Selected Data", Table, default=True)
annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Table)
components = Output("Components", Table)
settings_version = 1
settingsHandler = settings.DomainContextHandler()
variable_state = settings.ContextSetting({})
auto_commit = settings.Setting(True)
graph = settings.SettingProvider(OWRadvizGraph)
vizrank = settings.SettingProvider(RadvizVizRank)
jitter_sizes = [0, 0.1, 0.5, 1.0, 2.0]
ReplotRequest = QEvent.registerEventType()
graph_name = "graph.plot_widget.plotItem"
class Information(widget.OWWidget.Information):
sql_sampled_data = widget.Msg("Data has been sampled")
class Warning(widget.OWWidget.Warning):
no_features = widget.Msg("At least 2 features have to be chosen")
class Error(widget.OWWidget.Error):
sparse_data = widget.Msg("Sparse data is not supported")
no_features = widget.Msg("At least 3 numeric or categorical variables are required")
no_instances = widget.Msg("At least 2 data instances are required")
def __init__(self):
super().__init__()
self.data = None
self.subset_data = None
self._subset_mask = None
self._selection = None # np.array
self.__replot_requested = False
self._new_plotdata()
self.variable_x = ContinuousVariable("radviz-x")
self.variable_y = ContinuousVariable("radviz-y")
box = gui.vBox(self.mainArea, True, margin=0)
self.graph = OWRadvizGraph(self, box, "Plot", view_box=RadvizInteractiveViewBox)
self.graph.hide_axes()
box.layout().addWidget(self.graph.plot_widget)
plot = self.graph.plot_widget
SIZE_POLICY = (QSizePolicy.Minimum, QSizePolicy.Maximum)
self.variables_selection = VariablesSelection()
self.model_selected = VariableListModel(enable_dnd=True)
self.model_other = VariableListModel(enable_dnd=True)
self.variables_selection(self, self.model_selected, self.model_other)
self.vizrank, self.btn_vizrank = RadvizVizRank.add_vizrank(
self.controlArea, self, "Suggest features", self.vizrank_set_attrs)
self.btn_vizrank.setSizePolicy(*SIZE_POLICY)
self.variables_selection.add_remove.layout().addWidget(self.btn_vizrank)
self.viewbox = plot.getViewBox()
self.replot = None
g = self.graph.gui
pp_box = g.point_properties_box(self.controlArea)
pp_box.setSizePolicy(*SIZE_POLICY)
self.models = g.points_models
box = gui.vBox(self.controlArea, "Plot Properties")
box.setSizePolicy(*SIZE_POLICY)
g.add_widget(g.JitterSizeSlider, box)
g.add_widgets([g.ShowLegend, g.ClassDensity, g.LabelOnlySelected], box)
zoom_select = self.graph.box_zoom_select(self.controlArea)
zoom_select.setSizePolicy(*SIZE_POLICY)
self.icons = gui.attributeIconDict
p = self.graph.plot_widget.palette()
self.graph.set_palette(p)
gui.auto_commit(self.controlArea, self, "auto_commit", "Send Selection",
auto_label="Send Automatically")
self.graph.zoom_actions(self)
self._circle = QGraphicsEllipseItem()
self._circle.setRect(QRectF(-1., -1., 2., 2.))
self._circle.setPen(pg.mkPen(QColor(0, 0, 0), width=2))
def resizeEvent(self, event):
self._update_points_labels()
def keyPressEvent(self, event):
super().keyPressEvent(event)
self.graph.update_tooltip(event.modifiers())
def keyReleaseEvent(self, event):
super().keyReleaseEvent(event)
self.graph.update_tooltip(event.modifiers())
def vizrank_set_attrs(self, attrs):
if not attrs:
return
self.variables_selection.display_none()
self.model_selected[:] = attrs[:]
self.model_other[:] = [v for v in self.model_other if v not in attrs]
def _new_plotdata(self):
self.plotdata = namespace(
valid_mask=None,
embedding_coords=None,
points=None,
arcarrows=[],
point_labels=[],
rand=None,
data=None,
)
def update_colors(self):
self._vizrank_color_change()
self.cb_class_density.setEnabled(self.graph.can_draw_density())
def sizeHint(self):
return QSize(800, 500)
def clear(self):
"""
Clear/reset the widget state
"""
self.data = None
self.model_selected.clear()
self.model_other.clear()
self._clear_plot()
def _clear_plot(self):
self._new_plotdata()
self.graph.plot_widget.clear()
def invalidate_plot(self):
"""
Schedule a delayed replot.
"""
if not self.__replot_requested:
self.__replot_requested = True
QApplication.postEvent(self, QEvent(self.ReplotRequest), Qt.LowEventPriority - 10)
def init_attr_values(self):
domain = self.data and len(self.data) and self.data.domain or None
for model in self.models:
model.set_domain(domain)
self.graph.attr_color = self.data.domain.class_var if domain else None
self.graph.attr_shape = None
self.graph.attr_size = None
self.graph.attr_label = None
def _vizrank_color_change(self):
attr_color = self.graph.attr_color
is_enabled = self.data is not None and not self.data.is_sparse() and \
(len(self.model_other) + len(self.model_selected)) > 3 and len(self.data) > 1
self.btn_vizrank.setEnabled(
is_enabled and attr_color is not None
and not np.isnan(self.data.get_column_view(attr_color)[0].astype(float)).all())
self.vizrank.initialize()
@Inputs.data
def set_data(self, data):
"""
Set the input dataset and check if data is valid.
Args:
data (Orange.data.table): data instances
"""
def sql(data):
self.Information.sql_sampled_data.clear()
if isinstance(data, SqlTable):
if data.approx_len() < 4000:
data = Table(data)
else:
self.Information.sql_sampled_data()
data_sample = data.sample_time(1, no_cache=True)
data_sample.download_data(2000, partial=True)
data = Table(data_sample)
return data
def settings(data):
# get the default encoded state, replacing the position with Inf
state = VariablesSelection.encode_var_state(
[list(self.model_selected), list(self.model_other)]
)
state = {key: (source_ind, np.inf) for key, (source_ind, _) in state.items()}
self.openContext(data.domain)
selected_keys = [key
for key, (sind, _) in self.variable_state.items()
if sind == 0]
if set(selected_keys).issubset(set(state.keys())):
pass
# update the defaults state (the encoded state must contain
# all variables in the input domain)
state.update(self.variable_state)
# ... and restore it with saved positions taking precedence over
# the defaults
selected, other = VariablesSelection.decode_var_state(
state, [list(self.model_selected), list(self.model_other)])
return selected, other
def is_sparse(data):
if data.is_sparse():
self.Error.sparse_data()
data = None
return data
def are_features(data):
domain = data.domain
vars = [var for var in chain(domain.class_vars, domain.metas, domain.attributes)
if var.is_primitive()]
if len(vars) < 3:
self.Error.no_features()
data = None
return data
def are_instances(data):
if len(data) < 2:
self.Error.no_instances()
data = None
return data
self.clear_messages()
self.btn_vizrank.setEnabled(False)
self.closeContext()
self.clear()
self.information()
self.Error.clear()
for f in [sql, is_sparse, are_features, are_instances]:
if data is None:
break
data = f(data)
if data is not None:
self.data = data
self.init_attr_values()
domain = data.domain
vars = [v for v in chain(domain.metas, domain.attributes)
if v.is_primitive()]
self.model_selected[:] = vars[:5]
self.model_other[:] = vars[5:] + list(domain.class_vars)
self.model_selected[:], self.model_other[:] = settings(data)
self._selection = np.zeros(len(data), dtype=np.uint8)
self.invalidate_plot()
else:
self.data = None
@Inputs.data_subset
def set_subset_data(self, subset):
"""
Set the supplementary input subset dataset.
Args:
subset (Orange.data.table): subset of data instances
"""
self.subset_data = subset
self._subset_mask = None
self.controls.graph.alpha_value.setEnabled(subset is None)
def handleNewSignals(self):
if self.data is not None:
self._clear_plot()
if self.subset_data is not None and self._subset_mask is None:
dataids = self.data.ids.ravel()
subsetids = np.unique(self.subset_data.ids)
self._subset_mask = np.in1d(
dataids, subsetids, assume_unique=True)
self.setup_plot(reset_view=True)
self.cb_class_density.setEnabled(self.graph.can_draw_density())
else:
self.init_attr_values()
self.graph.new_data(None)
self._vizrank_color_change()
self.commit()
def customEvent(self, event):
if event.type() == OWRadviz.ReplotRequest:
self.__replot_requested = False
self._clear_plot()
self.setup_plot(reset_view=True)
else:
super().customEvent(event)
def closeContext(self):
self.variable_state = VariablesSelection.encode_var_state(
[list(self.model_selected), list(self.model_other)]
)
super().closeContext()
def prepare_radviz_data(self, variables):
ec, points, valid_mask = radviz(self.data, variables, self.plotdata.points)
self.plotdata.embedding_coords = ec
self.plotdata.points = points
self.plotdata.valid_mask = valid_mask
def setup_plot(self, reset_view=True):
if self.data is None:
return
self.graph.jitter_continuous = True
self.__replot_requested = False
variables = list(self.model_selected)
if len(variables) < 2:
self.Warning.no_features()
self.graph.new_data(None)
return
self.Warning.clear()
self.prepare_radviz_data(variables)
if self.plotdata.embedding_coords is None:
return
domain = self.data.domain
new_metas = domain.metas + (self.variable_x, self.variable_y)
domain = Domain(attributes=domain.attributes,
class_vars=domain.class_vars,
metas=new_metas)
mask = self.plotdata.valid_mask
array = np.zeros((len(self.data), 2), dtype=np.float)
array[mask] = self.plotdata.embedding_coords
data = Table.from_numpy(
domain, X=self.data.X, Y=self.data.Y, metas=np.hstack((self.data.metas, array)))
subset_data = data[self._subset_mask & mask]\
if self._subset_mask is not None and len(self._subset_mask) else None
self.plotdata.data = data
self.graph.new_data(data[mask], subset_data)
if self._selection is not None:
self.graph.selection = self._selection[self.plotdata.valid_mask]
self.graph.update_data(self.variable_x, self.variable_y, reset_view=reset_view)
self.graph.plot_widget.addItem(self._circle)
self.graph.scatterplot_points = ScatterPlotItem(
x=self.plotdata.points[:, 0],
y=self.plotdata.points[:, 1]
)
self._update_points_labels()
self.graph.plot_widget.addItem(self.graph.scatterplot_points)
def randomize_indices(self):
ec = self.plotdata.embedding_coords
self.plotdata.rand = np.random.choice(len(ec), MAX_POINTS, replace=False) \
if len(ec) > MAX_POINTS else None
def manual_move(self):
self.__replot_requested = False
if self.plotdata.rand is not None:
rand = self.plotdata.rand
valid_mask = self.plotdata.valid_mask
data = self.data[valid_mask]
selection = self._selection[valid_mask]
selection = selection[rand]
ec, _, valid_mask = radviz(data, list(self.model_selected), self.plotdata.points)
assert sum(valid_mask) == len(data)
data = data[rand]
ec = ec[rand]
data_x = data.X
data_y = data.Y
data_metas = data.metas
else:
self.prepare_radviz_data(list(self.model_selected))
ec = self.plotdata.embedding_coords
valid_mask = self.plotdata.valid_mask
data_x = self.data.X[valid_mask]
data_y = self.data.Y[valid_mask]
data_metas = self.data.metas[valid_mask]
selection = self._selection[valid_mask]
attributes = (self.variable_x, self.variable_y) + self.data.domain.attributes
domain = Domain(attributes=attributes,
class_vars=self.data.domain.class_vars,
metas=self.data.domain.metas)
data = Table.from_numpy(domain, X=np.hstack((ec, data_x)), Y=data_y, metas=data_metas)
self.graph.new_data(data, None)
self.graph.selection = selection
self.graph.update_data(self.variable_x, self.variable_y, reset_view=True)
self.graph.plot_widget.addItem(self._circle)
self.graph.scatterplot_points = ScatterPlotItem(
x=self.plotdata.points[:, 0], y=self.plotdata.points[:, 1])
self._update_points_labels()
self.graph.plot_widget.addItem(self.graph.scatterplot_points)
def _update_points_labels(self):
if self.plotdata.points is None:
return
for point_label in self.plotdata.point_labels:
self.graph.plot_widget.removeItem(point_label)
self.plotdata.point_labels = []
sx, sy = self.graph.view_box.viewPixelSize()
for row in self.plotdata.points:
ti = TextItem()
metrics = QFontMetrics(ti.textItem.font())
text_width = ((RANGE.width())/2. - np.abs(row[0])) / sx
name = row[2].name
ti.setText(name)
ti.setTextWidth(text_width)
ti.setColor(QColor(0, 0, 0))
br = ti.boundingRect()
width = metrics.width(name) if metrics.width(name) < br.width() else br.width()
width = sx * (width + 5)
height = sy * br.height()
ti.setPos(row[0] - (row[0] < 0) * width, row[1] + (row[1] > 0) * height)
self.plotdata.point_labels.append(ti)
self.graph.plot_widget.addItem(ti)
def _update_jitter(self):
self.invalidate_plot()
def reset_graph_data(self, *_):
if self.data is not None:
self.graph.rescale_data()
self._update_graph()
def _update_graph(self, reset_view=True, **_):
self.graph.zoomStack = []
if self.graph.data is None:
return
self.graph.update_data(self.variable_x, self.variable_y, reset_view=reset_view)
def update_density(self):
self._update_graph(reset_view=True)
def selection_changed(self):
if self.graph.selection is not None:
self._selection[self.plotdata.valid_mask] = self.graph.selection
self.commit()
def prepare_data(self):
pass
def commit(self):
selected = annotated = components = None
graph = self.graph
if self.plotdata.data is not None:
name = self.data.name
data = self.plotdata.data
mask = self.plotdata.valid_mask.astype(int)
mask[mask == 1] = graph.selection if graph.selection is not None \
else [False * len(mask)]
selection = np.array([], dtype=np.uint8) if mask is None else np.flatnonzero(mask)
if len(selection):
selected = data[selection]
selected.name = name + ": selected"
selected.attributes = self.data.attributes
if graph.selection is not None and np.max(graph.selection) > 1:
annotated = create_groups_table(data, mask)
else:
annotated = create_annotated_table(data, selection)
annotated.attributes = self.data.attributes
annotated.name = name + ": annotated"
comp_domain = Domain(
self.plotdata.points[:, 2],
metas=[StringVariable(name='component')])
metas = np.array([["RX"], ["RY"], ["angle"]])
angle = np.arctan2(np.array(self.plotdata.points[:, 1].T, dtype=float),
np.array(self.plotdata.points[:, 0].T, dtype=float))
components = Table.from_numpy(
comp_domain,
X=np.row_stack((self.plotdata.points[:, :2].T, angle)),
metas=metas)
components.name = name + ": components"
self.Outputs.selected_data.send(selected)
self.Outputs.annotated_data.send(annotated)
self.Outputs.components.send(components)
def send_report(self):
if self.data is None:
return
def name(var):
return var and var.name
caption = report.render_items_vert((
("Color", name(self.graph.attr_color)),
("Label", name(self.graph.attr_label)),
("Shape", name(self.graph.attr_shape)),
("Size", name(self.graph.attr_size)),
("Jittering", self.graph.jitter_size != 0 and "{} %".format(self.graph.jitter_size))))
self.report_plot()
if caption:
self.report_caption(caption)
def __init__(self, state):
QEvent.__init__(self, StateChangedEvent.StateChanged)
self._state = state
class FutureWatcher(QObject):
"""
An `QObject` watching the state changes of a `concurrent.futures.Future`
Note
----
The state change notification signals (`done`, `finished`, ...)
are always emitted when the control flow reaches the event loop
(even if the future is already completed when set).
Note
----
An event loop must be running, otherwise the notifier signals will
not be emitted.
Parameters
----------
parent : QObject
Parent object.
future : Future
The future instance to watch.
Example
-------
>>> app = QCoreApplication.instance() or QCoreApplication([])
>>> f = submit(lambda i, j: i ** j, 10, 3)
>>> watcher = FutureWatcher(f)
>>> watcher.resultReady.connect(lambda res: print("Result:", res))
>>> watcher.done.connect(app.quit)
>>> _ = app.exec()
Result: 1000
>>> f.result()
1000
"""
#: Signal emitted when the future is done (cancelled or finished)
done = Signal(Future)
#: Signal emitted when the future is finished (i.e. returned a result
#: or raised an exception - but not if cancelled)
finished = Signal(Future)
#: Signal emitted when the future was cancelled
cancelled = Signal(Future)
#: Signal emitted with the future's result when successfully finished.
resultReady = Signal(object)
#: Signal emitted with the future's exception when finished with an
#: exception.
exceptionReady = Signal(BaseException)
# A private event type used to notify the watcher of a Future's completion
__FutureDone = QEvent.registerEventType()
def __init__(self, future=None, parent=None, **kwargs):
super().__init__(parent, **kwargs)
self.__future = None
if future is not None:
self.setFuture(future)
def setFuture(self, future):
# type: (Future) -> None
"""
Set the future to watch.
Raise a `RuntimeError` if a future is already set.
Parameters
----------
future : Future
"""
if self.__future is not None:
raise RuntimeError("Future already set")
self.__future = future
selfweakref = weakref.ref(self)
def on_done(f):
assert f is future
selfref = selfweakref()
if selfref is None:
return
try:
QCoreApplication.postEvent(selfref,
QEvent(FutureWatcher.__FutureDone))
except RuntimeError:
# Ignore RuntimeErrors (when C++ side of QObject is deleted)
# (? Use QObject.destroyed and remove the done callback ?)
pass
future.add_done_callback(on_done)
def future(self):
# type: () -> Future
"""
Return the future instance.
"""
return self.__future
def isCancelled(self):
warnings.warn("isCancelled is deprecated",
DeprecationWarning,
stacklevel=2)
return self.__future.cancelled()
def isDone(self):
warnings.warn("isDone is deprecated", DeprecationWarning, stacklevel=2)
return self.__future.done()
def result(self):
# type: () -> Any
"""
Return the future's result.
Note
----
This method is non-blocking. If the future has not yet completed
it will raise an error.
"""
try:
return self.__future.result(timeout=0)
except TimeoutError:
raise RuntimeError("Future is not yet done")
def exception(self):
# type: () -> Optional[BaseException]
"""
Return the future's exception.
Note
----
This method is non-blocking. If the future has not yet completed
it will raise an error.
"""
try:
return self.__future.exception(timeout=0)
except TimeoutError:
raise RuntimeError("Future is not yet done")
def __emitSignals(self):
assert self.__future is not None
assert self.__future.done()
if self.__future.cancelled():
self.cancelled.emit(self.__future)
self.done.emit(self.__future)
elif self.__future.done():
self.finished.emit(self.__future)
self.done.emit(self.__future)
if self.__future.exception():
self.exceptionReady.emit(self.__future.exception())
else:
self.resultReady.emit(self.__future.result())
else:
assert False
def customEvent(self, event):
# Reimplemented.
if event.type() == FutureWatcher.__FutureDone:
self.__emitSignals()
super().customEvent(event)
class RuntimeEvent(QEvent):
Init = QEvent.registerEventType()
def _invalidate(self):
self.__invalidated = True
QApplication.postEvent(self, QEvent(self.Invalidate))
def event(self, event: QEvent) -> bool:
if event.type() == QEvent.LayoutRequest:
self.__layout()
elif event.type() == QEvent.ContentsRectChange:
self.__layout()
return super().event(event)
def __scheduleLayout(self):
if not self.__reflowPending:
self.__reflowPending = True
QApplication.postEvent(self, QEvent(QEvent.LayoutRequest),
Qt.HighEventPriority)
class OWCorrespondenceAnalysis(widget.OWWidget):
name = "Correspondence Analysis"
description = "Correspondence analysis for categorical multivariate data."
icon = "icons/CorrespondenceAnalysis.svg"
keywords = []
class Inputs:
data = Input("Data", Table)
class Outputs:
coordinates = Output("Coordinates", Table)
Invalidate = QEvent.registerEventType()
settingsHandler = settings.DomainContextHandler()
selected_var_indices = settings.ContextSetting([])
auto_commit = Setting(True)
graph_name = "plot.plotItem"
class Error(widget.OWWidget.Error):
empty_data = widget.Msg("Empty dataset")
no_disc_vars = widget.Msg("No categorical data")
def __init__(self):
super().__init__()
self.data = None
self.component_x = 0
self.component_y = 1
self._set_input_summary(None)
self._set_output_summary(None)
box = gui.vBox(self.controlArea, "Variables")
self.varlist = itemmodels.VariableListModel()
self.varview = view = ListViewSearch(
selectionMode=QListView.MultiSelection,
uniformItemSizes=True
)
view.setModel(self.varlist)
view.selectionModel().selectionChanged.connect(self._var_changed)
box.layout().addWidget(view)
axes_box = gui.vBox(self.controlArea, "Axes")
self.axis_x_cb = gui.comboBox(
axes_box, self, "component_x", label="X:",
callback=self._component_changed, orientation=Qt.Horizontal,
sizePolicy=(QSizePolicy.MinimumExpanding,
QSizePolicy.Preferred)
)
self.axis_y_cb = gui.comboBox(
axes_box, self, "component_y", label="Y:",
callback=self._component_changed, orientation=Qt.Horizontal,
sizePolicy=(QSizePolicy.MinimumExpanding,
QSizePolicy.Preferred)
)
self.infotext = gui.widgetLabel(
gui.vBox(self.controlArea, "Contribution to Inertia"), "\n"
)
gui.auto_send(self.buttonsArea, self, "auto_commit")
self.plot = pg.PlotWidget(background="w")
self.plot.setMenuEnabled(False)
self.mainArea.layout().addWidget(self.plot)
@Inputs.data
def set_data(self, data):
self.closeContext()
self.clear()
self.Error.clear()
if data is not None and not len(data):
self.Error.empty_data()
data = None
self.data = data
self._set_input_summary(self.data)
if data is not None:
self.varlist[:] = [var for var in data.domain.variables
if var.is_discrete]
if not len(self.varlist[:]):
self.Error.no_disc_vars()
self.data = None
else:
self.selected_var_indices = [0, 1][:len(self.varlist)]
# This widget's update flow is broken in many ways, starting
# from using context domain handler without having any valid
# context settings. Getting rid of these warnings would require
# rewriting large portins; @ales-erjavec is doing it and will
# finish it eventually, so let us these warnings are
# uninformative and would better be silenced.
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore", "combo box 'component_[xy]' .*", UserWarning)
self.component_x = 0
self.component_y = int(len(self.varlist[self.selected_var_indices[-1]].values) > 1)
self.openContext(data)
self._restore_selection()
self._update_CA()
def commit(self):
output_table = None
if self.ca is not None:
sel_vars = self.selected_vars()
if len(sel_vars) == 2:
rf = np.vstack((self.ca.row_factors, self.ca.col_factors))
else:
rf = self.ca.row_factors
vars_data = [(val.name, var) for val in sel_vars for var in val.values]
output_table = Table(
Domain([ContinuousVariable(f"Component {i + 1}")
for i in range(rf.shape[1])],
metas=[StringVariable("Variable"),
StringVariable("Value")]),
rf, metas=vars_data
)
self._set_output_summary(output_table)
self.Outputs.coordinates.send(output_table)
def clear(self):
self.data = None
self.ca = None
self.plot.clear()
self.varlist[:] = []
def _set_input_summary(self, data):
summary = len(data) if data else self.info.NoInput
details = format_summary_details(data) if data else ""
self.info.set_input_summary(summary, details)
def _set_output_summary(self, output):
summary = len(output) if output else self.info.NoOutput
details = format_summary_details(output) if output else ""
self.info.set_output_summary(summary, details)
def selected_vars(self):
rows = sorted(
ind.row() for ind in self.varview.selectionModel().selectedRows())
return [self.varlist[i] for i in rows]
def _restore_selection(self):
def restore(view, indices):
with itemmodels.signal_blocking(view.selectionModel()):
select_rows(view, indices)
restore(self.varview, self.selected_var_indices)
def _p_axes(self):
return self.component_x, self.component_y
def _var_changed(self):
self.selected_var_indices = sorted(
ind.row() for ind in self.varview.selectionModel().selectedRows())
rfs = self.update_XY()
if rfs is not None:
if self.component_x >= rfs:
self.component_x = rfs-1
if self.component_y >= rfs:
self.component_y = rfs-1
self._invalidate()
def _component_changed(self):
if self.ca is not None:
self._setup_plot()
self._update_info()
def _invalidate(self):
self.__invalidated = True
QApplication.postEvent(self, QEvent(self.Invalidate))
def customEvent(self, event):
if event.type() == self.Invalidate:
self.ca = None
self.plot.clear()
self._update_CA()
return
return super().customEvent(event)
def _update_CA(self):
self.update_XY()
# See the comment about catch_warnings above.
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore", "combo box 'component_[xy]' .*", UserWarning)
self.component_x, self.component_y = \
self.component_x, self.component_y
self._setup_plot()
self._update_info()
self.commit()
def update_XY(self):
self.axis_x_cb.clear()
self.axis_y_cb.clear()
ca_vars = self.selected_vars()
if len(ca_vars) == 0:
return
multi = len(ca_vars) != 2
if multi:
_, ctable = burt_table(self.data, ca_vars)
else:
ctable = contingency.get_contingency(self.data, *ca_vars[::-1])
self.ca = correspondence(ctable, )
rfs = self.ca.row_factors.shape[1]
axes = ["{}".format(i + 1)
for i in range(rfs)]
self.axis_x_cb.addItems(axes)
self.axis_y_cb.addItems(axes)
return rfs
def _setup_plot(self):
def get_minmax(points):
minmax = [float('inf'),
float('-inf'),
float('inf'),
float('-inf')]
for pp in points:
for p in pp:
minmax[0] = min(p[0], minmax[0])
minmax[1] = max(p[0], minmax[1])
minmax[2] = min(p[1], minmax[2])
minmax[3] = max(p[1], minmax[3])
return minmax
self.plot.clear()
points = self.ca
variables = self.selected_vars()
colors = colorpalettes.LimitedDiscretePalette(len(variables))
p_axes = self._p_axes()
if points is None:
return
if len(variables) == 2:
row_points = self.ca.row_factors[:, p_axes]
col_points = self.ca.col_factors[:, p_axes]
points = [row_points, col_points]
else:
points = self.ca.row_factors[:, p_axes]
counts = [len(var.values) for var in variables]
range_indices = np.cumsum([0] + counts)
ranges = zip(range_indices, range_indices[1:])
points = [points[s:e] for s, e in ranges]
minmax = get_minmax(points)
margin = abs(minmax[0] - minmax[1])
margin = margin * 0.05 if margin > 1e-10 else 1
self.plot.setXRange(minmax[0] - margin, minmax[1] + margin)
margin = abs(minmax[2] - minmax[3])
margin = margin * 0.05 if margin > 1e-10 else 1
self.plot.setYRange(minmax[2] - margin, minmax[3] + margin)
for i, (v, points) in enumerate(zip(variables, points)):
color_outline = colors[i]
color_outline.setAlpha(200)
color = QColor(color_outline)
color.setAlpha(120)
item = ScatterPlotItem(
x=points[:, 0], y=points[:, 1], brush=QBrush(color),
pen=pg.mkPen(color_outline.darker(120), width=1.5),
size=np.full((points.shape[0],), 10.1),
)
self.plot.addItem(item)
for name, point in zip(v.values, points):
item = pg.TextItem(name, anchor=(0.5, 0))
self.plot.addItem(item)
item.setPos(point[0], point[1])
inertia = self.ca.inertia_of_axis()
if np.sum(inertia) == 0:
inertia = 100 * inertia
else:
inertia = 100 * inertia / np.sum(inertia)
ax = self.plot.getAxis("bottom")
ax.setLabel("Component {} ({:.1f}%)"
.format(p_axes[0] + 1, inertia[p_axes[0]]))
ax = self.plot.getAxis("left")
ax.setLabel("Component {} ({:.1f}%)"
.format(p_axes[1] + 1, inertia[p_axes[1]]))
def _update_info(self):
if self.ca is None:
self.infotext.setText("\n\n")
else:
fmt = ("Axis 1: {:.2f}\n"
"Axis 2: {:.2f}")
inertia = self.ca.inertia_of_axis()
if np.sum(inertia) == 0:
inertia = 100 * inertia
else:
inertia = 100 * inertia / np.sum(inertia)
ax1, ax2 = self._p_axes()
self.infotext.setText(fmt.format(inertia[ax1], inertia[ax2]))
def send_report(self):
if self.data is None:
return
vars = self.selected_vars()
if not vars:
return
items = OrderedDict()
items["Data instances"] = len(self.data)
if len(vars) == 1:
items["Selected variable"] = vars[0]
else:
items["Selected variables"] = "{} and {}".format(
", ".join(var.name for var in vars[:-1]), vars[-1].name)
self.report_items(items)
self.report_plot()
def commit(self):
if not self._invalidated:
self._invalidated = True
QApplication.postEvent(self, QEvent(QEvent.User))
class OWFreeViz(widget.OWWidget):
name = "FreeViz"
description = "Displays FreeViz projection"
icon = "icons/Freeviz.svg"
priority = 240
class Inputs:
data = Input("Data", Table, default=True)
data_subset = Input("Data Subset", Table)
class Outputs:
selected_data = Output("Selected Data", Table, default=True)
annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Table)
components = Output("Components", Table)
#: Initialization type
Circular, Random = 0, 1
jitter_sizes = [0, 0.1, 0.5, 1, 2]
settings_version = 2
settingsHandler = settings.DomainContextHandler()
radius = settings.Setting(0)
initialization = settings.Setting(Circular)
auto_commit = settings.Setting(True)
resolution = 256
graph = settings.SettingProvider(OWFreeVizGraph)
ReplotRequest = QEvent.registerEventType()
graph_name = "graph.plot_widget.plotItem"
class Warning(widget.OWWidget.Warning):
sparse_not_supported = widget.Msg("Sparse data is ignored.")
class Error(widget.OWWidget.Error):
no_class_var = widget.Msg("Need a class variable")
not_enough_class_vars = widget.Msg("Needs discrete class variable " \
"with at lest 2 values")
features_exceeds_instances = widget.Msg("Algorithm should not be used when " \
"number of features exceeds the number " \
"of instances.")
too_many_data_instances = widget.Msg("Cannot handle so large data.")
no_valid_data = widget.Msg("No valid data.")
def __init__(self):
super().__init__()
self.data = None
self.subset_data = None
self._subset_mask = None
self._validmask = None
self._X = None
self._Y = None
self._selection = None
self.__replot_requested = False
self.variable_x = ContinuousVariable("freeviz-x")
self.variable_y = ContinuousVariable("freeviz-y")
box0 = gui.vBox(self.mainArea, True, margin=0)
self.graph = OWFreeVizGraph(self, box0, "Plot", view_box=FreeVizInteractiveViewBox)
box0.layout().addWidget(self.graph.plot_widget)
plot = self.graph.plot_widget
box = gui.widgetBox(self.controlArea, "Optimization", spacing=10)
form = QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10
)
form.addRow(
"Initialization",
gui.comboBox(box, self, "initialization",
items=["Circular", "Random"],
callback=self.reset_initialization)
)
box.layout().addLayout(form)
self.btn_start = gui.button(widget=box, master=self, label="Optimize",
callback=self.toogle_start, enabled=False)
self.viewbox = plot.getViewBox()
self.replot = None
g = self.graph.gui
g.point_properties_box(self.controlArea)
self.models = g.points_models
box = gui.widgetBox(self.controlArea, "Show anchors")
self.rslider = gui.hSlider(
box, self, "radius", minValue=0, maxValue=100,
step=5, label="Radius", createLabel=False, ticks=True,
callback=self.update_radius)
self.rslider.setTickInterval(0)
self.rslider.setPageStep(10)
box = gui.vBox(self.controlArea, "Plot Properties")
g.add_widgets([g.JitterSizeSlider], box)
g.add_widgets([g.ShowLegend,
g.ClassDensity,
g.LabelOnlySelected],
box)
self.graph.box_zoom_select(self.controlArea)
self.controlArea.layout().addStretch(100)
self.icons = gui.attributeIconDict
p = self.graph.plot_widget.palette()
self.graph.set_palette(p)
gui.auto_commit(self.controlArea, self, "auto_commit",
"Send Selection", "Send Automatically")
self.graph.zoom_actions(self)
# FreeViz
self._loop = AsyncUpdateLoop(parent=self)
self._loop.yielded.connect(self.__set_projection)
self._loop.finished.connect(self.__freeviz_finished)
self._loop.raised.connect(self.__on_error)
self._new_plotdata()
def keyPressEvent(self, event):
super().keyPressEvent(event)
self.graph.update_tooltip(event.modifiers())
def keyReleaseEvent(self, event):
super().keyReleaseEvent(event)
self.graph.update_tooltip(event.modifiers())
def update_radius(self):
# Update the anchor/axes visibility
assert not self.plotdata is None
if self.plotdata.hidecircle is None:
return
minradius = self.radius / 100 + 1e-5
for anchor, item in zip(self.plotdata.anchors,
self.plotdata.anchoritem):
item.setVisible(np.linalg.norm(anchor) > minradius)
self.plotdata.hidecircle.setRect(
QRectF(-minradius, -minradius,
2 * minradius, 2 * minradius))
def toogle_start(self):
if self._loop.isRunning():
self._loop.cancel()
if isinstance(self, OWFreeViz):
self.btn_start.setText("Optimize")
self.progressBarFinished(processEvents=False)
else:
self._start()
def _start(self):
"""
Start the projection optimization.
"""
assert not self.plotdata is None
X, Y = self.plotdata.X, self.plotdata.Y
anchors = self.plotdata.anchors
def update_freeviz(interval, initial):
anchors = initial
while True:
res = FreeViz.freeviz(X, Y, scale=False, center=False,
initial=anchors, maxiter=interval)
_, anchors_new = res[:2]
yield res[:2]
if np.allclose(anchors, anchors_new, rtol=1e-5, atol=1e-4):
return
anchors = anchors_new
interval = 10 # TODO
self._loop.setCoroutine(
update_freeviz(interval, anchors))
self.btn_start.setText("Stop")
self.progressBarInit(processEvents=False)
self.setBlocking(True)
self.setStatusMessage("Optimizing")
def reset_initialization(self):
"""
Reset the current 'anchor' initialization, and restart the
optimization if necessary.
"""
running = self._loop.isRunning()
if running:
self._loop.cancel()
if self.data is not None:
self._clear_plot()
self.setup_plot()
if running:
self._start()
def __set_projection(self, res):
# Set/update the projection matrix and coordinate embeddings
# assert self.plotdata is not None, "__set_projection call unexpected"
assert not self.plotdata is None
increment = 1 # TODO
self.progressBarAdvance(
increment * 100. / MAX_ITERATIONS, processEvents=False) # TODO
embedding_coords, projection = res
self.plotdata.embedding_coords = embedding_coords
self.plotdata.anchors = projection
self._update_xy()
self.update_radius()
self.update_density()
def __freeviz_finished(self):
# Projection optimization has finished
self.btn_start.setText("Optimize")
self.setStatusMessage("")
self.setBlocking(False)
self.progressBarFinished(processEvents=False)
self.commit()
def __on_error(self, err):
sys.excepthook(type(err), err, getattr(err, "__traceback__"))
def _update_xy(self):
# Update the plotted embedding coordinates
self.graph.plot_widget.clear()
coords = self.plotdata.embedding_coords
radius = np.max(np.linalg.norm(coords, axis=1))
self.plotdata.embedding_coords = coords / radius
self.plot(show_anchors=(len(self.data.domain.attributes) < MAX_ANCHORS))
def _new_plotdata(self):
self.plotdata = namespace(
validmask=None,
embedding_coords=None,
anchors=[],
anchoritem=[],
X=None,
Y=None,
indicators=[],
hidecircle=None,
data=None,
items=[],
topattrs=None,
rand=None,
selection=None, # np.array
)
def _anchor_circle(self):
# minimum visible anchor radius (radius)
minradius = self.radius / 100 + 1e-5
for item in chain(self.plotdata.anchoritem, self.plotdata.items):
self.viewbox.removeItem(item)
self.plotdata.anchoritem = []
self.plotdata.items = []
for anchor, var in zip(self.plotdata.anchors, self.data.domain.attributes):
if True or np.linalg.norm(anchor) > minradius:
axitem = AnchorItem(
line=QLineF(0, 0, *anchor), text=var.name,)
axitem.setVisible(np.linalg.norm(anchor) > minradius)
axitem.setPen(pg.mkPen((100, 100, 100)))
axitem.setArrowVisible(True)
self.plotdata.anchoritem.append(axitem)
self.viewbox.addItem(axitem)
hidecircle = QGraphicsEllipseItem()
hidecircle.setRect(
QRectF(-minradius, -minradius,
2 * minradius, 2 * minradius))
_pen = QPen(Qt.lightGray, 1)
_pen.setCosmetic(True)
hidecircle.setPen(_pen)
self.viewbox.addItem(hidecircle)
self.plotdata.items.append(hidecircle)
self.plotdata.hidecircle = hidecircle
def update_colors(self):
pass
def sizeHint(self):
return QSize(800, 500)
def _clear(self):
"""
Clear/reset the widget state
"""
self._loop.cancel()
self.data = None
self._selection = None
self._clear_plot()
def _clear_plot(self):
for item in chain(self.plotdata.anchoritem, self.plotdata.items):
self.viewbox.removeItem(item)
self.graph.plot_widget.clear()
self._new_plotdata()
def init_attr_values(self):
self.graph.set_domain(self.data)
@Inputs.data
def set_data(self, data):
self.clear_messages()
self._clear()
self.closeContext()
if data is not None:
if data and data.is_sparse():
self.Warning.sparse_not_supported()
data = None
elif data.domain.class_var is None:
self.Error.no_class_var()
data = None
elif data.domain.class_var.is_discrete and \
len(data.domain.class_var.values) < 2:
self.Error.not_enough_class_vars()
data = None
if data and len(data.domain.attributes) > data.X.shape[0]:
self.Error.features_exceeds_instances()
data = None
if data is not None:
valid_instances_count = self._prepare_freeviz_data(data)
if valid_instances_count > MAX_INSTANCES:
self.Error.too_many_data_instances()
data = None
elif valid_instances_count == 0:
self.Error.no_valid_data()
data = None
self.data = data
self.init_attr_values()
if data is not None:
self.cb_class_density.setEnabled(data.domain.has_discrete_class)
self.openContext(data)
self.btn_start.setEnabled(True)
else:
self.btn_start.setEnabled(False)
self._X = self._Y = None
self.graph.new_data(None, None)
@Inputs.data_subset
def set_subset_data(self, subset):
self.subset_data = subset
self.plotdata.subset_mask = None
self.controls.graph.alpha_value.setEnabled(subset is None)
def handleNewSignals(self):
if all(v is not None for v in [self.data, self.subset_data]):
dataids = self.data.ids.ravel()
subsetids = np.unique(self.subset_data.ids)
self._subset_mask = np.in1d(dataids, subsetids, assume_unique=True)
if self._X is not None:
self.setup_plot(True)
self.commit()
def customEvent(self, event):
if event.type() == OWFreeViz.ReplotRequest:
self.__replot_requested = False
self.setup_plot()
else:
super().customEvent(event)
def _prepare_freeviz_data(self, data):
X = data.X
Y = data.Y
mask = np.bitwise_or.reduce(np.isnan(X), axis=1)
mask |= np.isnan(Y)
validmask = ~mask
X = X[validmask, :]
Y = Y[validmask]
if not len(X):
self._X = None
return 0
if data.domain.class_var.is_discrete:
Y = Y.astype(int)
X = (X - np.mean(X, axis=0))
span = np.ptp(X, axis=0)
X[:, span > 0] /= span[span > 0].reshape(1, -1)
self._X = X
self._Y = Y
self._validmask = validmask
return len(X)
def setup_plot(self, reset_view=True):
assert not self._X is None
self.graph.jitter_continuous = True
self.__replot_requested = False
X = self.plotdata.X = self._X
self.plotdata.Y = self._Y
self.plotdata.validmask = self._validmask
self.plotdata.selection = self._selection if self._selection is not None else \
np.zeros(len(self._validmask), dtype=np.uint8)
anchors = self.plotdata.anchors
if len(anchors) == 0:
if self.initialization == self.Circular:
anchors = FreeViz.init_radial(X.shape[1])
else:
anchors = FreeViz.init_random(X.shape[1], 2)
EX = np.dot(X, anchors)
c = np.zeros((X.shape[0], X.shape[1]))
for i in range(X.shape[0]):
c[i] = np.argsort((np.power(X[i] * anchors[:, 0], 2) +
np.power(X[i] * anchors[:, 1], 2)))[::-1]
self.plotdata.topattrs = np.array(c, dtype=int)[:, :10]
radius = np.max(np.linalg.norm(EX, axis=1))
self.plotdata.anchors = anchors
coords = (EX / radius)
self.plotdata.embedding_coords = coords
if reset_view:
self.viewbox.setRange(RANGE)
self.viewbox.setAspectLocked(True, 1)
self.plot(reset_view=reset_view)
def randomize_indices(self):
X = self._X
self.plotdata.rand = np.random.choice(len(X), MAX_POINTS, replace=False) \
if len(X) > MAX_POINTS else None
def manual_move_anchor(self, show_anchors=True):
self.__replot_requested = False
X = self.plotdata.X = self._X
anchors = self.plotdata.anchors
validmask = self.plotdata.validmask
EX = np.dot(X, anchors)
data_x = self.data.X[validmask]
data_y = self.data.Y[validmask]
radius = np.max(np.linalg.norm(EX, axis=1))
if self.plotdata.rand is not None:
rand = self.plotdata.rand
EX = EX[rand]
data_x = data_x[rand]
data_y = data_y[rand]
selection = self.plotdata.selection[validmask]
selection = selection[rand]
else:
selection = self.plotdata.selection[validmask]
coords = (EX / radius)
if show_anchors:
self._anchor_circle()
attributes = () + self.data.domain.attributes + (self.variable_x, self.variable_y)
domain = Domain(attributes=attributes,
class_vars=self.data.domain.class_vars)
data = Table.from_numpy(domain, X=np.hstack((data_x, coords)),
Y=data_y)
self.graph.new_data(data, None)
self.graph.selection = selection
self.graph.update_data(self.variable_x, self.variable_y, reset_view=False)
def plot(self, reset_view=False, show_anchors=True):
if show_anchors:
self._anchor_circle()
attributes = () + self.data.domain.attributes + (self.variable_x, self.variable_y)
domain = Domain(attributes=attributes,
class_vars=self.data.domain.class_vars,
metas=self.data.domain.metas)
mask = self.plotdata.validmask
array = np.zeros((len(self.data), 2), dtype=np.float)
array[mask] = self.plotdata.embedding_coords
data = self.data.transform(domain)
data[:, self.variable_x] = array[:, 0].reshape(-1, 1)
data[:, self.variable_y] = array[:, 1].reshape(-1, 1)
subset_data = data[self._subset_mask & mask]\
if self._subset_mask is not None and len(self._subset_mask) else None
self.plotdata.data = data
self.graph.new_data(data[mask], subset_data)
if self.plotdata.selection is not None:
self.graph.selection = self.plotdata.selection[self.plotdata.validmask]
self.graph.update_data(self.variable_x, self.variable_y, reset_view=reset_view)
def reset_graph_data(self, *_):
if self.data is not None:
self.graph.rescale_data()
self._update_graph()
def _update_graph(self, reset_view=True, **_):
self.graph.zoomStack = []
assert not self.graph.data is None
self.graph.update_data(self.variable_x, self.variable_y, reset_view)
def update_density(self):
if self.graph.data is None:
return
self._update_graph(reset_view=False)
def selection_changed(self):
if self.graph.selection is not None:
pd = self.plotdata
pd.selection[pd.validmask] = self.graph.selection
self._selection = pd.selection
self.commit()
def prepare_data(self):
pass
def commit(self):
selected = annotated = components = None
graph = self.graph
if self.data is not None and self.plotdata.validmask is not None:
name = self.data.name
metas = () + self.data.domain.metas + (self.variable_x, self.variable_y)
domain = Domain(attributes=self.data.domain.attributes,
class_vars=self.data.domain.class_vars,
metas=metas)
data = self.plotdata.data.transform(domain)
validmask = self.plotdata.validmask
mask = np.array(validmask, dtype=int)
mask[mask == 1] = graph.selection if graph.selection is not None \
else [False * len(mask)]
selection = np.array([], dtype=np.uint8) if mask is None else np.flatnonzero(mask)
if len(selection):
selected = data[selection]
selected.name = name + ": selected"
selected.attributes = self.data.attributes
if graph.selection is not None and np.max(graph.selection) > 1:
annotated = create_groups_table(data, mask)
else:
annotated = create_annotated_table(data, selection)
annotated.attributes = self.data.attributes
annotated.name = name + ": annotated"
comp_domain = Domain(
self.data.domain.attributes,
metas=[StringVariable(name='component')])
metas = np.array([["FreeViz 1"], ["FreeViz 2"]])
components = Table.from_numpy(
comp_domain,
X=self.plotdata.anchors.T,
metas=metas)
components.name = name + ": components"
self.Outputs.selected_data.send(selected)
self.Outputs.annotated_data.send(annotated)
self.Outputs.components.send(components)
def send_report(self):
if self.data is None:
return
def name(var):
return var and var.name
caption = report.render_items_vert((
("Color", name(self.graph.attr_color)),
("Label", name(self.graph.attr_label)),
("Shape", name(self.graph.attr_shape)),
("Size", name(self.graph.attr_size)),
("Jittering", self.graph.jitter_size != 0 and "{} %".format(self.graph.jitter_size))))
self.report_plot()
if caption:
self.report_caption(caption)
def __init__(self, state):
QEvent.__init__(self, StateChangedEvent.StateChanged)
self._state = state
class OWCorrespondenceAnalysis(widget.OWWidget):
name = "Correspondence Analysis"
description = "Correspondence analysis for categorical multivariate data."
icon = "icons/CorrespondenceAnalysis.svg"
inputs = [("Data", Orange.data.Table, "set_data")]
Invalidate = QEvent.registerEventType()
settingsHandler = settings.DomainContextHandler()
selected_var_indices = settings.ContextSetting([])
graph_name = "plot.plotItem"
class Error(widget.OWWidget.Error):
empty_data = widget.Msg("Empty data set")
def __init__(self):
super().__init__()
self.data = None
self.component_x = 0
self.component_y = 1
box = gui.vBox(self.controlArea, "Variables")
self.varlist = itemmodels.VariableListModel()
self.varview = view = QListView(selectionMode=QListView.MultiSelection)
view.setModel(self.varlist)
view.selectionModel().selectionChanged.connect(self._var_changed)
box.layout().addWidget(view)
axes_box = gui.vBox(self.controlArea, "Axes")
box = gui.vBox(axes_box, "Axis X", margin=0)
box.setFlat(True)
self.axis_x_cb = gui.comboBox(box,
self,
"component_x",
callback=self._component_changed)
box = gui.vBox(axes_box, "Axis Y", margin=0)
box.setFlat(True)
self.axis_y_cb = gui.comboBox(box,
self,
"component_y",
callback=self._component_changed)
self.infotext = gui.widgetLabel(
gui.vBox(self.controlArea, "Contribution to Inertia"), "\n")
gui.rubber(self.controlArea)
self.plot = pg.PlotWidget(background="w")
self.plot.setMenuEnabled(False)
self.mainArea.layout().addWidget(self.plot)
def set_data(self, data):
self.closeContext()
self.clear()
if data is not None and not len(data):
self.Error.empty_data()
data = None
else:
self.Error.empty_data.clear()
self.data = data
if data is not None:
self.varlist[:] = [
var for var in data.domain.variables if var.is_discrete
]
self.selected_var_indices = [0, 1][:len(self.varlist)]
self.component_x, self.component_y = 0, 1
self.openContext(data)
self._restore_selection()
# self._invalidate()
self._update_CA()
def clear(self):
self.data = None
self.ca = None
self.plot.clear()
self.varlist[:] = []
def selected_vars(self):
rows = sorted(ind.row()
for ind in self.varview.selectionModel().selectedRows())
return [self.varlist[i] for i in rows]
def _restore_selection(self):
def restore(view, indices):
with itemmodels.signal_blocking(view.selectionModel()):
select_rows(view, indices)
restore(self.varview, self.selected_var_indices)
def _p_axes(self):
# return (0, 1)
return (self.component_x, self.component_y)
def _var_changed(self):
self.selected_var_indices = sorted(
ind.row() for ind in self.varview.selectionModel().selectedRows())
rfs = self.update_XY()
if rfs is not None:
if self.component_x >= rfs:
self.component_x = rfs - 1
if self.component_y >= rfs:
self.component_y = rfs - 1
self._invalidate()
def _component_changed(self):
if self.ca is not None:
self._setup_plot()
self._update_info()
def _invalidate(self):
self.__invalidated = True
QApplication.postEvent(self, QEvent(self.Invalidate))
def customEvent(self, event):
if event.type() == self.Invalidate:
self.ca = None
self.plot.clear()
self._update_CA()
return
return super().customEvent(event)
def _update_CA(self):
self.update_XY()
self.component_x, self.component_y = self.component_x, self.component_y
self._setup_plot()
self._update_info()
def update_XY(self):
self.axis_x_cb.clear()
self.axis_y_cb.clear()
ca_vars = self.selected_vars()
if len(ca_vars) == 0:
return
multi = len(ca_vars) != 2
if multi:
_, ctable = burt_table(self.data, ca_vars)
else:
ctable = contingency.get_contingency(self.data, *ca_vars[::-1])
self.ca = correspondence(ctable, )
rfs = self.ca.row_factors.shape[1]
axes = ["{}".format(i + 1) for i in range(rfs)]
self.axis_x_cb.addItems(axes)
self.axis_y_cb.addItems(axes)
return rfs
def _setup_plot(self):
self.plot.clear()
points = self.ca
variables = self.selected_vars()
colors = colorpalette.ColorPaletteGenerator(len(variables))
p_axes = self._p_axes()
if points == None:
return
if len(variables) == 2:
row_points = self.ca.row_factors[:, p_axes]
col_points = self.ca.col_factors[:, p_axes]
points = [row_points, col_points]
else:
points = self.ca.row_factors[:, p_axes]
counts = [len(var.values) for var in variables]
range_indices = numpy.cumsum([0] + counts)
ranges = zip(range_indices, range_indices[1:])
points = [points[s:e] for s, e in ranges]
for i, (v, points) in enumerate(zip(variables, points)):
color_outline = colors[i]
color_outline.setAlpha(200)
color = QColor(color_outline)
color.setAlpha(120)
item = ScatterPlotItem(
x=points[:, 0],
y=points[:, 1],
brush=QBrush(color),
pen=pg.mkPen(color_outline.darker(120), width=1.5),
size=numpy.full((points.shape[0], ), 10.1),
)
self.plot.addItem(item)
for name, point in zip(v.values, points):
item = pg.TextItem(name, anchor=(0.5, 0))
self.plot.addItem(item)
item.setPos(point[0], point[1])
inertia = self.ca.inertia_of_axis()
if numpy.sum(inertia) == 0:
inertia = 100 * inertia
else:
inertia = 100 * inertia / numpy.sum(inertia)
ax = self.plot.getAxis("bottom")
ax.setLabel("Component {} ({:.1f}%)".format(p_axes[0] + 1,
inertia[p_axes[0]]))
ax = self.plot.getAxis("left")
ax.setLabel("Component {} ({:.1f}%)".format(p_axes[1] + 1,
inertia[p_axes[1]]))
def _update_info(self):
if self.ca is None:
self.infotext.setText("\n\n")
else:
fmt = ("Axis 1: {:.2f}\n" "Axis 2: {:.2f}")
inertia = self.ca.inertia_of_axis()
if numpy.sum(inertia) == 0:
inertia = 100 * inertia
else:
inertia = 100 * inertia / numpy.sum(inertia)
ax1, ax2 = self._p_axes()
self.infotext.setText(fmt.format(inertia[ax1], inertia[ax2]))
def send_report(self):
if self.data is None:
return
vars = self.selected_vars()
if not vars:
return
items = OrderedDict()
items["Data instances"] = len(self.data)
if len(vars) == 1:
items["Selected variable"] = vars[0]
else:
items["Selected variables"] = "{} and {}".format(
", ".join(var.name for var in vars[:-1]), vars[-1].name)
self.report_items(items)
self.report_plot()
def scheduleDelayedActivate(self):
if self.isEnabled() and not self.__layoutPending:
self.__layoutPending = True
QApplication.postEvent(self, QEvent(QEvent.LayoutRequest))
def close(self):
QCoreApplication.sendEvent(self, QEvent(QEvent.Close))
def start(self):
QCoreApplication.postEvent(self, QEvent(Task.__ExecuteCall))
class ActivateParentEvent(QEvent):
ActivateParent = QEvent.registerEventType()
def __init__(self):
QEvent.__init__(self, self.ActivateParent)
def __init__(self):
QEvent.__init__(self, ExecuteCallEvent.ExecuteCall)
def __init__(self):
QEvent.__init__(self, self.ActivateParent)
def showPopup(self):
# type: () -> None
"""
Reimplemented from QComboBox.showPopup
Popup up a customized view and filter edit line.
Note
----
The .popup(), .lineEdit(), .completer() of the base class are not used.
"""
if self.__popup is not None:
# We have user entered state that cannot be disturbed
# (entered filter text, scroll offset, ...)
return # pragma: no cover
if self.count() == 0:
return
opt = QStyleOptionComboBox()
self.initStyleOption(opt)
popup = QListView(
uniformItemSizes=True,
horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff,
verticalScrollBarPolicy=Qt.ScrollBarAsNeeded,
iconSize=self.iconSize(),
)
popup.setFocusProxy(self.__searchline)
popup.setParent(self, Qt.Popup | Qt.FramelessWindowHint)
popup.setItemDelegate(_ComboBoxListDelegate(popup))
proxy = QSortFilterProxyModel(popup,
filterCaseSensitivity=Qt.CaseInsensitive)
proxy.setFilterKeyColumn(self.modelColumn())
proxy.setSourceModel(self.model())
popup.setModel(proxy)
root = proxy.mapFromSource(self.rootModelIndex())
popup.setRootIndex(root)
self.__popup = popup
self.__proxy = proxy
self.__searchline.setText("")
self.__searchline.setPlaceholderText("Filter...")
self.__searchline.setVisible(True)
self.__searchline.textEdited.connect(proxy.setFilterFixedString)
style = self.style() # type: QStyle
popuprect_origin = style.subControlRect(QStyle.CC_ComboBox, opt,
QStyle.SC_ComboBoxListBoxPopup,
self) # type: QRect
if sys.platform == "darwin":
slmargin = self.__searchline.style() \
.pixelMetric(QStyle.PM_FocusFrameVMargin)
popuprect_origin.adjust(slmargin / 2, 0, -slmargin * 1.5, slmargin)
popuprect_origin = QRect(self.mapToGlobal(popuprect_origin.topLeft()),
popuprect_origin.size())
editrect = style.subControlRect(QStyle.CC_ComboBox, opt,
QStyle.SC_ComboBoxEditField,
self) # type: QRect
self.__searchline.setGeometry(editrect)
desktop = QApplication.desktop()
screenrect = desktop.availableGeometry(self) # type: QRect
# get the height for the view
listrect = QRect()
for i in range(min(proxy.rowCount(root), self.maxVisibleItems())):
index = proxy.index(i, self.modelColumn(), root)
if index.isValid():
listrect = listrect.united(popup.visualRect(index))
if listrect.height() >= screenrect.height():
break
window = popup.window() # type: QWidget
window.ensurePolished()
if window.layout() is not None:
window.layout().activate()
else:
QApplication.sendEvent(window, QEvent(QEvent.LayoutRequest))
margins = qwidget_margin_within(popup.viewport(), window)
height = (listrect.height() + 2 * popup.spacing() + margins.top() +
margins.bottom())
popup_size = (QSize(popuprect_origin.width(), height).expandedTo(
window.minimumSize()).boundedTo(window.maximumSize()).boundedTo(
screenrect.size()))
popuprect = QRect(popuprect_origin.bottomLeft(), popup_size)
popuprect = dropdown_popup_geometry(popuprect, popuprect_origin,
screenrect)
popup.setGeometry(popuprect)
current = proxy.mapFromSource(self.model().index(
self.currentIndex(), self.modelColumn(), self.rootModelIndex()))
popup.setCurrentIndex(current)
popup.scrollTo(current, QAbstractItemView.EnsureVisible)
popup.show()
popup.setFocus(Qt.PopupFocusReason)
popup.installEventFilter(self)
popup.viewport().installEventFilter(self)
popup.viewport().setMouseTracking(True)
self.update()
self.__popupTimer.restart()
def __init__(self):
super().__init__()
#: widget's runtime state
self.__state = State.NoState
self.corpus = None
self.n_text_categories = 0
self.n_text_data = 0
self.n_skipped = 0
self.__invalidated = False
self.__pendingTask = None
vbox = gui.vBox(self.controlArea)
hbox = gui.hBox(vbox)
self.recent_cb = QComboBox(
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon,
minimumContentsLength=16,
acceptDrops=True
)
self.recent_cb.installEventFilter(self)
self.recent_cb.activated[int].connect(self.__onRecentActivated)
browseaction = QAction(
"Open/Load Documents", self,
iconText="\N{HORIZONTAL ELLIPSIS}",
icon=self.style().standardIcon(QStyle.SP_DirOpenIcon),
toolTip="Select a folder from which to load the documents"
)
browseaction.triggered.connect(self.__runOpenDialog)
reloadaction = QAction(
"Reload", self,
icon=self.style().standardIcon(QStyle.SP_BrowserReload),
toolTip="Reload current document set"
)
reloadaction.triggered.connect(self.reload)
self.__actions = namespace(
browse=browseaction,
reload=reloadaction,
)
browsebutton = QPushButton(
browseaction.iconText(),
icon=browseaction.icon(),
toolTip=browseaction.toolTip(),
clicked=browseaction.trigger
)
reloadbutton = QPushButton(
reloadaction.iconText(),
icon=reloadaction.icon(),
clicked=reloadaction.trigger,
default=True,
)
hbox.layout().addWidget(self.recent_cb)
hbox.layout().addWidget(browsebutton)
hbox.layout().addWidget(reloadbutton)
self.addActions([browseaction, reloadaction])
reloadaction.changed.connect(
lambda: reloadbutton.setEnabled(reloadaction.isEnabled())
)
box = gui.vBox(vbox, "Info")
self.infostack = QStackedWidget()
self.info_area = QLabel(
text="No document set selected",
wordWrap=True
)
self.progress_widget = QProgressBar(
minimum=0, maximum=100
)
self.cancel_button = QPushButton(
"Cancel", icon=self.style().standardIcon(QStyle.SP_DialogCancelButton),
)
self.cancel_button.clicked.connect(self.cancel)
w = QWidget()
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.addWidget(self.progress_widget)
hlayout.addWidget(self.cancel_button)
vlayout.addLayout(hlayout)
self.pathlabel = TextLabel()
self.pathlabel.setTextElideMode(Qt.ElideMiddle)
self.pathlabel.setAttribute(Qt.WA_MacSmallSize)
vlayout.addWidget(self.pathlabel)
w.setLayout(vlayout)
self.infostack.addWidget(self.info_area)
self.infostack.addWidget(w)
box.layout().addWidget(self.infostack)
self.__initRecentItemsModel()
self.__invalidated = True
self.__executor = ThreadExecutor(self)
QApplication.postEvent(self, QEvent(RuntimeEvent.Init))
def setPalette(self, palette):
# type: (QPalette) -> None
if self.__palette != palette:
self.__palette = QPalette(palette)
QApplication.sendEvent(self, QEvent(QEvent.PaletteChange))
class WorkflowEvent(QEvent):
#: Delivered to Scheme when a node has been added
NodeAdded = QEvent.registerEventType()
#: Delivered to Scheme when a node has been removed
NodeRemoved = QEvent.registerEventType()
#: A Link has been added to the scheme
LinkAdded = QEvent.registerEventType()
#: A Link has been removed from the scheme
LinkRemoved = QEvent.registerEventType()
#: Node's (runtime) state has changed
NodeStateChange = QEvent.registerEventType()
#: Link's (runtime) state has changed
LinkStateChange = QEvent.registerEventType()
#: Request for Node's runtime initialization (e.g.
#: load required data, establish connection, ...)
NodeInitialize = QEvent.registerEventType()
#: Restore the node from serialized state
NodeRestore = QEvent.registerEventType()
NodeSaveStateRequest = QEvent.registerEventType() # ?
#: Node user activate request (e.g. on double click in the
#: canvas GUI)
NodeActivateRequest = QEvent.registerEventType()
# Workflow runtime changed (Running/Paused/Stopped, ...)
RuntimeStateChange = QEvent.registerEventType()
#: Workflow resource changed (e.g. work directory, env variable)
WorkflowResourceChange = QEvent.registerEventType()
#: Workflow is about to close.
WorkflowAboutToClose = QEvent.registerEventType()
WorkflowClose = QEvent.registerEventType()
AnnotationAdded = QEvent.registerEventType()
AnnotationRemoved = QEvent.registerEventType()
AnnotationChange = QEvent.registerEventType()
#: Request activation (show and raise) of the window containing
#: the workflow view
ActivateParentRequest = QEvent.registerEventType()
def __init__(self, etype):
QEvent.__init__(self, etype)
def eventFilter(self, obj: QDateTimeEdit, event: QEvent) -> bool:
if event.type() == QEvent.Wheel:
return True
return super().eventFilter(obj, event)
def __init__(self, etype):
QEvent.__init__(self, etype)
def viewportEvent(self, event: QEvent) -> bool:
if event.type() == QEvent.Resize:
self._layout()
return super().viewportEvent(event)
class AsyncUpdateLoop(QObject):
"""
Run/drive an coroutine from the event loop.
This is a utility class which can be used for implementing
asynchronous update loops. I.e. coroutines which periodically yield
control back to the Qt event loop.
"""
Next = QEvent.registerEventType()
#: State flags
Idle, Running, Cancelled, Finished = 0, 1, 2, 3
#: The coroutine has yielded control to the caller (with `object`)
yielded = Signal(object)
#: The coroutine has finished/exited (either with an exception
#: or with a return statement)
finished = Signal()
#: The coroutine has returned (normal return statement / StopIteration)
returned = Signal(object)
#: The coroutine has exited with with an exception.
raised = Signal(object)
#: The coroutine was cancelled/closed.
cancelled = Signal()
def __init__(self, parent=None, **kwargs):
super().__init__(parent, **kwargs)
self.__coroutine = None
self.__next_pending = False # Flag for compressing scheduled events
self.__in_next = False
self.__state = AsyncUpdateLoop.Idle
@Slot(object)
def setCoroutine(self, loop):
"""
Set the coroutine.
The coroutine will be resumed (repeatedly) from the event queue.
If there is an existing coroutine set it is first closed/cancelled.
Raises an RuntimeError if the current coroutine is running.
"""
if self.__coroutine is not None:
self.__coroutine.close()
self.__coroutine = None
self.__state = AsyncUpdateLoop.Cancelled
self.cancelled.emit()
self.finished.emit()
if loop is not None:
self.__coroutine = loop
self.__state = AsyncUpdateLoop.Running
self.__schedule_next()
@Slot()
def cancel(self):
"""
Cancel/close the current coroutine.
Raises an RuntimeError if the current coroutine is running.
"""
self.setCoroutine(None)
def state(self):
"""
Return the current state.
"""
return self.__state
def isRunning(self):
return self.__state == AsyncUpdateLoop.Running
def __schedule_next(self):
if not self.__next_pending:
self.__next_pending = True
QTimer.singleShot(10, self.__on_timeout)
def __next(self):
if self.__coroutine is not None:
try:
rval = next(self.__coroutine)
except StopIteration as stop:
self.__state = AsyncUpdateLoop.Finished
self.returned.emit(stop.value)
self.finished.emit()
self.__coroutine = None
except BaseException as er:
self.__state = AsyncUpdateLoop.Finished
self.raised.emit(er)
self.finished.emit()
self.__coroutine = None
else:
self.yielded.emit(rval)
self.__schedule_next()
@Slot()
def __on_timeout(self):
assert self.__next_pending
self.__next_pending = False
if not self.__in_next:
self.__in_next = True
try:
self.__next()
finally:
self.__in_next = False
else:
# warn
self.__schedule_next()
def customEvent(self, event):
if event.type() == AsyncUpdateLoop.Next:
self.__on_timeout()
else:
super().customEvent(event)
def __init__(self):
QEvent.__init__(self, ExecuteCallEvent.ExecuteCall)
def __init__(self):
super().__init__()
#: widget's runtime state
self.__state = State.NoState
self.corpus = None
self.n_text_categories = 0
self.n_text_data = 0
self.skipped_documents = []
self.__invalidated = False
self.__pendingTask = None
layout = QGridLayout()
layout.setSpacing(4)
gui.widgetBox(self.controlArea, orientation=layout, box='Source')
source_box = gui.radioButtons(None, self, "source", box=True,
callback=self.start, addToLayout=False)
rb_button = gui.appendRadioButton(source_box, "Folder:",
addToLayout=False)
layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter)
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.Fixed)
self.recent_cb = QComboBox(
sizeAdjustPolicy=QComboBox.AdjustToMinimumContentsLengthWithIcon,
minimumContentsLength=16,
acceptDrops=True
)
self.recent_cb.installEventFilter(self)
self.recent_cb.activated[int].connect(self.__onRecentActivated)
browseaction = QAction(
"Open/Load Documents", self,
iconText="\N{HORIZONTAL ELLIPSIS}",
icon=self.style().standardIcon(QStyle.SP_DirOpenIcon),
toolTip="Select a folder from which to load the documents"
)
browseaction.triggered.connect(self.__runOpenDialog)
reloadaction = QAction(
"Reload", self,
icon=self.style().standardIcon(QStyle.SP_BrowserReload),
toolTip="Reload current document set"
)
reloadaction.triggered.connect(self.reload)
self.__actions = namespace(
browse=browseaction,
reload=reloadaction,
)
browsebutton = QPushButton(
browseaction.iconText(),
icon=browseaction.icon(),
toolTip=browseaction.toolTip(),
clicked=browseaction.trigger,
default=False,
autoDefault=False,
)
reloadbutton = QPushButton(
reloadaction.iconText(),
icon=reloadaction.icon(),
clicked=reloadaction.trigger,
default=False,
autoDefault=False,
)
box.layout().addWidget(self.recent_cb)
layout.addWidget(box, 0, 1)
layout.addWidget(browsebutton, 0, 2)
layout.addWidget(reloadbutton, 0, 3)
rb_button = gui.appendRadioButton(source_box, "URL:", addToLayout=False)
layout.addWidget(rb_button, 3, 0, Qt.AlignVCenter)
self.url_combo = url_combo = QComboBox()
url_model = PyListModel()
url_model.wrap(self.recent_urls)
url_combo.setLineEdit(LineEditSelectOnFocus())
url_combo.setModel(url_model)
url_combo.setSizePolicy(QSizePolicy.Ignored, QSizePolicy.Fixed)
url_combo.setEditable(True)
url_combo.setInsertPolicy(url_combo.InsertAtTop)
url_edit = url_combo.lineEdit()
l, t, r, b = url_edit.getTextMargins()
url_edit.setTextMargins(l + 5, t, r, b)
layout.addWidget(url_combo, 3, 1, 1, 3)
url_combo.activated.connect(self._url_set)
# whit completer we set that combo box is case sensitive when
# matching the history
completer = QCompleter()
completer.setCaseSensitivity(Qt.CaseSensitive)
url_combo.setCompleter(completer)
self.addActions([browseaction, reloadaction])
reloadaction.changed.connect(
lambda: reloadbutton.setEnabled(reloadaction.isEnabled())
)
box = gui.vBox(self.controlArea, "Info")
self.infostack = QStackedWidget()
self.info_area = QLabel(
text="No document set selected",
wordWrap=True
)
self.progress_widget = QProgressBar(
minimum=0, maximum=100
)
self.cancel_button = QPushButton(
"Cancel",
icon=self.style().standardIcon(QStyle.SP_DialogCancelButton),
default=False,
autoDefault=False,
)
self.cancel_button.clicked.connect(self.cancel)
w = QWidget()
vlayout = QVBoxLayout()
vlayout.setContentsMargins(0, 0, 0, 0)
hlayout = QHBoxLayout()
hlayout.setContentsMargins(0, 0, 0, 0)
hlayout.addWidget(self.progress_widget)
hlayout.addWidget(self.cancel_button)
vlayout.addLayout(hlayout)
self.pathlabel = TextLabel()
self.pathlabel.setTextElideMode(Qt.ElideMiddle)
self.pathlabel.setAttribute(Qt.WA_MacSmallSize)
vlayout.addWidget(self.pathlabel)
w.setLayout(vlayout)
self.infostack.addWidget(self.info_area)
self.infostack.addWidget(w)
box.layout().addWidget(self.infostack)
self.__initRecentItemsModel()
self.__invalidated = True
self.__executor = ThreadExecutor(self)
QApplication.postEvent(self, QEvent(RuntimeEvent.Init))
def __init__(self):
QEvent.__init__(self, self.ActivateParent)
def main(argv=None):
app = QApplication(list(argv) if argv else [])
argv = app.arguments()
parser = argparse.ArgumentParser(
description=(
"Run an orange workflow without showing a GUI and exit "
"when it completes.\n\n"
"WARNING: This is experimental as Orange is not designed to run "
"non-interactive."
)
)
parser.add_argument("--log-level", "-l", metavar="LEVEL", type=int,
default=logging.CRITICAL, dest="log_level")
parser.add_argument("--config", default="Orange.canvas.config.Config",
type=str)
parser.add_argument("file")
args = parser.parse_args(argv[1:])
log_level = args.log_level
filename = args.file
logging.basicConfig(level=log_level)
cfg_class = utils.name_lookup(args.config)
cfg: config.Config = cfg_class()
config.set_default(cfg)
config.init()
reg = WidgetRegistry()
widget_discovery = cfg.widget_discovery(
reg, cached_descriptions=cache.registry_cache()
)
widget_discovery.run(cfg.widgets_entry_points())
model = cfg.workflow_constructor()
model.set_runtime_env(
"basedir", os.path.abspath(os.path.dirname(filename))
)
sigprop = model.findChild(signalmanager.SignalManager)
sigprop.pause() # Pause signal propagation during load
with open(filename, "rb") as f:
model.load_from(f, registry=reg)
# Ensure all widgets are created (this is required for the workflow
# to even start - relies to much on OWWidget behaviour).
for _ in map(model.widget_for_node, model.nodes):
pass
sigprop.resume() # Resume inter-widget signal propagation
def on_finished():
severity = 0
for node in model.nodes:
for msg in node.state_messages():
if msg.contents and msg.severity == msg.Error:
print(msg.contents, msg.message_id, file=sys.stderr)
severity = msg.Error
if severity == UserMessage.Error:
app.exit(1)
else:
app.exit()
sigprop.finished.connect(on_finished)
rval = app.exec_()
model.clear()
# Notify the workflow model to 'close'.
QApplication.sendEvent(model, QEvent(QEvent.Close))
app.processEvents()
return rval