def __init__(self, pixmap, title="", parent=None): QGraphicsWidget.__init__(self, parent) self._title = None self._size = QSizeF() layout = QGraphicsLinearLayout(Qt.Vertical, self) layout.setSpacing(2) layout.setContentsMargins(5, 5, 5, 5) self.setContentsMargins(0, 0, 0, 0) self.pixmapWidget = GraphicsPixmapWidget(pixmap, self) self.labelWidget = GraphicsTextWidget(title, self) layout.addItem(self.pixmapWidget) layout.addItem(self.labelWidget) layout.setAlignment(self.pixmapWidget, Qt.AlignCenter) layout.setAlignment(self.labelWidget, Qt.AlignHCenter | Qt.AlignBottom) self.setLayout(layout) self.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding) self.setFlag(QGraphicsItem.ItemIsSelectable, True) self.setTitle(title) self.setTitleWidth(100)
def __init__(self, pixmap, title="", parentItem=None, **kwargs): super().__init__(parentItem, **kwargs) self.setFocusPolicy(Qt.StrongFocus) self._title = None self._size = QSizeF() layout = QGraphicsLinearLayout(Qt.Vertical, self) layout.setSpacing(2) layout.setContentsMargins(5, 5, 5, 5) self.setContentsMargins(0, 0, 0, 0) self.pixmapWidget = GraphicsPixmapWidget(pixmap, self) self.labelWidget = GraphicsTextWidget(title, self) layout.addItem(self.pixmapWidget) layout.addItem(self.labelWidget) layout.addStretch() layout.setAlignment(self.pixmapWidget, Qt.AlignCenter) layout.setAlignment(self.labelWidget, Qt.AlignHCenter | Qt.AlignBottom) self.setLayout(layout) self.setSizePolicy(QSizePolicy.Minimum, QSizePolicy.Minimum) self.setFlag(QGraphicsItem.ItemIsSelectable, True) self.setTitle(title) self.setTitleWidth(100)
class OWHierarchicalClustering(widget.OWWidget): name = "Hierarchical Clustering" description = ("Hierarchical clustering based on distance matrix, and " "a dendrogram viewer.") icon = "icons/HierarchicalClustering.svg" priority = 2100 inputs = [("Distances", Orange.misc.DistMatrix, "set_distances")] outputs = [("Selected Data", Orange.data.Table), ("Other Data", Orange.data.Table)] #: Selected linkage linkage = settings.Setting(1) #: Index of the selected annotation item (variable, ...) annotation_idx = settings.Setting(0) #: Selected tree pruning (none/max depth) pruning = settings.Setting(0) #: Maximum depth when max depth pruning is selected max_depth = settings.Setting(10) #: Selected cluster selection method (none, cut distance, top n) selection_method = settings.Setting(0) #: Cut height ratio wrt root height cut_ratio = settings.Setting(75.0) #: Number of top clusters to select top_n = settings.Setting(3) append_clusters = settings.Setting(True) cluster_role = settings.Setting(2) cluster_name = settings.Setting("Cluster") autocommit = settings.Setting(False) #: Cluster variable domain role AttributeRole, ClassRole, MetaRole = 0, 1, 2 def __init__(self, parent=None): super().__init__(parent) self.matrix = None self.items = None self.linkmatrix = None self.root = None self._displayed_root = None self.cutoff_height = 0.0 self._invalidated = False gui.comboBox(gui.widgetBox(self.controlArea, "Linkage"), self, "linkage", items=LINKAGE, callback=self._invalidate_clustering) box = gui.widgetBox(self.controlArea, "Annotation") self.label_cb = gui.comboBox(box, self, "annotation_idx", callback=self._update_labels) self.label_cb.setModel(itemmodels.VariableListModel()) self.label_cb.model()[:] = ["None", "Enumeration"] box = gui.radioButtons(self.controlArea, self, "pruning", box="Pruning", callback=self._invalidate_pruning) grid = QGridLayout() box.layout().addLayout(grid) grid.addWidget(gui.appendRadioButton(box, "None", addToLayout=False), 0, 0) self.max_depth_spin = gui.spin(box, self, "max_depth", minv=1, maxv=100, callback=self._invalidate_pruning, keyboardTracking=False) grid.addWidget( gui.appendRadioButton(box, "Max depth", addToLayout=False), 1, 0) grid.addWidget(self.max_depth_spin, 1, 1) box = gui.radioButtons(self.controlArea, self, "selection_method", box="Selection", callback=self._selection_method_changed) grid = QGridLayout() box.layout().addLayout(grid) grid.addWidget(gui.appendRadioButton(box, "Manual", addToLayout=False), 0, 0) grid.addWidget( gui.appendRadioButton(box, "Height ratio", addToLayout=False), 1, 0) self.cut_ratio_spin = gui.spin(box, self, "cut_ratio", 0, 100, step=1e-1, spinType=float, callback=self._selection_method_changed) self.cut_ratio_spin.setSuffix("%") grid.addWidget(self.cut_ratio_spin, 1, 1) grid.addWidget(gui.appendRadioButton(box, "Top N", addToLayout=False), 2, 0) self.top_n_spin = gui.spin(box, self, "top_n", 1, 20, callback=self._selection_method_changed) grid.addWidget(self.top_n_spin, 2, 1) box.layout().addLayout(grid) self.controlArea.layout().addStretch() box = gui.widgetBox(self.controlArea, "Output") gui.checkBox(box, self, "append_clusters", "Append cluster IDs", callback=self._invalidate_output) ibox = gui.indentedBox(box) name_edit = gui.lineEdit(ibox, self, "cluster_name") name_edit.editingFinished.connect(self._invalidate_output) cb = gui.comboBox( ibox, self, "cluster_role", callback=self._invalidate_output, items=["Attribute", "Class variable", "Meta variable"]) form = QFormLayout(fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow, labelAlignment=Qt.AlignLeft, spacing=8) form.addRow("Name", name_edit) form.addRow("Place", cb) ibox.layout().addSpacing(5) ibox.layout().addLayout(form) ibox.layout().addSpacing(5) cb = gui.checkBox(box, self, "autocommit", "Commit automatically") b = gui.button(box, self, "Commit", callback=self.commit, default=True) gui.setStopper(self, b, cb, "_invalidated", callback=self.commit) self.scene = QGraphicsScene() self.view = QGraphicsView( self.scene, horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff, verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn, alignment=Qt.AlignLeft | Qt.AlignVCenter) def axis_view(orientation): ax = pg.AxisItem(orientation=orientation, maxTickLength=7) scene = QGraphicsScene() scene.addItem(ax) view = QGraphicsView( scene, horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff, verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn, alignment=Qt.AlignLeft | Qt.AlignVCenter) view.setFixedHeight(ax.size().height()) ax.line = SliderLine(orientation=Qt.Horizontal, length=ax.size().height()) scene.addItem(ax.line) return view, ax self.top_axis_view, self.top_axis = axis_view("top") self.mainArea.layout().setSpacing(1) self.mainArea.layout().addWidget(self.top_axis_view) self.mainArea.layout().addWidget(self.view) self.bottom_axis_view, self.bottom_axis = axis_view("bottom") self.mainArea.layout().addWidget(self.bottom_axis_view) self._main_graphics = QGraphicsWidget() self._main_layout = QGraphicsLinearLayout(Qt.Horizontal) self._main_layout.setSpacing(1) self._main_graphics.setLayout(self._main_layout) self.scene.addItem(self._main_graphics) self.dendrogram = DendrogramWidget() self.dendrogram.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding) self.dendrogram.selectionChanged.connect(self._invalidate_output) self.dendrogram.selectionEdited.connect(self._selection_edited) fm = self.fontMetrics() self.dendrogram.setContentsMargins(5, fm.lineSpacing() / 2, 5, fm.lineSpacing() / 2) self.labels = GraphicsSimpleTextList() self.labels.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Preferred) self.labels.setAlignment(Qt.AlignLeft) self.labels.setMaximumWidth(200) self.labels.layout().setSpacing(0) self._main_layout.addItem(self.dendrogram) self._main_layout.addItem(self.labels) self._main_layout.setAlignment(self.dendrogram, Qt.AlignLeft | Qt.AlignVCenter) self._main_layout.setAlignment(self.labels, Qt.AlignLeft | Qt.AlignVCenter) self.view.viewport().installEventFilter(self) self.top_axis_view.viewport().installEventFilter(self) self.bottom_axis_view.viewport().installEventFilter(self) self._main_graphics.installEventFilter(self) self.cut_line = SliderLine(self.dendrogram, orientation=Qt.Horizontal) self.cut_line.valueChanged.connect(self._dendrogram_slider_changed) self.cut_line.hide() self.bottom_axis.line.valueChanged.connect(self._axis_slider_changed) self.top_axis.line.valueChanged.connect(self._axis_slider_changed) self.dendrogram.geometryChanged.connect(self._dendrogram_geom_changed) self._set_cut_line_visible(self.selection_method == 1) def set_distances(self, matrix): self.matrix = matrix self._invalidate_clustering() self._set_items(matrix.row_items if matrix is not None else None) def _set_items(self, items): self.items = items if items is None: self.label_cb.model()[:] = ["None", "Enumeration"] elif isinstance(items, Orange.data.Table): vars = list(items.domain) self.label_cb.model()[:] = ["None", "Enumeration"] + vars elif isinstance(items, list) and \ all(isinstance(var, Orange.data.Variable) for var in items): self.label_cb.model()[:] = ["None", "Enumeration", "Name"] else: self.label_cb.model()[:] = ["None", "Enumeration"] self.annotation_idx = min(self.annotation_idx, len(self.label_cb.model()) - 1) def handleNewSignals(self): self._update_labels() def _clear_plot(self): self.labels.set_labels([]) self.dendrogram.set_root(None) def _set_displayed_root(self, root): self._clear_plot() self._displayed_root = root self.dendrogram.set_root(root) self._update_labels() self._main_graphics.resize( self._main_graphics.size().width(), self._main_graphics.sizeHint(Qt.PreferredSize).height()) self._main_graphics.layout().activate() def _update(self): self._clear_plot() distances = self.matrix if distances is not None: # Convert to flat upper triangular distances i, j = numpy.triu_indices(distances.X.shape[0], k=1) distances = distances.X[i, j] method = LINKAGE[self.linkage].lower() Z = scipy.cluster.hierarchy.linkage(distances, method=method) tree = tree_from_linkage(Z) self.linkmatrix = Z self.root = tree self.top_axis.setRange(tree.value.height, 0.0) self.bottom_axis.setRange(tree.value.height, 0.0) if self.pruning: self._set_displayed_root(prune(tree, level=self.max_depth)) else: self._set_displayed_root(tree) else: self.linkmatrix = None self.root = None self._set_displayed_root(None) self._apply_selection() def _update_labels(self): labels = [] if self.root and self._displayed_root: indices = [leaf.value.index for leaf in leaves(self.root)] if self.annotation_idx == 0: labels = [] elif self.annotation_idx == 1: labels = [str(i) for i in indices] elif isinstance(self.items, Orange.data.Table): var = self.label_cb.model()[self.annotation_idx] col = self.items[:, var] labels = [var.repr_val(next(iter(row))) for row in col] labels = [labels[idx] for idx in indices] else: labels = [] if labels and self._displayed_root is not self.root: joined = leaves(self._displayed_root) labels = [ ", ".join(labels[leaf.value.first:leaf.value.last]) for leaf in joined ] self.labels.set_labels(labels) self.labels.setMinimumWidth(1 if labels else -1) def _invalidate_clustering(self): self._update() self._update_labels() def _invalidate_output(self): self._invalidated = True if self.autocommit: self.commit() def _invalidate_pruning(self): if self.root: selection = self.dendrogram.selected_nodes() ranges = [node.value.range for node in selection] if self.pruning: self._set_displayed_root(prune(self.root, level=self.max_depth)) else: self._set_displayed_root(self.root) selected = [ node for node in preorder(self._displayed_root) if node.value.range in ranges ] self.dendrogram.set_selected_clusters(selected) self._apply_selection() def commit(self): self._invalidated = False items = getattr(self.matrix, "items", self.items) if not items: # nothing to commit return selection = self.dendrogram.selected_nodes() selection = sorted(selection, key=lambda c: c.value.first) indices = [leaf.value.index for leaf in leaves(self.root)] maps = [ indices[node.value.first:node.value.last] for node in selection ] selected_indices = list(chain(*maps)) unselected_indices = sorted( set(range(self.root.value.last)) - set(selected_indices)) selected = [items[k] for k in selected_indices] unselected = [items[k] for k in unselected_indices] if not selected: self.send("Selected Data", None) self.send("Other Data", None) return selected_data = unselected_data = None if isinstance(items, Orange.data.Table): c = numpy.zeros(len(items)) for i, indices in enumerate(maps): c[indices] = i c[unselected_indices] = len(maps) mask = c != len(maps) if self.append_clusters: clust_var = Orange.data.DiscreteVariable( str(self.cluster_name), values=[ "Cluster {}".format(i + 1) for i in range(len(maps)) ] + ["Other"]) data, domain = items, items.domain attrs = domain.attributes class_ = domain.class_vars metas = domain.metas X, Y, M = data.X, data.Y, data.metas if self.cluster_role == self.AttributeRole: attrs = attrs + (clust_var, ) X = numpy.c_[X, c] elif self.cluster_role == self.ClassRole: class_ = class_ + (clust_var, ) Y = numpy.c_[Y, c] elif self.cluster_role == self.MetaRole: metas = metas + (clust_var, ) M = numpy.c_[M, c] domain = Orange.data.Domain(attrs, class_, metas) data = Orange.data.Table(domain, X, Y, M) else: data = items if selected: selected_data = data[mask] if unselected: unselected_data = data[~mask] self.send("Selected Data", selected_data) self.send("Other Data", unselected_data) def sizeHint(self): return QSize(800, 500) def eventFilter(self, obj, event): if obj is self.view.viewport() and event.type() == QEvent.Resize: width = self.view.viewport().width() - 2 self._main_graphics.setMaximumWidth(width) self._main_graphics.setMinimumWidth(width) self._main_graphics.layout().activate() elif event.type() == QEvent.MouseButtonPress and \ (obj is self.top_axis_view.viewport() or obj is self.bottom_axis_view.viewport()): self.selection_method = 1 # Map click point to cut line local coordinates pos = self.top_axis_view.mapToScene(event.pos()) cut = self.top_axis.line.mapFromScene(pos) self.top_axis.line.setValue(cut.x()) # update the line visibility, output, ... self._selection_method_changed() return super().eventFilter(obj, event) def _dendrogram_geom_changed(self): pos = self.dendrogram.pos_at_height(self.cutoff_height) geom = self.dendrogram.geometry() crect = self.dendrogram.contentsRect() self._set_slider_value(pos.x(), geom.width()) self.cut_line.setLength(geom.height()) self.top_axis.resize(crect.width(), self.top_axis.height()) self.top_axis.setPos(geom.left() + crect.left(), 0) self.top_axis.line.setPos(self.cut_line.scenePos().x(), 0) self.bottom_axis.resize(crect.width(), self.bottom_axis.height()) self.bottom_axis.setPos(geom.left() + crect.left(), 0) self.bottom_axis.line.setPos(self.cut_line.scenePos().x(), 0) geom = self._main_graphics.geometry() assert geom.topLeft() == QPointF(0, 0) self.scene.setSceneRect(geom) geom.setHeight(self.top_axis.size().height()) self.top_axis.scene().setSceneRect(geom) self.bottom_axis.scene().setSceneRect(geom) def _axis_slider_changed(self, value): self.cut_line.setValue(value) def _dendrogram_slider_changed(self, value): p = QPointF(value, 0) cl_height = self.dendrogram.height_at(p) self.set_cutoff_height(cl_height) # Sync the cut positions between the dendrogram and the axis. self._set_slider_value(value, self.dendrogram.size().width()) def _set_slider_value(self, value, span): with blocked(self.cut_line): self.cut_line.setValue(value) self.cut_line.setRange(0, span) with blocked(self.top_axis.line): self.top_axis.line.setValue(value) self.top_axis.line.setRange(0, span) with blocked(self.bottom_axis.line): self.bottom_axis.line.setValue(value) self.bottom_axis.line.setRange(0, span) def set_cutoff_height(self, height): self.cutoff_height = height if self.root: self.cut_ratio = 100 * height / self.root.value.height self.select_max_height(height) def _set_cut_line_visible(self, visible): self.cut_line.setVisible(visible) self.top_axis.line.setVisible(visible) self.bottom_axis.line.setVisible(visible) def select_top_n(self, n): root = self._displayed_root if root: clusters = top_clusters(root, n) self.dendrogram.set_selected_clusters(clusters) def select_max_height(self, height): root = self._displayed_root if root: clusters = clusters_at_height(root, height) self.dendrogram.set_selected_clusters(clusters) def _selection_method_changed(self): self._set_cut_line_visible(self.selection_method == 1) if self.root: self._apply_selection() def _apply_selection(self): if not self.root: return if self.selection_method == 0: pass elif self.selection_method == 1: height = self.cut_ratio * self.root.value.height / 100 self.set_cutoff_height(height) pos = self.dendrogram.pos_at_height(height) self._set_slider_value(pos.x(), self.dendrogram.size().width()) elif self.selection_method == 2: self.select_top_n(self.top_n) def _selection_edited(self): # Selection was edited by clicking on a cluster in the # dendrogram view. self.selection_method = 0 self._selection_method_changed()
class OWHierarchicalClustering(widget.OWWidget): name = "Hierarchical Clustering" description = ("Hierarchical clustering based on distance matrix, and " "a dendrogram viewer.") icon = "icons/HierarchicalClustering.svg" priority = 2100 inputs = [("Distances", Orange.misc.DistMatrix, "set_distances")] outputs = [("Selected Data", Orange.data.Table), ("Other Data", Orange.data.Table)] #: Selected linkage linkage = settings.Setting(1) #: Index of the selected annotation item (variable, ...) annotation_idx = settings.Setting(0) #: Selected tree pruning (none/max depth) pruning = settings.Setting(0) #: Maximum depth when max depth pruning is selected max_depth = settings.Setting(10) #: Selected cluster selection method (none, cut distance, top n) selection_method = settings.Setting(0) #: Cut height ratio wrt root height cut_ratio = settings.Setting(75.0) #: Number of top clusters to select top_n = settings.Setting(3) append_clusters = settings.Setting(True) cluster_role = settings.Setting(2) cluster_name = settings.Setting("Cluster") autocommit = settings.Setting(False) #: Cluster variable domain role AttributeRole, ClassRole, MetaRole = 0, 1, 2 def __init__(self, parent=None): super().__init__(parent) self.matrix = None self.items = None self.linkmatrix = None self.root = None self._displayed_root = None self.cutoff_height = 0.0 gui.comboBox(gui.widgetBox(self.controlArea, "Linkage"), self, "linkage", items=LINKAGE, callback=self._invalidate_clustering) box = gui.widgetBox(self.controlArea, "Annotation") self.label_cb = gui.comboBox( box, self, "annotation_idx", callback=self._update_labels) self.label_cb.setModel(itemmodels.VariableListModel()) self.label_cb.model()[:] = ["None", "Enumeration"] box = gui.radioButtons( self.controlArea, self, "pruning", box="Pruning", callback=self._invalidate_pruning ) grid = QGridLayout() box.layout().addLayout(grid) grid.addWidget( gui.appendRadioButton(box, "None", addToLayout=False), 0, 0 ) self.max_depth_spin = gui.spin( box, self, "max_depth", minv=1, maxv=100, callback=self._invalidate_pruning, keyboardTracking=False ) grid.addWidget( gui.appendRadioButton(box, "Max depth", addToLayout=False), 1, 0) grid.addWidget(self.max_depth_spin, 1, 1) box = gui.radioButtons( self.controlArea, self, "selection_method", box="Selection", callback=self._selection_method_changed) grid = QGridLayout() box.layout().addLayout(grid) grid.addWidget( gui.appendRadioButton(box, "Manual", addToLayout=False), 0, 0 ) grid.addWidget( gui.appendRadioButton(box, "Height ratio", addToLayout=False), 1, 0 ) self.cut_ratio_spin = gui.spin( box, self, "cut_ratio", 0, 100, step=1e-1, spinType=float, callback=self._selection_method_changed ) self.cut_ratio_spin.setSuffix("%") grid.addWidget(self.cut_ratio_spin, 1, 1) grid.addWidget( gui.appendRadioButton(box, "Top N", addToLayout=False), 2, 0 ) self.top_n_spin = gui.spin(box, self, "top_n", 1, 20, callback=self._selection_method_changed) grid.addWidget(self.top_n_spin, 2, 1) box.layout().addLayout(grid) self.controlArea.layout().addStretch() box = gui.widgetBox(self.controlArea, "Output") gui.checkBox(box, self, "append_clusters", "Append cluster IDs", callback=self._invalidate_output) ibox = gui.indentedBox(box) name_edit = gui.lineEdit(ibox, self, "cluster_name") name_edit.editingFinished.connect(self._invalidate_output) cb = gui.comboBox( ibox, self, "cluster_role", callback=self._invalidate_output, items=["Attribute", "Class variable", "Meta variable"] ) form = QFormLayout( fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow, labelAlignment=Qt.AlignLeft, spacing=8 ) form.addRow("Name", name_edit) form.addRow("Place", cb) ibox.layout().addSpacing(5) ibox.layout().addLayout(form) ibox.layout().addSpacing(5) gui.auto_commit(box, self, "autocommit", "Send data", "Auto send is on", box=False) self.scene = QGraphicsScene() self.view = QGraphicsView( self.scene, horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff, verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn, alignment=Qt.AlignLeft | Qt.AlignVCenter ) def axis_view(orientation): ax = pg.AxisItem(orientation=orientation, maxTickLength=7) scene = QGraphicsScene() scene.addItem(ax) view = QGraphicsView( scene, horizontalScrollBarPolicy=Qt.ScrollBarAlwaysOff, verticalScrollBarPolicy=Qt.ScrollBarAlwaysOn, alignment=Qt.AlignLeft | Qt.AlignVCenter ) view.setFixedHeight(ax.size().height()) ax.line = SliderLine(orientation=Qt.Horizontal, length=ax.size().height()) scene.addItem(ax.line) return view, ax self.top_axis_view, self.top_axis = axis_view("top") self.mainArea.layout().setSpacing(1) self.mainArea.layout().addWidget(self.top_axis_view) self.mainArea.layout().addWidget(self.view) self.bottom_axis_view, self.bottom_axis = axis_view("bottom") self.mainArea.layout().addWidget(self.bottom_axis_view) self._main_graphics = QGraphicsWidget() self._main_layout = QGraphicsLinearLayout(Qt.Horizontal) self._main_layout.setSpacing(1) self._main_graphics.setLayout(self._main_layout) self.scene.addItem(self._main_graphics) self.dendrogram = DendrogramWidget() self.dendrogram.setSizePolicy(QSizePolicy.MinimumExpanding, QSizePolicy.MinimumExpanding) self.dendrogram.selectionChanged.connect(self._invalidate_output) self.dendrogram.selectionEdited.connect(self._selection_edited) fm = self.fontMetrics() self.dendrogram.setContentsMargins( 5, fm.lineSpacing() / 2, 5, fm.lineSpacing() / 2 ) self.labels = GraphicsSimpleTextList() self.labels.setSizePolicy(QSizePolicy.Preferred, QSizePolicy.Preferred) self.labels.setAlignment(Qt.AlignLeft) self.labels.setMaximumWidth(200) self.labels.layout().setSpacing(0) self._main_layout.addItem(self.dendrogram) self._main_layout.addItem(self.labels) self._main_layout.setAlignment( self.dendrogram, Qt.AlignLeft | Qt.AlignVCenter) self._main_layout.setAlignment( self.labels, Qt.AlignLeft | Qt.AlignVCenter) self.view.viewport().installEventFilter(self) self.top_axis_view.viewport().installEventFilter(self) self.bottom_axis_view.viewport().installEventFilter(self) self._main_graphics.installEventFilter(self) self.cut_line = SliderLine(self.dendrogram, orientation=Qt.Horizontal) self.cut_line.valueChanged.connect(self._dendrogram_slider_changed) self.cut_line.hide() self.bottom_axis.line.valueChanged.connect(self._axis_slider_changed) self.top_axis.line.valueChanged.connect(self._axis_slider_changed) self.dendrogram.geometryChanged.connect(self._dendrogram_geom_changed) self._set_cut_line_visible(self.selection_method == 1) def set_distances(self, matrix): self.matrix = matrix self._invalidate_clustering() self._set_items(matrix.row_items if matrix is not None else None) def _set_items(self, items): self.items = items if items is None: self.label_cb.model()[:] = ["None", "Enumeration"] elif isinstance(items, Orange.data.Table): vars = list(items.domain) self.label_cb.model()[:] = ["None", "Enumeration"] + vars elif isinstance(items, list) and \ all(isinstance(var, Orange.data.Variable) for var in items): self.label_cb.model()[:] = ["None", "Enumeration", "Name"] else: self.label_cb.model()[:] = ["None", "Enumeration"] self.annotation_idx = min(self.annotation_idx, len(self.label_cb.model()) - 1) def handleNewSignals(self): self._update_labels() def _clear_plot(self): self.labels.set_labels([]) self.dendrogram.set_root(None) def _set_displayed_root(self, root): self._clear_plot() self._displayed_root = root self.dendrogram.set_root(root) self._update_labels() self._main_graphics.resize( self._main_graphics.size().width(), self._main_graphics.sizeHint(Qt.PreferredSize).height() ) self._main_graphics.layout().activate() def _update(self): self._clear_plot() distances = self.matrix if distances is not None: # Convert to flat upper triangular distances i, j = numpy.triu_indices(distances.X.shape[0], k=1) distances = distances.X[i, j] method = LINKAGE[self.linkage].lower() Z = scipy.cluster.hierarchy.linkage( distances, method=method ) tree = tree_from_linkage(Z) self.linkmatrix = Z self.root = tree self.top_axis.setRange(tree.value.height, 0.0) self.bottom_axis.setRange(tree.value.height, 0.0) if self.pruning: self._set_displayed_root(prune(tree, level=self.max_depth)) else: self._set_displayed_root(tree) else: self.linkmatrix = None self.root = None self._set_displayed_root(None) self._apply_selection() def _update_labels(self): labels = [] if self.root and self._displayed_root: indices = [leaf.value.index for leaf in leaves(self.root)] if self.annotation_idx == 0: labels = [] elif self.annotation_idx == 1: labels = [str(i) for i in indices] elif isinstance(self.items, Orange.data.Table): var = self.label_cb.model()[self.annotation_idx] col = self.items[:, var] labels = [var.repr_val(next(iter(row))) for row in col] labels = [labels[idx] for idx in indices] else: labels = [] if labels and self._displayed_root is not self.root: joined = leaves(self._displayed_root) labels = [", ".join(labels[leaf.value.first: leaf.value.last]) for leaf in joined] self.labels.set_labels(labels) self.labels.setMinimumWidth(1 if labels else -1) def _invalidate_clustering(self): self._update() self._update_labels() def _invalidate_output(self): self.commit() def _invalidate_pruning(self): if self.root: selection = self.dendrogram.selected_nodes() ranges = [node.value.range for node in selection] if self.pruning: self._set_displayed_root( prune(self.root, level=self.max_depth)) else: self._set_displayed_root(self.root) selected = [node for node in preorder(self._displayed_root) if node.value.range in ranges] self.dendrogram.set_selected_clusters(selected) self._apply_selection() def commit(self): items = getattr(self.matrix, "items", self.items) if not items: # nothing to commit return selection = self.dendrogram.selected_nodes() selection = sorted(selection, key=lambda c: c.value.first) indices = [leaf.value.index for leaf in leaves(self.root)] maps = [indices[node.value.first:node.value.last] for node in selection] selected_indices = list(chain(*maps)) unselected_indices = sorted(set(range(self.root.value.last)) - set(selected_indices)) selected = [items[k] for k in selected_indices] unselected = [items[k] for k in unselected_indices] if not selected: self.send("Selected Data", None) self.send("Other Data", None) return selected_data = unselected_data = None if isinstance(items, Orange.data.Table): c = numpy.zeros(len(items)) for i, indices in enumerate(maps): c[indices] = i c[unselected_indices] = len(maps) mask = c != len(maps) if self.append_clusters: clust_var = Orange.data.DiscreteVariable( str(self.cluster_name), values=["Cluster {}".format(i + 1) for i in range(len(maps))] + ["Other"], ordered=True ) data, domain = items, items.domain attrs = domain.attributes class_ = domain.class_vars metas = domain.metas if self.cluster_role == self.AttributeRole: attrs = attrs + (clust_var,) elif self.cluster_role == self.ClassRole: class_ = class_ + (clust_var,) elif self.cluster_role == self.MetaRole: metas = metas + (clust_var,) domain = Orange.data.Domain(attrs, class_, metas) data = Orange.data.Table(domain, data) data.get_column_view(clust_var)[0][:] = c else: data = items if selected: selected_data = data[mask] if unselected: unselected_data = data[~mask] self.send("Selected Data", selected_data) self.send("Other Data", unselected_data) def sizeHint(self): return QSize(800, 500) def eventFilter(self, obj, event): if obj is self.view.viewport() and event.type() == QEvent.Resize: width = self.view.viewport().width() - 2 self._main_graphics.setMaximumWidth(width) self._main_graphics.setMinimumWidth(width) self._main_graphics.layout().activate() elif event.type() == QEvent.MouseButtonPress and \ (obj is self.top_axis_view.viewport() or obj is self.bottom_axis_view.viewport()): self.selection_method = 1 # Map click point to cut line local coordinates pos = self.top_axis_view.mapToScene(event.pos()) cut = self.top_axis.line.mapFromScene(pos) self.top_axis.line.setValue(cut.x()) # update the line visibility, output, ... self._selection_method_changed() return super().eventFilter(obj, event) def _dendrogram_geom_changed(self): pos = self.dendrogram.pos_at_height(self.cutoff_height) geom = self.dendrogram.geometry() crect = self.dendrogram.contentsRect() self._set_slider_value(pos.x(), geom.width()) self.cut_line.setLength(geom.height()) self.top_axis.resize(crect.width(), self.top_axis.height()) self.top_axis.setPos(geom.left() + crect.left(), 0) self.top_axis.line.setPos(self.cut_line.scenePos().x(), 0) self.bottom_axis.resize(crect.width(), self.bottom_axis.height()) self.bottom_axis.setPos(geom.left() + crect.left(), 0) self.bottom_axis.line.setPos(self.cut_line.scenePos().x(), 0) geom = self._main_graphics.geometry() assert geom.topLeft() == QPointF(0, 0) self.scene.setSceneRect(geom) geom.setHeight(self.top_axis.size().height()) self.top_axis.scene().setSceneRect(geom) self.bottom_axis.scene().setSceneRect(geom) def _axis_slider_changed(self, value): self.cut_line.setValue(value) def _dendrogram_slider_changed(self, value): p = QPointF(value, 0) cl_height = self.dendrogram.height_at(p) self.set_cutoff_height(cl_height) # Sync the cut positions between the dendrogram and the axis. self._set_slider_value(value, self.dendrogram.size().width()) def _set_slider_value(self, value, span): with blocked(self.cut_line): self.cut_line.setValue(value) self.cut_line.setRange(0, span) with blocked(self.top_axis.line): self.top_axis.line.setValue(value) self.top_axis.line.setRange(0, span) with blocked(self.bottom_axis.line): self.bottom_axis.line.setValue(value) self.bottom_axis.line.setRange(0, span) def set_cutoff_height(self, height): self.cutoff_height = height if self.root: self.cut_ratio = 100 * height / self.root.value.height self.select_max_height(height) def _set_cut_line_visible(self, visible): self.cut_line.setVisible(visible) self.top_axis.line.setVisible(visible) self.bottom_axis.line.setVisible(visible) def select_top_n(self, n): root = self._displayed_root if root: clusters = top_clusters(root, n) self.dendrogram.set_selected_clusters(clusters) def select_max_height(self, height): root = self._displayed_root if root: clusters = clusters_at_height(root, height) self.dendrogram.set_selected_clusters(clusters) def _selection_method_changed(self): self._set_cut_line_visible(self.selection_method == 1) if self.root: self._apply_selection() def _apply_selection(self): if not self.root: return if self.selection_method == 0: pass elif self.selection_method == 1: height = self.cut_ratio * self.root.value.height / 100 self.set_cutoff_height(height) pos = self.dendrogram.pos_at_height(height) self._set_slider_value(pos.x(), self.dendrogram.size().width()) elif self.selection_method == 2: self.select_top_n(self.top_n) def _selection_edited(self): # Selection was edited by clicking on a cluster in the # dendrogram view. self.selection_method = 0 self._selection_method_changed()