def rect(self):
if getattr(self, "_rect", QRectF()).isValid():
return self._rect
else:
return QRectF(QPointF(0, 0), self.document().size()) | \
getattr(self, "_rect", QRectF(0, 0, 1, 1))
def setup_plot(self, scoreindex, scores, nulldist=None):
"""
Setup the score histogram plot
Parameters
----------
scoreindex : int
Score index (into OWFeatureSelection.Scores)
scores : (N, ) array
The scores obtained
nulldist (P, N) array optional
The scores obtained under P permutations of labels.
"""
score_name, side, test_type, _ = self.Scores[scoreindex]
low, high = self.thresholds.get(score_name, (-np.inf, np.inf))
validmask = np.isfinite(scores)
validscores = scores[validmask]
nbins = int(max(np.ceil(np.sqrt(len(validscores))), 20))
freq, edges = np.histogram(validscores, bins=nbins)
self.histogram.setHistogramCurve(
pg.PlotCurveItem(x=edges,
y=freq,
stepMode=True,
pen=pg.mkPen("b", width=2)))
if nulldist is not None:
nulldist = nulldist.ravel()
validmask = np.isfinite(nulldist)
validnulldist = nulldist[validmask]
nullbins = edges # XXX: extend to the full range of nulldist
nullfreq, _ = np.histogram(validnulldist, bins=nullbins)
nullfreq = nullfreq * (freq.sum() / nullfreq.sum())
nullitem = pg.PlotCurveItem(x=nullbins,
y=nullfreq,
stepMode=True,
pen=pg.mkPen((50, 50, 50, 100)))
# Ensure it stacks behind the main curve
nullitem.setZValue(nullitem.zValue() - 10)
self.histogram.addItem(nullitem)
# Restore saved thresholds
eps = np.finfo(float).eps
minx, maxx = edges[0] - eps, edges[-1] + eps
low, high = max(low, minx), min(high, maxx)
if side == OWFeatureSelection.LowTail:
mode = Histogram.Low
elif side == OWFeatureSelection.HighTail:
mode = Histogram.High
elif side == OWFeatureSelection.TwoTail:
mode = Histogram.TwoSided
else:
assert False
self.histogram.setSelectionMode(mode)
self.histogram.setBoundary(low, high)
# If this is a two sample test add markers to the left and right
# plot indicating which group is over-expressed in that part
if test_type == OWFeatureSelection.TwoSampleTest and \
side == OWFeatureSelection.TwoTail:
maxy = np.max(freq)
# XXX: Change use of integer constant
if scoreindex == 0: # fold change is centered on 1.0
x1, y1 = (minx + 1) / 2, maxy
x2, y2 = (maxx + 1) / 2, maxy
else:
x1, y1 = minx / 2, maxy
x2, y2 = maxx / 2, maxy
grp, selected_indices = self.selected_split()
values = grp.values
selected_values = [values[i] for i in selected_indices]
left = ", ".join(v for v in values if v not in selected_values)
right = ", ".join(v for v in selected_values)
labelitem = pg.TextItem(left, color=(40, 40, 40))
labelitem.setPos(x1, y1)
self.histogram.addItem(labelitem)
labelitem = pg.TextItem(right, color=(40, 40, 40))
labelitem.setPos(x2, y2)
self.histogram.addItem(labelitem)
miny, maxy = 0.0, np.max(freq)
if nulldist is not None:
maxy = max(np.max(nullfreq), maxy)
if not np.any(np.isnan([maxx, minx, maxy])):
self.histogram.setRange(QRectF(minx, miny, maxx - minx,
maxy - miny),
padding=0.05)
def _select_data(self):
self.widget.graph.select_by_rectangle(QRectF(4, 3, 3, 1))
return self.widget.graph.get_selection()
def boundingRect(self):
return QRectF(-self.r, -self.r, 2 * self.r, 2 * self.r)
def boundingRect(self):
return QRectF(0, 0, 40 + self.text_width, 20 + self.scale.bins * 15)
def _ensureSceneRect(self, scene):
r = scene.addRect(QRectF(0, 0, 400, 400))
scene.sceneRect()
scene.removeItem(r)
def update_data(self, attr_x, attr_y, reset_view=True):
self.master.Warning.missing_coords.clear()
self.master.Information.missing_coords.clear()
self._clear_plot_widget()
self.shown_x, self.shown_y = attr_x, attr_y
if self.jittered_data is None or not len(self.jittered_data):
self.valid_data = None
else:
index_x = self.domain.index(attr_x)
index_y = self.domain.index(attr_y)
self.valid_data = self.get_valid_list([index_x, index_y])
if not np.any(self.valid_data):
self.valid_data = None
if self.valid_data is None:
self.selection = None
self.n_points = 0
self.master.Warning.missing_coords(
self.shown_x.name, self.shown_y.name)
return
x_data, y_data = self.get_xy_data_positions(
attr_x, attr_y, self.valid_data)
self.n_points = len(x_data)
if reset_view:
min_x, max_x = np.nanmin(x_data), np.nanmax(x_data)
min_y, max_y = np.nanmin(y_data), np.nanmax(y_data)
self.view_box.setRange(
QRectF(min_x, min_y, max_x - min_x, max_y - min_y),
padding=0.025)
self.view_box.init_history()
self.view_box.tag_history()
[min_x, max_x], [min_y, max_y] = self.view_box.viewRange()
for axis, name, index in (("bottom", attr_x, index_x),
("left", attr_y, index_y)):
self.set_axis_title(axis, name)
var = self.domain[index]
if var.is_discrete:
self.set_labels(axis, get_variable_values_sorted(var))
else:
self.set_labels(axis, None)
color_data, brush_data = self.compute_colors()
color_data_sel, brush_data_sel = self.compute_colors_sel()
size_data = self.compute_sizes()
shape_data = self.compute_symbols()
if self.should_draw_density():
rgb_data = [pen.color().getRgb()[:3] for pen in color_data]
self.density_img = classdensity.class_density_image(
min_x, max_x, min_y, max_y, self.resolution,
x_data, y_data, rgb_data)
self.plot_widget.addItem(self.density_img)
data_indices = np.flatnonzero(self.valid_data)
if len(data_indices) != self.original_data.shape[1]:
self.master.Information.missing_coords(
self.shown_x.name, self.shown_y.name)
self.scatterplot_item = ScatterPlotItem(
x=x_data, y=y_data, data=data_indices,
symbol=shape_data, size=size_data, pen=color_data, brush=brush_data
)
self.scatterplot_item_sel = ScatterPlotItem(
x=x_data, y=y_data, data=data_indices,
symbol=shape_data, size=size_data + SELECTION_WIDTH,
pen=color_data_sel, brush=brush_data_sel
)
self.plot_widget.addItem(self.scatterplot_item_sel)
self.plot_widget.addItem(self.scatterplot_item)
self.scatterplot_item.selected_points = []
self.scatterplot_item.sigClicked.connect(self.select_by_click)
self.update_labels()
self.make_legend()
self.plot_widget.replot()
def setSelectionRect(self, rect):
if self._selection_rect != rect:
self._selection_rect = QRectF(rect)
self._item.setRect(self._selection_rect)
def _reset(self):
self.setSelectionRect(QRectF())
self._item.setVisible(False)
self._mouse_dragging = False
def basic_scene():
scene = QGraphicsScene()
scene.addRect(QRectF(0, 0, 100, 100))
return scene
def rect(self):
return QRectF(self.pos(), QSizeF(*self.size()))
def boundingRect(self):
return QRectF(0, 0, self.width, self.height)
def clear_scene(self):
self.scene.clear()
self.scene.setSceneRect(QRectF())
def boundingRect(self):
return self._rect if getattr(self, "_rect", QRectF()).isValid() \
else super().boundingRect()
def boundingRect(self):
return QRectF()
def setData(self, data, nsamples, sample_range=None, color=Qt.magenta):
assert np.all(np.isfinite(data))
if data.size > 0:
xmin, xmax = np.min(data), np.max(data)
else:
xmin = xmax = 0.0
if sample_range is None:
xrange = xmax - xmin
sample_min = xmin - xrange * 0.025
sample_max = xmax + xrange * 0.025
else:
sample_min, sample_max = sample_range
sample = np.linspace(sample_min, sample_max, nsamples)
if data.size < 2:
est = np.full(sample.size, 1. / sample.size, )
else:
try:
density = stats.gaussian_kde(data)
est = density.evaluate(sample)
except np.linalg.LinAlgError:
est = np.zeros(sample.size)
item = QGraphicsPathItem(violin_shape(sample, est))
color = QColor(color)
color.setAlphaF(0.5)
item.setBrush(QBrush(color))
pen = QPen(self.palette().color(QPalette.Shadow))
pen.setCosmetic(True)
item.setPen(pen)
est_max = np.max(est)
x = np.random.RandomState(0xD06F00D).uniform(
-est_max, est_max, size=data.size
)
dots = ScatterPlotItem(
x=x, y=data, size=3,
)
dots.setVisible(self.__dataPointsVisible)
pen = QPen(self.palette().color(QPalette.Shadow), 1)
hoverPen = QPen(self.palette().color(QPalette.Highlight), 1.5)
cmax = SelectionLine(
angle=0, pos=xmax, movable=True, bounds=(sample_min, sample_max),
pen=pen, hoverPen=hoverPen
)
cmin = SelectionLine(
angle=0, pos=xmin, movable=True, bounds=(sample_min, sample_max),
pen=pen, hoverPen=hoverPen
)
cmax.setCursor(Qt.SizeVerCursor)
cmin.setCursor(Qt.SizeVerCursor)
selection_item = QGraphicsRectItem(
QRectF(-est_max, xmin, est_max * 2, xmax - xmin)
)
selection_item.setPen(QPen(Qt.NoPen))
selection_item.setBrush(QColor(0, 250, 0, 50))
def update_selection_rect():
mode = self.__selectionMode
p = selection_item.parentItem() # type: Optional[QGraphicsItem]
while p is not None and not isinstance(p, pg.ViewBox):
p = p.parentItem()
if p is not None:
viewbox = p # type: pg.ViewBox
else:
viewbox = None
rect = selection_item.rect() # type: QRectF
if mode & ViolinPlot.High:
rect.setTop(cmax.value())
elif viewbox is not None:
rect.setTop(viewbox.viewRect().bottom())
else:
rect.setTop(cmax.maxRange[1])
if mode & ViolinPlot.Low:
rect.setBottom(cmin.value())
elif viewbox is not None:
rect.setBottom(viewbox.viewRect().top())
else:
rect.setBottom(cmin.maxRange[0])
selection_item.setRect(rect.normalized())
cmax.sigPositionChanged.connect(update_selection_rect)
cmin.sigPositionChanged.connect(update_selection_rect)
cmax.visibleChanged.connect(update_selection_rect)
cmin.visibleChanged.connect(update_selection_rect)
def setupper(line):
ebound = self.__effectiveBoundary()
elower, eupper = ebound
mode = self.__selectionMode
if not mode & ViolinPlot.High:
return
upper = line.value()
lower = min(elower, upper)
if lower != elower and mode & ViolinPlot.Low:
self.__min = lower
cmin.setValue(lower)
if upper != eupper:
self.__max = upper
if ebound != self.__effectiveBoundary():
self.selectionEdited.emit()
self.selectionChanged.emit()
def setlower(line):
ebound = self.__effectiveBoundary()
elower, eupper = ebound
mode = self.__selectionMode
if not mode & ViolinPlot.Low:
return
lower = line.value()
upper = max(eupper, lower)
if upper != eupper and mode & ViolinPlot.High:
self.__max = upper
cmax.setValue(upper)
if lower != elower:
self.__min = lower
if ebound != self.__effectiveBoundary():
self.selectionEdited.emit()
self.selectionChanged.emit()
cmax.sigPositionChanged.connect(setupper)
cmin.sigPositionChanged.connect(setlower)
selmode = self.__selectionMode
cmax.setVisible(selmode & ViolinPlot.High)
cmin.setVisible(selmode & ViolinPlot.Low)
selection_item.setVisible(selmode)
self.addItem(dots)
self.addItem(item)
self.addItem(cmax)
self.addItem(cmin)
self.addItem(selection_item)
self.setRange(
QRectF(-est_max, np.min(sample), est_max * 2, np.ptp(sample))
)
self._plotitems = SimpleNamespace(
pointsitem=dots,
densityitem=item,
cmax=cmax,
cmin=cmin,
selection_item=selection_item
)
self.__min = xmin
self.__max = xmax
def set_view_box_range(self):
self.view_box.setRange(QRectF(-1.05, -1.05, 2.1, 2.1))
def clear_scene(self):
self.scene.clear()
self.scene.setSceneRect(QRectF())
self.view.setSceneRect(QRectF())
self._stripe_plot = None
def adjustLeft(rect):
rect = QRectF(rect)
rect.setLeft(geom.left())
return rect
def update_data(self, attr_x, attr_y, reset_view=True):
self.master.Warning.missing_coords.clear()
self.master.Information.missing_coords.clear()
self._clear_plot_widget()
if self.shown_y != attr_y:
# 'reset' the axis text width estimation. Without this the left
# axis tick labels space only ever expands
yaxis = self.plot_widget.getAxis("left")
yaxis.textWidth = 30
self.shown_x, self.shown_y = attr_x, attr_y
if attr_x not in self.data.domain or attr_y not in self.data.domain:
data = self.sparse_to_dense()
self.set_data(data)
if self.jittered_data is None or not len(self.jittered_data):
self.valid_data = None
else:
self.valid_data = self.get_valid_list([attr_x, attr_y])
if not np.any(self.valid_data):
self.valid_data = None
if self.valid_data is None:
self.selection = None
self.n_points = 0
self.master.Warning.missing_coords(self.shown_x.name,
self.shown_y.name)
return
x_data, y_data = self.get_xy_data_positions(attr_x, attr_y,
self.valid_data)
self.n_points = len(x_data)
if reset_view:
min_x, max_x = np.nanmin(x_data), np.nanmax(x_data)
min_y, max_y = np.nanmin(y_data), np.nanmax(y_data)
self.view_box.setRange(QRectF(min_x, min_y, max_x - min_x,
max_y - min_y),
padding=0.025)
self.view_box.init_history()
self.view_box.tag_history()
[min_x, max_x], [min_y, max_y] = self.view_box.viewRange()
for axis, var in (("bottom", attr_x), ("left", attr_y)):
self.set_axis_title(axis, var)
if var.is_discrete:
self.set_labels(axis, get_variable_values_sorted(var))
else:
self.set_labels(axis, None)
color_data, brush_data = self.compute_colors()
color_data_sel, brush_data_sel = self.compute_colors_sel()
size_data = self.compute_sizes()
shape_data = self.compute_symbols()
if self.should_draw_density():
rgb_data = [pen.color().getRgb()[:3] for pen in color_data]
self.density_img = classdensity.class_density_image(
min_x, max_x, min_y, max_y, self.resolution, x_data, y_data,
rgb_data)
self.plot_widget.addItem(self.density_img)
self.data_indices = np.flatnonzero(self.valid_data)
if len(self.data_indices) != len(self.data):
self.master.Information.missing_coords(self.shown_x.name,
self.shown_y.name)
self.scatterplot_item = ScatterPlotItem(x=x_data,
y=y_data,
data=self.data_indices,
symbol=shape_data,
size=size_data,
pen=color_data,
brush=brush_data)
self.scatterplot_item_sel = ScatterPlotItem(x=x_data,
y=y_data,
data=self.data_indices,
symbol=shape_data,
size=size_data +
SELECTION_WIDTH,
pen=color_data_sel,
brush=brush_data_sel)
self.plot_widget.addItem(self.scatterplot_item_sel)
self.plot_widget.addItem(self.scatterplot_item)
self.scatterplot_item.selected_points = []
self.scatterplot_item.sigClicked.connect(self.select_by_click)
if self.show_reg_line:
_x_data = self.data.get_column_view(self.shown_x)[0]
_y_data = self.data.get_column_view(self.shown_y)[0]
_x_data = _x_data[self.valid_data]
_y_data = _y_data[self.valid_data]
assert _x_data.size
assert _y_data.size
self.draw_regression_line(_x_data, _y_data, np.min(_x_data),
np.max(_y_data))
self.update_labels()
self.make_legend()
self.plot_widget.replot()
def _select_data(self):
rect = QRectF(QPointF(-20, -20), QPointF(20, 20))
self.widget.graph.select_by_rectangle(rect)
return self.widget.graph.get_selection()
def update_scene(self):
self.clear_scene()
if self.domain is None or not len(self.points[0]):
return
n_attrs = self.n_attributes if self.display_index else int(1e10)
attr_inds, attributes = zip(*self.get_ordered_attributes()[:n_attrs])
name_items = [QGraphicsTextItem(attr.name) for attr in attributes]
point_text = QGraphicsTextItem("Points")
probs_text = QGraphicsTextItem("Probabilities (%)")
all_items = name_items + [point_text, probs_text]
name_offset = -max(t.boundingRect().width() for t in all_items) - 10
w = self.view.viewport().rect().width()
max_width = w + name_offset - 30
points = [self.points[i][self.target_class_index] for i in attr_inds]
if self.align == OWNomogram.ALIGN_LEFT:
points = [p - p.min() for p in points]
max_ = np.nan_to_num(max(max(abs(p)) for p in points))
d = 100 / max_ if max_ else 1
minimums = [p[self.target_class_index].min() for p in self.points]
if self.scale == OWNomogram.POINT_SCALE:
points = [p * d for p in points]
if self.align == OWNomogram.ALIGN_LEFT:
self.scale_marker_values = lambda x: (x - minimums) * d
else:
self.scale_marker_values = lambda x: x * d
else:
if self.align == OWNomogram.ALIGN_LEFT:
self.scale_marker_values = lambda x: x - minimums
else:
self.scale_marker_values = lambda x: x
point_item, nomogram_head = self.create_main_nomogram(
attributes, attr_inds, name_items, points, max_width, point_text,
name_offset)
probs_item, nomogram_foot = self.create_footer_nomogram(
probs_text, d, minimums, max_width, name_offset)
for item in self.feature_items.values():
item.dot.point_dot = point_item.dot
item.dot.probs_dot = probs_item.dot
item.dot.vertical_line = self.hidden_vertical_line
self.nomogram = nomogram = NomogramItem()
nomogram.add_items([nomogram_head, self.nomogram_main, nomogram_foot])
self.scene.addItem(nomogram)
self.set_feature_marker_values()
rect = QRectF(self.scene.itemsBoundingRect().x(),
self.scene.itemsBoundingRect().y(),
self.scene.itemsBoundingRect().width(),
self.nomogram.preferredSize().height()).adjusted(
10, 0, 20, 0)
self.scene.setSceneRect(rect)
# Clip top and bottom (60 and 150) parts from the main view
self.view.setSceneRect(rect.x(),
rect.y() + 80,
rect.width() - 10,
rect.height() - 160)
self.view.viewport().setMaximumHeight(rect.height() - 160)
# Clip main part from top/bottom views
# below point values are imprecise (less/more than required) but this
# is not a problem due to clipped scene content still being drawn
self.top_view.setSceneRect(rect.x(),
rect.y() + 3,
rect.width() - 10, 20)
self.bottom_view.setSceneRect(rect.x(),
rect.height() - 110,
rect.width() - 10, 30)
def display_contingency(self):
"""
Set the contingency to display.
"""
cont = self.contingencies
var, cvar = self.var, self.cvar
if cont is None or not len(cont):
return
self.plot.clear()
self.plot_prob.clear()
self._legend.clear()
self.tooltip_items = []
if self.show_prob:
self.ploti.showAxis('right')
else:
self.ploti.hideAxis('right')
bottomaxis = self.ploti.getAxis("bottom")
bottomaxis.setLabel(var.name)
bottomaxis.resizeEvent()
cvar_values = cvar.values
colors = [QColor(*col) for col in cvar.colors]
if var and var.is_continuous:
bottomaxis.setTicks(None)
weights, cols, cvar_values, curves = [], [], [], []
for i, dist in enumerate(cont):
v, W = dist
if len(v):
weights.append(numpy.sum(W))
cols.append(colors[i])
cvar_values.append(cvar.values[i])
curves.append(
ash_curve(dist,
cont,
m=OWDistributions.ASH_HIST,
smoothing_factor=self.smoothing_factor))
weights = numpy.array(weights)
sumw = numpy.sum(weights)
weights /= sumw
colors = cols
curves = [(X, Y * w) for (X, Y), w in zip(curves, weights)]
curvesline = [] #from histograms to lines
for X, Y in curves:
X = X + (X[1] - X[0]) / 2
X = X[:-1]
X = numpy.array(X)
Y = numpy.array(Y)
curvesline.append((X, Y))
for t in ["fill", "line"]:
curve_data = list(zip(curvesline, colors, weights,
cvar_values))
for (X, Y), color, w, cval in reversed(curve_data):
item = pg.PlotCurveItem()
pen = QPen(QBrush(color), 3)
pen.setCosmetic(True)
color = QColor(color)
color.setAlphaF(0.2)
item.setData(X,
Y / (w if self.relative_freq else 1),
antialias=True,
stepMode=False,
fillLevel=0 if t == "fill" else None,
brush=QBrush(color),
pen=pen)
self.plot.addItem(item)
if t == "line":
item.tooltip = "{}\n{}={}".format(
"Normalized density " if self.relative_freq else
"Density ", cvar.name, cval)
self.tooltip_items.append((self.plot, item))
if self.show_prob:
all_X = numpy.array(
numpy.unique(numpy.hstack([X for X, _ in curvesline])))
inter_X = numpy.array(
numpy.linspace(all_X[0], all_X[-1],
len(all_X) * 2))
curvesinterp = [
numpy.interp(inter_X, X, Y) for (X, Y) in curvesline
]
sumprob = numpy.sum(curvesinterp, axis=0)
legal = sumprob > 0.05 * numpy.max(sumprob)
i = len(curvesinterp) + 1
show_all = self.show_prob == i
for Y, color, cval in reversed(
list(zip(curvesinterp, colors, cvar_values))):
i -= 1
if show_all or self.show_prob == i:
item = pg.PlotCurveItem()
pen = QPen(QBrush(color), 3, style=Qt.DotLine)
pen.setCosmetic(True)
prob = Y[legal] / sumprob[legal]
item.setData(inter_X[legal],
prob,
antialias=True,
stepMode=False,
fillLevel=None,
brush=None,
pen=pen)
self.plot_prob.addItem(item)
item.tooltip = "Probability that \n" + cvar.name + "=" + cval
self.tooltip_items.append((self.plot_prob, item))
elif var and var.is_discrete:
bottomaxis.setTicks([list(enumerate(var.values))])
cont = numpy.array(cont)
maxh = 0 #maximal column height
maxrh = 0 #maximal relative column height
scvar = cont.sum(axis=1)
#a cvar with sum=0 with allways have distribution counts 0,
#therefore we can divide it by anything
scvar[scvar == 0] = 1
for i, (value, dist) in enumerate(zip(var.values, cont.T)):
maxh = max(maxh, max(dist))
maxrh = max(maxrh, max(dist / scvar))
for i, (value, dist) in enumerate(zip(var.values, cont.T)):
dsum = sum(dist)
geom = QRectF(i - 0.333, 0, 0.666,
maxrh if self.relative_freq else maxh)
if self.show_prob:
prob = dist / dsum
ci = 1.96 * numpy.sqrt(prob * (1 - prob) / dsum)
else:
ci = None
item = DistributionBarItem(
geom, dist / scvar /
maxrh if self.relative_freq else dist / maxh, colors)
self.plot.addItem(item)
tooltip = "\n".join("%s: %.*f" %
(n, 3 if self.relative_freq else 1, v)
for n, v in zip(
cvar_values, dist /
scvar if self.relative_freq else dist))
item.tooltip = "{} ({}={}):\n{}".format(
"Normalized frequency " if self.relative_freq else
"Frequency ", cvar.name, value, tooltip)
self.tooltip_items.append((self.plot, item))
if self.show_prob:
item.tooltip += "\n\nProbabilities:"
for ic, a in enumerate(dist):
if self.show_prob - 1 != ic and \
self.show_prob - 1 != len(dist):
continue
position = -0.333 + ((ic + 0.5) * 0.666 / len(dist))
if dsum < 1e-6:
continue
prob = a / dsum
if not 1e-6 < prob < 1 - 1e-6:
continue
ci = 1.96 * sqrt(prob * (1 - prob) / dsum)
item.tooltip += "\n%s: %.3f ± %.3f" % (cvar_values[ic],
prob, ci)
mark = pg.ScatterPlotItem()
errorbar = pg.ErrorBarItem()
pen = QPen(QBrush(QColor(0)), 1)
pen.setCosmetic(True)
errorbar.setData(x=[i + position],
y=[prob],
bottom=min(numpy.array([ci]), prob),
top=min(numpy.array([ci]), 1 - prob),
beam=numpy.array([0.05]),
brush=QColor(1),
pen=pen)
mark.setData([i + position], [prob],
antialias=True,
symbol="o",
fillLevel=None,
pxMode=True,
size=10,
brush=QColor(colors[ic]),
pen=pen)
self.plot_prob.addItem(errorbar)
self.plot_prob.addItem(mark)
for color, name in zip(colors, cvar_values):
self._legend.addItem(
ScatterPlotItem(pen=color, brush=color, size=10, shape="s"),
escape(name))
self._legend.show()
def paint(self, p, opt, widget):
def get_arrows():
# Compute (n, 4) array of coordinates of arrows' ends
# Arrows are at 15 degrees; length is 10, clipped to edge length
x0, y0, x1, y1 = edge_coords.T
arr_len = np.clip(lengths - sizes1 - w3, 0, 10)
cos12 = arr_len * np.cos(np.pi / 12)
sin12 = arr_len * np.sin(np.pi / 12)
# cos(a ± 15) = cos(a) cos(15) ∓ sin(a) sin(15)
tx = sins * (fx * sin12)
x1a = x1 - coss * (fx * cos12)
x2a = x1a - tx
x1a += tx
# sin(a ± 15) = sin(a) cos(15) ± sin(15) cos(a)
ty = (fy * sin12) * coss
y1a = y1 + sins * (fy * cos12)
y2a = y1a - ty
y1a += ty
return np.vstack((x1a, y1a, x2a, y2a)).T
def get_short_edge_coords():
# Compute the target-side coordinates of edges with arrows
# Such edges are shorted by 8 pixels + width / 3
off = 8 + w3
return edge_coords[:, 2:] + (off * np.vstack((-fxcos, fysin))).T
if self.xData is None or len(self.xData) == 0:
return
# Widths of edges, divided by 3; used for adjusting sizes
w3 = (self.widths if self.widths is not None else self.pen.width()) / 3
# Sizes of source and target nodes; they are used for adjusting the
# edge lengths, so we increase the sizes by edge widths / 3
sizes0, sizes1 = self.sizes[::2] + w3, self.sizes[1::2] + w3
# Coordinates of vertices for all end points (in real world)
x0s, x1s = self.xData[::2], self.xData[1::2]
y0s, y1s = self.yData[::2], self.yData[1::2]
# Factors for transforming real-worlds coordinates into pixels
fx = 1 / p.worldTransform().m11()
fy = 1 / p.worldTransform().m22()
# Computations of angles (lengths are also used to clip the arrows)
# We need sine and cosine of angles, and never the actual angles.
# Sine and cosine are compute as ratios in triangles rather than with
# trigonometric functions
diffx, diffy = (x1s - x0s) / fx, -(y1s - y0s) / fy
lengths = np.sqrt(diffx**2 + diffy**2)
arcs = lengths == 0
coss, sins = np.nan_to_num(diffx / lengths), np.nan_to_num(diffy /
lengths)
# A slower version of the above, with trigonometry
# angles = np.arctan2(-(y1s - y0s) / fy, (x1s - x0s) / fx)
# return np.cos(angles), np.sin(angles)
# Sin and cos are mostly used as mulitplied with fx and fy; precompute
fxcos, fysin = fx * coss, fy * sins
# Coordinates of edges' end points: coordinates of vertices, adjusted
# by sizes. When drawing arraws, the target coordinate is used for
# the tip of the arrow, not the edge
edge_coords = np.vstack((x0s + fxcos * sizes0, y0s - fysin * sizes0,
x1s - fxcos * sizes1, y1s + fysin * sizes1)).T
pen = QPen(self.pen)
p.setRenderHint(p.Antialiasing, True)
p.setCompositionMode(p.CompositionMode_SourceOver)
if self.widths is None:
p.setPen(pen)
if self.directed:
for (x0, y0, x1,
y1), (x1w,
y1w), (xa1, ya1, xa2,
ya2), arc in zip(edge_coords,
get_short_edge_coords(),
get_arrows(), arcs):
if not arc:
p.drawLine(QLineF(x0, y0, x1w, y1w))
p.drawLine(QLineF(xa1, ya1, x1, y1))
p.drawLine(QLineF(xa2, ya2, x1, y1))
else:
for ecoords in edge_coords[~arcs]:
p.drawLine(QLineF(*ecoords))
else:
if self.directed:
for (x0, y0, x1,
y1), (x1w,
y1w), (xa1, ya1, xa2,
ya2), w, arc in zip(edge_coords,
get_short_edge_coords(),
get_arrows(),
self.widths, arcs):
if not arc:
pen.setWidth(w)
p.setPen(pen)
p.drawLine(QLineF(x0, y0, x1w, y1w))
p.drawLine(QLineF(xa1, ya1, x1, y1))
p.drawLine(QLineF(xa2, ya2, x1, y1))
else:
for ecoords, w in zip(edge_coords[~arcs], self.widths[~arcs]):
pen.setWidth(w)
p.setPen(pen)
p.drawLine(QLineF(*ecoords))
# This part is not so optimized because there can't be that many loops
if np.any(arcs):
xs, ys = self.xData[::2][arcs], self.yData[1::2][arcs]
sizes = self.sizes[::2][arcs]
sizes += w3 if isinstance(w3, float) else w3[arcs]
# if radius of loop would be size, then distance betwween
# vertex and loop centers would be
# d = np.sqrt(size ** 2 - r ** 2 / 2) + r / np.sqrt(2) + r / 2
ds = sizes * (1 + np.sqrt(2) / 4)
rxs = xs - ds * fx
rys = ys - ds * fy
rfxs = sizes * fx
rfys = sizes * fy
ax0o = 6 * np.cos(np.pi * 5 / 6) * fx
ax1o = 6 * np.cos(np.pi * 7 / 12) * fx
ay0o = 6 * np.sin(np.pi * 5 / 6) * fy
ay1o = 6 * np.sin(np.pi * 7 / 12) * fy
if self.widths is None:
widths = np.full(len(rxs), pen.width())
else:
widths = self.widths[arcs]
for rx, ry, rfx, rfy, w in zip(rxs, rys, rfxs, rfys, widths):
rect = QRectF(rx, ry, rfx, rfy)
pen.setWidth(w)
p.setPen(pen)
p.drawArc(rect, 100 * 16, 250 * 16)
if self.directed:
rx += 1.1 * rfx
ry += rfy / 2
p.drawLine(QLineF(rx, ry, rx + ax0o, ry - ay0o))
p.drawLine(QLineF(rx, ry, rx + ax1o, ry - ay1o))
def update_circle(self):
if self.scatterplot_item is not None and not self.circle_item:
self.circle_item = QGraphicsEllipseItem()
self.circle_item.setRect(QRectF(-1, -1, 2, 2))
self.circle_item.setPen(pg.mkPen(QColor(0, 0, 0), width=2))
self.plot_widget.addItem(self.circle_item)
def get_mapped_rect():
p1, p2 = ev.buttonDownPos(ev.button()), ev.pos()
p1 = self.mapToView(p1)
p2 = self.mapToView(p2)
return QRectF(p1, p2)
def extend_horizontal(rect):
# type: (QRectF) -> QRectF
rect = QRectF(rect)
rect.setLeft(geom.left())
rect.setRight(geom.right())
return rect
def boundingRect(self):
return QRectF(0, 0,
25 + self.text_width + self.bin_height,
20 + self.scale.bins * self.bin_height)
def boundingRect(self):
# type: () -> QRectF
return QRectF()
def set_rect(self, rect):
self.prepareGeometryChange()
rect = QRectF() if rect is None else rect
self._rect = rect
self.update_contents()
self.update()
