class OWNxExplorer(widget.OWWidget):
name = "Network Explorer"
description = "Visually explore the network and its properties."
icon = "icons/NetworkExplorer.svg"
priority = 6420
inputs = [
("Network", network.Graph, "set_graph", widget.Default),
("Node Subset", Table, 'set_marking_items'),
("Node Data", Table, "set_items"),
("Node Distances", Orange.misc.DistMatrix, "set_items_distance_matrix"),
]
outputs = [(Output.SUBGRAPH, network.Graph),
(Output.DISTANCE, Orange.misc.DistMatrix),
(Output.SELECTED, Table),
(Output.HIGHLIGHTED, Table),
(Output.REMAINING, Table)]
settingsList = ["lastVertexSizeColumn", "lastColorColumn",
"lastLabelColumns", "lastTooltipColumns",]
# TODO: set settings
UserAdviceMessages = [
widget.Message('When selecting nodes on the Marking tab, '
'press <b><tt>Enter</tt></b> key to add '
'<b><font color="{}">highlighted</font></b> nodes to '
'<b><font color="{}">selection</font></b>.'
.format(Node.Pen.HIGHLIGHTED.color().name(),
Node.Pen.SELECTED.color().name()),
'marking-info',
widget.Message.Information),
widget.Message('Left-click to select nodes '
'(hold <b><tt>Shift</tt></b> to append to selection). '
'Right-click to pan/move the view. Scroll to zoom.',
'mouse-info',
widget.Message.Information),
]
do_auto_commit = settings.Setting(True)
maxNodeSize = settings.Setting(50)
minNodeSize = settings.Setting(8)
selectionMode = settings.Setting(0)
tabIndex = settings.Setting(0)
showEdgeWeights = settings.Setting(False)
relativeEdgeWidths = settings.Setting(False)
invertNodeSize = settings.Setting(False)
markDistance = settings.Setting(1)
markSearchString = settings.Setting("")
markNBest = settings.Setting(1)
markNConnections = settings.Setting(2)
def __init__(self):
super().__init__()
#self.contextHandlers = {"": DomainContextHandler("", [ContextField("attributes", selected="node_label_attrs"), ContextField("attributes", selected="tooltipAttributes"), "color"])}
self.view = GraphView(self)
self.mainArea.layout().addWidget(self.view)
self.graph_attrs = []
self.acceptingEnterKeypress = False
self.node_label_attrs = []
self.tooltipAttributes = []
self.searchStringTimer = QTimer(self)
self.markInputItems = None
self.node_color_attr = 0
self.node_size_attr = 0
self.nHighlighted = 0
self.nSelected = 0
self.verticesPerEdge = 0
self.edgesPerVertex = 0
self.lastVertexSizeColumn = ''
self.lastColorColumn = ''
self.lastLabelColumns = set()
self.lastTooltipColumns = set()
self.items_matrix = None
self.number_of_nodes_label = 0
self.number_of_edges_label = 0
self.graph = None
self.setMinimumWidth(600)
self.tabs = gui.tabWidget(self.controlArea)
self.displayTab = gui.createTabPage(self.tabs, "Display")
self.markTab = gui.createTabPage(self.tabs, "Marking")
def on_tab_changed(index):
self.tabIndex = index
self.set_selection_mode()
self.tabs.currentChanged.connect(on_tab_changed)
self.tabs.setCurrentIndex(self.tabIndex)
ib = gui.widgetBox(self.displayTab, "Info")
gui.label(ib, self, "Nodes: %(number_of_nodes_label)i (%(verticesPerEdge).2f per edge)")
gui.label(ib, self, "Edges: %(number_of_edges_label)i (%(edgesPerVertex).2f per node)")
box = gui.widgetBox(self.displayTab, "Nodes")
self.relayout_button = gui.button(box, self, 'Re-layout',
callback=self.relayout, autoDefault=False)
self.view.positionsChanged.connect(lambda _: self.progressbar.advance())
def animationFinished():
self.relayout_button.setEnabled(True)
self.progressbar.finish()
self.view.animationFinished.connect(animationFinished)
self.colorCombo = gui.comboBox(
box, self, "node_color_attr", label='Color:',
orientation='horizontal', callback=self.set_node_colors)
self.invertNodeSizeCheck = self.maxNodeSizeSpin = QWidget() # Forward declaration
self.nodeSizeCombo = gui.comboBox(
box, self, "node_size_attr",
label='Size:',
orientation='horizontal',
callback=self.set_node_sizes)
hb = gui.widgetBox(box, orientation="horizontal")
hb.layout().addStretch(1)
self.minNodeSizeSpin = gui.spin(
hb, self, "minNodeSize", 1, 50, step=1, label="Min:",
callback=self.set_node_sizes)
self.minNodeSizeSpin.setValue(8)
gui.separator(hb)
self.maxNodeSizeSpin = gui.spin(
hb, self, "maxNodeSize", 10, 200, step=5, label="Max:",
callback=self.set_node_sizes)
self.maxNodeSizeSpin.setValue(50)
gui.separator(hb)
self.invertNodeSizeCheck = gui.checkBox(
hb, self, "invertNodeSize", "Invert",
callback=self.set_node_sizes)
hb = gui.widgetBox(self.displayTab, box="Node labels | tooltips",
orientation="horizontal", addSpace=False)
self.attListBox = gui.listBox(
hb, self, "node_label_attrs", "graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._on_node_label_attrs_changed)
self.tooltipListBox = gui.listBox(
hb, self, "tooltipAttributes", "graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._clicked_tooltip_lstbox)
eb = gui.widgetBox(self.displayTab, "Edges", orientation="vertical")
self.checkbox_relative_edges = gui.checkBox(
eb, self, 'relativeEdgeWidths', 'Relative edge widths',
callback=self.set_edge_sizes)
self.checkbox_show_weights = gui.checkBox(
eb, self, 'showEdgeWeights', 'Show edge weights',
callback=self.set_edge_labels)
ib = gui.widgetBox(self.markTab, "Info", orientation="vertical")
gui.label(ib, self, "Nodes: %(number_of_nodes_label)i")
gui.label(ib, self, "Selected: %(nSelected)i")
gui.label(ib, self, "Highlighted: %(nHighlighted)i")
def on_selection_change():
self.nSelected = len(self.view.getSelected())
self.nHighlighted = len(self.view.getHighlighted())
self.set_selection_mode()
self.commit()
self.view.selectionChanged.connect(on_selection_change)
ib = gui.widgetBox(self.markTab, "Highlight nodes ...")
ribg = gui.radioButtonsInBox(ib, self, "selectionMode", callback=self.set_selection_mode)
gui.appendRadioButton(ribg, "None")
gui.appendRadioButton(ribg, "... whose attributes contain:")
self.ctrlMarkSearchString = gui.lineEdit(gui.indentedBox(ribg), self, "markSearchString", callback=self._set_search_string_timer, callbackOnType=True)
self.searchStringTimer.timeout.connect(self.set_selection_mode)
gui.appendRadioButton(ribg, "... neighbours of selected, ≤ N hops away")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkDistance = gui.spin(ib, self, "markDistance", 1, 100, 1, label="Hops:",
callback=lambda: self.set_selection_mode(SelectionMode.NEIGHBORS))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg, "... with at least N connections")
gui.appendRadioButton(ribg, "... with at most N connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNConnections = gui.spin(ib, self, "markNConnections", 0, 1000000, 1, label="Connections:",
callback=lambda: self.set_selection_mode(SelectionMode.AT_MOST_N if self.selectionMode == SelectionMode.AT_MOST_N else SelectionMode.AT_LEAST_N))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg, "... with more connections than any neighbor")
gui.appendRadioButton(ribg, "... with more connections than average neighbor")
gui.appendRadioButton(ribg, "... with most connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNumber = gui.spin(ib, self, "markNBest", 1, 1000000, 1,
label="Number of nodes:",
callback=lambda: self.set_selection_mode(SelectionMode.MOST_CONN))
ib.layout().addStretch(1)
self.markInputRadioButton = gui.appendRadioButton(ribg, "... given in the ItemSubset input signal")
self.markInput = 0
ib = gui.indentedBox(ribg)
self.markInputCombo = gui.comboBox(ib, self, 'markInput',
callback=lambda: self.set_selection_mode(SelectionMode.FROM_INPUT))
self.markInputRadioButton.setEnabled(False)
gui.auto_commit(ribg, self, 'do_auto_commit', 'Output changes')
self.markTab.layout().addStretch(1)
self.set_graph(None)
self.set_selection_mode()
def commit(self):
self.send_data()
def set_items_distance_matrix(self, matrix):
assert matrix is None or isinstance(matrix, Orange.misc.DistMatrix)
self.items_matrix = matrix
self.relayout()
def _set_search_string_timer(self):
self.selectionMode = SelectionMode.SEARCH
self.searchStringTimer.stop()
self.searchStringTimer.start(300)
def switchTab(self, index=None):
index = index or self.tabs.currentIndex()
curTab = self.tabs.widget(index)
self.acceptingEnterKeypress = False
if curTab == self.markTab and self.selectionMode != SelectionMode.NONE:
self.acceptingEnterKeypress = True
@non_reentrant
def set_selection_mode(self, selectionMode=None):
self.searchStringTimer.stop()
selectionMode = self.selectionMode = selectionMode or self.selectionMode
self.switchTab()
if (self.graph is None or
self.tabs.widget(self.tabs.currentIndex()) != self.markTab):
return
if selectionMode == SelectionMode.NONE:
self.view.setHighlighted([])
elif selectionMode == SelectionMode.SEARCH:
table, txt = self.graph.items(), self.markSearchString.lower()
if not table or not txt: return
toMark = set(i for i, instance in enumerate(table)
if txt in " ".join(map(str, instance.list)).lower())
self.view.setHighlighted(toMark)
elif selectionMode == SelectionMode.NEIGHBORS:
selected = set(self.view.getSelected())
neighbors = selected.copy()
for _ in range(self.markDistance):
for neigh in list(neighbors):
neighbors |= set(self.graph[neigh].keys())
neighbors -= selected
self.view.setHighlighted(neighbors)
elif selectionMode == SelectionMode.AT_LEAST_N:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree().items()
if degree >= self.markNConnections))
elif selectionMode == SelectionMode.AT_MOST_N:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree().items()
if degree <= self.markNConnections))
elif selectionMode == SelectionMode.ANY_NEIGH:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree().items()
if degree > max(self.graph.degree(self.graph[node]).values(), default=0)))
elif selectionMode == SelectionMode.AVG_NEIGH:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree().items()
if degree > np.nan_to_num(np.mean(list(self.graph.degree(self.graph[node]).values())))))
elif selectionMode == SelectionMode.MOST_CONN:
degrees = np.array(sorted(self.graph.degree().items(), key=lambda i: i[1], reverse=True))
cut_ind = max(1, min(self.markNBest, self.graph.number_of_nodes()))
cut_degree = degrees[cut_ind - 1, 1]
toMark = set(degrees[degrees[:, 1] >= cut_degree, 0])
self.view.setHighlighted(toMark)
elif selectionMode == SelectionMode.FROM_INPUT:
var = self.markInputCombo.currentText()
tomark = {}
if self.markInputItems:
if var == 'ID':
values = {x.id for x in self.markInputItems}
tomark = {x for x in self.graph.nodes()
if self.graph.items()[x].id in values}
else:
clean = lambda s: str(s).strip().upper()
values = {clean(x[var]) for x in self.markInputItems}
tomark = {x for x in self.graph.nodes()
if clean(self.graph.items()[x][var]) in values}
self.view.setHighlighted(tomark)
def keyReleaseEvent(self, ev):
"""On Enter, expand the selected set with the highlighted"""
if (not self.acceptingEnterKeypress or
ev.key() not in (Qt.Key_Return, Qt.Key_Enter)):
super().keyReleaseEvent(ev)
return
highlighted = self.view.getHighlighted()
self.view.setSelected(highlighted, extend=True)
self.view.setHighlighted([])
self.set_selection_mode()
def save_network(self):
# TODO: this was never reviewed since Orange2
if self.view is None or self.graph is None:
return
filename = QFileDialog.getSaveFileName(
self, 'Save Network', '',
'NetworkX graph as Python pickle (*.gpickle)\n'
'NetworkX edge list (*.edgelist)\n'
'Pajek network (*.net *.pajek)\n'
'GML network (*.gml)')
if filename:
_, ext = os.path.splitext(filename)
if not ext: filename += ".net"
items = self.graph.items()
for i in range(self.graph.number_of_nodes()):
graph_node = self.graph.node[i]
plot_node = self.networkCanvas.networkCurve.nodes()[i]
if items is not None:
ex = items[i]
if 'x' in ex.domain: ex['x'] = plot_node.x()
if 'y' in ex.domain: ex['y'] = plot_node.y()
graph_node['x'] = plot_node.x()
graph_node['y'] = plot_node.y()
network.readwrite.write(self.graph, filename)
def send_data(self):
if not self.graph:
for output in Output.all:
self.send(output, None)
return
selected = self.view.getSelected()
self.send(Output.SUBGRAPH,
self.graph.subgraph(selected) if selected else None)
self.send(Output.DISTANCE,
self.items_matrix.submatrix(sorted(selected)) if self.items_matrix is not None and selected else None)
items = self.graph.items()
if not items:
self.send(Output.SELECTED, None)
self.send(Output.HIGHLIGHTED, None)
self.send(Output.REMAINING, None)
else:
highlighted = self.view.getHighlighted()
self.send(Output.SELECTED, items[sorted(selected), :] if selected else None)
self.send(Output.HIGHLIGHTED, items[sorted(highlighted), :] if highlighted else None)
remaining = sorted(set(self.graph) - set(selected) - set(highlighted))
self.send(Output.REMAINING, items[remaining, :] if remaining else None)
def _set_combos(self):
self._clear_combos()
self.graph_attrs = self.graph.items_vars()
lastLabelColumns = self.lastLabelColumns
lastTooltipColumns = self.lastTooltipColumns
for var in self.graph_attrs:
if var.is_discrete or var.is_continuous:
self.colorCombo.addItem(gui.attributeIconDict[gui.vartype(var)], var.name, var)
if var.is_continuous:
self.nodeSizeCombo.addItem(gui.attributeIconDict[gui.vartype(var)], var.name, var)
elif var.is_string:
try: value = self.graph.items()[0][var].value
except (IndexError, TypeError): pass
else:
# can value be a list?
if len(value.split(',')) > 1:
self.nodeSizeCombo.addItem(gui.attributeIconDict[gui.vartype(var)], var.name, var)
self.nodeSizeCombo.setDisabled(not self.graph_attrs)
self.colorCombo.setDisabled(not self.graph_attrs)
for i in range(self.nodeSizeCombo.count()):
if self.lastVertexSizeColumn == \
self.nodeSizeCombo.itemText(i):
self.node_size_attr = i
self.set_node_sizes()
break
for i in range(self.colorCombo.count()):
if self.lastColorColumn == self.colorCombo.itemText(i):
self.node_color_attr = i
self.set_node_colors()
break
for i in range(self.attListBox.count()):
if str(self.attListBox.item(i).text()) in lastLabelColumns:
self.attListBox.item(i).setSelected(True)
self._on_node_label_attrs_changed()
for i in range(self.tooltipListBox.count()):
if (self.tooltipListBox.item(i).text() in lastTooltipColumns or
not lastTooltipColumns):
self.tooltipListBox.item(i).setSelected(True)
self._clicked_tooltip_lstbox()
self.lastLabelColumns = lastLabelColumns
self.lastTooltipColumns = lastTooltipColumns
def _clear_combos(self):
self.graph_attrs = []
self.colorCombo.clear()
self.nodeSizeCombo.clear()
self.colorCombo.addItem('(none)', None)
self.nodeSizeCombo.addItem("(uniform)")
def set_graph_none(self):
self.graph = None
self.graph_base = None
self._clear_combos()
self.number_of_nodes_label = 0
self.number_of_edges_label = 0
self.verticesPerEdge = 0
self.edgesPerVertex = 0
self._items = None
self.view.set_graph(None)
def set_graph(self, graph):
if not graph:
return self.set_graph_none()
if graph.number_of_nodes() < 2:
self.set_graph_none()
self.information('I\'m not really in a mood to visualize just one node. Try again tomorrow.')
return
self.information()
all_edges_equal = bool(1 == len(set(w for u,v,w in graph.edges_iter(data='weight'))))
self.checkbox_show_weights.setEnabled(not all_edges_equal)
self.checkbox_relative_edges.setEnabled(not all_edges_equal)
self.graph_base = graph
self.graph = graph.copy()
# Set items table from the separate signal
if self._items: self.set_items(self._items)
self.view.set_graph(self.graph, relayout=False)
# Set labels
self.number_of_nodes_label = self.graph.number_of_nodes()
self.number_of_edges_label = self.graph.number_of_edges()
self.verticesPerEdge = self.graph.number_of_nodes() / max(1, self.graph.number_of_edges())
self.edgesPerVertex = self.graph.number_of_edges() / max(1, self.graph.number_of_nodes())
self._set_combos()
if self.graph.number_of_nodes() + self.graph.number_of_edges() > 30000:
self.set_graph_none()
self.error('Network is too large to visualize. Sorry.')
return
self.error()
self.set_selection_mode()
self.relayout()
def set_items(self, items=None):
self._items = items
if items is None:
return self.set_graph(self.graph_base)
if not self.graph:
self.warning('No graph found!')
return
self.warning()
if len(items) != self.graph.number_of_nodes():
self.error('Items table must have one instance for each network node.')
return
self.error()
self.graph.set_items(items)
self._set_combos()
def set_marking_items(self, items):
self.markInputCombo.clear()
self.markInputRadioButton.setEnabled(False)
self.markInputItems = items
self.warning()
if items is None:
return
if self.graph is None or self.graph.items() is None:
self.warning('No graph provided or no items attached to the graph.')
return
graph_items = self.graph.items()
domain = graph_items.domain
if len(items) > 0:
commonVars = (set(x.name for x in chain(items.domain.variables,
items.domain.metas))
& set(x.name for x in chain(domain.variables,
domain.metas)))
self.markInputCombo.addItem(gui.attributeIconDict[gui.vartype(DiscreteVariable())], "ID")
for var in commonVars:
orgVar, mrkVar = domain[var], items.domain[var]
if type(orgVar) == type(mrkVar) == StringVariable:
self.markInputCombo.addItem(gui.attributeIconDict[gui.vartype(orgVar)], orgVar.name)
self.markInputRadioButton.setEnabled(True)
def relayout(self):
if self.graph is None or self.graph.number_of_nodes() <= 1:
return
self.progressbar = gui.ProgressBar(self, FR_ITERATIONS)
distmatrix = self.items_matrix
if distmatrix is not None and distmatrix.shape[0] != self.graph.number_of_nodes():
self.warning(17, "Distance matrix size doesn't match the number of network nodes. Not using it.")
distmatrix = None
self.warning(17)
self.relayout_button.setDisabled(True)
self.view.relayout(randomize=False, weight=distmatrix)
def _on_node_label_attrs_changed(self):
if not self.graph: return
attributes = self.lastLabelColumns = [self.graph_attrs[i] for i in self.node_label_attrs]
if attributes:
table = self.graph.items()
if not table: return
for i, node in enumerate(self.view.nodes):
text = ', '.join(map(str, table[i, attributes][0].list))
node.setText(text)
else:
for node in self.view.nodes:
node.setText('')
def _clicked_tooltip_lstbox(self):
if not self.graph: return
attributes = self.lastTooltipColumns = [self.graph_attrs[i] for i in self.tooltipAttributes]
if attributes:
table = self.graph.items()
if not table: return
assert self.view.nodes
for i, node in enumerate(self.view.nodes):
node.setTooltip(lambda row=i, attributes=attributes, table=table:
'<br>'.join('<b>{.name}:</b> {}'.format(i[0], str(i[1]).replace('<', '<'))
for i in zip(attributes, table[row, attributes][0].list))
)
else:
for node in self.view.nodes:
node.setTooltip(None)
def set_edge_labels(self):
if self.showEdgeWeights:
weights = (str(w or '') for u, v, w in self.graph.edges_iter(data='weight'))
else:
weights = ('' for i in range(self.graph.number_of_edges()))
for edge, weight in zip(self.view.edges, weights):
edge.setText(weight)
def set_node_colors(self):
if not self.graph: return
self.lastColorColumn = self.colorCombo.currentText()
attribute = self.colorCombo.itemData(self.colorCombo.currentIndex())
assert not attribute or isinstance(attribute, Orange.data.Variable)
if not attribute:
for node in self.view.nodes:
node.setColor(None)
return
table = self.graph.items()
if not table: return
if attribute in table.domain.class_vars:
values = table[:, attribute].Y
if values.ndim > 1:
values = values.T
elif attribute in table.domain.metas:
values = table[:, attribute].metas[:, 0]
elif attribute in table.domain.attributes:
values = table[:, attribute].X[:, 0]
else: raise RuntimeError("Shouldn't be able to select this column")
if attribute.is_continuous:
colors = CONTINUOUS_PALETTE[scale(values)]
elif attribute.is_discrete:
DISCRETE_PALETTE = ColorPaletteGenerator(len(attribute.values))
colors = DISCRETE_PALETTE[values]
for node, color in zip(self.view.nodes, colors):
node.setColor(color)
def set_node_sizes(self):
attribute = self.nodeSizeCombo.itemData(self.nodeSizeCombo.currentIndex())
depending_widgets = (self.invertNodeSizeCheck, self.maxNodeSizeSpin)
for w in depending_widgets:
w.setDisabled(not attribute)
if not self.graph: return
table = self.graph.items()
if not table: return
if attribute in table.domain.class_vars:
values = table[:, attribute].Y
if values.ndim > 1:
values = values.T
elif attribute in table.domain.metas:
values = table[:, attribute].metas[:, 0]
elif attribute in table.domain.attributes:
values = table[:, attribute].X[:, 0]
else:
for node in self.view.nodes:
node.setSize(self.minNodeSize)
return
values = np.array(values)
if self.invertNodeSize:
values += np.nanmin(values) + 1
values = 1/values
nodemin, nodemax = np.nanmin(values), np.nanmax(values)
if nodemin == nodemax:
# np.polyfit borks on this condition
sizes = (self.minNodeSize for i in range(len(self.view.nodes)))
else:
k, n = np.polyfit([nodemin, nodemax],
[self.minNodeSize, self.maxNodeSize], 1)
sizes = values * k + n
sizes[np.isnan(sizes)] = np.nanmean(sizes)
for node, size in zip(self.view.nodes, sizes):
node.setSize(size)
def set_edge_sizes(self):
if not self.graph: return
if self.relativeEdgeWidths:
widths = [self.graph.edge[u][v].get('weight', 1)
for u, v in self.graph.edges()]
widths = scale(widths, .7, 8)
else:
widths = (.7 for i in range(self.graph.number_of_edges()))
for edge, width in zip(self.view.edges, widths):
edge.setSize(width)
def sendReport(self):
self.reportSettings("Graph data",
[("Number of vertices", self.graph.number_of_nodes()),
("Number of edges", self.graph.number_of_edges()),
("Vertices per edge", "%.3f" % self.verticesPerEdge),
("Edges per vertex", "%.3f" % self.edgesPerVertex),
])
if self.node_color_attr or self.node_size_attr or self.node_label_attrs:
self.reportSettings("Visual settings",
[self.node_color_attr and ("Vertex color", self.colorCombo.currentText()),
self.node_size_attr and ("Vertex size", str(self.nodeSizeCombo.currentText()) + " (inverted)" if self.invertNodeSize else ""),
self.node_label_attrs and ("Labels", ", ".join(self.graph_attrs[i].name for i in self.node_label_attrs)),
])
self.reportSection("Graph")
self.reportImage(self.view)
class OWNxExplorer(widget.OWWidget):
name = "Network Explorer"
description = "Visually explore the network and its properties."
icon = "icons/NetworkExplorer.svg"
priority = 6420
inputs = [
("Network", network.Graph, "set_graph", widget.Default),
("Node Subset", Table, 'set_marking_items'),
("Node Data", Table, "set_items"),
("Node Distances", Orange.misc.DistMatrix,
"set_items_distance_matrix"),
]
outputs = [(Output.SUBGRAPH, network.Graph),
(Output.UNSELECTED_SUBGRAPH, network.Graph),
(Output.DISTANCE, Orange.misc.DistMatrix),
(Output.SELECTED, Table), (Output.HIGHLIGHTED, Table),
(Output.REMAINING, Table)]
settingsList = [
"lastVertexSizeColumn",
"lastColorColumn",
"lastLabelColumns",
"lastTooltipColumns",
]
# TODO: set settings
UserAdviceMessages = [
widget.Message(
'When selecting nodes on the Marking tab, '
'press <b><tt>Enter</tt></b> key to add '
'<b><font color="{}">highlighted</font></b> nodes to '
'<b><font color="{}">selection</font></b>.'.format(
Node.Pen.HIGHLIGHTED.color().name(),
Node.Pen.SELECTED.color().name()), 'marking-info',
widget.Message.Information),
widget.Message(
'Left-click to select nodes '
'(hold <b><tt>Shift</tt></b> to append to selection). '
'Right-click to pan/move the view. Scroll to zoom.', 'mouse-info',
widget.Message.Information),
]
do_auto_commit = settings.Setting(True)
maxNodeSize = settings.Setting(50)
minNodeSize = settings.Setting(8)
selectionMode = settings.Setting(SelectionMode.FROM_INPUT)
tabIndex = settings.Setting(0)
showEdgeWeights = settings.Setting(False)
relativeEdgeWidths = settings.Setting(False)
invertNodeSize = settings.Setting(False)
markDistance = settings.Setting(1)
markSearchString = settings.Setting("")
markNBest = settings.Setting(1)
markNConnections = settings.Setting(2)
graph_name = 'view'
def __init__(self):
super().__init__()
#self.contextHandlers = {"": DomainContextHandler("", [ContextField("attributes", selected="node_label_attrs"), ContextField("attributes", selected="tooltipAttributes"), "color"])}
self.view = GraphView(self)
self.mainArea.layout().addWidget(self.view)
self.graph_attrs = []
self.acceptingEnterKeypress = False
self.node_label_attrs = []
self.tooltipAttributes = []
self.searchStringTimer = QTimer(self)
self.markInputItems = None
self.node_color_attr = 0
self.node_size_attr = 0
self.nHighlighted = 0
self.nSelected = 0
self.verticesPerEdge = 0
self.edgesPerVertex = 0
self.lastVertexSizeColumn = ''
self.lastColorColumn = ''
self.lastLabelColumns = set()
self.lastTooltipColumns = set()
self.items_matrix = None
self.number_of_nodes_label = 0
self.number_of_edges_label = 0
self.graph = None
self.setMinimumWidth(600)
self.tabs = gui.tabWidget(self.controlArea)
self.displayTab = gui.createTabPage(self.tabs, "Display")
self.markTab = gui.createTabPage(self.tabs, "Marking")
def on_tab_changed(index):
self.tabIndex = index
self.set_selection_mode()
self.tabs.currentChanged.connect(on_tab_changed)
self.tabs.setCurrentIndex(self.tabIndex)
ib = gui.widgetBox(self.displayTab, "Info")
gui.label(
ib, self,
"Nodes: %(number_of_nodes_label)i (%(verticesPerEdge).2f per edge)"
)
gui.label(
ib, self,
"Edges: %(number_of_edges_label)i (%(edgesPerVertex).2f per node)")
box = gui.widgetBox(self.displayTab, "Nodes")
self.relayout_button = gui.button(box,
self,
'Re-layout',
callback=self.relayout,
autoDefault=False)
self.view.positionsChanged.connect(
lambda _: self.progressbar.advance())
def animationFinished():
self.relayout_button.setEnabled(True)
self.progressbar.finish()
self.view.animationFinished.connect(animationFinished)
self.colorCombo = gui.comboBox(box,
self,
"node_color_attr",
label='Color:',
orientation='horizontal',
callback=self.set_node_colors)
self.invertNodeSizeCheck = self.maxNodeSizeSpin = QWidget(
) # Forward declaration
self.nodeSizeCombo = gui.comboBox(box,
self,
"node_size_attr",
label='Size:',
orientation='horizontal',
callback=self.set_node_sizes)
hb = gui.widgetBox(box, orientation="horizontal")
hb.layout().addStretch(1)
self.minNodeSizeSpin = gui.spin(hb,
self,
"minNodeSize",
1,
50,
step=1,
label="Min:",
callback=self.set_node_sizes)
self.minNodeSizeSpin.setValue(8)
gui.separator(hb)
self.maxNodeSizeSpin = gui.spin(hb,
self,
"maxNodeSize",
10,
200,
step=5,
label="Max:",
callback=self.set_node_sizes)
self.maxNodeSizeSpin.setValue(50)
gui.separator(hb)
self.invertNodeSizeCheck = gui.checkBox(hb,
self,
"invertNodeSize",
"Invert",
callback=self.set_node_sizes)
hb = gui.widgetBox(self.displayTab,
box="Node labels | tooltips",
orientation="horizontal",
addSpace=False)
self.attListBox = gui.listBox(
hb,
self,
"node_label_attrs",
"graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._on_node_label_attrs_changed)
self.tooltipListBox = gui.listBox(
hb,
self,
"tooltipAttributes",
"graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._clicked_tooltip_lstbox)
eb = gui.widgetBox(self.displayTab, "Edges", orientation="vertical")
self.checkbox_relative_edges = gui.checkBox(
eb,
self,
'relativeEdgeWidths',
'Relative edge widths',
callback=self.set_edge_sizes)
self.checkbox_show_weights = gui.checkBox(
eb,
self,
'showEdgeWeights',
'Show edge weights',
callback=self.set_edge_labels)
ib = gui.widgetBox(self.markTab, "Info", orientation="vertical")
gui.label(ib, self, "Nodes: %(number_of_nodes_label)i")
gui.label(ib, self, "Selected: %(nSelected)i")
gui.label(ib, self, "Highlighted: %(nHighlighted)i")
def on_selection_change():
self.nSelected = len(self.view.getSelected())
self.nHighlighted = len(self.view.getHighlighted())
self.set_selection_mode()
self.commit()
self.view.selectionChanged.connect(on_selection_change)
ib = gui.widgetBox(self.markTab, "Highlight nodes ...")
ribg = gui.radioButtonsInBox(ib,
self,
"selectionMode",
callback=self.set_selection_mode)
gui.appendRadioButton(ribg, "None")
gui.appendRadioButton(ribg, "... whose attributes contain:")
self.ctrlMarkSearchString = gui.lineEdit(
gui.indentedBox(ribg),
self,
"markSearchString",
callback=self._set_search_string_timer,
callbackOnType=True)
self.searchStringTimer.timeout.connect(self.set_selection_mode)
gui.appendRadioButton(ribg,
"... neighbours of selected, ≤ N hops away")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkDistance = gui.spin(
ib,
self,
"markDistance",
1,
100,
1,
label="Hops:",
callback=lambda: self.set_selection_mode(SelectionMode.NEIGHBORS))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg, "... with at least N connections")
gui.appendRadioButton(ribg, "... with at most N connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNConnections = gui.spin(
ib,
self,
"markNConnections",
0,
1000000,
1,
label="Connections:",
callback=lambda: self.set_selection_mode(
SelectionMode.AT_MOST_N if self.selectionMode == SelectionMode.
AT_MOST_N else SelectionMode.AT_LEAST_N))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg,
"... with more connections than any neighbor")
gui.appendRadioButton(
ribg, "... with more connections than average neighbor")
gui.appendRadioButton(ribg, "... with most connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNumber = gui.spin(
ib,
self,
"markNBest",
1,
1000000,
1,
label="Number of nodes:",
callback=lambda: self.set_selection_mode(SelectionMode.MOST_CONN))
ib.layout().addStretch(1)
self.markInputRadioButton = gui.appendRadioButton(
ribg, "... from Node Subset input signal")
self.markInputRadioButton.setEnabled(True)
gui.auto_commit(ribg, self, 'do_auto_commit', 'Output changes')
self.markTab.layout().addStretch(1)
self.set_graph(None)
self.set_selection_mode()
def commit(self):
self.send_data()
def set_items_distance_matrix(self, matrix):
assert matrix is None or isinstance(matrix, Orange.misc.DistMatrix)
self.items_matrix = matrix
self.relayout()
def _set_search_string_timer(self):
self.selectionMode = SelectionMode.SEARCH
self.searchStringTimer.stop()
self.searchStringTimer.start(300)
def switchTab(self, index=None):
index = index or self.tabs.currentIndex()
curTab = self.tabs.widget(index)
self.acceptingEnterKeypress = False
if curTab == self.markTab and self.selectionMode != SelectionMode.NONE:
self.acceptingEnterKeypress = True
@non_reentrant
def set_selection_mode(self, selectionMode=None):
self.searchStringTimer.stop()
selectionMode = self.selectionMode = selectionMode or self.selectionMode
self.switchTab()
if (self.graph is None
or self.tabs.widget(self.tabs.currentIndex()) != self.markTab
and selectionMode != SelectionMode.FROM_INPUT):
return
if selectionMode == SelectionMode.NONE:
self.view.setHighlighted([])
elif selectionMode == SelectionMode.SEARCH:
table, txt = self.graph.items(), self.markSearchString.lower()
if not table or not txt: return
toMark = set(i for i, instance in enumerate(table)
if txt in " ".join(map(str, instance.list)).lower())
self.view.setHighlighted(toMark)
elif selectionMode == SelectionMode.NEIGHBORS:
selected = set(self.view.getSelected())
neighbors = selected.copy()
for _ in range(self.markDistance):
for neigh in list(neighbors):
neighbors |= set(self.graph[neigh].keys())
neighbors -= selected
self.view.setHighlighted(neighbors)
elif selectionMode == SelectionMode.AT_LEAST_N:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree().items()
if degree >= self.markNConnections))
elif selectionMode == SelectionMode.AT_MOST_N:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree().items()
if degree <= self.markNConnections))
elif selectionMode == SelectionMode.ANY_NEIGH:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree().items() if
degree > max(self.graph.degree(self.graph[node]).values(),
default=0)))
elif selectionMode == SelectionMode.AVG_NEIGH:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree().items(
) if degree > np.nan_to_num(
np.mean(list(self.graph.degree(
self.graph[node]).values())))))
elif selectionMode == SelectionMode.MOST_CONN:
degrees = np.array(
sorted(self.graph.degree().items(),
key=lambda i: i[1],
reverse=True))
cut_ind = max(1, min(self.markNBest, self.graph.number_of_nodes()))
cut_degree = degrees[cut_ind - 1, 1]
toMark = set(degrees[degrees[:, 1] >= cut_degree, 0])
self.view.setHighlighted(toMark)
elif selectionMode == SelectionMode.FROM_INPUT:
tomark = {}
if self.markInputItems:
ids = set(self.markInputItems.ids)
tomark = {
x
for x in self.graph.nodes()
if self.graph.items()[x].id in ids
}
self.view.setHighlighted(tomark)
def keyReleaseEvent(self, ev):
"""On Enter, expand the selected set with the highlighted"""
if (not self.acceptingEnterKeypress
or ev.key() not in (Qt.Key_Return, Qt.Key_Enter)):
super().keyReleaseEvent(ev)
return
highlighted = self.view.getHighlighted()
self.view.setSelected(highlighted, extend=True)
self.view.setHighlighted([])
self.set_selection_mode()
def save_network(self):
# TODO: this was never reviewed since Orange2
if self.view is None or self.graph is None:
return
filename = QFileDialog.getSaveFileName(
self, 'Save Network', '',
'NetworkX graph as Python pickle (*.gpickle)\n'
'NetworkX edge list (*.edgelist)\n'
'Pajek network (*.net *.pajek)\n'
'GML network (*.gml)')
if filename:
_, ext = os.path.splitext(filename)
if not ext: filename += ".net"
items = self.graph.items()
for i in range(self.graph.number_of_nodes()):
graph_node = self.graph.node[i]
plot_node = self.networkCanvas.networkCurve.nodes()[i]
if items is not None:
ex = items[i]
if 'x' in ex.domain: ex['x'] = plot_node.x()
if 'y' in ex.domain: ex['y'] = plot_node.y()
graph_node['x'] = plot_node.x()
graph_node['y'] = plot_node.y()
network.readwrite.write(self.graph, filename)
def send_data(self):
if not self.graph:
for output in Output.all:
self.send(output, None)
return
selected = self.view.getSelected()
self.send(Output.SUBGRAPH,
self.graph.subgraph(selected) if selected else None)
self.send(
Output.UNSELECTED_SUBGRAPH,
self.graph.subgraph(self.view.getUnselected())
if selected else self.graph)
self.send(
Output.DISTANCE,
self.items_matrix.submatrix(sorted(selected))
if self.items_matrix is not None and selected else None)
items = self.graph.items()
if not items:
self.send(Output.SELECTED, None)
self.send(Output.HIGHLIGHTED, None)
self.send(Output.REMAINING, None)
else:
highlighted = self.view.getHighlighted()
self.send(Output.SELECTED,
items[sorted(selected), :] if selected else None)
self.send(Output.HIGHLIGHTED,
items[sorted(highlighted), :] if highlighted else None)
remaining = sorted(
set(self.graph) - set(selected) - set(highlighted))
self.send(Output.REMAINING,
items[remaining, :] if remaining else None)
def _set_combos(self):
self._clear_combos()
self.graph_attrs = self.graph.items_vars()
lastLabelColumns = self.lastLabelColumns
lastTooltipColumns = self.lastTooltipColumns
for var in self.graph_attrs:
if var.is_discrete or var.is_continuous:
self.colorCombo.addItem(
gui.attributeIconDict[gui.vartype(var)], var.name, var)
if var.is_continuous:
self.nodeSizeCombo.addItem(
gui.attributeIconDict[gui.vartype(var)], var.name, var)
elif var.is_string:
try:
value = self.graph.items()[0][var].value
except (IndexError, TypeError):
pass
else:
# can value be a list?
if len(value.split(',')) > 1:
self.nodeSizeCombo.addItem(
gui.attributeIconDict[gui.vartype(var)], var.name,
var)
self.nodeSizeCombo.setDisabled(not self.graph_attrs)
self.colorCombo.setDisabled(not self.graph_attrs)
for i in range(self.nodeSizeCombo.count()):
if self.lastVertexSizeColumn == \
self.nodeSizeCombo.itemText(i):
self.node_size_attr = i
self.set_node_sizes()
break
for i in range(self.colorCombo.count()):
if self.lastColorColumn == self.colorCombo.itemText(i):
self.node_color_attr = i
self.set_node_colors()
break
for i in range(self.attListBox.count()):
if str(self.attListBox.item(i).text()) in lastLabelColumns:
self.attListBox.item(i).setSelected(True)
self._on_node_label_attrs_changed()
for i in range(self.tooltipListBox.count()):
if (self.tooltipListBox.item(i).text() in lastTooltipColumns
or not lastTooltipColumns):
self.tooltipListBox.item(i).setSelected(True)
self._clicked_tooltip_lstbox()
self.lastLabelColumns = lastLabelColumns
self.lastTooltipColumns = lastTooltipColumns
def _clear_combos(self):
self.graph_attrs = []
self.colorCombo.clear()
self.nodeSizeCombo.clear()
self.colorCombo.addItem('(none)', None)
self.nodeSizeCombo.addItem("(uniform)")
def set_graph_none(self):
self.graph = None
self.graph_base = None
self._clear_combos()
self.number_of_nodes_label = 0
self.number_of_edges_label = 0
self.verticesPerEdge = 0
self.edgesPerVertex = 0
self._items = None
self.view.set_graph(None)
def set_graph(self, graph):
if not graph:
return self.set_graph_none()
if graph.number_of_nodes() < 2:
self.set_graph_none()
self.information(
'I\'m not really in a mood to visualize just one node. Try again tomorrow.'
)
return
if graph.number_of_nodes() + graph.number_of_edges() > 30000:
self.set_graph_none()
self.error('Network is too large to visualize. Sorry.')
return
self.information()
all_edges_equal = bool(
1 == len(set(w for u, v, w in graph.edges_iter(data='weight'))))
self.checkbox_show_weights.setEnabled(not all_edges_equal)
self.checkbox_relative_edges.setEnabled(not all_edges_equal)
self.graph_base = graph
self.graph = graph.copy()
# Set items table from the separate signal
if self._items: self.set_items(self._items)
self.view.set_graph(self.graph, relayout=False)
# Set labels
self.number_of_nodes_label = self.graph.number_of_nodes()
self.number_of_edges_label = self.graph.number_of_edges()
self.verticesPerEdge = self.graph.number_of_nodes() / max(
1, self.graph.number_of_edges())
self.edgesPerVertex = self.graph.number_of_edges() / max(
1, self.graph.number_of_nodes())
self._set_combos()
self.error()
self.set_selection_mode()
self.relayout()
def set_items(self, items=None):
self._items = items
if items is None:
return self.set_graph(self.graph_base)
if not self.graph:
self.warning('No graph found!')
return
self.warning()
if len(items) != self.graph.number_of_nodes():
self.error(
'Items table must have one instance for each network node.')
return
self.error()
self.graph.set_items(items)
self._set_combos()
def set_marking_items(self, items):
self.markInputRadioButton.setEnabled(False)
self.markInputItems = items
self.warning()
if items is None:
self.view.selectionChanged.emit()
return
if self.graph is None or self.graph.items() is None:
self.warning(
'No graph provided or no items attached to the graph.')
return
graph_items = self.graph.items()
domain = graph_items.domain
if len(items) > 0:
commonVars = (
set(x.name
for x in chain(items.domain.variables, items.domain.metas))
& set(x.name for x in chain(domain.variables, domain.metas)))
self.markInputRadioButton.setEnabled(True)
self.view.selectionChanged.emit()
def relayout(self):
if self.graph is None or self.graph.number_of_nodes() <= 1:
return
self.progressbar = gui.ProgressBar(self, FR_ITERATIONS)
distmatrix = self.items_matrix
if distmatrix is not None and distmatrix.shape[
0] != self.graph.number_of_nodes():
self.warning(
17,
"Distance matrix size doesn't match the number of network nodes. Not using it."
)
distmatrix = None
self.warning(17)
self.relayout_button.setDisabled(True)
self.view.relayout(randomize=False, weight=distmatrix)
def _on_node_label_attrs_changed(self):
if not self.graph: return
attributes = self.lastLabelColumns = [
self.graph_attrs[i] for i in self.node_label_attrs
]
if attributes:
table = self.graph.items()
if not table: return
for i, node in enumerate(self.view.nodes):
text = ', '.join(map(str, table[i, attributes][0].list))
node.setText(text)
else:
for node in self.view.nodes:
node.setText('')
def _clicked_tooltip_lstbox(self):
if not self.graph: return
attributes = self.lastTooltipColumns = [
self.graph_attrs[i] for i in self.tooltipAttributes
]
if attributes:
table = self.graph.items()
if not table: return
assert self.view.nodes
for i, node in enumerate(self.view.nodes):
node.setTooltip(
lambda row=i, attributes=attributes, table=table: '<br>'.
join('<b>{.name}:</b> {}'.format(
i[0],
str(i[1]).replace('<', '<')) for i in zip(
attributes, table[row, attributes][0].list)))
else:
for node in self.view.nodes:
node.setTooltip(None)
def set_edge_labels(self):
if self.showEdgeWeights:
weights = (str(w or '')
for u, v, w in self.graph.edges_iter(data='weight'))
else:
weights = ('' for i in range(self.graph.number_of_edges()))
for edge, weight in zip(self.view.edges, weights):
edge.setText(weight)
def set_node_colors(self):
if not self.graph: return
self.lastColorColumn = self.colorCombo.currentText()
attribute = self.colorCombo.itemData(self.colorCombo.currentIndex())
assert not attribute or isinstance(attribute, Orange.data.Variable)
if not attribute:
for node in self.view.nodes:
node.setColor(None)
return
table = self.graph.items()
if not table: return
if attribute in table.domain.class_vars:
values = table[:, attribute].Y
if values.ndim > 1:
values = values.T
elif attribute in table.domain.metas:
values = table[:, attribute].metas[:, 0]
elif attribute in table.domain.attributes:
values = table[:, attribute].X[:, 0]
else:
raise RuntimeError("Shouldn't be able to select this column")
if attribute.is_continuous:
colors = CONTINUOUS_PALETTE[scale(values)]
elif attribute.is_discrete:
DISCRETE_PALETTE = ColorPaletteGenerator(len(attribute.values))
colors = DISCRETE_PALETTE[values]
for node, color in zip(self.view.nodes, colors):
node.setColor(color)
def set_node_sizes(self):
attribute = self.nodeSizeCombo.itemData(
self.nodeSizeCombo.currentIndex())
depending_widgets = (self.invertNodeSizeCheck, self.maxNodeSizeSpin)
for w in depending_widgets:
w.setDisabled(not attribute)
if not self.graph:
return
table = self.graph.items()
if table is None:
return
try:
values = table.get_column_view(attribute)[0]
except Exception:
for node in self.view.nodes:
node.setSize(self.minNodeSize)
return
if isinstance(table.domain[attribute], StringVariable):
values = np.array([(s.count(',') + 1) if s else np.nan
for s in values])
if self.invertNodeSize:
values += np.nanmin(values) + 1
values = 1 / values
nodemin, nodemax = np.nanmin(values), np.nanmax(values)
if nodemin == nodemax:
# np.polyfit borks on this condition
sizes = (self.minNodeSize for i in range(len(self.view.nodes)))
else:
k, n = np.polyfit([nodemin, nodemax],
[self.minNodeSize, self.maxNodeSize], 1)
sizes = values * k + n
sizes[np.isnan(sizes)] = np.nanmean(sizes)
for node, size in zip(self.view.nodes, sizes):
node.setSize(size)
def set_edge_sizes(self):
if not self.graph: return
if self.relativeEdgeWidths:
widths = [
self.graph.edge[u][v].get('weight', 1)
for u, v in self.graph.edges()
]
widths = scale(widths, .7, 8)
else:
widths = (.7 for i in range(self.graph.number_of_edges()))
for edge, width in zip(self.view.edges, widths):
edge.setSize(width)
def send_report(self):
self.report_data("Data", self.graph.items())
self.report_items('Graph info', [
("Number of vertices", self.graph.number_of_nodes()),
("Number of edges", self.graph.number_of_edges()),
("Vertices per edge", "%.3f" % self.verticesPerEdge),
("Edges per vertex", "%.3f" % self.edgesPerVertex),
])
if self.node_color_attr or self.node_size_attr or self.node_label_attrs:
self.report_items("Visual settings", [
("Vertex color", self.colorCombo.currentText()),
("Vertex size", str(self.nodeSizeCombo.currentText()) +
" (inverted)" if self.invertNodeSize else ""),
("Labels", ", ".join(self.graph_attrs[i].name
for i in self.node_label_attrs)),
])
self.report_plot("Graph", self.view)
class OWNxExplorer(widget.OWWidget):
name = "Network Explorer"
description = "Visually explore the network and its properties."
icon = "icons/NetworkExplorer.svg"
priority = 6420
class Inputs:
network = Input("Network", network.Graph, default=True)
node_subset = Input("Node Subset", Table)
node_data = Input("Node Data", Table)
node_distances = Input("Node Distances", Orange.misc.DistMatrix)
class Outputs:
subgraph = Output("Selected sub-network", network.Graph)
unselected_subgraph = Output("Remaining sub-network", network.Graph)
distances = Output("Distance matrix", Orange.misc.DistMatrix)
selected = Output("Selected items", Table)
highlighted = Output("Highlighted items", Table)
remaining = Output("Remaining items", Table)
UserAdviceMessages = [
widget.Message(
'When selecting nodes on the Marking tab, '
'press <b><tt>Enter</tt></b> key to add '
'<b><font color="{}">highlighted</font></b> nodes to '
'<b><font color="{}">selection</font></b>.'.format(
Node.Pen.HIGHLIGHTED.color().name(),
Node.Pen.SELECTED.color().name()), 'marking-info',
widget.Message.Information),
widget.Message(
'Left-click to select nodes '
'(hold <b><tt>Shift</tt></b> to append to selection). '
'Right-click to pan/move the view. Scroll to zoom.', 'mouse-info',
widget.Message.Information),
]
settingsHandler = DomainContextHandler()
do_auto_commit = Setting(True)
selectionMode = Setting(SelectionMode.FROM_INPUT)
tabIndex = Setting(0)
showEdgeWeights = Setting(False)
relativeEdgeWidths = Setting(False)
randomizePositions = Setting(True)
invertNodeSize = Setting(False)
markDistance = Setting(1)
markSearchString = Setting("")
markNBest = Setting(1)
markNConnections = Setting(2)
point_width = Setting(10)
edge_width = Setting(1)
attr_size = ContextSetting(None)
attr_color = ContextSetting(None)
attrs_label = ContextSetting({})
attrs_tooltip = ContextSetting({})
graph_name = 'view'
class Warning(widget.OWWidget.Warning):
distance_matrix_size = widget.Msg(
"Distance matrix size doesn't match the number of network nodes. Not using it."
)
no_graph_found = widget.Msg('No graph found!')
no_graph_or_items = widget.Msg(
'No graph provided or no items attached to the graph.')
class Error(widget.OWWidget.Error):
instance_for_each_node = widget.Msg(
'Items table must have one instance for each network node.')
network_too_large = widget.Msg(
'Network is too large to visualize. Sorry.')
def __init__(self):
super().__init__()
#self.contextHandlers = {"": DomainContextHandler("", [ContextField("attributes", selected="node_label_attrs"), ContextField("attributes", selected="tooltipAttributes"), "color"])}
self.view = GraphView(self)
self.mainArea.layout().addWidget(self.view)
self.graph_attrs = []
self.acceptingEnterKeypress = False
self.node_label_attrs = []
self.tooltipAttributes = []
self.searchStringTimer = QTimer(self)
self.markInputItems = None
self.node_color_attr = 0
self.node_size_attr = 0
self.nHighlighted = 0
self.nSelected = 0
self.verticesPerEdge = 0
self.edgesPerVertex = 0
self.items_matrix = None
self.number_of_nodes_label = 0
self.number_of_edges_label = 0
self.graph = None
self.setMinimumWidth(600)
self.tabs = gui.tabWidget(self.controlArea)
self.displayTab = gui.createTabPage(self.tabs, "Display")
self.markTab = gui.createTabPage(self.tabs, "Marking")
def on_tab_changed(index):
self.tabIndex = index
self.set_selection_mode()
self.tabs.currentChanged.connect(on_tab_changed)
self.tabs.setCurrentIndex(self.tabIndex)
ib = gui.widgetBox(self.displayTab, "Info")
gui.label(
ib, self,
"Nodes: %(number_of_nodes_label)i (%(verticesPerEdge).2f per edge)"
)
gui.label(
ib, self,
"Edges: %(number_of_edges_label)i (%(edgesPerVertex).2f per node)")
box = gui.widgetBox(self.displayTab, "Nodes")
self.relayout_button = gui.button(box,
self,
'Re-layout',
callback=self.relayout,
autoDefault=False)
self.randomize_cb = gui.checkBox(box, self, "randomizePositions",
"Randomize positions")
self.view.positionsChanged.connect(
lambda positions, progress: self.progressbar.widget.progressBarSet(
int(round(100 * progress))))
def animationFinished():
self.relayout_button.setEnabled(True)
self.progressbar.finish()
self.view.animationFinished.connect(animationFinished)
self.color_model = VariableListModel(placeholder="(Same color)")
self.color_combo = gui.comboBox(box,
self,
"attr_color",
label='Color:',
orientation='horizontal',
callback=self.set_node_colors,
model=self.color_model)
self.size_model = VariableListModel(placeholder="(Same size)")
self.size_combo = gui.comboBox(box,
self,
"attr_size",
label='Size:',
orientation='horizontal',
callback=self.set_node_sizes,
model=self.size_model)
gui.hSlider(box,
self,
'point_width',
label="Symbol size: ",
minValue=1,
maxValue=10,
step=1,
createLabel=False,
callback=self.set_node_sizes)
hb = gui.widgetBox(box, orientation="horizontal")
hb.layout().addStretch(1)
self.invertNodeSizeCheck = gui.checkBox(hb,
self,
"invertNodeSize",
"Invert",
callback=self.set_node_sizes)
hb = gui.widgetBox(self.displayTab,
box="Node labels | tooltips",
orientation="horizontal",
addSpace=False)
self.attListBox = gui.listBox(
hb,
self,
"node_label_attrs",
"graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._on_node_label_attrs_changed)
self.tooltipListBox = gui.listBox(
hb,
self,
"tooltipAttributes",
"graph_attrs",
selectionMode=QListWidget.MultiSelection,
sizeHint=QSize(100, 100),
callback=self._clicked_tooltip_lstbox)
eb = gui.widgetBox(self.displayTab, "Edges", orientation="vertical")
self.checkbox_relative_edges = gui.checkBox(
eb,
self,
'relativeEdgeWidths',
'Relative edge widths',
callback=self.set_edge_sizes)
gui.hSlider(eb,
self,
'edge_width',
label="Edge width: ",
minValue=1,
maxValue=10,
step=1,
createLabel=False,
callback=self.set_edge_sizes)
self.checkbox_show_weights = gui.checkBox(
eb,
self,
'showEdgeWeights',
'Show edge weights',
callback=self.set_edge_labels)
ib = gui.widgetBox(self.markTab, "Info", orientation="vertical")
gui.label(ib, self, "Nodes: %(number_of_nodes_label)i")
gui.label(ib, self, "Selected: %(nSelected)i")
gui.label(ib, self, "Highlighted: %(nHighlighted)i")
def on_selection_change():
self.nSelected = len(self.view.getSelected())
self.nHighlighted = len(self.view.getHighlighted())
self.set_selection_mode()
self.commit()
self.view.selectionChanged.connect(on_selection_change)
ib = gui.widgetBox(self.markTab, "Highlight nodes ...")
ribg = gui.radioButtonsInBox(ib,
self,
"selectionMode",
callback=self.set_selection_mode)
gui.appendRadioButton(ribg, "None")
gui.appendRadioButton(ribg, "... whose attributes contain:")
self.ctrlMarkSearchString = gui.lineEdit(
gui.indentedBox(ribg),
self,
"markSearchString",
callback=self._set_search_string_timer,
callbackOnType=True)
self.searchStringTimer.timeout.connect(self.set_selection_mode)
gui.appendRadioButton(ribg,
"... neighbours of selected, ≤ N hops away")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkDistance = gui.spin(
ib,
self,
"markDistance",
1,
100,
1,
label="Hops:",
callback=lambda: self.set_selection_mode(SelectionMode.NEIGHBORS))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg, "... with at least N connections")
gui.appendRadioButton(ribg, "... with at most N connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNConnections = gui.spin(
ib,
self,
"markNConnections",
0,
1000000,
1,
label="Connections:",
callback=lambda: self.set_selection_mode(
SelectionMode.AT_MOST_N if self.selectionMode == SelectionMode.
AT_MOST_N else SelectionMode.AT_LEAST_N))
ib.layout().addStretch(1)
gui.appendRadioButton(ribg,
"... with more connections than any neighbor")
gui.appendRadioButton(
ribg, "... with more connections than average neighbor")
gui.appendRadioButton(ribg, "... with most connections")
ib = gui.indentedBox(ribg, orientation=0)
self.ctrlMarkNumber = gui.spin(
ib,
self,
"markNBest",
1,
1000000,
1,
label="Number of nodes:",
callback=lambda: self.set_selection_mode(SelectionMode.MOST_CONN))
ib.layout().addStretch(1)
self.markInputRadioButton = gui.appendRadioButton(
ribg, "... from Node Subset input signal")
self.markInputRadioButton.setEnabled(True)
gui.auto_commit(ribg, self, 'do_auto_commit', 'Output changes')
self.markTab.layout().addStretch(1)
self.set_graph(None)
self.set_selection_mode()
def sizeHint(self):
return QSize(800, 600)
def commit(self):
self.send_data()
@Inputs.node_distances
def set_items_distance_matrix(self, matrix):
assert matrix is None or isinstance(matrix, Orange.misc.DistMatrix)
self.items_matrix = matrix
self.relayout()
def _set_search_string_timer(self):
self.selectionMode = SelectionMode.SEARCH
self.searchStringTimer.stop()
self.searchStringTimer.start(300)
def switchTab(self, index=None):
index = index or self.tabs.currentIndex()
curTab = self.tabs.widget(index)
self.acceptingEnterKeypress = False
if curTab == self.markTab and self.selectionMode != SelectionMode.NONE:
self.acceptingEnterKeypress = True
@non_reentrant
def set_selection_mode(self, selectionMode=None):
self.searchStringTimer.stop()
selectionMode = self.selectionMode = selectionMode or self.selectionMode
self.switchTab()
if (self.graph is None
or self.tabs.widget(self.tabs.currentIndex()) != self.markTab
and selectionMode != SelectionMode.FROM_INPUT):
return
if selectionMode == SelectionMode.NONE:
self.view.setHighlighted([])
elif selectionMode == SelectionMode.SEARCH:
table, txt = self.graph.items(), self.markSearchString.lower()
if not table or not txt: return
toMark = set(i for i, instance in enumerate(table)
if txt in " ".join(map(str, instance.list)).lower())
self.view.setHighlighted(toMark)
elif selectionMode == SelectionMode.NEIGHBORS:
selected = set(self.view.getSelected())
neighbors = selected.copy()
for _ in range(self.markDistance):
for neigh in list(neighbors):
neighbors |= set(self.graph[neigh].keys())
neighbors -= selected
self.view.setHighlighted(neighbors)
elif selectionMode == SelectionMode.AT_LEAST_N:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree()
if degree >= self.markNConnections))
elif selectionMode == SelectionMode.AT_MOST_N:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree()
if degree <= self.markNConnections))
elif selectionMode == SelectionMode.ANY_NEIGH:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree() if degree >
max(dict(self.graph.degree(self.graph[node])).values(),
default=0)))
elif selectionMode == SelectionMode.AVG_NEIGH:
self.view.setHighlighted(
set(node for node, degree in self.graph.degree()
if degree > np.nan_to_num(
np.mean(
list(
dict(self.graph.degree(
self.graph[node])).values())))))
elif selectionMode == SelectionMode.MOST_CONN:
degrees = np.array(
sorted(self.graph.degree(), key=lambda i: i[1], reverse=True))
cut_ind = max(1, min(self.markNBest, self.graph.number_of_nodes()))
cut_degree = degrees[cut_ind - 1, 1]
toMark = set(degrees[degrees[:, 1] >= cut_degree, 0])
self.view.setHighlighted(toMark)
elif selectionMode == SelectionMode.FROM_INPUT:
tomark = {}
if self.markInputItems:
ids = set(self.markInputItems.ids)
tomark = {
x
for x in self.graph if self.graph.items()[x].id in ids
}
self.view.setHighlighted(tomark)
def keyReleaseEvent(self, ev):
"""On Enter, expand the selected set with the highlighted"""
if (not self.acceptingEnterKeypress
or ev.key() not in (Qt.Key_Return, Qt.Key_Enter)):
super().keyReleaseEvent(ev)
return
highlighted = self.view.getHighlighted()
self.view.setSelected(highlighted, extend=True)
self.view.setHighlighted([])
self.set_selection_mode()
def save_network(self):
# TODO: this was never reviewed since Orange2
if self.view is None or self.graph is None:
return
filename = QFileDialog.getSaveFileName(
self, 'Save Network', '',
'NetworkX graph as Python pickle (*.gpickle)\n'
'NetworkX edge list (*.edgelist)\n'
'Pajek network (*.net *.pajek)\n'
'GML network (*.gml)')
if filename:
_, ext = os.path.splitext(filename)
if not ext: filename += ".net"
items = self.graph.items()
for i in range(self.graph.number_of_nodes()):
graph_node = self.graph.node[i]
plot_node = self.networkCanvas.networkCurve.nodes()[i]
if items is not None:
ex = items[i]
if 'x' in ex.domain: ex['x'] = plot_node.x()
if 'y' in ex.domain: ex['y'] = plot_node.y()
graph_node['x'] = plot_node.x()
graph_node['y'] = plot_node.y()
network.readwrite.write(self.graph, filename)
def send_data(self):
if not self.graph:
for output in dir(self.Outputs):
if not output.startswith('__'):
getattr(self.Outputs, output).send(None)
return
selected = self.view.getSelected()
self.Outputs.subgraph.send(
self.graph.subgraph(selected) if selected else None)
self.Outputs.unselected_subgraph.send(
self.graph.subgraph(self.view.getUnselected()
) if selected else self.graph)
self.Outputs.distances.send(
self.items_matrix.submatrix(sorted(selected))
if self.items_matrix is not None and selected else None)
items = self.graph.items()
if not items:
self.Outputs.selected.send(None)
self.Outputs.highlighted.send(None)
self.Outputs.remaining.send(None)
else:
highlighted = self.view.getHighlighted()
self.Outputs.selected.send(items[
sorted(selected), :] if selected else None)
self.Outputs.highlighted.send(items[
sorted(highlighted), :] if highlighted else None)
remaining = sorted(
set(self.graph) - set(selected) - set(highlighted))
self.Outputs.remaining.send(items[
remaining, :] if remaining else None)
def _set_combos(self):
self._clear_combos()
self.graph_attrs = self.graph.items_vars()
self.color_model[:] = [None] + [
v for v in self.graph_attrs if v.is_primitive()
]
self.size_model[:] = [None] + [
v for v in self.graph_attrs if v.is_continuous
]
self.size_combo.setDisabled(not self.graph_attrs)
self.color_combo.setDisabled(not self.graph_attrs)
self.set_node_sizes()
self.set_node_colors()
self.set_edge_sizes()
for columns, box in ((self.attrs_label, self.attListBox),
(self.attrs_tooltip, self.tooltipListBox)):
columns = [var.name for var in columns]
if columns:
selection = QItemSelection()
model = box.model()
for i in range(box.count()):
if str(box.item(i).text()) in columns:
selection.append(QItemSelectionRange(model.index(i,
0)))
selmodel = box.selectionModel()
selmodel.select(selection, selmodel.Select | selmodel.Clear)
else:
box.selectionModel().clearSelection()
self._on_node_label_attrs_changed()
self._clicked_tooltip_lstbox()
def _clear_combos(self):
self.graph_attrs = []
self.color_combo.clear()
self.size_combo.clear()
def set_graph_none(self):
self.graph = None
self.graph_base = None
self._clear_combos()
self.number_of_nodes_label = 0
self.number_of_edges_label = 0
self.verticesPerEdge = 0
self.edgesPerVertex = 0
self._items = None
self.view.set_graph(None)
@Inputs.network
def set_graph(self, graph):
if not graph:
return self.set_graph_none()
if graph.number_of_nodes() < 2:
self.set_graph_none()
self.information(
'I\'m not really in a mood to visualize just one node. Try again tomorrow.'
)
return
if graph.number_of_nodes() + graph.number_of_edges() > 30000:
self.set_graph_none()
self.Error.network_too_large()
return
self.information()
self.closeContext()
all_edges_equal = bool(
1 == len(set(w for u, v, w in graph.edges(data='weight'))))
self.checkbox_show_weights.setEnabled(not all_edges_equal)
self.checkbox_relative_edges.setEnabled(not all_edges_equal)
self.graph_base = graph
self.graph = graph.copy()
# Set items table from the separate signal
if self._items: self.set_items(self._items)
self.view.set_graph(self.graph, relayout=False)
# Set labels
self.number_of_nodes_label = self.graph.number_of_nodes()
self.number_of_edges_label = self.graph.number_of_edges()
self.verticesPerEdge = self.graph.number_of_nodes() / max(
1, self.graph.number_of_edges())
self.edgesPerVertex = self.graph.number_of_edges() / max(
1, self.graph.number_of_nodes())
self._set_combos()
if self.graph.items():
self.openContext(self.graph.items().domain)
self.Error.clear()
self.set_selection_mode()
self.randomizePositions = True
self.relayout()
@Inputs.node_data
def set_items(self, items=None):
self._items = items
if items is None:
return self.set_graph(self.graph_base)
if not self.graph:
self.Warning.no_graph_found()
return
self.Warning.clear()
if len(items) != self.graph.number_of_nodes():
self.Error.instance_for_each_node()
return
self.Error.instance_for_each_node.clear()
self.graph.set_items(items)
self._set_combos()
@Inputs.node_subset
def set_marking_items(self, items):
self.markInputRadioButton.setEnabled(False)
self.markInputItems = items
self.Warning.clear()
if self.selectionMode == SelectionMode.FROM_INPUT and \
(items is None or self.graph is None or self.graph.items() is None):
self.selectionMode = SelectionMode.NONE
if items is None:
self.view.selectionChanged.emit()
return
if self.graph is None or self.graph.items() is None:
self.Warning.no_graph_or_items()
return
if len(items) > 0:
self.markInputRadioButton.setEnabled(True)
self.view.selectionChanged.emit()
def relayout(self):
if self.graph is None or self.graph.number_of_nodes() <= 1:
return
self.progressbar = gui.ProgressBar(self, FR_ITERATIONS)
distmatrix = self.items_matrix
if distmatrix is not None and distmatrix.shape[
0] != self.graph.number_of_nodes():
self.Warning.distance_matrix_size()
distmatrix = None
self.Warning.distance_matrix_size.clear()
self.relayout_button.setDisabled(True)
self.view.relayout(randomize=self.randomizePositions,
weight=distmatrix)
def _on_node_label_attrs_changed(self):
if not self.graph: return
attributes = self.attrs_label = [
self.graph_attrs[i] for i in self.node_label_attrs
]
if attributes:
table = self.graph.items()
if not table: return
for i, node in enumerate(self.view.nodes):
text = ', '.join(map(str, table[i, attributes][0].list))
node.setText(text)
else:
for node in self.view.nodes:
node.setText('')
def _clicked_tooltip_lstbox(self):
if not self.graph: return
attributes = self.attrs_tooltip = [
self.graph_attrs[i] for i in self.tooltipAttributes
]
if attributes:
table = self.graph.items()
if not table: return
assert self.view.nodes
for i, node in enumerate(self.view.nodes):
node.setTooltip(
lambda row=i, attributes=attributes, table=table: '<br>'.
join('<b>{.name}:</b> {}'.format(
i[0],
str(i[1]).replace('<', '<')) for i in zip(
attributes, table[row, attributes][0].list)))
else:
for node in self.view.nodes:
node.setTooltip(None)
def set_edge_labels(self):
if not self.graph:
return
if self.showEdgeWeights:
weights = (str(w or '')
for u, v, w in self.graph.edges(data='weight'))
else:
weights = ('' for i in range(self.graph.number_of_edges()))
for edge, weight in zip(self.view.edges, weights):
edge.setText(weight)
def set_node_colors(self):
if not self.graph: return
attribute = self.attr_color
assert not attribute or isinstance(attribute, Orange.data.Variable)
if self.view.legend is not None:
self.view.scene().removeItem(self.view.legend)
self.view.legend.clear()
else:
self.view.legend = LegendItem()
self.view.legend.set_parent(self.view)
if not attribute:
for node in self.view.nodes:
node.setColor(None)
return
table = self.graph.items()
if not table: return
if attribute in table.domain.class_vars:
values = table[:, attribute].Y
if values.ndim > 1:
values = values.T
elif attribute in table.domain.metas:
values = table[:, attribute].metas[:, 0]
elif attribute in table.domain.attributes:
values = table[:, attribute].X[:, 0]
else:
raise RuntimeError("Shouldn't be able to select this column")
if attribute.is_continuous:
colors = CONTINUOUS_PALETTE[scale(values)]
label = PaletteItemSample(
CONTINUOUS_PALETTE,
DiscretizedScale(np.nanmin(values), np.nanmax(values)))
self.view.legend.addItem(label, "")
self.view.legend.setGeometry(label.boundingRect())
elif attribute.is_discrete:
DISCRETE_PALETTE = ColorPaletteGenerator(len(attribute.values))
colors = DISCRETE_PALETTE[values]
for value, color in zip(attribute.values, DISCRETE_PALETTE):
self.view.legend.addItem(
ScatterPlotItem(pen=Node.Pen.DEFAULT,
brush=QBrush(QColor(color)),
size=10,
symbol="o"), escape(value))
for node, color in zip(self.view.nodes, colors):
node.setColor(color)
self.view.scene().addItem(self.view.legend)
self.view.legend.geometry_changed()
def set_node_sizes(self):
self.invertNodeSizeCheck.setDisabled(not self.attr_size)
if not self.graph:
return
table = self.graph.items()
if table is None:
return
try:
a = table.get_column_view(self.attr_size)[0]
values = a.copy()
except Exception:
for node in self.view.nodes:
node.setSize(MIN_NODE_SIZE * self.point_width)
return
if self.invertNodeSize:
values += np.nanmin(values) + 1
values = 1 / values
nodemin, nodemax = np.nanmin(values), np.nanmax(values)
if nodemin == nodemax:
# np.polyfit borks on this condition
sizes = (MIN_NODE_SIZE for _ in range(len(self.view.nodes)))
else:
k, n = np.polyfit([nodemin, nodemax],
[MIN_NODE_SIZE, MAX_NODE_SIZE], 1)
sizes = values * k + n
sizes[np.isnan(sizes)] = np.nanmean(sizes)
for node, size in zip(self.view.nodes, sizes):
node.setSize(size * self.point_width)
def set_edge_sizes(self):
if not self.graph: return
if self.relativeEdgeWidths:
widths = [
self.graph.adj[u][v].get('weight', 1)
for u, v in self.graph.edges()
]
widths = scale(widths, .7, 8) * np.log2(self.edge_width / 4 + 1)
else:
widths = (.7 * self.edge_width
for _ in range(self.graph.number_of_edges()))
for edge, width in zip(self.view.edges, widths):
edge.setSize(width)
def send_report(self):
self.report_data("Data", self.graph.items())
self.report_items('Graph info', [
("Number of vertices", self.graph.number_of_nodes()),
("Number of edges", self.graph.number_of_edges()),
("Vertices per edge", "%.3f" % self.verticesPerEdge),
("Edges per vertex", "%.3f" % self.edgesPerVertex),
])
if self.node_color_attr or self.node_size_attr or self.node_label_attrs:
self.report_items("Visual settings", [
("Vertex color", self.colorCombo.currentText()),
("Vertex size", str(self.nodeSizeCombo.currentText()) +
" (inverted)" if self.invertNodeSize else ""),
("Labels", ", ".join(self.graph_attrs[i].name
for i in self.node_label_attrs)),
])
self.report_plot("Graph", self.view)