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)
palette_name = settings.Setting(colorpalettes.DefaultContinuousPaletteName)
color_gamma = settings.Setting(0.0)
color_low = settings.Setting(0.0)
color_high = settings.Setting(1.0)
annotation_idx = settings.ContextSetting(0)
pending_selection = settings.Setting(None, schema_only=True)
autocommit = settings.Setting(True)
graph_name = "grid_widget"
# Disable clustering for inputs bigger than this
_MaxClustering = 25000
# Disable cluster leaf ordering for inputs bigger than this
_MaxOrderedClustering = 2000
def __init__(self):
super().__init__()
self.matrix = None
self._matrix_range = 0.
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.color_map_widget = cmw = ColorGradientSelection(
thresholds=(self.color_low, self.color_high), )
model = itemmodels.ContinuousPalettesModel(parent=self)
cmw.setModel(model)
idx = cmw.findData(self.palette_name, model.KeyRole)
if idx != -1:
cmw.setCurrentIndex(idx)
cmw.activated.connect(self._update_color)
def _set_thresholds(low, high):
self.color_low, self.color_high = low, high
self._update_color()
cmw.thresholdsChanged.connect(_set_thresholds)
box.layout().addWidget(self.color_map_widget)
self.annot_combo = gui.comboBox(self.controlArea,
self,
"annotation_idx",
box="Annotations",
contentsLength=12,
searchable=True,
callback=self._invalidate_annotations)
self.annot_combo.setModel(itemmodels.VariableListModel())
self.annot_combo.model()[:] = ["None", "Enumeration"]
gui.rubber(self.controlArea)
gui.auto_send(self.buttonsArea, self, "autocommit")
self.view = GraphicsView(background=None)
self.mainArea.layout().addWidget(self.view)
self.grid_widget = pg.GraphicsWidget()
self.grid = QGraphicsGridLayout()
self.grid_widget.setLayout(self.grid)
self.gradient_legend = GradientLegendWidget(0, 1, self._color_map())
self.gradient_legend.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Fixed)
self.gradient_legend.setMaximumWidth(250)
self.grid.addItem(self.gradient_legend, 0, 1)
self.viewbox = pg.ViewBox(enableMouse=False, enableMenu=False)
self.viewbox.setAcceptedMouseButtons(Qt.NoButton)
self.viewbox.setAcceptHoverEvents(False)
self.grid.addItem(self.viewbox, 2, 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, 2, 0)
self.grid.addItem(self.top_dendrogram, 1, 1)
self.right_labels = TextList(alignment=Qt.AlignLeft | Qt.AlignVCenter,
sizePolicy=QSizePolicy(
QSizePolicy.Fixed,
QSizePolicy.Expanding))
self.bottom_labels = TextList(
orientation=Qt.Horizontal,
alignment=Qt.AlignRight | Qt.AlignVCenter,
sizePolicy=QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed))
self.grid.addItem(self.right_labels, 2, 2)
self.grid.addItem(self.bottom_labels, 3, 1)
self.view.setCentralItem(self.grid_widget)
self.gradient_legend.hide()
self.left_dendrogram.hide()
self.top_dendrogram.hide()
self.right_labels.hide()
self.bottom_labels.hide()
self.matrix_item = None
self.dendrogram = None
self.settingsAboutToBePacked.connect(self.pack_settings)
def pack_settings(self):
if self.matrix_item is not None:
self.pending_selection = self.matrix_item.selections()
else:
self.pending_selection = None
@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._matrix_range = numpy.nanmax(matrix)
self.set_items(matrix.row_items, matrix.axis)
else:
self._matrix_range = 0.
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._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()
if self.pending_selection is not None:
self.matrix_item.set_selections(self.pending_selection)
self.pending_selection = None
self.commit.now()
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)
self.gradient_legend.hide()
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.setItems(labels or [])
textlist.setVisible(bool(labels))
constraint = -1 if labels else 0
self.right_labels.setMaximumWidth(constraint)
self.bottom_labels.setMaximumHeight(constraint)
def _color_map(self) -> GradientColorMap:
palette = self.color_map_widget.currentData()
return GradientColorMap(palette.lookup_table(),
thresholds=(self.color_low,
max(self.color_high,
self.color_low)),
span=(0., self._matrix_range))
def _update_color(self):
palette = self.color_map_widget.currentData()
self.palette_name = palette.name
if self.matrix_item:
cmap = self._color_map().replace(span=(0., 1.))
colors = cmap.apply(numpy.arange(256) / 255.)
self.matrix_item.setLookupTable(colors)
self.gradient_legend.show()
self.gradient_legend.setRange(0, self._matrix_range)
self.gradient_legend.setColorMap(self._color_map())
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.deferred()
@gui.deferred
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._matrix_range = 0.
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.color_map_widget = cmw = ColorGradientSelection(
thresholds=(self.color_low, self.color_high), )
model = itemmodels.ContinuousPalettesModel(parent=self)
cmw.setModel(model)
idx = cmw.findData(self.palette_name, model.KeyRole)
if idx != -1:
cmw.setCurrentIndex(idx)
cmw.activated.connect(self._update_color)
def _set_thresholds(low, high):
self.color_low, self.color_high = low, high
self._update_color()
cmw.thresholdsChanged.connect(_set_thresholds)
box.layout().addWidget(self.color_map_widget)
self.annot_combo = gui.comboBox(self.controlArea,
self,
"annotation_idx",
box="Annotations",
contentsLength=12,
searchable=True,
callback=self._invalidate_annotations)
self.annot_combo.setModel(itemmodels.VariableListModel())
self.annot_combo.model()[:] = ["None", "Enumeration"]
gui.rubber(self.controlArea)
gui.auto_send(self.buttonsArea, self, "autocommit")
self.view = GraphicsView(background=None)
self.mainArea.layout().addWidget(self.view)
self.grid_widget = pg.GraphicsWidget()
self.grid = QGraphicsGridLayout()
self.grid_widget.setLayout(self.grid)
self.gradient_legend = GradientLegendWidget(0, 1, self._color_map())
self.gradient_legend.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Fixed)
self.gradient_legend.setMaximumWidth(250)
self.grid.addItem(self.gradient_legend, 0, 1)
self.viewbox = pg.ViewBox(enableMouse=False, enableMenu=False)
self.viewbox.setAcceptedMouseButtons(Qt.NoButton)
self.viewbox.setAcceptHoverEvents(False)
self.grid.addItem(self.viewbox, 2, 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, 2, 0)
self.grid.addItem(self.top_dendrogram, 1, 1)
self.right_labels = TextList(alignment=Qt.AlignLeft | Qt.AlignVCenter,
sizePolicy=QSizePolicy(
QSizePolicy.Fixed,
QSizePolicy.Expanding))
self.bottom_labels = TextList(
orientation=Qt.Horizontal,
alignment=Qt.AlignRight | Qt.AlignVCenter,
sizePolicy=QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed))
self.grid.addItem(self.right_labels, 2, 2)
self.grid.addItem(self.bottom_labels, 3, 1)
self.view.setCentralItem(self.grid_widget)
self.gradient_legend.hide()
self.left_dendrogram.hide()
self.top_dendrogram.hide()
self.right_labels.hide()
self.bottom_labels.hide()
self.matrix_item = None
self.dendrogram = None
self.settingsAboutToBePacked.connect(self.pack_settings)
def __init__(self):
super().__init__()
self.matrix = None
self._matrix_range = 0.
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.color_box = gui.palette_combo_box(self.palette_name)
self.color_box.currentIndexChanged.connect(self._update_color)
box.layout().addWidget(self.color_box)
form = QFormLayout(formAlignment=Qt.AlignLeft,
labelAlignment=Qt.AlignLeft,
fieldGrowthPolicy=QFormLayout.AllNonFixedFieldsGrow)
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",
contentsLength=12,
searchable=True,
callback=self._invalidate_annotations)
self.annot_combo.setModel(itemmodels.VariableListModel())
self.annot_combo.model()[:] = ["None", "Enumeration"]
self.controlArea.layout().addStretch()
gui.auto_send(self.controlArea, self, "autocommit")
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.gradient_legend = GradientLegendWidget(0, 1, self._color_map())
self.gradient_legend.setSizePolicy(QSizePolicy.Preferred,
QSizePolicy.Fixed)
self.gradient_legend.setMaximumWidth(250)
self.grid.addItem(self.gradient_legend, 0, 1)
self.viewbox = pg.ViewBox(enableMouse=False, enableMenu=False)
self.viewbox.setAcceptedMouseButtons(Qt.NoButton)
self.viewbox.setAcceptHoverEvents(False)
self.grid.addItem(self.viewbox, 2, 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, 2, 0)
self.grid.addItem(self.top_dendrogram, 1, 1)
self.right_labels = TextList(alignment=Qt.AlignLeft | Qt.AlignVCenter,
sizePolicy=QSizePolicy(
QSizePolicy.Fixed,
QSizePolicy.Expanding))
self.bottom_labels = TextList(
orientation=Qt.Horizontal,
alignment=Qt.AlignRight | Qt.AlignVCenter,
sizePolicy=QSizePolicy(QSizePolicy.Expanding, QSizePolicy.Fixed))
self.grid.addItem(self.right_labels, 2, 2)
self.grid.addItem(self.bottom_labels, 3, 1)
self.view.setCentralItem(self.grid_widget)
self.gradient_legend.hide()
self.left_dendrogram.hide()
self.top_dendrogram.hide()
self.right_labels.hide()
self.bottom_labels.hide()
self.matrix_item = None
self.dendrogram = None
self.settingsAboutToBePacked.connect(self.pack_settings)