def setPlot(self, plot):
"""setting the ScatterPlotWidget for the node"""
self.plot = plot
# ScatterPlotItem for the current position of the 'Pointer'
self.spiPos = pg.ScatterPlotItem(size=3,
pen=pg.mkPen(None),
brush=pg.mkBrush(255, 255, 255, 255))
# ScatterPlotItem for the path, while drawing
self.spiPath = pg.ScatterPlotItem(size=3,
pen=pg.mkPen(None),
brush=pg.mkBrush(255, 0, 0, 255))
# ScatterPlotItem for the recognized template
self.spiTemplate = pg.ScatterPlotItem(size=3,
pen=pg.mkPen(None),
brush=pg.mkBrush(0,
100, 255, 255))
# setting the x and y range to width and height of the ir camera field
self.plot.setXRange(0, 1024)
self.plot.setYRange(0, 768)
# appending legend to display which color shows which data
self.legend = pg.LegendItem(offset=(-1, 1))
self.legend.addItem(self.spiPos, 'position')
self.legend.addItem(self.spiPath, 'path')
self.legend.addItem(self.spiTemplate, 'template')
self.legend.setParentItem(self.plot)
def __init__(self,name=None,items=None,colors=None):
super(CParameterTree,self).__init__()
self.name = name
self.setColumnCount(4)
self.setHeaderHidden(True)
self.setDragEnabled(False)
self.header = pg.TreeWidgetItem([name])
self.setIndentation(0)
headerBackgroundColor = pg.mkBrush(color=(100,100,100))
fontcolor = pg.mkBrush(color=(255,255,255))
self.setupHeader()
# self.header.setBackground(0,headerBackgroundColor)
# self.header.setBackground(1,headerBackgroundColor)
# self.header.setBackground(2,headerBackgroundColor)
# self.header.setBackground(3,headerBackgroundColor)
# self.header.setForeground(0,fontcolor)
# self.addTopLevelItem(self.header)
# self.header.setSizeHint(0,QtCore.QSize(-1, 25))
# self.setColumnWidth (0, 100)
# self.setColumnWidth (1, 50)
# self.setColumnWidth (2, 70)
self.setColumnWidth (3, 5)
if items is not None: self.names = items
else: self.names = []
self.items = {} # main widgets
self.colors = {} # color widgets
self.boxes = {} # checkbox widgets
self.groups = {} # just empty items
if items: self.addItems(items,colors)
def add_measure_rois(self):
# First, remove existing rois
for roi in self._rois:
self._plot_item.removeItem(roi)
if len(self._measure_rois) == 0:
for i in range(3):
view_range = self._plot_item.viewRange()
x_vrange = view_range[0][1] - view_range[0][0]
x_len = x_vrange * 0.25
x_pos = view_range[0][0] + x_vrange * 0.1 + x_len * 1.1 * i
roi = LinearRegionItem(values=[x_pos, x_pos + x_len],
brush=pg.mkBrush(
QColor(152, 251, 152, 50)),
removable=False)
if i == 1:
roi.setBrush(pg.mkBrush(QColor(255, 69, 0, 50)))
self._measure_rois.append(roi)
for roi in self._measure_rois:
roi.sigRemoveRequested.connect(
lambda: Dispatch.on_updated_roi.emit(
measure_rois=self._measure_rois))
roi.sigRegionChangeFinished.connect(
lambda: Dispatch.on_updated_roi.emit(
measure_rois=self._measure_rois))
# Connect events
Dispatch.on_updated_roi.emit(measure_rois=self._measure_rois)
for roi in self._measure_rois:
self._plot_item.addItem(roi)
def __init__(self, pen=None, brush=None, **opts):
"""
Arguments for each surface are:
x1,x2 - position of center of _physical surface_
r1,r2 - radius of curvature
d1,d2 - diameter of optic
"""
defaults = dict(x1=-2, r1=100, d1=25.4, x2=2, r2=100, d2=25.4)
defaults.update(opts)
ParamObj.__init__(self)
self.surfaces = [CircleSurface(defaults['r1'], defaults['d1']), CircleSurface(-defaults['r2'], defaults['d2'])]
pg.GraphicsObject.__init__(self)
for s in self.surfaces:
s.setParentItem(self)
if pen is None:
self.pen = pg.mkPen((220,220,255,200), width=1, cosmetic=True)
else:
self.pen = pg.mkPen(pen)
if brush is None:
self.brush = pg.mkBrush((230, 230, 255, 30))
else:
self.brush = pg.mkBrush(brush)
self.setParams(**defaults)
def plotMA(self, G, R, z_scores, z_cuttof):
ratio, intensity = expression.ratio_intensity(G, R)
validmask = (numpy.isfinite(ratio) &
numpy.isfinite(intensity) &
numpy.isfinite(z_scores))
for array in [ratio, intensity, z_scores]:
if numpy.ma.is_masked(array):
validmask &= ~array.mask
filtered_ind = numpy.ma.where(validmask)
ratio = numpy.take(ratio, filtered_ind)
intensity = numpy.take(intensity, filtered_ind)
z_scores = numpy.take(z_scores, filtered_ind)
red_ind = numpy.ma.where(numpy.ma.abs(z_scores) >= z_cuttof)
blue_ind = numpy.ma.where(numpy.ma.abs(z_scores) < z_cuttof)
red_xdata, red_ydata = intensity[red_ind], ratio[red_ind]
blue_xdata, blue_ydata = intensity[blue_ind], ratio[blue_ind]
self.graph.clear()
line = pg.InfiniteLine(pos=(0, 0), angle=0, pen=pg.mkPen((0, 0, 0)))
self.graph.addItem(line)
red_points = ScatterPlotItem(
x=red_xdata, y=red_ydata,
brush=pg.mkBrush((255, 0, 0, 100)), size=6, antialias=True)
blue_points = ScatterPlotItem(
x=blue_xdata, y=blue_ydata,
brush=pg.mkBrush((0, 0, 255, 100)), size=6, antialias=True)
self.graph.addItem(red_points)
self.graph.addItem(blue_points)
def updateSelectedPenPointsGraphics(self, selectedpendata=None):
if selectedpendata is None:
selectedpendata = MarkWriteMainWindow.instance().project.selectedpendata
pen=pen2=None
brush=brush2=None
psize=SETTINGS['spatialplot_selectedpoint_size']
if MarkWriteMainWindow.instance().project.isSelectedDataValidForNewSegment():
pen = pg.mkPen(SETTINGS['spatialplot_selectedvalid_color'],
width=SETTINGS['spatialplot_selectedpoint_size'])
pen2 = pg.mkPen(SETTINGS['spatialplot_selectedvalid_color'].darker(300),
width=SETTINGS['spatialplot_selectedpoint_size'])
brush = pg.mkBrush(SETTINGS['spatialplot_selectedvalid_color'])
brush2 = pg.mkBrush(SETTINGS['spatialplot_selectedvalid_color'].darker(300))
else:
pen = pg.mkPen(SETTINGS['spatialplot_selectedinvalid_color'],
width=SETTINGS['spatialplot_selectedpoint_size'])
brush = pg.mkBrush(SETTINGS['spatialplot_selectedinvalid_color'])
pen2 = pg.mkPen(SETTINGS['spatialplot_selectedinvalid_color'].darker(300),
width=SETTINGS['spatialplot_selectedpoint_size'])
brush2 = pg.mkBrush(SETTINGS['spatialplot_selectedinvalid_color'].darker(300))
penarray = np.empty(selectedpendata.shape[0], dtype=object)
penarray[:] = pen
penarray[selectedpendata['pressure'] == 0] = pen2
brusharray = np.empty(selectedpendata.shape[0], dtype=object)
brusharray[:] = brush
brusharray[selectedpendata['pressure'] == 0] = brush2
self.selectedPlotDataItem.setData(x=selectedpendata[X_FIELD],
y=selectedpendata[Y_FIELD], pen=None,
symbol='o', symbolSize=psize,
symbolBrush=brusharray, symbolPen=penarray)
def generatePicture(self):
## pre-computing a QPicture object allows paint() to run much more quickly,
## rather than re-drawing the shapes every time.
self.picture = QtGui.QPicture()
p = QtGui.QPainter(self.picture)
p.setPen(pg.mkPen('w'))
barWidth = (self.data[1][0] - self.data[0][0]) / 3.
for index,item in enumerate(self.data):
time = item[0]
open = item[1]
high = item[2]
low = item[3]
close = item[4]
# 01.draw high-low line,when high == low,it means the symbol is not traded.
if(high != low):
p.drawLine(QtCore.QPointF(index, low), QtCore.QPointF(index, high))
# 02.decide the color of candle
if open > close:
p.setBrush(pg.mkBrush('g'))
else:
p.setBrush(pg.mkBrush('r'))
# 03.draw the candle rect
x=index-barWidth
y=open
width= barWidth*2
height=close-open
p.drawRect(QtCore.QRectF(x,y ,width,height))
p.end()
def __init__(self, parent = None):
QtGui.QWidget.__init__(self, parent)
pg.setConfigOption('background', 'w')
pg.setConfigOption('foreground', 'k')
pg.setConfigOptions(antialias=False)
self.scopeWidget = pg.PlotWidget()
self.scopeWidget.setTitle('Scope trace', size='12')
self.vbl = QtGui.QVBoxLayout()
self.vbl.addWidget(self.scopeWidget)
self.setLayout(self.vbl)
self.scopeWidget.setLabel('left', 'Signal', units='V')
self.scopeWidget.setLabel('bottom', 'Time', units='s')
self.scopeWidget.showGrid(x=False, y=True)
self.scopeWidget.clear()
self.lr1 = pg.LinearRegionItem([0,0], brush=pg.mkBrush(0,0,160,80))
self.lr2 = pg.LinearRegionItem([0,0], brush=pg.mkBrush(52,124,23,80))
self.lr1.setZValue(10)
self.lr2.setZValue(10)
self.scopeWidget.addItem(self.lr2)
self.scopeWidget.addItem(self.lr1)
self.lr1.setMovable(False)
self.lr2.setMovable(False)
def makeGraph(self):
#g1 = pg.GraphItem(pos=self.pos, adj=self.links[self.rope], pen=0.2, symbol=None)
brushes = np.where(self.fixed, pg.mkBrush(0,0,0,255), pg.mkBrush(50,50,200,255))
g2 = pg.GraphItem(pos=self.pos, adj=self.links[self.push & self.pull], pen=0.5, brush=brushes, symbol='o', size=(self.mass**0.33), pxMode=False)
p = pg.ItemGroup()
#p.addItem(g1)
p.addItem(g2)
return p
def generatePicture(self):
## pre-computing a QPicture object allows paint() to run much more quickly,
## rather than re-drawing the shapes every time.
self.picture = QtGui.QPicture()
p = QtGui.QPainter(self.picture)
p.setPen(pg.mkPen('w'))
halfBarWidth = (self.data[1][0] - self.data[0][0]) / 3.
for index,item in enumerate(self.data):
time = item[0]
open = item[1]
high = item[2]
low = item[3]
close = item[4]
if(True):
x = time
else:
x = index
# 01.draw high-low line,when high == low,it means the symbol is not traded.
if(high != low):
p.drawLine(QtCore.QPointF(x, low), QtCore.QPointF(x, high))
# 02.decide the color of candle
if open > close:
p.setBrush(pg.mkBrush('g'))
else:
p.setBrush(pg.mkBrush('r'))
# 03.draw the candle rect
x=x-halfBarWidth
y=open
barWidth= halfBarWidth*2
height=close-open
rectToDraw = QtCore.QRectF(x,y ,barWidth,height)
if(not self.bSelected):
for lastRect in self.lastClicked:
for newRect in self.ptsClicked:
if(lastRect == newRect):
self.bSelected = True
if(not self.bSelected):
for rect in self.ptsClicked:
if(rect == rectToDraw):
self.lastClicked = self.ptsClicked
p.setPen(pg.mkPen('w'))
p.setBrush(pg.mkBrush('w'))
else:
self.bSelected = False
p.drawRect(QtCore.QRectF(x,y ,barWidth,height))
self.dataRects[index]=QtCore.QRectF(x,y ,barWidth,height)
p.end()
def setupGUI(self):
self.setWindowTitle("Edit effectibve stress formula")
self.setGeometry(500, 300, 350, 200)
# self.centralWidget = QtGui.QWidget()
# self.setCentralWidget(self.centralWidget)
self.centralLayout = QtGui.QVBoxLayout()
# self.centralWidget.setLayout(self.centralLayout)
self.setLayout(self.centralLayout)
self.variablesText = QtGui.QLabel('')
tree = pg.TreeWidget()
tree.setHeaderHidden(True)
tree.setIndentation(0)
tree.setColumnCount(3)
# stuff to make gray background for tree widget
g = pg.mkBrush(240,240,240)
b = pg.mkBrush(0,0,0)
w = pg.mkBrush(255,255,255)
bgBrush = pg.mkBrush(255,0,0)
tree.setFrameShape(QtGui.QFrame.NoFrame)
palette = QtGui.QPalette(g, g, g, g, g, b, b, g, g)
# tree.setPalette(palette)
axStressItem = pg.TreeWidgetItem(['Axial stress'])
# axStressItem.setTextAlignment(0,0)
# axStressItem.setBackground(1,w)
confStressItem = pg.TreeWidgetItem(['Confining pressure'])
# confStressItem.setTextAlignment(0,0)
porePressItem = pg.TreeWidgetItem(['Pore pressure'])
biotItem = pg.TreeWidgetItem(['Biot coefficient'])
porePressItem.setTextAlignment(0,0)
self.axStressBox = QtGui.QLineEdit()
self.confStressBox = QtGui.QLineEdit()
self.porePressBox = QtGui.QLineEdit()
self.biotBox = pg.SpinBox(value=1, bounds=[0.5, 1],step=0.1)
axStressItem.setWidget(1,self.axStressBox)
confStressItem.setWidget(1,self.confStressBox)
biotItem.setWidget(1,self.biotBox)
porePressItem.setWidget(1,self.porePressBox)
tree.addTopLevelItem(axStressItem)
tree.addTopLevelItem(confStressItem)
tree.addTopLevelItem(porePressItem)
tree.addTopLevelItem(biotItem)
self.centralLayout.addWidget(self.variablesText)
self.centralLayout.addWidget(tree)
# self.centralLayout.addWidget(self.buttonsWidget)
tree.setColumnWidth(0,120)
tree.setColumnWidth(1,170)
tree.setColumnWidth(2,10)
def change_to_image(self, image):
""" Set curTrace to TRACE. Update all the buttons/table_slice
and then highlight the proper row in the table_traces."""
# Deselecting the previous curTrace
if self.curImage is not None:
index = -1
for row in range(self.table_images.rowCount()):
item = self.table_images.item(row, 0)
if str(item.text()) == self.curImage.name:
index = row
if index != -1:
item = self.table_images.item(index, 0)
item.setBackground(pqg.mkBrush((255, 255, 255, 255)))
# Selecting the current trace
index = -1
for row in range(self.table_images.rowCount()):
item = self.table_images.item(row, 0)
if str(item.text()) == image.name:
index = row
if index != -1:
item = self.table_images.item(index, 0)
item.setBackground(pqg.mkBrush((0, 255, 127, 100)))
if self.curImage is not None:
self.curImage.gradient = self.plot.getHistogramWidget().gradient.saveState()
self.curImage.levels = self.plot.getHistogramWidget().getLevels()
if self.plot.axes.get('t', None) is not None:
self.curImage.time = self.plot.timeLine.value()
self.curImage.savedGradient = self.gradient_isocurve.saveState()
self.curImage.remove_isocurves()
self.curImage = image
image.update_slice_table(self.table_slice)
self.sync_buttons()
if image.gradient is not None:
self.plot.getHistogramWidget().gradient.restoreState(image.gradient)
if image.valName is not None:
image.display_image()
else:
self.plot.clear()
if image.levels is not None:
self.plot.setLevels(*image.levels)
if image.time is not None and self.plot.axes['t'] is not None:
self.plot.timeLine.setValue(image.time)
self.plot.timeLineChanged()
if image.savedGradient is not None:
self.gradient_isocurve.restoreState(image.savedGradient)
self.table_isocurve.setRowCount(0)
image.init_isocurves()
def setPlot(self, plot):
self.plot = plot
self.spi = pg.ScatterPlotItem(size=10,
pen=pg.mkPen(None),
brush=pg.mkBrush(255, 255, 255, 255))
self.spi2 = pg.ScatterPlotItem(size=10,
pen=pg.mkPen(None),
brush=pg.mkBrush(255, 0, 0, 255))
self.plot.setXRange(0, 1024)
self.plot.setYRange(0, 768)
def test_scatterplotitem():
plot = pg.PlotWidget()
# set view range equal to its bounding rect.
# This causes plots to look the same regardless of pxMode.
plot.setRange(rect=plot.boundingRect())
# test SymbolAtlas accepts custom symbol
s = pg.ScatterPlotItem()
symbol = QtGui.QPainterPath()
symbol.addEllipse(QtCore.QRectF(-0.5, -0.5, 1, 1))
s.addPoints([{'pos': [0,0], 'data': 1, 'symbol': symbol}])
for i, pxMode in enumerate([True, False]):
for j, useCache in enumerate([True, False]):
s = pg.ScatterPlotItem()
s.opts['useCache'] = useCache
plot.addItem(s)
s.setData(x=np.array([10,40,20,30])+i*100, y=np.array([40,60,10,30])+j*100, pxMode=pxMode)
s.addPoints(x=np.array([60, 70])+i*100, y=np.array([60, 70])+j*100, size=[20, 30])
# Test uniform spot updates
s.setSize(10)
s.setBrush('r')
s.setPen('g')
s.setSymbol('+')
app.processEvents()
# Test list spot updates
s.setSize([10] * 6)
s.setBrush([pg.mkBrush('r')] * 6)
s.setPen([pg.mkPen('g')] * 6)
s.setSymbol(['+'] * 6)
s.setPointData([s] * 6)
app.processEvents()
# Test array spot updates
s.setSize(np.array([10] * 6))
s.setBrush(np.array([pg.mkBrush('r')] * 6))
s.setPen(np.array([pg.mkPen('g')] * 6))
s.setSymbol(np.array(['+'] * 6))
s.setPointData(np.array([s] * 6))
app.processEvents()
# Test per-spot updates
spot = s.points()[0]
spot.setSize(20)
spot.setBrush('b')
spot.setPen('g')
spot.setSymbol('o')
spot.setData(None)
app.processEvents()
plot.clear()
def generatePicture(self):
self.picture = QtGui.QPicture()
p = QtGui.QPainter(self.picture)
p.setPen(pg.mkPen('w'))
w = (self.data[1][0] - self.data[0][0]) / 3.
for (t, open, close, min, max) in self.data:
p.drawLine(QtCore.QPointF(t, min), QtCore.QPointF(t, max))
if open > close:
p.setBrush(pg.mkBrush('r'))
else:
p.setBrush(pg.mkBrush('g'))
p.drawRect(QtCore.QRectF(t-w, open, w*2, close-open))
p.end()
def createDefaultPenBrushForData(self, pdat):
pen = pg.mkPen(SETTINGS['spatialplot_default_color'],
width=SETTINGS['spatialplot_default_point_size'])
pen2 = pg.mkPen(SETTINGS['spatialplot_default_color'].lighter(),
width=SETTINGS['spatialplot_default_point_size'])
brush = pg.mkBrush(SETTINGS['spatialplot_default_color'])
brush2 = pg.mkBrush(SETTINGS['spatialplot_default_color'].lighter())
penarray = np.empty(pdat.shape[0], dtype=object)
penarray[:] = pen
penarray[pdat['pressure'] == 0] = pen2
brusharray = np.empty(pdat.shape[0], dtype=object)
brusharray[:] = brush
brusharray[pdat['pressure'] == 0] = brush2
return brusharray, penarray
def plotData(self, sz, wx, wy):
self.plot(sz, wx,
pen = None,
symbol = 'o',
symbolPen = pyqtgraph.mkPen(255,0,0),
symbolBrush = pyqtgraph.mkBrush(0,0,255),
symbolSize = 6)
self.plot(sz, wy,
pen = None,
symbol = 'o',
symbolPen = pyqtgraph.mkPen(0,255,0),
symbolBrush = pyqtgraph.mkBrush(0,0,255),
symbolSize = 6)
def generatePicture(self):
## pre-computing a QPicture object allows paint() to run much more quickly,
## rather than re-drawing the shapes every time.
self.picture = QtGui.QPicture()
p = QtGui.QPainter(self.picture)
p.setPen(pg.mkPen('w'))
w = (self.data[1][0] - self.data[0][0]) / 3.
for (t, open, close, min, max) in self.data:
p.drawLine(QtCore.QPointF(t, min), QtCore.QPointF(t, max))
if open > close:
p.setBrush(pg.mkBrush('r'))
else:
p.setBrush(pg.mkBrush('g'))
p.drawRect(QtCore.QRectF(t-w, open, w*2, close-open))
p.end()
def setupHeader(self):
self.header = pg.TreeWidgetItem([self.name])
self.setIndentation(0)
headerBackgroundColor = pg.mkBrush(color=(100,100,100))
fontcolor = pg.mkBrush(color=(255,255,255))
self.header.setBackground(0,headerBackgroundColor)
self.header.setBackground(1,headerBackgroundColor)
self.header.setBackground(2,headerBackgroundColor)
self.header.setBackground(3,headerBackgroundColor)
self.header.setForeground(0,fontcolor)
self.addTopLevelItem(self.header)
self.header.setSizeHint(0,QtCore.QSize(-1, 25))
self.setColumnWidth (0, 100)
self.setColumnWidth (1, 50)
self.setColumnWidth (2, 70)
def generatePicture(self):
# pre-computing a QPicture object allows paint() to run much more quickly,
# rather than re-drawing the shapes every time.
self.picture = QtGui.QPicture()
p = QtGui.QPainter(self.picture)
p.setPen(pg.mkPen('w'))
barWidth = 1 / 3.
for (open, close, min, max, index) in self.data:
p.drawLine(QtCore.QPointF(index, min), QtCore.QPointF(index, max))
if open > close:
p.setBrush(pg.mkBrush('r'))
else:
p.setBrush(pg.mkBrush('g'))
p.drawRect(QtCore.QRectF(index - barWidth, open, barWidth * 2, close - open))
p.end()
def __init__(self):
QtGui.QMainWindow.__init__(self)
# variables
self.columnSize = 20
self.rowSize = 20
self.xInitPos = 0
self.yInitPos = 0
self.state = conway.CONWAY(self.rowSize,self.columnSize)
self.alive = 0
self.aliveEvolution = []
self.color1 = pg.mkBrush(255,255,255)
self.color2 = pg.mkBrush(0,0,0)
self.brushes = []
self.fileName = ''
self.pause = True
self.generation = 0
# se carga la ui
self.ui = uic.loadUi('ventana.ui',self)
# se conectan los botones en la ui a sus funciones
self.ui.connect(self.ui.tick, QtCore.SIGNAL('clicked()'), self.nextState)
self.ui.connect(self.ui.botonStartPause, QtCore.SIGNAL('clicked()'), self.startPause)
self.ui.connect(self.ui.botonRestart, QtCore.SIGNAL('clicked()'), self.reloadState)
self.ui.connect(self.ui.botonClean, QtCore.SIGNAL('clicked()'), self.cleanState)
self.ui.connect(self.ui.botonOpen, QtCore.SIGNAL('clicked()'), self.openFileDialog)
self.ui.sizeOptions.valueChanged.connect(self.gridSize)
self.ui.speedSlide.valueChanged.connect(self.changeSpeed)
self.ui.xPosValue.textEdited.connect(self.changeXInitPos)
self.ui.yPosValue.textEdited.connect(self.changeYInitPos)
# se crea el plot con la matriz de celdas
self.gfx = self.ui.PlotView.addPlot()
self.restartPlot()
self.createGrid()
self.updateGrid()
# se crea el plot con la grafica de celdas vivas
self.gfx2 = self.ui.PlotView2.addPlot(title='Celdas Vivas')
self.restartPlot2()
# Timer
self.timer = pg.QtCore.QTimer()
self.timer.timeout.connect(self.updateTimer)
self.TIME_INTERVAL = 1000
self.TIME_INTERVAL_MAX = 2000
def __init__(self, parent=None, **kwargs):
pg.PlotWidget.__init__(self, parent, **kwargs)
self.getAxis("bottom").setLabel("Score")
self.getAxis("left").setLabel("Counts")
self.__data = None
self.__histcurve = None
self.__mode = Histogram.NoSelection
self.__min = 0
self.__max = 0
def makeline(pos):
pen = QtGui.QPen(Qt.darkGray, 1)
pen.setCosmetic(True)
line = InfiniteLine(angle=90, pos=pos, pen=pen, movable=True)
line.setCursor(Qt.SizeHorCursor)
return line
self.__cuthigh = makeline(self.__max)
self.__cuthigh.sigPositionChanged.connect(self.__on_cuthigh_changed)
self.__cuthigh.sigPositionChangeFinished.connect(self.selectionEdited)
self.__cutlow = makeline(self.__min)
self.__cutlow.sigPositionChanged.connect(self.__on_cutlow_changed)
self.__cutlow.sigPositionChangeFinished.connect(self.selectionEdited)
brush = pg.mkBrush((200, 200, 200, 180))
self.__taillow = pg.PlotCurveItem(
fillLevel=0, brush=brush, pen=QtGui.QPen(Qt.NoPen))
self.__taillow.setVisible(False)
self.__tailhigh = pg.PlotCurveItem(
fillLevel=0, brush=brush, pen=QtGui.QPen(Qt.NoPen))
self.__tailhigh.setVisible(False)
def draw_path(self):
path = self.combineXYPoints()
points = []
for i in range(0, len(path)):
points.append(Point(path[i][0], path[i][1]))
# display points
if len(points) >= 3:
points = resample(points, self.sample_size)
if points is not None:
path = []
for i in range(0, len(points)):
path.append([points[i].x, points[i].y])
self.pathScatter.addPoints(
pos=np.array(path), brush=pg.mkBrush(255, 255, 255, 120))
# handle pressed keys
if self.pressed_key is 'A':
self.compare_template()
elif self.pressed_key is 'B':
self.create_template()
self.path['x'] = []
self.path['y'] = []
self.pressed_key = None
def colorSelected(self, color): if color.isValid(): self.color=QColor(color.name()) self.pen.setColor(self.color) self.path_item.setPen(self.pen) self.ti.fill = pg.mkBrush(self.color) self.update()
def __start(self, plot_points, frame_rate, title = 'RPLIDAR Data Plot'):
self.x = [0]*plot_points # x value data generated from dist*sin(theta)
self.y = [0]*plot_points # y value data generated from dist*cos(theta)
self.plot_points = plot_points
# Create GUI Graphics and Window; Set up parameters
app = QtGui.QApplication([])
mw = QtGui.QMainWindow()
mw.resize(800,800)
view = pg.GraphicsLayoutWidget() ## GraphicsView with GraphicsLayout inserted by default
mw.setCentralWidget(view)
mw.show() # Show the created GUI
mw.setWindowTitle(title)
# Create plot and set plot parameters
w1 = view.addPlot() # Returns a PlotItem object
w1.showGrid(x=True,y=True)
w1.setMenuEnabled()
w1.getViewBox().setXRange(min=-0.8,max=0.8)
w1.getViewBox().setYRange(min=-1.0,max=1.0)
w1.setLabel(axis='left',text='Y Distance',units='m')
w1.setLabel(axis='bottom',text='X Distance',units='m')
w1.setTitle(title=title)
# Create scatter plot
s1 = pg.ScatterPlotItem(size=3, pen=pg.mkPen(None), brush=pg.mkBrush(255, 0, 0, 120))
s1.addPoints(self.x,self.y)
# Add scatter plot to the window
w1.addItem(s1)
self.s1 = s1
# Create plot GUI update timer
timer = pg.QtCore.QTimer()
timer.timeout.connect(self.__update_plot)
timer.start(frame_rate)
# Load plot
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
def plot_trace(xy, ids = None, depth = 0, colormap = 'rainbow', line_color = 'k', line_width = 1, point_size = 5, title = None):
"""Plot trajectories with positions color coded according to discrete ids"""
#if ids is not None:
uids = np.unique(ids);
cmap = cm.get_cmap(colormap);
n = len(uids);
colors = cmap(range(n), bytes = True);
#lines
if line_width is not None:
#plt.plot(xy[:,0], xy[:,1], color = lines);
plot = pg.plot(xy[:,0], xy[:,1], pen = pg.mkPen(color = line_color, width = line_width))
else:
plot = pg.plot(title = title);
if ids is None:
sp = pg.ScatterPlotItem(pos = xy, size=point_size, pen=pg.mkPen(colors[0])); #, pxMode=True);
else:
sp = pg.ScatterPlotItem(size=point_size); #, pxMode=True);
spots = [];
for j,i in enumerate(uids):
idx = ids == i;
spots.append({'pos': xy[idx,:].T, 'data': 1, 'brush':pg.mkBrush(colors[j])}); #, 'size': point_size});
sp.addPoints(spots)
plot.addItem(sp);
return plot;
def violin_plot(ax, data, pos, dist=.0, bp=False):
'''
create violin plots on an axis
'''
if data is None or len(data) == 0:
return # skip trying to do the plot
dist = max(pos)-min(pos)
w = min(0.15*max(dist,1.0),0.5)
for i, d in enumerate(data):
if d == [] or len(d) == 0:
continue
k = scipy.stats.gaussian_kde(d) #calculates the kernel density
m = k.dataset.min() #lower bound of violin
M = k.dataset.max() #upper bound of violin
y = np.arange(m, M, (M-m)/100.) # support for violin
v = k.evaluate(y) #violin profile (density curve)
v = v / v.max() * w #scaling the violin to the available space
c1 = pg.PlotDataItem(y=y, x=pos[i]+v, pen=pg.mkPen('k', width=0.5))
c2 = pg.PlotDataItem(y=y, x=pos[i]-v, pen=pg.mkPen('k', width=0.5))
#mean = k.dataset.mean()
#vm = k.evaluate(mean)
#vm = vm * w
#ax.plot(x=np.array([pos[i]-vm[0], pos[i]+vm[0]]), y=np.array([mean, mean]), pen=pg.mkPen('k', width=1.0))
ax.addItem(c1)
ax.addItem(c2)
#ax.addItem(hbar)
f = pg.FillBetweenItem(curve1=c1, curve2=c2, brush=pg.mkBrush((255, 255, 0, 96)))
ax.addItem(f)
if bp:
pass
def show(self):
if self._view is None:
pg.mkQApp()
self._view_widget = pg.GraphicsLayoutWidget()
self._view = self._view_widget.addViewBox(0, 0)
v = self._view
cell_ids = sorted(self.cells.keys())
pos = np.array([self.cells[i].position[:2] for i in cell_ids])
if len(self.connections) == 0:
adj = np.empty((0,2), dtype='int')
else:
adj = np.array(self.connections) - 1
colors = []
for cid in cell_ids:
cell = self.cells[cid]
color = [0, 0, 0]
for i,cre in enumerate(self.cre_types):
if cell.labels[cre] == '+':
color[i] = 255
colors.append(color)
brushes = [pg.mkBrush(c) for c in colors]
print(pos)
print(adj)
print(colors)
self._graph = pg.GraphItem(pos=pos, adj=adj, size=30, symbolBrush=brushes)
v.addItem(self._graph)
self._view_widget.show()
def __init__(self, clock):
pg.ItemGroup.__init__(self)
self.size = clock.size
self.item = QtGui.QGraphicsEllipseItem(QtCore.QRectF(0, 0, self.size, self.size))
self.item.translate(-self.size*0.5, -self.size*0.5)
self.item.setPen(pg.mkPen(100,100,100))
self.item.setBrush(clock.brush)
self.hand = QtGui.QGraphicsLineItem(0, 0, 0, self.size*0.5)
self.hand.setPen(pg.mkPen('w'))
self.hand.setZValue(10)
self.flare = QtGui.QGraphicsPolygonItem(QtGui.QPolygonF([
QtCore.QPointF(0, -self.size*0.25),
QtCore.QPointF(0, self.size*0.25),
QtCore.QPointF(self.size*1.5, 0),
QtCore.QPointF(0, -self.size*0.25),
]))
self.flare.setPen(pg.mkPen('y'))
self.flare.setBrush(pg.mkBrush(255,150,0))
self.flare.setZValue(-10)
self.addItem(self.hand)
self.addItem(self.item)
self.addItem(self.flare)
self.clock = clock
self.i = 1
self._spaceline = None
def plotWxWyData(self, wx, wy, cat):
self.plot(wx, wy,
pen = None,
symbol = 'o',
symbolPen = pyqtgraph.mkPen(255,0,0),
symbolBrush = pyqtgraph.mkBrush(0,0,255),
symbolSize = 6)
w2.setAspectLocked(True)
view.nextRow()
w3 = view.addPlot()
w4 = view.addPlot()
print("Generating data, this takes a few seconds...")
# There are a few different ways we can draw scatter plots; each is optimized for different types of data:
# 1) All spots identical and transform-invariant (top-left plot).
# In this case we can get a huge performance boost by pre-rendering the spot
# image and just drawing that image repeatedly.
n = 300
s1 = pg.ScatterPlotItem(size=10, pen=pg.mkPen(
None), brush=pg.mkBrush(255, 255, 255, 120))
pos = np.random.normal(size=(2, n), scale=1e-5)
spots = [{'pos': pos[:, i], 'data': 1}
for i in range(n)] + [{'pos': [0, 0], 'data': 1}]
s1.addPoints(spots)
w1.addItem(s1)
# Make all plots clickable
lastClicked = []
def clicked(plot, points):
global lastClicked
for p in lastClicked:
p.resetPen()
print("clicked points", points)
def pg_brush_cycler(i=0):
return pg.mkBrush(color_cycler(i))
def plot_stepsAndSpikes(self, data, posSpike, negSpike):
self.glmProcTimeSeries = np.append(self.glmProcTimeSeries, data, axis=1)
sz, l = self.glmProcTimeSeries.shape
for i in range(sz):
if posSpike[i] == 1:
if self.posSpikes[str(i)].any():
self.posSpikes[str(i)] = np.append(self.posSpikes[str(i)], l-1)
else:
self.posSpikes[str(i)] = np.array([l-1])
if negSpike[i] == 1:
if self.negSpikes[str(i)].any():
self.negSpikes[str(i)] = np.append(self.negSpikes[str(i)], l-1)
else:
self.negSpikes[str(i)] = np.array([l-1])
x = np.arange(0, l, dtype=np.float64)
plotitem = self.spikes_plot.getPlotItem()
plotitem.clear()
plots = []
muster = self.drawMusterPlot(plotitem)
for i, c in zip(range(sz), config.ROI_PLOT_COLORS):
pen = pg.mkPen(color=c, width=config.ROI_PLOT_WIDTH)
p = plotitem.plot(pen=pen)
plots.append(p)
self.plot_stepsAndSpikes.__dict__[plotitem] = plots, muster
for p, y in zip(self.plot_stepsAndSpikes.__dict__[plotitem][0], self.glmProcTimeSeries):
p.setData(x=x, y=np.array(y))
for i, c in zip(range(sz), config.ROI_PLOT_COLORS):
if self.posSpikes[str(i)].any():
brush = pg.mkBrush(color=c)
p = plotitem.scatterPlot(symbol='o', size=20, brush=brush)
plots.append(p)
plots[-1].setData(x=x[self.posSpikes[str(i)]], y=self.glmProcTimeSeries[i, self.posSpikes[str(i)]])
pen = pg.mkPen(color=pg.mkColor(0, 0, 0), width=1.5*config.ROI_PLOT_WIDTH)
p = plotitem.plot(pen=pen)
plots.append(p)
inds = self.posSpikes[str(i)]
inds = np.array(list(itertools.chain.from_iterable(zip(inds, inds-1))))
y = np.array(self.glmProcTimeSeries[i,inds])
x1 = inds
plots[-1].setData(x=x1, y=y, connect='pairs')
if self.negSpikes[str(i)].any():
brush = pg.mkBrush(color=c)
p = plotitem.scatterPlot(symbol='d', size=20, brush=brush)
plots.append(p)
plots[-1].setData(x=x[self.negSpikes[str(i)]], y=self.glmProcTimeSeries[i, self.negSpikes[str(i)]])
pen = pg.mkPen(color=pg.mkColor(0, 0, 0), width=1.5*config.ROI_PLOT_WIDTH)
p = plotitem.plot(pen=pen)
plots.append(p)
inds = self.negSpikes[str(i)]
inds = np.array(list(itertools.chain.from_iterable(zip(inds, inds - 1))))
y = np.array(self.glmProcTimeSeries[i,inds])
x1 = inds
plots[-1].setData(x=x1, y=y, connect='pairs')
cnt = 0;
for i in range(sz):
cnt = cnt + np.count_nonzero(self.posSpikes[str(i)])
names = ['( Circles ) <br>Positive spikes: ' + str(int(cnt))]
cnt = 0;
for i in range(sz):
cnt = cnt + np.count_nonzero(self.negSpikes[str(i)])
names.append('<br>( Diamonds )<br>Negative spikes: ' + str(int(cnt)))
pens = [pg.mkPen(color=config.STAT_PLOT_COLORS[0], width=1.2), pg.mkPen(color=config.STAT_PLOT_COLORS[0], width=1.2)]
self.makeTextValueLabel(self.spikesLabel, names, pens)
items = plotitem.listDataItems()
for m in self.plot_stepsAndSpikes.__dict__[plotitem][1]:
items.remove(m)
if data.any():
plotitem.setYRange(np.min(self.glmProcTimeSeries), np.max(self.glmProcTimeSeries), padding=0.0)
from PyQt5 import QtCore, QtGui, QtWidgets
import numpy as np
import pyqtgraph as pg
STYLE = {
'pen': pg.mkPen(0, 0, 0),
'pen-hover': pg.mkPen(255, 255, 255, width=1),
'brush': pg.mkBrush(100, 100, 100),
'brush-hover': pg.mkBrush(150, 150, 150),
'brush-selected': pg.mkBrush(200, 200, 200),
'underline-central': pg.mkPen(176, 35, 48, width=3),
'underline-flanker': pg.mkPen(51, 152, 188, width=3)
}
STYLE['underline-central'].setCapStyle(QtCore.Qt.FlatCap)
STYLE['underline-flanker'].setCapStyle(QtCore.Qt.FlatCap)
class ClickableBar(QtWidgets.QGraphicsRectItem):
def __init__(self, barplot, x, y, w, h):
self.barplot = barplot
self.x = x
_scale = 10000
QtWidgets.QGraphicsRectItem.__init__(self, QtCore.QRectF(x * _scale, y * _scale, w * _scale, h * _scale))
self.setScale(1 / _scale)
self.setPen(STYLE['pen'])
self.setBrush(STYLE['brush'])
self.setAcceptHoverEvents(True)
self.is_current_flag = False
def hoverEnterEvent(self, ev):
self.savedPen = self.pen()
'lomid': "#4f98ca",
'dark': "#272727",
'darker': "#23374d",
}
numlabelsize = 22
txtlabelsize = 20
# STYLING
numfont = QtGui.QFont("Avenir Next") # requires macos
numfont.setPixelSize(numlabelsize)
txtfont = QtGui.QFont("Avenir Next") # requires macos
txtfont.setPixelSize(txtlabelsize)
brushes = {k: pg.mkBrush(c) for k, c in colors.items()}
pg.setConfigOptions(antialias=True)
pg.setConfigOption('background', colors['dark'])
pg.setConfigOption('foreground', colors['light'])
QPushButton_style = f"""
QPushButton{{
color: {colors['light']};
background-color: transparent;
border: 1px solid #4589b2;
padding: 5px;
}}
QPushButton::hover{{
def paint(self, painter: QPainter, *_):
painter.save()
painter.setPen(pg.mkPen((255, 255, 0), width=1))
painter.setBrush(pg.mkBrush(255, 255, 0, 100))
painter.drawRect(self.__rect)
painter.restore()
app = TaurusApplication()
# a standard pyqtgraph plot_item
w = pg.PlotWidget()
# add legend to the plot, for that we have to give a name to plot items
w.addLegend()
# adding a regular data item (non-taurus)
c1 = pg.PlotDataItem(name="st plot", pen="b", fillLevel=0, brush="c")
c1.setData(numpy.arange(300) / 300.0)
w.addItem(c1)
pen = pg.mkPen(color="r", style=4)
brush = pg.mkBrush(color="b")
brush.setStyle(3)
# adding a taurus data item
# c2 = TaurusPlotDataItem(name='st2 plot', pen='r', symbol='o')
c2 = TaurusPlotDataItem(pen=pen, name="foo")
# c2 = TaurusPlotDataItem()
# c2.loadConfigFile('tmp/conf.cfg')
c2.setModel('eval:Quantity(rand(256),"m")')
# c2.setModel('sys/tg_test/1/wave')
# c2.setModel(None)
# c2.setXModel(None)
# c2.setXModel('eval:Quantity(rand(256),"m")')
def load_course(self):
if len(self.config.logger.course.latitude) == 0:
return
t = datetime.datetime.utcnow()
cp = pg.CoursePlotItem(
x=self.config.logger.course.longitude,
y=self.get_mod_lat_np(self.config.logger.course.latitude),
brushes=self.config.logger.course.colored_altitude,
width=6)
self.plot.addItem(cp)
#test
if not self.config.G_IS_RASPI:
plot_verification = pg.ScatterPlotItem(pxMode=True)
test_points = []
for i in range(len(self.config.logger.course.longitude)):
p = {
'pos': [
self.config.logger.course.longitude[i],
self.get_mod_lat(self.config.logger.course.latitude[i])
],
'size':
2,
'pen': {
'color': 'w',
'width': 1
},
'brush':
pg.mkBrush(color=(255, 0, 0))
}
test_points.append(p)
plot_verification.setData(test_points)
self.plot.addItem(plot_verification)
print("\tpyqt_graph : course_plot : ",
(datetime.datetime.utcnow() - t).total_seconds(), "sec")
#course point
if len(self.config.logger.course.point_longitude) == 0:
return
t = datetime.datetime.utcnow()
self.course_points_plot = pg.ScatterPlotItem(pxMode=True, symbol="t")
self.course_points = []
for i in reversed(range(len(
self.config.logger.course.point_longitude))):
#if self.config.logger.course.point_type[i] == "Straight":
# continue
cp = {
'pos': [
self.config.logger.course.point_longitude[i],
self.get_mod_lat(
self.config.logger.course.point_latitude[i])
],
'size':
10,
'pen': {
'color': 'r',
'width': 1
},
'brush':
pg.mkBrush(color=(255, 0, 0))
}
self.course_points.append(cp)
self.course_points_plot.setData(self.course_points)
self.plot.addItem(self.course_points_plot)
print("\tpyqt_graph : load course_points_plot : ",
(datetime.datetime.utcnow() - t).total_seconds(), "sec")
t = datetime.datetime.utcnow()
self.course_points_label = []
if self.config.G_FONT_NAME != "":
self.font = QtGui.QFont(self.config.G_FONT_NAME)
for i in reversed(range(len(
self.config.logger.course.point_longitude))):
#if self.config.logger.course.point_type[i] == "Straight":
# continue
#CoursePointType from TCX schema
# https://www8.garmin.com/xmlschemas/TrainingCenterDatabasev2.xsd
# Generic, Summit, Valley, Water, Food, Danger,
# Left, Right, Straight, First Aid,
# 4th Category, 3rd Category, 2nd Category, 1st Category,
# Hors Category, Sprint,
#arrow = ""
#if self.config.logger.course.point_type[i] == "Left":
# arrow ="backarrow_black.png"
#elif self.config.logger.course.point_type[i] == "Right":
# arrow ="nextarrow_black.png"
#else:
# continue
# Create text object, use HTML tags to specify color/size
# http://www.pyqtgraph.org/documentation/graphicsItems/textitem.html
text = pg.TextItem(
#html = '<div style="text-align: center">' + '<img src="img/' + arrow + '" /></div>',
#html = '<div style="text-align: center">' + self.config.logger.course.point_name[i] + '</div>',
text=self.config.logger.course.point_name[i],
anchor=(-0.1, 1.2),
angle=0,
border=(255, 0, 0),
fill=(255, 255, 255),
color=(0, 0, 0),
)
#text.setTextWidth(int(self.config.G_WIDTH/2.5))
if self.config.G_FONT_NAME != "":
text.setFont(self.font)
self.plot.addItem(text)
text.setPos(
self.config.logger.course.point_longitude[i],
self.get_mod_lat(self.config.logger.course.point_latitude[i]))
self.course_points_label.append(text)
print("\tpyqt_graph : display course_points_plot : ",
(datetime.datetime.utcnow() - t).total_seconds(), "sec")
def brush(color):
return pg.mkBrush(color)
def load_course(self):
if len(self.config.logger.course.distance) == 0:
return
t = datetime.datetime.utcnow()
if not self.config.logger.sensor.sensor_gps.hasGPS():
self.zoom = self.config.G_MAX_ZOOM
self.plot.showGrid(x=True, y=True, alpha=1)
self.plot.showAxis('left')
self.plot.showAxis('bottom')
font = QtGui.QFont()
font.setPixelSize(16)
font.setBold(True)
self.plot.getAxis("bottom").tickFont = font
#self.plot.getAxis("bottom").setStyle(tickTextOffset = 5)
self.plot.getAxis("left").tickFont = font
#self.plot.getAxis("left").setStyle(tickTextOffset = 5)
#self.plot.setAutoPan()
print("\tpyqt_graph : load course profile : ",
(datetime.datetime.utcnow() - t).total_seconds(), "sec")
t = datetime.datetime.utcnow()
bg = pg.CourseProfileGraphItem(
x=self.config.logger.course.distance,
y=self.config.logger.course.altitude,
brushes=self.config.logger.course.colored_altitude,
pen=pg.mkPen(color=(255, 255, 255, 0),
width=0.01)) #transparent(alpha=0) and thin line
self.plot.addItem(bg)
self.course_points_plot = pg.ScatterPlotItem(pxMode=True, symbol="t")
self.course_points = []
for i in reversed(range(len(
self.config.logger.course.point_distance))):
cp = {
'pos': [
self.config.logger.course.point_distance[i],
self.config.logger.course.point_altitude[i]
],
'size':
10,
'pen': {
'color': 'r',
'width': 1
},
'brush':
pg.mkBrush(color=(255, 0, 0))
}
self.course_points.append(cp)
self.course_points_plot.setData(self.course_points)
self.plot.addItem(self.course_points_plot)
self.course_points_label = []
if self.config.G_FONT_NAME != "":
self.font = QtGui.QFont(self.config.G_FONT_NAME)
for i in reversed(range(len(
self.config.logger.course.point_distance))):
text = pg.TextItem(
text=self.config.logger.course.point_name[i],
anchor=(-0.1, 1.2),
angle=0,
border=(255, 0, 0),
fill=(255, 255, 255),
color=(0, 0, 0),
)
#text.setTextWidth(int(self.config.G_WIDTH/2.5))
if self.config.G_FONT_NAME != "":
text.setFont(self.font)
self.plot.addItem(text)
text.setPos(self.config.logger.course.point_distance[i],
self.config.logger.course.point_altitude[i])
self.course_points_label.append(text)
print("\tpyqt_graph : plot course profile : ",
(datetime.datetime.utcnow() - t).total_seconds(), "sec")
conn_data = np.empty((len(cell_classes), 3))
n_probed = []
n_connected = []
brushes = []
pens = []
for i,class_info in enumerate(cell_classes):
cell_class, _, color = class_info
class_results = results[(cell_class, cell_class)]
conn_data[i] = class_results['connection_probability']
n_probed.append(class_results['n_probed'])
n_connected.append(class_results['n_connected'])
print("Cell class: %s connected: %d probed: %d probability: %0.3f min_ci: %0.3f max_ci: %0.3f" % (
cell_class.name, class_results['n_connected'], class_results['n_probed'],
class_results['connection_probability'][0], class_results['connection_probability'][1], class_results['connection_probability'][2],
))
brushes.append(pg.mkBrush(color))
# Add confidence interval line for this class
errbar = pg.QtGui.QGraphicsLineItem(i, class_results['connection_probability'][1], i, class_results['connection_probability'][2])
errbar.setPen(pg.mkPen(color, width=3))
conn_plot.addItem(errbar)
write_csv(csv_file, class_names, "Figure 4%s cell classes" % fig_letter)
write_csv(csv_file, n_connected, "Figure 4%s n connected pairs < 100um" % fig_letter)
write_csv(csv_file, n_probed, "Figure 4%s n probed pairs < 100um" % fig_letter)
# plot connection probability points
conn_plot.plot(conn_data[:,0], pen=None, symbol='o', symbolBrush=brushes, symbolPen='k')
write_csv(csv_file, conn_data[:, 0], "Figure 4%s connection probability < 100um" % fig_letter)
# write confidence intervals into csv
def on_activate(self):
""" Definition and initialisation of the GUI.
"""
self._wm_logger_logic = self.wavemeterloggerlogic1()
self._save_logic = self.savelogic()
# setting up the window
self._mw = WavemeterLogWindow()
## giving the plots names allows us to link their axes together
self._pw = self._mw.plotWidget # pg.PlotWidget(name='Counter1')
self._plot_item = self._pw.plotItem
## create a new ViewBox, link the right axis to its coordinate system
self._right_axis = pg.ViewBox()
self._plot_item.showAxis('right')
self._plot_item.scene().addItem(self._right_axis)
self._plot_item.getAxis('right').linkToView(self._right_axis)
self._right_axis.setXLink(self._plot_item)
## create a new ViewBox, link the right axis to its coordinate system
self._top_axis = pg.ViewBox()
self._plot_item.showAxis('top')
self._plot_item.scene().addItem(self._top_axis)
self._plot_item.getAxis('top').linkToView(self._top_axis)
self._top_axis.setYLink(self._plot_item)
self._top_axis.invertX(b=True)
# handle resizing of any of the elements
self._update_plot_views()
self._plot_item.vb.sigResized.connect(self._update_plot_views)
self._pw.setLabel('left', 'Fluorescence', units='counts/s')
self._pw.setLabel('right', 'Number of Points', units='#')
self._pw.setLabel('bottom', 'Wavelength', units='nm')
self._pw.setLabel('top', 'Relative Frequency', units='Hz')
self._mw.actionStop_resume_scan.triggered.connect(
self.stop_resume_clicked)
self._mw.actionSave_histogram.triggered.connect(self.save_clicked)
self._mw.actionStart_scan.triggered.connect(self.start_clicked)
self._mw.actionAuto_range.triggered.connect(self.set_auto_range)
# defining the parameters to edit
self._mw.binSpinBox.setValue(self._wm_logger_logic.get_bins())
self._mw.binSpinBox.editingFinished.connect(self.recalculate_histogram)
self._mw.minDoubleSpinBox.setValue(
self._wm_logger_logic.get_min_wavelength())
self._mw.minDoubleSpinBox.editingFinished.connect(
self.recalculate_histogram)
self._mw.maxDoubleSpinBox.setValue(
self._wm_logger_logic.get_max_wavelength())
self._mw.maxDoubleSpinBox.editingFinished.connect(
self.recalculate_histogram)
self._mw.show()
## Create an empty plot curve to be filled later, set its pen
self.curve_data_points = pg.PlotDataItem(pen=pg.mkPen(palette.c1),
symbol=None)
self.curve_nm_counts = pg.PlotDataItem(pen=pg.mkPen(
palette.c2, style=QtCore.Qt.DotLine),
symbol=None)
self.curve_hz_counts = pg.PlotDataItem(pen=pg.mkPen(
palette.c6, style=QtCore.Qt.DotLine),
symbol=None)
self.curve_envelope = pg.PlotDataItem(pen=pg.mkPen(
palette.c3, style=QtCore.Qt.DotLine),
symbol=None)
self.curve_fit = pg.PlotDataItem(pen=pg.mkPen(palette.c2, width=3),
symbol=None)
self._pw.addItem(self.curve_data_points)
self._pw.addItem(self.curve_envelope)
self._right_axis.addItem(self.curve_nm_counts)
self._top_axis.addItem(self.curve_hz_counts)
# scatter plot for time series
self._spw = self._mw.scatterPlotWidget
self._spi = self._spw.plotItem
self._spw.setLabel('bottom', 'Wavelength', units='nm')
self._spw.setLabel('left', 'Time', units='s')
self._scatterplot = pg.ScatterPlotItem(size=10,
pen=pg.mkPen(None),
brush=pg.mkBrush(
255, 255, 255, 20))
self._spw.addItem(self._scatterplot)
self._spw.setXLink(self._plot_item)
self._wm_logger_logic.sig_new_data_point.connect(self.add_data_point)
self._wm_logger_logic.sig_data_updated.connect(self.updateData)
# fit settings
self._fsd = FitSettingsDialog(self._wm_logger_logic.fc)
self._fsd.sigFitsUpdated.connect(
self._mw.fit_methods_ComboBox.setFitFunctions)
self._fsd.applySettings()
# self._mw.action_FitSettings.triggered.connect(self._fsd.show) #commented to debug
self._mw.do_fit_PushButton.clicked.connect(self.doFit)
self.sigDoFit.connect(self._wm_logger_logic.do_fit)
self.sigFitChanged.connect(self._wm_logger_logic.fc.set_current_fit)
self._wm_logger_logic.sig_fit_updated.connect(self.updateFit)
def __init__(self, parent):
# graph
self.name = "Transfer functions"
super(IirGraphWidget, self).__init__(parent)
self.parent = parent
self.module = self.parent.module
self.layout = QtWidgets.QVBoxLayout(self)
self.win = MyGraphicsWindow(title="Amplitude", parent=self)
self.win_phase = MyGraphicsWindow(title="Phase", parent=self)
# self.proxy = pg.SignalProxy(self.win.scene().sigMouseClicked,
# rateLimit=60, slot=self.mouse_clicked)
self.mag = self.win.addPlot(title="Magnitude (dB)")
self.phase = self.win_phase.addPlot(title="Phase (deg)")
self.phase.setXLink(self.mag)
# self.proxy_phase = pg.SignalProxy(self.win_phase.scene().sigMouseClicked,
# rateLimit=60, slot=self.mouse_clicked)
# we will plot the following curves:
# poles, zeros -> large dots and crosses
# design (designed filter) - yellow line
# measured filter with na - orange dots
# data (measruement data) - green line
# data x design (or data/design) - red line
self.plots = OrderedDict()
# make scatterplot items
for name, style in [('filter_measurement', dict(pen=pg.mkPen(None),
symbol='o',
size=5,
brush=pg.mkBrush(255, 100, 0, 180))),
('zeros', dict(pen=pg.mkPen(None),
symbol='o',
size=10,
brush=pg.mkBrush(255, 0, 255, 120))),
('poles', dict(pen=pg.mkPen(None),
symbol='x',
size=10,
brush=pg.mkBrush(255, 0, 255, 120))),
# ('actpole', dict(size=30,
# symbol='x',
# pen='r',
# brush=pg.mkBrush(255, 0, 255,
# 120))),
# ('actzero', dict(size=30,
# symbol='o',
# pen='r',
# brush=pg.mkBrush(255, 0, 255,
# 120)))
]:
item = pg.ScatterPlotItem(**style)
self.mag.addItem(item)
self.plots[name] = item
item = pg.ScatterPlotItem(**style)
self.phase.addItem(item)
self.plots[name+'_phase'] = item
# make lines
for name, style in [('data', dict(pen='g')),
('filter_design', dict(pen='y')),
('data_x_design', dict(pen='r'))]:
self.plots[name] = self.mag.plot(**style)
self.plots[name + "_phase"] = self.phase.plot(**style)
self.plots[name].setLogMode(xMode=self.xlog, yMode=None)
self.plots[name + '_phase'].setLogMode(xMode=self.xlog, yMode=None)
# also set logscale for the xaxis
# make scatter plots
self.mag.setLogMode(x=self.xlog, y=None)
self.phase.setLogMode(x=self.xlog, y=None)
self.layout.addWidget(self.win)
self.layout.addWidget(self.win_phase)
def setup(self):
## Dummy data Structures (override in func:self.load_data())
self.hyperspec_data = np.arange(10 * 10 * 34).reshape((10, 10, 34))
self.display_image = self.hyperspec_data.sum(
-1) # np.random.rand(10,10)
self.spec_x_array = np.arange(34)
# Call :func:set_scalebar_params() during self.load_data() to add a scalebar!
self.scalebar_type = None
# Will be filled derived maps and x_arrays
self.display_images = dict()
self.spec_x_arrays = dict()
## Graphs and Interface
self.line_colors = ['w', 'r', 'b', 'y', 'm', 'c', 'g']
self.plot_n_fit = PlotNFit(Ndata_lines=2,
pens=['g'] + self.line_colors)
# Docks
self.ui = self.dockarea = dockarea.DockArea()
self.image_dock = self.dockarea.addDock(name='Image')
self.spec_dock = self.dockarea.addDock(self.plot_n_fit.graph_dock)
self.settings_dock = self.dockarea.addDock(name='settings',
position='left',
relativeTo=self.image_dock)
self.export_dock = self.dockarea.addDock(name='export & adv. settings',
position='below',
relativeTo=self.settings_dock)
self.dockarea.addDock(self.plot_n_fit.settings_dock,
relativeTo=self.settings_dock,
position='below')
self.corr_dock = self.dockarea.addDock(name='correlation',
position='right',
relativeTo=self.spec_dock)
# Image View
self.imview = pg.ImageView()
self.imview.getView().invertY(False) # lower left origin
self.image_dock.addWidget(self.imview)
self.graph_layout = self.plot_n_fit.graph_layout
# Rectangle ROI
self.rect_roi = pg.RectROI([20, 20], [20, 20], pen=self.line_colors[0])
self.rect_roi.addTranslateHandle((0.5, 0.5))
self.imview.getView().addItem(self.rect_roi)
self.rect_roi.sigRegionChanged[object].connect(self.on_change_rect_roi)
# Point ROI
self.circ_roi = pg.CircleROI((0, 0), (2, 2),
movable=True,
pen=self.line_colors[1])
#self.circ_roi.removeHandle(self.circ_roi.getHandles()[0])
h = self.circ_roi.addTranslateHandle((0.5, .5))
h.pen = pg.mkPen(pen=self.line_colors[1])
h.update()
self.imview.getView().addItem(self.circ_roi)
self.circ_roi.removeHandle(0)
self.circ_roi_plotline = pg.PlotCurveItem([0], pen=self.line_colors[1])
self.imview.getView().addItem(self.circ_roi_plotline)
self.circ_roi.sigRegionChanged[object].connect(self.on_update_circ_roi)
# Spec plot
self.spec_plot = self.plot_n_fit.plot
self.spec_plot.setLabel('left', 'Intensity', units='counts')
self.rect_plotdata = self.plot_n_fit.data_lines[0]
self.point_plotdata = self.plot_n_fit.data_lines[1]
self.point_plotdata.setZValue(-1)
#settings
S = self.settings
self.default_display_image_choices = ['default', 'sum']
S.New('display_image',
str,
choices=self.default_display_image_choices,
initial='default')
S.display_image.add_listener(self.on_change_display_image)
self.default_x_axis_choices = ['default', 'index']
self.x_axis = S.New('x_axis',
str,
initial='default',
choices=self.default_x_axis_choices)
self.x_axis.add_listener(self.on_change_x_axis)
bg_subtract_choices = ('None', 'bg_slice', 'costum_const')
self.bg_subtract = S.New('bg_subtract',
str,
initial='None',
choices=bg_subtract_choices)
self.bg_counts = S.New('bg_value', initial=0, unit='cts/bin')
self.bg_counts.add_listener(self.update_display)
self.binning = S.New('binning', int, initial=1, vmin=1)
self.binning.add_listener(self.update_display)
self.norm_data = S.New('norm_data', bool, initial=False)
self.norm_data.add_listener(self.update_display)
S.New('default_view_on_load', bool, initial=True)
self.spatial_binning = S.New('spatial_binning', int, initial=1, vmin=1)
self.spatial_binning.add_listener(self.bin_spatially)
self.show_lines = ['show_circ_line', 'show_rect_line']
for x in self.show_lines:
lq = S.New(x, bool, initial=True)
lq.add_listener(self.on_change_show_lines)
# Settings Widgets
self.settings_widgets = [
] # Hack part 1/2: allows to use settings.New_UI() and have settings defined in scan_specific_setup()
font = QtGui.QFont("Times", 12)
font.setBold(True)
self.x_slicer = RegionSlicer(
self.spec_plot,
name='x_slice',
#slicer_updated_func=self.update_display,
brush=QtGui.QColor(0, 255, 0, 50),
ZValue=10,
font=font,
initial=[100, 511],
activated=True)
self.bg_slicer = RegionSlicer(
self.spec_plot,
name='bg_slice',
#slicer_updated_func=self.update_display,
brush=QtGui.QColor(255, 255, 255, 50),
ZValue=11,
font=font,
initial=[0, 80],
label_line=0)
self.x_slicer.region_changed_signal.connect(self.update_display)
self.bg_slicer.region_changed_signal.connect(self.update_display)
self.bg_slicer.activated.add_listener(
lambda: self.bg_subtract.update_value('bg_slice')
if self.bg_slicer.activated.val else None)
self.settings_widgets.append(self.x_slicer.New_UI())
self.settings_widgets.append(self.bg_slicer.New_UI())
## Setting widgets, (w/o logged quantities)
self.update_display_pushButton = QtWidgets.QPushButton(
text='update display')
self.settings_widgets.append(self.update_display_pushButton)
self.update_display_pushButton.clicked.connect(self.update_display)
self.default_view_pushButton = QtWidgets.QPushButton(
text='default img view')
self.settings_widgets.append(self.default_view_pushButton)
self.default_view_pushButton.clicked.connect(self.default_image_view)
self.recalc_median_pushButton = QtWidgets.QPushButton(
text='recalc median map')
self.settings_widgets.append(self.recalc_median_pushButton)
self.recalc_median_pushButton.clicked.connect(self.recalc_median_map)
self.recalc_sum_pushButton = QtWidgets.QPushButton(
text='recalc sum map')
self.settings_widgets.append(self.recalc_sum_pushButton)
self.recalc_sum_pushButton.clicked.connect(self.recalc_sum_map)
self.delete_current_display_image_pushButton = QtWidgets.QPushButton(
text='delete image')
self.settings_widgets.append(
self.delete_current_display_image_pushButton)
self.delete_current_display_image_pushButton.clicked.connect(
self.delete_current_display_image)
#correlation plot
self.corr_layout = pg.GraphicsLayoutWidget()
self.corr_plot = self.corr_layout.addPlot()
self.corr_plotdata = pg.ScatterPlotItem(x=[0, 1, 2, 3, 4],
y=[0, 2, 1, 3, 2],
size=17,
pen=pg.mkPen(None),
brush=pg.mkBrush(
255, 255, 255, 60))
self.corr_plot.addItem(self.corr_plotdata)
self.corr_plotdata.sigClicked.connect(self.corr_plot_clicked)
self.corr_dock.addWidget(self.corr_layout)
self.corr_settings = CS = LQCollection()
self.cor_X_data = self.corr_settings.New(
'cor_X_data',
str,
choices=self.default_display_image_choices,
initial='default')
self.cor_Y_data = self.corr_settings.New(
'cor_Y_data',
str,
choices=self.default_display_image_choices,
initial='sum')
self.cor_X_data.add_listener(self.on_change_corr_settings)
self.cor_Y_data.add_listener(self.on_change_corr_settings)
self.corr_ui = self.corr_settings.New_UI()
self.corr_dock.addWidget(self.corr_ui)
# map exporter
self.map_export_settings = MES = LQCollection()
MES.New('include_scale_bar', bool, initial=True)
MES.New('scale_bar_width', float, initial=1, spinbox_decimals=3)
MES.New('scale_bar_text', str, ro=False)
map_export_ui = MES.New_UI()
self.export_dock.addWidget(map_export_ui)
self.export_maps_as_jpegs_pushButton = QtWidgets.QPushButton(
'export maps as jpegs')
self.export_maps_as_jpegs_pushButton.clicked.connect(
self.export_maps_as_jpegs)
self.export_dock.addWidget(self.export_maps_as_jpegs_pushButton)
self.save_state_pushButton = QtWidgets.QPushButton(text='save state')
self.export_dock.addWidget(self.save_state_pushButton)
self.save_state_pushButton.clicked.connect(self.save_state)
# finalize settings widgets
self.scan_specific_setup(
) # there could more settings_widgets generated here (part 2/2)
hide_settings = [
'norm_data', 'show_circ_line', 'show_rect_line',
'default_view_on_load', 'spatial_binning', 'x_axis'
]
self.settings_ui = self.settings.New_UI(exclude=hide_settings)
self.settings_dock.addWidget(self.settings_ui)
self.hidden_settings_ui = self.settings.New_UI(include=hide_settings)
self.export_dock.addWidget(self.hidden_settings_ui)
ui_widget = QtWidgets.QWidget()
gridLayout = QtWidgets.QGridLayout()
gridLayout.setSpacing(0)
gridLayout.setContentsMargins(0, 0, 0, 0)
ui_widget.setLayout(gridLayout)
for i, w in enumerate(self.settings_widgets):
gridLayout.addWidget(w, int(i / 2), i % 2)
self.settings_dock.addWidget(ui_widget)
self.plot_n_fit.add_button('fit_map', self.fit_map)
self.settings_dock.raiseDock()
self.plot_n_fit.settings_dock.setStretch(1, 1)
self.export_dock.setStretch(1, 1)
self.settings_dock.setStretch(1, 1)
for layout in [
self.settings_ui.layout(),
self.export_dock.layout,
]:
VSpacerItem = QtWidgets.QSpacerItem(
0, 0, QtWidgets.QSizePolicy.Minimum,
QtWidgets.QSizePolicy.Expanding)
layout.addItem(VSpacerItem)
def paint(self, p, *args):
p.setPen(pg.mkPen(self.border_color))
p.setBrush(pg.mkBrush(self.fill_color))
p.drawRect(self.boundingRect())
def __init__(self, populations):
self.pops = populations
pg.PlotWidget.__init__(self)
self.setLogMode(x=True, y=False)
self.cells = pg.ScatterPlotItem(clickable=True)
self.cells.setZValue(10)
self.addItem(self.cells)
self.cells.sigClicked.connect(self.cells_clicked)
self.selected = pg.ScatterPlotItem()
self.selected.setZValue(20)
self.addItem(self.selected)
self.connections = pg.PlotCurveItem()
self.addItem(self.connections)
# first assign positions of all cells
cells = []
for y, pop in enumerate(self.pops.values()):
pop.cell_spots = []
pop.fwd_connections = {}
for i, cell in enumerate(pop._cells):
pos = (np.log10(cell['cf']), y)
real = cell['cell'] != 0
if not real:
pop.cell_spots.append(None)
continue
brush = pg.mkBrush('b') if real else pg.mkBrush(
255, 255, 255, 30)
spot = {
'x': pos[0],
'y': pos[1],
'symbol': 'o' if real else 'x',
'brush': brush,
'pen': None,
'data': (pop, i)
}
cells.append(spot)
pop.cell_spots.append(spot)
self.cells.setData(cells)
self.getAxis('left').setTicks([list(enumerate(self.pops.keys()))])
# now assign connection lines and record forward connectivity
con_x = []
con_y = []
for pop in self.pops.values():
for i, cell in enumerate(pop._cells):
conns = cell['connections']
if conns == 0:
continue
for prepop, precells in conns.items():
spot = pop.cell_spots[i]
if spot is None:
continue
p1 = spot['x'], spot['y']
for j in precells:
prepop.fwd_connections.setdefault(j, [])
prepop.fwd_connections[j].append((pop, i))
spot2 = prepop.cell_spots[j]
if spot2 is None:
return
p2 = spot2['x'], spot2['y']
con_x.extend([p1[0], p2[0]])
con_y.extend([p1[1], p2[1]])
self.connections.setData(x=con_x,
y=con_y,
connect='pairs',
pen=(255, 255, 255, 60))
def __clear_hover(self):
for item in self.__fill_items:
item.setBrush(pg.mkBrush(*item.rgb))
self.__clear_tooltips()
def generatePicture(self, data=None, redraw=False):
"""重新生成图形对象"""
# 重画或者只更新最后一个K线
if redraw:
self.pictures = []
elif self.pictures:
self.pictures.pop()
w = 0.4
bPen = self.bPen
bBrush = self.bBrush
rPen = self.rPen
rBrush = self.rBrush
low, high = (data[0]['low'], data[0]['high']) if len(data) > 0 else (0, 1)
prehigh= 0
prelow =0
# '''
for (t, open0, close0, low0, high0) in data:
if t >= len(self.pictures):
tShift = t
low, high = (min(low, low0), max(high, high0))
picture = QtGui.QPicture()
p = QtGui.QPainter(picture)
# # 下跌蓝色（实心）, 上涨红色（空心）
pen, brush, pmin, pmax = (bPen, bBrush, close0, open0) \
if open0 > close0 else (rPen, rBrush, open0, close0)
p.setPen(pen)
p.setBrush(brush)
# 画K线方块和上下影线
if pmin > low0:
p.drawLine(QtCore.QPointF(tShift, low0), QtCore.QPointF(tShift, pmin))
if high0 > pmax:
p.drawLine(QtCore.QPointF(tShift, pmax), QtCore.QPointF(tShift, high0))
# 指定图片绘制的区域 QRect,画方块
p.drawRect(QtCore.QRectF(tShift - w, open0, w * 2, close0 - open0))
if self.flag:
p.setPen(pg.mkPen('w'))
p.setBrush(pg.mkBrush('w'))
if prehigh==0:
p.drawLine(QtCore.QPointF(t, high0+5), QtCore.QPointF(t, high0+5))
else:
p.drawLine(QtCore.QPointF(t-1, prehigh), QtCore.QPointF(t, high0+5))
prehigh = high0+5
p.setPen(pg.mkPen(color=(255,215,0)))
if prelow == 0:
p.drawLine(QtCore.QPointF(t, low0-3), QtCore.QPointF(t, low0-3))
else:
p.drawLine(QtCore.QPointF(t - 1, prelow), QtCore.QPointF(t, low0-3))
prelow = low0-3
p.end()
self.pictures.append(picture)
self.new_pictures[t] = p
# '''
# prehigh= 0
# prelow = 0
# t = 0
# for (t, open0, close0, low0, high0) in data:
# p = self.new_pictures[t]
# p.setPen(pg.mkPen('w'))
# p.setBrush(pg.mkBrush('w'))
# if prehigh==0:
# p.drawLine(QtCore.QPointF(t, high0), QtCore.QPointF(t, high0))
# else:
# p.drawLine(QtCore.QPointF(t-1, prehigh), QtCore.QPointF(t, high0))
# prehigh = high0
# p.end()
self.low, self.high = low, high
w2 = view.addViewBox()
w2.setAspectLocked(True)
view.nextRow()
w3 = view.addPlot()
w4 = view.addPlot()
print("Generating data, this takes a few seconds...")
## There are a few different ways we can draw scatter plots; each is optimized for different types of data:
## 1) All spots identical and transform-invariant (top-left plot).
## In this case we can get a huge performance boost by pre-rendering the spot
## image and just drawing that image repeatedly.
n = 300
s1 = pg.ScatterPlotItem(size=10, pen=pg.mkPen(None), brush=pg.mkBrush(255, 255, 255, 120))
pos = np.random.normal(size=(2,n), scale=1e-5)
spots = [{'pos': pos[:,i], 'data': 1} for i in range(n)] + [{'pos': [0,0], 'data': 1}]
s1.addPoints(spots)
w1.addItem(s1)
## Make all plots clickable
lastClicked = []
def clicked(plot, points):
global lastClicked
for p in lastClicked:
p.resetPen()
print("clicked points", points)
for p in points:
p.setPen('b', width=2)
lastClicked = points
def handle_checker_record(self, rec):
expt = rec['experiment']
if expt in self.records_by_expt:
# use old record / item
index = self.records_by_expt[expt]
item = self.records[index]['item']
else:
# add new record / item
item = pg.TreeWidgetItem()
self.expt_tree.addTopLevelItem(item)
rec['item'] = item
index = self.records.add_record({})
item.index = index
record = self.records[index]
record['item'] = item
self.records_by_expt[expt] = index
# update item/record fields
update_filter = False
for field, val in rec.items():
if field in self.field_indices and isinstance(val, tuple):
# if a tuple was given, interpret it as (text, color)
val, color = val
else:
# otherwise make a guess on a good color
color = 'w'
if val is True:
color = pass_color
elif val is False:
color = fail_color
elif val in ('ERROR', 'MISSING', 'FAILED'):
color = fail_color
elif val == '-':
# dash means item is incomplete but still acceptable
color = [c * 0.5 + 128 for c in pass_color]
display_val = str(val)
if field == 'timestamp' and rec.get('error') is not None:
color = fail_color
# update this field in the record
record[field] = val
# update this field in the tree item
try:
i = self.field_indices[field]
except KeyError:
continue
item.setText(i, display_val)
if color is not None:
item.setBackground(i, pg.mkBrush(color))
# update filter fields
filter_field = self.filter_fields.get(field)
if filter_field is not None and filter_field['mode'] == 'enum' and display_val not in filter_field['values']:
filter_field['values'][display_val] = True
update_filter = True
if update_filter:
self.filter.setFields(self.filter_fields)
self.filter_items(self.records[index:index+1])
def init_bar_graph_caract(self):
brushes = [pg.mkBrush(i) for i in range(len(self.gv.waves))]
x = [w.get_half_pos() for w in self.gv.waves.values()]
width = [w.get_delta_range() for w in self.gv.waves.values()]
return brushes, x, width
# # option1: only for .plot(), following c1,c2 for example-----------------------
# win.addLegend(frame=False, colCount=2)
# bar graph
x = np.arange(10)
y = np.sin(x+2) * 3
bg1 = pg.BarGraphItem(x=x, height=y, width=0.3, brush='b', pen='w', name='bar')
win.addItem(bg1)
# curve
c1 = win.plot([np.random.randint(0,8) for i in range(10)], pen='r', symbol='t', symbolPen='r', symbolBrush='g', name='curve1')
c2 = win.plot([2,1,4,3,1,3,2,4,3,2], pen='g', fillLevel=0, fillBrush=(255,255,255,30), name='curve2')
# scatter plot
s1 = pg.ScatterPlotItem(size=10, pen=pg.mkPen(None), brush=pg.mkBrush(255, 255, 255, 120), name='scatter')
spots = [{'pos': [i, np.random.randint(-3, 3)], 'data': 1} for i in range(10)]
s1.addPoints(spots)
win.addItem(s1)
# # option2: generic method------------------------------------------------
legend = pg.LegendItem((80,60), offset=(70,20))
legend.setParentItem(win.graphicsItem())
legend.addItem(bg1, 'bar')
legend.addItem(c1, 'curve1')
legend.addItem(c2, 'curve2')
legend.addItem(s1, 'scatter')
if __name__ == '__main__':
pg.mkQApp().exec_()
def makeColoredBrush(self, percent, value):
color = self.legend.getColor(percent)
print("Value: ", value, " Percent: ", percent, " Color: ",
color.getRgb())
return pg.mkBrush(color)
def __init__(self, parent=None):
super(TSNEPlot, self).__init__(parent=parent)
self.model = ResultsTableModel()
self.layout = QtGui.QGridLayout(self)
self.layout.setAlignment(QtCore.Qt.AlignTop)
self.random_seed = np.random.randint(1, 99999)
self.perplexity = 30
self.lr = 200.0
self.plot_widget = pg.PlotWidget()
self.tsne_plot = pg.ScatterPlotItem(
symbol="o",
size=10,
pen=pg.mkPen(width=0.2, color="b"),
brush=pg.mkBrush(0.7),
antialias=True,
)
self.tsne_plot.sigClicked.connect(self.pointClicked)
self.selectedPt = None
self.plot_widget.hideAxis("left")
self.plot_widget.hideAxis("bottom")
self.plot_widget.addItem(self.tsne_plot)
self.random_seed_edit = QtGui.QLineEdit(str(self.random_seed))
self.random_seed_edit.setValidator(QtGui.QIntValidator(1, 99999))
self.random_seed_edit.setMaximumWidth(75)
self.perplexity_edit = QtGui.QLineEdit(str(self.perplexity))
self.perplexity_edit.setValidator(QtGui.QIntValidator(1, 50))
self.perplexity_edit.setMaximumWidth(75)
self.lr_edit = QtGui.QLineEdit(str(self.lr))
self.lr_edit.setValidator(QtGui.QDoubleValidator(10, 1000, 3))
self.lr_edit.setMaximumWidth(75)
self.select_feature = QtGui.QComboBox()
self.run_button = QtGui.QPushButton("Run t-SNE")
self.back_button = QtGui.QPushButton("<<< Feature Selection")
self.save_button = QtGui.QPushButton("Export Image")
self.save_button.setIcon(self.style().standardIcon(
QtGui.QStyle.SP_FileDialogStart))
self.legend = pg.GradientWidget(orientation="right")
self.legend.setMaximumWidth(50)
self.legend.sigGradientChangeFinished.connect(self.colorChange)
# print(self.legend.colorMap())
self.layout.addWidget(QtGui.QLabel("Perplexity"), 0, 0, 1, 1)
self.layout.addWidget(self.perplexity_edit, 0, 1, 1, 1)
self.layout.addWidget(QtGui.QLabel("Random Seed"), 1, 0, 1, 1)
self.layout.addWidget(self.random_seed_edit, 1, 1, 1, 1)
self.layout.addWidget(QtGui.QLabel("Learning Rate"), 2, 0, 1, 1)
self.layout.addWidget(self.lr_edit, 2, 1, 1, 1)
self.layout.addWidget(self.save_button, 3, 0, 1, 1)
self.layout.addWidget(self.run_button, 3, 1, 1, 2)
self.layout.addWidget(self.plot_widget, 4, 0, 4, 3)
self.layout.addWidget(self.select_feature, 8, 0, 1, 3)
self.layout.addWidget(self.back_button, 9, 0, 1, 3)
self.layout.addWidget(self.legend, 4, 4, 4, 1)
# self.layout.setColumnStretch(4, 1)
self.select_feature.activated[str].connect(self.setBrushes)
def setup(self, win):
# Data plots
self.data_plots = []
self.data_curves = []
for i in range(self.num_depths):
title = "{:.0f} cm".format(100 * self.depths[i])
plot = win.addPlot(row=0, col=i, title=title)
plot.setMenuEnabled(False)
plot.setMouseEnabled(x=False, y=False)
plot.hideButtons()
plot.showGrid(x=True, y=True)
plot.setYRange(0, 2**16)
plot.hideAxis("left")
plot.hideAxis("bottom")
plot.plot(np.arange(self.sweeps_per_frame),
2**15 * np.ones(self.sweeps_per_frame))
curve = plot.plot(pen=utils.pg_pen_cycler())
self.data_plots.append(plot)
self.data_curves.append(curve)
# Spectral density plot
self.sd_plot = win.addPlot(row=1, col=0, colspan=self.num_depths)
self.sd_plot.setMenuEnabled(False)
self.sd_plot.setMouseEnabled(x=False, y=False)
self.sd_plot.hideButtons()
self.sd_plot.setLabel("left", "Normalized PSD (dB)")
self.sd_plot.showGrid(x=True, y=True)
self.sd_curve = self.sd_plot.plot(pen=utils.pg_pen_cycler())
dashed_pen = pg.mkPen("k", width=2, style=QtCore.Qt.DashLine)
self.sd_threshold_line = pg.InfiniteLine(angle=0, pen=dashed_pen)
self.sd_plot.addItem(self.sd_threshold_line)
self.smooth_max = utils.SmoothMax(
self.est_update_rate,
tau_decay=0.5,
tau_grow=0,
hysteresis=0.2,
)
# Rolling speed plot
self.vel_plot = pg.PlotItem()
self.vel_plot.setMenuEnabled(False)
self.vel_plot.setMouseEnabled(x=False, y=False)
self.vel_plot.hideButtons()
self.vel_plot.setLabel("bottom", "Time (s)")
self.vel_plot.showGrid(x=True, y=True)
self.vel_plot.setXRange(-EST_VEL_HISTORY_LENGTH, 0)
self.vel_max_line = pg.InfiniteLine(angle=0,
pen=pg.mkPen("k", width=1))
self.vel_plot.addItem(self.vel_max_line)
self.vel_scatter = pg.ScatterPlotItem(size=8)
self.vel_plot.addItem(self.vel_scatter)
self.vel_html_fmt = '<span style="color:#000;font-size:24pt;">{:.1f} {}</span>'
self.vel_text_item = pg.TextItem(anchor=(0.5, 0))
self.vel_plot.addItem(self.vel_text_item)
# Sequence speed plot
self.sequences_plot = pg.PlotItem()
self.sequences_plot.setMenuEnabled(False)
self.sequences_plot.setMouseEnabled(x=False, y=False)
self.sequences_plot.hideButtons()
self.sequences_plot.setLabel("bottom", "History")
self.sequences_plot.showGrid(y=True)
self.sequences_plot.setXRange(-NUM_SAVED_SEQUENCES + 0.5, 0.5)
tmp = np.flip(np.arange(NUM_SAVED_SEQUENCES) == 0)
brushes = [pg.mkBrush(utils.color_cycler(n)) for n in tmp]
self.bar_graph = pg.BarGraphItem(
x=np.arange(-NUM_SAVED_SEQUENCES, 0) + 1,
height=np.zeros(NUM_SAVED_SEQUENCES),
width=0.8,
brushes=brushes,
)
self.sequences_plot.addItem(self.bar_graph)
self.sequences_text_item = pg.TextItem(anchor=(0.5, 0))
self.sequences_plot.addItem(self.sequences_text_item)
sublayout = win.addLayout(row=2, col=0, colspan=self.num_depths)
sublayout.addItem(self.vel_plot, col=0)
sublayout.addItem(self.sequences_plot, col=1)
self.setup_is_done = True
self.update_processing_config()
def __graph_results(self):
yes_votes = self.poll_data[:, NUM_YES]
no_votes = self.poll_data[:, NUM_NO]
cycle = self.poll_data[:, ROUND]
# Std processing
std_votes = yes_votes[self.std_gamemode_mask] + no_votes[
self.std_gamemode_mask]
std_percent_yes_votes = yes_votes[self.std_gamemode_mask] / std_votes
std_cycle = cycle[self.std_gamemode_mask]
# Taiko processing
taiko_votes = yes_votes[self.taiko_gamemode_mask] + no_votes[
self.taiko_gamemode_mask]
taiko_percent_yes_votes = yes_votes[
self.taiko_gamemode_mask] / taiko_votes
taiko_cycle = cycle[self.taiko_gamemode_mask]
# Catch processing
catch_votes = yes_votes[self.catch_gamemode_mask] + no_votes[
self.catch_gamemode_mask]
catch_percent_yes_votes = yes_votes[
self.catch_gamemode_mask] / catch_votes
catch_cycle = cycle[self.catch_gamemode_mask]
# Mania processing
mania_votes = yes_votes[self.mania_gamemode_mask] + no_votes[
self.mania_gamemode_mask]
mania_percent_yes_votes = yes_votes[
self.mania_gamemode_mask] / mania_votes
mania_cycle = cycle[self.mania_gamemode_mask]
# Scatter plot highlighting
brush_fail = (255, 100, 100, 200)
brush_pass = (100, 100, 255, 200)
std_scatter_brush = [
pyqtgraph.mkBrush(
brush_fail if std_percent_yes_vote <= 0.85 else brush_pass)
for std_percent_yes_vote in std_percent_yes_votes
]
taiko_scatter_brush = [
pyqtgraph.mkBrush(
brush_fail if taiko_percent_yes_vote <= 0.85 else brush_pass)
for taiko_percent_yes_vote in taiko_percent_yes_votes
]
catch_scatter_brush = [
pyqtgraph.mkBrush(
brush_fail if catch_percent_yes_vote <= 0.85 else brush_pass)
for catch_percent_yes_vote in catch_percent_yes_votes
]
mania_scatter_brush = [
pyqtgraph.mkBrush(
brush_fail if mania_percent_yes_vote <= 0.85 else brush_pass)
for mania_percent_yes_vote in mania_percent_yes_votes
]
# Graphing
self.graphs['std']['plot'].setData(std_cycle,
std_votes,
pen=None,
symbol='o',
symbolPen=None,
symbolSize=2,
symbolBrush=std_scatter_brush)
self.graphs['taiko']['plot'].setData(taiko_cycle,
taiko_votes,
pen=None,
symbol='o',
symbolPen=None,
symbolSize=2,
symbolBrush=taiko_scatter_brush)
self.graphs['catch']['plot'].setData(catch_cycle,
catch_votes,
pen=None,
symbol='o',
symbolPen=None,
symbolSize=2,
symbolBrush=catch_scatter_brush)
self.graphs['mania']['plot'].setData(mania_cycle,
mania_votes,
pen=None,
symbol='o',
symbolPen=None,
symbolSize=2,
symbolBrush=mania_scatter_brush)
import numpy as np
import pyqtgraph as pg
from bwplot import cbox
from pyqtgraph.Qt import QtGui, QtCore
plt = pg.plot()
plt.setWindowTitle('pyqtgraph example: Legend')
plt.addLegend()
for i in range(100):
x = np.array([3, 5, 5, 3, 3, 7, 9, 9, 7, 7, 7]) + i
y = [2, 2, 4, 4, 2, 6, 6, 7, 7, 6, 6]
connect = np.array([1, 1, 1, 1, 0, 1, 1, 1, 1, 1, 0])
pen = 'w'
brush = pg.mkBrush(cbox(0, as255=True, alpha=80))
# c = plt.plot(x, y, pen='w', connect=connect, fillBrush=brush, fillLevel='enclosed', name="fillLevel='enclosed'")
# item = pg.PlotDataItem(x, y, pen='w', connect=connect, fillBrush=brush, fillLevel='enclosed', name="fillLevel='enclosed'")
item = pg.GraphicsObject
item.yData = y
item.xData = x
item.z
plt.addItem(item, params={})
if __name__ == '__main__':
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
def __init__(self,
data_filename,
bgimg,
delta_video_filename,
load_original=False,
clickable_width=6,
draw_interesting_time_points=True,
draw_config_function=False):
self.load_original = load_original
TemplateBaseClass.__init__(self)
self.setWindowTitle('Trajectory Viewer GUI v2')
# Create the main window
#self.app = QtGui.QApplication([])
self.ui = WindowTemplate()
self.ui.setupUi(self)
#self.show()
# options
self.draw_interesting_time_points = draw_interesting_time_points
self.draw_config_function = draw_config_function
# Buttons
self.ui.save_trajecs.clicked.connect(self.save_trajectories)
self.ui.movie_save.clicked.connect(self.save_image_sequence)
self.ui.movie_speed.sliderMoved.connect(self.set_movie_speed)
self.ui.trajec_undo.clicked.connect(self.trajec_undo)
self.ui.movie_play.clicked.connect(self.movie_play)
self.ui.movie_pause.clicked.connect(self.movie_pause)
self.ui.trajec_delete.clicked.connect(self.toggle_trajec_delete)
self.ui.trajec_cut.clicked.connect(self.toggle_trajec_cut)
self.ui.trajec_join_collect.clicked.connect(
self.toggle_trajec_join_collect)
self.ui.trajec_select_all.clicked.connect(self.select_all_trajecs)
self.ui.trajec_join_add_data.clicked.connect(
self.toggle_trajec_join_add_data)
self.ui.trajec_join_save.clicked.connect(self.trajec_join_save)
self.ui.trajec_join_clear.clicked.connect(
self.toggle_trajec_join_clear)
self.ui.save_annotation.clicked.connect(self.save_annotation)
self.ui.load_annotations.clicked.connect(self.load_annotations)
self.ui.annotated_color_checkbox.stateChanged.connect(
self.toggle_annotated_colors)
self.ui.annotated_hide_checkbox.stateChanged.connect(
self.toggle_annotated_hide)
if not SMALL:
self.ui.get_original_objid.clicked.connect(
self.trajec_get_original_objid)
self.ui.save_colors.clicked.connect(self.save_trajec_colors)
self.ui.min_selection_length.setPlainText(str(0))
self.ui.max_selection_length.setPlainText(str(-1)) # -1 means all
# parameters
self.data_filename = data_filename
self.load_data()
self.backgroundimg_filename = bgimg
self.backgroundimg = None
self.binsx = None
self.binsy = None
trange = np.float(
np.max(self.pd.time_epoch.values) -
np.min(self.pd.time_epoch.values))
self.troi = [
np.min(self.pd.time_epoch.values),
np.min(self.pd.time_epoch.values) + trange * 0.1
]
self.skip_frames = 1
self.frame_delay = 0.03
self.path = os.path.dirname(data_filename)
self.clickable_width = clickable_width
# load delta video bag
if delta_video_filename != 'none':
self.dvbag = rosbag.Bag(delta_video_filename)
else:
self.dvbag = None
# Initialize
self.trajec_width_dict = {}
try:
fname = os.path.join(self.path, 'trajec_to_color_dict.pickle')
f = open(fname, 'r+')
self.trajec_to_color_dict = pickle.load(f)
f.close()
except:
self.trajec_to_color_dict = {}
for key in self.pd.objid.unique():
color = get_random_color()
self.trajec_to_color_dict.setdefault(key, color)
self.plotted_traces_keys = []
self.plotted_traces = []
self.trajectory_ends_vlines = []
self.data_to_add = []
self.selected_trajectory_ends = []
self.object_id_numbers = []
self.annotations = os.path.join(self.path, 'annotations.pickle')
if os.path.exists(self.annotations):
f = open(self.annotations, 'r+')
data = pickle.load(f)
f.close()
self.annotated_keys = data.keys()
else:
self.annotated_keys = []
self.time_mouse_click = time.time()
self.cut_objects = False
self.delete_objects = False
self.join_objects = False
self.add_data = False
self.crosshair_pen = pg.mkPen('w', width=1)
self.ui.qtplot_timetrace.enableAutoRange('xy', False)
if self.config is not None:
print('**** Sensory stimulus: ', self.config.sensory_stimulus_on)
for r, row in enumerate(self.config.sensory_stimulus_on):
v1 = pg.PlotDataItem([
self.config.sensory_stimulus_on[r][0],
self.config.sensory_stimulus_on[r][0]
], [0, 10])
v2 = pg.PlotDataItem([
self.config.sensory_stimulus_on[r][-1],
self.config.sensory_stimulus_on[r][-1]
], [0, 10])
try:
f12 = pg.FillBetweenItem(
curve1=v1,
curve2=v2,
brush=pg.mkBrush(self.config.sensory_stimulus_rgba[r]))
except:
f12 = pg.FillBetweenItem(curve1=v1,
curve2=v2,
brush=pg.mkBrush(
(255, 0, 0, 150)))
self.ui.qtplot_timetrace.addItem(f12)
lr = pg.LinearRegionItem(values=self.troi)
f = 'update_time_region'
lr.sigRegionChanged.connect(self.__getattribute__(f))
self.ui.qtplot_timetrace.addItem(lr)
print('drawing interesting time points')
self.draw_timeseries_vlines_for_interesting_timepoints()
print('done drawing interesting time points')
self.ui.qtplot_timetrace.setRange(xRange=[
np.min(self.time_epoch_continuous),
np.max(self.time_epoch_continuous)
],
yRange=[0, np.max(self.nflies)])
self.ui.qtplot_timetrace.setLimits(yMin=0, yMax=np.max(self.nflies))
self.ui.qtplot_timetrace.setLimits(minYRange=np.max(self.nflies),
maxYRange=np.max(self.nflies))
self.current_time_vline = pg.InfiniteLine(angle=90, movable=False)
self.ui.qtplot_timetrace.addItem(self.current_time_vline,
ignoreBounds=True)
self.current_time_vline.setPos(0)
pen = pg.mkPen((255, 255, 255), width=2)
self.current_time_vline.setPen(pen)
# hide a bunch of the axes
self.ui.qtplot_timetrace.hideAxis('left')
self.ui.qtplot_timetrace.hideAxis('bottom')
self.ui.qtplot_trajectory.hideAxis('left')
self.ui.qtplot_trajectory.hideAxis('bottom')
def update_plot(self):
# first, we compile the line plot data, then we iterate over them and
# plot them. we then plot the scatter plots in the same manner
tfargs = {} # args to the call of iir.transfer_function
frequencies = self.frequencies
plot = OrderedDict()
# plot data curve (measurement)
try:
_, plot['data'] = self.module._data_curve_object.data
except AttributeError: # no curve for plotting available
plot['data'] = []
# plot designed filter
plot['filter_design'] = self.module.transfer_function(frequencies, **tfargs)
# plot product
plot['data_x_design'] = []
if self.module.plot_data_times_filter:
try:
plot['data_x_design'] = plot['data'] * plot['filter_design']
except ValueError:
pass
# disable data plot if this is desired
if not self.module.plot_data:
plot['data'] = []
# plot everything (all lines) up to here
for k, v in plot.items():
self.graph_widget.plots[k].setData(frequencies[:len(v)],
self._magnitude(v))
self.graph_widget.plots[k+'_phase'].setData(frequencies[:len(v)],
self._phase(v))
# plot poles and zeros
aws = self.attribute_widgets
for end in ['poles', 'zeros']:
mag, phase = [], []
for start in ['complex', 'real']:
key = start+'_'+end
freq = getattr(self.module, key)
if start == 'complex':
freq = np.imag(freq)
defsize = 15 # complex (double) PZ's are plotted with larger symbols
else:
defsize = 10
freq = np.abs(freq)
tf = self.module.transfer_function(freq, **tfargs)
selected = aws[key].attribute_value.selected
brush = [pg.mkBrush(color='m')
if (num == selected)
else pg.mkBrush(color='y')
for num in range(aws[key].number)]
size = [defsize*1.0 if (num == selected) else defsize
for num in range(aws[key].number)]
mag += [{'pos': (fr, val), 'data': i, 'brush': br, 'size': si}
for (i, (fr, val, br, si))
in enumerate(zip(list(np.log10(freq)),
list(self._magnitude(tf)),
brush,
size))]
phase += [{'pos': (fr, val), 'data': i, 'brush': br, 'size': si}
for (i, (fr, val, br, si))
in enumerate(zip(list(np.log10(freq)),
list(self._phase(tf)),
brush,
size))]
self.graph_widget.plots[end].setPoints(mag)
self.graph_widget.plots[end+'_phase'].setPoints(phase)
# plot the measurement data if desired
if self.module.plot_measurement and hasattr(self.module, '_measurement_data'):
f, v = self.module._measurement_data
f[f<=0] = sys.float_info.epsilon
f = np.asarray(np.log10(f), dtype=float)
self.graph_widget.plots['filter_measurement'].setData(x=f[:len(v)],
y=self._magnitude(v))
self.graph_widget.plots['filter_measurement_phase'].setData(x=f[:len(v)],
y=self._phase(v))
def __init__(self):
super(ImageViewer, self).__init__()
self.createActions()
self.createMenus()
self.resize(800, 600)
win = QWidget()
self.setCentralWidget(win)
# creates plot
self.plot = pg.PlotWidget(name="VES Locations")
layout = BorderLayout()
layout.add(QWidgetItem(self.plot), BorderLayout.Center)
# List items
# self.list_w = myListWidget()
self.list_w = QListWidget()
self.listitem.append(QListWidgetItem('Welcome to ResLayer!!!'))
self.list_w.setFrameStyle(QFrame.Box | QFrame.Raised)
layout.add(QWidgetItem(self.list_w), BorderLayout.West)
win.setLayout(layout)
self.list_w.addItem(self.listitem[0])
# text=self.list_w.itemClicked.connect(self.list_w.Clicked)
self.list_w.itemClicked.connect(self.OnSingleClick)
# print(text)
self.setWindowTitle("Border Layout")
mypen = pg.mkPen('y', width=1)
self.vesdf, self.data_dfs = load_pkl(self.base_folder +
'vesdf_datadf.pkl')
self.lith_dict = load_pkl(self.base_folder + 'lith_dict.pkl')
new_ves = load_pkl(self.base_folder + 'new_ves.pkl')
try:
self.boundaries = load_pkl(self.base_folder + 'boundaries.pkl')
except:
self.boundaries = []
try:
self.drilldf = load_pkl(self.base_folder + 'drill_info.pkl')
except:
self.drilldf = []
try:
self.profiles = load_pkl(self.base_folder + 'profiles.pkl')
# print(self.profiles)
for profile in self.profiles:
self.listitem.append(
QListWidgetItem('Profile: ' +
'-'.join([p for p, q in profile])))
self.list_w.addItem(self.listitem[-1])
except:
self.profiles = []
self.VES,self.E,self.N,self.Ele,self.block=self.vesdf['VES No.'].values,self.vesdf.Easting.values.astype(np.float), \
self.vesdf.Northing.values.astype(np.float), \
str_array2floats(self.vesdf.RL.values),self.vesdf.Block.values
self.coords = [[xi, yi] for xi, yi in zip(self.E, self.N)]
self.plot.setLabel('left', "Northing", units='deg')
self.plot.setLabel('bottom', "Easting", units='deg')
self.plot.showGrid(x=1, y=1, alpha=None)
self.plot.showAxis('right')
self.plot.showAxis('top')
self.plot.getViewBox().setAspectLocked(True)
# self.curve = pg.ScatterPlotItem(size=20, pen=pg.mkPen(None), brush=pg.mkBrush(255, 255, 255, 120))
# spots = [{'pos': j, 'data': 1} for j in zip(self.E,self.N)]
# self.curve.addPoints(spots)
self.curve = self.plot.plot(
x=self.E, y=self.N, size=10, pen=pg.mkPen(None),
symbol='o') #brush=pg.mkBrush(255, 100, 255, 120),pen=None,
#drill information
if len(self.drilldf) > 0:
drillE, drillN, drill_labels = self.drilldf.Easting.values.astype(
np.float), self.drilldf.Northing.values.astype(
np.float), self.drilldf.Location.values
self.plot.plot(x=drillE,
y=drillN,
size=30,
pen=pg.mkPen(None),
symbol='s',
brush=pg.mkBrush('r'),
fc='r')
self.plot_labels(self.plot, drillE, drillN, drill_labels)
#district and block boundaries
if len(self.boundaries) > 0:
for b in self.boundaries:
self.plot.plot(x=[g for g in b[0]], y=[g for g in b[1]])
self.plot.addItem(self.curve)
# labels=['{}-{}'.format(ves,blk) for ves,blk in zip(self.VES,self.block)]
self.plot_labels(self.plot, self.E, self.N, self.VES, self.block)
self.curve.scene().sigMouseMoved.connect(self.onMouseMoved)
self.curve.scene().sigMouseClicked.connect(self.decideWhere2go)