def __init__(self): super().__init__() self.matrix = None self._tree = None self._ordered_tree = None self._sorted_matrix = None self._sort_indices = None self._selection = None self.sorting_cb = gui.comboBox( self.controlArea, self, "sorting", box="Element Sorting", items=["None", "Clustering", "Clustering with ordered leaves"], callback=self._invalidate_ordering) box = gui.vBox(self.controlArea, "Colors") self.colormap_cb = gui.comboBox(box, self, "colormap", callback=self._update_color) self.colormap_cb.setIconSize(QSize(64, 16)) self.palettes = list(_color_palettes) init_color_combo(self.colormap_cb, self.palettes, QSize(64, 16)) self.colormap_cb.setCurrentIndex(self.colormap) form = QFormLayout(formAlignment=Qt.AlignLeft, labelAlignment=Qt.AlignLeft, fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow) # form.addRow( # "Gamma", # gui.hSlider(box, self, "color_gamma", minValue=0.0, maxValue=1.0, # step=0.05, ticks=True, intOnly=False, # createLabel=False, callback=self._update_color) # ) form.addRow( "Low:", gui.hSlider(box, self, "color_low", minValue=0.0, maxValue=1.0, step=0.05, ticks=True, intOnly=False, createLabel=False, callback=self._update_color)) form.addRow( "High:", gui.hSlider(box, self, "color_high", minValue=0.0, maxValue=1.0, step=0.05, ticks=True, intOnly=False, createLabel=False, callback=self._update_color)) box.layout().addLayout(form) self.annot_combo = gui.comboBox(self.controlArea, self, "annotation_idx", box="Annotations", callback=self._invalidate_annotations, contentsLength=12) self.annot_combo.setModel(itemmodels.VariableListModel()) self.annot_combo.model()[:] = ["None", "Enumeration"] self.controlArea.layout().addStretch() gui.auto_commit(self.controlArea, self, "autocommit", "Send Selected") self.view = pg.GraphicsView(background="w") self.mainArea.layout().addWidget(self.view) self.grid_widget = pg.GraphicsWidget() self.grid = QGraphicsGridLayout() self.grid_widget.setLayout(self.grid) self.viewbox = pg.ViewBox(enableMouse=False, enableMenu=False) self.viewbox.setAcceptedMouseButtons(Qt.NoButton) self.viewbox.setAcceptHoverEvents(False) self.grid.addItem(self.viewbox, 1, 1) self.left_dendrogram = DendrogramWidget( self.grid_widget, orientation=DendrogramWidget.Left, selectionMode=DendrogramWidget.NoSelection, hoverHighlightEnabled=False) self.left_dendrogram.setAcceptedMouseButtons(Qt.NoButton) self.left_dendrogram.setAcceptHoverEvents(False) self.top_dendrogram = DendrogramWidget( self.grid_widget, orientation=DendrogramWidget.Top, selectionMode=DendrogramWidget.NoSelection, hoverHighlightEnabled=False) self.top_dendrogram.setAcceptedMouseButtons(Qt.NoButton) self.top_dendrogram.setAcceptHoverEvents(False) self.grid.addItem(self.left_dendrogram, 1, 0) self.grid.addItem(self.top_dendrogram, 0, 1) self.right_labels = TextList(alignment=Qt.AlignLeft) self.bottom_labels = TextList(orientation=Qt.Horizontal, alignment=Qt.AlignRight) self.grid.addItem(self.right_labels, 1, 2) self.grid.addItem(self.bottom_labels, 2, 1) self.view.setCentralItem(self.grid_widget) self.left_dendrogram.hide() self.top_dendrogram.hide() self.right_labels.hide() self.bottom_labels.hide() self.matrix_item = None self.dendrogram = None self.grid_widget.scene().installEventFilter(self)
class OWDistanceMap(widget.OWWidget): name = "Distance Map" description = "Visualize a distance matrix." icon = "icons/DistanceMap.svg" priority = 1200 keywords = [] class Inputs: distances = Input("Distances", Orange.misc.DistMatrix) class Outputs: selected_data = Output("Selected Data", Orange.data.Table, default=True) annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Orange.data.Table) features = Output("Features", widget.AttributeList, dynamic=False) settingsHandler = settings.PerfectDomainContextHandler() #: type of ordering to apply to matrix rows/columns NoOrdering, Clustering, OrderedClustering = 0, 1, 2 sorting = settings.Setting(NoOrdering) colormap = settings.Setting(_default_colormap_index) color_gamma = settings.Setting(0.0) color_low = settings.Setting(0.0) color_high = settings.Setting(1.0) annotation_idx = settings.ContextSetting(0) autocommit = settings.Setting(True) graph_name = "grid_widget" # Disable clustering for inputs bigger than this if hierarchical._HAS_NN_CHAIN: _MaxClustering = 25000 else: _MaxClustering = 3000 # Disable cluster leaf ordering for inputs bigger than this _MaxOrderedClustering = 1000 def __init__(self): super().__init__() self.matrix = None self._tree = None self._ordered_tree = None self._sorted_matrix = None self._sort_indices = None self._selection = None self.sorting_cb = gui.comboBox( self.controlArea, self, "sorting", box="Element Sorting", items=["None", "Clustering", "Clustering with ordered leaves"], callback=self._invalidate_ordering) box = gui.vBox(self.controlArea, "Colors") self.colormap_cb = gui.comboBox(box, self, "colormap", callback=self._update_color) self.colormap_cb.setIconSize(QSize(64, 16)) self.palettes = list(_color_palettes) init_color_combo(self.colormap_cb, self.palettes, QSize(64, 16)) self.colormap_cb.setCurrentIndex(self.colormap) form = QFormLayout(formAlignment=Qt.AlignLeft, labelAlignment=Qt.AlignLeft, fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow) # form.addRow( # "Gamma", # gui.hSlider(box, self, "color_gamma", minValue=0.0, maxValue=1.0, # step=0.05, ticks=True, intOnly=False, # createLabel=False, callback=self._update_color) # ) form.addRow( "Low:", gui.hSlider(box, self, "color_low", minValue=0.0, maxValue=1.0, step=0.05, ticks=True, intOnly=False, createLabel=False, callback=self._update_color)) form.addRow( "High:", gui.hSlider(box, self, "color_high", minValue=0.0, maxValue=1.0, step=0.05, ticks=True, intOnly=False, createLabel=False, callback=self._update_color)) box.layout().addLayout(form) self.annot_combo = gui.comboBox(self.controlArea, self, "annotation_idx", box="Annotations", callback=self._invalidate_annotations, contentsLength=12) self.annot_combo.setModel(itemmodels.VariableListModel()) self.annot_combo.model()[:] = ["None", "Enumeration"] self.controlArea.layout().addStretch() gui.auto_commit(self.controlArea, self, "autocommit", "Send Selected") self.view = pg.GraphicsView(background="w") self.mainArea.layout().addWidget(self.view) self.grid_widget = pg.GraphicsWidget() self.grid = QGraphicsGridLayout() self.grid_widget.setLayout(self.grid) self.viewbox = pg.ViewBox(enableMouse=False, enableMenu=False) self.viewbox.setAcceptedMouseButtons(Qt.NoButton) self.viewbox.setAcceptHoverEvents(False) self.grid.addItem(self.viewbox, 1, 1) self.left_dendrogram = DendrogramWidget( self.grid_widget, orientation=DendrogramWidget.Left, selectionMode=DendrogramWidget.NoSelection, hoverHighlightEnabled=False) self.left_dendrogram.setAcceptedMouseButtons(Qt.NoButton) self.left_dendrogram.setAcceptHoverEvents(False) self.top_dendrogram = DendrogramWidget( self.grid_widget, orientation=DendrogramWidget.Top, selectionMode=DendrogramWidget.NoSelection, hoverHighlightEnabled=False) self.top_dendrogram.setAcceptedMouseButtons(Qt.NoButton) self.top_dendrogram.setAcceptHoverEvents(False) self.grid.addItem(self.left_dendrogram, 1, 0) self.grid.addItem(self.top_dendrogram, 0, 1) self.right_labels = TextList(alignment=Qt.AlignLeft) self.bottom_labels = TextList(orientation=Qt.Horizontal, alignment=Qt.AlignRight) self.grid.addItem(self.right_labels, 1, 2) self.grid.addItem(self.bottom_labels, 2, 1) self.view.setCentralItem(self.grid_widget) self.left_dendrogram.hide() self.top_dendrogram.hide() self.right_labels.hide() self.bottom_labels.hide() self.matrix_item = None self.dendrogram = None self.grid_widget.scene().installEventFilter(self) @Inputs.distances def set_distances(self, matrix): self.closeContext() self.clear() self.error() if matrix is not None: N, _ = matrix.shape if N < 2: self.error("Empty distance matrix.") matrix = None self.matrix = matrix if matrix is not None: self.set_items(matrix.row_items, matrix.axis) else: self.set_items(None) if matrix is not None: N, _ = matrix.shape else: N = 0 model = self.sorting_cb.model() item = model.item(2) msg = None if N > OWDistanceMap._MaxOrderedClustering: item.setFlags(item.flags() & ~Qt.ItemIsEnabled) if self.sorting == OWDistanceMap.OrderedClustering: self.sorting = OWDistanceMap.Clustering msg = "Cluster ordering was disabled due to the input " \ "matrix being to big" else: item.setFlags(item.flags() | Qt.ItemIsEnabled) item = model.item(1) if N > OWDistanceMap._MaxClustering: item.setFlags(item.flags() & ~Qt.ItemIsEnabled) if self.sorting == OWDistanceMap.Clustering: self.sorting = OWDistanceMap.NoOrdering msg = "Clustering was disabled due to the input " \ "matrix being to big" else: item.setFlags(item.flags() | Qt.ItemIsEnabled) self.information(msg) def set_items(self, items, axis=1): self.items = items model = self.annot_combo.model() if items is None: model[:] = ["None", "Enumeration"] elif not axis: model[:] = ["None", "Enumeration", "Attribute names"] elif isinstance(items, Orange.data.Table): annot_vars = list(filter_visible(items.domain.variables)) + list( items.domain.metas) model[:] = ["None", "Enumeration"] + annot_vars self.annotation_idx = 0 self.openContext(items.domain) elif isinstance(items, list) and \ all(isinstance(item, Orange.data.Variable) for item in items): model[:] = ["None", "Enumeration", "Name"] else: model[:] = ["None", "Enumeration"] self.annotation_idx = min(self.annotation_idx, len(model) - 1) def clear(self): self.matrix = None self.cluster = None self._tree = None self._ordered_tree = None self._sorted_matrix = None self._selection = [] self._clear_plot() def handleNewSignals(self): if self.matrix is not None: self._update_ordering() self._setup_scene() self._update_labels() self.unconditional_commit() def _clear_plot(self): def remove(item): item.setParentItem(None) item.scene().removeItem(item) if self.matrix_item is not None: self.matrix_item.selectionChanged.disconnect( self._invalidate_selection) remove(self.matrix_item) self.matrix_item = None self._set_displayed_dendrogram(None) self._set_labels(None) def _cluster_tree(self): if self._tree is None: self._tree = hierarchical.dist_matrix_clustering(self.matrix) return self._tree def _ordered_cluster_tree(self): if self._ordered_tree is None: tree = self._cluster_tree() self._ordered_tree = \ hierarchical.optimal_leaf_ordering(tree, self.matrix) return self._ordered_tree def _setup_scene(self): self._clear_plot() self.matrix_item = DistanceMapItem(self._sorted_matrix) # Scale the y axis to compensate for pg.ViewBox's y axis invert self.matrix_item.setTransform(QTransform.fromScale(1, -1), ) self.viewbox.addItem(self.matrix_item) # Set fixed view box range. h, w = self._sorted_matrix.shape self.viewbox.setRange(QRectF(0, -h, w, h), padding=0) self.matrix_item.selectionChanged.connect(self._invalidate_selection) if self.sorting == OWDistanceMap.NoOrdering: tree = None elif self.sorting == OWDistanceMap.Clustering: tree = self._cluster_tree() elif self.sorting == OWDistanceMap.OrderedClustering: tree = self._ordered_cluster_tree() self._set_displayed_dendrogram(tree) self._update_color() def _set_displayed_dendrogram(self, root): self.left_dendrogram.set_root(root) self.top_dendrogram.set_root(root) self.left_dendrogram.setVisible(root is not None) self.top_dendrogram.setVisible(root is not None) constraint = 0 if root is None else -1 # 150 self.left_dendrogram.setMaximumWidth(constraint) self.top_dendrogram.setMaximumHeight(constraint) def _invalidate_ordering(self): self._sorted_matrix = None if self.matrix is not None: self._update_ordering() self._setup_scene() self._update_labels() self._invalidate_selection() def _update_ordering(self): if self.sorting == OWDistanceMap.NoOrdering: self._sorted_matrix = self.matrix self._sort_indices = None else: if self.sorting == OWDistanceMap.Clustering: tree = self._cluster_tree() elif self.sorting == OWDistanceMap.OrderedClustering: tree = self._ordered_cluster_tree() leaves = hierarchical.leaves(tree) indices = numpy.array([leaf.value.index for leaf in leaves]) X = self.matrix self._sorted_matrix = X[indices[:, numpy.newaxis], indices[numpy.newaxis, :]] self._sort_indices = indices def _invalidate_annotations(self): if self.matrix is not None: self._update_labels() def _update_labels(self, ): if self.annotation_idx == 0: # None labels = None elif self.annotation_idx == 1: # Enumeration labels = [str(i + 1) for i in range(self.matrix.shape[0])] elif self.annot_combo.model()[ self.annotation_idx] == "Attribute names": attr = self.matrix.row_items.domain.attributes labels = [str(attr[i]) for i in range(self.matrix.shape[0])] elif self.annotation_idx == 2 and \ isinstance(self.items, widget.AttributeList): labels = [v.name for v in self.items] elif isinstance(self.items, Orange.data.Table): var = self.annot_combo.model()[self.annotation_idx] column, _ = self.items.get_column_view(var) labels = [var.str_val(value) for value in column] self._set_labels(labels) def _set_labels(self, labels): self._labels = labels if labels and self.sorting != OWDistanceMap.NoOrdering: sortind = self._sort_indices labels = [labels[i] for i in sortind] for textlist in [self.right_labels, self.bottom_labels]: textlist.set_labels(labels or []) textlist.setVisible(bool(labels)) constraint = -1 if labels else 0 self.right_labels.setMaximumWidth(constraint) self.bottom_labels.setMaximumHeight(constraint) def _update_color(self): if self.matrix_item: name, colors = self.palettes[self.colormap] n, colors = max(colors.items()) colors = numpy.array(colors, dtype=numpy.ubyte) low, high = self.color_low * 255, self.color_high * 255 points = numpy.linspace(low, high, n) space = numpy.linspace(0, 255, 255) r = numpy.interp(space, points, colors[:, 0], left=255, right=0) g = numpy.interp(space, points, colors[:, 1], left=255, right=0) b = numpy.interp(space, points, colors[:, 2], left=255, right=0) colortable = numpy.c_[r, g, b] self.matrix_item.setLookupTable(colortable) def _invalidate_selection(self): ranges = self.matrix_item.selections() ranges = reduce(iadd, ranges, []) indices = reduce(iadd, ranges, []) if self.sorting != OWDistanceMap.NoOrdering: sortind = self._sort_indices indices = [sortind[i] for i in indices] self._selection = list(sorted(set(indices))) self.commit() def commit(self): datasubset = None featuresubset = None if not self._selection: pass elif isinstance(self.items, Orange.data.Table): indices = self._selection if self.matrix.axis == 1: datasubset = self.items.from_table_rows(self.items, indices) elif self.matrix.axis == 0: domain = Orange.data.Domain( [self.items.domain[i] for i in indices], self.items.domain.class_vars, self.items.domain.metas) datasubset = self.items.transform(domain) elif isinstance(self.items, widget.AttributeList): subset = [self.items[i] for i in self._selection] featuresubset = widget.AttributeList(subset) self.Outputs.selected_data.send(datasubset) self.Outputs.annotated_data.send( create_annotated_table(self.items, self._selection)) self.Outputs.features.send(featuresubset) def onDeleteWidget(self): super().onDeleteWidget() self.clear() def send_report(self): annot = self.annot_combo.currentText() if self.annotation_idx <= 1: annot = annot.lower() self.report_items((("Sorting", self.sorting_cb.currentText().lower()), ("Annotations", annot))) if self.matrix is not None: self.report_plot()
class OWDistanceMap(widget.OWWidget): name = "Distance Map" description = "Visualize a distance matrix." icon = "icons/DistanceMap.svg" priority = 1200 keywords = [] class Inputs: distances = Input("Distances", Orange.misc.DistMatrix) class Outputs: selected_data = Output("Selected Data", Orange.data.Table, default=True) annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Orange.data.Table) features = Output("Features", widget.AttributeList, dynamic=False) settingsHandler = settings.PerfectDomainContextHandler() #: type of ordering to apply to matrix rows/columns NoOrdering, Clustering, OrderedClustering = 0, 1, 2 sorting = settings.Setting(NoOrdering) colormap = settings.Setting(_default_colormap_index) color_gamma = settings.Setting(0.0) color_low = settings.Setting(0.0) color_high = settings.Setting(1.0) annotation_idx = settings.ContextSetting(0) autocommit = settings.Setting(True) graph_name = "grid_widget" # Disable clustering for inputs bigger than this if hierarchical._HAS_NN_CHAIN: _MaxClustering = 25000 else: _MaxClustering = 3000 # Disable cluster leaf ordering for inputs bigger than this _MaxOrderedClustering = 1000 def __init__(self): super().__init__() self.matrix = None self._tree = None self._ordered_tree = None self._sorted_matrix = None self._sort_indices = None self._selection = None self.sorting_cb = gui.comboBox( self.controlArea, self, "sorting", box="Element Sorting", items=["None", "Clustering", "Clustering with ordered leaves"], callback=self._invalidate_ordering) box = gui.vBox(self.controlArea, "Colors") self.colormap_cb = gui.comboBox( box, self, "colormap", callback=self._update_color) self.colormap_cb.setIconSize(QSize(64, 16)) self.palettes = list(_color_palettes) init_color_combo(self.colormap_cb, self.palettes, QSize(64, 16)) self.colormap_cb.setCurrentIndex(self.colormap) form = QFormLayout( formAlignment=Qt.AlignLeft, labelAlignment=Qt.AlignLeft, fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow ) # form.addRow( # "Gamma", # gui.hSlider(box, self, "color_gamma", minValue=0.0, maxValue=1.0, # step=0.05, ticks=True, intOnly=False, # createLabel=False, callback=self._update_color) # ) form.addRow( "Low:", gui.hSlider(box, self, "color_low", minValue=0.0, maxValue=1.0, step=0.05, ticks=True, intOnly=False, createLabel=False, callback=self._update_color) ) form.addRow( "High:", gui.hSlider(box, self, "color_high", minValue=0.0, maxValue=1.0, step=0.05, ticks=True, intOnly=False, createLabel=False, callback=self._update_color) ) box.layout().addLayout(form) self.annot_combo = gui.comboBox( self.controlArea, self, "annotation_idx", box="Annotations", callback=self._invalidate_annotations, contentsLength=12) self.annot_combo.setModel(itemmodels.VariableListModel()) self.annot_combo.model()[:] = ["None", "Enumeration"] self.controlArea.layout().addStretch() gui.auto_commit(self.controlArea, self, "autocommit", "Send Selected") self.view = pg.GraphicsView(background="w") self.mainArea.layout().addWidget(self.view) self.grid_widget = pg.GraphicsWidget() self.grid = QGraphicsGridLayout() self.grid_widget.setLayout(self.grid) self.viewbox = pg.ViewBox(enableMouse=False, enableMenu=False) self.viewbox.setAcceptedMouseButtons(Qt.NoButton) self.viewbox.setAcceptHoverEvents(False) self.grid.addItem(self.viewbox, 1, 1) self.left_dendrogram = DendrogramWidget( self.grid_widget, orientation=DendrogramWidget.Left, selectionMode=DendrogramWidget.NoSelection, hoverHighlightEnabled=False ) self.left_dendrogram.setAcceptedMouseButtons(Qt.NoButton) self.left_dendrogram.setAcceptHoverEvents(False) self.top_dendrogram = DendrogramWidget( self.grid_widget, orientation=DendrogramWidget.Top, selectionMode=DendrogramWidget.NoSelection, hoverHighlightEnabled=False ) self.top_dendrogram.setAcceptedMouseButtons(Qt.NoButton) self.top_dendrogram.setAcceptHoverEvents(False) self.grid.addItem(self.left_dendrogram, 1, 0) self.grid.addItem(self.top_dendrogram, 0, 1) self.right_labels = TextList( alignment=Qt.AlignLeft) self.bottom_labels = TextList( orientation=Qt.Horizontal, alignment=Qt.AlignRight) self.grid.addItem(self.right_labels, 1, 2) self.grid.addItem(self.bottom_labels, 2, 1) self.view.setCentralItem(self.grid_widget) self.left_dendrogram.hide() self.top_dendrogram.hide() self.right_labels.hide() self.bottom_labels.hide() self.matrix_item = None self.dendrogram = None self.grid_widget.scene().installEventFilter(self) @Inputs.distances def set_distances(self, matrix): self.closeContext() self.clear() self.error() if matrix is not None: N, _ = matrix.shape if N < 2: self.error("Empty distance matrix.") matrix = None self.matrix = matrix if matrix is not None: self.set_items(matrix.row_items, matrix.axis) else: self.set_items(None) if matrix is not None: N, _ = matrix.shape else: N = 0 model = self.sorting_cb.model() item = model.item(2) msg = None if N > OWDistanceMap._MaxOrderedClustering: item.setFlags(item.flags() & ~Qt.ItemIsEnabled) if self.sorting == OWDistanceMap.OrderedClustering: self.sorting = OWDistanceMap.Clustering msg = "Cluster ordering was disabled due to the input " \ "matrix being to big" else: item.setFlags(item.flags() | Qt.ItemIsEnabled) item = model.item(1) if N > OWDistanceMap._MaxClustering: item.setFlags(item.flags() & ~Qt.ItemIsEnabled) if self.sorting == OWDistanceMap.Clustering: self.sorting = OWDistanceMap.NoOrdering msg = "Clustering was disabled due to the input " \ "matrix being to big" else: item.setFlags(item.flags() | Qt.ItemIsEnabled) self.information(msg) def set_items(self, items, axis=1): self.items = items model = self.annot_combo.model() if items is None: model[:] = ["None", "Enumeration"] elif not axis: model[:] = ["None", "Enumeration", "Attribute names"] elif isinstance(items, Orange.data.Table): annot_vars = list(filter_visible(items.domain.variables)) + list(items.domain.metas) model[:] = ["None", "Enumeration"] + annot_vars self.annotation_idx = 0 self.openContext(items.domain) elif isinstance(items, list) and \ all(isinstance(item, Orange.data.Variable) for item in items): model[:] = ["None", "Enumeration", "Name"] else: model[:] = ["None", "Enumeration"] self.annotation_idx = min(self.annotation_idx, len(model) - 1) def clear(self): self.matrix = None self.cluster = None self._tree = None self._ordered_tree = None self._sorted_matrix = None self._selection = [] self._clear_plot() def handleNewSignals(self): if self.matrix is not None: self._update_ordering() self._setup_scene() self._update_labels() self.unconditional_commit() def _clear_plot(self): def remove(item): item.setParentItem(None) item.scene().removeItem(item) if self.matrix_item is not None: self.matrix_item.selectionChanged.disconnect( self._invalidate_selection) remove(self.matrix_item) self.matrix_item = None self._set_displayed_dendrogram(None) self._set_labels(None) def _cluster_tree(self): if self._tree is None: self._tree = hierarchical.dist_matrix_clustering(self.matrix) return self._tree def _ordered_cluster_tree(self): if self._ordered_tree is None: tree = self._cluster_tree() self._ordered_tree = \ hierarchical.optimal_leaf_ordering(tree, self.matrix) return self._ordered_tree def _setup_scene(self): self._clear_plot() self.matrix_item = DistanceMapItem(self._sorted_matrix) # Scale the y axis to compensate for pg.ViewBox's y axis invert self.matrix_item.setTransform(QTransform.fromScale(1, -1), ) self.viewbox.addItem(self.matrix_item) # Set fixed view box range. h, w = self._sorted_matrix.shape self.viewbox.setRange(QRectF(0, -h, w, h), padding=0) self.matrix_item.selectionChanged.connect(self._invalidate_selection) if self.sorting == OWDistanceMap.NoOrdering: tree = None elif self.sorting == OWDistanceMap.Clustering: tree = self._cluster_tree() elif self.sorting == OWDistanceMap.OrderedClustering: tree = self._ordered_cluster_tree() self._set_displayed_dendrogram(tree) self._update_color() def _set_displayed_dendrogram(self, root): self.left_dendrogram.set_root(root) self.top_dendrogram.set_root(root) self.left_dendrogram.setVisible(root is not None) self.top_dendrogram.setVisible(root is not None) constraint = 0 if root is None else -1 # 150 self.left_dendrogram.setMaximumWidth(constraint) self.top_dendrogram.setMaximumHeight(constraint) def _invalidate_ordering(self): self._sorted_matrix = None if self.matrix is not None: self._update_ordering() self._setup_scene() self._update_labels() self._invalidate_selection() def _update_ordering(self): if self.sorting == OWDistanceMap.NoOrdering: self._sorted_matrix = self.matrix self._sort_indices = None else: if self.sorting == OWDistanceMap.Clustering: tree = self._cluster_tree() elif self.sorting == OWDistanceMap.OrderedClustering: tree = self._ordered_cluster_tree() leaves = hierarchical.leaves(tree) indices = numpy.array([leaf.value.index for leaf in leaves]) X = self.matrix self._sorted_matrix = X[indices[:, numpy.newaxis], indices[numpy.newaxis, :]] self._sort_indices = indices def _invalidate_annotations(self): if self.matrix is not None: self._update_labels() def _update_labels(self, ): if self.annotation_idx == 0: # None labels = None elif self.annotation_idx == 1: # Enumeration labels = [str(i + 1) for i in range(self.matrix.shape[0])] elif self.annot_combo.model()[self.annotation_idx] == "Attribute names": attr = self.matrix.row_items.domain.attributes labels = [str(attr[i]) for i in range(self.matrix.shape[0])] elif self.annotation_idx == 2 and \ isinstance(self.items, widget.AttributeList): labels = [v.name for v in self.items] elif isinstance(self.items, Orange.data.Table): var = self.annot_combo.model()[self.annotation_idx] column, _ = self.items.get_column_view(var) labels = [var.str_val(value) for value in column] self._set_labels(labels) def _set_labels(self, labels): self._labels = labels if labels and self.sorting != OWDistanceMap.NoOrdering: sortind = self._sort_indices labels = [labels[i] for i in sortind] for textlist in [self.right_labels, self.bottom_labels]: textlist.set_labels(labels or []) textlist.setVisible(bool(labels)) constraint = -1 if labels else 0 self.right_labels.setMaximumWidth(constraint) self.bottom_labels.setMaximumHeight(constraint) def _update_color(self): if self.matrix_item: name, colors = self.palettes[self.colormap] n, colors = max(colors.items()) colors = numpy.array(colors, dtype=numpy.ubyte) low, high = self.color_low * 255, self.color_high * 255 points = numpy.linspace(low, high, n) space = numpy.linspace(0, 255, 255) r = numpy.interp(space, points, colors[:, 0], left=255, right=0) g = numpy.interp(space, points, colors[:, 1], left=255, right=0) b = numpy.interp(space, points, colors[:, 2], left=255, right=0) colortable = numpy.c_[r, g, b] self.matrix_item.setLookupTable(colortable) def _invalidate_selection(self): ranges = self.matrix_item.selections() ranges = reduce(iadd, ranges, []) indices = reduce(iadd, ranges, []) if self.sorting != OWDistanceMap.NoOrdering: sortind = self._sort_indices indices = [sortind[i] for i in indices] self._selection = list(sorted(set(indices))) self.commit() def commit(self): datasubset = None featuresubset = None if not self._selection: pass elif isinstance(self.items, Orange.data.Table): indices = self._selection if self.matrix.axis == 1: datasubset = self.items.from_table_rows(self.items, indices) elif self.matrix.axis == 0: domain = Orange.data.Domain( [self.items.domain[i] for i in indices], self.items.domain.class_vars, self.items.domain.metas) datasubset = self.items.transform(domain) elif isinstance(self.items, widget.AttributeList): subset = [self.items[i] for i in self._selection] featuresubset = widget.AttributeList(subset) self.Outputs.selected_data.send(datasubset) self.Outputs.annotated_data.send(create_annotated_table(self.items, self._selection)) self.Outputs.features.send(featuresubset) def onDeleteWidget(self): super().onDeleteWidget() self.clear() def send_report(self): annot = self.annot_combo.currentText() if self.annotation_idx <= 1: annot = annot.lower() self.report_items(( ("Sorting", self.sorting_cb.currentText().lower()), ("Annotations", annot) )) if self.matrix is not None: self.report_plot()
def __init__(self): super().__init__() self.matrix = None self._tree = None self._ordered_tree = None self._sorted_matrix = None self._sort_indices = None self._selection = None self.sorting_cb = gui.comboBox( self.controlArea, self, "sorting", box="Element Sorting", items=["None", "Clustering", "Clustering with ordered leaves"], callback=self._invalidate_ordering) box = gui.vBox(self.controlArea, "Colors") self.colormap_cb = gui.comboBox( box, self, "colormap", callback=self._update_color) self.colormap_cb.setIconSize(QSize(64, 16)) self.palettes = list(_color_palettes) init_color_combo(self.colormap_cb, self.palettes, QSize(64, 16)) self.colormap_cb.setCurrentIndex(self.colormap) form = QFormLayout( formAlignment=Qt.AlignLeft, labelAlignment=Qt.AlignLeft, fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow ) # form.addRow( # "Gamma", # gui.hSlider(box, self, "color_gamma", minValue=0.0, maxValue=1.0, # step=0.05, ticks=True, intOnly=False, # createLabel=False, callback=self._update_color) # ) form.addRow( "Low:", gui.hSlider(box, self, "color_low", minValue=0.0, maxValue=1.0, step=0.05, ticks=True, intOnly=False, createLabel=False, callback=self._update_color) ) form.addRow( "High:", gui.hSlider(box, self, "color_high", minValue=0.0, maxValue=1.0, step=0.05, ticks=True, intOnly=False, createLabel=False, callback=self._update_color) ) box.layout().addLayout(form) self.annot_combo = gui.comboBox( self.controlArea, self, "annotation_idx", box="Annotations", callback=self._invalidate_annotations, contentsLength=12) self.annot_combo.setModel(itemmodels.VariableListModel()) self.annot_combo.model()[:] = ["None", "Enumeration"] self.controlArea.layout().addStretch() gui.auto_commit(self.controlArea, self, "autocommit", "Send Selected") self.view = pg.GraphicsView(background="w") self.mainArea.layout().addWidget(self.view) self.grid_widget = pg.GraphicsWidget() self.grid = QGraphicsGridLayout() self.grid_widget.setLayout(self.grid) self.viewbox = pg.ViewBox(enableMouse=False, enableMenu=False) self.viewbox.setAcceptedMouseButtons(Qt.NoButton) self.viewbox.setAcceptHoverEvents(False) self.grid.addItem(self.viewbox, 1, 1) self.left_dendrogram = DendrogramWidget( self.grid_widget, orientation=DendrogramWidget.Left, selectionMode=DendrogramWidget.NoSelection, hoverHighlightEnabled=False ) self.left_dendrogram.setAcceptedMouseButtons(Qt.NoButton) self.left_dendrogram.setAcceptHoverEvents(False) self.top_dendrogram = DendrogramWidget( self.grid_widget, orientation=DendrogramWidget.Top, selectionMode=DendrogramWidget.NoSelection, hoverHighlightEnabled=False ) self.top_dendrogram.setAcceptedMouseButtons(Qt.NoButton) self.top_dendrogram.setAcceptHoverEvents(False) self.grid.addItem(self.left_dendrogram, 1, 0) self.grid.addItem(self.top_dendrogram, 0, 1) self.right_labels = TextList( alignment=Qt.AlignLeft) self.bottom_labels = TextList( orientation=Qt.Horizontal, alignment=Qt.AlignRight) self.grid.addItem(self.right_labels, 1, 2) self.grid.addItem(self.bottom_labels, 2, 1) self.view.setCentralItem(self.grid_widget) self.left_dendrogram.hide() self.top_dendrogram.hide() self.right_labels.hide() self.bottom_labels.hide() self.matrix_item = None self.dendrogram = None self.grid_widget.scene().installEventFilter(self)
def setUp(self) -> None: super().setUp() self.scene = QGraphicsScene() self.view = QGraphicsView(self.scene) self.widget = DendrogramWidget() self.scene.addItem(self.widget)