def test_create(self, SettingProvider):
""":type SettingProvider: unittest.mock.Mock"""
with patch.object(SettingsHandler, 'read_defaults'):
handler = SettingsHandler.create(SimpleWidget)
self.assertEqual(handler.widget_class, SimpleWidget)
# create needs to create a SettingProvider which traverses
# the widget definition and collects all settings and read
# all settings and for widget class
SettingProvider.assert_called_once_with(SimpleWidget)
SettingsHandler.read_defaults.assert_called_once_with()
def test_initialize_with_no_provider(self, SettingProvider):
""":type SettingProvider: unittest.mock.Mock"""
handler = SettingsHandler()
handler.provider = Mock(get_provider=Mock(return_value=None))
provider = Mock()
SettingProvider.return_value = provider
widget = SimpleWidget()
# initializing an undeclared provider should display a warning
with warnings.catch_warnings(record=True) as w:
handler.initialize(widget)
self.assertEqual(1, len(w))
SettingProvider.assert_called_once_with(SimpleWidget)
provider.initialize.assert_called_once_with(widget, None)
class BaseWidget:
settingsHandler = None
show_graph = Setting(True)
graph = SettingProvider(Graph)
def __init__(self):
initialize_settings(self)
self.graph = Graph()
class MockWidget(OWWidget):
name = 'MockWidget'
want_main_area = False
filter_component = SettingProvider(CollapsibleFilterComponent)
pagination_component = SettingProvider(PaginationComponent)
pagination_availability = pyqtSignal(bool, bool)
@patch(
'orangecontrib.bioinformatics.widgets.components.resolwe.get_credential_manager',
return_value=CredentialManager('resolwe_credentials_test'),
)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.filter_component = CollapsibleFilterComponent(
self, self.controlArea)
self.pagination_component = PaginationComponent(self, self.controlArea)
self.sign_in_dialog = SignIn(self)
class Widget(BaseWidget):
show_zoom_toolbar = Setting(True)
zoom_toolbar = SettingProvider(ZoomToolbar)
def __init__(self):
super().__init__()
initialize_settings(self)
self.zoom_toolbar = ZoomToolbar()
class MyWidget(OWWidget):
name = "Dummy"
field = Setting(42)
component = SettingProvider(DummyComponent)
def __init__(self):
super().__init__()
self.component = DummyComponent(self)
self.widget = None
class MockWidget(OWWidget):
name = 'Mock'
want_main_area = False
selection_component = SettingProvider(GeneSetSelection)
class Error(OWWidget.Error):
custom_gene_sets_table_format = Msg('FooBar')
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.selection_component = GeneSetSelection(self, self.controlArea)
class MyWidget(OWWidget):
foo = True
component = SettingProvider(DummyComponent)
def __init__(self):
super().__init__()
self.component = DummyComponent(self)
self.foo_control = gui.checkBox(self.controlArea, self, "foo", "")
self.component_foo_control = gui.checkBox(self.controlArea, self,
"component.foo", "")
class OWCurves(OWWidget):
name = "Curves"
inputs = [("Data", Orange.data.Table, 'set_data', Default),
("Data subset", Orange.data.Table, 'set_subset', Default)]
outputs = [("Selection", Orange.data.Table), ("Data", Orange.data.Table)]
icon = "icons/curves.svg"
settingsHandler = DomainContextHandler(metas_in_res=True)
curveplot = SettingProvider(CurvePlot)
class Information(OWWidget.Information):
showing_sample = Msg("Showing {} of {} curves.")
class Warning(OWWidget.Warning):
no_x = Msg("No continuous features in input data.")
def __init__(self):
super().__init__()
self.controlArea.hide()
self.curveplot = CurvePlot(self, select=SELECTMANY)
self.mainArea.layout().addWidget(self.curveplot)
self.resize(900, 700)
self.graph_name = "curveplot.plotview"
def set_data(self, data):
self.Information.showing_sample.clear()
self.Warning.no_x.clear()
self.closeContext()
self.curveplot.set_data(data)
self.openContext(data)
self.curveplot.update_view()
if data is not None and not len(self.curveplot.data_x):
self.Warning.no_x()
if self.curveplot.sampled_indices \
and len(self.curveplot.sampled_indices) != len(self.curveplot.data):
self.Information.showing_sample(
len(self.curveplot.sampled_indices), len(data))
self.selection_changed()
def set_subset(self, data):
self.curveplot.set_data_subset(data.ids if data else None)
def selection_changed(self):
annotated = create_annotated_table(
self.curveplot.data, sorted(self.curveplot.selected_indices))
self.send("Data", annotated)
selected = None
if self.curveplot.selected_indices and self.curveplot.data:
selected = self.curveplot.data[sorted(
self.curveplot.selected_indices)]
self.send("Selection", selected)
class SimpleWidget:
settings_version = 1
setting = Setting(42)
schema_only_setting = Setting(None, schema_only=True)
non_setting = 5
component = SettingProvider(Component)
def __init__(self):
self.component = Component()
migrate_settings = Mock()
migrate_context = Mock()
class SimpleWidget(QObject):
settings_version = 1
setting = Setting(42)
schema_only_setting = Setting(None, schema_only=True)
list_setting = Setting([])
non_setting = 5
component = SettingProvider(Component)
settingsAboutToBePacked = Signal()
def __init__(self):
super().__init__()
self.component = Component()
migrate_settings = Mock()
migrate_context = Mock()
class OWManifoldLearning(OWWidget):
name = "流形学习(Manifold Learning)"
description = "非线性降维。"
icon = "icons/Manifold.svg"
priority = 2200
keywords = []
settings_version = 2
class Inputs:
data = Input("数据(Data)", Table, replaces=['Data'])
class Outputs:
transformed_data = Output("转换的数据(Transformed data)", Table, dynamic=False, replaces=['Transformed data'])
MANIFOLD_METHODS = (TSNE, MDS, Isomap, LocallyLinearEmbedding,
SpectralEmbedding)
tsne_editor = SettingProvider(TSNEParametersEditor)
mds_editor = SettingProvider(MDSParametersEditor)
isomap_editor = SettingProvider(IsomapParametersEditor)
lle_editor = SettingProvider(LocallyLinearEmbeddingParametersEditor)
spectral_editor = SettingProvider(SpectralEmbeddingParametersEditor)
resizing_enabled = False
want_main_area = False
manifold_method_index = Setting(0)
n_components = Setting(2)
auto_apply = Setting(True)
class Error(OWWidget.Error):
n_neighbors_too_small = Msg("For chosen method and components, "
"neighbors must be greater than {}")
manifold_error = Msg("{}")
sparse_not_supported = Msg("Sparse data is not supported.")
out_of_memory = Msg("Out of memory")
class Warning(OWWidget.Warning):
graph_not_connected = Msg("Disconnected graph, embedding may not work")
@classmethod
def migrate_settings(cls, settings, version):
if version < 2:
tsne_settings = settings.get('tsne_editor', {})
# Fixup initialization index
if 'init_index' in tsne_settings:
idx = tsne_settings.pop('init_index')
idx = min(idx, len(TSNEParametersEditor.initialization_values))
tsne_settings['initialization_index'] = idx
# We removed several metrics here
if 'metric_index' in tsne_settings:
idx = tsne_settings['metric_index']
idx = min(idx, len(TSNEParametersEditor.metric_values))
tsne_settings['metric_index'] = idx
def __init__(self):
self.data = None
# GUI
method_box = gui.vBox(self.controlArea, "方法")
self.manifold_methods_combo = gui.comboBox(
method_box, self, "manifold_method_index",
items=[m.name for m in self.MANIFOLD_METHODS],
callback=self.manifold_method_changed)
self.params_box = gui.vBox(self.controlArea, "参数")
self.tsne_editor = TSNEParametersEditor(self)
self.mds_editor = MDSParametersEditor(self)
self.isomap_editor = IsomapParametersEditor(self)
self.lle_editor = LocallyLinearEmbeddingParametersEditor(self)
self.spectral_editor = SpectralEmbeddingParametersEditor(self)
self.parameter_editors = [
self.tsne_editor, self.mds_editor, self.isomap_editor,
self.lle_editor, self.spectral_editor]
for editor in self.parameter_editors:
self.params_box.layout().addWidget(editor)
editor.hide()
self.params_widget = self.parameter_editors[self.manifold_method_index]
self.params_widget.show()
output_box = gui.vBox(self.controlArea, "输出")
self.n_components_spin = gui.spin(
output_box, self, "n_components", 1, 10, label="成分:",
alignment=Qt.AlignRight, callbackOnReturn=True,
callback=self.settings_changed)
self.apply_button = gui.auto_apply(self.controlArea, self, box=False, commit=self.apply)
def manifold_method_changed(self):
self.params_widget.hide()
self.params_widget = self.parameter_editors[self.manifold_method_index]
self.params_widget.show()
self.apply()
def settings_changed(self):
self.apply()
@Inputs.data
def set_data(self, data):
self.data = data
self.n_components_spin.setMaximum(len(self.data.domain.attributes)
if self.data else 10)
self.unconditional_apply()
def apply(self):
builtin_warn = warnings.warn
def _handle_disconnected_graph_warning(msg, *args, **kwargs):
if msg.startswith("Graph is not fully connected"):
self.Warning.graph_not_connected()
else:
builtin_warn(msg, *args, **kwargs)
out = None
data = self.data
method = self.MANIFOLD_METHODS[self.manifold_method_index]
have_data = data is not None and len(data)
self.Error.clear()
self.Warning.clear()
if have_data and data.is_sparse():
self.Error.sparse_not_supported()
elif have_data:
domain = Domain([ContinuousVariable("C{}".format(i))
for i in range(self.n_components)],
data.domain.class_vars,
data.domain.metas)
try:
warnings.warn = _handle_disconnected_graph_warning
projector = method(**self.get_method_parameters(data, method))
model = projector(data)
if isinstance(model, TSNEModel):
out = model.embedding
else:
X = model.embedding_
out = Table(domain, X, data.Y, data.metas)
except ValueError as e:
if e.args[0] == "for method='hessian', n_neighbors " \
"must be greater than [n_components" \
" * (n_components + 3) / 2]":
n = self.n_components * (self.n_components + 3) / 2
self.Error.n_neighbors_too_small("{}".format(n))
else:
self.Error.manifold_error(e.args[0])
except MemoryError:
self.Error.out_of_memory()
except np.linalg.linalg.LinAlgError as e:
self.Error.manifold_error(str(e))
finally:
warnings.warn = builtin_warn
self.Outputs.transformed_data.send(out)
def get_method_parameters(self, data, method):
parameters = dict(n_components=self.n_components)
parameters.update(self.params_widget.get_parameters())
return parameters
def send_report(self):
method = self.MANIFOLD_METHODS[self.manifold_method_index]
self.report_items((("Method", method.name),))
parameters = self.get_method_parameters(self.data, method)
self.report_items("Method parameters", tuple(parameters.items()))
if self.data:
self.report_data("Data", self.data)
class OWKaplanMeier(OWWidget):
name = 'Kaplan-Meier Plot'
# TODO
description = ''
# TODO
icon = ''
priority = 0
show_confidence_interval: bool
show_confidence_interval = Setting(False)
show_median_line: bool
show_median_line = Setting(False)
show_censored_data: bool
show_censored_data = Setting(False)
settingsHandler = PerfectDomainContextHandler()
time_var = ContextSetting(None)
event_var = ContextSetting(None)
group_var: Optional[DiscreteVariable] = ContextSetting(None)
graph = SettingProvider(KaplanMeierPlot)
auto_commit: bool = Setting(False, schema_only=True)
class Inputs:
data = Input('Data', Table)
class Outputs:
selected_data = Output('Data', Table)
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.data: Optional[Table] = None
self.plot_curves = None
time_var_model = DomainModel(valid_types=(ContinuousVariable, ))
event_var_model = DomainModel(valid_types=DomainModel.PRIMITIVE)
group_var_model = DomainModel(placeholder='(None)',
valid_types=(DiscreteVariable, ))
box = gui.vBox(self.controlArea, 'Time', margin=0)
gui.comboBox(box,
self,
'time_var',
model=time_var_model,
callback=self.on_controls_changed)
box = gui.vBox(self.controlArea, 'Event', margin=0)
gui.comboBox(box,
self,
'event_var',
model=event_var_model,
callback=self.on_controls_changed)
box = gui.vBox(self.controlArea, 'Group', margin=0)
gui.comboBox(box,
self,
'group_var',
model=group_var_model,
callback=self.on_controls_changed)
box = gui.vBox(self.controlArea, 'Display options')
gui.checkBox(
box,
self,
'show_confidence_interval',
label='Confidence intervals',
callback=self.on_display_option_changed,
)
gui.checkBox(
box,
self,
'show_median_line',
label='Median',
callback=self.on_display_option_changed,
)
gui.checkBox(
box,
self,
'show_censored_data',
label='Censored data',
callback=self.on_display_option_changed,
)
self.graph: KaplanMeierPlot = KaplanMeierPlot(parent=self)
self.graph.selection_changed.connect(self.commit)
self.mainArea.layout().addWidget(self.graph)
plot_gui = OWPlotGUI(self)
plot_gui.box_zoom_select(self.controlArea)
gui.rubber(self.controlArea)
self.commit_button = gui.auto_commit(self.controlArea,
self,
'auto_commit',
'&Commit',
box=False)
@Inputs.data
def set_data(self, data: Table):
self.closeContext()
if not data:
return
self.data = data
self.controls.time_var.model().set_domain(data.domain)
self.controls.event_var.model().set_domain(data.domain)
self.controls.group_var.model().set_domain(data.domain)
self.time_var = None
self.event_var = None
self.group_var = None
self.graph.selection = {}
self.openContext(data.domain)
self.graph.curves = {
curve_id: curve
for curve_id, curve in enumerate(self.generate_plot_curves())
}
self.graph.update_plot(**self._get_plot_options())
self.commit()
def _get_plot_options(self):
return {
'confidence_interval': self.show_confidence_interval,
'median': self.show_median_line,
'censored': self.show_censored_data,
}
def on_display_option_changed(self) -> None:
self.graph.update_plot(**self._get_plot_options())
def on_controls_changed(self):
if not self.data:
return
self.graph.curves = {
curve_id: curve
for curve_id, curve in enumerate(self.generate_plot_curves())
}
self.graph.clear_selection()
self.graph.update_plot(**self._get_plot_options())
self.commit()
def _get_discrete_var_color(self, index: Optional[int]):
if self.group_var is not None and index is not None:
return list(self.group_var.colors[index])
def generate_plot_curves(self) -> List[EstimatedFunctionCurve]:
if self.time_var is None or self.event_var is None:
return []
time, _ = self.data.get_column_view(self.time_var)
events, _ = self.data.get_column_view(self.event_var)
# time = np.array([2.5, 4, 4, 5, 6, 6])
# events = np.array([1, 1, 1, 1, 0, 0])
if self.group_var:
groups, _ = self.data.get_column_view(self.group_var)
group_indexes = [
index for index, _ in enumerate(self.group_var.values)
]
colors = [
self._get_discrete_var_color(index) for index in group_indexes
]
masks = groups == np.reshape(group_indexes, (-1, 1))
return [
EstimatedFunctionCurve(time[mask],
events[mask],
color=color,
label=label) for mask, color, label in
zip(masks, colors, self.group_var.values) if mask.any()
]
else:
return [EstimatedFunctionCurve(time, events)]
def commit(self):
if not self.graph.selection:
self.Outputs.selected_data.send(None)
return
time, _ = self.data.get_column_view(self.time_var)
if self.group_var is None:
time_interval = self.graph.selection[0].x
start, end = time_interval[0], time_interval[-1]
selection = np.argwhere((time >= start)
& (time <= end)).reshape(-1).astype(int)
else:
selection = []
group, _ = self.data.get_column_view(self.group_var)
for group_id, time_interval in self.graph.selection.items():
start, end = time_interval.x[0], time_interval.x[-1]
selection += (np.argwhere((time >= start) & (time <= end) & (
group == group_id)).reshape(-1).astype(int).tolist())
selection = sorted(selection)
self.Outputs.selected_data.send(self.data[selection, :])
def sizeHint(self):
return QSize(1280, 620)
class OWRadviz(OWAnchorProjectionWidget):
name = "Radviz"
description = "显示Radviz投影"
icon = "icons/Radviz.svg"
priority = 241
keywords = ["viz"]
settings_version = 2
selected_vars = ContextSetting([])
vizrank = SettingProvider(RadvizVizRank)
GRAPH_CLASS = OWRadvizGraph
graph = SettingProvider(OWRadvizGraph)
class Warning(OWAnchorProjectionWidget.Warning):
invalid_embedding = widget.Msg("选择的特征没有投影")
removed_vars = widget.Msg("不显示具有两个以上值的分类变量")
def __init__(self):
self.model_selected = VariableListModel(enable_dnd=True)
self.model_selected.removed.connect(self.__model_selected_changed)
self.model_other = VariableListModel(enable_dnd=True)
self.vizrank, self.btn_vizrank = RadvizVizRank.add_vizrank(
None, self, "Suggest features", self.vizrank_set_attrs)
super().__init__()
def _add_controls(self):
self.variables_selection = VariablesSelection(self,
self.model_selected,
self.model_other,
self.controlArea)
self.variables_selection.added.connect(self.__model_selected_changed)
self.variables_selection.removed.connect(self.__model_selected_changed)
self.variables_selection.add_remove.layout().addWidget(
self.btn_vizrank)
super()._add_controls()
self.controlArea.layout().removeWidget(self.control_area_stretch)
self.control_area_stretch.setParent(None)
@property
def primitive_variables(self):
if self.data is None or self.data.domain is None:
return []
dom = self.data.domain
return [
v for v in chain(dom.variables, dom.metas)
if v.is_continuous or v.is_discrete and len(v.values) == 2
]
@property
def effective_variables(self):
return self.model_selected[:]
def vizrank_set_attrs(self, *attrs):
if not attrs:
return
self.model_selected[:] = attrs[:]
self.model_other[:] = [
var for var in self.primitive_variables if var not in attrs
]
self.__model_selected_changed()
def __model_selected_changed(self):
self.selected_vars = [(var.name, vartype(var))
for var in self.model_selected]
self.init_projection()
self.setup_plot()
self.commit()
def colors_changed(self):
super().colors_changed()
self._init_vizrank()
def set_data(self, data):
super().set_data(data)
self._init_vizrank()
self.init_projection()
def use_context(self):
self.model_selected.clear()
self.model_other.clear()
if self.data is not None and len(self.selected_vars):
d, selected = self.data.domain, [v[0] for v in self.selected_vars]
self.model_selected[:] = [d[name] for name in selected]
self.model_other[:] = [
d[attr.name] for attr in self.primitive_variables
if attr.name not in selected
]
elif self.data is not None:
d, variables = self.data.domain, self.primitive_variables
class_var = [variables.pop(variables.index(d.class_var))] \
if d.class_var in variables else []
self.model_selected[:] = variables[:5]
self.model_other[:] = variables[5:] + class_var
def _init_vizrank(self):
is_enabled = self.data is not None and \
len(self.primitive_variables) > 3 and \
self.attr_color is not None and \
not np.isnan(self.data.get_column_view(
self.attr_color)[0].astype(float)).all() and \
len(self.data[self.valid_data]) > 1 and \
np.all(np.nan_to_num(np.nanstd(self.data.X, 0)) != 0)
self.btn_vizrank.setEnabled(is_enabled)
if is_enabled:
self.vizrank.initialize()
def check_data(self):
super().check_data()
if self.data is not None:
domain = self.data.domain
vars_ = chain(domain.variables, domain.metas)
n_vars = sum(v.is_primitive() for v in vars_)
if len(self.primitive_variables) < n_vars:
self.Warning.removed_vars()
def init_attr_values(self):
super().init_attr_values()
self.selected_vars = []
def _manual_move(self, anchor_idx, x, y):
angle = np.arctan2(y, x)
super()._manual_move(anchor_idx, np.cos(angle), np.sin(angle))
def _send_components_x(self):
components_ = super()._send_components_x()
angle = np.arctan2(*components_[::-1])
return np.row_stack((components_, angle))
def _send_components_metas(self):
return np.vstack((super()._send_components_metas(), ["angle"]))
def clear(self):
super().clear()
self.projector = RadViz()
@classmethod
def migrate_context(cls, context, version):
if version < 2:
values = context.values
values["attr_color"] = values["graph"]["attr_color"]
values["attr_size"] = values["graph"]["attr_size"]
values["attr_shape"] = values["graph"]["attr_shape"]
values["attr_label"] = values["graph"]["attr_label"]
class OWScatterPlot(OWDataProjectionWidget):
"""Scatterplot visualization with explorative analysis and intelligent
data visualization enhancements."""
name = 'Scatter Plot'
description = "Interactive scatter plot visualization with " \
"intelligent data visualization enhancements."
icon = "icons/ScatterPlot.svg"
priority = 140
keywords = []
class Inputs(OWDataProjectionWidget.Inputs):
features = Input("Features", AttributeList)
class Outputs(OWDataProjectionWidget.Outputs):
features = Output("Features", AttributeList, dynamic=False)
settings_version = 5
auto_sample = Setting(True)
attr_x = ContextSetting(None)
attr_y = ContextSetting(None)
tooltip_shows_all = Setting(True)
GRAPH_CLASS = OWScatterPlotGraph
graph = SettingProvider(OWScatterPlotGraph)
embedding_variables_names = None
xy_changed_manually = Signal(Variable, Variable)
class Warning(OWDataProjectionWidget.Warning):
missing_coords = Msg("Plot cannot be displayed because '{}' or '{}' "
"is missing for all data points.")
class Information(OWDataProjectionWidget.Information):
sampled_sql = Msg("Large SQL table; showing a sample.")
missing_coords = Msg(
"Points with missing '{}' or '{}' are not displayed")
def __init__(self):
self.attr_box: QGroupBox = None
self.xy_model: DomainModel = None
self.cb_attr_x: ComboBoxSearch = None
self.cb_attr_y: ComboBoxSearch = None
self.vizrank: ScatterPlotVizRank = None
self.vizrank_button: QPushButton = None
self.sampling: QGroupBox = None
self.sql_data = None # Orange.data.sql.table.SqlTable
self.attribute_selection_list = None # list of Orange.data.Variable
self.__timer = QTimer(self, interval=1200)
self.__timer.timeout.connect(self.add_data)
super().__init__()
# manually register Matplotlib file writers
self.graph_writers = self.graph_writers.copy()
for w in [MatplotlibFormat, MatplotlibPDFFormat]:
self.graph_writers.append(w)
def _add_controls(self):
self._add_controls_axis()
self._add_controls_sampling()
super()._add_controls()
self.gui.add_widget(self.gui.JitterNumericValues, self._effects_box)
self.gui.add_widgets([
self.gui.ShowGridLines, self.gui.ToolTipShowsAll,
self.gui.RegressionLine
], self._plot_box)
gui.checkBox(
self._plot_box,
self,
value="graph.orthonormal_regression",
label="Treat variables as independent",
callback=self.graph.update_regression_line,
tooltip=
"If checked, fit line to group (minimize distance from points);\n"
"otherwise fit y as a function of x (minimize vertical distances)",
disabledBy=self.cb_reg_line)
def _add_controls_axis(self):
common_options = dict(labelWidth=50,
orientation=Qt.Horizontal,
sendSelectedValue=True,
contentsLength=12,
searchable=True)
self.attr_box = gui.vBox(self.controlArea,
'Axes',
spacing=2 if gui.is_macstyle() else 8)
dmod = DomainModel
self.xy_model = DomainModel(dmod.MIXED, valid_types=dmod.PRIMITIVE)
self.cb_attr_x = gui.comboBox(
self.attr_box,
self,
"attr_x",
label="Axis x:",
callback=self.set_attr_from_combo,
model=self.xy_model,
**common_options,
)
self.cb_attr_y = gui.comboBox(
self.attr_box,
self,
"attr_y",
label="Axis y:",
callback=self.set_attr_from_combo,
model=self.xy_model,
**common_options,
)
vizrank_box = gui.hBox(self.attr_box)
self.vizrank, self.vizrank_button = ScatterPlotVizRank.add_vizrank(
vizrank_box, self, "Find Informative Projections", self.set_attr)
def _add_controls_sampling(self):
self.sampling = gui.auto_commit(self.controlArea,
self,
"auto_sample",
"Sample",
box="Sampling",
callback=self.switch_sampling,
commit=lambda: self.add_data(1))
self.sampling.setVisible(False)
@property
def effective_variables(self):
return [self.attr_x, self.attr_y
] if self.attr_x and self.attr_y else []
@property
def effective_data(self):
eff_var = self.effective_variables
if eff_var and self.attr_x.name == self.attr_y.name:
eff_var = [self.attr_x]
return self.data.transform(Domain(eff_var))
def _vizrank_color_change(self):
self.vizrank.initialize()
err_msg = ""
if self.data is None:
err_msg = "No data on input"
elif self.data.is_sparse():
err_msg = "Data is sparse"
elif len(self.xy_model) < 3:
err_msg = "Not enough features for ranking"
elif self.attr_color is None:
err_msg = "Color variable is not selected"
elif np.isnan(
self.data.get_column_view(
self.attr_color)[0].astype(float)).all():
err_msg = "Color variable has no values"
self.vizrank_button.setEnabled(not err_msg)
self.vizrank_button.setToolTip(err_msg)
def set_data(self, data):
super().set_data(data)
self._vizrank_color_change()
def findvar(name, iterable):
"""Find a Orange.data.Variable in `iterable` by name"""
for el in iterable:
if isinstance(el, Variable) and el.name == name:
return el
return None
# handle restored settings from < 3.3.9 when attr_* were stored
# by name
if isinstance(self.attr_x, str):
self.attr_x = findvar(self.attr_x, self.xy_model)
if isinstance(self.attr_y, str):
self.attr_y = findvar(self.attr_y, self.xy_model)
if isinstance(self.attr_label, str):
self.attr_label = findvar(self.attr_label, self.gui.label_model)
if isinstance(self.attr_color, str):
self.attr_color = findvar(self.attr_color, self.gui.color_model)
if isinstance(self.attr_shape, str):
self.attr_shape = findvar(self.attr_shape, self.gui.shape_model)
if isinstance(self.attr_size, str):
self.attr_size = findvar(self.attr_size, self.gui.size_model)
def check_data(self):
super().check_data()
self.__timer.stop()
self.sampling.setVisible(False)
self.sql_data = None
if isinstance(self.data, SqlTable):
if self.data.approx_len() < 4000:
self.data = Table(self.data)
else:
self.Information.sampled_sql()
self.sql_data = self.data
data_sample = self.data.sample_time(0.8, no_cache=True)
data_sample.download_data(2000, partial=True)
self.data = Table(data_sample)
self.sampling.setVisible(True)
if self.auto_sample:
self.__timer.start()
if self.data is not None and (len(self.data) == 0
or len(self.data.domain.variables) == 0):
self.data = None
def get_embedding(self):
self.valid_data = None
if self.data is None:
return None
x_data = self.get_column(self.attr_x, filter_valid=False)
y_data = self.get_column(self.attr_y, filter_valid=False)
if x_data is None or y_data is None:
return None
self.Warning.missing_coords.clear()
self.Information.missing_coords.clear()
self.valid_data = np.isfinite(x_data) & np.isfinite(y_data)
if self.valid_data is not None and not np.all(self.valid_data):
msg = self.Information if np.any(self.valid_data) else self.Warning
msg.missing_coords(self.attr_x.name, self.attr_y.name)
return np.vstack((x_data, y_data)).T
# Tooltip
def _point_tooltip(self, point_id, skip_attrs=()):
point_data = self.data[point_id]
xy_attrs = (self.attr_x, self.attr_y)
text = "<br/>".join(
escape('{} = {}'.format(var.name, point_data[var]))
for var in xy_attrs)
if self.tooltip_shows_all:
others = super()._point_tooltip(point_id, skip_attrs=xy_attrs)
if others:
text = "<b>{}</b><br/><br/>{}".format(text, others)
return text
def can_draw_regresssion_line(self):
return self.data is not None and \
self.data.domain is not None and \
self.attr_x.is_continuous and \
self.attr_y.is_continuous
def add_data(self, time=0.4):
if self.data and len(self.data) > 2000:
self.__timer.stop()
return
data_sample = self.sql_data.sample_time(time, no_cache=True)
if data_sample:
data_sample.download_data(2000, partial=True)
data = Table(data_sample)
self.data = Table.concatenate((self.data, data), axis=0)
self.handleNewSignals()
def init_attr_values(self):
super().init_attr_values()
data = self.data
domain = data.domain if data and len(data) else None
self.xy_model.set_domain(domain)
self.attr_x = self.xy_model[0] if self.xy_model else None
self.attr_y = self.xy_model[1] if len(self.xy_model) >= 2 \
else self.attr_x
def switch_sampling(self):
self.__timer.stop()
if self.auto_sample and self.sql_data:
self.add_data()
self.__timer.start()
def set_subset_data(self, subset_data):
self.warning()
if isinstance(subset_data, SqlTable):
if subset_data.approx_len() < AUTO_DL_LIMIT:
subset_data = Table(subset_data)
else:
self.warning("Data subset does not support large Sql tables")
subset_data = None
super().set_subset_data(subset_data)
# called when all signals are received, so the graph is updated only once
def handleNewSignals(self):
self.attr_box.setEnabled(True)
self.vizrank.setEnabled(True)
if self.attribute_selection_list and self.data is not None and \
self.data.domain is not None and \
all(attr in self.data.domain for attr
in self.attribute_selection_list):
self.attr_x, self.attr_y = self.attribute_selection_list[:2]
self.attr_box.setEnabled(False)
self.vizrank.setEnabled(False)
super().handleNewSignals()
if self._domain_invalidated:
self.graph.update_axes()
self._domain_invalidated = False
self.cb_reg_line.setEnabled(self.can_draw_regresssion_line())
@Inputs.features
def set_shown_attributes(self, attributes):
if attributes and len(attributes) >= 2:
self.attribute_selection_list = attributes[:2]
self._invalidated = self._invalidated \
or self.attr_x != attributes[0] \
or self.attr_y != attributes[1]
else:
self.attribute_selection_list = None
def set_attr(self, attr_x, attr_y):
if attr_x != self.attr_x or attr_y != self.attr_y:
self.attr_x, self.attr_y = attr_x, attr_y
self.attr_changed()
def set_attr_from_combo(self):
self.attr_changed()
self.xy_changed_manually.emit(self.attr_x, self.attr_y)
def attr_changed(self):
self.cb_reg_line.setEnabled(self.can_draw_regresssion_line())
self.setup_plot()
self.commit.deferred()
def get_axes(self):
return {"bottom": self.attr_x, "left": self.attr_y}
def colors_changed(self):
super().colors_changed()
self._vizrank_color_change()
@gui.deferred
def commit(self):
super().commit()
self.send_features()
def send_features(self):
features = [attr for attr in [self.attr_x, self.attr_y] if attr]
self.Outputs.features.send(AttributeList(features) or None)
def get_widget_name_extension(self):
if self.data is not None:
return "{} vs {}".format(self.attr_x.name, self.attr_y.name)
return None
def _get_send_report_caption(self):
return report.render_items_vert(
(("Color", self._get_caption_var_name(self.attr_color)),
("Label", self._get_caption_var_name(self.attr_label)),
("Shape", self._get_caption_var_name(self.attr_shape)),
("Size", self._get_caption_var_name(self.attr_size)),
("Jittering", (self.attr_x.is_discrete or self.attr_y.is_discrete
or self.graph.jitter_continuous)
and self.graph.jitter_size)))
@classmethod
def migrate_settings(cls, settings, version):
if version < 2 and "selection" in settings and settings["selection"]:
settings["selection_group"] = [(a, 1)
for a in settings["selection"]]
if version < 3:
if "auto_send_selection" in settings:
settings["auto_commit"] = settings["auto_send_selection"]
if "selection_group" in settings:
settings["selection"] = settings["selection_group"]
if version < 5:
if "graph" in settings and \
"jitter_continuous" not in settings["graph"]:
settings["graph"]["jitter_continuous"] = True
@classmethod
def migrate_context(cls, context, version):
values = context.values
if version < 3:
values["attr_color"] = values["graph"]["attr_color"]
values["attr_size"] = values["graph"]["attr_size"]
values["attr_shape"] = values["graph"]["attr_shape"]
values["attr_label"] = values["graph"]["attr_label"]
if version < 4:
if values["attr_x"][1] % 100 == 1 or values["attr_y"][1] % 100 == 1:
raise IncompatibleContext()
class OWDataProjectionWidget(OWProjectionWidgetBase, openclass=True):
"""
Base widget for widgets that get Data and Data Subset (both
Orange.data.Table) on the input, and output Selected Data and Data
(both Orange.data.Table).
Beside that the widget displays data as two-dimensional projection
of points.
"""
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)
class Warning(OWProjectionWidgetBase.Warning):
too_many_labels = Msg(
"Too many labels to show (zoom in or label only selected)")
subset_not_subset = Msg(
"Subset data contains some instances that do not appear in "
"input data")
subset_independent = Msg(
"No subset data instances appear in input data")
transparent_subset = Msg(
"Increase opacity if subset is difficult to see")
settingsHandler = DomainContextHandler()
selection = Setting(None, schema_only=True)
visual_settings = Setting({}, schema_only=True)
auto_commit = Setting(True)
GRAPH_CLASS = OWScatterPlotBase
graph = SettingProvider(OWScatterPlotBase)
graph_name = "graph.plot_widget.plotItem"
embedding_variables_names = ("proj-x", "proj-y")
buttons_area_orientation = Qt.Vertical
input_changed = Signal(object)
output_changed = Signal(object)
def __init__(self):
super().__init__()
self.subset_data = None
self.subset_indices = None
self.__pending_selection = self.selection
self._invalidated = True
self._domain_invalidated = True
self.setup_gui()
VisualSettingsDialog(self,
self.graph.parameter_setter.initial_settings)
# GUI
def setup_gui(self):
self._add_graph()
self._add_controls()
self._add_buttons()
self.input_changed.emit(None)
self.output_changed.emit(None)
def _add_graph(self):
box = gui.vBox(self.mainArea, True, margin=0)
self.graph = self.GRAPH_CLASS(self, box)
box.layout().addWidget(self.graph.plot_widget)
self.graph.too_many_labels.connect(
lambda too_many: self.Warning.too_many_labels(shown=too_many))
def _add_controls(self):
self.gui = OWPlotGUI(self)
area = self.controlArea
self._point_box = self.gui.point_properties_box(area)
self._effects_box = self.gui.effects_box(area)
self._plot_box = self.gui.plot_properties_box(area)
def _add_buttons(self):
gui.rubber(self.controlArea)
self.gui.box_zoom_select(self.buttonsArea)
gui.auto_send(self.buttonsArea, self, "auto_commit")
@property
def effective_variables(self):
return self.data.domain.attributes
@property
def effective_data(self):
return self.data.transform(
Domain(self.effective_variables, self.data.domain.class_vars,
self.data.domain.metas))
# Input
@Inputs.data
@check_sql_input
def set_data(self, data):
data_existed = self.data is not None
effective_data = self.effective_data if data_existed else None
self.closeContext()
self.data = data
self.check_data()
self.init_attr_values()
self.openContext(self.data)
self._invalidated = not (data_existed
and self.data is not None and array_equal(
effective_data.X, self.effective_data.X))
self._domain_invalidated = not (
data_existed and self.data is not None
and effective_data.domain.checksum()
== self.effective_data.domain.checksum())
if self._invalidated:
self.clear()
self.input_changed.emit(data)
self.enable_controls()
def check_data(self):
self.clear_messages()
def enable_controls(self):
self.cb_class_density.setEnabled(self.can_draw_density())
@Inputs.data_subset
@check_sql_input
def set_subset_data(self, subset):
self.subset_data = subset
def handleNewSignals(self):
self._handle_subset_data()
if self._invalidated:
self._invalidated = False
self.setup_plot()
else:
self.graph.update_point_props()
self._update_opacity_warning()
self.unconditional_commit()
def _handle_subset_data(self):
self.Warning.subset_independent.clear()
self.Warning.subset_not_subset.clear()
if self.data is None or self.subset_data is None:
self.subset_indices = set()
else:
self.subset_indices = set(self.subset_data.ids)
ids = set(self.data.ids)
if not self.subset_indices & ids:
self.Warning.subset_independent()
elif self.subset_indices - ids:
self.Warning.subset_not_subset()
def _update_opacity_warning(self):
self.Warning.transparent_subset(
shown=self.subset_indices and self.graph.alpha_value < 128)
def get_subset_mask(self):
if not self.subset_indices:
return None
valid_data = self.data[self.valid_data]
return np.fromiter((ex.id in self.subset_indices for ex in valid_data),
dtype=bool,
count=len(valid_data))
# Plot
def get_embedding(self):
"""A get embedding method.
Derived classes must override this method. The overridden method
should return embedding for all data (valid and invalid). Invalid
data embedding coordinates should be set to 0 (in some cases to Nan).
The method should also set self.valid_data.
Returns:
np.array: Array of embedding coordinates with shape
len(self.data) x 2
"""
raise NotImplementedError
def get_coordinates_data(self):
embedding = self.get_embedding()
if embedding is not None and len(embedding[self.valid_data]):
return embedding[self.valid_data].T
return None, None
def setup_plot(self):
self.graph.reset_graph()
self.__pending_selection = self.selection or self.__pending_selection
self.apply_selection()
# Selection
def apply_selection(self):
pending = self.__pending_selection
if self.data is not None and pending is not None and len(pending) \
and max(i for i, _ in pending) < self.graph.n_valid:
index_group = np.array(pending).T
selection = np.zeros(self.graph.n_valid, dtype=np.uint8)
selection[index_group[0]] = index_group[1]
self.selection = self.__pending_selection
self.__pending_selection = None
self.graph.selection = selection
self.graph.update_selection_colors()
if self.graph.label_only_selected:
self.graph.update_labels()
def selection_changed(self):
sel = None if self.data and isinstance(self.data, SqlTable) \
else self.graph.selection
self.selection = [(i, x) for i, x in enumerate(sel) if x] \
if sel is not None else None
self.commit()
# Output
def commit(self):
self.send_data()
def send_data(self):
group_sel, data, graph = None, self._get_projection_data(), self.graph
if graph.selection is not None:
group_sel = np.zeros(len(data), dtype=int)
group_sel[self.valid_data] = graph.selection
selected = self._get_selected_data(data, graph.get_selection(),
group_sel)
self.output_changed.emit(selected)
self.Outputs.selected_data.send(selected)
self.Outputs.annotated_data.send(
self._get_annotated_data(data, group_sel, graph.selection))
def _get_projection_data(self):
if self.data is None or self.embedding_variables_names is None:
return self.data
variables = self._get_projection_variables()
data = self.data.transform(
Domain(self.data.domain.attributes, self.data.domain.class_vars,
self.data.domain.metas + variables))
with data.unlocked(data.metas):
data.metas[:, -2:] = self.get_embedding()
return data
def _get_projection_variables(self):
names = get_unique_names(self.data.domain,
self.embedding_variables_names)
return ContinuousVariable(names[0]), ContinuousVariable(names[1])
@staticmethod
def _get_selected_data(data, selection, group_sel):
return create_groups_table(data, group_sel, False, "Group") \
if len(selection) else None
@staticmethod
def _get_annotated_data(data, group_sel, graph_sel):
if data is None:
return None
if graph_sel is not None and np.max(graph_sel) > 1:
return create_groups_table(data, group_sel)
else:
if group_sel is None:
mask = np.full((len(data), ), False)
else:
mask = np.nonzero(group_sel)[0]
return create_annotated_table(data, mask)
# Report
def send_report(self):
if self.data is None:
return
caption = self._get_send_report_caption()
self.report_plot()
if caption:
self.report_caption(caption)
def _get_send_report_caption(self):
return report.render_items_vert(
(("Color", self._get_caption_var_name(self.attr_color)),
("Label", self._get_caption_var_name(self.attr_label)),
("Shape", self._get_caption_var_name(self.attr_shape)),
("Size", self._get_caption_var_name(self.attr_size)),
("Jittering", self.graph.jitter_size != 0
and "{} %".format(self.graph.jitter_size))))
# Customize plot
def set_visual_settings(self, key, value):
self.graph.parameter_setter.set_parameter(key, value)
self.visual_settings[key] = value
@staticmethod
def _get_caption_var_name(var):
return var.name if isinstance(var, Variable) else var
# Misc
def sizeHint(self):
return QSize(1132, 708)
def clear(self):
self.selection = None
self.graph.selection = None
def onDeleteWidget(self):
super().onDeleteWidget()
self.graph.plot_widget.getViewBox().deleteLater()
self.graph.plot_widget.clear()
self.graph.clear()
class OWDataProjectionWidget(OWProjectionWidgetBase):
"""
Base widget for widgets that get Data and Data Subset (both
Orange.data.Table) on the input, and output Selected Data and Data
(both Orange.data.Table).
Beside that the widget displays data as two-dimensional projection
of points.
"""
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)
settingsHandler = DomainContextHandler()
selection = Setting(None, schema_only=True)
auto_commit = Setting(True)
GRAPH_CLASS = OWScatterPlotBase
graph = SettingProvider(OWScatterPlotBase)
graph_name = "graph.plot_widget.plotItem"
embedding_variables_names = ("proj-x", "proj-y")
def __init__(self):
super().__init__()
self.subset_data = None
self.subset_indices = None
self.__pending_selection = self.selection
self.setup_gui()
# GUI
def setup_gui(self):
self._add_graph()
self._add_controls()
def _add_graph(self):
box = gui.vBox(self.mainArea, True, margin=0)
self.graph = self.GRAPH_CLASS(self, box)
box.layout().addWidget(self.graph.plot_widget)
def _add_controls(self):
self._point_box = self.graph.gui.point_properties_box(self.controlArea)
self._effects_box = self.graph.gui.effects_box(self.controlArea)
self._plot_box = self.graph.gui.plot_properties_box(self.controlArea)
self.control_area_stretch = gui.widgetBox(self.controlArea)
self.control_area_stretch.layout().addStretch(100)
self.graph.box_zoom_select(self.controlArea)
gui.auto_commit(self.controlArea, self, "auto_commit",
"Send Selection", "Send Automatically")
# Input
@Inputs.data
@check_sql_input
def set_data(self, data):
same_domain = (self.data and data and
data.domain.checksum() == self.data.domain.checksum())
self.closeContext()
self.clear()
self.data = data
self.check_data()
if not same_domain:
self.init_attr_values()
self.openContext(self.data)
self.cb_class_density.setEnabled(self.can_draw_density())
def check_data(self):
self.clear_messages()
@Inputs.data_subset
@check_sql_input
def set_subset_data(self, subset):
self.subset_data = subset
self.subset_indices = {e.id for e in subset} \
if subset is not None else {}
self.controls.graph.alpha_value.setEnabled(subset is None)
def handleNewSignals(self):
self.setup_plot()
self.commit()
def get_subset_mask(self):
if self.subset_indices:
return np.array([ex.id in self.subset_indices
for ex in self.data[self.valid_data]])
return None
# Plot
def get_embedding(self):
"""A get embedding method.
Derived classes must override this method. The overridden method
should return embedding for all data (valid and invalid). Invalid
data embedding coordinates should be set to 0 (in some cases to Nan).
The method should also sets self.valid_data.
Returns:
np.array: Array of embedding coordinates with shape
len(self.data) x 2
"""
raise NotImplementedError
def get_coordinates_data(self):
embedding = self.get_embedding()
return embedding[self.valid_data].T[:2] if embedding is not None \
else (None, None)
def setup_plot(self):
self.graph.reset_graph()
self.__pending_selection = self.selection or self.__pending_selection
self.apply_selection()
# Selection
def apply_selection(self):
if self.data is not None and self.__pending_selection is not None \
and self.graph.n_valid:
index_group = [(index, group) for index, group in
self.__pending_selection if index < len(self.data)]
index_group = np.array(index_group).T
selection = np.zeros(self.graph.n_valid, dtype=np.uint8)
selection[index_group[0]] = index_group[1]
self.selection = self.__pending_selection
self.__pending_selection = None
self.graph.selection = selection
self.graph.update_selection_colors()
def selection_changed(self):
sel = None if self.data and isinstance(self.data, SqlTable) \
else self.graph.selection
self.selection = [(i, x) for i, x in enumerate(sel) if x] \
if sel is not None else None
self.commit()
# Output
def commit(self):
self.send_data()
def send_data(self):
group_sel, data, graph = None, self._get_projection_data(), self.graph
if graph.selection is not None:
group_sel = np.zeros(len(data), dtype=int)
group_sel[self.valid_data] = graph.selection
self.Outputs.selected_data.send(
self._get_selected_data(data, graph.get_selection(), group_sel))
self.Outputs.annotated_data.send(
self._get_annotated_data(data, graph.get_selection(), group_sel,
graph.selection))
def _get_projection_data(self):
if self.data is None or self.embedding_variables_names is None:
return self.data
variables = self._get_projection_variables()
data = self.data.transform(Domain(self.data.domain.attributes,
self.data.domain.class_vars,
self.data.domain.metas + variables))
data.metas[:, -2:] = self.get_embedding()
return data
def _get_projection_variables(self):
domain = self.data.domain
names = get_unique_names(
[v.name for v in domain.variables + domain.metas],
self.embedding_variables_names
)
return ContinuousVariable(names[0]), ContinuousVariable(names[1])
@staticmethod
def _get_selected_data(data, selection, group_sel):
return create_groups_table(data, group_sel, False, "Group") \
if len(selection) else None
@staticmethod
def _get_annotated_data(data, selection, group_sel, graph_sel):
if graph_sel is not None and np.max(graph_sel) > 1:
return create_groups_table(data, group_sel)
else:
return create_annotated_table(data, selection)
# Report
def send_report(self):
if self.data is None:
return
caption = self._get_send_report_caption()
self.report_plot()
if caption:
self.report_caption(caption)
def _get_send_report_caption(self):
return report.render_items_vert((
("Color", self._get_caption_var_name(self.attr_color)),
("Label", self._get_caption_var_name(self.attr_label)),
("Shape", self._get_caption_var_name(self.attr_shape)),
("Size", self._get_caption_var_name(self.attr_size)),
("Jittering", self.graph.jitter_size != 0 and
"{} %".format(self.graph.jitter_size))))
@staticmethod
def _get_caption_var_name(var):
return var.name if isinstance(var, Variable) else var
# Misc
def sizeHint(self):
return QSize(1132, 708)
def clear(self):
self.data = None
self.valid_data = None
self.selection = None
self.graph.selection = None
def onDeleteWidget(self):
super().onDeleteWidget()
self.graph.plot_widget.getViewBox().deleteLater()
self.graph.plot_widget.clear()
class OWtSNE(OWDataProjectionWidget, ConcurrentWidgetMixin):
name = "t-SNE"
description = "Two-dimensional data projection with t-SNE."
icon = "icons/TSNE.svg"
priority = 920
keywords = ["tsne"]
settings_version = 4
perplexity = ContextSetting(30)
multiscale = ContextSetting(False)
exaggeration = ContextSetting(1)
pca_components = ContextSetting(_DEFAULT_PCA_COMPONENTS)
normalize = ContextSetting(True)
GRAPH_CLASS = OWtSNEGraph
graph = SettingProvider(OWtSNEGraph)
embedding_variables_names = ("t-SNE-x", "t-SNE-y")
# Use `invalidated` descriptor so we don't break the usage of
# `_invalidated` in `OWDataProjectionWidget`, but still allow finer control
# over which parts of the embedding to invalidate
_invalidated = invalidated()
class Information(OWDataProjectionWidget.Information):
modified = Msg("The parameter settings have been changed. Press "
"\"Start\" to rerun with the new settings.")
class Error(OWDataProjectionWidget.Error):
not_enough_rows = Msg("Input data needs at least 2 rows")
not_enough_cols = Msg("Input data needs at least 2 attributes")
constant_data = Msg("Input data is constant")
no_valid_data = Msg("No projection due to no valid data")
def __init__(self):
OWDataProjectionWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
self.pca_projection = None # type: Optional[Table]
self.initialization = None # type: Optional[np.ndarray]
self.affinities = None # type: Optional[openTSNE.affinity.Affinities]
self.tsne_embedding = None # type: Optional[manifold.TSNEModel]
self.iterations_done = 0 # type: int
def _add_controls(self):
self._add_controls_start_box()
super()._add_controls()
def _add_controls_start_box(self):
box = gui.vBox(self.controlArea, box="Optimize")
form = QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
)
self.perplexity_spin = gui.spin(
box, self, "perplexity", 1, 500, step=1, alignment=Qt.AlignRight,
callback=self._invalidate_affinities, addToLayout=False
)
self.controls.perplexity.setDisabled(self.multiscale)
form.addRow("Perplexity:", self.perplexity_spin)
form.addRow(gui.checkBox(
box, self, "multiscale", label="Preserve global structure",
callback=self._multiscale_changed, addToLayout=False
))
sbe = gui.hBox(self.controlArea, False, addToLayout=False)
gui.hSlider(
sbe, self, "exaggeration", minValue=1, maxValue=4, step=1,
callback=self._invalidate_tsne_embedding,
)
form.addRow("Exaggeration:", sbe)
sbp = gui.hBox(self.controlArea, False, addToLayout=False)
gui.hSlider(
sbp, self, "pca_components", minValue=2, maxValue=_MAX_PCA_COMPONENTS,
step=1, callback=self._invalidate_pca_projection,
)
form.addRow("PCA components:", sbp)
self.normalize_cbx = gui.checkBox(
box, self, "normalize", "Normalize data",
callback=self._invalidate_pca_projection, addToLayout=False
)
form.addRow(self.normalize_cbx)
box.layout().addLayout(form)
self.run_button = gui.button(box, self, "Start", callback=self._toggle_run)
def _multiscale_changed(self):
self.controls.perplexity.setDisabled(self.multiscale)
self._invalidate_affinities()
def _invalidate_pca_projection(self):
self._invalidated.pca_projection = True
self._invalidate_affinities()
def _invalidate_affinities(self):
self._invalidated.affinities = True
self._invalidate_tsne_embedding()
def _invalidate_tsne_embedding(self):
self._invalidated.tsne_embedding = True
self._stop_running_task()
self._set_modified(True)
def _stop_running_task(self):
self.cancel()
self.run_button.setText("Start")
def _set_modified(self, state):
"""Mark the widget (GUI) as containing modified state."""
if self.data is None:
# Does not apply when we have no data
state = False
self.Information.modified(shown=state)
def check_data(self):
def error(err):
err()
self.data = None
# `super().check_data()` clears all messages so we have to remember if
# it was shown
# pylint: disable=assignment-from-no-return
should_show_modified_message = self.Information.modified.is_shown()
super().check_data()
if self.data is None:
return
self.Information.modified(shown=should_show_modified_message)
if len(self.data) < 2:
error(self.Error.not_enough_rows)
elif len(self.data.domain.attributes) < 2:
error(self.Error.not_enough_cols)
elif not self.data.is_sparse():
if np.all(~np.isfinite(self.data.X)):
error(self.Error.no_valid_data)
else:
with warnings.catch_warnings():
warnings.filterwarnings(
"ignore", "Degrees of freedom .*", RuntimeWarning)
if np.nan_to_num(np.nanstd(self.data.X, axis=0)).sum() \
== 0:
error(self.Error.constant_data)
def get_embedding(self):
if self.tsne_embedding is None:
self.valid_data = None
return None
embedding = self.tsne_embedding.embedding.X
self.valid_data = np.ones(len(embedding), dtype=bool)
return embedding
def _toggle_run(self):
# If no data, there's nothing to do
if self.data is None:
return
# Pause task
if self.task is not None:
self.cancel()
self.run_button.setText("Resume")
self.commit.deferred()
# Resume task
else:
self.run()
def handleNewSignals(self):
# We don't bother with the granular invalidation flags because
# `super().handleNewSignals` will just set all of them to False or will
# do nothing. However, it's important we remember its state because we
# won't call `run` if needed. `run` also relies on the state of
# `_invalidated` to properly set the intermediate values to None
prev_invalidated = bool(self._invalidated)
super().handleNewSignals()
self._invalidated = prev_invalidated
if self._invalidated:
self.run()
def init_attr_values(self):
super().init_attr_values()
if self.data is not None:
n_attrs = len(self.data.domain.attributes)
max_components = min(_MAX_PCA_COMPONENTS, n_attrs)
else:
max_components = _MAX_PCA_COMPONENTS
# We set this to the default number of components here so it resets
# properly, any previous settings will be restored from context
# settings a little later
self.controls.pca_components.setMaximum(max_components)
self.controls.pca_components.setValue(_DEFAULT_PCA_COMPONENTS)
self.exaggeration = 1
def enable_controls(self):
super().enable_controls()
if self.data is not None:
# PCA doesn't support normalization on sparse data, as this would
# require centering and normalizing the matrix
self.normalize_cbx.setDisabled(self.data.is_sparse())
if self.data.is_sparse():
self.normalize = False
self.normalize_cbx.setToolTip(
"Data normalization is not supported on sparse matrices."
)
else:
self.normalize_cbx.setToolTip("")
# Disable the perplexity spin box if multiscale is turned on
self.controls.perplexity.setDisabled(self.multiscale)
def run(self):
# Reset invalidated values as indicated by the flags
if self._invalidated.pca_projection:
self.pca_projection = None
if self._invalidated.affinities:
self.affinities = None
if self._invalidated.tsne_embedding:
self.iterations_done = 0
self.tsne_embedding = None
self._set_modified(False)
self._invalidated = False
# When the data is invalid, it is set to `None` and an error is set,
# therefore it would be erroneous to clear the error here
if self.data is not None:
self.run_button.setText("Stop")
# Cancel current running task
self.cancel()
if self.data is None:
return
task = Task(
data=self.data,
normalize=self.normalize,
pca_components=self.pca_components,
pca_projection=self.pca_projection,
perplexity=self.perplexity,
multiscale=self.multiscale,
exaggeration=self.exaggeration,
initialization=self.initialization,
affinities=self.affinities,
tsne_embedding=self.tsne_embedding,
iterations_done=self.iterations_done,
)
return self.start(TSNERunner.run, task)
def __ensure_task_same_for_pca(self, task: Task):
assert self.data is not None
assert task.normalize == self.normalize
assert task.pca_components == self.pca_components
assert isinstance(task.pca_projection, Table) and \
len(task.pca_projection) == len(self.data)
def __ensure_task_same_for_initialization(self, task: Task):
assert isinstance(task.initialization, np.ndarray) and \
len(task.initialization) == len(self.data)
def __ensure_task_same_for_affinities(self, task: Task):
assert task.perplexity == self.perplexity
assert task.multiscale == self.multiscale
def __ensure_task_same_for_embedding(self, task: Task):
assert task.exaggeration == self.exaggeration
assert isinstance(task.tsne_embedding, manifold.TSNEModel) and \
len(task.tsne_embedding.embedding) == len(self.data)
def on_partial_result(self, value):
# type: (Tuple[str, Task]) -> None
which, task = value
if which == "pca_projection":
self.__ensure_task_same_for_pca(task)
self.pca_projection = task.pca_projection
elif which == "initialization":
self.__ensure_task_same_for_pca(task)
self.__ensure_task_same_for_initialization(task)
self.initialization = task.initialization
elif which == "affinities":
self.__ensure_task_same_for_pca(task)
self.__ensure_task_same_for_affinities(task)
self.affinities = task.affinities
elif which == "tsne_embedding":
self.__ensure_task_same_for_pca(task)
self.__ensure_task_same_for_initialization(task)
self.__ensure_task_same_for_affinities(task)
self.__ensure_task_same_for_embedding(task)
prev_embedding, self.tsne_embedding = self.tsne_embedding, task.tsne_embedding
self.iterations_done = task.iterations_done
# If this is the first partial result we've gotten, we've got to
# setup the plot
if prev_embedding is None:
self.setup_plot()
# Otherwise, just update the point positions
else:
self.graph.update_coordinates()
self.graph.update_density()
else:
raise RuntimeError(
"Unrecognized partial result called with `%s`" % which
)
def on_done(self, task):
# type: (Task) -> None
self.run_button.setText("Start")
# NOTE: All of these have already been set by on_partial_result,
# we double check that they are aliases
if task.pca_projection is not None:
self.__ensure_task_same_for_pca(task)
assert task.pca_projection is self.pca_projection
if task.initialization is not None:
self.__ensure_task_same_for_initialization(task)
assert task.initialization is self.initialization
if task.affinities is not None:
assert task.affinities is self.affinities
if task.tsne_embedding is not None:
self.__ensure_task_same_for_embedding(task)
assert task.tsne_embedding is self.tsne_embedding
self.commit.deferred()
def _get_projection_data(self):
if self.data is None:
return None
data = self.data.transform(
Domain(
self.data.domain.attributes,
self.data.domain.class_vars,
self.data.domain.metas + self._get_projection_variables()
)
)
with data.unlocked(data.metas):
data.metas[:, -2:] = self.get_embedding()
if self.tsne_embedding is not None:
data.domain = Domain(
self.data.domain.attributes,
self.data.domain.class_vars,
self.data.domain.metas + self.tsne_embedding.domain.attributes,
)
return data
def clear(self):
"""Clear widget state. Note that this doesn't clear the data."""
super().clear()
self.run_button.setText("Start")
self.cancel()
self.pca_projection = None
self.initialization = None
self.affinities = None
self.tsne_embedding = None
self.iterations_done = 0
def onDeleteWidget(self):
self.clear()
self.data = None
self.shutdown()
super().onDeleteWidget()
@classmethod
def migrate_settings(cls, settings, version):
if version < 3:
if "selection_indices" in settings:
settings["selection"] = settings["selection_indices"]
if version < 4:
settings.pop("max_iter", None)
@classmethod
def migrate_context(cls, context, version):
if version < 3:
values = context.values
values["attr_color"] = values["graph"]["attr_color"]
values["attr_size"] = values["graph"]["attr_size"]
values["attr_shape"] = values["graph"]["attr_shape"]
values["attr_label"] = values["graph"]["attr_label"]
class OWMDS(OWDataProjectionWidget, ConcurrentWidgetMixin):
name = "MDS"
description = "Two-dimensional data projection by multidimensional " \
"scaling constructed from a distance matrix."
icon = "icons/MDS.svg"
keywords = ["multidimensional scaling", "multi dimensional scaling"]
class Inputs(OWDataProjectionWidget.Inputs):
distances = Input("Distances", DistMatrix)
settings_version = 3
#: Initialization type
PCA, Random, Jitter = 0, 1, 2
#: Refresh rate
RefreshRate = [("Every iteration", 1), ("Every 5 steps", 5),
("Every 10 steps", 10), ("Every 25 steps", 25),
("Every 50 steps", 50), ("None", -1)]
max_iter = settings.Setting(300)
initialization = settings.Setting(PCA)
refresh_rate = settings.Setting(3)
GRAPH_CLASS = OWMDSGraph
graph = SettingProvider(OWMDSGraph)
embedding_variables_names = ("mds-x", "mds-y")
class Error(OWDataProjectionWidget.Error):
not_enough_rows = Msg("Input data needs at least 2 rows")
matrix_too_small = Msg("Input matrix must be at least 2x2")
no_attributes = Msg("Data has no attributes")
mismatching_dimensions = \
Msg("Data and distances dimensions do not match.")
out_of_memory = Msg("Out of memory")
optimization_error = Msg("Error during optimization\n{}")
def __init__(self):
OWDataProjectionWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
#: Input dissimilarity matrix
self.matrix = None # type: Optional[DistMatrix]
#: Data table from the `self.matrix.row_items` (if present)
self.matrix_data = None # type: Optional[Table]
#: Input data table
self.signal_data = None
self.embedding = None # type: Optional[np.ndarray]
self.effective_matrix = None # type: Optional[DistMatrix]
self.graph.pause_drawing_pairs()
self.size_model = self.gui.points_models[2]
self.size_model.order = \
self.gui.points_models[2].order[:1] \
+ ("Stress", ) + \
self.gui.points_models[2].order[1:]
def _add_controls(self):
self._add_controls_optimization()
super()._add_controls()
self.gui.add_control(self._effects_box,
gui.hSlider,
"Show similar pairs:",
master=self.graph,
value="connected_pairs",
minValue=0,
maxValue=20,
createLabel=False,
callback=self._on_connected_changed)
def _add_controls_optimization(self):
box = gui.vBox(self.controlArea, box=True)
self.run_button = gui.button(box, self, "Start", self._toggle_run)
gui.comboBox(box,
self,
"refresh_rate",
label="Refresh: ",
orientation=Qt.Horizontal,
items=[t for t, _ in OWMDS.RefreshRate],
callback=self.__refresh_rate_combo_changed)
hbox = gui.hBox(box, margin=0)
gui.button(hbox, self, "PCA", callback=self.do_PCA)
gui.button(hbox, self, "Randomize", callback=self.do_random)
gui.button(hbox, self, "Jitter", callback=self.do_jitter)
def __refresh_rate_combo_changed(self):
if self.task is not None:
self._run()
def set_data(self, data):
"""Set the input dataset.
Parameters
----------
data : Optional[Table]
"""
if data is not None and len(data) < 2:
self.Error.not_enough_rows()
data = None
else:
self.Error.not_enough_rows.clear()
self.signal_data = data
@Inputs.distances
def set_disimilarity(self, matrix):
"""Set the dissimilarity (distance) matrix.
Parameters
----------
matrix : Optional[Orange.misc.DistMatrix]
"""
if matrix is not None and len(matrix) < 2:
self.Error.matrix_too_small()
matrix = None
else:
self.Error.matrix_too_small.clear()
self.matrix = matrix
self.matrix_data = matrix.row_items if matrix is not None else None
def clear(self):
super().clear()
self.cancel()
self.embedding = None
self.graph.set_effective_matrix(None)
def _initialize(self):
matrix_existed = self.effective_matrix is not None
effective_matrix = self.effective_matrix
self._invalidated = True
self.data = None
self.effective_matrix = None
self.closeContext()
self.clear_messages()
# if no data nor matrix is present reset plot
if self.signal_data is None and self.matrix is None:
self.clear()
self.init_attr_values()
return
if self.signal_data is not None and self.matrix is not None and \
len(self.signal_data) != len(self.matrix):
self.Error.mismatching_dimensions()
self.clear()
self.init_attr_values()
return
if self.signal_data is not None:
self.data = self.signal_data
elif self.matrix_data is not None:
self.data = self.matrix_data
if self.matrix is not None:
self.effective_matrix = self.matrix
if self.matrix.axis == 0 and self.data is not None \
and self.data is self.matrix_data:
names = [[attr.name] for attr in self.data.domain.attributes]
domain = Domain([], metas=[StringVariable("labels")])
self.data = Table.from_list(domain, names)
elif self.data.domain.attributes:
preprocessed_data = MDS().preprocess(self.data)
self.effective_matrix = Euclidean(preprocessed_data)
else:
self.Error.no_attributes()
self.clear()
self.init_attr_values()
return
self.init_attr_values()
self.openContext(self.data)
self._invalidated = not (
matrix_existed and self.effective_matrix is not None
and array_equal(effective_matrix, self.effective_matrix))
if self._invalidated:
self.clear()
self.graph.set_effective_matrix(self.effective_matrix)
def init_attr_values(self):
super().init_attr_values()
if self.matrix is not None and self.matrix.axis == 0 and \
self.data is not None and len(self.data):
self.attr_label = self.data.domain["labels"]
def _toggle_run(self):
if self.task is not None:
self.cancel()
self.run_button.setText("Resume")
self.commit()
else:
self._run()
def _run(self):
if self.effective_matrix is None:
return
self.graph.pause_drawing_pairs()
self.run_button.setText("Stop")
_, step_size = OWMDS.RefreshRate[self.refresh_rate]
if step_size == -1:
step_size = self.max_iter
init_type = "PCA" if self.initialization == OWMDS.PCA else "random"
self.start(run_mds, self.effective_matrix, self.max_iter, step_size,
init_type, self.embedding)
# ConcurrentWidgetMixin
def on_partial_result(self, result: Result):
assert isinstance(result.embedding, np.ndarray)
assert len(result.embedding) == len(self.effective_matrix)
first_result = self.embedding is None
new_embedding = result.embedding
need_update = new_embedding is not self.embedding
self.embedding = new_embedding
if first_result:
self.setup_plot()
else:
if need_update:
self.graph.update_coordinates()
self.graph.update_density()
def on_done(self, result: Result):
assert isinstance(result.embedding, np.ndarray)
assert len(result.embedding) == len(self.effective_matrix)
self.embedding = result.embedding
self.graph.resume_drawing_pairs()
self.run_button.setText("Start")
self.commit()
def on_exception(self, ex: Exception):
if isinstance(ex, MemoryError):
self.Error.out_of_memory()
else:
self.Error.optimization_error(str(ex))
self.graph.resume_drawing_pairs()
self.run_button.setText("Start")
def do_PCA(self):
self.do_initialization(self.PCA)
def do_random(self):
self.do_initialization(self.Random)
def do_jitter(self):
self.do_initialization(self.Jitter)
def do_initialization(self, init_type: int):
self.run_button.setText("Start")
self.__invalidate_embedding(init_type)
self.setup_plot()
self.commit()
def __invalidate_embedding(self, initialization=PCA):
def jitter_coord(part):
span = np.max(part) - np.min(part)
part += np.random.uniform(-span / 20, span / 20, len(part))
# reset/invalidate the MDS embedding, to the default initialization
# (Random or PCA), restarting the optimization if necessary.
if self.effective_matrix is None:
self.graph.reset_graph()
return
X = self.effective_matrix
if initialization == OWMDS.PCA:
self.embedding = torgerson(X)
elif initialization == OWMDS.Random:
self.embedding = np.random.rand(len(X), 2)
else:
jitter_coord(self.embedding[:, 0])
jitter_coord(self.embedding[:, 1])
# restart the optimization if it was interrupted.
if self.task is not None:
self._run()
def handleNewSignals(self):
self._initialize()
self.input_changed.emit(self.data)
if self._invalidated:
self.graph.pause_drawing_pairs()
self.__invalidate_embedding()
self.enable_controls()
if self.effective_matrix is not None:
self._run()
super().handleNewSignals()
def _on_connected_changed(self):
self.graph.set_effective_matrix(self.effective_matrix)
self.graph.update_pairs(reconnect=True)
def setup_plot(self):
super().setup_plot()
if self.embedding is not None:
self.graph.update_pairs(reconnect=True)
def get_size_data(self):
if self.attr_size == "Stress":
return stress(self.embedding, self.effective_matrix)
else:
return super().get_size_data()
def get_embedding(self):
self.valid_data = np.ones(len(self.embedding), dtype=bool) \
if self.embedding is not None else None
return self.embedding
def _get_projection_data(self):
if self.embedding is None:
return None
if self.data is None:
x_name, y_name = self.embedding_variables_names
variables = ContinuousVariable(x_name), ContinuousVariable(y_name)
return Table(Domain(variables), self.embedding)
return super()._get_projection_data()
def onDeleteWidget(self):
self.shutdown()
super().onDeleteWidget()
@classmethod
def migrate_settings(cls, settings_, version):
if version < 2:
settings_graph = {}
for old, new in (("label_only_selected", "label_only_selected"),
("symbol_opacity", "alpha_value"),
("symbol_size", "point_width"), ("jitter",
"jitter_size")):
settings_graph[new] = settings_[old]
settings_["graph"] = settings_graph
settings_["auto_commit"] = settings_["autocommit"]
if version < 3:
if "connected_pairs" in settings_:
connected_pairs = settings_["connected_pairs"]
settings_["graph"]["connected_pairs"] = connected_pairs
@classmethod
def migrate_context(cls, context, version):
if version < 2:
domain = context.ordered_domain
n_domain = [t for t in context.ordered_domain if t[1] == 2]
c_domain = [t for t in context.ordered_domain if t[1] == 1]
context_values = {}
for _, old_val, new_val in ((domain, "color_value", "attr_color"),
(c_domain, "shape_value",
"attr_shape"),
(n_domain, "size_value", "attr_size"),
(domain, "label_value", "attr_label")):
tmp = context.values[old_val]
if tmp[1] >= 0:
context_values[new_val] = (tmp[0], tmp[1] + 100)
elif tmp[0] != "Stress":
context_values[new_val] = None
else:
context_values[new_val] = tmp
context.values = context_values
if version < 3 and "graph" in context.values:
values = context.values
values["attr_color"] = values["graph"]["attr_color"]
values["attr_size"] = values["graph"]["attr_size"]
values["attr_shape"] = values["graph"]["attr_shape"]
values["attr_label"] = values["graph"]["attr_label"]
class OWScatterPlot(OWWidget):
"""Scatterplot visualization with explorative analysis and intelligent
data visualization enhancements."""
name = 'Scatter Plot'
description = "Interactive scatter plot visualization with " \
"intelligent data visualization enhancements."
icon = "icons/ScatterPlot.svg"
priority = 140
class Inputs:
data = Input("Data", Table, default=True)
data_subset = Input("Data Subset", Table)
features = Input("Features", AttributeList)
class Outputs:
selected_data = Output("Selected Data", Table, default=True)
annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Table)
features = Output("Features", Table, dynamic=False)
settingsHandler = DomainContextHandler()
auto_send_selection = Setting(True)
auto_sample = Setting(True)
toolbar_selection = Setting(0)
attr_x = ContextSetting(None)
attr_y = ContextSetting(None)
selection = Setting(None, schema_only=True)
graph = SettingProvider(OWScatterPlotGraph)
jitter_sizes = [0, 0.1, 0.5, 1, 2, 3, 4, 5, 7, 10]
graph_name = "graph.plot_widget.plotItem"
class Information(OWWidget.Information):
sampled_sql = Msg("Large SQL table; showing a sample.")
def __init__(self):
super().__init__()
box = gui.vBox(self.mainArea, True, margin=0)
self.graph = OWScatterPlotGraph(self, box, "ScatterPlot")
box.layout().addWidget(self.graph.plot_widget)
plot = self.graph.plot_widget
axispen = QPen(self.palette().color(QPalette.Text))
axis = plot.getAxis("bottom")
axis.setPen(axispen)
axis = plot.getAxis("left")
axis.setPen(axispen)
self.data = None # Orange.data.Table
self.subset_data = None # Orange.data.Table
self.data_metas_X = None # self.data, where primitive metas are moved to X
self.sql_data = None # Orange.data.sql.table.SqlTable
self.attribute_selection_list = None # list of Orange.data.Variable
self.__timer = QTimer(self, interval=1200)
self.__timer.timeout.connect(self.add_data)
common_options = dict(
labelWidth=50, orientation=Qt.Horizontal, sendSelectedValue=True,
valueType=str)
box = gui.vBox(self.controlArea, "Axis Data")
dmod = DomainModel
self.xy_model = DomainModel(dmod.MIXED, valid_types=dmod.PRIMITIVE)
self.cb_attr_x = gui.comboBox(
box, self, "attr_x", label="Axis x:", callback=self.update_attr,
model=self.xy_model, **common_options)
self.cb_attr_y = gui.comboBox(
box, self, "attr_y", label="Axis y:", callback=self.update_attr,
model=self.xy_model, **common_options)
vizrank_box = gui.hBox(box)
gui.separator(vizrank_box, width=common_options["labelWidth"])
self.vizrank, self.vizrank_button = ScatterPlotVizRank.add_vizrank(
vizrank_box, self, "Find Informative Projections", self.set_attr)
gui.separator(box)
gui.valueSlider(
box, self, value='graph.jitter_size', label='Jittering: ',
values=self.jitter_sizes, callback=self.reset_graph_data,
labelFormat=lambda x:
"None" if x == 0 else ("%.1f %%" if x < 1 else "%d %%") % x)
gui.checkBox(
gui.indentedBox(box), self, 'graph.jitter_continuous',
'Jitter numeric values', callback=self.reset_graph_data)
self.sampling = gui.auto_commit(
self.controlArea, self, "auto_sample", "Sample", box="Sampling",
callback=self.switch_sampling, commit=lambda: self.add_data(1))
self.sampling.setVisible(False)
g = self.graph.gui
g.point_properties_box(self.controlArea)
self.models = [self.xy_model] + g.points_models
box = gui.vBox(self.controlArea, "Plot Properties")
g.add_widgets([g.ShowLegend, g.ShowGridLines], box)
gui.checkBox(
box, self, value='graph.tooltip_shows_all',
label='Show all data on mouse hover')
self.cb_class_density = gui.checkBox(
box, self, value='graph.class_density', label='Show class density',
callback=self.update_density)
self.cb_reg_line = gui.checkBox(
box, self, value='graph.show_reg_line',
label='Show regression line', callback=self.update_regression_line)
gui.checkBox(
box, self, 'graph.label_only_selected',
'Label only selected points', callback=self.graph.update_labels)
self.zoom_select_toolbar = g.zoom_select_toolbar(
gui.vBox(self.controlArea, "Zoom/Select"), nomargin=True,
buttons=[g.StateButtonsBegin, g.SimpleSelect, g.Pan, g.Zoom,
g.StateButtonsEnd, g.ZoomReset]
)
buttons = self.zoom_select_toolbar.buttons
buttons[g.Zoom].clicked.connect(self.graph.zoom_button_clicked)
buttons[g.Pan].clicked.connect(self.graph.pan_button_clicked)
buttons[g.SimpleSelect].clicked.connect(self.graph.select_button_clicked)
buttons[g.ZoomReset].clicked.connect(self.graph.reset_button_clicked)
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_send_selection",
"Send Selection", "Send Automatically")
def zoom(s):
"""Zoom in/out by factor `s`."""
viewbox = plot.getViewBox()
# scaleBy scales the view's bounds (the axis range)
viewbox.scaleBy((1 / s, 1 / s))
def fit_to_view():
viewbox = plot.getViewBox()
viewbox.autoRange()
zoom_in = QAction(
"Zoom in", self, triggered=lambda: zoom(1.25)
)
zoom_in.setShortcuts([QKeySequence(QKeySequence.ZoomIn),
QKeySequence(self.tr("Ctrl+="))])
zoom_out = QAction(
"Zoom out", self, shortcut=QKeySequence.ZoomOut,
triggered=lambda: zoom(1 / 1.25)
)
zoom_fit = QAction(
"Fit in view", self,
shortcut=QKeySequence(Qt.ControlModifier | Qt.Key_0),
triggered=fit_to_view
)
self.addActions([zoom_in, zoom_out, zoom_fit])
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 settingsFromWidgetCallback(self, handler, context):
# context.selectionPolygons = []
# for curve in self.graph.selectionCurveList:
# xs = [curve.x(i) for i in range(curve.dataSize())]
# ys = [curve.y(i) for i in range(curve.dataSize())]
# context.selectionPolygons.append((xs, ys))
# def settingsToWidgetCallback(self, handler, context):
# selections = getattr(context, "selectionPolygons", [])
# for (xs, ys) in selections:
# c = SelectionCurve("")
# c.setData(xs,ys)
# c.attach(self.graph)
# self.graph.selectionCurveList.append(c)
def reset_graph_data(self, *_):
if self.data is not None:
self.graph.rescale_data()
self.update_graph()
@Inputs.data
def set_data(self, data):
self.clear_messages()
self.Information.sampled_sql.clear()
self.__timer.stop()
self.sampling.setVisible(False)
self.sql_data = None
if isinstance(data, SqlTable):
if data.approx_len() < 4000:
data = Table(data)
else:
self.Information.sampled_sql()
self.sql_data = data
data_sample = data.sample_time(0.8, no_cache=True)
data_sample.download_data(2000, partial=True)
data = Table(data_sample)
self.sampling.setVisible(True)
if self.auto_sample:
self.__timer.start()
if data is not None and (len(data) == 0 or len(data.domain) == 0):
data = None
if self.data and data and self.data.checksum() == data.checksum():
return
self.closeContext()
same_domain = (self.data and data and
data.domain.checksum() == self.data.domain.checksum())
self.data = data
self.data_metas_X = self.move_primitive_metas_to_X(data)
if not same_domain:
self.init_attr_values()
self.vizrank.initialize()
self.vizrank.attrs = self.data.domain.attributes if self.data is not None else []
self.vizrank_button.setEnabled(
self.data is not None and not self.data.is_sparse() and
self.data.domain.class_var is not None and
len(self.data.domain.attributes) > 1 and len(self.data) > 1)
if self.data is not None and self.data.domain.class_var is None \
and len(self.data.domain.attributes) > 1 and len(self.data) > 1:
self.vizrank_button.setToolTip(
"Data with a class variable is required.")
else:
self.vizrank_button.setToolTip("")
self.openContext(self.data)
def findvar(name, iterable):
"""Find a Orange.data.Variable in `iterable` by name"""
for el in iterable:
if isinstance(el, Orange.data.Variable) and el.name == name:
return el
return None
# handle restored settings from < 3.3.9 when attr_* were stored
# by name
if isinstance(self.attr_x, str):
self.attr_x = findvar(self.attr_x, self.xy_model)
if isinstance(self.attr_y, str):
self.attr_y = findvar(self.attr_y, self.xy_model)
if isinstance(self.graph.attr_label, str):
self.graph.attr_label = findvar(
self.graph.attr_label, self.graph.gui.label_model)
if isinstance(self.graph.attr_color, str):
self.graph.attr_color = findvar(
self.graph.attr_color, self.graph.gui.color_model)
if isinstance(self.graph.attr_shape, str):
self.graph.attr_shape = findvar(
self.graph.attr_shape, self.graph.gui.shape_model)
if isinstance(self.graph.attr_size, str):
self.graph.attr_size = findvar(
self.graph.attr_size, self.graph.gui.size_model)
def add_data(self, time=0.4):
if self.data and len(self.data) > 2000:
return self.__timer.stop()
data_sample = self.sql_data.sample_time(time, no_cache=True)
if data_sample:
data_sample.download_data(2000, partial=True)
data = Table(data_sample)
self.data = Table.concatenate((self.data, data), axis=0)
self.data_metas_X = self.move_primitive_metas_to_X(self.data)
self.handleNewSignals()
def switch_sampling(self):
self.__timer.stop()
if self.auto_sample and self.sql_data:
self.add_data()
self.__timer.start()
def move_primitive_metas_to_X(self, data):
if data is not None:
new_attrs = [a for a in data.domain.attributes + data.domain.metas
if a.is_primitive()]
new_metas = [m for m in data.domain.metas if not m.is_primitive()]
new_domain = Domain(new_attrs, data.domain.class_vars, new_metas)
data = data.transform(new_domain)
return data
@Inputs.data_subset
def set_subset_data(self, subset_data):
self.warning()
if isinstance(subset_data, SqlTable):
if subset_data.approx_len() < AUTO_DL_LIMIT:
subset_data = Table(subset_data)
else:
self.warning("Data subset does not support large Sql tables")
subset_data = None
self.subset_data = self.move_primitive_metas_to_X(subset_data)
self.controls.graph.alpha_value.setEnabled(subset_data is None)
# called when all signals are received, so the graph is updated only once
def handleNewSignals(self):
self.graph.new_data(self.sparse_to_dense(self.data_metas_X),
self.sparse_to_dense(self.subset_data))
if self.attribute_selection_list and self.graph.domain and \
all(attr in self.graph.domain
for attr in self.attribute_selection_list):
self.attr_x = self.attribute_selection_list[0]
self.attr_y = self.attribute_selection_list[1]
self.attribute_selection_list = None
self.update_graph()
self.cb_class_density.setEnabled(self.graph.can_draw_density())
self.cb_reg_line.setEnabled(self.graph.can_draw_regresssion_line())
self.apply_selection()
self.unconditional_commit()
def prepare_data(self):
"""
Only when dealing with sparse matrices.
GH-2152
"""
self.graph.new_data(self.sparse_to_dense(self.data_metas_X),
self.sparse_to_dense(self.subset_data),
new=False)
def sparse_to_dense(self, input_data=None):
if input_data is None or not input_data.is_sparse():
return input_data
keys = []
attrs = {self.attr_x,
self.attr_y,
self.graph.attr_color,
self.graph.attr_shape,
self.graph.attr_size,
self.graph.attr_label}
for i, attr in enumerate(input_data.domain):
if attr in attrs:
keys.append(i)
new_domain = input_data.domain.select_columns(keys)
dmx = input_data.transform(new_domain)
dmx.X = dmx.X.toarray()
# TODO: remove once we make sure Y is always dense.
if sp.issparse(dmx.Y):
dmx.Y = dmx.Y.toarray()
return dmx
def apply_selection(self):
"""Apply selection saved in workflow."""
if self.data is not None and self.selection is not None:
self.graph.selection = np.zeros(len(self.data), dtype=np.uint8)
self.selection = [x for x in self.selection if x < len(self.data)]
self.graph.selection[self.selection] = 1
self.graph.update_colors(keep_colors=True)
@Inputs.features
def set_shown_attributes(self, attributes):
if attributes and len(attributes) >= 2:
self.attribute_selection_list = attributes[:2]
else:
self.attribute_selection_list = None
def get_shown_attributes(self):
return self.attr_x, self.attr_y
def init_attr_values(self):
domain = self.data and self.data.domain
for model in self.models:
model.set_domain(domain)
self.attr_x = self.xy_model[0] if self.xy_model else None
self.attr_y = self.xy_model[1] if len(self.xy_model) >= 2 \
else self.attr_x
self.graph.attr_color = domain and self.data.domain.class_var or None
self.graph.attr_shape = None
self.graph.attr_size = None
self.graph.attr_label = None
def set_attr(self, attr_x, attr_y):
self.attr_x, self.attr_y = attr_x, attr_y
self.update_attr()
def update_attr(self):
self.prepare_data()
self.update_graph()
self.cb_class_density.setEnabled(self.graph.can_draw_density())
self.cb_reg_line.setEnabled(self.graph.can_draw_regresssion_line())
self.send_features()
def update_colors(self):
self.prepare_data()
self.cb_class_density.setEnabled(self.graph.can_draw_density())
def update_density(self):
self.update_graph(reset_view=False)
def update_regression_line(self):
self.update_graph(reset_view=False)
def update_graph(self, reset_view=True, **_):
self.graph.zoomStack = []
if self.graph.data is None:
return
self.graph.update_data(self.attr_x, self.attr_y, reset_view)
def selection_changed(self):
self.send_data()
@staticmethod
def create_groups_table(data, selection):
if data is None:
return None
names = [var.name for var in data.domain.variables + data.domain.metas]
name = get_next_name(names, "Selection group")
metas = data.domain.metas + (
DiscreteVariable(
name,
["Unselected"] + ["G{}".format(i + 1)
for i in range(np.max(selection))]),
)
domain = Domain(data.domain.attributes, data.domain.class_vars, metas)
table = data.transform(domain)
table.metas[:, len(data.domain.metas):] = \
selection.reshape(len(data), 1)
return table
def send_data(self):
selected = None
selection = None
# TODO: Implement selection for sql data
graph = self.graph
if isinstance(self.data, SqlTable):
selected = self.data
elif self.data is not None:
selection = graph.get_selection()
if len(selection) > 0:
selected = self.data[selection]
if graph.selection is not None and np.max(graph.selection) > 1:
annotated = self.create_groups_table(self.data, graph.selection)
else:
annotated = create_annotated_table(self.data, selection)
self.Outputs.selected_data.send(selected)
self.Outputs.annotated_data.send(annotated)
# Store current selection in a setting that is stored in workflow
if self.selection is not None and len(selection):
self.selection = list(selection)
def send_features(self):
features = None
if self.attr_x or self.attr_y:
dom = Domain([], metas=(StringVariable(name="feature"),))
features = Table(dom, [[self.attr_x], [self.attr_y]])
features.name = "Features"
self.Outputs.features.send(features)
def commit(self):
self.send_data()
self.send_features()
def get_widget_name_extension(self):
if self.data is not None:
return "{} vs {}".format(self.attr_x.name, self.attr_y.name)
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.attr_x.is_discrete or
self.attr_y.is_discrete or
self.graph.jitter_continuous) and
self.graph.jitter_size)))
self.report_plot()
if caption:
self.report_caption(caption)
def onDeleteWidget(self):
super().onDeleteWidget()
self.graph.plot_widget.getViewBox().deleteLater()
self.graph.plot_widget.clear()
class OWMosaicDisplay(OWWidget):
name = "Mosaic Display"
description = "Display data in a mosaic plot."
icon = "icons/MosaicDisplay.svg"
priority = 220
keywords = []
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)
settingsHandler = DomainContextHandler()
vizrank = SettingProvider(MosaicVizRank)
settings_version = 2
use_boxes = Setting(True)
variable1: Variable = ContextSetting(None)
variable2: Variable = ContextSetting(None)
variable3: Variable = ContextSetting(None)
variable4: Variable = ContextSetting(None)
variable_color: DiscreteVariable = ContextSetting(None)
selection = Setting(set(), schema_only=True)
BAR_WIDTH = 5
SPACING = 4
ATTR_NAME_OFFSET = 20
ATTR_VAL_OFFSET = 3
BLUE_COLORS = [
QColor(255, 255, 255),
QColor(210, 210, 255),
QColor(110, 110, 255),
QColor(0, 0, 255)
]
RED_COLORS = [
QColor(255, 255, 255),
QColor(255, 200, 200),
QColor(255, 100, 100),
QColor(255, 0, 0)
]
graph_name = "canvas"
attrs_changed_manually = Signal(list)
class Warning(OWWidget.Warning):
incompatible_subset = Msg("Data subset is incompatible with Data")
no_valid_data = Msg("No valid data")
no_cont_selection_sql = \
Msg("Selection of numeric features on SQL is not supported")
def __init__(self):
super().__init__()
self.data = None
self.discrete_data = None
self.subset_data = None
self.subset_indices = None
self.__pending_selection = self.selection
self.selection = set()
self.color_data = None
self.areas = []
self.canvas = QGraphicsScene(self)
self.canvas_view = ViewWithPress(self.canvas,
handler=self.clear_selection)
self.mainArea.layout().addWidget(self.canvas_view)
self.canvas_view.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.canvas_view.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.canvas_view.setRenderHint(QPainter.Antialiasing)
box = gui.vBox(self.controlArea, box=True)
self.model_1 = DomainModel(order=DomainModel.MIXED,
valid_types=DomainModel.PRIMITIVE)
self.model_234 = DomainModel(order=DomainModel.MIXED,
valid_types=DomainModel.PRIMITIVE,
placeholder="(None)")
self.attr_combos = [
gui.comboBox(box,
self,
value="variable{}".format(i),
orientation=Qt.Horizontal,
contentsLength=12,
searchable=True,
callback=self.attr_changed,
model=self.model_1 if i == 1 else self.model_234)
for i in range(1, 5)
]
self.vizrank, self.vizrank_button = MosaicVizRank.add_vizrank(
box, self, "Find Informative Mosaics", self.set_attr)
box2 = gui.vBox(self.controlArea, box="Interior Coloring")
self.color_model = DomainModel(order=DomainModel.MIXED,
valid_types=DomainModel.PRIMITIVE,
placeholder="(Pearson residuals)")
self.cb_attr_color = gui.comboBox(box2,
self,
value="variable_color",
orientation=Qt.Horizontal,
contentsLength=12,
labelWidth=50,
searchable=True,
callback=self.set_color_data,
model=self.color_model)
self.bar_button = gui.checkBox(box2,
self,
'use_boxes',
label='Compare with total',
callback=self.update_graph)
gui.rubber(self.controlArea)
def sizeHint(self):
return QSize(720, 530)
def _get_discrete_data(self, data):
"""
Discretize continuous attributes.
Return None when there is no data, no rows, or no primitive attributes.
"""
if (data is None or not len(data) or not any(
attr.is_discrete or attr.is_continuous
for attr in chain(data.domain.variables, data.domain.metas))):
return None
elif any(attr.is_continuous for attr in data.domain.variables):
return Discretize(method=EqualFreq(n=4),
remove_const=False,
discretize_classes=True,
discretize_metas=True)(data)
else:
return data
def init_combos(self, data):
def set_combos(value):
self.model_1.set_domain(value)
self.model_234.set_domain(value)
self.color_model.set_domain(value)
if data is None:
set_combos(None)
self.variable1 = self.variable2 = self.variable3 \
= self.variable4 = self.variable_color = None
return
set_combos(self.data.domain)
if len(self.model_1) > 0:
self.variable1 = self.model_1[0]
self.variable2 = self.model_1[min(1, len(self.model_1) - 1)]
self.variable3 = self.variable4 = None
self.variable_color = self.data.domain.class_var # None is OK, too
def get_disc_attr_list(self):
return [
self.discrete_data.domain[var.name]
for var in (self.variable1, self.variable2, self.variable3,
self.variable4) if var
]
def set_attr(self, *attrs):
self.variable1, self.variable2, self.variable3, self.variable4 = [
attr and self.data.domain[attr.name] for attr in attrs
]
self.reset_graph()
def attr_changed(self):
self.attrs_changed_manually.emit(self.get_disc_attr_list())
self.reset_graph()
def resizeEvent(self, e):
OWWidget.resizeEvent(self, e)
self.update_graph()
def showEvent(self, ev):
OWWidget.showEvent(self, ev)
self.update_graph()
@Inputs.data
def set_data(self, data):
if isinstance(data, SqlTable) and data.approx_len() > LARGE_TABLE:
data = data.sample_time(DEFAULT_SAMPLE_TIME)
self.closeContext()
self.data = data
self.vizrank.stop_and_reset()
self.vizrank_button.setEnabled(
self.data is not None and len(self.data) > 1
and len(self.data.domain.attributes) >= 1)
if self.data is None:
self.discrete_data = None
self.init_combos(None)
return
self.init_combos(self.data)
self.openContext(self.data)
@Inputs.data_subset
def set_subset_data(self, data):
self.subset_data = data
# this is called by widget after setData and setSubsetData are called.
# this way the graph is updated only once
def handleNewSignals(self):
self.Warning.incompatible_subset.clear()
self.subset_indices = None
if self.data is not None and self.subset_data:
transformed = self.subset_data.transform(self.data.domain)
if np.all(np.isnan(transformed.X)) \
and np.all(np.isnan(transformed.Y)):
self.Warning.incompatible_subset()
else:
indices = {e.id for e in transformed}
self.subset_indices = [ex.id in indices for ex in self.data]
if self.data is not None and self.__pending_selection is not None:
self.selection = self.__pending_selection
self.__pending_selection = None
else:
self.selection = set()
self.set_color_data()
self.update_graph()
self.send_selection()
def clear_selection(self):
self.selection = set()
self.update_selection_rects()
self.send_selection()
def coloring_changed(self):
self.vizrank.coloring_changed()
self.update_graph()
def reset_graph(self):
self.clear_selection()
self.update_graph()
def set_color_data(self):
if self.data is None:
return
self.bar_button.setEnabled(self.variable_color is not None)
attrs = [v for v in self.model_1 if v and v is not self.variable_color]
domain = Domain(attrs, self.variable_color, None)
self.color_data = self.data.from_table(domain, self.data)
self.discrete_data = self._get_discrete_data(self.color_data)
self.vizrank.stop_and_reset()
self.vizrank_button.setEnabled(True)
self.coloring_changed()
def update_selection_rects(self):
pens = (QPen(), QPen(Qt.black, 3, Qt.DotLine))
for i, (_, _, area) in enumerate(self.areas):
area.setPen(pens[i in self.selection])
def select_area(self, index, ev):
if ev.button() != Qt.LeftButton:
return
if ev.modifiers() & Qt.ControlModifier:
self.selection ^= {index}
else:
self.selection = {index}
self.update_selection_rects()
self.send_selection()
def send_selection(self):
if not self.selection or self.data is None:
self.Outputs.selected_data.send(None)
self.Outputs.annotated_data.send(
create_annotated_table(self.data, []))
return
filters = []
self.Warning.no_cont_selection_sql.clear()
if self.discrete_data is not self.data:
if isinstance(self.data, SqlTable):
self.Warning.no_cont_selection_sql()
for i in self.selection:
cols, vals, _ = self.areas[i]
filters.append(
filter.Values(
filter.FilterDiscrete(col, [val])
for col, val in zip(cols, vals)))
if len(filters) > 1:
filters = filter.Values(filters, conjunction=False)
else:
filters = filters[0]
selection = filters(self.discrete_data)
idset = set(selection.ids)
sel_idx = [i for i, id in enumerate(self.data.ids) if id in idset]
if self.discrete_data is not self.data:
selection = self.data[sel_idx]
self.Outputs.selected_data.send(selection)
self.Outputs.annotated_data.send(
create_annotated_table(self.data, sel_idx))
def send_report(self):
self.report_plot(self.canvas)
def update_graph(self):
spacing = self.SPACING
bar_width = self.BAR_WIDTH
def get_counts(attr_vals, values):
"""Calculate rectangles' widths; if all are 0, they are set to 1."""
if not attr_vals:
counts = [conditionaldict[val] for val in values]
else:
counts = [
conditionaldict[attr_vals + "-" + val] for val in values
]
total = sum(counts)
if total == 0:
counts = [1] * len(values)
total = sum(counts)
return total, counts
def draw_data(attr_list,
x0_x1,
y0_y1,
side,
condition,
total_attrs,
used_attrs,
used_vals,
attr_vals=""):
x0, x1 = x0_x1
y0, y1 = y0_y1
if conditionaldict[attr_vals] == 0:
add_rect(x0,
x1,
y0,
y1,
"",
used_attrs,
used_vals,
attr_vals=attr_vals)
# store coordinates for later drawing of labels
draw_text(side, attr_list[0], (x0, x1), (y0, y1), total_attrs,
used_attrs, used_vals, attr_vals)
return
attr = attr_list[0]
# how much smaller rectangles do we draw
edge = len(attr_list) * spacing
values = get_variable_values_sorted(attr)
if side % 2:
values = values[::-1] # reverse names if necessary
if side % 2 == 0: # we are drawing on the x axis
# remove the space needed for separating different attr. values
whole = max(0, (x1 - x0) - edge * (len(values) - 1))
if whole == 0:
edge = (x1 - x0) / float(len(values) - 1)
else: # we are drawing on the y axis
whole = max(0, (y1 - y0) - edge * (len(values) - 1))
if whole == 0:
edge = (y1 - y0) / float(len(values) - 1)
total, counts = get_counts(attr_vals, values)
# when visualizing the third attribute and the first attribute has
# the last value, reverse the order in which the boxes are drawn;
# otherwise, if the last cell, nearest to the labels of the fourth
# attribute, is empty, we wouldn't be able to position the labels
valrange = list(range(len(values)))
if len(attr_list + used_attrs) == 4 and len(used_attrs) == 2:
attr1values = get_variable_values_sorted(used_attrs[0])
if used_vals[0] == attr1values[-1]:
valrange = valrange[::-1]
for i in valrange:
start = i * edge + whole * float(sum(counts[:i]) / total)
end = i * edge + whole * float(sum(counts[:i + 1]) / total)
val = values[i]
htmlval = to_html(val)
newattrvals = attr_vals + "-" + val if attr_vals else val
tooltip = "{} {}: <b>{}</b><br/>".format(
condition, attr.name, htmlval)
attrs = used_attrs + [attr]
vals = used_vals + [val]
args = attrs, vals, newattrvals
if side % 2 == 0: # if we are moving horizontally
if len(attr_list) == 1:
add_rect(x0 + start, x0 + end, y0, y1, tooltip, *args)
else:
draw_data(attr_list[1:], (x0 + start, x0 + end),
(y0, y1), side + 1, tooltip, total_attrs,
*args)
else:
if len(attr_list) == 1:
add_rect(x0, x1, y0 + start, y0 + end, tooltip, *args)
else:
draw_data(attr_list[1:], (x0, x1),
(y0 + start, y0 + end), side + 1, tooltip,
total_attrs, *args)
draw_text(side, attr_list[0], (x0, x1), (y0, y1), total_attrs,
used_attrs, used_vals, attr_vals)
def draw_text(side, attr, x0_x1, y0_y1, total_attrs, used_attrs,
used_vals, attr_vals):
x0, x1 = x0_x1
y0, y1 = y0_y1
if side in drawn_sides:
return
# the text on the right will be drawn when we are processing
# visualization of the last value of the first attribute
if side == 3:
attr1values = get_variable_values_sorted(used_attrs[0])
if used_vals[0] != attr1values[-1]:
return
if not conditionaldict[attr_vals]:
if side not in draw_positions:
draw_positions[side] = (x0, x1, y0, y1)
return
else:
if side in draw_positions:
# restore the positions of attribute values and name
(x0, x1, y0, y1) = draw_positions[side]
drawn_sides.add(side)
values = get_variable_values_sorted(attr)
if side % 2:
values = values[::-1]
spaces = spacing * (total_attrs - side) * (len(values) - 1)
width = x1 - x0 - spaces * (side % 2 == 0)
height = y1 - y0 - spaces * (side % 2 == 1)
# calculate position of first attribute
currpos = 0
total, counts = get_counts(attr_vals, values)
aligns = [
Qt.AlignTop | Qt.AlignHCenter, Qt.AlignRight | Qt.AlignVCenter,
Qt.AlignBottom | Qt.AlignHCenter,
Qt.AlignLeft | Qt.AlignVCenter
]
align = aligns[side]
for i, val in enumerate(values):
if distributiondict[val] != 0:
perc = counts[i] / float(total)
rwidth = width * perc
xs = [
x0 + currpos + rwidth / 2, x0 - self.ATTR_VAL_OFFSET,
x0 + currpos + rwidth / 2, x1 + self.ATTR_VAL_OFFSET
]
ys = [
y1 + self.ATTR_VAL_OFFSET,
y0 + currpos + height * 0.5 * perc,
y0 - self.ATTR_VAL_OFFSET,
y0 + currpos + height * 0.5 * perc
]
CanvasText(self.canvas,
val,
xs[side],
ys[side],
align,
max_width=rwidth if side == 0 else None)
space = height if side % 2 else width
currpos += perc * space + spacing * (total_attrs - side)
xs = [
x0 + (x1 - x0) / 2, x0 - max_ylabel_w1 - self.ATTR_VAL_OFFSET,
x0 + (x1 - x0) / 2, x1 + max_ylabel_w2 + self.ATTR_VAL_OFFSET
]
ys = [
y1 + self.ATTR_VAL_OFFSET + self.ATTR_NAME_OFFSET,
y0 + (y1 - y0) / 2,
y0 - self.ATTR_VAL_OFFSET - self.ATTR_NAME_OFFSET,
y0 + (y1 - y0) / 2
]
CanvasText(self.canvas,
attr.name,
xs[side],
ys[side],
align,
bold=True,
vertical=side % 2)
def add_rect(x0,
x1,
y0,
y1,
condition,
used_attrs,
used_vals,
attr_vals=""):
area_index = len(self.areas)
x1 += (x0 == x1)
y1 += (y0 == y1)
# rectangles of width and height 1 are not shown - increase
y1 += (x1 - x0 + y1 - y0 == 2)
colors = class_var and [QColor(*col) for col in class_var.colors]
def select_area(_, ev):
self.select_area(area_index, ev)
def rect(x, y, w, h, z, pen_color=None, brush_color=None, **args):
if pen_color is None:
return CanvasRectangle(self.canvas,
x,
y,
w,
h,
z=z,
onclick=select_area,
**args)
if brush_color is None:
brush_color = pen_color
return CanvasRectangle(self.canvas,
x,
y,
w,
h,
pen_color,
brush_color,
z=z,
onclick=select_area,
**args)
def line(x1, y1, x2, y2):
r = QGraphicsLineItem(x1, y1, x2, y2, None)
self.canvas.addItem(r)
r.setPen(QPen(Qt.white, 2))
r.setZValue(30)
outer_rect = rect(x0, y0, x1 - x0, y1 - y0, 30)
self.areas.append((used_attrs, used_vals, outer_rect))
if not conditionaldict[attr_vals]:
return
if self.variable_color is None:
s = sum(apriori_dists[0])
expected = s * reduce(
mul, (apriori_dists[i][used_vals[i]] / float(s)
for i in range(len(used_vals))))
actual = conditionaldict[attr_vals]
pearson = float((actual - expected) / sqrt(expected))
if pearson == 0:
ind = 0
else:
ind = max(0, min(int(log(abs(pearson), 2)), 3))
color = [self.RED_COLORS, self.BLUE_COLORS][pearson > 0][ind]
rect(x0, y0, x1 - x0, y1 - y0, -20, color)
outer_rect.setToolTip(
condition + "<hr/>" + "Expected instances: %.1f<br>"
"Actual instances: %d<br>"
"Standardized (Pearson) residual: %.1f" %
(expected, conditionaldict[attr_vals], pearson))
else:
cls_values = get_variable_values_sorted(class_var)
prior = get_distribution(data, class_var.name)
total = 0
for i, value in enumerate(cls_values):
val = conditionaldict[attr_vals + "-" + value]
if val == 0:
continue
if i == len(cls_values) - 1:
v = y1 - y0 - total
else:
v = ((y1 - y0) * val) / conditionaldict[attr_vals]
rect(x0, y0 + total, x1 - x0, v, -20, colors[i])
total += v
if self.use_boxes and \
abs(x1 - x0) > bar_width and abs(y1 - y0) > bar_width:
total = 0
line(x0 + bar_width, y0, x0 + bar_width, y1)
n = sum(prior)
for i, (val, color) in enumerate(zip(prior, colors)):
if i == len(prior) - 1:
h = y1 - y0 - total
else:
h = (y1 - y0) * val / n
rect(x0, y0 + total, bar_width, h, 20, color)
total += h
if conditionalsubsetdict:
if conditionalsubsetdict[attr_vals]:
if self.subset_indices is not None:
line(x1 - bar_width, y0, x1 - bar_width, y1)
total = 0
n = conditionalsubsetdict[attr_vals]
if n:
for i, (cls, color) in \
enumerate(zip(cls_values, colors)):
val = conditionalsubsetdict[attr_vals +
"-" + cls]
if val == 0:
continue
if i == len(prior) - 1:
v = y1 - y0 - total
else:
v = ((y1 - y0) * val) / n
rect(x1 - bar_width, y0 + total, bar_width,
v, 15, color)
total += v
actual = [
conditionaldict[attr_vals + "-" + cls_values[i]]
for i in range(len(prior))
]
n_actual = sum(actual)
if n_actual > 0:
apriori = [prior[key] for key in cls_values]
n_apriori = sum(apriori)
text = "<br/>".join(
"<b>%s</b>: %d / %.1f%% (Expected %.1f / %.1f%%)" %
(cls, act, 100.0 * act / n_actual,
apr / n_apriori * n_actual, 100.0 * apr / n_apriori)
for cls, act, apr in zip(cls_values, actual, apriori))
else:
text = ""
outer_rect.setToolTip("{}<hr>Instances: {}<br><br>{}".format(
condition, n_actual, text[:-4]))
def create_legend():
if self.variable_color is None:
names = [
"<-8", "-8:-4", "-4:-2", "-2:2", "2:4", "4:8", ">8",
"Residuals:"
]
colors = self.RED_COLORS[::-1] + self.BLUE_COLORS[1:]
edges = repeat(Qt.black)
else:
names = get_variable_values_sorted(class_var)
edges = colors = [QColor(*col) for col in class_var.colors]
items = []
size = 8
for name, color, edgecolor in zip(names, colors, edges):
item = QGraphicsItemGroup()
item.addToGroup(
CanvasRectangle(None, -size / 2, -size / 2, size, size,
edgecolor, color))
item.addToGroup(
CanvasText(None, name, size, 0, Qt.AlignVCenter))
items.append(item)
return wrap_legend_items(items,
hspacing=20,
vspacing=16 + size,
max_width=self.canvas_view.width() - xoff)
self.canvas.clear()
self.areas = []
data = self.discrete_data
if data is None:
return
attr_list = self.get_disc_attr_list()
class_var = data.domain.class_var
# TODO: check this
# data = Preprocessor_dropMissing(data)
unique = [v.name for v in set(attr_list + [class_var]) if v]
if len(data[:, unique]) == 0:
self.Warning.no_valid_data()
return
else:
self.Warning.no_valid_data.clear()
attrs = [attr for attr in attr_list if not attr.values]
if attrs:
CanvasText(self.canvas,
"Feature {} has no values".format(attrs[0]),
(self.canvas_view.width() - 120) / 2,
self.canvas_view.height() / 2)
return
if self.variable_color is None:
apriori_dists = [
get_distribution(data, attr) for attr in attr_list
]
else:
apriori_dists = []
def get_max_label_width(attr):
values = get_variable_values_sorted(attr)
maxw = 0
for val in values:
t = CanvasText(self.canvas, val, 0, 0, bold=0, show=False)
maxw = max(int(t.boundingRect().width()), maxw)
return maxw
xoff = 20
# get the maximum width of rectangle
width = 20
max_ylabel_w1 = max_ylabel_w2 = 0
if len(attr_list) > 1:
text = CanvasText(self.canvas, attr_list[1].name, bold=1, show=0)
max_ylabel_w1 = min(get_max_label_width(attr_list[1]), 150)
width = 5 + text.boundingRect().height() + \
self.ATTR_VAL_OFFSET + max_ylabel_w1
xoff = width
if len(attr_list) == 4:
text = CanvasText(self.canvas,
attr_list[3].name,
bold=1,
show=0)
max_ylabel_w2 = min(get_max_label_width(attr_list[3]), 150)
width += text.boundingRect().height() + \
self.ATTR_VAL_OFFSET + max_ylabel_w2 - 10
legend = create_legend()
# get the maximum height of rectangle
yoff = 45
legendoff = yoff + self.ATTR_NAME_OFFSET + self.ATTR_VAL_OFFSET + 35
square_size = min(
self.canvas_view.width() - width - 20,
self.canvas_view.height() - legendoff -
legend.boundingRect().height())
if square_size < 0:
return # canvas is too small to draw rectangles
self.canvas_view.setSceneRect(0, 0, self.canvas_view.width(),
self.canvas_view.height())
drawn_sides = set()
draw_positions = {}
conditionaldict, distributiondict = \
get_conditional_distribution(data, attr_list)
conditionalsubsetdict = None
if self.subset_indices:
conditionalsubsetdict, _ = get_conditional_distribution(
self.discrete_data[self.subset_indices], attr_list)
# draw rectangles
draw_data(attr_list, (xoff, xoff + square_size),
(yoff, yoff + square_size), 0, "", len(attr_list), [], [])
self.canvas.addItem(legend)
legend.setPos(
xoff - legend.boundingRect().x() +
max(0, (square_size - legend.boundingRect().width()) / 2),
legendoff + square_size)
self.update_selection_rects()
@classmethod
def migrate_context(cls, context, version):
if version < 2:
settings.migrate_str_to_variable(context,
none_placeholder="(None)")
class OWLinearProjection(OWAnchorProjectionWidget):
name = "Linear Projection"
description = "A multi-axis projection of data onto " \
"a two-dimensional plane."
icon = "icons/LinearProjection.svg"
priority = 240
keywords = []
Projection_name = {Placement.Circular: "Circular Placement",
Placement.LDA: "Linear Discriminant Analysis",
Placement.PCA: "Principal Component Analysis"}
settings_version = 6
placement = Setting(Placement.Circular)
selected_vars = ContextSetting([])
vizrank = SettingProvider(LinearProjectionVizRank)
GRAPH_CLASS = OWLinProjGraph
graph = SettingProvider(OWLinProjGraph)
left_side_scrolling = True
class Error(OWAnchorProjectionWidget.Error):
no_cont_features = Msg("Plotting requires numeric features")
def _add_controls(self):
self._add_controls_variables()
self._add_controls_placement()
super()._add_controls()
self.gui.add_control(
self._effects_box, gui.hSlider, "Hide radius:", master=self.graph,
value="hide_radius", minValue=0, maxValue=100, step=10,
createLabel=False, callback=self.__radius_slider_changed
)
self.controlArea.layout().removeWidget(self.control_area_stretch)
self.control_area_stretch.setParent(None)
def _add_controls_variables(self):
self.model_selected = VariableSelectionModel(self.selected_vars)
variables_selection(self.controlArea, self, self.model_selected)
self.model_selected.selection_changed.connect(
self.__model_selected_changed)
self.vizrank, self.btn_vizrank = LinearProjectionVizRank.add_vizrank(
None, self, "Suggest Features", self.__vizrank_set_attrs)
self.controlArea.layout().addWidget(self.btn_vizrank)
def _add_controls_placement(self):
box = gui.widgetBox(
self.controlArea, True,
sizePolicy=(QSizePolicy.Minimum, QSizePolicy.Maximum)
)
self.radio_placement = gui.radioButtonsInBox(
box, self, "placement",
btnLabels=[self.Projection_name[x] for x in Placement],
callback=self.__placement_radio_changed
)
@property
def continuous_variables(self):
if self.data is None or self.data.domain is None:
return []
dom = self.data.domain
return [v for v in chain(dom.variables, dom.metas) if v.is_continuous]
@property
def effective_variables(self):
return self.selected_vars
def __vizrank_set_attrs(self, attrs):
if not attrs:
return
self.selected_vars[:] = attrs
# Ugly, but the alternative is to have yet another signal to which
# the view will have to connect
self.model_selected.selection_changed.emit()
def __model_selected_changed(self):
self.projection = None
self._check_options()
self.init_projection()
self.setup_plot()
self.commit()
def __placement_radio_changed(self):
self.controls.graph.hide_radius.setEnabled(
self.placement != Placement.Circular)
self.projection = self.projector = None
self._init_vizrank()
self.init_projection()
self.setup_plot()
self.commit()
def __radius_slider_changed(self):
self.graph.update_radius()
def colors_changed(self):
super().colors_changed()
self._init_vizrank()
def set_data(self, data):
super().set_data(data)
self._check_options()
self._init_vizrank()
self.init_projection()
def _check_options(self):
buttons = self.radio_placement.buttons
for btn in buttons:
btn.setEnabled(True)
if self.data is not None:
has_discrete_class = self.data.domain.has_discrete_class
if not has_discrete_class or len(np.unique(self.data.Y)) < 3:
buttons[Placement.LDA].setEnabled(False)
if self.placement == Placement.LDA:
self.placement = Placement.Circular
self.controls.graph.hide_radius.setEnabled(
self.placement != Placement.Circular)
def _init_vizrank(self):
is_enabled, msg = False, ""
if self.data is None:
msg = "There is no data."
elif self.attr_color is None:
msg = "Color variable has to be selected"
elif self.attr_color.is_continuous and \
self.placement == Placement.LDA:
msg = "Suggest Features does not work for Linear " \
"Discriminant Analysis Projection when " \
"continuous color variable is selected."
elif len([v for v in self.continuous_variables
if v is not self.attr_color]) < 3:
msg = "Not enough available continuous variables"
elif np.sum(np.all(np.isfinite(self.data.X), axis=1)) < 2:
msg = "Not enough valid data instances"
else:
is_enabled = not np.isnan(self.data.get_column_view(
self.attr_color)[0].astype(float)).all()
self.btn_vizrank.setToolTip(msg)
self.btn_vizrank.setEnabled(is_enabled)
if is_enabled:
self.vizrank.initialize()
def check_data(self):
def error(err):
err()
self.data = None
super().check_data()
if self.data is not None:
if not len(self.continuous_variables):
error(self.Error.no_cont_features)
def init_attr_values(self):
super().init_attr_values()
self.selected_vars[:] = self.continuous_variables[:3]
self.model_selected[:] = self.continuous_variables
def init_projection(self):
if self.placement == Placement.Circular:
self.projector = CircularPlacement()
elif self.placement == Placement.LDA:
self.projector = LDA(solver="eigen", n_components=2)
elif self.placement == Placement.PCA:
self.projector = PCA(n_components=2)
self.projector.component = 2
self.projector.preprocessors = PCA.preprocessors + [Normalize()]
super().init_projection()
def get_coordinates_data(self):
def normalized(a):
span = np.max(a, axis=0) - np.min(a, axis=0)
span[span == 0] = 1
return (a - np.mean(a, axis=0)) / span
embedding = self.get_embedding()
if embedding is None:
return None, None
norm_emb = normalized(embedding[self.valid_data])
return (norm_emb.ravel(), np.zeros(len(norm_emb), dtype=float)) \
if embedding.shape[1] == 1 else norm_emb.T
def _get_send_report_caption(self):
def projection_name():
return self.Projection_name[self.placement]
return report.render_items_vert((
("Projection", projection_name()),
("Color", self._get_caption_var_name(self.attr_color)),
("Label", self._get_caption_var_name(self.attr_label)),
("Shape", self._get_caption_var_name(self.attr_shape)),
("Size", self._get_caption_var_name(self.attr_size)),
("Jittering", self.graph.jitter_size != 0 and
"{} %".format(self.graph.jitter_size))))
@classmethod
def migrate_settings(cls, settings_, version):
if version < 2:
settings_["point_width"] = settings_["point_size"]
if version < 3:
settings_graph = {}
settings_graph["jitter_size"] = settings_["jitter_value"]
settings_graph["point_width"] = settings_["point_width"]
settings_graph["alpha_value"] = settings_["alpha_value"]
settings_graph["class_density"] = settings_["class_density"]
settings_["graph"] = settings_graph
if version < 4:
if "radius" in settings_:
settings_["graph"]["hide_radius"] = settings_["radius"]
if "selection_indices" in settings_ and \
settings_["selection_indices"] is not None:
selection = settings_["selection_indices"]
settings_["selection"] = [(i, 1) for i, selected in
enumerate(selection) if selected]
if version < 5:
if "placement" in settings_ and \
settings_["placement"] not in Placement:
settings_["placement"] = Placement.Circular
@classmethod
def migrate_context(cls, context, version):
values = context.values
if version < 2:
domain = context.ordered_domain
c_domain = [t for t in context.ordered_domain if t[1] == 2]
d_domain = [t for t in context.ordered_domain if t[1] == 1]
for d, old_val, new_val in ((domain, "color_index", "attr_color"),
(d_domain, "shape_index", "attr_shape"),
(c_domain, "size_index", "attr_size")):
index = context.values[old_val][0] - 1
values[new_val] = (d[index][0], d[index][1] + 100) \
if 0 <= index < len(d) else None
if version < 3:
values["graph"] = {
"attr_color": values["attr_color"],
"attr_shape": values["attr_shape"],
"attr_size": values["attr_size"]
}
if version == 3:
values["attr_color"] = values["graph"]["attr_color"]
values["attr_size"] = values["graph"]["attr_size"]
values["attr_shape"] = values["graph"]["attr_shape"]
values["attr_label"] = values["graph"]["attr_label"]
if version < 6 and "selected_vars" in values:
values["selected_vars"] = (values["selected_vars"], -3)
# for backward compatibility with settings < 6, pull the enum from global
# namespace into class
Placement = Placement
class OWFile(widget.OWWidget, RecentPathsWComboMixin):
name = "File"
id = "orange.widgets.data.file"
description = "Read data from an input file or network " \
"and send a data table to the output."
icon = "icons/File.svg"
priority = 10
category = "Data"
keywords = ["data", "file", "load", "read"]
outputs = [
widget.OutputSignal(
"Data",
Table,
doc="Attribute-valued data set read from the input file.")
]
want_main_area = False
SEARCH_PATHS = [("sample-datasets", get_sample_datasets_dir())]
SIZE_LIMIT = 1e7
LOCAL_FILE, URL = range(2)
settingsHandler = PerfectDomainContextHandler()
# Overload RecentPathsWidgetMixin.recent_paths to set defaults
recent_paths = Setting([
RecentPath("", "sample-datasets", "iris.tab"),
RecentPath("", "sample-datasets", "titanic.tab"),
RecentPath("", "sample-datasets", "housing.tab"),
RecentPath("", "sample-datasets", "heart_disease.tab"),
])
recent_urls = Setting([])
source = Setting(LOCAL_FILE)
xls_sheet = ContextSetting("")
sheet_names = Setting({})
url = Setting("")
variables = ContextSetting([])
dlg_formats = ("All readable files ({});;".format(
'*' + ' *'.join(FileFormat.readers.keys())) + ";;".join(
"{} (*{})".format(f.DESCRIPTION, ' *'.join(f.EXTENSIONS))
for f in sorted(set(FileFormat.readers.values()),
key=list(FileFormat.readers.values()).index)))
domain_editor = SettingProvider(DomainEditor)
class Warning(widget.OWWidget.Warning):
file_too_big = widget.Msg(
"The file is too large to load automatically."
" Press Reload to load.")
class Error(widget.OWWidget.Error):
file_not_found = widget.Msg("File not found.")
def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.data = None
self.loaded_file = ""
self.reader = None
layout = QGridLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
vbox = gui.radioButtons(None,
self,
"source",
box=True,
addSpace=True,
callback=self.load_data,
addToLayout=False)
rb_button = gui.appendRadioButton(vbox, "File:", addToLayout=False)
layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter)
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.activated[int].connect(self.select_file)
box.layout().addWidget(self.file_combo)
layout.addWidget(box, 0, 1)
file_button = gui.button(None,
self,
'...',
callback=self.browse_file,
autoDefault=False)
file_button.setIcon(self.style().standardIcon(QStyle.SP_DirOpenIcon))
file_button.setSizePolicy(Policy.Maximum, Policy.Fixed)
layout.addWidget(file_button, 0, 2)
reload_button = gui.button(None,
self,
"Reload",
callback=self.load_data,
autoDefault=False)
reload_button.setIcon(self.style().standardIcon(
QStyle.SP_BrowserReload))
reload_button.setSizePolicy(Policy.Fixed, Policy.Fixed)
layout.addWidget(reload_button, 0, 3)
self.sheet_box = gui.hBox(None, addToLayout=False, margin=0)
self.sheet_combo = gui.comboBox(
None,
self,
"xls_sheet",
callback=self.select_sheet,
sendSelectedValue=True,
)
self.sheet_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_label = QLabel()
self.sheet_label.setText('Sheet')
self.sheet_label.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_box.layout().addWidget(self.sheet_label, Qt.AlignLeft)
self.sheet_box.layout().addWidget(self.sheet_combo, Qt.AlignVCenter)
layout.addWidget(self.sheet_box, 2, 1)
self.sheet_box.hide()
rb_button = gui.appendRadioButton(vbox, "URL:", addToLayout=False)
layout.addWidget(rb_button, 3, 0, Qt.AlignVCenter)
self.url_combo = url_combo = QComboBox()
url_model = NamedURLModel(self.sheet_names)
url_model.wrap(self.recent_urls)
url_combo.setLineEdit(LineEditSelectOnFocus())
url_combo.setModel(url_model)
url_combo.setSizePolicy(Policy.MinimumExpanding, Policy.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, 3, 3)
url_combo.activated.connect(self._url_set)
box = gui.vBox(self.controlArea, "Info")
self.info = gui.widgetLabel(box, 'No data loaded.')
self.warnings = gui.widgetLabel(box, '')
box = gui.widgetBox(self.controlArea, "Columns (Double click to edit)")
self.domain_editor = DomainEditor(self)
self.editor_model = self.domain_editor.model()
box.layout().addWidget(self.domain_editor)
box = gui.hBox(self.controlArea)
gui.button(box,
self,
"Browse documentation data sets",
callback=lambda: self.browse_file(True),
autoDefault=False)
gui.rubber(box)
box.layout().addWidget(self.report_button)
self.report_button.setFixedWidth(170)
self.apply_button = gui.button(box,
self,
"Apply",
callback=self.apply_domain_edit)
self.apply_button.setEnabled(False)
self.apply_button.setFixedWidth(170)
self.editor_model.dataChanged.connect(
lambda: self.apply_button.setEnabled(True))
self.set_file_list()
# Must not call open_file from within __init__. open_file
# explicitly re-enters the event loop (by a progress bar)
self.setAcceptDrops(True)
if self.source == self.LOCAL_FILE:
last_path = self.last_path()
if last_path and os.path.exists(last_path) and \
os.path.getsize(last_path) > self.SIZE_LIMIT:
self.Warning.file_too_big()
return
QTimer.singleShot(0, self.load_data)
def sizeHint(self):
return QSize(600, 550)
def select_file(self, n):
assert n < len(self.recent_paths)
super().select_file(n)
if self.recent_paths:
self.source = self.LOCAL_FILE
self.load_data()
self.set_file_list()
def select_sheet(self):
self.recent_paths[0].sheet = self.sheet_combo.currentText()
self.load_data()
def _url_set(self):
self.source = self.URL
self.load_data()
def browse_file(self, in_demos=False):
if in_demos:
start_file = get_sample_datasets_dir()
if not os.path.exists(start_file):
QMessageBox.information(
None, "File",
"Cannot find the directory with documentation data sets")
return
else:
start_file = self.last_path() or os.path.expanduser("~/")
filename, _ = QFileDialog.getOpenFileName(self,
'Open Orange Data File',
start_file, self.dlg_formats)
if not filename:
return
self.add_path(filename)
self.source = self.LOCAL_FILE
self.load_data()
# Open a file, create data from it and send it over the data channel
def load_data(self):
# We need to catch any exception type since anything can happen in
# file readers
# pylint: disable=broad-except
self.closeContext()
self.domain_editor.set_domain(None)
self.apply_button.setEnabled(False)
self.clear_messages()
self.set_file_list()
if self.last_path() and not os.path.exists(self.last_path()):
self.Error.file_not_found()
self.send("Data", None)
self.info.setText("No data.")
return
error = None
try:
self.reader = self._get_reader()
if self.reader is None:
self.data = None
self.send("Data", None)
self.info.setText("No data.")
self.sheet_box.hide()
return
except Exception as ex:
error = ex
if not error:
self._update_sheet_combo()
with catch_warnings(record=True) as warnings:
try:
data = self.reader.read()
except Exception as ex:
log.exception(ex)
error = ex
self.warning(warnings[-1].message.args[0] if warnings else '')
if error:
self.data = None
self.send("Data", None)
self.info.setText("An error occurred:\n{}".format(error))
self.sheet_box.hide()
return
self.info.setText(self._describe(data))
self.loaded_file = self.last_path()
add_origin(data, self.loaded_file)
self.data = data
self.openContext(data.domain)
self.apply_domain_edit() # sends data
def _get_reader(self):
"""
Returns
-------
FileFormat
"""
if self.source == self.LOCAL_FILE:
reader = FileFormat.get_reader(self.last_path())
if self.recent_paths and self.recent_paths[0].sheet:
reader.select_sheet(self.recent_paths[0].sheet)
return reader
elif self.source == self.URL:
url = self.url_combo.currentText().strip()
if url:
return UrlReader(url)
def _update_sheet_combo(self):
if len(self.reader.sheets) < 2:
self.sheet_box.hide()
self.reader.select_sheet(None)
return
self.sheet_combo.clear()
self.sheet_combo.addItems(self.reader.sheets)
self._select_active_sheet()
self.sheet_box.show()
def _select_active_sheet(self):
if self.reader.sheet:
try:
idx = self.reader.sheets.index(self.reader.sheet)
self.sheet_combo.setCurrentIndex(idx)
except ValueError:
# Requested sheet does not exist in this file
self.reader.select_sheet(None)
else:
self.sheet_combo.setCurrentIndex(0)
def _describe(self, table):
domain = table.domain
text = ""
attrs = getattr(table, "attributes", {})
descs = [
attrs[desc] for desc in ("Name", "Description") if desc in attrs
]
if len(descs) == 2:
descs[0] = "<b>{}</b>".format(descs[0])
if descs:
text += "<p>{}</p>".format("<br/>".join(descs))
text += "<p>{} instance(s), {} feature(s), {} meta attribute(s)".\
format(len(table), len(domain.attributes), len(domain.metas))
if domain.has_continuous_class:
text += "<br/>Regression; numerical class."
elif domain.has_discrete_class:
text += "<br/>Classification; discrete class with {} values.".\
format(len(domain.class_var.values))
elif table.domain.class_vars:
text += "<br/>Multi-target; {} target variables.".format(
len(table.domain.class_vars))
else:
text += "<br/>Data has no target variable."
text += "</p>"
if 'Timestamp' in table.domain:
# Google Forms uses this header to timestamp responses
text += '<p>First entry: {}<br/>Last entry: {}</p>'.format(
table[0, 'Timestamp'], table[-1, 'Timestamp'])
return text
def storeSpecificSettings(self):
self.current_context.modified_variables = self.variables[:]
def retrieveSpecificSettings(self):
if hasattr(self.current_context, "modified_variables"):
self.variables[:] = self.current_context.modified_variables
def apply_domain_edit(self):
if self.data is not None:
domain, cols = self.domain_editor.get_domain(
self.data.domain, self.data)
X, y, m = cols
X = np.array(X).T if len(X) else np.empty((len(self.data), 0))
y = np.array(y).T if len(y) else None
dtpe = object if any(
isinstance(m, StringVariable) for m in domain.metas) else float
m = np.array(m, dtype=dtpe).T if len(m) else None
table = Table.from_numpy(domain, X, y, m, self.data.W)
table.name = self.data.name
table.ids = np.array(self.data.ids)
table.attributes = getattr(self.data, 'attributes', {})
else:
table = self.data
self.send("Data", table)
self.apply_button.setEnabled(False)
def get_widget_name_extension(self):
_, name = os.path.split(self.loaded_file)
return os.path.splitext(name)[0]
def send_report(self):
def get_ext_name(filename):
try:
return FileFormat.names[os.path.splitext(filename)[1]]
except KeyError:
return "unknown"
if self.data is None:
self.report_paragraph("File", "No file.")
return
if self.source == self.LOCAL_FILE:
home = os.path.expanduser("~")
if self.loaded_file.startswith(home):
# os.path.join does not like ~
name = "~" + os.path.sep + \
self.loaded_file[len(home):].lstrip("/").lstrip("\\")
else:
name = self.loaded_file
if self.sheet_combo.isVisible():
name += " ({})".format(self.sheet_combo.currentText())
self.report_items("File", [("File name", name),
("Format", get_ext_name(name))])
else:
self.report_items("Data", [("Resource", self.url),
("Format", get_ext_name(self.url))])
self.report_data("Data", self.data)
def dragEnterEvent(self, event):
"""Accept drops of valid file urls"""
urls = event.mimeData().urls()
if urls:
try:
FileFormat.get_reader(
OSX_NSURL_toLocalFile(urls[0]) or urls[0].toLocalFile())
event.acceptProposedAction()
except IOError:
pass
def dropEvent(self, event):
"""Handle file drops"""
urls = event.mimeData().urls()
if urls:
self.add_path(
OSX_NSURL_toLocalFile(urls[0])
or urls[0].toLocalFile()) # add first file
self.source = self.LOCAL_FILE
self.load_data()
class OWMDS(OWWidget):
name = "MDS"
description = "Two-dimensional data projection by multidimensional " \
"scaling constructed from a distance matrix."
icon = "icons/MDS.svg"
class Inputs:
data = Input("Data", Orange.data.Table, default=True)
distances = Input("Distances", Orange.misc.DistMatrix)
data_subset = Input("Data Subset", Orange.data.Table)
class Outputs:
selected_data = Output("Selected Data",
Orange.data.Table,
default=True)
annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Orange.data.Table)
settings_version = 2
#: Initialization type
PCA, Random = 0, 1
#: Refresh rate
RefreshRate = [("Every iteration", 1), ("Every 5 steps", 5),
("Every 10 steps", 10), ("Every 25 steps", 25),
("Every 50 steps", 50), ("None", -1)]
#: Runtime state
Running, Finished, Waiting = 1, 2, 3
settingsHandler = settings.DomainContextHandler()
max_iter = settings.Setting(300)
initialization = settings.Setting(PCA)
refresh_rate = settings.Setting(3)
# output embedding role.
NoRole, AttrRole, AddAttrRole, MetaRole = 0, 1, 2, 3
auto_commit = settings.Setting(True)
selection_indices = settings.Setting(None, schema_only=True)
#: Percentage of all pairs displayed (ranges from 0 to 20)
connected_pairs = settings.Setting(5)
legend_anchor = settings.Setting(((1, 0), (1, 0)))
graph = SettingProvider(OWMDSGraph)
jitter_sizes = [0, 0.1, 0.5, 1, 2, 3, 4, 5, 7, 10]
graph_name = "graph.plot_widget.plotItem"
class Error(OWWidget.Error):
not_enough_rows = Msg("Input data needs at least 2 rows")
matrix_too_small = Msg("Input matrix must be at least 2x2")
no_attributes = Msg("Data has no attributes")
mismatching_dimensions = \
Msg("Data and distances dimensions do not match.")
out_of_memory = Msg("Out of memory")
optimization_error = Msg("Error during optimization\n{}")
def __init__(self):
super().__init__()
#: Input dissimilarity matrix
self.matrix = None # type: Optional[Orange.misc.DistMatrix]
#: Effective data used for plot styling/annotations. Can be from the
#: input signal (`self.signal_data`) or the input matrix
#: (`self.matrix.data`)
self.data = None # type: Optional[Orange.data.Table]
#: Input subset data table
self.subset_data = None # type: Optional[Orange.data.Table]
#: Data table from the `self.matrix.row_items` (if present)
self.matrix_data = None # type: Optional[Orange.data.Table]
#: Input data table
self.signal_data = None
self._similar_pairs = None
self._subset_mask = None # type: Optional[np.ndarray]
self._invalidated = False
self.effective_matrix = None
self._curve = None
self.variable_x = ContinuousVariable("mds-x")
self.variable_y = ContinuousVariable("mds-y")
self.__update_loop = None
# timer for scheduling updates
self.__timer = QTimer(self, singleShot=True, interval=0)
self.__timer.timeout.connect(self.__next_step)
self.__state = OWMDS.Waiting
self.__in_next_step = False
self.__draw_similar_pairs = False
box = gui.vBox(self.controlArea, "MDS Optimization")
form = QFormLayout(labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10)
form.addRow("Max iterations:",
gui.spin(box, self, "max_iter", 10, 10**4, step=1))
form.addRow(
"Initialization:",
gui.radioButtons(box,
self,
"initialization",
btnLabels=("PCA (Torgerson)", "Random"),
callback=self.__invalidate_embedding))
box.layout().addLayout(form)
form.addRow(
"Refresh:",
gui.comboBox(box,
self,
"refresh_rate",
items=[t for t, _ in OWMDS.RefreshRate],
callback=self.__invalidate_refresh))
gui.separator(box, 10)
self.runbutton = gui.button(box,
self,
"Run",
callback=self._toggle_run)
box = gui.vBox(self.mainArea, True, margin=0)
self.graph = OWMDSGraph(self,
box,
"MDSGraph",
view_box=MDSInteractiveViewBox)
box.layout().addWidget(self.graph.plot_widget)
self.plot = self.graph.plot_widget
g = self.graph.gui
box = g.point_properties_box(self.controlArea)
self.models = g.points_models
self.models[2].order = \
self.models[2].order[:1] + ("Stress", ) + self.models[2].order[1:]
gui.hSlider(box,
self,
"connected_pairs",
label="Show similar pairs:",
minValue=0,
maxValue=20,
createLabel=False,
callback=self._on_connected_changed)
g.add_widgets(ids=[g.JitterSizeSlider], widget=box)
box = gui.vBox(self.controlArea, "Plot Properties")
g.add_widgets([
g.ShowLegend, g.ToolTipShowsAll, g.ClassDensity,
g.LabelOnlySelected
], box)
self.controlArea.layout().addStretch(100)
self.icons = gui.attributeIconDict
palette = self.graph.plot_widget.palette()
self.graph.set_palette(palette)
gui.rubber(self.controlArea)
self.graph.box_zoom_select(self.controlArea)
gui.auto_commit(box,
self,
"auto_commit",
"Send Selected",
checkbox_label="Send selected automatically",
box=None)
self.plot.getPlotItem().hideButtons()
self.plot.setRenderHint(QPainter.Antialiasing)
self.graph.jitter_continuous = True
self._initialize()
def reset_graph_data(self, *_):
if self.data is not None:
self.graph.rescale_data()
self.update_graph()
self.connect_pairs()
def update_colors(self):
pass
def update_density(self):
self.update_graph(reset_view=False)
def update_regression_line(self):
self.update_graph(reset_view=False)
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 prepare_data(self):
pass
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, True)
def selection_changed(self):
self.commit()
@Inputs.data
@check_sql_input
def set_data(self, data):
"""Set the input data set.
Parameters
----------
data : Optional[Orange.data.Table]
"""
if data is not None and len(data) < 2:
self.Error.not_enough_rows()
data = None
else:
self.Error.not_enough_rows.clear()
self.signal_data = data
if self.matrix is not None and data is not None and len(
self.matrix) == len(data):
self.closeContext()
self.data = data
self.init_attr_values()
self.openContext(data)
else:
self._invalidated = True
@Inputs.distances
def set_disimilarity(self, matrix):
"""Set the dissimilarity (distance) matrix.
Parameters
----------
matrix : Optional[Orange.misc.DistMatrix]
"""
if matrix is not None and len(matrix) < 2:
self.Error.matrix_too_small()
matrix = None
else:
self.Error.matrix_too_small.clear()
self.matrix = matrix
if matrix is not None and matrix.row_items:
self.matrix_data = matrix.row_items
if matrix is None:
self.matrix_data = None
self._invalidated = True
@Inputs.data_subset
def set_subset_data(self, subset_data):
"""Set a subset of `data` input to highlight in the plot.
Parameters
----------
subset_data: Optional[Orange.data.Table]
"""
self.subset_data = subset_data
# invalidate the pen/brush when the subset is changed
self._subset_mask = None # type: Optional[np.ndarray]
self.controls.graph.alpha_value.setEnabled(subset_data is None)
def _clear(self):
self._similar_pairs = None
self.__set_update_loop(None)
self.__state = OWMDS.Waiting
def _clear_plot(self):
self.graph.plot_widget.clear()
def _initialize(self):
# clear everything
self.closeContext()
self._clear()
self.Error.clear()
self.data = None
self.effective_matrix = None
self.embedding = None
self.init_attr_values()
# if no data nor matrix is present reset plot
if self.signal_data is None and self.matrix is None:
return
if self.signal_data is not None and self.matrix is not None and \
len(self.signal_data) != len(self.matrix):
self.Error.mismatching_dimensions()
self._update_plot()
return
if self.signal_data is not None:
self.data = self.signal_data
elif self.matrix_data is not None:
self.data = self.matrix_data
if self.matrix is not None:
self.effective_matrix = self.matrix
if self.matrix.axis == 0 and self.data is self.matrix_data:
self.data = None
elif self.data.domain.attributes:
preprocessed_data = Orange.projection.MDS().preprocess(self.data)
self.effective_matrix = Orange.distance.Euclidean(
preprocessed_data)
else:
self.Error.no_attributes()
return
self.init_attr_values()
self.openContext(self.data)
def _toggle_run(self):
if self.__state == OWMDS.Running:
self.stop()
self._invalidate_output()
else:
self.start()
def start(self):
if self.__state == OWMDS.Running:
return
elif self.__state == OWMDS.Finished:
# Resume/continue from a previous run
self.__start()
elif self.__state == OWMDS.Waiting and \
self.effective_matrix is not None:
self.__start()
def stop(self):
if self.__state == OWMDS.Running:
self.__set_update_loop(None)
def __start(self):
self.__draw_similar_pairs = False
X = self.effective_matrix
init = self.embedding
# number of iterations per single GUI update step
_, step_size = OWMDS.RefreshRate[self.refresh_rate]
if step_size == -1:
step_size = self.max_iter
def update_loop(X, max_iter, step, init):
"""
return an iterator over successive improved MDS point embeddings.
"""
# NOTE: this code MUST NOT call into QApplication.processEvents
done = False
iterations_done = 0
oldstress = np.finfo(np.float).max
init_type = "PCA" if self.initialization == OWMDS.PCA else "random"
while not done:
step_iter = min(max_iter - iterations_done, step)
mds = Orange.projection.MDS(dissimilarity="precomputed",
n_components=2,
n_init=1,
max_iter=step_iter,
init_type=init_type,
init_data=init)
mdsfit = mds(X)
iterations_done += step_iter
embedding, stress = mdsfit.embedding_, mdsfit.stress_
stress /= np.sqrt(np.sum(embedding**2, axis=1)).sum()
if iterations_done >= max_iter:
done = True
elif (oldstress - stress) < mds.params["eps"]:
done = True
init = embedding
oldstress = stress
yield embedding, mdsfit.stress_, iterations_done / max_iter
self.__set_update_loop(update_loop(X, self.max_iter, step_size, init))
self.progressBarInit(processEvents=None)
def __set_update_loop(self, loop):
"""
Set the update `loop` coroutine.
The `loop` is a generator yielding `(embedding, stress, progress)`
tuples where `embedding` is a `(N, 2) ndarray` of current updated
MDS points, `stress` is the current stress and `progress` a float
ratio (0 <= progress <= 1)
If an existing update coroutine loop is already in place it is
interrupted (i.e. closed).
.. note::
The `loop` must not explicitly yield control flow to the event
loop (i.e. call `QApplication.processEvents`)
"""
if self.__update_loop is not None:
self.__update_loop.close()
self.__update_loop = None
self.progressBarFinished(processEvents=None)
self.__update_loop = loop
if loop is not None:
self.setBlocking(True)
self.progressBarInit(processEvents=None)
self.setStatusMessage("Running")
self.runbutton.setText("Stop")
self.__state = OWMDS.Running
self.__timer.start()
else:
self.setBlocking(False)
self.setStatusMessage("")
self.runbutton.setText("Start")
self.__state = OWMDS.Finished
self.__timer.stop()
def __next_step(self):
if self.__update_loop is None:
return
assert not self.__in_next_step
self.__in_next_step = True
loop = self.__update_loop
self.Error.out_of_memory.clear()
try:
embedding, _, progress = next(self.__update_loop)
assert self.__update_loop is loop
except StopIteration:
self.__set_update_loop(None)
self.unconditional_commit()
self.__draw_similar_pairs = True
self._update_plot()
except MemoryError:
self.Error.out_of_memory()
self.__set_update_loop(None)
self.__draw_similar_pairs = True
except Exception as exc:
self.Error.optimization_error(str(exc))
self.__set_update_loop(None)
self.__draw_similar_pairs = True
else:
self.progressBarSet(100.0 * progress, processEvents=None)
self.embedding = embedding
self._update_plot()
# schedule next update
self.__timer.start()
self.__in_next_step = False
def __invalidate_embedding(self):
# reset/invalidate the MDS embedding, to the default initialization
# (Random or PCA), restarting the optimization if necessary.
if self.embedding is None:
return
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
X = self.effective_matrix
if self.initialization == OWMDS.PCA:
self.embedding = torgerson(X)
else:
self.embedding = np.random.rand(len(X), 2)
self._update_plot()
# restart the optimization if it was interrupted.
if state == OWMDS.Running:
self.__start()
def __invalidate_refresh(self):
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
# restart the optimization if it was interrupted.
# TODO: decrease the max iteration count by the already
# completed iterations count.
if state == OWMDS.Running:
self.__start()
def handleNewSignals(self):
if self._invalidated:
self.__draw_similar_pairs = False
self._invalidated = False
self._initialize()
self.start()
if self._subset_mask is None and self.subset_data is not None and \
self.data is not None:
self._subset_mask = np.in1d(self.data.ids, self.subset_data.ids)
self._update_plot(new=True)
self.unconditional_commit()
def _invalidate_output(self):
self.commit()
def _on_connected_changed(self):
self._similar_pairs = None
self.connect_pairs()
def _update_plot(self, new=False):
self._clear_plot()
if self.embedding is not None:
self._setup_plot(new=new)
else:
self.graph.new_data(None)
def connect_pairs(self):
if self._curve:
self.graph.plot_widget.removeItem(self._curve)
if not (self.connected_pairs and self.__draw_similar_pairs):
return
emb_x, emb_y = self.graph.get_xy_data_positions(
self.variable_x, self.variable_y, self.graph.valid_data)
if self._similar_pairs is None:
# This code requires storing lower triangle of X (n x n / 2
# doubles), n x n / 2 * 2 indices to X, n x n / 2 indices for
# argsort result. If this becomes an issue, it can be reduced to
# n x n argsort indices by argsorting the entire X. Then we
# take the first n + 2 * p indices. We compute their coordinates
# i, j in the original matrix. We keep those for which i < j.
# n + 2 * p will suffice to exclude the diagonal (i = j). If the
# number of those for which i < j is smaller than p, we instead
# take i > j. Among those that remain, we take the first p.
# Assuming that MDS can't show so many points that memory could
# become an issue, I preferred using simpler code.
m = self.effective_matrix
n = len(m)
p = min(n * (n - 1) // 2 * self.connected_pairs // 100,
MAX_N_PAIRS * self.connected_pairs // 20)
indcs = np.triu_indices(n, 1)
sorted = np.argsort(m[indcs])[:p]
self._similar_pairs = fpairs = np.empty(2 * p, dtype=int)
fpairs[::2] = indcs[0][sorted]
fpairs[1::2] = indcs[1][sorted]
emb_x_pairs = emb_x[self._similar_pairs].reshape((-1, 2))
emb_y_pairs = emb_y[self._similar_pairs].reshape((-1, 2))
# Filter out zero distance lines (in embedding coords).
# Null (zero length) line causes bad rendering artifacts
# in Qt when using the raster graphics system (see gh-issue: 1668).
(x1, x2), (y1, y2) = (emb_x_pairs.T, emb_y_pairs.T)
pairs_mask = ~(np.isclose(x1, x2) & np.isclose(y1, y2))
emb_x_pairs = emb_x_pairs[pairs_mask, :]
emb_y_pairs = emb_y_pairs[pairs_mask, :]
self._curve = pg.PlotCurveItem(emb_x_pairs.ravel(),
emb_y_pairs.ravel(),
pen=pg.mkPen(0.8,
width=2,
cosmetic=True),
connect="pairs",
antialias=True)
self.graph.plot_widget.addItem(self._curve)
def _setup_plot(self, new=False):
emb_x, emb_y = self.embedding[:, 0], self.embedding[:, 1]
coords = np.vstack((emb_x, emb_y)).T
data = self.data
attributes = data.domain.attributes + (self.variable_x,
self.variable_y)
domain = Domain(attributes=attributes,
class_vars=data.domain.class_vars,
metas=data.domain.metas)
data = Table.from_numpy(domain,
X=hstack((data.X, coords)),
Y=data.Y,
metas=data.metas)
subset_data = data[
self._subset_mask] if self._subset_mask is not None else None
self.graph.new_data(data, subset_data=subset_data, new=new)
self.graph.update_data(self.variable_x, self.variable_y, True)
self.connect_pairs()
def commit(self):
if self.embedding is not None:
names = get_unique_names(
[v.name for v in self.data.domain.variables],
["mds-x", "mds-y"])
output = embedding = Orange.data.Table.from_numpy(
Orange.data.Domain([
ContinuousVariable(names[0]),
ContinuousVariable(names[1])
]), self.embedding)
else:
output = embedding = None
if self.embedding is not None and self.data is not None:
domain = self.data.domain
domain = Orange.data.Domain(
domain.attributes, domain.class_vars,
domain.metas + embedding.domain.attributes)
output = self.data.transform(domain)
output.metas[:, -2:] = embedding.X
selection = self.graph.get_selection()
if output is not None and len(selection) > 0:
selected = output[selection]
else:
selected = None
if self.graph.selection is not None and np.max(
self.graph.selection) > 1:
annotated = create_groups_table(output, self.graph.selection)
else:
annotated = create_annotated_table(output, selection)
self.Outputs.selected_data.send(selected)
self.Outputs.annotated_data.send(annotated)
def onDeleteWidget(self):
super().onDeleteWidget()
self._clear_plot()
self._clear()
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)
@classmethod
def migrate_settings(cls, settings_, version):
if version < 2:
settings_graph = {}
for old, new in (("label_only_selected", "label_only_selected"),
("symbol_opacity", "alpha_value"),
("symbol_size", "point_width"), ("jitter",
"jitter_size")):
settings_graph[new] = settings_[old]
settings_["graph"] = settings_graph
settings_["auto_commit"] = settings_["autocommit"]
@classmethod
def migrate_context(cls, context, version):
if version < 2:
domain = context.ordered_domain
n_domain = [t for t in context.ordered_domain if t[1] == 2]
c_domain = [t for t in context.ordered_domain if t[1] == 1]
context_values_graph = {}
for _, old_val, new_val in ((domain, "color_value", "attr_color"),
(c_domain, "shape_value",
"attr_shape"),
(n_domain, "size_value", "attr_size"),
(domain, "label_value", "attr_label")):
tmp = context.values[old_val]
if tmp[1] >= 0:
context_values_graph[new_val] = (tmp[0], tmp[1] + 100)
elif tmp[0] != "Stress":
context_values_graph[new_val] = None
else:
context_values_graph[new_val] = tmp
context.values["graph"] = context_values_graph
class OWNxExplorer(OWDataProjectionWidget):
name = "Network Explorer"
description = "Visually explore the network and its properties."
icon = "icons/NetworkExplorer.svg"
priority = 6420
class Inputs:
node_data = Input("Node Data", Table)
node_subset = Input("Node Subset", Table)
network = Input("Network", Network, default=True)
node_distances = Input("Node Distances", Orange.misc.DistMatrix)
class Outputs(OWDataProjectionWidget.Outputs):
subgraph = Output("Selected sub-network", Network)
unselected_subgraph = Output("Remaining sub-network", Network)
distances = Output("Distance matrix", Orange.misc.DistMatrix)
UserAdviceMessages = [
widget.Message("Double clicks select connected components",
widget.Message.Information),
]
GRAPH_CLASS = GraphView
graph = SettingProvider(GraphView)
layout_density = Setting(10)
observe_weights = Setting(True)
mark_hops = Setting(1)
mark_min_conn = Setting(5)
mark_max_conn = Setting(5)
mark_most_conn = Setting(1)
alpha_value = 255 # Override the setting from parent
class Warning(OWDataProjectionWidget.Warning):
distance_matrix_mismatch = widget.Msg(
"Distance matrix size doesn't match the number of network nodes "
"and will be ignored.")
no_graph_found = widget.Msg("Node data is given, graph data is missing.")
class Error(OWDataProjectionWidget.Error):
data_size_mismatch = widget.Msg(
"Length of the data does not match the number of nodes.")
network_too_large = widget.Msg("Network is too large to visualize.")
single_node_graph = widget.Msg("I don't do single-node graphs today.")
def __init__(self):
# These are already needed in super().__init__()
self.number_of_nodes = 0
self.number_of_edges = 0
self.nHighlighted = 0
self.nSelected = 0
self.nodes_per_edge = 0
self.edges_per_node = 0
self.mark_mode = 0
self.mark_text = ""
super().__init__()
self.network = None
self.node_data = None
self.distance_matrix = None
self.edges = None
self.positions = None
self._optimizer = None
self._animation_thread = None
self._stop_optimization = False
self.marked_nodes = None
self.searchStringTimer = QTimer(self)
self.searchStringTimer.timeout.connect(self.update_marks)
self.set_mark_mode()
self.setMinimumWidth(600)
def sizeHint(self):
return QSize(800, 600)
def _add_controls(self):
self.gui = OWPlotGUI(self)
self._add_info_box()
self.gui.point_properties_box(self.controlArea)
self._add_effects_box()
self.gui.plot_properties_box(self.controlArea)
self._add_mark_box()
self.controls.attr_label.activated.connect(self.on_change_label_attr)
def _add_info_box(self):
info = gui.vBox(self.controlArea, box="Layout")
gui.label(
info, self,
"Nodes: %(number_of_nodes)i (%(nodes_per_edge).2f per edge); "
"%(nSelected)i selected")
gui.label(
info, self,
"Edges: %(number_of_edges)i (%(edges_per_node).2f per node)")
lbox = gui.hBox(info)
self.relayout_button = gui.button(
lbox, self, 'Improve', callback=self.improve, autoDefault=False,
tooltip="Optimize the current layout, with a small initial jerk")
self.stop_button = gui.button(
lbox, self, 'Stop', callback=self.stop_relayout, autoDefault=False,
hidden=True)
self.randomize_button = gui.button(
lbox, self, 'Re-layout', callback=self.restart, autoDefault=False,
tooltip="Restart laying out from random positions")
gui.hSlider(info, self, "layout_density", minValue=1, maxValue=50,
label="Gravity", orientation=Qt.Horizontal,
callback_finished=self.improve,
tooltip="Lower values improve optimization,\n"
"higher work better for graph with many small "
"components")
gui.checkBox(info, self, "observe_weights",
label="Make edges with large weights shorter",
callback=self.improve)
def _add_effects_box(self):
gbox = self.gui.create_gridbox(self.controlArea, box="Widths and Sizes")
self.gui.add_widget(self.gui.PointSize, gbox)
gbox.layout().itemAtPosition(1, 0).widget().setText("Node Size:")
self.gui.add_control(
gbox, gui.hSlider, "Edge width:",
master=self, value='graph.edge_width',
minValue=1, maxValue=10, step=1,
callback=self.graph.update_edges)
box = gui.vBox(None)
gbox.layout().addWidget(box, 3, 0, 1, 2)
gui.separator(box)
self.checkbox_relative_edges = gui.checkBox(
box, self, 'graph.relative_edge_widths',
'Scale edge widths to weights',
callback=self.graph.update_edges)
self.checkbox_show_weights = gui.checkBox(
box, self, 'graph.show_edge_weights',
'Show edge weights',
callback=self.graph.update_edge_labels)
self.checkbox_show_weights = gui.checkBox(
box, self, 'graph.label_selected_edges',
'Label only edges of selected nodes',
callback=self.graph.update_edge_labels)
# This is ugly: create a slider that controls alpha_value so that
# parent can enable and disable it - although it's never added to any
# layout and visible to the user
gui.hSlider(None, self, "graph.alpha_value")
def _add_mark_box(self):
hbox = gui.hBox(None, box=True)
self.mainArea.layout().addWidget(hbox)
vbox = gui.hBox(hbox)
def spin(value, label, minv, maxv):
return gui.spin(
vbox, self, value, label=label, minv=minv, maxv=maxv,
step=1,
alignment=Qt.AlignRight, callback=self.update_marks).box
def text_line():
def set_search_string_timer():
self.searchStringTimer.stop()
self.searchStringTimer.start(300)
return gui.lineEdit(
gui.hBox(vbox), self, "mark_text", label="Text: ",
orientation=Qt.Horizontal, minimumWidth=50,
callback=set_search_string_timer, callbackOnType=True).box
def _mark_by_labels(marker):
txt = self.mark_text.lower()
if not txt:
return None
labels = self.get_label_data()
if labels is None:
return None
return marker(np.char.array(labels), txt)
def mark_label_starts():
return _mark_by_labels(
lambda labels, txt: np.flatnonzero(labels.lower().startswith(txt)))
def mark_label_contains():
return _mark_by_labels(
lambda labels, txt: np.flatnonzero(labels.lower().find(txt) != -1))
def mark_text():
txt = self.mark_text.lower()
if not txt or self.data is None:
return None
return np.array(
[i for i, inst in enumerate(self.data)
if txt in "\x00".join(map(str, inst.list)).lower()])
def mark_reachable():
selected = self.graph.get_selection()
if selected is None:
return None
return self.get_reachable(selected)
def mark_close():
selected = self.graph.get_selection()
if selected is None:
return None
neighbours = set(selected)
last_round = list(neighbours)
for _ in range(self.mark_hops):
next_round = set()
for neigh in last_round:
next_round |= set(self.network.neighbours(neigh))
neighbours |= next_round
last_round = next_round
neighbours -= set(selected)
return np.array(list(neighbours))
def mark_from_input():
if self.subset_data is None or self.data is None:
return None
ids = set(self.subset_data.ids)
return np.array(
[i for i, ex in enumerate(self.data) if ex.id in ids])
def mark_most_connections():
n = self.mark_most_conn
if n >= self.number_of_nodes:
return np.arange(self.number_of_nodes)
degrees = self.network.degrees()
# pylint: disable=invalid-unary-operand-type
min_degree = np.partition(degrees, -n)[-n]
return np.flatnonzero(degrees >= min_degree)
def mark_more_than_any_neighbour():
degrees = self.network.degrees()
return np.array(
[node for node, degree in enumerate(degrees)
if degree > np.max(degrees[self.network.neighbours(node)],
initial=0)])
def mark_more_than_average_neighbour():
degrees = self.network.degrees()
return np.array(
[node for node, degree, neighbours in (
(node, degree, self.network.neighbours(node))
for node, degree in enumerate(degrees))
if degree > (np.mean(degrees[neighbours]) if neighbours.size else 0)
]
)
self.mark_criteria = [
("(Select criteria for marking)", None, lambda: np.zeros((0,))),
("Mark nodes whose label starts with", text_line(), mark_label_starts),
("Mark nodes whose label contains", text_line(), mark_label_contains),
("Mark nodes whose data that contains", text_line(), mark_text),
("Mark nodes reachable from selected", None, mark_reachable),
("Mark nodes in vicinity of selection",
spin("mark_hops", "Number of hops:", 1, 20),
mark_close),
("Mark nodes from subset signal", None, mark_from_input),
("Mark nodes with few connections",
spin("mark_max_conn", "Max. connections:", 0, 1000),
lambda: np.flatnonzero(self.network.degrees() <= self.mark_max_conn)),
("Mark nodes with many connections",
spin("mark_min_conn", "Min. connections:", 1, 1000),
lambda: np.flatnonzero(self.network.degrees() >= self.mark_min_conn)),
("Mark nodes with most connections",
spin("mark_most_conn", "Number of marked:", 1, 1000),
mark_most_connections),
("Mark nodes with more connections than any neighbour", None,
mark_more_than_any_neighbour),
("Mark nodes with more connections than average neighbour", None,
mark_more_than_average_neighbour)
]
cb = gui.comboBox(
hbox, self, "mark_mode",
items=[item for item, *_ in self.mark_criteria],
maximumContentsLength=-1, callback=self.set_mark_mode)
hbox.layout().insertWidget(0, cb)
gui.rubber(hbox)
self.btselect = gui.button(
hbox, self, "Select", callback=self.select_marked)
self.btadd = gui.button(
hbox, self, "Add to Selection", callback=self.select_add_marked)
self.btgroup = gui.button(
hbox, self, "Add New Group", callback=self.select_as_group)
def set_mark_mode(self, mode=None):
if mode is not None:
self.mark_mode = mode
for i, (_, widget, _) in enumerate(self.mark_criteria):
if widget:
if i == self.mark_mode:
widget.show()
else:
widget.hide()
self.searchStringTimer.stop()
self.update_marks()
def update_marks(self):
if self.network is None:
return
self.marked_nodes = self.mark_criteria[self.mark_mode][2]()
if self.marked_nodes is not None and not self.marked_nodes.size:
self.marked_nodes = None
self.graph.update_marks()
if self.graph.label_only_selected:
self.graph.update_labels()
self.update_selection_buttons()
def update_selection_buttons(self):
if self.marked_nodes is None:
self.btselect.hide()
self.btadd.hide()
self.btgroup.hide()
return
else:
self.btselect.show()
selection = self.graph.get_selection()
if not len(selection) or np.max(selection) == 0:
self.btadd.hide()
self.btgroup.hide()
elif np.max(selection) == 1:
self.btadd.setText("Add to Selection")
self.btadd.show()
self.btgroup.hide()
else:
self.btadd.setText("Add to Group")
self.btadd.show()
self.btgroup.show()
def selection_changed(self):
super().selection_changed()
self.nSelected = 0 if self.selection is None else len(self.selection)
self.update_selection_buttons()
self.update_marks()
def select_marked(self):
self.graph.selection_select(self.marked_nodes)
def select_add_marked(self):
self.graph.selection_append(self.marked_nodes)
def select_as_group(self):
self.graph.selection_new_group(self.marked_nodes)
def on_change_label_attr(self):
if self.mark_mode in (1, 2):
self.update_marks()
@Inputs.node_data
def set_node_data(self, data):
self.node_data = data
@Inputs.node_subset
def set_node_subset(self, data):
# It would be better to call super, but this fails because super
# is decorated to set the partial summary for signal "Subset Data",
# which does not exist for this widget (OWNxExplorer.Inputs is not
# derived from OWDataProjectionWidget.Inputs in order to rename the
# signal)
self.subset_data = data
@Inputs.node_distances
def set_items_distance_matrix(self, matrix):
self.distance_matrix = matrix
self.positions = None
@Inputs.network
def set_graph(self, graph):
def set_graph_none(error=None):
if error is not None:
error()
self.network = None
self.number_of_nodes = self.edges_per_node = 0
self.number_of_edges = self.nodes_per_edge = 0
def compute_stats():
self.number_of_nodes = graph.number_of_nodes()
self.number_of_edges = graph.number_of_edges()
self.edges_per_node = self.number_of_edges / self.number_of_nodes
self.nodes_per_edge = \
self.number_of_nodes / max(1, self.number_of_edges)
self.mark_text = ""
self.set_mark_mode(0)
self.positions = None
if not graph or graph.number_of_nodes() == 0:
set_graph_none()
return
if graph.number_of_nodes() + graph.number_of_edges() > 100000:
set_graph_none(self.Error.network_too_large)
return
self.Error.clear()
self.network = graph
compute_stats()
def handleNewSignals(self):
network = self.network
def set_actual_data():
self.closeContext()
self.Error.data_size_mismatch.clear()
self.Warning.no_graph_found.clear()
self._invalid_data = False
if network is None:
if self.node_data is not None:
self.Warning.no_graph_found()
return
n_nodes = len(self.network.nodes)
if self.node_data is not None:
if len(self.node_data) != n_nodes:
self.Error.data_size_mismatch()
self._invalid_data = True
self.data = None
else:
self.data = self.node_data
if self.node_data is None:
if isinstance(network.nodes, Table):
self.data = network.nodes
elif isinstance(network.nodes, np.ndarray) \
and (len(network.nodes.shape) == 1
or network.nodes.shape[1] == 1):
self.data = Table.from_numpy(
Domain([], None, [StringVariable("label")]),
np.zeros((len(network.nodes),0)),
None,
metas=network.nodes.reshape((n_nodes, 1))
)
else:
self.data = None
if self.data is not None:
# Replicate the necessary parts of set_data
self.valid_data = np.full(len(self.data), True, dtype=bool)
self.init_attr_values()
self.openContext(self.data)
self.cb_class_density.setEnabled(self.can_draw_density())
def set_actual_edges():
def set_checkboxes(value):
self.checkbox_show_weights.setEnabled(value)
self.checkbox_relative_edges.setEnabled(value)
self.Warning.distance_matrix_mismatch.clear()
if self.network is None:
self.edges = None
set_checkboxes(False)
return
set_checkboxes(True)
if network.number_of_edges(0):
self.edges = network.edges[0].edges.tocoo()
else:
self.edges = sp.coo_matrix((0, 3))
if self.distance_matrix is not None:
if len(self.distance_matrix) != self.number_of_nodes:
self.Warning.distance_matrix_mismatch()
else:
self.edges.data = np.fromiter(
(self.distance_matrix[u, v]
for u, v in zip(self.edges.row, self.edges.col)),
dtype=np.int32, count=len(self.edges.row)
)
if np.allclose(self.edges.data, 0):
self.edges.data[:] = 1
set_checkboxes(False)
elif len(set(self.edges.data)) == 1:
set_checkboxes(False)
self.stop_optimization_and_wait()
set_actual_data()
super()._handle_subset_data()
if self.positions is None:
set_actual_edges()
self.set_random_positions()
self.graph.reset_graph()
self.relayout(True)
else:
self.graph.update_point_props()
self.update_marks()
self.update_selection_buttons()
def init_attr_values(self):
super().init_attr_values()
if self.node_data is None \
and self.data is not None \
and isinstance(self.network.nodes, np.ndarray):
assert len(self.data.domain.metas) == 1
self.attr_label = self.data.domain.metas[0]
def randomize(self):
self.set_random_positions()
self.graph.update_coordinates()
def set_random_positions(self):
if self.network is None:
self.position = None
else:
self.positions = np.random.uniform(size=(self.number_of_nodes, 2))
def get_reachable(self, initial):
to_check = list(initial)
reachable = set(to_check)
for node in to_check:
new_checks = set(self.network.neighbours(node)) - reachable
to_check += new_checks
reachable |= new_checks
return np.array(to_check)
def send_data(self):
super().send_data()
Outputs = self.Outputs
selected_indices = self.graph.get_selection()
if selected_indices is None or len(selected_indices) == 0:
Outputs.subgraph.send(None)
Outputs.unselected_subgraph.send(self.network)
Outputs.distances.send(None)
return
selection = self.graph.selection
subgraph = self.network.subgraph(selected_indices)
subgraph.nodes = \
self._get_selected_data(self.data, selected_indices, selection)
Outputs.subgraph.send(subgraph)
Outputs.unselected_subgraph.send(
self.network.subgraph(np.flatnonzero(selection == 0)))
distances = self.distance_matrix
if distances is None:
Outputs.distances.send(None)
else:
Outputs.distances.send(distances.submatrix(sorted(selected_indices)))
def get_coordinates_data(self):
if self.positions is not None:
return self.positions.T
else:
return None, None
def get_embedding(self):
return self.positions
def get_subset_mask(self):
if self.data is None:
return None
return super().get_subset_mask()
def get_edges(self):
return self.edges
def is_directed(self):
return self.network is not None and self.network.edges[0].directed
def get_marked_nodes(self):
return self.marked_nodes
def set_buttons(self, running):
self.stop_button.setHidden(not running)
self.relayout_button.setHidden(running)
self.randomize_button.setHidden(running)
def stop_relayout(self):
self._stop_optimization = True
self.set_buttons(running=False)
def restart(self):
self.relayout(restart=True)
def improve(self):
self.relayout(restart=False)
# TODO: Stop relayout if new data is received
def relayout(self, restart):
if self.edges is None:
return
if restart or self.positions is None:
self.set_random_positions()
self.progressbar = gui.ProgressBar(self, 100)
self.set_buttons(running=True)
self._stop_optimization = False
Simplifications = self.graph.Simplifications
self.graph.set_simplifications(
Simplifications.NoDensity
+ Simplifications.NoLabels * (len(self.graph.labels) > 20)
+ Simplifications.NoEdgeLabels * (len(self.graph.edge_labels) > 20)
+ Simplifications.NoEdges * (self.number_of_edges > 30000))
large_graph = self.number_of_nodes + self.number_of_edges > 30000
class LayoutOptimizer(QObject):
update = Signal(np.ndarray, float)
done = Signal(np.ndarray)
stopped = Signal()
def __init__(self, widget):
super().__init__()
self.widget = widget
def send_update(self, positions, progress):
if not large_graph:
self.update.emit(np.array(positions), progress)
return not self.widget._stop_optimization
def run(self):
widget = self.widget
edges = widget.edges
nnodes = widget.number_of_nodes
init_temp = 0.05 if restart else 0.2
k = widget.layout_density / 10 / np.sqrt(nnodes)
sample_ratio = None if nnodes < 1000 else 1000 / nnodes
fruchterman_reingold(
widget.positions, edges, widget.observe_weights,
FR_ALLOWED_TIME, k, init_temp, sample_ratio,
callback_step=4, callback=self.send_update)
self.done.emit(widget.positions)
self.stopped.emit()
def update(positions, progress):
self.progressbar.advance(progress)
self.positions = positions
self.graph.update_coordinates()
def done(positions):
self.positions = positions
self.set_buttons(running=False)
self.graph.set_simplifications(
self.graph.Simplifications.NoSimplifications)
self.graph.update_coordinates()
self.progressbar.finish()
def thread_finished():
self._optimizer = None
self._animation_thread = None
self._optimizer = LayoutOptimizer(self)
self._animation_thread = QThread()
self._optimizer.update.connect(update)
self._optimizer.done.connect(done)
self._optimizer.stopped.connect(self._animation_thread.quit)
self._optimizer.moveToThread(self._animation_thread)
self._animation_thread.started.connect(self._optimizer.run)
self._animation_thread.finished.connect(thread_finished)
self._animation_thread.start()
def stop_optimization_and_wait(self):
if self._animation_thread is not None:
self._stop_optimization = True
self._animation_thread.quit()
self._animation_thread.wait()
self._animation_thread = None
def onDeleteWidget(self):
self.stop_optimization_and_wait()
super().onDeleteWidget()
def send_report(self):
if self.network is None:
return
self.report_items('Graph info', [
("Number of vertices", self.network.number_of_nodes()),
("Number of edges", self.network.number_of_edges()),
("Vertices per edge", round(self.nodes_per_edge, 3)),
("Edges per vertex", round(self.edges_per_node, 3)),
])
if self.data is not None:
self.report_data("Data", self.data)
if any((self.attr_color, self.attr_shape,
self.attr_size, self.attr_label)):
self.report_items(
"Visual settings",
[("Color", self._get_caption_var_name(self.attr_color)),
("Label", self._get_caption_var_name(self.attr_label)),
("Shape", self._get_caption_var_name(self.attr_shape)),
("Size", self._get_caption_var_name(self.attr_size))])
self.report_plot()
class OWtSNE(OWDataProjectionWidget):
name = "t-SNE"
description = "Two-dimensional data projection with t-SNE."
icon = "icons/TSNE.svg"
priority = 920
keywords = ["tsne"]
settings_version = 3
max_iter = Setting(300)
perplexity = Setting(30)
pca_components = Setting(20)
GRAPH_CLASS = OWtSNEGraph
graph = SettingProvider(OWtSNEGraph)
embedding_variables_names = ("t-SNE-x", "t-SNE-y")
#: Runtime state
Running, Finished, Waiting = 1, 2, 3
class Outputs(OWDataProjectionWidget.Outputs):
preprocessor = Output("Preprocessor", Preprocess)
class Error(OWDataProjectionWidget.Error):
not_enough_rows = Msg("Input data needs at least 2 rows")
constant_data = Msg("Input data is constant")
no_attributes = Msg("Data has no attributes")
out_of_memory = Msg("Out of memory")
optimization_error = Msg("Error during optimization\n{}")
no_valid_data = Msg("No projection due to no valid data")
def __init__(self):
super().__init__()
self.pca_data = None
self.projection = None
self.__update_loop = None
# timer for scheduling updates
self.__timer = QTimer(self, singleShot=True, interval=1,
timeout=self.__next_step)
self.__state = OWtSNE.Waiting
self.__in_next_step = False
self.__draw_similar_pairs = False
def _add_controls(self):
self._add_controls_start_box()
super()._add_controls()
# Because sc data frequently has many genes,
# showing all attributes in combo boxes can cause problems
# QUICKFIX: Remove a separator and attributes from order
# (leaving just the class and metas)
self.models = self.gui.points_models
for model in self.models:
model.order = model.order[:-2]
def _add_controls_start_box(self):
box = gui.vBox(self.controlArea, True)
form = QFormLayout(
labelAlignment=Qt.AlignLeft,
formAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow,
verticalSpacing=10
)
form.addRow(
"Max iterations:",
gui.spin(box, self, "max_iter", 1, 2000, step=50))
form.addRow(
"Perplexity:",
gui.spin(box, self, "perplexity", 1, 100, step=1))
box.layout().addLayout(form)
gui.separator(box, 10)
self.runbutton = gui.button(box, self, "Run", callback=self._toggle_run)
gui.separator(box, 10)
gui.hSlider(box, self, "pca_components", label="PCA components:",
minValue=2, maxValue=50, step=1)
def check_data(self):
def error(err):
err()
self.data = None
super().check_data()
if self.data is not None:
if len(self.data) < 2:
error(self.Error.not_enough_rows)
elif not self.data.domain.attributes:
error(self.Error.no_attributes)
elif not self.data.is_sparse() and \
np.allclose(self.data.X - self.data.X[0], 0):
error(self.Error.constant_data)
elif not self.data.is_sparse() and \
np.all(~np.isfinite(self.data.X)):
error(self.Error.no_valid_data)
def get_embedding(self):
if self.data is None:
self.valid_data = None
return None
elif self.projection is None:
embedding = np.random.normal(size=(len(self.data), 2))
else:
embedding = self.projection.embedding.X
self.valid_data = np.ones(len(embedding), dtype=bool)
return embedding
def _toggle_run(self):
if self.__state == OWtSNE.Running:
self.stop()
self.commit()
else:
self.start()
def start(self):
if not self.data or self.__state == OWtSNE.Running:
self.graph.update_coordinates()
elif self.__state in (OWtSNE.Finished, OWtSNE.Waiting):
self.__start()
def stop(self):
if self.__state == OWtSNE.Running:
self.__set_update_loop(None)
def pca_preprocessing(self):
if self.pca_data is not None and \
self.pca_data.X.shape[1] == self.pca_components:
return
pca = PCA(n_components=self.pca_components, random_state=0)
model = pca(self.data)
self.pca_data = model(self.data)
def __start(self):
self.pca_preprocessing()
initial = 'random' if self.projection is None \
else self.projection.embedding.X
step_size = 50
def update_loop(data, max_iter, step, embedding):
# NOTE: this code MUST NOT call into QApplication.processEvents
done = False
iterations_done = 0
while not done:
step_iter = min(max_iter - iterations_done, step)
projection = compute_tsne(
data, self.perplexity, step_iter, embedding)
embedding = projection.embedding.X
iterations_done += step_iter
if iterations_done >= max_iter:
done = True
yield projection, iterations_done / max_iter
self.__set_update_loop(update_loop(
self.pca_data, self.max_iter, step_size, initial))
self.progressBarInit(processEvents=None)
def __set_update_loop(self, loop):
if self.__update_loop is not None:
self.__update_loop.close()
self.__update_loop = None
self.progressBarFinished(processEvents=None)
self.__update_loop = loop
if loop is not None:
self.setBlocking(True)
self.progressBarInit(processEvents=None)
self.setStatusMessage("Running")
self.runbutton.setText("Stop")
self.__state = OWtSNE.Running
self.__timer.start()
else:
self.setBlocking(False)
self.setStatusMessage("")
self.runbutton.setText("Start")
self.__state = OWtSNE.Finished
self.__timer.stop()
def __next_step(self):
if self.__update_loop is None:
return
assert not self.__in_next_step
self.__in_next_step = True
loop = self.__update_loop
self.Error.out_of_memory.clear()
self.Error.optimization_error.clear()
try:
projection, progress = next(self.__update_loop)
assert self.__update_loop is loop
except StopIteration:
self.__set_update_loop(None)
self.unconditional_commit()
except MemoryError:
self.Error.out_of_memory()
self.__set_update_loop(None)
except Exception as exc:
self.Error.optimization_error(str(exc))
self.__set_update_loop(None)
else:
self.progressBarSet(100.0 * progress, processEvents=None)
self.projection = projection
self.graph.update_coordinates()
self.graph.update_density()
# schedule next update
self.__timer.start()
self.__in_next_step = False
def setup_plot(self):
super().setup_plot()
self.start()
def commit(self):
super().commit()
self.send_preprocessor()
def _get_projection_data(self):
if self.data is None or self.projection is None:
return None
data = self.data.transform(
Domain(self.data.domain.attributes,
self.data.domain.class_vars,
self.data.domain.metas + self.projection.domain.attributes))
data.metas[:, -2:] = self.get_embedding()
return data
def send_preprocessor(self):
prep = None
if self.data is not None and self.projection is not None:
prep = ApplyDomain(self.projection.domain, self.projection.name)
self.Outputs.preprocessor.send(prep)
def clear(self):
super().clear()
self.__set_update_loop(None)
self.__state = OWtSNE.Waiting
self.pca_data = None
self.projection = None
@classmethod
def migrate_settings(cls, settings, version):
if version < 3:
if "selection_indices" in settings:
settings["selection"] = settings["selection_indices"]
@classmethod
def migrate_context(cls, context, version):
if version < 3:
values = context.values
values["attr_color"] = values["graph"]["attr_color"]
values["attr_size"] = values["graph"]["attr_size"]
values["attr_shape"] = values["graph"]["attr_shape"]
values["attr_label"] = values["graph"]["attr_label"]
class OWFile(widget.OWWidget, RecentPathsWComboMixin):
name = "File"
id = "orange.widgets.data.file"
description = "Read data from an input file or network " \
"and send a data table to the output."
icon = "icons/File.svg"
priority = 10
category = "Data"
keywords = ["file", "load", "read", "open"]
class Outputs:
data = Output("Data",
Table,
doc="Attribute-valued dataset read from the input file.")
want_main_area = False
SEARCH_PATHS = [("sample-datasets", get_sample_datasets_dir())]
SIZE_LIMIT = 1e7
LOCAL_FILE, URL = range(2)
settingsHandler = PerfectDomainContextHandler(
match_values=PerfectDomainContextHandler.MATCH_VALUES_ALL)
# pylint seems to want declarations separated from definitions
recent_paths: List[RecentPath]
recent_urls: List[str]
variables: list
# Overload RecentPathsWidgetMixin.recent_paths to set defaults
recent_paths = Setting([
RecentPath("", "sample-datasets", "iris.tab"),
RecentPath("", "sample-datasets", "titanic.tab"),
RecentPath("", "sample-datasets", "housing.tab"),
RecentPath("", "sample-datasets", "heart_disease.tab"),
RecentPath("", "sample-datasets", "brown-selected.tab"),
RecentPath("", "sample-datasets", "zoo.tab"),
])
recent_urls = Setting([])
source = Setting(LOCAL_FILE)
xls_sheet = ContextSetting("")
sheet_names = Setting({})
url = Setting("")
variables = ContextSetting([])
domain_editor = SettingProvider(DomainEditor)
class Warning(widget.OWWidget.Warning):
file_too_big = widget.Msg(
"The file is too large to load automatically."
" Press Reload to load.")
load_warning = widget.Msg("Read warning:\n{}")
class Error(widget.OWWidget.Error):
file_not_found = widget.Msg("File not found.")
missing_reader = widget.Msg("Missing reader.")
sheet_error = widget.Msg("Error listing available sheets.")
unknown = widget.Msg("Read error:\n{}")
class NoFileSelected:
pass
UserAdviceMessages = [
widget.Message(
"Use CSV File Import widget for advanced options "
"for comma-separated files", "use-csv-file-import"),
widget.Message(
"This widget loads only tabular data. Use other widgets to load "
"other data types like models, distance matrices and networks.",
"other-data-types")
]
def __init__(self):
super().__init__()
RecentPathsWComboMixin.__init__(self)
self.domain = None
self.data = None
self.loaded_file = ""
self.reader = None
layout = QGridLayout()
gui.widgetBox(self.controlArea, margin=0, orientation=layout)
vbox = gui.radioButtons(None,
self,
"source",
box=True,
addSpace=True,
callback=self.load_data,
addToLayout=False)
rb_button = gui.appendRadioButton(vbox, "File:", addToLayout=False)
layout.addWidget(rb_button, 0, 0, Qt.AlignVCenter)
box = gui.hBox(None, addToLayout=False, margin=0)
box.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.file_combo.activated[int].connect(self.select_file)
box.layout().addWidget(self.file_combo)
layout.addWidget(box, 0, 1)
file_button = gui.button(None,
self,
'...',
callback=self.browse_file,
autoDefault=False)
file_button.setIcon(self.style().standardIcon(QStyle.SP_DirOpenIcon))
file_button.setSizePolicy(Policy.Maximum, Policy.Fixed)
layout.addWidget(file_button, 0, 2)
reload_button = gui.button(None,
self,
"Reload",
callback=self.load_data,
autoDefault=False)
reload_button.setIcon(self.style().standardIcon(
QStyle.SP_BrowserReload))
reload_button.setSizePolicy(Policy.Fixed, Policy.Fixed)
layout.addWidget(reload_button, 0, 3)
self.sheet_box = gui.hBox(None, addToLayout=False, margin=0)
self.sheet_combo = gui.comboBox(
None,
self,
"xls_sheet",
callback=self.select_sheet,
sendSelectedValue=True,
)
self.sheet_combo.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_label = QLabel()
self.sheet_label.setText('Sheet')
self.sheet_label.setSizePolicy(Policy.MinimumExpanding, Policy.Fixed)
self.sheet_box.layout().addWidget(self.sheet_label, Qt.AlignLeft)
self.sheet_box.layout().addWidget(self.sheet_combo, Qt.AlignVCenter)
layout.addWidget(self.sheet_box, 2, 1)
self.sheet_box.hide()
rb_button = gui.appendRadioButton(vbox, "URL:", addToLayout=False)
layout.addWidget(rb_button, 3, 0, Qt.AlignVCenter)
self.url_combo = url_combo = QComboBox()
url_model = NamedURLModel(self.sheet_names)
url_model.wrap(self.recent_urls)
url_combo.setLineEdit(LineEditSelectOnFocus())
url_combo.setModel(url_model)
url_combo.setSizePolicy(Policy.Ignored, Policy.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, 3, 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)
box = gui.vBox(self.controlArea, "Info")
self.infolabel = gui.widgetLabel(box, 'No data loaded.')
self.warnings = gui.widgetLabel(box, '')
box = gui.widgetBox(self.controlArea, "Columns (Double click to edit)")
self.domain_editor = DomainEditor(self)
self.editor_model = self.domain_editor.model()
box.layout().addWidget(self.domain_editor)
box = gui.hBox(self.controlArea)
gui.button(box,
self,
"Browse documentation datasets",
callback=lambda: self.browse_file(True),
autoDefault=False)
gui.rubber(box)
gui.button(box, self, "Reset", callback=self.reset_domain_edit)
self.apply_button = gui.button(box,
self,
"Apply",
callback=self.apply_domain_edit)
self.apply_button.setEnabled(False)
self.apply_button.setFixedWidth(170)
self.editor_model.dataChanged.connect(
lambda: self.apply_button.setEnabled(True))
self.set_file_list()
# Must not call open_file from within __init__. open_file
# explicitly re-enters the event loop (by a progress bar)
self.setAcceptDrops(True)
if self.source == self.LOCAL_FILE:
last_path = self.last_path()
if last_path and os.path.exists(last_path) and \
os.path.getsize(last_path) > self.SIZE_LIMIT:
self.Warning.file_too_big()
return
QTimer.singleShot(0, self.load_data)
@staticmethod
def sizeHint():
return QSize(600, 550)
def select_file(self, n):
assert n < len(self.recent_paths)
super().select_file(n)
if self.recent_paths:
self.source = self.LOCAL_FILE
self.load_data()
self.set_file_list()
def select_sheet(self):
self.recent_paths[0].sheet = self.sheet_combo.currentText()
self.load_data()
def _url_set(self):
url = self.url_combo.currentText()
pos = self.recent_urls.index(url)
url = url.strip()
if not urlparse(url).scheme:
url = 'http://' + url
self.url_combo.setItemText(pos, url)
self.recent_urls[pos] = url
self.source = self.URL
self.load_data()
def browse_file(self, in_demos=False):
if in_demos:
start_file = get_sample_datasets_dir()
if not os.path.exists(start_file):
QMessageBox.information(
None, "File",
"Cannot find the directory with documentation datasets")
return
else:
start_file = self.last_path() or os.path.expanduser("~/")
readers = [
f for f in FileFormat.formats
if getattr(f, 'read', None) and getattr(f, "EXTENSIONS", None)
]
filename, reader, _ = open_filename_dialog(start_file, None, readers)
if not filename:
return
self.add_path(filename)
if reader is not None:
self.recent_paths[0].file_format = reader.qualified_name()
self.source = self.LOCAL_FILE
self.load_data()
# Open a file, create data from it and send it over the data channel
def load_data(self):
# We need to catch any exception type since anything can happen in
# file readers
self.closeContext()
self.domain_editor.set_domain(None)
self.apply_button.setEnabled(False)
self.clear_messages()
self.set_file_list()
error = self._try_load()
if error:
error()
self.data = None
self.sheet_box.hide()
self.Outputs.data.send(None)
self.infolabel.setText("No data.")
def _try_load(self):
# pylint: disable=broad-except
if self.last_path() and not os.path.exists(self.last_path()):
return self.Error.file_not_found
try:
self.reader = self._get_reader()
assert self.reader is not None
except Exception:
return self.Error.missing_reader
if self.reader is self.NoFileSelected:
self.Outputs.data.send(None)
return None
try:
self._update_sheet_combo()
except Exception:
return self.Error.sheet_error
with catch_warnings(record=True) as warnings:
try:
data = self.reader.read()
except Exception as ex:
log.exception(ex)
return lambda x=ex: self.Error.unknown(str(x))
if warnings:
self.Warning.load_warning(warnings[-1].message.args[0])
self.infolabel.setText(self._describe(data))
self.loaded_file = self.last_path()
add_origin(data, self.loaded_file)
self.data = data
self.openContext(data.domain)
self.apply_domain_edit() # sends data
return None
def _get_reader(self) -> FileFormat:
if self.source == self.LOCAL_FILE:
path = self.last_path()
if path is None:
return self.NoFileSelected
if self.recent_paths and self.recent_paths[0].file_format:
qname = self.recent_paths[0].file_format
reader_class = class_from_qualified_name(qname)
reader = reader_class(path)
else:
reader = FileFormat.get_reader(path)
if self.recent_paths and self.recent_paths[0].sheet:
reader.select_sheet(self.recent_paths[0].sheet)
return reader
else:
url = self.url_combo.currentText().strip()
if url:
return UrlReader(url)
else:
return self.NoFileSelected
def _update_sheet_combo(self):
if len(self.reader.sheets) < 2:
self.sheet_box.hide()
self.reader.select_sheet(None)
return
self.sheet_combo.clear()
self.sheet_combo.addItems(self.reader.sheets)
self._select_active_sheet()
self.sheet_box.show()
def _select_active_sheet(self):
if self.reader.sheet:
try:
idx = self.reader.sheets.index(self.reader.sheet)
self.sheet_combo.setCurrentIndex(idx)
except ValueError:
# Requested sheet does not exist in this file
self.reader.select_sheet(None)
else:
self.sheet_combo.setCurrentIndex(0)
@staticmethod
def _describe(table):
def missing_prop(prop):
if prop:
return f"({prop * 100:.1f}% missing values)"
else:
return "(no missing values)"
domain = table.domain
text = ""
attrs = getattr(table, "attributes", {})
descs = [
attrs[desc] for desc in ("Name", "Description") if desc in attrs
]
if len(descs) == 2:
descs[0] = f"<b>{descs[0]}</b>"
if descs:
text += f"<p>{'<br/>'.join(descs)}</p>"
text += f"<p>{len(table)} instance(s)"
missing_in_attr = missing_prop(table.has_missing_attribute()
and table.get_nan_frequency_attribute())
missing_in_class = missing_prop(table.has_missing_class()
and table.get_nan_frequency_class())
text += f"<br/>{len(domain.attributes)} feature(s) {missing_in_attr}"
if domain.has_continuous_class:
text += f"<br/>Regression; numerical class {missing_in_class}"
elif domain.has_discrete_class:
text += "<br/>Classification; categorical class " \
f"with {len(domain.class_var.values)} values {missing_in_class}"
elif table.domain.class_vars:
text += "<br/>Multi-target; " \
f"{len(table.domain.class_vars)} target variables " \
f"{missing_in_class}"
else:
text += "<br/>Data has no target variable."
text += f"<br/>{len(domain.metas)} meta attribute(s)"
text += "</p>"
if 'Timestamp' in table.domain:
# Google Forms uses this header to timestamp responses
text += f"<p>First entry: {table[0, 'Timestamp']}<br/>" \
f"Last entry: {table[-1, 'Timestamp']}</p>"
return text
def storeSpecificSettings(self):
self.current_context.modified_variables = self.variables[:]
def retrieveSpecificSettings(self):
if hasattr(self.current_context, "modified_variables"):
self.variables[:] = self.current_context.modified_variables
def reset_domain_edit(self):
self.domain_editor.reset_domain()
self.apply_domain_edit()
def apply_domain_edit(self):
if self.data is None:
table = None
else:
domain, cols = self.domain_editor.get_domain(
self.data.domain, self.data)
if not (domain.variables or domain.metas):
table = None
else:
X, y, m = cols
table = Table.from_numpy(domain, X, y, m, self.data.W)
table.name = self.data.name
table.ids = np.array(self.data.ids)
table.attributes = getattr(self.data, 'attributes', {})
self.Outputs.data.send(table)
self.apply_button.setEnabled(False)
def get_widget_name_extension(self):
_, name = os.path.split(self.loaded_file)
return os.path.splitext(name)[0]
def send_report(self):
def get_ext_name(filename):
try:
return FileFormat.names[os.path.splitext(filename)[1]]
except KeyError:
return "unknown"
if self.data is None:
self.report_paragraph("File", "No file.")
return
if self.source == self.LOCAL_FILE:
home = os.path.expanduser("~")
if self.loaded_file.startswith(home):
# os.path.join does not like ~
name = "~" + os.path.sep + \
self.loaded_file[len(home):].lstrip("/").lstrip("\\")
else:
name = self.loaded_file
if self.sheet_combo.isVisible():
name += f" ({self.sheet_combo.currentText()})"
self.report_items("File", [("File name", name),
("Format", get_ext_name(name))])
else:
self.report_items("Data", [("Resource", self.url),
("Format", get_ext_name(self.url))])
self.report_data("Data", self.data)
@staticmethod
def dragEnterEvent(event):
"""Accept drops of valid file urls"""
urls = event.mimeData().urls()
if urls:
try:
FileFormat.get_reader(urls[0].toLocalFile())
event.acceptProposedAction()
except IOError:
pass
def dropEvent(self, event):
"""Handle file drops"""
urls = event.mimeData().urls()
if urls:
self.add_path(urls[0].toLocalFile()) # add first file
self.source = self.LOCAL_FILE
self.load_data()
def workflowEnvChanged(self, key, value, oldvalue):
"""
Function called when environment changes (e.g. while saving the scheme)
It make sure that all environment connected values are modified
(e.g. relative file paths are changed)
"""
self.update_file_list(key, value, oldvalue)
class OWHyper(OWWidget):
name = "Hyperspectra"
inputs = [("Data", Orange.data.Table, 'set_data', Default)]
outputs = [("Selection", Orange.data.Table), ("Data", Orange.data.Table)]
icon = "icons/hyper.svg"
settings_version = 2
settingsHandler = DomainContextHandler(metas_in_res=True)
imageplot = SettingProvider(ImagePlot)
curveplot = SettingProvider(CurvePlotHyper)
integration_method = Setting(0)
integration_methods = [Integrate.Simple, Integrate.Baseline,
Integrate.PeakMax, Integrate.PeakBaseline, Integrate.PeakAt]
value_type = Setting(0)
attr_value = ContextSetting(None)
lowlim = Setting(None)
highlim = Setting(None)
choose = Setting(None)
class Warning(OWWidget.Warning):
threshold_error = Msg("Low slider should be less than High")
class Error(OWWidget.Warning):
image_too_big = Msg("Image for chosen features is too big ({} x {}).")
@classmethod
def migrate_settings(cls, settings_, version):
if version < 2:
# delete the saved attr_value to prevent crashes
try:
del settings_["context_settings"][0].values["attr_value"]
except:
pass
def __init__(self):
super().__init__()
dbox = gui.widgetBox(self.controlArea, "Image values")
rbox = gui.radioButtons(
dbox, self, "value_type", callback=self._change_integration)
gui.appendRadioButton(rbox, "From spectra")
self.box_values_spectra = gui.indentedBox(rbox)
gui.comboBox(
self.box_values_spectra, self, "integration_method", valueType=int,
items=(a.name for a in self.integration_methods),
callback=self._change_integral_type)
gui.rubber(self.controlArea)
gui.appendRadioButton(rbox, "Use feature")
self.box_values_feature = gui.indentedBox(rbox)
self.feature_value_model = DomainModel(DomainModel.METAS | DomainModel.CLASSES,
valid_types=DomainModel.PRIMITIVE)
self.feature_value = gui.comboBox(
self.box_values_feature, self, "attr_value",
callback=self.update_feature_value, model=self.feature_value_model,
sendSelectedValue=True, valueType=str)
splitter = QSplitter(self)
splitter.setOrientation(Qt.Vertical)
self.imageplot = ImagePlot(self, self.image_selection_changed)
self.curveplot = CurvePlotHyper(self, select=SELECTONE)
self.curveplot.plot.vb.x_padding = 0.005 # pad view so that lines are not hidden
splitter.addWidget(self.imageplot)
splitter.addWidget(self.curveplot)
self.mainArea.layout().addWidget(splitter)
self.line1 = MovableVlineWD(position=self.lowlim, label="", setvalfn=self.set_lowlim,
confirmfn=self.edited, report=self.curveplot)
self.line2 = MovableVlineWD(position=self.highlim, label="", setvalfn=self.set_highlim,
confirmfn=self.edited, report=self.curveplot)
self.line3 = MovableVlineWD(position=self.choose, label="", setvalfn=self.set_choose,
confirmfn=self.edited, report=self.curveplot)
self.curveplot.add_marking(self.line1)
self.curveplot.add_marking(self.line2)
self.curveplot.add_marking(self.line3)
self.line1.hide()
self.line2.hide()
self.line3.hide()
self.data = None
self.resize(900, 700)
self.graph_name = "imageplot.plotview"
self._update_integration_type()
def image_selection_changed(self, indices):
annotated = create_annotated_table(self.data, indices)
self.send("Data", annotated)
if self.data:
selected = self.data[indices]
self.send("Selection", selected if selected else None)
if selected:
self.curveplot.set_data(selected)
else:
self.curveplot.set_data(self.data)
else:
self.send("Selection", None)
self.curveplot.set_data(None)
self.curveplot.update_view()
def selection_changed(self):
self.redraw_data()
def init_attr_values(self):
domain = self.data.domain if self.data is not None else None
self.feature_value_model.set_domain(domain)
self.attr_value = self.feature_value_model[0] if self.feature_value_model else None
def set_lowlim(self, v):
self.lowlim = v
def set_highlim(self, v):
self.highlim = v
def set_choose(self, v):
self.choose = v
def redraw_data(self):
self.imageplot.set_integral_limits()
def update_feature_value(self):
self.redraw_data()
def _update_integration_type(self):
self.line1.hide()
self.line2.hide()
self.line3.hide()
if self.value_type == 0:
self.box_values_spectra.setDisabled(False)
self.box_values_feature.setDisabled(True)
if self.integration_methods[self.integration_method] != Integrate.PeakAt:
self.line1.show()
self.line2.show()
else:
self.line3.show()
elif self.value_type == 1:
self.box_values_spectra.setDisabled(True)
self.box_values_feature.setDisabled(False)
QTest.qWait(1) # first update the interface
def _change_integration(self):
# change what to show on the image
self._update_integration_type()
self.redraw_data()
def edited(self):
self.redraw_data()
def _change_integral_type(self):
self._change_integration()
def set_data(self, data):
self.closeContext()
self.curveplot.set_data(data)
if data is not None:
same_domain = (self.data and
data.domain.checksum() == self.data.domain.checksum())
self.data = data
if not same_domain:
self.init_attr_values()
else:
self.data = None
if self.curveplot.data_x is not None and len(self.curveplot.data_x):
minx = self.curveplot.data_x[0]
maxx = self.curveplot.data_x[-1]
if self.lowlim is None or not minx <= self.lowlim <= maxx:
self.lowlim = minx
self.line1.setValue(self.lowlim)
if self.highlim is None or not minx <= self.highlim <= maxx:
self.highlim = maxx
self.line2.setValue(self.highlim)
if self.choose is None:
self.choose = (minx + maxx)/2
elif self.choose < minx:
self.choose = minx
elif self.choose > maxx:
self.choose = maxx
self.line3.setValue(self.choose)
self.imageplot.set_data(data)
self.openContext(data)
self.curveplot.update_view()
self.imageplot.update_view()
# store selection as a list due to a bug in checking if numpy settings changed
def storeSpecificSettings(self):
selection = self.imageplot.selection
if selection is not None:
selection = list(selection)
self.current_context.selection = selection
def retrieveSpecificSettings(self):
selection = getattr(self.current_context, "selection", None)
if selection is not None:
selection = np.array(selection, dtype="bool")
self.imageplot.selection = selection
class OWAnchorProjectionWidget(OWDataProjectionWidget, openclass=True):
""" Base widget for widgets with graphs with anchors. """
SAMPLE_SIZE = 100
GRAPH_CLASS = OWGraphWithAnchors
graph = SettingProvider(OWGraphWithAnchors)
class Outputs(OWDataProjectionWidget.Outputs):
components = Output("Components", Table)
class Error(OWDataProjectionWidget.Error):
sparse_data = Msg("Sparse data is not supported")
no_valid_data = Msg("No projection due to no valid data")
no_instances = Msg("At least two data instances are required")
proj_error = Msg("An error occurred while projecting data.\n{}")
def __init__(self):
self.projector = self.projection = None
super().__init__()
self.graph.view_box.started.connect(self._manual_move_start)
self.graph.view_box.moved.connect(self._manual_move)
self.graph.view_box.finished.connect(self._manual_move_finish)
def check_data(self):
def error(err):
err()
self.data = None
super().check_data()
if self.data is not None:
if self.data.is_sparse():
error(self.Error.sparse_data)
elif len(self.data) < 2:
error(self.Error.no_instances)
else:
if not np.sum(np.all(np.isfinite(self.data.X), axis=1)):
error(self.Error.no_valid_data)
def init_projection(self):
self.projection = None
if not self.effective_variables:
return
try:
self.projection = self.projector(self.effective_data)
except Exception as ex: # pylint: disable=broad-except
self.Error.proj_error(ex)
def get_embedding(self):
self.valid_data = None
if self.data is None or self.projection is None:
return None
embedding = self.projection(self.data).X
self.valid_data = np.all(np.isfinite(embedding), axis=1)
return embedding
def get_anchors(self):
if self.projection is None:
return None, None
components = self.projection.components_
if components.shape == (1, 1):
components = np.array([[1.], [0.]])
return components.T, [a.name for a in self.effective_variables]
def _manual_move_start(self):
self.graph.set_sample_size(self.SAMPLE_SIZE)
def _manual_move(self, anchor_idx, x, y):
self.projection.components_[:, anchor_idx] = [x, y]
self.graph.update_coordinates()
def _manual_move_finish(self, anchor_idx, x, y):
self._manual_move(anchor_idx, x, y)
self.graph.set_sample_size(None)
self.commit()
def _get_projection_data(self):
if self.data is None or self.projection is None:
return None
proposed = [a.name for a in self.projection.domain.attributes]
names = get_unique_names(self.data.domain, proposed)
if proposed != names:
attributes = tuple([
attr.copy(name=name)
for name, attr in zip(names, self.projection.domain.attributes)
])
else:
attributes = self.projection.domain.attributes
return self.data.transform(
Domain(self.data.domain.attributes, self.data.domain.class_vars,
self.data.domain.metas + attributes))
def commit(self):
super().commit()
self.send_components()
def send_components(self):
components = None
if self.data is not None and self.projection is not None:
proposed = [var.name for var in self.effective_variables]
comp_name = get_unique_names(proposed, 'component')
meta_attrs = [StringVariable(name=comp_name)]
domain = Domain(self.effective_variables, metas=meta_attrs)
components = Table(domain,
self._send_components_x().copy(),
metas=self._send_components_metas())
components.name = "components"
self.Outputs.components.send(components)
def _send_components_x(self):
return self.projection.components_
def _send_components_metas(self):
variable_names = [a.name for a in self.projection.domain.attributes]
return np.array(variable_names, dtype=object)[:, None]
def clear(self):
super().clear()
self.projector = self.projection = None
class OWManifoldLearning(OWWidget):
name = "Manifold Learning"
description = "Nonlinear dimensionality reduction."
icon = "icons/Manifold.svg"
priority = 2200
inputs = [("Data", Table, "set_data")]
outputs = [("Transformed data", Table)]
MANIFOLD_METHODS = (TSNE, MDS, Isomap, LocallyLinearEmbedding,
SpectralEmbedding)
tsne_editor = SettingProvider(TSNEParametersEditor)
mds_editor = SettingProvider(MDSParametersEditor)
isomap_editor = SettingProvider(IsomapParametersEditor)
lle_editor = SettingProvider(LocallyLinearEmbeddingParametersEditor)
spectral_editor = SettingProvider(SpectralEmbeddingParametersEditor)
resizing_enabled = False
want_main_area = False
manifold_method_index = Setting(0)
n_components = Setting(2)
auto_apply = Setting(True)
class Error(OWWidget.Error):
n_neighbors_too_small = Msg("Neighbors must be greater than {}.")
manifold_error = Msg("{}")
sparse_not_supported = Msg("Sparse data is not supported.")
def __init__(self):
self.data = None
# GUI
method_box = gui.vBox(self.controlArea, "Method")
self.manifold_methods_combo = gui.comboBox(
method_box, self, "manifold_method_index",
items=[m.name for m in self.MANIFOLD_METHODS],
callback=self.manifold_method_changed)
self.params_box = gui.vBox(self.controlArea, "Parameters")
self.tsne_editor = TSNEParametersEditor(self)
self.mds_editor = MDSParametersEditor(self)
self.isomap_editor = IsomapParametersEditor(self)
self.lle_editor = LocallyLinearEmbeddingParametersEditor(self)
self.spectral_editor = SpectralEmbeddingParametersEditor(self)
self.parameter_editors = [
self.tsne_editor, self.mds_editor, self.isomap_editor,
self.lle_editor, self.spectral_editor]
for editor in self.parameter_editors:
self.params_box.layout().addWidget(editor)
editor.hide()
self.params_widget = self.parameter_editors[self.manifold_method_index]
self.params_widget.show()
output_box = gui.vBox(self.controlArea, "Output")
self.n_components_spin = gui.spin(
output_box, self, "n_components", 1, 10, label="Components:",
alignment=Qt.AlignRight, callbackOnReturn=True,
callback=self.settings_changed)
self.apply_button = gui.auto_commit(
output_box, self, "auto_apply", "&Apply",
box=False, commit=self.apply)
def manifold_method_changed(self):
self.params_widget.hide()
self.params_widget = self.parameter_editors[self.manifold_method_index]
self.params_widget.show()
self.apply()
def settings_changed(self):
self.apply()
def set_data(self, data):
self.data = data
self.n_components_spin.setMaximum(len(self.data.domain.attributes)
if self.data else 10)
self.apply()
def apply(self):
data = None
self.clear_messages()
if self.data:
if self.data.is_sparse():
self.Error.sparse_not_supported()
else:
with self.progressBar():
self.progressBarSet(10)
domain = Domain([ContinuousVariable("C{}".format(i))
for i in range(self.n_components)],
self.data.domain.class_vars,
self.data.domain.metas)
method = self.MANIFOLD_METHODS[self.manifold_method_index]
projector = method(**self.get_method_parameters())
try:
self.progressBarSet(20)
X = projector(self.data).embedding_
data = Table(domain, X, self.data.Y, self.data.metas)
except ValueError as e:
if e.args[0] == "for method='hessian', n_neighbors " \
"must be greater than [n_components" \
" * (n_components + 3) / 2]":
n = self.n_components * (self.n_components + 3) / 2
self.Error.n_neighbors_too_small("{}".format(n))
else:
self.Error.manifold_error(e.args[0])
except np.linalg.linalg.LinAlgError as e:
self.Error.manifold_error(str(e))
self.send("Transformed data", data)
def get_method_parameters(self):
parameters = dict(n_components=self.n_components)
parameters.update(self.params_widget.parameters)
return parameters
def send_report(self):
method_name = self.MANIFOLD_METHODS[self.manifold_method_index].name
self.report_items((("Method", method_name),))
parameters = self.get_method_parameters()
self.report_items("Method parameters", tuple(parameters.items()))
if self.data:
self.report_data("Data", self.data)
class OWScatterPlot(OWDataProjectionWidget):
"""Scatterplot visualization with explorative analysis and intelligent
data visualization enhancements."""
name = 'Scatter Plot'
description = "Interactive scatter plot visualization with " \
"intelligent data visualization enhancements."
icon = "icons/ScatterPlot.svg"
priority = 140
keywords = []
class Inputs(OWDataProjectionWidget.Inputs):
features = Input("Features", AttributeList)
class Outputs(OWDataProjectionWidget.Outputs):
features = Output("Features", AttributeList, dynamic=False)
settings_version = 3
auto_sample = Setting(True)
attr_x = ContextSetting(None)
attr_y = ContextSetting(None)
tooltip_shows_all = Setting(True)
GRAPH_CLASS = OWScatterPlotGraph
graph = SettingProvider(OWScatterPlotGraph)
embedding_variables_names = None
class Warning(OWDataProjectionWidget.Warning):
missing_coords = Msg("Plot cannot be displayed because '{}' or '{}' "
"is missing for all data points")
class Information(OWDataProjectionWidget.Information):
sampled_sql = Msg("Large SQL table; showing a sample.")
missing_coords = Msg(
"Points with missing '{}' or '{}' are not displayed")
def __init__(self):
self.sql_data = None # Orange.data.sql.table.SqlTable
self.attribute_selection_list = None # list of Orange.data.Variable
self.__timer = QTimer(self, interval=1200)
self.__timer.timeout.connect(self.add_data)
super().__init__()
# manually register Matplotlib file writers
self.graph_writers = self.graph_writers.copy()
for w in [MatplotlibFormat, MatplotlibPDFFormat]:
for ext in w.EXTENSIONS:
self.graph_writers[ext] = w
def _add_controls(self):
self._add_controls_axis()
self._add_controls_sampling()
super()._add_controls()
self.gui.add_widget(self.gui.JitterNumericValues, self._effects_box)
self.gui.add_widgets([
self.gui.ShowGridLines, self.gui.ToolTipShowsAll,
self.gui.RegressionLine
], self._plot_box)
def _add_controls_axis(self):
common_options = dict(labelWidth=50,
orientation=Qt.Horizontal,
sendSelectedValue=True,
valueType=str,
contentsLength=14)
box = gui.vBox(self.controlArea, True)
dmod = DomainModel
self.xy_model = DomainModel(dmod.MIXED, valid_types=dmod.PRIMITIVE)
self.cb_attr_x = gui.comboBox(box,
self,
"attr_x",
label="Axis x:",
callback=self.attr_changed,
model=self.xy_model,
**common_options)
self.cb_attr_y = gui.comboBox(box,
self,
"attr_y",
label="Axis y:",
callback=self.attr_changed,
model=self.xy_model,
**common_options)
vizrank_box = gui.hBox(box)
self.vizrank, self.vizrank_button = ScatterPlotVizRank.add_vizrank(
vizrank_box, self, "Find Informative Projections", self.set_attr)
def _add_controls_sampling(self):
self.sampling = gui.auto_commit(self.controlArea,
self,
"auto_sample",
"Sample",
box="Sampling",
callback=self.switch_sampling,
commit=lambda: self.add_data(1))
self.sampling.setVisible(False)
@property
def effective_variables(self):
return [self.attr_x, self.attr_y]
def _vizrank_color_change(self):
self.vizrank.initialize()
is_enabled = self.data is not None and not self.data.is_sparse() and \
len(self.xy_model) > 2 and len(self.data[self.valid_data]) > 1 \
and np.all(np.nan_to_num(np.nanstd(self.data.X, 0)) != 0)
self.vizrank_button.setEnabled(
is_enabled and self.attr_color is not None and not np.isnan(
self.data.get_column_view(
self.attr_color)[0].astype(float)).all())
text = "Color variable has to be selected." \
if is_enabled and self.attr_color is None else ""
self.vizrank_button.setToolTip(text)
def set_data(self, data):
if self.data and data and self.data.checksum() == data.checksum():
return
super().set_data(data)
def findvar(name, iterable):
"""Find a Orange.data.Variable in `iterable` by name"""
for el in iterable:
if isinstance(el, Variable) and el.name == name:
return el
return None
# handle restored settings from < 3.3.9 when attr_* were stored
# by name
if isinstance(self.attr_x, str):
self.attr_x = findvar(self.attr_x, self.xy_model)
if isinstance(self.attr_y, str):
self.attr_y = findvar(self.attr_y, self.xy_model)
if isinstance(self.attr_label, str):
self.attr_label = findvar(self.attr_label, self.gui.label_model)
if isinstance(self.attr_color, str):
self.attr_color = findvar(self.attr_color, self.gui.color_model)
if isinstance(self.attr_shape, str):
self.attr_shape = findvar(self.attr_shape, self.gui.shape_model)
if isinstance(self.attr_size, str):
self.attr_size = findvar(self.attr_size, self.gui.size_model)
def check_data(self):
self.clear_messages()
self.__timer.stop()
self.sampling.setVisible(False)
self.sql_data = None
if isinstance(self.data, SqlTable):
if self.data.approx_len() < 4000:
self.data = Table(self.data)
else:
self.Information.sampled_sql()
self.sql_data = self.data
data_sample = self.data.sample_time(0.8, no_cache=True)
data_sample.download_data(2000, partial=True)
self.data = Table(data_sample)
self.sampling.setVisible(True)
if self.auto_sample:
self.__timer.start()
if self.data is not None and (len(self.data) == 0
or len(self.data.domain) == 0):
self.data = None
def get_embedding(self):
self.valid_data = None
if self.data is None:
return None
x_data = self.get_column(self.attr_x, filter_valid=False)
y_data = self.get_column(self.attr_y, filter_valid=False)
if x_data is None or y_data is None:
return None
self.Warning.missing_coords.clear()
self.Information.missing_coords.clear()
self.valid_data = np.isfinite(x_data) & np.isfinite(y_data)
if self.valid_data is not None and not np.all(self.valid_data):
msg = self.Information if np.any(self.valid_data) else self.Warning
msg.missing_coords(self.attr_x.name, self.attr_y.name)
return np.vstack((x_data, y_data)).T
# Tooltip
def _point_tooltip(self, point_id, skip_attrs=()):
point_data = self.data[point_id]
xy_attrs = (self.attr_x, self.attr_y)
text = "<br/>".join(
escape('{} = {}'.format(var.name, point_data[var]))
for var in xy_attrs)
if self.tooltip_shows_all:
others = super()._point_tooltip(point_id, skip_attrs=xy_attrs)
if others:
text = "<b>{}</b><br/><br/>{}".format(text, others)
return text
def can_draw_regresssion_line(self):
return self.data is not None and\
self.data.domain is not None and \
self.attr_x.is_continuous and \
self.attr_y.is_continuous
def add_data(self, time=0.4):
if self.data and len(self.data) > 2000:
self.__timer.stop()
return
data_sample = self.sql_data.sample_time(time, no_cache=True)
if data_sample:
data_sample.download_data(2000, partial=True)
data = Table(data_sample)
self.data = Table.concatenate((self.data, data), axis=0)
self.handleNewSignals()
def init_attr_values(self):
super().init_attr_values()
data = self.data
domain = data.domain if data and len(data) else None
self.xy_model.set_domain(domain)
self.attr_x = self.xy_model[0] if self.xy_model else None
self.attr_y = self.xy_model[1] if len(self.xy_model) >= 2 \
else self.attr_x
def switch_sampling(self):
self.__timer.stop()
if self.auto_sample and self.sql_data:
self.add_data()
self.__timer.start()
def set_subset_data(self, subset_data):
self.warning()
if isinstance(subset_data, SqlTable):
if subset_data.approx_len() < AUTO_DL_LIMIT:
subset_data = Table(subset_data)
else:
self.warning("Data subset does not support large Sql tables")
subset_data = None
super().set_subset_data(subset_data)
# called when all signals are received, so the graph is updated only once
def handleNewSignals(self):
if self.attribute_selection_list and self.data is not None and \
self.data.domain is not None and \
all(attr in self.data.domain for attr
in self.attribute_selection_list):
self.set_attr(self.attribute_selection_list[0],
self.attribute_selection_list[1])
self.attribute_selection_list = None
else:
super().handleNewSignals()
self._vizrank_color_change()
self.cb_reg_line.setEnabled(self.can_draw_regresssion_line())
@Inputs.features
def set_shown_attributes(self, attributes):
if attributes and len(attributes) >= 2:
self.attribute_selection_list = attributes[:2]
else:
self.attribute_selection_list = None
def set_attr(self, attr_x, attr_y):
if attr_x != self.attr_x or attr_y != self.attr_y:
self.attr_x, self.attr_y = attr_x, attr_y
self.attr_changed()
def attr_changed(self):
self.cb_reg_line.setEnabled(self.can_draw_regresssion_line())
self.setup_plot()
self.commit()
def setup_plot(self):
super().setup_plot()
for axis, var in (("bottom", self.attr_x), ("left", self.attr_y)):
self.graph.set_axis_title(axis, var)
if var and var.is_discrete:
self.graph.set_axis_labels(axis,
get_variable_values_sorted(var))
else:
self.graph.set_axis_labels(axis, None)
def colors_changed(self):
super().colors_changed()
self._vizrank_color_change()
def commit(self):
super().commit()
self.send_features()
def send_features(self):
features = [attr for attr in [self.attr_x, self.attr_y] if attr]
self.Outputs.features.send(features or None)
def get_widget_name_extension(self):
if self.data is not None:
return "{} vs {}".format(self.attr_x.name, self.attr_y.name)
return None
def _get_send_report_caption(self):
return report.render_items_vert(
(("Color", self._get_caption_var_name(self.attr_color)),
("Label", self._get_caption_var_name(self.attr_label)),
("Shape", self._get_caption_var_name(self.attr_shape)),
("Size", self._get_caption_var_name(self.attr_size)),
("Jittering", (self.attr_x.is_discrete or self.attr_y.is_discrete
or self.graph.jitter_continuous)
and self.graph.jitter_size)))
@classmethod
def migrate_settings(cls, settings, version):
if version < 2 and "selection" in settings and settings["selection"]:
settings["selection_group"] = [(a, 1)
for a in settings["selection"]]
if version < 3:
if "auto_send_selection" in settings:
settings["auto_commit"] = settings["auto_send_selection"]
if "selection_group" in settings:
settings["selection"] = settings["selection_group"]
@classmethod
def migrate_context(cls, context, version):
if version < 3:
values = context.values
values["attr_color"] = values["graph"]["attr_color"]
values["attr_size"] = values["graph"]["attr_size"]
values["attr_shape"] = values["graph"]["attr_shape"]
values["attr_label"] = values["graph"]["attr_label"]
class OWMDS(OWDataProjectionWidget):
name = "多维标度分析"
description = "由距离矩阵构造的多维标度的二维数据投影。"
icon = "icons/MDS.svg"
keywords = ["multidimensional scaling", "multi dimensional scaling"]
class Inputs(OWDataProjectionWidget.Inputs):
distances = Input("Distances", DistMatrix)
settings_version = 3
#: Initialization type
PCA, Random, Jitter = 0, 1, 2
#: Refresh rate
RefreshRate = [("Every iteration", 1), ("Every 5 steps", 5),
("Every 10 steps", 10), ("Every 25 steps", 25),
("Every 50 steps", 50), ("None", -1)]
#: Runtime state
Running, Finished, Waiting = 1, 2, 3
max_iter = settings.Setting(300)
initialization = settings.Setting(PCA)
refresh_rate = settings.Setting(3)
GRAPH_CLASS = OWMDSGraph
graph = SettingProvider(OWMDSGraph)
embedding_variables_names = ("mds-x", "mds-y")
class Error(OWDataProjectionWidget.Error):
not_enough_rows = Msg("Input data needs at least 2 rows")
matrix_too_small = Msg("Input matrix must be at least 2x2")
no_attributes = Msg("Data has no attributes")
mismatching_dimensions = \
Msg("Data and distances dimensions do not match.")
out_of_memory = Msg("Out of memory")
optimization_error = Msg("Error during optimization\n{}")
def __init__(self):
super().__init__()
#: Input dissimilarity matrix
self.matrix = None # type: Optional[DistMatrix]
#: Data table from the `self.matrix.row_items` (if present)
self.matrix_data = None # type: Optional[Table]
#: Input data table
self.signal_data = None
self.__invalidated = True
self.embedding = None
self.effective_matrix = None
self.__update_loop = None
# timer for scheduling updates
self.__timer = QTimer(self, singleShot=True, interval=0)
self.__timer.timeout.connect(self.__next_step)
self.__state = OWMDS.Waiting
self.__in_next_step = False
self.graph.pause_drawing_pairs()
self.size_model = self.gui.points_models[2]
self.size_model.order = \
self.gui.points_models[2].order[:1] \
+ ("Stress", ) + \
self.gui.points_models[2].order[1:]
# self._initialize()
def _add_controls(self):
self._add_controls_optimization()
super()._add_controls()
self.gui.add_control(self._effects_box,
gui.hSlider,
"Show similar pairs:",
master=self.graph,
value="connected_pairs",
minValue=0,
maxValue=20,
createLabel=False,
callback=self._on_connected_changed)
def _add_controls_optimization(self):
box = gui.vBox(self.controlArea, box=True)
self.runbutton = gui.button(box,
self,
"运行优化",
callback=self._toggle_run)
gui.comboBox(box,
self,
"refresh_rate",
label="刷新: ",
orientation=Qt.Horizontal,
items=[t for t, _ in OWMDS.RefreshRate],
callback=self.__invalidate_refresh)
hbox = gui.hBox(box, margin=0)
gui.button(hbox, self, "PCA", callback=self.do_PCA)
gui.button(hbox, self, "Randomize", callback=self.do_random)
gui.button(hbox, self, "Jitter", callback=self.do_jitter)
def set_data(self, data):
"""Set the input dataset.
Parameters
----------
data : Optional[Table]
"""
if data is not None and len(data) < 2:
self.Error.not_enough_rows()
data = None
else:
self.Error.not_enough_rows.clear()
self.signal_data = data
@Inputs.distances
def set_disimilarity(self, matrix):
"""Set the dissimilarity (distance) matrix.
Parameters
----------
matrix : Optional[Orange.misc.DistMatrix]
"""
if matrix is not None and len(matrix) < 2:
self.Error.matrix_too_small()
matrix = None
else:
self.Error.matrix_too_small.clear()
self.matrix = matrix
self.matrix_data = matrix.row_items if matrix is not None else None
def clear(self):
super().clear()
self.embedding = None
self.graph.set_effective_matrix(None)
self.__set_update_loop(None)
self.__state = OWMDS.Waiting
def _initialize(self):
matrix_existed = self.effective_matrix is not None
effective_matrix = self.effective_matrix
self.__invalidated = True
self.data = None
self.effective_matrix = None
self.closeContext()
self.clear_messages()
# if no data nor matrix is present reset plot
if self.signal_data is None and self.matrix is None:
self.clear()
self.init_attr_values()
return
if self.signal_data is not None and self.matrix is not None and \
len(self.signal_data) != len(self.matrix):
self.Error.mismatching_dimensions()
self.clear()
self.init_attr_values()
return
if self.signal_data is not None:
self.data = self.signal_data
elif self.matrix_data is not None:
self.data = self.matrix_data
if self.matrix is not None:
self.effective_matrix = self.matrix
if self.matrix.axis == 0 and self.data is self.matrix_data:
self.data = None
elif self.data.domain.attributes:
preprocessed_data = MDS().preprocess(self.data)
self.effective_matrix = Euclidean(preprocessed_data)
else:
self.Error.no_attributes()
self.clear()
self.init_attr_values()
return
self.init_attr_values()
self.openContext(self.data)
self.__invalidated = not (
matrix_existed and self.effective_matrix is not None
and np.array_equal(effective_matrix, self.effective_matrix))
if self.__invalidated:
self.clear()
self.graph.set_effective_matrix(self.effective_matrix)
def _toggle_run(self):
if self.__state == OWMDS.Running:
self.stop()
self._invalidate_output()
else:
self.start()
def start(self):
if self.__state == OWMDS.Running:
return
elif self.__state == OWMDS.Finished:
# Resume/continue from a previous run
self.__start()
elif self.__state == OWMDS.Waiting and \
self.effective_matrix is not None:
self.__start()
def stop(self):
if self.__state == OWMDS.Running:
self.__set_update_loop(None)
def __start(self):
self.graph.pause_drawing_pairs()
X = self.effective_matrix
init = self.embedding
# number of iterations per single GUI update step
_, step_size = OWMDS.RefreshRate[self.refresh_rate]
if step_size == -1:
step_size = self.max_iter
def update_loop(X, max_iter, step, init):
"""
return an iterator over successive improved MDS point embeddings.
"""
# NOTE: this code MUST NOT call into QApplication.processEvents
done = False
iterations_done = 0
oldstress = np.finfo(np.float).max
init_type = "PCA" if self.initialization == OWMDS.PCA else "random"
while not done:
step_iter = min(max_iter - iterations_done, step)
mds = MDS(dissimilarity="precomputed",
n_components=2,
n_init=1,
max_iter=step_iter,
init_type=init_type,
init_data=init)
mdsfit = mds(X)
iterations_done += step_iter
embedding, stress = mdsfit.embedding_, mdsfit.stress_
stress /= np.sqrt(np.sum(embedding**2, axis=1)).sum()
if iterations_done >= max_iter:
done = True
elif (oldstress - stress) < mds.params["eps"]:
done = True
init = embedding
oldstress = stress
yield embedding, mdsfit.stress_, iterations_done / max_iter
self.__set_update_loop(update_loop(X, self.max_iter, step_size, init))
self.progressBarInit(processEvents=None)
def __set_update_loop(self, loop):
"""
Set the update `loop` coroutine.
The `loop` is a generator yielding `(embedding, stress, progress)`
tuples where `embedding` is a `(N, 2) ndarray` of current updated
MDS points, `stress` is the current stress and `progress` a float
ratio (0 <= progress <= 1)
If an existing update coroutine loop is already in place it is
interrupted (i.e. closed).
.. note::
The `loop` must not explicitly yield control flow to the event
loop (i.e. call `QApplication.processEvents`)
"""
if self.__update_loop is not None:
self.__update_loop.close()
self.__update_loop = None
self.progressBarFinished(processEvents=None)
self.__update_loop = loop
if loop is not None:
self.setBlocking(True)
self.progressBarInit(processEvents=None)
self.setStatusMessage("Running")
self.runbutton.setText("Stop")
self.__state = OWMDS.Running
self.__timer.start()
else:
self.setBlocking(False)
self.setStatusMessage("")
self.runbutton.setText("Start")
self.__state = OWMDS.Finished
self.__timer.stop()
def __next_step(self):
if self.__update_loop is None:
return
assert not self.__in_next_step
self.__in_next_step = True
loop = self.__update_loop
self.Error.out_of_memory.clear()
try:
embedding, _, progress = next(self.__update_loop)
assert self.__update_loop is loop
except StopIteration:
self.__set_update_loop(None)
self.unconditional_commit()
self.graph.resume_drawing_pairs()
except MemoryError:
self.Error.out_of_memory()
self.__set_update_loop(None)
self.graph.resume_drawing_pairs()
except Exception as exc:
self.Error.optimization_error(str(exc))
self.__set_update_loop(None)
self.graph.resume_drawing_pairs()
else:
self.progressBarSet(100.0 * progress, processEvents=None)
self.embedding = embedding
self.graph.update_coordinates()
# schedule next update
self.__timer.start()
self.__in_next_step = False
def do_PCA(self):
self.__invalidate_embedding(self.PCA)
def do_random(self):
self.__invalidate_embedding(self.Random)
def do_jitter(self):
self.__invalidate_embedding(self.Jitter)
def __invalidate_embedding(self, initialization=PCA):
def jitter_coord(part):
span = np.max(part) - np.min(part)
part += np.random.uniform(-span / 20, span / 20, len(part))
# reset/invalidate the MDS embedding, to the default initialization
# (Random or PCA), restarting the optimization if necessary.
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
if self.effective_matrix is None:
self.graph.reset_graph()
return
X = self.effective_matrix
if initialization == OWMDS.PCA:
self.embedding = torgerson(X)
elif initialization == OWMDS.Random:
self.embedding = np.random.rand(len(X), 2)
else:
jitter_coord(self.embedding[:, 0])
jitter_coord(self.embedding[:, 1])
self.setup_plot()
# restart the optimization if it was interrupted.
if state == OWMDS.Running:
self.__start()
def __invalidate_refresh(self):
state = self.__state
if self.__update_loop is not None:
self.__set_update_loop(None)
# restart the optimization if it was interrupted.
# TODO: decrease the max iteration count by the already
# completed iterations count.
if state == OWMDS.Running:
self.__start()
def handleNewSignals(self):
self._initialize()
if self.__invalidated:
self.graph.pause_drawing_pairs()
self.__invalidated = False
self.__invalidate_embedding()
self.cb_class_density.setEnabled(self.can_draw_density())
self.start()
else:
self.graph.update_point_props()
self.commit()
def _invalidate_output(self):
self.commit()
def _on_connected_changed(self):
self.graph.set_effective_matrix(self.effective_matrix)
self.graph.update_pairs(reconnect=True)
def setup_plot(self):
super().setup_plot()
if self.embedding is not None:
self.graph.update_pairs(reconnect=True)
def get_size_data(self):
if self.attr_size == "Stress":
return stress(self.embedding, self.effective_matrix)
else:
return super().get_size_data()
def get_embedding(self):
self.valid_data = np.ones(len(self.embedding), dtype=bool) \
if self.embedding is not None else None
return self.embedding
def _get_projection_data(self):
if self.embedding is None:
return None
if self.data is None:
x_name, y_name = self.embedding_variables_names
variables = ContinuousVariable(x_name), ContinuousVariable(y_name)
return Table(Domain(variables), self.embedding)
return super()._get_projection_data()
@classmethod
def migrate_settings(cls, settings_, version):
if version < 2:
settings_graph = {}
for old, new in (("label_only_selected", "label_only_selected"),
("symbol_opacity", "alpha_value"),
("symbol_size", "point_width"), ("jitter",
"jitter_size")):
settings_graph[new] = settings_[old]
settings_["graph"] = settings_graph
settings_["auto_commit"] = settings_["autocommit"]
if version < 3:
if "connected_pairs" in settings_:
connected_pairs = settings_["connected_pairs"]
settings_["graph"]["connected_pairs"] = connected_pairs
@classmethod
def migrate_context(cls, context, version):
if version < 2:
domain = context.ordered_domain
n_domain = [t for t in context.ordered_domain if t[1] == 2]
c_domain = [t for t in context.ordered_domain if t[1] == 1]
context_values = {}
for _, old_val, new_val in ((domain, "color_value", "attr_color"),
(c_domain, "shape_value",
"attr_shape"),
(n_domain, "size_value", "attr_size"),
(domain, "label_value", "attr_label")):
tmp = context.values[old_val]
if tmp[1] >= 0:
context_values[new_val] = (tmp[0], tmp[1] + 100)
elif tmp[0] != "Stress":
context_values[new_val] = None
else:
context_values[new_val] = tmp
context.values = context_values
if version < 3 and "graph" in context.values:
values = context.values
values["attr_color"] = values["graph"]["attr_color"]
values["attr_size"] = values["graph"]["attr_size"]
values["attr_shape"] = values["graph"]["attr_shape"]
values["attr_label"] = values["graph"]["attr_label"]