def test_task(self):
results = []
task = Task(function=QThread.currentThread)
task.resultReady.connect(results.append)
task.start()
self.app.processEvents()
self.assertSequenceEqual(results, [QThread.currentThread()])
thread = QThread()
thread.start()
try:
task = Task(function=QThread.currentThread)
task.moveToThread(thread)
self.assertIsNot(task.thread(), QThread.currentThread())
self.assertIs(task.thread(), thread)
results = Future()
def record(value):
# record the result value and the calling thread
results.set_result((QThread.currentThread(), value))
task.resultReady.connect(record, Qt.DirectConnection)
task.start()
f = task.future()
emit_thread, thread_ = results.result(3)
self.assertIs(f.result(3), thread)
self.assertIs(emit_thread, thread)
self.assertIs(thread_, thread)
finally:
thread.quit()
thread.wait()
def test_task(self):
results = []
task = Task(function=QThread.currentThread)
task.resultReady.connect(results.append)
task.start()
self.app.processEvents()
self.assertSequenceEqual(results, [QThread.currentThread()])
thread = QThread()
thread.start()
try:
task = Task(function=QThread.currentThread)
task.moveToThread(thread)
self.assertIsNot(task.thread(), QThread.currentThread())
self.assertIs(task.thread(), thread)
results = Future()
def record(value):
# record the result value and the calling thread
results.set_result((QThread.currentThread(), value))
task.resultReady.connect(record, Qt.DirectConnection)
task.start()
f = task.future()
emit_thread, thread_ = results.result(3)
self.assertIs(f.result(3), thread)
self.assertIs(emit_thread, thread)
self.assertIs(thread_, thread)
finally:
thread.quit()
thread.wait()
class X11EventPoller(QObject):
keyPressed = pyqtSignal(object, object)
def __init__(self):
QObject.__init__(self)
self._display = Display()
self._thread = QThread()
self.moveToThread(self._thread)
self._thread.start()
def start(self):
QTimer.singleShot(0, self.run)
def run(self):
ctx = self._display.record_create_context(0,
[record.CurrentClients],
[{
'core_requests': (0, 0),
'core_replies': (0, 0),
'ext_requests': (0, 0, 0, 0),
'ext_replies': (0, 0, 0, 0),
'delivered_events': (0, 0),
'device_events': (X.KeyPress, X.KeyRelease),
'errors': (0, 0),
'client_started': False,
'client_died': False,
}])
self._display.record_enable_context(ctx, self._record_callback)
self._display.record_free_context(ctx)
def _record_callback(self, reply):
QApplication.processEvents()
if reply.category != record.FromServer:
return
if reply.client_swapped:
# received swapped protocol data, cowardly ignored
return
if not len(reply.data) or reply.data[0] < 2:
# not an event
return
data = reply.data
while len(data):
event, data = rq.EventField(None).parse_binary_value(data, self._display.display, None, None)
self.keyPressed.emit(event, data)
def destroy(self):
# self._thread.terminate()
self._thread.wait()
class OWSOM(OWWidget):
name = "Self-Organizing Map"
description = "Computation of self-organizing map."
icon = "icons/SOM.svg"
keywords = ["SOM"]
class Inputs:
data = Input("Data", Table)
class Outputs:
selected_data = Output("Selected Data", Table, default=True)
annotated_data = Output(ANNOTATED_DATA_SIGNAL_NAME, Table)
settingsHandler = DomainContextHandler()
auto_dimension = Setting(True)
size_x = Setting(10)
size_y = Setting(10)
hexagonal = Setting(1)
initialization = Setting(0)
attr_color = ContextSetting(None)
size_by_instances = Setting(True)
pie_charts = Setting(False)
selection = Setting(None, schema_only=True)
graph_name = "view"
_grid_pen = QPen(QBrush(QColor(224, 224, 224)), 2)
_grid_pen.setCosmetic(True)
OptControls = namedtuple(
"OptControls",
("shape", "auto_dim", "spin_x", "spin_y", "initialization", "start"))
class Warning(OWWidget.Warning):
ignoring_disc_variables = Msg("SOM ignores discrete variables.")
missing_colors = \
Msg("Some data instances have undefined value of '{}'.")
missing_values = \
Msg("{} data instance{} with undefined value(s) {} not shown.")
single_attribute = Msg("Data contains a single numeric column.")
class Error(OWWidget.Error):
no_numeric_variables = Msg("Data contains no numeric columns.")
no_defined_rows = Msg("All rows contain at least one undefined value.")
def __init__(self):
super().__init__()
self.__pending_selection = self.selection
self._optimizer = None
self._optimizer_thread = None
self.stop_optimization = False
self.data = self.cont_x = None
self.cells = self.member_data = None
self.selection = None
self.colors = self.thresholds = self.bin_labels = None
self._set_input_summary(None)
self._set_output_summary(None)
box = gui.vBox(self.controlArea, box="SOM")
shape = gui.comboBox(box,
self,
"",
items=("Hexagonal grid", "Square grid"))
shape.setCurrentIndex(1 - self.hexagonal)
box2 = gui.indentedBox(box, 10)
auto_dim = gui.checkBox(box2,
self,
"auto_dimension",
"Set dimensions automatically",
callback=self.on_auto_dimension_changed)
self.manual_box = box3 = gui.hBox(box2)
spinargs = dict(value="",
widget=box3,
master=self,
minv=5,
maxv=100,
step=5,
alignment=Qt.AlignRight)
spin_x = gui.spin(**spinargs)
spin_x.setValue(self.size_x)
gui.widgetLabel(box3, "×")
spin_y = gui.spin(**spinargs)
spin_y.setValue(self.size_y)
gui.rubber(box3)
self.manual_box.setEnabled(not self.auto_dimension)
initialization = gui.comboBox(box,
self,
"initialization",
items=("Initialize with PCA",
"Random initialization",
"Replicable random"))
start = gui.button(box,
self,
"Restart",
callback=self.restart_som_pressed,
sizePolicy=(QSizePolicy.MinimumExpanding,
QSizePolicy.Fixed))
self.opt_controls = self.OptControls(shape, auto_dim, spin_x, spin_y,
initialization, start)
box = gui.vBox(self.controlArea, "Color")
gui.comboBox(box,
self,
"attr_color",
searchable=True,
callback=self.on_attr_color_change,
model=DomainModel(placeholder="(Same color)",
valid_types=DomainModel.PRIMITIVE))
gui.checkBox(box,
self,
"pie_charts",
label="Show pie charts",
callback=self.on_pie_chart_change)
gui.checkBox(box,
self,
"size_by_instances",
label="Size by number of instances",
callback=self.on_attr_size_change)
gui.rubber(self.controlArea)
self.scene = QGraphicsScene(self)
self.view = SomView(self.scene)
self.view.setMinimumWidth(400)
self.view.setMinimumHeight(400)
self.view.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.view.setVerticalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
self.view.setRenderHint(QPainter.Antialiasing)
self.view.selection_changed.connect(self.on_selection_change)
self.view.selection_moved.connect(self.on_selection_move)
self.view.selection_mark_changed.connect(self.on_selection_mark_change)
self.mainArea.layout().addWidget(self.view)
self.elements = None
self.grid = None
self.grid_cells = None
self.legend = None
@Inputs.data
def set_data(self, data):
def prepare_data():
if len(cont_attrs) < len(attrs):
self.Warning.ignoring_disc_variables()
if len(cont_attrs) == 1:
self.Warning.single_attribute()
x = Table.from_table(Domain(cont_attrs), data).X
if sp.issparse(x):
self.data = data
self.cont_x = x.tocsr()
else:
mask = np.all(np.isfinite(x), axis=1)
if not np.any(mask):
self.Error.no_defined_rows()
else:
if np.all(mask):
self.data = data
self.cont_x = x.copy()
else:
self.data = data[mask]
self.cont_x = x[mask]
self.cont_x -= np.min(self.cont_x, axis=0)[None, :]
sums = np.sum(self.cont_x, axis=0)[None, :]
sums[sums == 0] = 1
self.cont_x /= sums
def set_warnings():
missing = len(data) - len(self.data)
if missing == 1:
self.Warning.missing_values(1, "", "is")
elif missing > 1:
self.Warning.missing_values(missing, "s", "are")
self.stop_optimization_and_wait()
self.closeContext()
self.clear()
self.Error.clear()
self.Warning.clear()
if data is not None:
attrs = data.domain.attributes
cont_attrs = [var for var in attrs if var.is_continuous]
if not cont_attrs:
self.Error.no_numeric_variables()
else:
prepare_data()
if self.data is not None:
self.controls.attr_color.model().set_domain(data.domain)
self.attr_color = data.domain.class_var
set_warnings()
self.openContext(self.data)
self.set_color_bins()
self.create_legend()
self.recompute_dimensions()
self._set_input_summary(data)
self.start_som()
def _set_input_summary(self, data):
summary = len(data) if data else self.info.NoInput
details = format_summary_details(data) if data else ""
self.info.set_input_summary(summary, details)
def _set_output_summary(self, output):
summary = len(output) if output else self.info.NoOutput
details = format_summary_details(output) if output else ""
self.info.set_output_summary(summary, details)
def clear(self):
self.data = self.cont_x = None
self.cells = self.member_data = None
self.attr_color = None
self.colors = self.thresholds = self.bin_labels = None
if self.elements is not None:
self.scene.removeItem(self.elements)
self.elements = None
self.clear_selection()
self.controls.attr_color.model().set_domain(None)
self.Warning.clear()
self.Error.clear()
def recompute_dimensions(self):
if not self.auto_dimension or self.cont_x is None:
return
dim = max(5, int(np.ceil(np.sqrt(5 * np.sqrt(self.cont_x.shape[0])))))
self.opt_controls.spin_x.setValue(dim)
self.opt_controls.spin_y.setValue(dim)
def on_auto_dimension_changed(self):
self.manual_box.setEnabled(not self.auto_dimension)
if self.auto_dimension:
self.recompute_dimensions()
else:
spin_x = self.opt_controls.spin_x
spin_y = self.opt_controls.spin_y
dimx = int(5 * np.round(spin_x.value() / 5))
dimy = int(5 * np.round(spin_y.value() / 5))
spin_x.setValue(dimx)
spin_y.setValue(dimy)
def on_attr_color_change(self):
self.controls.pie_charts.setEnabled(self.attr_color is not None)
self.set_color_bins()
self.create_legend()
self.rescale()
self._redraw()
def on_attr_size_change(self):
self._redraw()
def on_pie_chart_change(self):
self._redraw()
def clear_selection(self):
self.selection = None
self.redraw_selection()
def on_selection_change(self, selection, action=SomView.SelectionSet):
if self.data is None: # clicks on empty canvas
return
if self.selection is None:
self.selection = np.zeros(self.grid_cells.T.shape, dtype=np.int16)
if action == SomView.SelectionSet:
self.selection[:] = 0
self.selection[selection] = 1
elif action == SomView.SelectionAddToGroup:
self.selection[selection] = max(1, np.max(self.selection))
elif action == SomView.SelectionNewGroup:
self.selection[selection] = 1 + np.max(self.selection)
elif action & SomView.SelectionRemove:
self.selection[selection] = 0
self.redraw_selection()
self.update_output()
def on_selection_move(self, event: QKeyEvent):
if self.selection is None or not np.any(self.selection):
if event.key() in (Qt.Key_Right, Qt.Key_Down):
x = y = 0
else:
x = self.size_x - 1
y = self.size_y - 1
else:
x, y = np.nonzero(self.selection)
if len(x) > 1:
return
if event.key() == Qt.Key_Up and y > 0:
y -= 1
if event.key() == Qt.Key_Down and y < self.size_y - 1:
y += 1
if event.key() == Qt.Key_Left and x:
x -= 1
if event.key() == Qt.Key_Right and x < self.size_x - 1:
x += 1
x -= self.hexagonal and x == self.size_x - 1 and y % 2
if self.selection is not None and self.selection[x, y]:
return
selection = np.zeros(self.grid_cells.shape, dtype=bool)
selection[x, y] = True
self.on_selection_change(selection)
def on_selection_mark_change(self, marks):
self.redraw_selection(marks=marks)
def redraw_selection(self, marks=None):
if self.grid_cells is None:
return
sel_pen = QPen(QBrush(QColor(128, 128, 128)), 2)
sel_pen.setCosmetic(True)
mark_pen = QPen(QBrush(QColor(128, 128, 128)), 4)
mark_pen.setCosmetic(True)
pens = [self._grid_pen, sel_pen]
mark_brush = QBrush(QColor(224, 255, 255))
sels = self.selection is not None and np.max(self.selection)
palette = LimitedDiscretePalette(number_of_colors=sels + 1)
brushes = [QBrush(Qt.NoBrush)] + \
[QBrush(palette[i].lighter(165)) for i in range(sels)]
for y in range(self.size_y):
for x in range(self.size_x - (y % 2) * self.hexagonal):
cell = self.grid_cells[y, x]
marked = marks is not None and marks[x, y]
sel_group = self.selection is not None and self.selection[x, y]
if marked:
cell.setBrush(mark_brush)
cell.setPen(mark_pen)
else:
cell.setBrush(brushes[sel_group])
cell.setPen(pens[bool(sel_group)])
cell.setZValue(marked or sel_group)
def restart_som_pressed(self):
if self._optimizer_thread is not None:
self.stop_optimization = True
self._optimizer.stop_optimization = True
else:
self.start_som()
def start_som(self):
self.read_controls()
self.update_layout()
self.clear_selection()
if self.cont_x is not None:
self.enable_controls(False)
self._recompute_som()
else:
self.update_output()
def read_controls(self):
c = self.opt_controls
self.hexagonal = c.shape.currentIndex() == 0
self.size_x = c.spin_x.value()
self.size_y = c.spin_y.value()
def enable_controls(self, enable):
c = self.opt_controls
c.shape.setEnabled(enable)
c.auto_dim.setEnabled(enable)
c.start.setText("Start" if enable else "Stop")
def update_layout(self):
self.set_legend_pos()
if self.elements: # Prevent having redrawn grid but with old elements
self.scene.removeItem(self.elements)
self.elements = None
self.redraw_grid()
self.rescale()
def _redraw(self):
self.Warning.missing_colors.clear()
if self.elements:
self.scene.removeItem(self.elements)
self.elements = None
self.view.set_dimensions(self.size_x, self.size_y, self.hexagonal)
if self.cells is None:
return
sizes = self.cells[:, :, 1] - self.cells[:, :, 0]
sizes = sizes.astype(float)
if not self.size_by_instances:
sizes[sizes != 0] = 0.8
else:
sizes *= 0.8 / np.max(sizes)
self.elements = QGraphicsItemGroup()
self.scene.addItem(self.elements)
if self.attr_color is None:
self._draw_same_color(sizes)
elif self.pie_charts:
self._draw_pie_charts(sizes)
else:
self._draw_colored_circles(sizes)
@property
def _grid_factors(self):
return (0.5, sqrt3_2) if self.hexagonal else (0, 1)
def _draw_same_color(self, sizes):
fx, fy = self._grid_factors
color = QColor(64, 64, 64)
for y in range(self.size_y):
for x in range(self.size_x - self.hexagonal * (y % 2)):
r = sizes[x, y]
n = len(self.get_member_indices(x, y))
if not r:
continue
ellipse = ColoredCircle(r / 2, color, 0)
ellipse.setPos(x + (y % 2) * fx, y * fy)
ellipse.setToolTip(f"{n} instances")
self.elements.addToGroup(ellipse)
def _get_color_column(self):
color_column = \
self.data.get_column_view(self.attr_color)[0].astype(float,
copy=False)
if self.attr_color.is_discrete:
with np.errstate(invalid="ignore"):
int_col = color_column.astype(int)
int_col[np.isnan(color_column)] = len(self.colors)
else:
int_col = np.zeros(len(color_column), dtype=int)
# The following line is unnecessary because rows with missing
# numeric data are excluded. Uncomment it if you change SOM to
# tolerate missing values.
# int_col[np.isnan(color_column)] = len(self.colors)
for i, thresh in enumerate(self.thresholds, start=1):
int_col[color_column >= thresh] = i
return int_col
def _tooltip(self, colors, distribution):
if self.attr_color.is_discrete:
values = self.attr_color.values
else:
values = self._bin_names()
tot = np.sum(distribution)
nbhp = "\N{NON-BREAKING HYPHEN}"
return '<table style="white-space: nowrap">' + "".join(f"""
<tr>
<td>
<font color={color.name()}>■</font>
<b>{escape(val).replace("-", nbhp)}</b>:
</td>
<td>
{n} ({n / tot * 100:.1f} %)
</td>
</tr>
""" for color, val, n in zip(colors, values, distribution) if n) \
+ "</table>"
def _draw_pie_charts(self, sizes):
fx, fy = self._grid_factors
color_column = self._get_color_column()
colors = self.colors.qcolors_w_nan
for y in range(self.size_y):
for x in range(self.size_x - self.hexagonal * (y % 2)):
r = sizes[x, y]
if not r:
self.grid_cells[y, x].setToolTip("")
continue
members = self.get_member_indices(x, y)
color_dist = np.bincount(color_column[members],
minlength=len(colors))
rel_color_dist = color_dist.astype(float) / len(members)
pie = PieChart(rel_color_dist, r / 2, colors)
pie.setToolTip(self._tooltip(colors, color_dist))
self.elements.addToGroup(pie)
pie.setPos(x + (y % 2) * fx, y * fy)
def _draw_colored_circles(self, sizes):
fx, fy = self._grid_factors
color_column = self._get_color_column()
qcolors = self.colors.qcolors_w_nan
for y in range(self.size_y):
for x in range(self.size_x - self.hexagonal * (y % 2)):
r = sizes[x, y]
if not r:
continue
members = self.get_member_indices(x, y)
color_dist = color_column[members]
color_dist = color_dist[color_dist < len(self.colors)]
if len(color_dist) != len(members):
self.Warning.missing_colors(self.attr_color.name)
bc = np.bincount(color_dist, minlength=len(self.colors))
color = qcolors[np.argmax(bc)]
ellipse = ColoredCircle(r / 2, color,
np.max(bc) / len(members))
ellipse.setPos(x + (y % 2) * fx, y * fy)
ellipse.setToolTip(self._tooltip(qcolors, bc))
self.elements.addToGroup(ellipse)
def redraw_grid(self):
if self.grid is not None:
self.scene.removeItem(self.grid)
self.grid = QGraphicsItemGroup()
self.grid.setZValue(-200)
self.grid_cells = np.full((self.size_y, self.size_x), None)
for y in range(self.size_y):
for x in range(self.size_x - (y % 2) * self.hexagonal):
if self.hexagonal:
cell = QGraphicsPathItem(_hexagon_path)
cell.setPos(x + (y % 2) / 2, y * sqrt3_2)
else:
cell = QGraphicsRectItem(x - 0.5, y - 0.5, 1, 1)
self.grid_cells[y, x] = cell
cell.setPen(self._grid_pen)
self.grid.addToGroup(cell)
self.scene.addItem(self.grid)
def get_member_indices(self, x, y):
i, j = self.cells[x, y]
return self.member_data[i:j]
def _recompute_som(self):
if self.cont_x is None:
return
som = SOM(self.size_x,
self.size_y,
hexagonal=self.hexagonal,
pca_init=self.initialization == 0,
random_seed=0 if self.initialization == 2 else None)
class Optimizer(QObject):
update = Signal(float, np.ndarray, np.ndarray)
done = Signal(SOM)
stopped = Signal()
stop_optimization = False
def __init__(self, data, som):
super().__init__()
self.som = som
self.data = data
def callback(self, progress):
self.update.emit(progress, self.som.weights.copy(),
self.som.ssum_weights.copy())
return not self.stop_optimization
def run(self):
try:
self.som.fit(self.data,
N_ITERATIONS,
callback=self.callback)
# Report an exception, but still remove the thread
finally:
self.done.emit(self.som)
self.stopped.emit()
def thread_finished():
self._optimizer = None
self._optimizer_thread = None
self.progressBarInit()
self._optimizer = Optimizer(self.cont_x, som)
self._optimizer_thread = QThread()
self._optimizer_thread.setStackSize(5 * 2**20)
self._optimizer.update.connect(self.__update)
self._optimizer.done.connect(self.__done)
self._optimizer.stopped.connect(self._optimizer_thread.quit)
self._optimizer.moveToThread(self._optimizer_thread)
self._optimizer_thread.started.connect(self._optimizer.run)
self._optimizer_thread.finished.connect(thread_finished)
self.stop_optimization = False
self._optimizer_thread.start()
@Slot(float, object, object)
def __update(self, _progress, weights, ssum_weights):
self.progressBarSet(_progress)
self._assign_instances(weights, ssum_weights)
self._redraw()
@Slot(object)
def __done(self, som):
self.enable_controls(True)
self.progressBarFinished()
self._assign_instances(som.weights, som.ssum_weights)
self._redraw()
# This is the first time we know what was selected (assuming that
# initialization is not set to random)
if self.__pending_selection is not None:
self.on_selection_change(self.__pending_selection)
self.__pending_selection = None
self.update_output()
def stop_optimization_and_wait(self):
if self._optimizer_thread is not None:
self.stop_optimization = True
self._optimizer.stop_optimization = True
self._optimizer_thread.quit()
self._optimizer_thread.wait()
self._optimizer_thread = None
def onDeleteWidget(self):
self.stop_optimization_and_wait()
self.clear()
super().onDeleteWidget()
def _assign_instances(self, weights, ssum_weights):
if self.cont_x is None:
return # the widget is shutting down while signals still processed
assignments = SOM.winner_from_weights(self.cont_x, weights,
ssum_weights, self.hexagonal)
members = defaultdict(list)
for i, (x, y) in enumerate(assignments):
members[(x, y)].append(i)
members.pop(None, None)
self.cells = np.empty((self.size_x, self.size_y, 2), dtype=int)
self.member_data = np.empty(self.cont_x.shape[0], dtype=int)
index = 0
for x in range(self.size_x):
for y in range(self.size_y):
nmembers = len(members[(x, y)])
self.member_data[index:index + nmembers] = members[(x, y)]
self.cells[x, y] = [index, index + nmembers]
index += nmembers
def resizeEvent(self, event):
super().resizeEvent(event)
self.create_legend() # re-wrap lines if necessary
self.rescale()
def rescale(self):
if self.legend:
leg_height = self.legend.boundingRect().height()
leg_extra = 1.5
else:
leg_height = 0
leg_extra = 1
vw, vh = self.view.width(), self.view.height() - leg_height
scale = min(vw / (self.size_x + 1),
vh / ((self.size_y + leg_extra) * self._grid_factors[1]))
self.view.setTransform(QTransform.fromScale(scale, scale))
if self.hexagonal:
self.view.setSceneRect(0, -1, self.size_x - 1,
(self.size_y + leg_extra) * sqrt3_2 +
leg_height / scale)
else:
self.view.setSceneRect(-0.25, -0.25, self.size_x - 0.5,
self.size_y - 0.5 + leg_height / scale)
def update_output(self):
if self.data is None:
self.Outputs.selected_data.send(None)
self.Outputs.annotated_data.send(None)
self._set_output_summary(None)
return
indices = np.zeros(len(self.data), dtype=int)
if self.selection is not None and np.any(self.selection):
for y in range(self.size_y):
for x in range(self.size_x):
rows = self.get_member_indices(x, y)
indices[rows] = self.selection[x, y]
if np.any(indices):
sel_data = create_groups_table(self.data, indices, False, "Group")
self.Outputs.selected_data.send(sel_data)
self._set_output_summary(sel_data)
else:
self.Outputs.selected_data.send(None)
self._set_output_summary(None)
if np.max(indices) > 1:
annotated = create_groups_table(self.data, indices)
else:
annotated = create_annotated_table(self.data,
np.flatnonzero(indices))
self.Outputs.annotated_data.send(annotated)
def set_color_bins(self):
if self.attr_color is None:
self.thresholds = self.bin_labels = self.colors = None
elif self.attr_color.is_discrete:
self.thresholds = self.bin_labels = None
self.colors = self.attr_color.palette
else:
col = self.data.get_column_view(self.attr_color)[0].astype(float)
if self.attr_color.is_time:
binning = time_binnings(col, min_bins=4)[-1]
else:
binning = decimal_binnings(col, min_bins=4)[-1]
self.thresholds = binning.thresholds[1:-1]
self.bin_labels = (binning.labels[1:-1],
binning.short_labels[1:-1])
palette = BinnedContinuousPalette.from_palette(
self.attr_color.palette, binning.thresholds)
self.colors = palette
def create_legend(self):
if self.legend is not None:
self.scene.removeItem(self.legend)
self.legend = None
if self.attr_color is None:
return
if self.attr_color.is_discrete:
names = self.attr_color.values
else:
names = self._bin_names()
items = []
size = 8
for name, color in zip(names, self.colors.qcolors):
item = QGraphicsItemGroup()
item.addToGroup(
CanvasRectangle(None, -size / 2, -size / 2, size, size,
Qt.gray, color))
item.addToGroup(CanvasText(None, name, size, 0, Qt.AlignVCenter))
items.append(item)
self.legend = wrap_legend_items(items,
hspacing=20,
vspacing=16 + size,
max_width=self.view.width() - 25)
self.legend.setFlags(self.legend.ItemIgnoresTransformations)
self.legend.setTransform(
QTransform.fromTranslate(-self.legend.boundingRect().width() / 2,
0))
self.scene.addItem(self.legend)
self.set_legend_pos()
def _bin_names(self):
labels, short_labels = self.bin_labels
return \
[f"< {labels[0]}"] \
+ [f"{x} - {y}" for x, y in zip(labels, short_labels[1:])] \
+ [f"≥ {labels[-1]}"]
def set_legend_pos(self):
if self.legend is None:
return
self.legend.setPos(self.size_x / 2,
(self.size_y + 0.2 + 0.3 * self.hexagonal) *
self._grid_factors[1])
def send_report(self):
self.report_plot()
if self.attr_color:
self.report_caption(
f"Self-organizing map colored by '{self.attr_color.name}'")
class OWNxExplorer(OWDataProjectionWidget):
name = "Network Explorer"
description = "Visually explore the network and its properties."
icon = "icons/NetworkExplorer.svg"
priority = 6420
class Inputs:
node_data = Input("Node Data", Table)
node_subset = Input("Node Subset", Table)
network = Input("Network", Network, default=True)
node_distances = Input("Node Distances", Orange.misc.DistMatrix)
class Outputs(OWDataProjectionWidget.Outputs):
subgraph = Output("Selected sub-network", Network)
unselected_subgraph = Output("Remaining sub-network", Network)
distances = Output("Distance matrix", Orange.misc.DistMatrix)
UserAdviceMessages = [
widget.Message("Double clicks select connected components",
widget.Message.Information),
]
GRAPH_CLASS = GraphView
graph = SettingProvider(GraphView)
layout_density = Setting(10)
observe_weights = Setting(True)
mark_hops = Setting(1)
mark_min_conn = Setting(5)
mark_max_conn = Setting(5)
mark_most_conn = Setting(1)
alpha_value = 255 # Override the setting from parent
class Warning(OWDataProjectionWidget.Warning):
distance_matrix_mismatch = widget.Msg(
"Distance matrix size doesn't match the number of network nodes "
"and will be ignored.")
no_graph_found = widget.Msg("Node data is given, graph data is missing.")
class Error(OWDataProjectionWidget.Error):
data_size_mismatch = widget.Msg(
"Length of the data does not match the number of nodes.")
network_too_large = widget.Msg("Network is too large to visualize.")
single_node_graph = widget.Msg("I don't do single-node graphs today.")
def __init__(self):
# These are already needed in super().__init__()
self.number_of_nodes = 0
self.number_of_edges = 0
self.nHighlighted = 0
self.nSelected = 0
self.nodes_per_edge = 0
self.edges_per_node = 0
self.mark_mode = 0
self.mark_text = ""
super().__init__()
self.network = None
self.node_data = None
self.distance_matrix = None
self.edges = None
self.positions = None
self._optimizer = None
self._animation_thread = None
self._stop_optimization = False
self.marked_nodes = None
self.searchStringTimer = QTimer(self)
self.searchStringTimer.timeout.connect(self.update_marks)
self.set_mark_mode()
self.setMinimumWidth(600)
def sizeHint(self):
return QSize(800, 600)
def _add_controls(self):
self.gui = OWPlotGUI(self)
self._add_info_box()
self.gui.point_properties_box(self.controlArea)
self._add_effects_box()
self.gui.plot_properties_box(self.controlArea)
self._add_mark_box()
self.controls.attr_label.activated.connect(self.on_change_label_attr)
def _add_info_box(self):
info = gui.vBox(self.controlArea, box="Layout")
gui.label(
info, self,
"Nodes: %(number_of_nodes)i (%(nodes_per_edge).2f per edge); "
"%(nSelected)i selected")
gui.label(
info, self,
"Edges: %(number_of_edges)i (%(edges_per_node).2f per node)")
lbox = gui.hBox(info)
self.relayout_button = gui.button(
lbox, self, 'Improve', callback=self.improve, autoDefault=False,
tooltip="Optimize the current layout, with a small initial jerk")
self.stop_button = gui.button(
lbox, self, 'Stop', callback=self.stop_relayout, autoDefault=False,
hidden=True)
self.randomize_button = gui.button(
lbox, self, 'Re-layout', callback=self.restart, autoDefault=False,
tooltip="Restart laying out from random positions")
gui.hSlider(info, self, "layout_density", minValue=1, maxValue=50,
label="Gravity", orientation=Qt.Horizontal,
callback_finished=self.improve,
tooltip="Lower values improve optimization,\n"
"higher work better for graph with many small "
"components")
gui.checkBox(info, self, "observe_weights",
label="Make edges with large weights shorter",
callback=self.improve)
def _add_effects_box(self):
gbox = self.gui.create_gridbox(self.controlArea, box="Widths and Sizes")
self.gui.add_widget(self.gui.PointSize, gbox)
gbox.layout().itemAtPosition(1, 0).widget().setText("Node Size:")
self.gui.add_control(
gbox, gui.hSlider, "Edge width:",
master=self, value='graph.edge_width',
minValue=1, maxValue=10, step=1,
callback=self.graph.update_edges)
box = gui.vBox(None)
gbox.layout().addWidget(box, 3, 0, 1, 2)
gui.separator(box)
self.checkbox_relative_edges = gui.checkBox(
box, self, 'graph.relative_edge_widths',
'Scale edge widths to weights',
callback=self.graph.update_edges)
self.checkbox_show_weights = gui.checkBox(
box, self, 'graph.show_edge_weights',
'Show edge weights',
callback=self.graph.update_edge_labels)
self.checkbox_show_weights = gui.checkBox(
box, self, 'graph.label_selected_edges',
'Label only edges of selected nodes',
callback=self.graph.update_edge_labels)
# This is ugly: create a slider that controls alpha_value so that
# parent can enable and disable it - although it's never added to any
# layout and visible to the user
gui.hSlider(None, self, "graph.alpha_value")
def _add_mark_box(self):
hbox = gui.hBox(None, box=True)
self.mainArea.layout().addWidget(hbox)
vbox = gui.hBox(hbox)
def spin(value, label, minv, maxv):
return gui.spin(
vbox, self, value, label=label, minv=minv, maxv=maxv,
step=1,
alignment=Qt.AlignRight, callback=self.update_marks).box
def text_line():
def set_search_string_timer():
self.searchStringTimer.stop()
self.searchStringTimer.start(300)
return gui.lineEdit(
gui.hBox(vbox), self, "mark_text", label="Text: ",
orientation=Qt.Horizontal, minimumWidth=50,
callback=set_search_string_timer, callbackOnType=True).box
def _mark_by_labels(marker):
txt = self.mark_text.lower()
if not txt:
return None
labels = self.get_label_data()
if labels is None:
return None
return marker(np.char.array(labels), txt)
def mark_label_starts():
return _mark_by_labels(
lambda labels, txt: np.flatnonzero(labels.lower().startswith(txt)))
def mark_label_contains():
return _mark_by_labels(
lambda labels, txt: np.flatnonzero(labels.lower().find(txt) != -1))
def mark_text():
txt = self.mark_text.lower()
if not txt or self.data is None:
return None
return np.array(
[i for i, inst in enumerate(self.data)
if txt in "\x00".join(map(str, inst.list)).lower()])
def mark_reachable():
selected = self.graph.get_selection()
if selected is None:
return None
return self.get_reachable(selected)
def mark_close():
selected = self.graph.get_selection()
if selected is None:
return None
neighbours = set(selected)
last_round = list(neighbours)
for _ in range(self.mark_hops):
next_round = set()
for neigh in last_round:
next_round |= set(self.network.neighbours(neigh))
neighbours |= next_round
last_round = next_round
neighbours -= set(selected)
return np.array(list(neighbours))
def mark_from_input():
if self.subset_data is None or self.data is None:
return None
ids = set(self.subset_data.ids)
return np.array(
[i for i, ex in enumerate(self.data) if ex.id in ids])
def mark_most_connections():
n = self.mark_most_conn
if n >= self.number_of_nodes:
return np.arange(self.number_of_nodes)
degrees = self.network.degrees()
# pylint: disable=invalid-unary-operand-type
min_degree = np.partition(degrees, -n)[-n]
return np.flatnonzero(degrees >= min_degree)
def mark_more_than_any_neighbour():
degrees = self.network.degrees()
return np.array(
[node for node, degree in enumerate(degrees)
if degree > np.max(degrees[self.network.neighbours(node)],
initial=0)])
def mark_more_than_average_neighbour():
degrees = self.network.degrees()
return np.array(
[node for node, degree, neighbours in (
(node, degree, self.network.neighbours(node))
for node, degree in enumerate(degrees))
if degree > (np.mean(degrees[neighbours]) if neighbours.size else 0)
]
)
self.mark_criteria = [
("(Select criteria for marking)", None, lambda: np.zeros((0,))),
("Mark nodes whose label starts with", text_line(), mark_label_starts),
("Mark nodes whose label contains", text_line(), mark_label_contains),
("Mark nodes whose data that contains", text_line(), mark_text),
("Mark nodes reachable from selected", None, mark_reachable),
("Mark nodes in vicinity of selection",
spin("mark_hops", "Number of hops:", 1, 20),
mark_close),
("Mark nodes from subset signal", None, mark_from_input),
("Mark nodes with few connections",
spin("mark_max_conn", "Max. connections:", 0, 1000),
lambda: np.flatnonzero(self.network.degrees() <= self.mark_max_conn)),
("Mark nodes with many connections",
spin("mark_min_conn", "Min. connections:", 1, 1000),
lambda: np.flatnonzero(self.network.degrees() >= self.mark_min_conn)),
("Mark nodes with most connections",
spin("mark_most_conn", "Number of marked:", 1, 1000),
mark_most_connections),
("Mark nodes with more connections than any neighbour", None,
mark_more_than_any_neighbour),
("Mark nodes with more connections than average neighbour", None,
mark_more_than_average_neighbour)
]
cb = gui.comboBox(
hbox, self, "mark_mode",
items=[item for item, *_ in self.mark_criteria],
maximumContentsLength=-1, callback=self.set_mark_mode)
hbox.layout().insertWidget(0, cb)
gui.rubber(hbox)
self.btselect = gui.button(
hbox, self, "Select", callback=self.select_marked)
self.btadd = gui.button(
hbox, self, "Add to Selection", callback=self.select_add_marked)
self.btgroup = gui.button(
hbox, self, "Add New Group", callback=self.select_as_group)
def set_mark_mode(self, mode=None):
if mode is not None:
self.mark_mode = mode
for i, (_, widget, _) in enumerate(self.mark_criteria):
if widget:
if i == self.mark_mode:
widget.show()
else:
widget.hide()
self.searchStringTimer.stop()
self.update_marks()
def update_marks(self):
if self.network is None:
return
self.marked_nodes = self.mark_criteria[self.mark_mode][2]()
if self.marked_nodes is not None and not self.marked_nodes.size:
self.marked_nodes = None
self.graph.update_marks()
if self.graph.label_only_selected:
self.graph.update_labels()
self.update_selection_buttons()
def update_selection_buttons(self):
if self.marked_nodes is None:
self.btselect.hide()
self.btadd.hide()
self.btgroup.hide()
return
else:
self.btselect.show()
selection = self.graph.get_selection()
if not len(selection) or np.max(selection) == 0:
self.btadd.hide()
self.btgroup.hide()
elif np.max(selection) == 1:
self.btadd.setText("Add to Selection")
self.btadd.show()
self.btgroup.hide()
else:
self.btadd.setText("Add to Group")
self.btadd.show()
self.btgroup.show()
def selection_changed(self):
super().selection_changed()
self.nSelected = 0 if self.selection is None else len(self.selection)
self.update_selection_buttons()
self.update_marks()
def select_marked(self):
self.graph.selection_select(self.marked_nodes)
def select_add_marked(self):
self.graph.selection_append(self.marked_nodes)
def select_as_group(self):
self.graph.selection_new_group(self.marked_nodes)
def on_change_label_attr(self):
if self.mark_mode in (1, 2):
self.update_marks()
@Inputs.node_data
def set_node_data(self, data):
self.node_data = data
@Inputs.node_subset
def set_node_subset(self, data):
# It would be better to call super, but this fails because super
# is decorated to set the partial summary for signal "Subset Data",
# which does not exist for this widget (OWNxExplorer.Inputs is not
# derived from OWDataProjectionWidget.Inputs in order to rename the
# signal)
self.subset_data = data
@Inputs.node_distances
def set_items_distance_matrix(self, matrix):
self.distance_matrix = matrix
self.positions = None
@Inputs.network
def set_graph(self, graph):
def set_graph_none(error=None):
if error is not None:
error()
self.network = None
self.number_of_nodes = self.edges_per_node = 0
self.number_of_edges = self.nodes_per_edge = 0
def compute_stats():
self.number_of_nodes = graph.number_of_nodes()
self.number_of_edges = graph.number_of_edges()
self.edges_per_node = self.number_of_edges / self.number_of_nodes
self.nodes_per_edge = \
self.number_of_nodes / max(1, self.number_of_edges)
self.mark_text = ""
self.set_mark_mode(0)
self.positions = None
if not graph or graph.number_of_nodes() == 0:
set_graph_none()
return
if graph.number_of_nodes() + graph.number_of_edges() > 100000:
set_graph_none(self.Error.network_too_large)
return
self.Error.clear()
self.network = graph
compute_stats()
def handleNewSignals(self):
network = self.network
def set_actual_data():
self.closeContext()
self.Error.data_size_mismatch.clear()
self.Warning.no_graph_found.clear()
self._invalid_data = False
if network is None:
if self.node_data is not None:
self.Warning.no_graph_found()
return
n_nodes = len(self.network.nodes)
if self.node_data is not None:
if len(self.node_data) != n_nodes:
self.Error.data_size_mismatch()
self._invalid_data = True
self.data = None
else:
self.data = self.node_data
if self.node_data is None:
if isinstance(network.nodes, Table):
self.data = network.nodes
elif isinstance(network.nodes, np.ndarray) \
and (len(network.nodes.shape) == 1
or network.nodes.shape[1] == 1):
self.data = Table.from_numpy(
Domain([], None, [StringVariable("label")]),
np.zeros((len(network.nodes),0)),
None,
metas=network.nodes.reshape((n_nodes, 1))
)
else:
self.data = None
if self.data is not None:
# Replicate the necessary parts of set_data
self.valid_data = np.full(len(self.data), True, dtype=bool)
self.init_attr_values()
self.openContext(self.data)
self.cb_class_density.setEnabled(self.can_draw_density())
def set_actual_edges():
def set_checkboxes(value):
self.checkbox_show_weights.setEnabled(value)
self.checkbox_relative_edges.setEnabled(value)
self.Warning.distance_matrix_mismatch.clear()
if self.network is None:
self.edges = None
set_checkboxes(False)
return
set_checkboxes(True)
if network.number_of_edges(0):
self.edges = network.edges[0].edges.tocoo()
else:
self.edges = sp.coo_matrix((0, 3))
if self.distance_matrix is not None:
if len(self.distance_matrix) != self.number_of_nodes:
self.Warning.distance_matrix_mismatch()
else:
self.edges.data = np.fromiter(
(self.distance_matrix[u, v]
for u, v in zip(self.edges.row, self.edges.col)),
dtype=np.int32, count=len(self.edges.row)
)
if np.allclose(self.edges.data, 0):
self.edges.data[:] = 1
set_checkboxes(False)
elif len(set(self.edges.data)) == 1:
set_checkboxes(False)
self.stop_optimization_and_wait()
set_actual_data()
super()._handle_subset_data()
if self.positions is None:
set_actual_edges()
self.set_random_positions()
self.graph.reset_graph()
self.relayout(True)
else:
self.graph.update_point_props()
self.update_marks()
self.update_selection_buttons()
def init_attr_values(self):
super().init_attr_values()
if self.node_data is None \
and self.data is not None \
and isinstance(self.network.nodes, np.ndarray):
assert len(self.data.domain.metas) == 1
self.attr_label = self.data.domain.metas[0]
def randomize(self):
self.set_random_positions()
self.graph.update_coordinates()
def set_random_positions(self):
if self.network is None:
self.position = None
else:
self.positions = np.random.uniform(size=(self.number_of_nodes, 2))
def get_reachable(self, initial):
to_check = list(initial)
reachable = set(to_check)
for node in to_check:
new_checks = set(self.network.neighbours(node)) - reachable
to_check += new_checks
reachable |= new_checks
return np.array(to_check)
def send_data(self):
super().send_data()
Outputs = self.Outputs
selected_indices = self.graph.get_selection()
if selected_indices is None or len(selected_indices) == 0:
Outputs.subgraph.send(None)
Outputs.unselected_subgraph.send(self.network)
Outputs.distances.send(None)
return
selection = self.graph.selection
subgraph = self.network.subgraph(selected_indices)
subgraph.nodes = \
self._get_selected_data(self.data, selected_indices, selection)
Outputs.subgraph.send(subgraph)
Outputs.unselected_subgraph.send(
self.network.subgraph(np.flatnonzero(selection == 0)))
distances = self.distance_matrix
if distances is None:
Outputs.distances.send(None)
else:
Outputs.distances.send(distances.submatrix(sorted(selected_indices)))
def get_coordinates_data(self):
if self.positions is not None:
return self.positions.T
else:
return None, None
def get_embedding(self):
return self.positions
def get_subset_mask(self):
if self.data is None:
return None
return super().get_subset_mask()
def get_edges(self):
return self.edges
def is_directed(self):
return self.network is not None and self.network.edges[0].directed
def get_marked_nodes(self):
return self.marked_nodes
def set_buttons(self, running):
self.stop_button.setHidden(not running)
self.relayout_button.setHidden(running)
self.randomize_button.setHidden(running)
def stop_relayout(self):
self._stop_optimization = True
self.set_buttons(running=False)
def restart(self):
self.relayout(restart=True)
def improve(self):
self.relayout(restart=False)
# TODO: Stop relayout if new data is received
def relayout(self, restart):
if self.edges is None:
return
if restart or self.positions is None:
self.set_random_positions()
self.progressbar = gui.ProgressBar(self, 100)
self.set_buttons(running=True)
self._stop_optimization = False
Simplifications = self.graph.Simplifications
self.graph.set_simplifications(
Simplifications.NoDensity
+ Simplifications.NoLabels * (len(self.graph.labels) > 20)
+ Simplifications.NoEdgeLabels * (len(self.graph.edge_labels) > 20)
+ Simplifications.NoEdges * (self.number_of_edges > 30000))
large_graph = self.number_of_nodes + self.number_of_edges > 30000
class LayoutOptimizer(QObject):
update = Signal(np.ndarray, float)
done = Signal(np.ndarray)
stopped = Signal()
def __init__(self, widget):
super().__init__()
self.widget = widget
def send_update(self, positions, progress):
if not large_graph:
self.update.emit(np.array(positions), progress)
return not self.widget._stop_optimization
def run(self):
widget = self.widget
edges = widget.edges
nnodes = widget.number_of_nodes
init_temp = 0.05 if restart else 0.2
k = widget.layout_density / 10 / np.sqrt(nnodes)
sample_ratio = None if nnodes < 1000 else 1000 / nnodes
fruchterman_reingold(
widget.positions, edges, widget.observe_weights,
FR_ALLOWED_TIME, k, init_temp, sample_ratio,
callback_step=4, callback=self.send_update)
self.done.emit(widget.positions)
self.stopped.emit()
def update(positions, progress):
self.progressbar.advance(progress)
self.positions = positions
self.graph.update_coordinates()
def done(positions):
self.positions = positions
self.set_buttons(running=False)
self.graph.set_simplifications(
self.graph.Simplifications.NoSimplifications)
self.graph.update_coordinates()
self.progressbar.finish()
def thread_finished():
self._optimizer = None
self._animation_thread = None
self._optimizer = LayoutOptimizer(self)
self._animation_thread = QThread()
self._optimizer.update.connect(update)
self._optimizer.done.connect(done)
self._optimizer.stopped.connect(self._animation_thread.quit)
self._optimizer.moveToThread(self._animation_thread)
self._animation_thread.started.connect(self._optimizer.run)
self._animation_thread.finished.connect(thread_finished)
self._animation_thread.start()
def stop_optimization_and_wait(self):
if self._animation_thread is not None:
self._stop_optimization = True
self._animation_thread.quit()
self._animation_thread.wait()
self._animation_thread = None
def onDeleteWidget(self):
self.stop_optimization_and_wait()
super().onDeleteWidget()
def send_report(self):
if self.network is None:
return
self.report_items('Graph info', [
("Number of vertices", self.network.number_of_nodes()),
("Number of edges", self.network.number_of_edges()),
("Vertices per edge", round(self.nodes_per_edge, 3)),
("Edges per vertex", round(self.edges_per_node, 3)),
])
if self.data is not None:
self.report_data("Data", self.data)
if any((self.attr_color, self.attr_shape,
self.attr_size, self.attr_label)):
self.report_items(
"Visual settings",
[("Color", self._get_caption_var_name(self.attr_color)),
("Label", self._get_caption_var_name(self.attr_label)),
("Shape", self._get_caption_var_name(self.attr_shape)),
("Size", self._get_caption_var_name(self.attr_size))])
self.report_plot()
class VizRankDialog(QDialog, ProgressBarMixin, WidgetMessagesMixin):
"""
Base class for VizRank dialogs, providing a GUI with a table and a button,
and the skeleton for managing the evaluation of visualizations.
Derived classes must provide methods
- `iterate_states` for generating combinations (e.g. pairs of attritutes),
- `compute_score(state)` for computing the score of a combination,
- `row_for_state(state)` that returns a list of items inserted into the
table for the given state.
and, optionally,
- `state_count` that returns the number of combinations (used for progress
bar)
- `on_selection_changed` that handles event triggered when the user selects
a table row. The method should emit signal
`VizRankDialog.selectionChanged(object)`.
- `bar_length` returns the length of the bar corresponding to the score.
The class provides a table and a button. A widget constructs a single
instance of this dialog in its `__init__`, like (in Sieve) by using a
convenience method :obj:`add_vizrank`::
self.vizrank, self.vizrank_button = SieveRank.add_vizrank(
box, self, "Score Combinations", self.set_attr)
When the widget receives new data, it must call the VizRankDialog's
method :obj:`VizRankDialog.initialize()` to clear the GUI and reset the
state.
Clicking the Start button calls method `run` (and renames the button to
Pause). Run sets up a progress bar by getting the number of combinations
from :obj:`VizRankDialog.state_count()`. It restores the paused state
(if any) and calls generator :obj:`VizRankDialog.iterate_states()`. For
each generated state, it calls :obj:`VizRankDialog.score(state)`, which
must return the score (lower is better) for this state. If the returned
state is not `None`, the data returned by `row_for_state` is inserted at
the appropriate place in the table.
Args:
master (Orange.widget.OWWidget): widget to which the dialog belongs
Attributes:
master (Orange.widget.OWWidget): widget to which the dialog belongs
captionTitle (str): the caption for the dialog. This can be a class
attribute. `captionTitle` is used by the `ProgressBarMixin`.
"""
captionTitle = ""
NEGATIVE_COLOR = QColor(70, 190, 250)
POSITIVE_COLOR = QColor(170, 242, 43)
processingStateChanged = Signal(int)
progressBarValueChanged = Signal(float)
messageActivated = Signal(Msg)
messageDeactivated = Signal(Msg)
selectionChanged = Signal(object)
class Information(WidgetMessagesMixin.Information):
nothing_to_rank = Msg("There is nothing to rank.")
def __init__(self, master):
"""Initialize the attributes and set up the interface"""
QDialog.__init__(self, master, windowTitle=self.captionTitle)
WidgetMessagesMixin.__init__(self)
self.setLayout(QVBoxLayout())
self.insert_message_bar()
self.layout().insertWidget(0, self.message_bar)
self.master = master
self.keep_running = False
self.scheduled_call = None
self.saved_state = None
self.saved_progress = 0
self.scores = []
self.add_to_model = queue.Queue()
self.update_timer = QTimer(self)
self.update_timer.timeout.connect(self._update)
self.update_timer.setInterval(200)
self._thread = None
self._worker = None
self.filter = QLineEdit()
self.filter.setPlaceholderText("Filter ...")
self.filter.textChanged.connect(self.filter_changed)
self.layout().addWidget(self.filter)
# Remove focus from line edit
self.setFocus(Qt.ActiveWindowFocusReason)
self.rank_model = QStandardItemModel(self)
self.model_proxy = QSortFilterProxyModel(self,
filterCaseSensitivity=False)
self.model_proxy.setSourceModel(self.rank_model)
self.rank_table = view = QTableView(
selectionBehavior=QTableView.SelectRows,
selectionMode=QTableView.SingleSelection,
showGrid=False,
editTriggers=gui.TableView.NoEditTriggers)
if self._has_bars:
view.setItemDelegate(TableBarItem())
else:
view.setItemDelegate(HorizontalGridDelegate())
view.setModel(self.model_proxy)
view.selectionModel().selectionChanged.connect(
self.on_selection_changed)
view.horizontalHeader().setStretchLastSection(True)
view.horizontalHeader().hide()
self.layout().addWidget(view)
self.button = gui.button(self,
self,
"Start",
callback=self.toggle,
default=True)
@property
def _has_bars(self):
return type(self).bar_length is not VizRankDialog.bar_length
@classmethod
def add_vizrank(cls, widget, master, button_label, set_attr_callback):
"""
Equip the widget with VizRank button and dialog, and monkey patch the
widget's `closeEvent` and `hideEvent` to close/hide the vizrank, too.
Args:
widget (QWidget): the widget into whose layout to insert the button
master (Orange.widgets.widget.OWWidget): the master widget
button_label: the label for the button
set_attr_callback: the callback for setting the projection chosen
in the vizrank
Returns:
tuple with Vizrank dialog instance and push button
"""
# Monkey patching could be avoided by mixing-in the class (not
# necessarily a good idea since we can make a mess of multiple
# defined/derived closeEvent and hideEvent methods). Furthermore,
# per-class patching would be better than per-instance, but we don't
# want to mess with meta-classes either.
vizrank = cls(master)
button = gui.button(widget,
master,
button_label,
callback=vizrank.reshow,
enabled=False)
vizrank.selectionChanged.connect(lambda args: set_attr_callback(*args))
master_close_event = master.closeEvent
master_hide_event = master.hideEvent
master_delete_event = master.onDeleteWidget
def closeEvent(event):
vizrank.close()
master_close_event(event)
def hideEvent(event):
vizrank.hide()
master_hide_event(event)
def deleteEvent():
vizrank.keep_running = False
if vizrank._thread is not None and vizrank._thread.isRunning():
vizrank._thread.quit()
vizrank._thread.wait()
master_delete_event()
master.closeEvent = closeEvent
master.hideEvent = hideEvent
master.onDeleteWidget = deleteEvent
return vizrank, button
def reshow(self):
"""Put the widget on top of all windows
"""
self.show()
self.raise_()
self.activateWindow()
def initialize(self):
"""
Clear and initialize the dialog.
This method must be called by the widget when the data is reset,
e.g. from `set_data` handler.
"""
if self._thread is not None and self._thread.isRunning():
self.keep_running = False
self._thread.quit()
self._thread.wait()
self.keep_running = False
self.scheduled_call = None
self.saved_state = None
self.saved_progress = 0
self.update_timer.stop()
self.progressBarFinished()
self.scores = []
self._update_model() # empty queue
self.rank_model.clear()
self.button.setText("Start")
self.button.setEnabled(self.check_preconditions())
self._thread = QThread(self)
self._worker = Worker(self)
self._worker.moveToThread(self._thread)
self._worker.stopped.connect(self._thread.quit)
self._worker.stopped.connect(self._select_first_if_none)
self._worker.stopped.connect(self._stopped)
self._worker.done.connect(self._done)
self._thread.started.connect(self._worker.do_work)
def filter_changed(self, text):
self.model_proxy.setFilterFixedString(text)
def stop_and_reset(self, reset_method=None):
if self.keep_running:
self.scheduled_call = reset_method or self.initialize
self.keep_running = False
else:
self.initialize()
def check_preconditions(self):
"""Check whether there is sufficient data for ranking."""
return True
def on_selection_changed(self, selected, deselected):
"""
Set the new visualization in the widget when the user select a
row in the table.
If derived class does not reimplement this, the table gives the
information but the user can't click it to select the visualization.
Args:
selected: the index of the selected item
deselected: the index of the previously selected item
"""
pass
def iterate_states(self, initial_state):
"""
Generate all possible states (e.g. attribute combinations) for the
given data. The content of the generated states is specific to the
visualization.
This method must be defined in the derived classes.
Args:
initial_state: initial state; None if this is the first call
"""
raise NotImplementedError
def state_count(self):
"""
Return the number of states for the progress bar.
Derived classes should implement this to ensure the proper behaviour of
the progress bar"""
return 0
def compute_score(self, state):
"""
Abstract method for computing the score for the given state. Smaller
scores are better.
Args:
state: the state, e.g. the combination of attributes as generated
by :obj:`state_count`.
"""
raise NotImplementedError
def bar_length(self, score):
"""Compute the bar length (between 0 and 1) corresponding to the score.
Return `None` if the score cannot be normalized.
"""
return None
def row_for_state(self, score, state):
"""
Abstract method that return the items that are inserted into the table.
Args:
score: score, computed by :obj:`compute_score`
state: the state, e.g. combination of attributes
"""
raise NotImplementedError
def _select_first_if_none(self):
if not self.rank_table.selectedIndexes():
self.rank_table.selectRow(0)
def _done(self):
self.button.setText("Finished")
self.button.setEnabled(False)
self.keep_running = False
self.saved_state = None
def _stopped(self):
self.update_timer.stop()
self.progressBarFinished()
self._update_model()
self.stopped()
if self.scheduled_call:
self.scheduled_call()
def _update(self):
self._update_model()
self._update_progress()
def _update_progress(self):
self.progressBarSet(
int(self.saved_progress * 100 / max(1, self.state_count())))
def _update_model(self):
try:
while True:
pos, row_items = self.add_to_model.get_nowait()
self.rank_model.insertRow(pos, row_items)
except queue.Empty:
pass
def toggle(self):
"""Start or pause the computation."""
self.keep_running = not self.keep_running
if self.keep_running:
self.button.setText("Pause")
self.progressBarInit()
self.update_timer.start()
self.before_running()
self._thread.start()
else:
self.button.setText("Continue")
self._thread.quit()
# Need to sync state (the worker must read the keep_running
# state and stop) for reliable restart.
self._thread.wait()
def before_running(self):
"""Code that is run before running vizrank in its own thread"""
pass
def stopped(self):
"""Code that is run after stopping the vizrank thread"""
pass
class VizRankDialog(QDialog, ProgressBarMixin, WidgetMessagesMixin):
"""
Base class for VizRank dialogs, providing a GUI with a table and a button,
and the skeleton for managing the evaluation of visualizations.
Derived classes must provide methods
- `iterate_states` for generating combinations (e.g. pairs of attritutes),
- `compute_score(state)` for computing the score of a combination,
- `row_for_state(state)` that returns a list of items inserted into the
table for the given state.
and, optionally,
- `state_count` that returns the number of combinations (used for progress
bar)
- `on_selection_changed` that handles event triggered when the user selects
a table row. The method should emit signal
`VizRankDialog.selectionChanged(object)`.
- `bar_length` returns the length of the bar corresponding to the score.
The class provides a table and a button. A widget constructs a single
instance of this dialog in its `__init__`, like (in Sieve) by using a
convenience method :obj:`add_vizrank`::
self.vizrank, self.vizrank_button = SieveRank.add_vizrank(
box, self, "Score Combinations", self.set_attr)
When the widget receives new data, it must call the VizRankDialog's
method :obj:`VizRankDialog.initialize()` to clear the GUI and reset the
state.
Clicking the Start button calls method `run` (and renames the button to
Pause). Run sets up a progress bar by getting the number of combinations
from :obj:`VizRankDialog.state_count()`. It restores the paused state
(if any) and calls generator :obj:`VizRankDialog.iterate_states()`. For
each generated state, it calls :obj:`VizRankDialog.score(state)`, which
must return the score (lower is better) for this state. If the returned
state is not `None`, the data returned by `row_for_state` is inserted at
the appropriate place in the table.
Args:
master (Orange.widget.OWWidget): widget to which the dialog belongs
Attributes:
master (Orange.widget.OWWidget): widget to which the dialog belongs
captionTitle (str): the caption for the dialog. This can be a class
attribute. `captionTitle` is used by the `ProgressBarMixin`.
"""
captionTitle = ""
processingStateChanged = Signal(int)
progressBarValueChanged = Signal(float)
messageActivated = Signal(Msg)
messageDeactivated = Signal(Msg)
selectionChanged = Signal(object)
class Information(WidgetMessagesMixin.Information):
nothing_to_rank = Msg("There is nothing to rank.")
def __init__(self, master):
"""Initialize the attributes and set up the interface"""
QDialog.__init__(self, master, windowTitle=self.captionTitle)
WidgetMessagesMixin.__init__(self)
self.setLayout(QVBoxLayout())
self.insert_message_bar()
self.layout().insertWidget(0, self.message_bar)
self.master = master
self.keep_running = False
self.scheduled_call = None
self.saved_state = None
self.saved_progress = 0
self.scores = []
self.add_to_model = queue.Queue()
self.update_timer = QTimer(self)
self.update_timer.timeout.connect(self._update)
self.update_timer.setInterval(200)
self._thread = None
self._worker = None
self.filter = QLineEdit()
self.filter.setPlaceholderText("Filter ...")
self.filter.textChanged.connect(self.filter_changed)
self.layout().addWidget(self.filter)
# Remove focus from line edit
self.setFocus(Qt.ActiveWindowFocusReason)
self.rank_model = QStandardItemModel(self)
self.model_proxy = QSortFilterProxyModel(
self, filterCaseSensitivity=False)
self.model_proxy.setSourceModel(self.rank_model)
self.rank_table = view = QTableView(
selectionBehavior=QTableView.SelectRows,
selectionMode=QTableView.SingleSelection,
showGrid=False,
editTriggers=gui.TableView.NoEditTriggers)
if self._has_bars:
view.setItemDelegate(TableBarItem())
else:
view.setItemDelegate(HorizontalGridDelegate())
view.setModel(self.model_proxy)
view.selectionModel().selectionChanged.connect(
self.on_selection_changed)
view.horizontalHeader().setStretchLastSection(True)
view.horizontalHeader().hide()
self.layout().addWidget(view)
self.button = gui.button(
self, self, "Start", callback=self.toggle, default=True)
@property
def _has_bars(self):
return type(self).bar_length is not VizRankDialog.bar_length
@classmethod
def add_vizrank(cls, widget, master, button_label, set_attr_callback):
"""
Equip the widget with VizRank button and dialog, and monkey patch the
widget's `closeEvent` and `hideEvent` to close/hide the vizrank, too.
Args:
widget (QWidget): the widget into whose layout to insert the button
master (Orange.widgets.widget.OWWidget): the master widget
button_label: the label for the button
set_attr_callback: the callback for setting the projection chosen
in the vizrank
Returns:
tuple with Vizrank dialog instance and push button
"""
# Monkey patching could be avoided by mixing-in the class (not
# necessarily a good idea since we can make a mess of multiple
# defined/derived closeEvent and hideEvent methods). Furthermore,
# per-class patching would be better than per-instance, but we don't
# want to mess with meta-classes either.
vizrank = cls(master)
button = gui.button(
widget, master, button_label, callback=vizrank.reshow,
enabled=False)
vizrank.selectionChanged.connect(lambda args: set_attr_callback(*args))
master_close_event = master.closeEvent
master_hide_event = master.hideEvent
master_delete_event = master.onDeleteWidget
def closeEvent(event):
vizrank.close()
master_close_event(event)
def hideEvent(event):
vizrank.hide()
master_hide_event(event)
def deleteEvent():
vizrank.keep_running = False
if vizrank._thread is not None and vizrank._thread.isRunning():
vizrank._thread.quit()
vizrank._thread.wait()
master_delete_event()
master.closeEvent = closeEvent
master.hideEvent = hideEvent
master.onDeleteWidget = deleteEvent
return vizrank, button
def reshow(self):
"""Put the widget on top of all windows
"""
self.show()
self.raise_()
self.activateWindow()
def initialize(self):
"""
Clear and initialize the dialog.
This method must be called by the widget when the data is reset,
e.g. from `set_data` handler.
"""
if self._thread is not None and self._thread.isRunning():
self.keep_running = False
self._thread.quit()
self._thread.wait()
self.keep_running = False
self.scheduled_call = None
self.saved_state = None
self.saved_progress = 0
self.update_timer.stop()
self.progressBarFinished()
self.scores = []
self._update_model() # empty queue
self.rank_model.clear()
self.button.setText("Start")
self.button.setEnabled(self.check_preconditions())
self._thread = QThread(self)
self._worker = Worker(self)
self._worker.moveToThread(self._thread)
self._worker.stopped.connect(self._thread.quit)
self._worker.stopped.connect(self._select_first_if_none)
self._worker.stopped.connect(self._stopped)
self._worker.done.connect(self._done)
self._thread.started.connect(self._worker.do_work)
def filter_changed(self, text):
self.model_proxy.setFilterFixedString(text)
def stop_and_reset(self, reset_method=None):
if self.keep_running:
self.scheduled_call = reset_method or self.initialize
self.keep_running = False
else:
self.initialize()
def check_preconditions(self):
"""Check whether there is sufficient data for ranking."""
return True
def on_selection_changed(self, selected, deselected):
"""
Set the new visualization in the widget when the user select a
row in the table.
If derived class does not reimplement this, the table gives the
information but the user can't click it to select the visualization.
Args:
selected: the index of the selected item
deselected: the index of the previously selected item
"""
pass
def iterate_states(self, initial_state):
"""
Generate all possible states (e.g. attribute combinations) for the
given data. The content of the generated states is specific to the
visualization.
This method must be defined in the derived classes.
Args:
initial_state: initial state; None if this is the first call
"""
raise NotImplementedError
def state_count(self):
"""
Return the number of states for the progress bar.
Derived classes should implement this to ensure the proper behaviour of
the progress bar"""
return 0
def compute_score(self, state):
"""
Abstract method for computing the score for the given state. Smaller
scores are better.
Args:
state: the state, e.g. the combination of attributes as generated
by :obj:`state_count`.
"""
raise NotImplementedError
def bar_length(self, score):
"""Compute the bar length (between 0 and 1) corresponding to the score.
Return `None` if the score cannot be normalized.
"""
return None
def row_for_state(self, score, state):
"""
Abstract method that return the items that are inserted into the table.
Args:
score: score, computed by :obj:`compute_score`
state: the state, e.g. combination of attributes
"""
raise NotImplementedError
def _select_first_if_none(self):
if not self.rank_table.selectedIndexes():
self.rank_table.selectRow(0)
def _done(self):
self.button.setText("Finished")
self.button.setEnabled(False)
self.keep_running = False
self.saved_state = None
def _stopped(self):
self.update_timer.stop()
self.progressBarFinished()
self._update_model()
self.stopped()
if self.scheduled_call:
self.scheduled_call()
def _update(self):
self._update_model()
self._update_progress()
def _update_progress(self):
self.progressBarSet(int(self.saved_progress * 100 / max(1, self.state_count())))
def _update_model(self):
try:
while True:
pos, row_items = self.add_to_model.get_nowait()
self.rank_model.insertRow(pos, row_items)
except queue.Empty:
pass
def toggle(self):
"""Start or pause the computation."""
self.keep_running = not self.keep_running
if self.keep_running:
self.button.setText("Pause")
self.progressBarInit()
self.update_timer.start()
self.before_running()
self._thread.start()
else:
self.button.setText("Continue")
self._thread.quit()
# Need to sync state (the worker must read the keep_running
# state and stop) for reliable restart.
self._thread.wait()
def before_running(self):
"""Code that is run before running vizrank in its own thread"""
pass
def stopped(self):
"""Code that is run after stopping the vizrank thread"""
pass
class OWDtoxsAlignment(widget.OWWidget):
name = "Dtoxs Alignment"
description = "Step 1 of the Dtoxs SOP. Uses a Burrows-Wheeler Aligner (BWA)."
category = "RNASeq"
icon = "icons/dtoxs-alignment2.svg"
priority = 10
image_name = "biodepot/dtoxs_alignment"
image_version = "latest"
inputs = [("References", str, "set_refs"), ("Seqs", str, "set_seqs")]
outputs = [("Counts", str)]
auto_run = Setting(True)
want_main_area = False
def __init__(self):
super().__init__()
# Docker Client
# This client talks to your local docker
self.docker = DockerClient('unix:///var/run/docker.sock', 'local')
# The directory of the seq data needed to run
# the container will be set by the user before the
# container can be run
self.host_ref_dir = None
self.host_seq_dir = None
self.ref_dir_set = False
self.seq_dir_set = False
# The default write location of all widgets should be
# ~/BioDepot/WidgetName/
# TODO is this an issue if multiple containers write to the same place?
# TODO add timestamp to directory name to differentiate runs
counts_dir = '~/BioDepot/Dtoxs_Alignment/Counts'
if not os.path.exists(counts_dir):
os.makedirs(counts_dir)
self.host_counts_dir = self.docker.toHostDir(counts_dir)
# GUI
box = gui.widgetBox(self.controlArea, "Info")
self.infoLabel = gui.widgetLabel(
box, 'Connect to a Directory widget '
'to specify location of reference '
'and seq fastq files')
self.infoLabel.setWordWrap(True)
gui.checkBox(self.controlArea, self, 'auto_run',
'Run automatically when input set')
self.btn_run = gui.button(self.controlArea,
self,
"Run",
callback=self.btn_run_pushed)
self.is_running = False
"""
Called when the user pushes 'Run'
"""
def btn_run_pushed(self):
self.start_container(run_btn_pushed=True)
"""
Set references
"""
def set_refs(self, path):
# When a user removes a connected Directory widget,
# it sends a signal with path=None
if path is None:
self.ref_dir_set = False
else:
self.host_ref_dir = self.docker.toHostDir(path)
if self.host_ref_dir is None:
# TODO emit error
self.ref_dir_set = False
print('References set to invalid directory')
else:
self.ref_dir_set = True
self.start_container(run_btn_pushed=False)
"""
Set seqs
"""
def set_seqs(self, path):
# When a user removes a connected Directory widget,
# it sends a signal with path=None
if path is None:
self.seq_dir_set = False
else:
self.host_seq_dir = self.docker.toHostDir(path)
if self.host_seq_dir is None:
# TODO emit error
self.seq_dir_set = False
print('Seq set to invalid directory')
else:
self.seq_dir_set = True
self.start_container(run_btn_pushed=False)
"""
Pull image
"""
def pull_image(self):
self.infoLabel.setText('Pulling \'' + self.image_name + ":" +
self.image_version + '\' from Dockerhub...')
self.setStatusMessage("Downloading...")
self.progressBarInit()
self.is_running = True
self.btn_run.setEnabled(False)
# Pull the image in a new thread
self.pull_image_thread = QThread()
self.pull_image_worker = PullImageWorker(self.docker, self.image_name,
self.image_version)
self.pull_image_worker.progress[int].connect(self.pull_image_progress)
self.pull_image_worker.finished.connect(self.pull_image_finished)
self.pull_image_worker.moveToThread(self.pull_image_thread)
self.pull_image_thread.started.connect(self.pull_image_worker.work)
self.pull_image_thread.start()
@pyqtSlot(int, name="pullImageProgress")
def pull_image_progress(self, val):
self.progressBarSet(val)
@pyqtSlot(name="pullImageFinished")
def pull_image_finished(self):
self.pull_image_thread.terminate()
self.pull_image_thread.wait()
self.infoLabel.setText('Finished pulling \'' + self.image_name + ":" +
self.image_version + '\'')
self.progressBarFinished()
self.start_container()
"""
Alignment
"""
def start_container(self, run_btn_pushed=True):
# Make sure both inputs are set
if self.ref_dir_set and self.seq_dir_set:
if not self.is_running and (self.auto_run or run_btn_pushed):
# Make sure the docker image is downloaded
if not self.docker.has_image(self.image_name,
self.image_version):
self.pull_image()
else:
self.run_container()
else:
self.infoLabel.setText(
'References and Seqs directories set.\nWaiting to run...')
elif self.ref_dir_set:
self.infoLabel.setText("Waiting for user to set Seqs directory.")
elif self.seq_dir_set:
self.infoLabel.setText(
"Waiting for user to set References directory.")
def run_container(self):
self.is_running = True
self.infoLabel.setText('Running alignment...')
self.setStatusMessage('Running...')
self.progressBarInit()
# Run the container in a new thread
self.run_container_thread = QThread()
self.run_container_worker = RunAlignmentWorker(self.docker,
self.image_name,
self.host_ref_dir,
self.host_seq_dir,
self.host_counts_dir)
self.run_container_worker.progress[int].connect(
self.run_container_progress)
self.run_container_worker.finished.connect(self.run_container_finished)
self.run_container_worker.moveToThread(self.run_container_thread)
self.run_container_thread.started.connect(
self.run_container_worker.work)
self.run_container_thread.start()
@pyqtSlot(int, name="runContainerProgress")
def run_container_progress(self, val):
self.progressBarSet(val)
@pyqtSlot(name="runContainerFinished")
def run_container_finished(self):
self.run_container_thread.terminate()
self.run_container_thread.wait()
self.infoLabel.setText("Finished running alignment!")
self.btn_run.setEnabled(True)
self.is_running = False
self.btn_run.setText('Run again')
self.setStatusMessage('Finished!')
self.progressBarFinished()
self.send("Counts", self.docker.toContainerDir(self.host_counts_dir))