def addPoint(self, text, color, border=None, size=20.0):
shape = QGraphicsEllipseItem(size / 2.0, size / 2.0, size, size)
brush = makeBrush(color)
shape.setBrush(brush)
shape.setPen(makePen(border))
self.addEntry(MapLegendEntryItem(shape, text))
def addPoint(self, text, color, border=None, size=20.0):
shape = QGraphicsEllipseItem(size / 2.0, size / 2.0, size, size)
brush = makeBrush(color)
shape.setBrush(brush)
shape.setPen(makePen(border))
self.addEntry(MapLegendEntryItem(shape, text))
class DataNode:
def __init__(self, data, radius=15):
self.data = data
# Add circular node
self.node = QGraphicsEllipseItem(0, 0, 1, 1)
# Set radius
self.radius = radius
# Add text label
self.label = QGraphicsTextItem(data.label)
font = self.label.font()
font.setPointSize(10)
self.label.setFont(font)
# Add line between label and node
self.line1 = QGraphicsLineItem(0, 0, 1, 1)
self.line2 = QGraphicsLineItem(0, 0, 1, 1)
self.node.setZValue(20)
self.label.setZValue(10)
self.line1.setZValue(10)
self.line2.setZValue(10)
self.line1.setPen(get_pen('0.5'))
self.line2.setPen(get_pen('0.5'))
self.color = '0.8'
@property
def radius(self):
return self._radius
@radius.setter
def radius(self, value):
self._radius = value
self.node.setRect(-value, -value, 2 * value, 2 * value)
def contains(self, point):
# Check label
if self.label.contains(self.label.mapFromScene(point)):
return True
# Check node
if self.node.contains(self.node.mapFromScene(point)):
return True
return False
def update(self):
self.node.update()
def add_to_scene(self, scene):
scene.addItem(self.node)
scene.addItem(self.label)
scene.addItem(self.line1)
scene.addItem(self.line2)
def remove_from_scene(self, scene):
scene.removeItem(self.node)
scene.removeItem(self.label)
scene.removeItem(self.line1)
scene.removeItem(self.line2)
@property
def node_position(self):
pos = self.node.pos()
return pos.x(), pos.y()
@node_position.setter
def node_position(self, value):
self.node.setPos(value[0], value[1])
self.update_lines()
@property
def label_position(self):
pos = self.label.pos()
return pos.x(), pos.y()
@label_position.setter
def label_position(self, value):
self.label.setPos(value[0], value[1])
self.update_lines()
def update_lines(self):
x0, y0 = self.label_position
x2, y2 = self.node_position
x1 = 0.5 * (x0 + x2)
y1 = y0
self.line1.setLine(x0, y0, x1, y1)
self.line2.setLine(x1, y1, x2, y2)
@property
def color(self):
return qt_to_mpl_color(self.node.brush().color())
@color.setter
def color(self, value):
self.node.setBrush(mpl_to_qt_color(value))
def updateTime(self, frame):
if frame == self.previousframe:
return
self.previousframe = frame
idx = self.currentPuff.currentIndex()
currentPuff = self.group.puffs[idx]
image1 = np.copy(self.I[frame])
mmax = np.max(self.I)
image1 = image1 / mmax
image2 = np.copy(self.I_fits[idx][frame])
image2 = image2 / mmax
self.puff_3D.update_images(image1, image2)
rel_frame = frame - (currentPuff.kinetics['t_start'] -
currentPuff.kinetics['before'])
for line in [self.vLine1, self.vLine2,
self.vLine5]: # self.vLine3,self.vLine4,self.vLine5]:
line.setValue(rel_frame)
for bar in self.error_bars:
bar.plot.removeItem(bar)
self.error_bars = []
for item in self.addedItems:
self.imageview.view.removeItem(item)
self.addedItems = []
scatter = pg.ScatterPlotItem(size=8, pen=pg.mkPen(None))
self.imageview.view.addItem(scatter)
self.addedItems.append(scatter)
spots = []
for i in np.arange(len(self.group.puffs)):
rel_frame2 = frame - ((currentPuff.kinetics['t_start'] -
currentPuff.kinetics['before']) -
(self.group.puffs[i].kinetics['t_start'] -
self.group.puffs[i].kinetics['before']))
if self.puffCheckBoxes[i].isChecked(
) and rel_frame2 >= 0 and rel_frame2 < self.params[i].shape[0]:
centers = self.params[i][:, :2] - self.bounds[1:, 0]
center = centers[rel_frame2, :]
amps = np.copy(self.params[i][:, -1])
amps[amps <= 0] = .00000001
amp = amps[rel_frame2]
std = self.group.puffs[0].clusters.standard_deviations[i]
color = np.array(self.colors[i])
color[3] = 50
### FIRST ADD THE POINT TO THE SCATTER PLOT
if 0.8 / amp < std: # if the amplitude>0 and the error (0.8/SNR) is within the fitting bounds
### FIRST PLOT THE
""" WARNING!!! the amp should really be the signal to noise ratio, so it is only valid when the image has been ratiod by the standard deviation of the noise """
sigma = 0.8 / amp
sigmas = 0.8 / amps
# add error bars to x and y
# first add X
color[3] = 255
err = pg.ErrorBarItem(
x=np.array([rel_frame]),
y=np.array([self.params[i][rel_frame2, 0]]),
top=np.array([sigma]),
bottom=np.array([sigma]),
beam=0.5,
pen=pg.mkPen(pg.mkColor(tuple(color))))
self.p3.addItem(err)
err.plot = self.p3
self.error_bars.append(err)
# second add Y
err = pg.ErrorBarItem(
x=np.array([rel_frame]),
y=np.array([self.params[i][rel_frame2, 1]]),
top=np.array([sigma]),
bottom=np.array([sigma]),
beam=0.5,
pen=pg.mkPen(pg.mkColor(tuple(color))))
self.p4.addItem(err)
err.plot = self.p4
self.error_bars.append(err)
reasonable_fit = sigmas < 2 * std
bounds = QRectF(
QPointF(center[0] - sigma, center[1] - sigma),
QSizeF(2 * sigma, 2 * sigma))
### plot outer circle
pathitem = QGraphicsEllipseItem(bounds)
color[-1] = 127 # alpha channel
pathitem.setPen(pg.mkPen(pg.mkColor(tuple(color))))
pathitem.setBrush(pg.mkColor((0, 0, 0, 0)))
self.imageview.view.addItem(pathitem)
self.addedItems.append(pathitem)
### plot line
frame_i = rel_frame2 - 6
if frame_i < 0:
frame_i = 0
alpha = 255
for ii in np.arange(rel_frame2, frame_i, -1) - 1:
if alpha <= 0 or not reasonable_fit[ii]:
break
color[-1] = alpha # alpha channel
alpha = alpha - (255 * 1. / 6.)
pathitem = QGraphicsPathItem()
pathitem.setPen(pg.mkColor(tuple(color)))
path = QPainterPath(QPointF(*centers[ii]))
path.lineTo(QPointF(*centers[ii + 1]))
pathitem.setPath(path)
self.imageview.view.addItem(pathitem)
self.addedItems.append(pathitem)
color[3] = 255 # make the spot transparent
spots.append({
'pos': center,
'brush': pg.mkBrush(pg.mkColor(tuple(color)))
})
scatter.addPoints(spots)
class DataNode:
def __init__(self, data, radius=15):
self.data = data
# Add circular node
self.node = QGraphicsEllipseItem(0, 0, 1, 1)
# Set radius
self.radius = radius
# Add text label
self.label = QGraphicsTextItem(data.label)
font = self.label.font()
font.setPointSize(10)
self.label.setFont(font)
# Add line between label and node
self.line1 = QGraphicsLineItem(0, 0, 1, 1)
self.line2 = QGraphicsLineItem(0, 0, 1, 1)
self.node.setZValue(20)
self.label.setZValue(10)
self.line1.setZValue(10)
self.line2.setZValue(10)
self.line1.setPen(get_pen('0.5'))
self.line2.setPen(get_pen('0.5'))
self.color = '0.8'
@property
def radius(self):
return self._radius
@radius.setter
def radius(self, value):
self._radius = value
self.node.setRect(-value, -value, 2 * value, 2 * value)
def contains(self, point):
# Check label
if self.label.contains(self.label.mapFromScene(point)):
return True
# Check node
if self.node.contains(self.node.mapFromScene(point)):
return True
return False
def update(self):
self.node.update()
def add_to_scene(self, scene):
scene.addItem(self.node)
scene.addItem(self.label)
scene.addItem(self.line1)
scene.addItem(self.line2)
def remove_from_scene(self, scene):
scene.removeItem(self.node)
scene.removeItem(self.label)
scene.removeItem(self.line1)
scene.removeItem(self.line2)
@property
def node_position(self):
pos = self.node.pos()
return pos.x(), pos.y()
@node_position.setter
def node_position(self, value):
self.node.setPos(value[0], value[1])
self.update_lines()
@property
def label_position(self):
pos = self.label.pos()
return pos.x(), pos.y()
@label_position.setter
def label_position(self, value):
self.label.setPos(value[0], value[1])
self.update_lines()
def update_lines(self):
x0, y0 = self.label_position
x2, y2 = self.node_position
x1 = 0.5 * (x0 + x2)
y1 = y0
self.line1.setLine(x0, y0, x1, y1)
self.line2.setLine(x1, y1, x2, y2)
@property
def color(self):
return qt_to_mpl_color(self.node.brush().color())
@color.setter
def color(self, value):
self.node.setBrush(mpl_to_qt_color(value))
