class OWFreeViz(OWAnchorProjectionWidget, ConcurrentWidgetMixin):
MAX_INSTANCES = 10000
name = "FreeViz"
description = "Displays FreeViz projection"
icon = "icons/Freeviz.svg"
priority = 240
keywords = ["viz"]
settings_version = 3
initialization = settings.Setting(InitType.Circular)
GRAPH_CLASS = OWFreeVizGraph
graph = settings.SettingProvider(OWFreeVizGraph)
class Error(OWAnchorProjectionWidget.Error):
no_class_var = widget.Msg("Data must have a target variable.")
multiple_class_vars = widget.Msg(
"Data must have a single target variable.")
not_enough_class_vars = widget.Msg(
"Target variable must have at least two unique values.")
features_exceeds_instances = widget.Msg(
"Number of features exceeds the number of instances.")
too_many_data_instances = widget.Msg("Data is too large.")
constant_data = widget.Msg("All data columns are constant.")
not_enough_features = widget.Msg("At least two features are required.")
class Warning(OWAnchorProjectionWidget.Warning):
removed_features = widget.Msg("Categorical features with more than"
" two values are not shown.")
def __init__(self):
OWAnchorProjectionWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
def _add_controls(self):
self.__add_controls_start_box()
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)
def __add_controls_start_box(self):
box = gui.vBox(self.controlArea, box="Optimize", spacing=0)
gui.comboBox(box,
self,
"initialization",
label="Initialization:",
items=InitType.items(),
orientation=Qt.Horizontal,
labelWidth=90,
callback=self.__init_combo_changed)
self.run_button = gui.button(box, self, "Start", self._toggle_run)
@property
def effective_variables(self):
return [
a for a in self.data.domain.attributes
if a.is_continuous or a.is_discrete and len(a.values) == 2
]
def __radius_slider_changed(self):
self.graph.update_radius()
def __init_combo_changed(self):
self.Error.proj_error.clear()
self.init_projection()
self.setup_plot()
self.commit.deferred()
if self.task is not None:
self._run()
def _toggle_run(self):
if self.task is not None:
self.cancel()
self.graph.set_sample_size(None)
self.run_button.setText("Resume")
self.commit.deferred()
else:
self._run()
def _run(self):
if self.data is None:
return
self.graph.set_sample_size(self.SAMPLE_SIZE)
self.run_button.setText("Stop")
self.start(run_freeviz, self.effective_data, self.projector)
# ConcurrentWidgetMixin
def on_partial_result(self, result: Result):
assert isinstance(result.projector, FreeViz)
assert isinstance(result.projection, FreeVizModel)
self.projector = result.projector
self.projection = result.projection
self.graph.update_coordinates()
self.graph.update_density()
def on_done(self, result: Result):
assert isinstance(result.projector, FreeViz)
assert isinstance(result.projection, FreeVizModel)
self.projector = result.projector
self.projection = result.projection
self.graph.set_sample_size(None)
self.run_button.setText("Start")
self.commit.deferred()
def on_exception(self, ex: Exception):
self.Error.proj_error(ex)
self.graph.set_sample_size(None)
self.run_button.setText("Start")
# OWAnchorProjectionWidget
def set_data(self, data):
super().set_data(data)
self.graph.set_sample_size(None)
if self._invalidated:
self.init_projection()
def init_projection(self):
if self.data is None:
return
anchors = FreeViz.init_radial(len(self.effective_variables)) \
if self.initialization == InitType.Circular \
else FreeViz.init_random(len(self.effective_variables), 2)
self.projector = FreeViz(scale=False,
center=False,
initial=anchors,
maxiter=10)
data = self.projector.preprocess(self.effective_data)
self.projector.domain = data.domain
self.projector.components_ = anchors.T
self.projection = FreeVizModel(self.projector, self.projector.domain,
2)
self.projection.pre_domain = data.domain
self.projection.name = self.projector.name
def check_data(self):
def error(err):
err()
self.data = None
super().check_data()
if self.data is not None:
class_vars, domain = self.data.domain.class_vars, self.data.domain
if not class_vars:
error(self.Error.no_class_var)
elif len(class_vars) > 1:
error(self.Error.multiple_class_vars)
elif class_vars[0].is_discrete and len(np.unique(self.data.Y)) < 2:
error(self.Error.not_enough_class_vars)
elif len(self.data.domain.attributes) < 2:
error(self.Error.not_enough_features)
elif len(self.data.domain.attributes) > self.data.X.shape[0]:
error(self.Error.features_exceeds_instances)
elif not np.sum(np.std(self.data.X, axis=0)):
error(self.Error.constant_data)
elif np.sum(np.all(np.isfinite(self.data.X),
axis=1)) > self.MAX_INSTANCES:
error(self.Error.too_many_data_instances)
else:
if len(self.effective_variables) < len(domain.attributes):
self.Warning.removed_features()
def enable_controls(self):
super().enable_controls()
self.run_button.setEnabled(self.data is not None)
self.run_button.setText("Start")
def get_coordinates_data(self):
embedding = self.get_embedding()
if embedding is None:
return None, None
valid_emb = embedding[self.valid_data]
return valid_emb.T / (np.max(np.linalg.norm(valid_emb, axis=1)) or 1)
def _manual_move(self, anchor_idx, x, y):
self.projector.initial[anchor_idx] = [x, y]
super()._manual_move(anchor_idx, x, y)
def clear(self):
super().clear()
self.cancel()
def onDeleteWidget(self):
self.shutdown()
super().onDeleteWidget()
@classmethod
def migrate_settings(cls, _settings, version):
if version < 3:
if "radius" in _settings:
_settings["graph"]["hide_radius"] = _settings["radius"]
@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 OWFreeViz(OWAnchorProjectionWidget):
MAX_ITERATIONS = 1000
MAX_INSTANCES = 10000
name = "FreeViz"
description = "Displays FreeViz projection"
icon = "icons/Freeviz.svg"
priority = 240
keywords = ["viz"]
settings_version = 3
initialization = settings.Setting(InitType.Circular)
GRAPH_CLASS = OWFreeVizGraph
graph = settings.SettingProvider(OWFreeVizGraph)
class Error(OWAnchorProjectionWidget.Error):
no_class_var = widget.Msg("Data has no target variable")
not_enough_class_vars = widget.Msg(
"Target variable is not at least binary")
features_exceeds_instances = widget.Msg(
"Number of features exceeds the number of instances.")
too_many_data_instances = widget.Msg("Data is too large.")
constant_data = widget.Msg("All data columns are constant.")
not_enough_features = widget.Msg("At least two features are required")
class Warning(OWAnchorProjectionWidget.Warning):
removed_features = widget.Msg("Categorical features with more than"
" two values are not shown.")
def __init__(self):
super().__init__()
self._loop = AsyncUpdateLoop(parent=self)
self._loop.yielded.connect(self.__set_projection)
self._loop.finished.connect(self.__freeviz_finished)
self._loop.raised.connect(self.__on_error)
def _add_controls(self):
self.__add_controls_start_box()
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
)
def __add_controls_start_box(self):
box = gui.vBox(self.controlArea, box=True)
gui.comboBox(
box, self, "initialization", label="Initialization:",
items=InitType.items(), orientation=Qt.Horizontal,
labelWidth=90, callback=self.__init_combo_changed)
self.btn_start = gui.button(
box, self, "Optimize", self.__toggle_start, enabled=False)
@property
def effective_variables(self):
return [a for a in self.data.domain.attributes
if a.is_continuous or a.is_discrete and len(a.values) == 2]
def __radius_slider_changed(self):
self.graph.update_radius()
def __toggle_start(self):
if self._loop.isRunning():
self._loop.cancel()
self.btn_start.setText("Optimize")
self.progressBarFinished(processEvents=False)
else:
self._start()
def __init_combo_changed(self):
if self.data is None:
return
running = self._loop.isRunning()
if running:
self._loop.cancel()
self.init_projection()
self.graph.update_coordinates()
self.commit()
if running:
self._start()
def _start(self):
def update_freeviz(anchors):
while True:
self.projection = self.projector(self.effective_data)
_anchors = self.projector.components_.T
self.projector.initial = _anchors
yield _anchors
if np.allclose(anchors, _anchors, rtol=1e-5, atol=1e-4):
return
anchors = _anchors
self.graph.set_sample_size(self.SAMPLE_SIZE)
self._loop.setCoroutine(update_freeviz(self.projector.components_.T))
self.btn_start.setText("Stop")
self.progressBarInit()
self.setBlocking(True)
self.setStatusMessage("Optimizing")
def __set_projection(self, _):
# Set/update the projection matrix and coordinate embeddings
self.progressBarAdvance(100. / self.MAX_ITERATIONS)
self.graph.update_coordinates()
def __freeviz_finished(self):
self.graph.set_sample_size(None)
self.btn_start.setText("Optimize")
self.setStatusMessage("")
self.setBlocking(False)
self.progressBarFinished()
self.commit()
def __on_error(self, err):
sys.excepthook(type(err), err, getattr(err, "__traceback__"))
def check_data(self):
def error(err):
err()
self.data = None
super().check_data()
if self.data is not None:
class_var, domain = self.data.domain.class_var, self.data.domain
if class_var is None:
error(self.Error.no_class_var)
elif class_var.is_discrete and len(np.unique(self.data.Y)) < 2:
error(self.Error.not_enough_class_vars)
elif len(self.data.domain.attributes) < 2:
error(self.Error.not_enough_features)
elif len(self.data.domain.attributes) > self.data.X.shape[0]:
error(self.Error.features_exceeds_instances)
elif not np.sum(np.std(self.data.X, axis=0)):
error(self.Error.constant_data)
elif np.sum(self.valid_data) > self.MAX_INSTANCES:
error(self.Error.too_many_data_instances)
else:
if len(self.effective_variables) < len(domain.attributes):
self.Warning.removed_features()
self.btn_start.setEnabled(self.data is not None)
def set_data(self, data):
super().set_data(data)
if self.data is not None:
self.init_projection()
def init_projection(self):
anchors = FreeViz.init_radial(len(self.effective_variables)) \
if self.initialization == InitType.Circular \
else FreeViz.init_random(len(self.effective_variables), 2)
self.projector = FreeViz(scale=False, center=False,
initial=anchors, maxiter=10)
data = self.projector.preprocess(self.effective_data)
self.projector.domain = data.domain
self.projector.components_ = anchors.T
self.projection = FreeVizModel(self.projector, self.projector.domain, 2)
self.projection.pre_domain = data.domain
self.projection.name = self.projector.name
def get_coordinates_data(self):
embedding = self.get_embedding()
if embedding is None:
return None, None
valid_emb = embedding[self.valid_data]
return valid_emb.T / (np.max(np.linalg.norm(valid_emb, axis=1)) or 1)
def _manual_move(self, anchor_idx, x, y):
self.projector.initial[anchor_idx] = [x, y]
super()._manual_move(anchor_idx, x, y)
def clear(self):
super().clear()
self._loop.cancel()
@classmethod
def migrate_settings(cls, _settings, version):
if version < 3:
if "radius" in _settings:
_settings["graph"]["hide_radius"] = _settings["radius"]
@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 OWFreeViz(OWAnchorProjectionWidget):
MAX_ITERATIONS = 1000
MAX_INSTANCES = 10000
name = "FreeViz"
description = "Displays FreeViz projection"
icon = "icons/Freeviz.svg"
priority = 240
keywords = ["viz"]
settings_version = 3
initialization = settings.Setting(InitType.Circular)
GRAPH_CLASS = OWFreeVizGraph
graph = settings.SettingProvider(OWFreeVizGraph)
class Error(OWAnchorProjectionWidget.Error):
no_class_var = widget.Msg("Data has no target variable")
not_enough_class_vars = widget.Msg(
"Target variable is not at least binary")
features_exceeds_instances = widget.Msg(
"Number of features exceeds the number of instances.")
too_many_data_instances = widget.Msg("Data is too large.")
constant_data = widget.Msg("All data columns are constant.")
not_enough_features = widget.Msg("At least two features are required")
class Warning(OWAnchorProjectionWidget.Warning):
removed_features = widget.Msg("Categorical features with more than"
" two values are not shown.")
def __init__(self):
super().__init__()
self._loop = AsyncUpdateLoop(parent=self)
self._loop.yielded.connect(self.__set_projection)
self._loop.finished.connect(self.__freeviz_finished)
self._loop.raised.connect(self.__on_error)
def _add_controls(self):
self.__add_controls_start_box()
super()._add_controls()
self.graph.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)
def __add_controls_start_box(self):
box = gui.vBox(self.controlArea, box=True)
gui.comboBox(box,
self,
"initialization",
label="Initialization:",
items=InitType.items(),
orientation=Qt.Horizontal,
labelWidth=90,
callback=self.__init_combo_changed)
self.btn_start = gui.button(box,
self,
"Optimize",
self.__toggle_start,
enabled=False)
@property
def effective_variables(self):
return [
a for a in self.data.domain.attributes
if a.is_continuous or a.is_discrete and len(a.values) == 2
]
def __radius_slider_changed(self):
self.graph.update_radius()
def __toggle_start(self):
if self._loop.isRunning():
self._loop.cancel()
self.btn_start.setText("Optimize")
self.progressBarFinished(processEvents=False)
else:
self._start()
def __init_combo_changed(self):
if self.data is None:
return
running = self._loop.isRunning()
if running:
self._loop.cancel()
self.init_projection()
self.graph.update_coordinates()
self.commit()
if running:
self._start()
def _start(self):
def update_freeviz(anchors):
while True:
self.projection = self.projector(self.effective_data)
_anchors = self.projector.components_.T
self.projector.initial = _anchors
yield _anchors
if np.allclose(anchors, _anchors, rtol=1e-5, atol=1e-4):
return
anchors = _anchors
self.graph.set_sample_size(self.SAMPLE_SIZE)
self._loop.setCoroutine(update_freeviz(self.projector.components_.T))
self.btn_start.setText("Stop")
self.progressBarInit()
self.setBlocking(True)
self.setStatusMessage("Optimizing")
def __set_projection(self, _):
# Set/update the projection matrix and coordinate embeddings
self.progressBarAdvance(100. / self.MAX_ITERATIONS)
self.graph.update_coordinates()
def __freeviz_finished(self):
self.graph.set_sample_size(None)
self.btn_start.setText("Optimize")
self.setStatusMessage("")
self.setBlocking(False)
self.progressBarFinished()
self.commit()
def __on_error(self, err):
sys.excepthook(type(err), err, getattr(err, "__traceback__"))
def check_data(self):
def error(err):
err()
self.data = None
super().check_data()
if self.data is not None:
class_var, domain = self.data.domain.class_var, self.data.domain
if class_var is None:
error(self.Error.no_class_var)
elif class_var.is_discrete and len(np.unique(self.data.Y)) < 2:
error(self.Error.not_enough_class_vars)
elif len(self.data.domain.attributes) < 2:
error(self.Error.not_enough_features)
elif len(self.data.domain.attributes) > self.data.X.shape[0]:
error(self.Error.features_exceeds_instances)
elif not np.sum(np.std(self.data.X, axis=0)):
error(self.Error.constant_data)
elif np.sum(self.valid_data) > self.MAX_INSTANCES:
error(self.Error.too_many_data_instances)
else:
if len(self.effective_variables) < len(domain.attributes):
self.Warning.removed_features()
self.btn_start.setEnabled(self.data is not None)
def set_data(self, data):
super().set_data(data)
if self.data is not None:
self.init_projection()
def init_projection(self):
anchors = FreeViz.init_radial(len(self.effective_variables)) \
if self.initialization == InitType.Circular \
else FreeViz.init_random(len(self.effective_variables), 2)
self.projector = FreeViz(scale=False,
center=False,
initial=anchors,
maxiter=10)
data = self.projector.preprocess(self.effective_data)
self.projector.domain = data.domain
self.projector.components_ = anchors.T
self.projection = FreeVizModel(self.projector, self.projector.domain)
self.projection.pre_domain = data.domain
self.projection.name = self.projector.name
def get_coordinates_data(self):
embedding = self.get_embedding()
if embedding is None:
return None, None
valid_emb = embedding[self.valid_data]
return valid_emb.T / (np.max(np.linalg.norm(valid_emb, axis=1)) or 1)
def _manual_move(self, anchor_idx, x, y):
self.projector.initial[anchor_idx] = [x, y]
super()._manual_move(anchor_idx, x, y)
def clear(self):
super().clear()
self._loop.cancel()
@classmethod
def migrate_settings(cls, _settings, version):
if version < 3:
if "radius" in _settings:
_settings["graph"]["hide_radius"] = _settings["radius"]
@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 OWFreeViz(OWAnchorProjectionWidget, ConcurrentWidgetMixin):
MAX_INSTANCES = 10000
name = "FreeViz"
description = "Displays FreeViz projection"
icon = "icons/Freeviz.svg"
priority = 240
keywords = ["viz"]
settings_version = 3
initialization = settings.Setting(InitType.Circular)
GRAPH_CLASS = OWFreeVizGraph
graph = settings.SettingProvider(OWFreeVizGraph)
left_side_scrolling = True
class Error(OWAnchorProjectionWidget.Error):
no_class_var = widget.Msg("Data has no target variable")
not_enough_class_vars = widget.Msg(
"Target variable is not at least binary")
features_exceeds_instances = widget.Msg(
"Number of features exceeds the number of instances.")
too_many_data_instances = widget.Msg("Data is too large.")
constant_data = widget.Msg("All data columns are constant.")
not_enough_features = widget.Msg("At least two features are required")
class Warning(OWAnchorProjectionWidget.Warning):
removed_features = widget.Msg("Categorical features with more than"
" two values are not shown.")
def __init__(self):
OWAnchorProjectionWidget.__init__(self)
ConcurrentWidgetMixin.__init__(self)
def _add_controls(self):
self.__add_controls_start_box()
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
)
def __add_controls_start_box(self):
box = gui.vBox(self.controlArea, box=True)
gui.comboBox(
box, self, "initialization", label="Initialization:",
items=InitType.items(), orientation=Qt.Horizontal,
labelWidth=90, callback=self.__init_combo_changed)
self.run_button = gui.button(box, self, "Start", self._toggle_run)
@property
def effective_variables(self):
return [a for a in self.data.domain.attributes
if a.is_continuous or a.is_discrete and len(a.values) == 2]
def __radius_slider_changed(self):
self.graph.update_radius()
def __init_combo_changed(self):
self.Error.proj_error.clear()
self.init_projection()
self.setup_plot()
self.commit()
if self.task is not None:
self._run()
def _toggle_run(self):
if self.task is not None:
self.cancel()
self.graph.set_sample_size(None)
self.run_button.setText("Resume")
self.commit()
else:
self._run()
def _run(self):
if self.data is None:
return
self.graph.set_sample_size(self.SAMPLE_SIZE)
self.run_button.setText("Stop")
self.start(run_freeviz, self.effective_data, self.projector)
# ConcurrentWidgetMixin
def on_partial_result(self, result: Result):
assert isinstance(result.projector, FreeViz)
assert isinstance(result.projection, FreeVizModel)
self.projector = result.projector
self.projection = result.projection
self.graph.update_coordinates()
self.graph.update_density()
def on_done(self, result: Result):
assert isinstance(result.projector, FreeViz)
assert isinstance(result.projection, FreeVizModel)
self.projector = result.projector
self.projection = result.projection
self.graph.set_sample_size(None)
self.run_button.setText("Start")
self.commit()
def on_exception(self, ex: Exception):
self.Error.proj_error(ex)
self.graph.set_sample_size(None)
self.run_button.setText("Start")
# OWAnchorProjectionWidget
def set_data(self, data):
super().set_data(data)
if self._invalidated:
self.init_projection()
def init_projection(self):
if self.data is None:
return
anchors = FreeViz.init_radial(len(self.effective_variables)) \
if self.initialization == InitType.Circular \
else FreeViz.init_random(len(self.effective_variables), 2)
self.projector = FreeViz(scale=False, center=False,
initial=anchors, maxiter=10)
data = self.projector.preprocess(self.effective_data)
self.projector.domain = data.domain
self.projector.components_ = anchors.T
self.projection = FreeVizModel(self.projector, self.projector.domain, 2)
self.projection.pre_domain = data.domain
self.projection.name = self.projector.name
def check_data(self):
def error(err):
err()
self.data = None
super().check_data()
if self.data is not None:
class_var, domain = self.data.domain.class_var, self.data.domain
if class_var is None:
error(self.Error.no_class_var)
elif class_var.is_discrete and len(np.unique(self.data.Y)) < 2:
error(self.Error.not_enough_class_vars)
elif len(self.data.domain.attributes) < 2:
error(self.Error.not_enough_features)
elif len(self.data.domain.attributes) > self.data.X.shape[0]:
error(self.Error.features_exceeds_instances)
elif not np.sum(np.std(self.data.X, axis=0)):
error(self.Error.constant_data)
elif np.sum(np.all(np.isfinite(self.data.X), axis=1)) > self.MAX_INSTANCES:
error(self.Error.too_many_data_instances)
else:
if len(self.effective_variables) < len(domain.attributes):
self.Warning.removed_features()
def enable_controls(self):
super().enable_controls()
self.run_button.setEnabled(self.data is not None)
self.run_button.setText("Start")
def get_coordinates_data(self):
embedding = self.get_embedding()
if embedding is None:
return None, None
valid_emb = embedding[self.valid_data]
return valid_emb.T / (np.max(np.linalg.norm(valid_emb, axis=1)) or 1)
def _manual_move(self, anchor_idx, x, y):
self.projector.initial[anchor_idx] = [x, y]
super()._manual_move(anchor_idx, x, y)
def clear(self):
super().clear()
self.cancel()
def onDeleteWidget(self):
self.shutdown()
super().onDeleteWidget()
@classmethod
def migrate_settings(cls, _settings, version):
if version < 3:
if "radius" in _settings:
_settings["graph"]["hide_radius"] = _settings["radius"]
@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"]