def createPlotRegion(self):
self.linearRegionItem = pg.LinearRegionItem(brush=pg.intColor(1,alpha=100))
self.linearRegionItem.setZValue(10)
self.regionLabel = pg.TextItem(self.trackableFeature.name, color=pg.intColor(1), anchor=(0,1))
self.regionLabel.setX(self.linearRegionItem.getRegion()[0])
self.plotWidget.addItem(self.regionLabel)
self.plotWidget.addItem(self.linearRegionItem, ignoreBounds=True)
self.linearRegionItem.sigRegionChanged.connect(self.linearRegionItem_RegionChanged)
self.regionObserver.bind(self.linearRegionItem,self.linearRegionItem.setRegion,self._linearRegionItem_regionChanged)
def matchFreq(self):
freq1,freq2,ok=matchDialog.getData()
pencil1=pg.mkPen(color=pg.intColor(1))
pencil2=pg.mkPen(color=pg.intColor(20))
pencil3=pg.mkPen(color=pg.intColor(30))
for k in range(1,4):
self.p3.plot([k*freq1,k*freq1],[0,1.],pen=pencil1)
self.p3.plot([k*freq2,k*freq2],[0,1.],pen=pencil2)
for l in range(1,3):
self.p3.plot([k*freq2-l*freq1,k*freq2-l*freq1],[0,.5],pen=pencil3)
self.p3.plot([k*freq2+l*freq1,k*freq2+l*freq1],[0,.5],pen=pencil3)
self.p3.addItem(pg.PlotDataItem(pen=pencil1,name='ICRF'))
self.p3.addItem(pg.PlotDataItem(pen=pencil2,name='Helicon'))
self.p3.addItem(pg.PlotDataItem(pen=pencil3,name='Beat'))
def redrawPlot(self):
self.graph.clearPushed()
for bnum in range(0, self.numKeys):
if self.enabledbytes[bnum]:
self.graph.setColorInt(bnum, self.numKeys)
self.graph.passTrace(self.SADList[bnum], pen=pg.mkPen(pg.intColor(bnum, 16)), idString = str(bnum))
def plotSignal(self,item):
indexColor=0
self.p1.clear()
self.p2.clear()
for fileName in self.fileName:
print fileName
self.Back=False
self.signalName=item
time,data,self.sampling=readHdf5.getData(fileName,item,self.env)
self.time=np.array(time)
self.data=np.array(data)
self.frqlabel.setText('sampling rate: '+str(self.sampling))
pencil=pg.mkPen(color=pg.intColor(indexColor))
self.p1.plot(self.time,self.data,pen=pencil)
self.p2.plot(self.time,self.data,pen=pencil)
indexColor=indexColor+1
if self.existingData:
self.lr=pg.LinearRegionItem([self.left,self.right])
else:
self.lr=pg.LinearRegionItem([self.time[0],self.time[-1]])
self.left=self.time[0]
self.right=self.time[-1]
self.lr.setZValue(-10)
self.p1.addItem(self.lr)
self.lr.sigRegionChanged.connect(self.updatePlot)
def updateBluetooth(self):
returnedList = blescan.parse_events(self.sock, 1)
for beacon in returnedList:
words = beacon.split(',')
mac = words[0]
uid = words[1]
major = words[2]
minor = words[3]
power = words[4]
rssi = words[5]
print mac, rssi, minor
#print "dict lenght" ,len(self.signalList)
if mac not in self.signalList:
#self.signalList[mac] = np.zeros(self.bufferLength,'f')
self.signalList[mac] = np.zeros(0,'f')
self.curveList[mac] = self.p.plot(pen=QtGui.QPen(pg.intColor(self.nextColor)))
self.nextColor += 1
s = self.signalList[mac]
val = 100 + float(rssi)
if s.size < self.bufferLength:
s = np.append(s,val)
# if s.size > 4:
# s[-1] = self.runningMeanFast(s,3)[0]
print "append" , val
else:
s = np.roll(s,-1)
s[-1] = val
# s[-1] = self.runningMeanFast(s,3)[0]
self.curveList[mac].setData(s)
self.signalList[mac] = s
self.timeElapsed()
self.app.processEvents() ## force complete redraw for every plot
def addTracesABR(self, x, ys, intensity, trace_num):
self.clearTraces()
nreps = ys.shape[0]
for irep in reversed(range(nreps)):
self.trace_stash.append(self.plot(x, ys[irep, :], pen=(irep, nreps)))
line = self.plot(pen=pg.intColor(irep, hues=nreps))
self.legend.addItem(line, 'trace_' + str(trace_num[irep]) + ': ' + str(intensity[irep]) + ' dB')
self.legend_names.append('trace_' + str(trace_num[irep]) + ': ' + str(intensity[irep]) + ' dB')
def displayPartitions(self, differences={"partclass":None, "diffs":None}, traces=None, tRange=(0, -1)):
if traces is None:
traces = self.traceManager()
if tRange[1] < 0:
tRange = (tRange[0], traces.numTrace() + 1 + tRange[1])
self.partObject.setPartMethod(differences["partclass"])
self.numKeys = len(self.partObject.partMethod.getPartitionNum(traces, 0))
self.SADList = differences["diffs"]
self.graph = self.parent.getGraphWidgets(["Partition Differences"])[0]
# Place byte selection option on graph
if hasattr(self, 'enabledbytes') and len(self.enabledbytes) == self.numKeys:
pass
else:
self.enabledbytes = [False] * self.numKeys
self.doRedraw = True
self.byteNumAct = []
for i in range(0, self.numKeys):
ql = QToolButton()
ql.setText('%d' % i)
color = pg.intColor(i, self.numKeys)
ql.setStyleSheet("color: rgb(%d, %d, %d)" % (color.red(), color.green(), color.blue()))
qa = QWidgetAction(self)
qa.setDefaultWidget(ql)
qa.setStatusTip('%d' % i)
ql.setCheckable(True)
ql.setChecked(self.enabledbytes[i])
ql.clicked[bool].connect(partial(self.setBytePlot, i))
self.byteNumAct.append(qa)
byteNumAllOn = QAction('All On', self)
byteNumAllOff = QAction('All Off', self)
byteNumAllOn.triggered.connect(partial(self.setByteAll, True))
byteNumAllOff.triggered.connect(partial(self.setByteAll, False))
bselection = QToolBar()
for i in range(0, self.numKeys):
bselection.addAction(self.byteNumAct[i])
bselection.addAction(byteNumAllOn)
bselection.addAction(byteNumAllOff)
self.graph.addWidget(bselection)
self.graph.setPersistance(True)
# self.poi.setDifferences(SADList)
# self.parent.findParam('poi-pointrng').setLimits((0, len(SADList[0])))
# self.parent.findParam('poi-pointrng').setValue((0, len(SADList[0])))
self.redrawPlot()
def doPlot(columns, first, last):
from pyqtgraph.Qt import QtGui, QtCore
import numpy as np
import pyqtgraph as pg
import pyqtgraph.exporters
import itertools
pg.setConfigOptions(
antialias=True,
background='w',
foreground='k',
)
app = QtGui.QApplication([])
win = pg.GraphicsWindow(title="Curve plotter")
win.setWindowTitle('Curve plotter')
plot = win.addPlot(title="Rights and Usage")
ndays=(last-first).days+1
timeAxis = plot.getAxis('bottom')
timeAxis.setTicks([[
(i*25, first+datetime.timedelta(days=i))
for i in xrange(ndays)
],[
(i, i%25)
for i in xrange(25*ndays)
]])
timeAxis.setStyle(
tickTextHeight=390,
)
timeAxis.setGrid(100)
plot.addLegend()
for i,column in enumerate(columns):
plot.plot(np.array(column[1:]),
pen=pg.intColor(i),
name=column[0],
symbol='o',
symbolBrush=pg.intColor(i),
)
win.show()
app.exec_()
def __init__(self, x0=0.0, v0=0.0, t0=0.0, prog=None, pen=None, brush=None):
if pen is None:
pen = pg.intColor(Clock.nClocks, 12)
if brush is None:
brush = (0,0,150)
Clock.nClocks += 1
self.x0 = x0
self.v0 = v0
self.t0 = t0
self.prog = prog
self.pen = pen
self.brush = brush
def __init__(self, groups, xlims=None, parent=None):
super(ProgressWidget, self).__init__(parent)
self.lines = []
self.legend = self.addLegend()
for iline in range(len(groups)):
# give each line a different color
line = self.plot(pen=pg.intColor(iline, hues=len(groups)))
self.lines.append(line)
self.legend.addItem(line, str(groups[iline]))
if xlims is not None:
self.setXlim((xlims[0], xlims[1]))
self.groups = groups
def new_curve(self, results, color=pg.intColor(0), **kwargs):
if 'pen' not in kwargs:
kwargs['pen'] = pg.mkPen(color=color, width=2)
if 'antialias' not in kwargs:
kwargs['antialias'] = False
curve = ResultsCurve(results,
x=self.plot_frame.x_axis,
y=self.plot_frame.y_axis,
**kwargs
)
curve.setSymbol(None)
curve.setSymbolBrush(None)
return curve
def __init__(self, dataForCandle=None):
super(pgCandleWidget, self).__init__()
# 0) adds candle
self.candleData = dataForCandle
self.item01 = CandlestickItem(dataForCandle)
#self.addItem(self.item01)
# 1)cross hair
self.vLine = pg.InfiniteLine(angle=90, movable=False)
self.hLine = pg.InfiniteLine(angle=0, movable=False)
self.addItem(self.vLine, ignoreBounds=True)
self.addItem(self.hLine, ignoreBounds=True)
# 2) adds textInfo
self.textInfo = pg.TextItem("test")
self.addItem(self.textInfo, ignoreBounds=True)
#vb = self.plotItem.vb
#vb.setAspectLocked(True)
n = 300
self.lastClicked = []
def clicked(plot, points):
for p in self.lastClicked:
p.resetPen()
print("clicked points", points)
for p in points:
p.setPen('b', width=2)
self.lastClicked = points
self.item02 = pg.ScatterPlotItem(size=10, pen=pg.mkPen('w'), pxMode=False)
pos = np.random.normal(size=(2,n), scale=1e-5)
spots3 = []
for i in range(10):
for j in range(10):
spots3.append({'pos': (1e-6*i, 1e-6*j), 'size': 1, 'pen': {'color': 'w', 'width': 2}, 'brush':pg.intColor(i*10+j, 100)})
n=5
spots = [{'pos': pos[:,i], 'brush':pg.intColor(i, n), 'symbol': i%5, 'size': 50+i/10.} for i in range(n)]
a1 = {'pos': (10, 20), 'data': 5,'size': 5, 'pen': {'color': 'w', 'width': 2}, 'symbol': 't', 'brush':pg.intColor(10, 100)}
a2 = {'pos': (15, 20), 'data': 5,'size': 5, 'pen': {'color': 'w', 'width': 2}, 'symbol': 'd', 'brush':pg.intColor(10, 100)}
a3 = {'pos': (20, 20), 'data': 5,'size': 5, 'pen': {'color': 'w', 'width': 2}, 'symbol': '+', 'brush':pg.intColor(10, 100)}
spots2 = []
spots2.append(a1)
spots2.append(a2)
spots2.append(a3)
self.item02.addPoints(spots2)
self.addItem(self.item02)
self.item02.sigClicked.connect(clicked)
self.proxy = pg.SignalProxy(self.scene().sigMouseMoved, rateLimit=60, slot=self.mouseMoved)
def receiveNewNames(self, newNames):
# print("Receiving new names")
self.names = newNames
self.dataColumns = len(self.names)
for i in range(self.dataColumns):
color = pg.intColor(i, self.dataColumns)
self.curveColors.append(color)
item = QtGui.QStandardItem(self.names[i])
item.setBackground(color)
item.setCheckState(Qt.Checked)
item.setCheckable(True)
self.listViewModel.appendRow(item)
self.nameCheckItems.append(item)
def addSource(self, sourceX=None, sourceY=None):
if (sourceX is not None and not (isinstance(sourceX.content(), int) or isinstance(sourceX.content(), float))) or \
(sourceY is not None and not (isinstance(sourceY.content(), int) or isinstance(sourceY.content(), float))):
print "cannot add this type as source"
return
sourceTarget=Curve2DBox("data", self, dataRange=[0,0], color=pg.intColor(len(self.targets)))
#if sourceX is not None:
# sourceTarget.sources[0].updateSource(sourceX)
if sourceY is not None:
sourceTarget.sources[1].updateSource(sourceY)
self.targets.append(sourceTarget)
self.targets_layout.addWidget(sourceTarget)
self.rebuildLegend()
def __init__(self, x0=0.0, y0=0.0, m0=1.0, v0=0.0, t0=0.0, pen=None, brush=None, prog=None):
if pen is None:
pen = pg.intColor(Clock.nClocks, 12)
if brush is None:
brush = (0,0,150)
Clock.nClocks += 1
self.pen = pg.mkPen(pen)
self.brush = pg.mkBrush(brush)
self.y0 = y0
self.x0 = x0
self.v0 = v0
self.m0 = m0
self.t0 = t0
self.prog = prog
def onViewRangeChanged(viewRange, x, y, barGraphItem):
"""Updates barGraphItem data depending on plotItem viewRange.
@param viewRange: PlotItem viewRange
@param x, y: Data of barGraphItem
@param barGraphItem: BarGraphItem which data is to be updated
"""
v = list()
v.append(max(x[0], viewRange[0]))
v.append(min(x[-1], viewRange[-1]))
# n = 1024
newX = np.linspace(v[0], v[1], n)
newY = np.interp(newX, x, y)
# colors must be interpolated either in my task, here I just create new list of random colors
colors = [pg.intColor(np.random.randint(1, 100)) for i in xrange(n)]
barGraphItem.setOpts(x0=newX[:-1], x1=newX[1:], y0=[0] * n, y1=newY, brushes=colors, pens=colors)
def setup_plot(self):
self.plot = self#.plot()
self.showGrid(x=True, y=True)
# don't show the default left & bottom axes
[self.plot.showAxis(o, False) for o in ('left', 'bottom')]
# create & add scatter item to plot
self.scatters = []
for i, ul in enumerate(self.ulabels):
mask = self.labels == ul
brush = pg.intColor(i, hues=len(self.ulabels), alpha=125)
spi = pg.ScatterPlotItem(x=self.x[mask], y=self.y[mask], pen=None, brush=brush)
self.scatters.append(spi)
map(self.plot.addItem, self.scatters)
def to_update(self,obj=None):
self.spots,self.adj = self.graphModel.to_plot()
self.pos = []
try:
selected = self.selectionModel().selectedRows()
selected = [x.row() for x in selected]
except AttributeError:
selected = []
for i,s in enumerate(self.spots):
if i in selected:
s['pen'] = pg.mkPen('r')
else:
s['pen'] = pg.mkPen('k')
for k,v in s.items():
if k == 'pos':
self.pos.append(v)
elif k == 'symbol':
if v is None:
val = symbols[0]
elif v[0] == 'factor':
if v[1] > len(symbols) - 1:
val = symbols[-1]
else:
val = symbols[v[1]]
else:
val = symbols[0]
s[k] = val
elif k == 'size':
if v is None:
val = s_r[0]
elif v[0] == 'factor':
val = ((s_r[1] - s_r[0]) * (v[1]/v[2])) + s_r[0]
else:
val = ((s_r[1] - s_r[0]) * v[1]) + s_r[0]
s[k] = val
elif k == 'brush':
if v is None:
val = pg.mkBrush('c')
elif v[0] == 'factor':
s[k] = pg.mkBrush(pg.intColor(v[1], hues = v[2]))
else:
s[k] = pg.mkBrush(0,0,((c_r[1] - c_r[0]) * v[1]) + c_r[0])
self.spots[i] = s
self.update_data()
def makeScatterPlot():
## 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)
s1.sigClicked.connect(clicked)
## 2) Spots are transform-invariant, but not identical (top-right plot).
## In this case, drawing is as fast as 1), but there is more startup overhead
## and memory usage since each spot generates its own pre-rendered image.
s2 = pg.ScatterPlotItem(size=10, pen=pg.mkPen('w'), pxMode=True)
pos = np.random.normal(size=(2,n), scale=1e-5)
spots = [{'pos': pos[:,i], 'data': 1, 'brush':pg.intColor(i, n), 'symbol': i%5, 'size': 5+i/10.} for i in range(n)]
s2.addPoints(spots)
w2.addItem(s2)
s2.sigClicked.connect(clicked)
## 3) Spots are not transform-invariant, not identical (bottom-left).
## This is the slowest case, since all spots must be completely re-drawn
## every time because their apparent transformation may have changed.
s3 = pg.ScatterPlotItem(pxMode=False) ## Set pxMode=False to allow spots to transform with the view
spots3 = []
for i in range(10):
for j in range(10):
spots3.append({'pos': (1e-6*i, 1e-6*j), 'size': 1e-6, 'pen': {'color': 'w', 'width': 2}, 'brush':pg.intColor(i*10+j, 100)})
s3.addPoints(spots3)
w3.addItem(s3)
s3.sigClicked.connect(clicked)
## Test performance of large scatterplots
s4 = pg.ScatterPlotItem(size=10, pen=pg.mkPen(None), brush=pg.mkBrush(255, 255, 255, 20))
pos = np.random.normal(size=(2,10000), scale=1e-9)
s4.addPoints(x=pos[0], y=pos[1])
w4.addItem(s4)
s4.sigClicked.connect(clicked)
QtGui.QApplication.instance().exec_()
def plot_data(self, X, y):
self.clear_plot()
# get the simple cross validation score
clf = LDA()
scores = cross_validation.cross_val_score(clf, X, y, cv=5)
score = np.mean(scores)
self.ui.titleLabel.setText("Accuracy: %.2f" % score)
# project the data to 3D for visualization
clf = LDA(n_components=3)
X_proj = clf.fit(X, y).transform(X)
labels = sorted(np.unique(y))
for i in labels:
plot = gl.GLScatterPlotItem(
pos=X_proj[y == i], color=pg.glColor(pg.intColor(i)))
self.plotWidget.addItem(plot)
self.plot_items.append(plot)
def color_by_layer(self, root=None):
try:
unblock = False
if not isinstance(root, pg.QtGui.QTreeWidgetItem):
self.blockSignals(True)
unblock = True
root = self.labels_by_acronym['Isocortex']['item']
name = str(root.text(1))
if ', layer' in name.lower():
layer = name.split(' ')[-1]
layer = {'1': 0, '2': 1, '2/3': 2, '4': 3, '5': 4, '6a': 5, '6b': 6}[layer]
self.set_label_color(root.id, pg.intColor(layer, 10), recursive=False, emit=False)
for i in range(root.childCount()):
self.color_by_layer(root.child(i))
finally:
if unblock:
self.blockSignals(False)
self.labels_changed.emit()
def __init__(self, plotter, refresh_time=0.1, parent=None):
super(PlotterWindow, self).__init__(parent)
self.plotter = plotter
columns = plotter.results.procedure.DATA_COLUMNS
self.setWindowTitle("Results Plotter")
self.main = QtGui.QWidget(self)
vbox = QtGui.QVBoxLayout(self.main)
vbox.setSpacing(0)
hbox1 = QtGui.QHBoxLayout()
hbox1.setSpacing(6)
hbox1.setContentsMargins(-1, 6, -1, -1)
file_label = QtGui.QLabel(self.main)
file_label.setText("Data Filename:")
self.file = QtGui.QLineEdit(self.main)
self.file.setText(plotter.results.data_filename)
hbox1.addWidget(file_label)
hbox1.addWidget(self.file)
vbox.addLayout(hbox1)
self.plot_widget = PlotWidget(columns, check_status=False)
self.plot = self.plot_widget.plot
vbox.addWidget(self.plot_widget)
self.main.setLayout(vbox)
self.setCentralWidget(self.main)
self.main.show()
self.resize(800, 600)
self.curve = ResultsCurve(
plotter.results, columns[0], columns[1], pen=pg.mkPen(color=pg.intColor(0), width=2), antialias=False
)
self.plot.addItem(self.curve)
self.plot_widget.updated.connect(self.check_stop)
def setup(self, buffer):
"""
Setup the graph with the number of sensors from the buffer.
"""
self._number_of_sensors = buffer.number_of_sensors
# Create the data lists for the graph.
self._graph_data = [[] for vehicle in range(1, self._number_of_sensors + 1)]
# Create the curves for the graph.
color_index = 0
for vehicle in range(1, self._number_of_sensors + 1):
index = vehicle - 1
color = pg.intColor(color_index, hues=len(self._graph_data), maxValue=200)
color_index += 1
curve = self._graph.plot()
curve.setData(self._graph_data[index], pen=pg.mkPen(color, width=1.5))
self._graph_curves.append(curve)
def calculatefft(self):
indexColor=0
self.p3.clear()
self.p3.addLegend()
for fileName in self.fileName:
time,data,self.sampling=readHdf5.getData(fileName,self.signalName,self.env)
self.time=np.array(time)
self.data=np.array(data)
rang=self.p2.getPlotItem().getViewBox().viewRange()
rang2=rang[0]
# Number of samplepoints
dataslice=self.data[(self.time>=rang2[0]) & (self.time<=rang2[1])]
N=len(dataslice)
# sample spacing
T = 1.0 / self.sampling
yf = scipy.fftpack.fft(dataslice)
xf = np.linspace(0.0, 1.0/(2.0*T), N/2)
pencil=pg.mkPen(color=pg.intColor(indexColor))
self.p3.plot(xf, 2.0/N * np.abs(yf[0:N/2]),pen=pencil,name=fileName[0:-5])
indexColor=indexColor+1
self.p3.setLabel('left', "Spectral power (SI)")
self.p3.setLabel('bottom', "Frequency (Hz)")
def main():
app = QtGui.QApplication(sys.argv)
tabs = QtGui.QTabWidget()
for family in families:
scroller = QtGui.QScrollArea()
vb = pg.GraphicsWindow()
vb.setMinimumHeight(3000)
vb.setMinimumWidth(1900)
scroller.setWidget(vb)
for i, name in enumerate(pywt.wavelist(family)):
pen = pg.intColor(i)
wavelet = pywt.Wavelet(name)
if wavelet.orthogonal:
phi, psi, x = wavelet.wavefun(level=5)
ax = vb.addPlot(title=wavelet.name + " phi")
ax.plot(phi, pen=pen)
bx = vb.addPlot(title=wavelet.name + " psi")
bx.plot(psi, pen=pen)
else:
phi, psi, phi_r, psi_r, x = wavelet.wavefun(level=5)
ax = vb.addPlot(title=wavelet.name + " phi")
ax.plot(phi, pen=pen)
bx = vb.addPlot(title=wavelet.name + " psi")
bx.plot(psi, pen=pen)
ax = vb.addPlot(title=wavelet.name + " phi_r")
ax.plot(phi_r, pen=pen)
bx = vb.addPlot(title=wavelet.name + " psi_r")
bx.plot(psi_r, pen=pen)
if i % 2 == 0:
vb.nextRow()
tabs.addTab(scroller, family)
tabs.setWindowTitle('Wavelets')
tabs.resize(1920, 1080)
tabs.show()
sys.exit(app.exec_())
def _check(self):
# Update progress bar completion percentage every time, not only when
# new iteration callback data has arrived.
self._progress.setValue(self._runner.get_iteration_current())
# Stop the runner and update timer if the planning is done, then check
# for updates and final data.
if self._runner.done or not self._running:
self._stop()
self._update_timer.stop()
if self._updated:
# Update the graph with updated iteration statistics.
c = 0
for name, data in self._graph_data.iteritems():
if name not in self._graph_plots:
color = pg.intColor(c, hues=len(self._graph_data),
maxValue=200)
plot = self._graph.plot(symbol='o', symbolBrush=color,
symbolSize=5, pen=color, name=name)
self._graph_plots[name] = plot
self._graph_plots[name].setData(data)
c += 1
self._draw_list_item(self._graph_label, self._graph)
if self._runner.done or self._updated:
# Draw the plots for the Pareto front and any selected solution.
self._runner.make_pareto_plot(self._front_axes)
self._front_canvas.draw()
self._draw_list_item(self._front_label, self._front_canvas)
self._draw_solutions()
self._updated = False
import numpy as np
win = pg.plot()
win.setWindowTitle('pyqtgraph example: beeswarm')
data = np.random.normal(size=(4,20))
data[0] += 5
data[1] += 7
data[2] += 5
data[3] = 10 + data[3] * 2
## Make bar graph
#bar = pg.BarGraphItem(x=range(4), height=data.mean(axis=1), width=0.5, brush=0.4)
#win.addItem(bar)
## add scatter plots on top
for i in range(4):
xvals = pg.pseudoScatter(data[i], spacing=0.4, bidir=True) * 0.2
win.plot(x=xvals+i, y=data[i], pen=None, symbol='o', symbolBrush=pg.intColor(i,6,maxValue=128))
## Make error bars
err = pg.ErrorBarItem(x=np.arange(4), y=data.mean(axis=1), height=data.std(axis=1), beam=0.5, pen={'color':'w', 'width':2})
win.addItem(err)
## Start Qt event loop unless running in interactive mode or using pyside.
if __name__ == '__main__':
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
def show(self):
self.win = pg.GraphicsWindow()
self.win.setBackground('w')
Fs = self.Fs
p1 = self.win.addPlot(title='Stimulus',
row=0,
col=0,
labels={
'bottom': 'T (ms)',
'left': 'V'
})
p1.plot(self.stim.time * 1000,
self.stim.sound,
pen=pg.mkPen('k', width=0.75))
p1.setXLink(p1)
p2 = self.win.addPlot(title='AN spikes',
row=1,
col=0,
labels={
'bottom': 'T (ms)',
'left': 'AN spikes (first trial)'
})
for nr in range(self.nrep):
xan = []
yan = []
for k in range(len(self.pre_cells[nr])):
r = self.pre_cells[nr][k]._spiketrain
xan.extend(r)
yr = k + np.zeros_like(r) + 0.2
yan.extend(yr)
c = pg.PlotCurveItem()
xp = np.repeat(np.array(xan), 2)
yp = np.repeat(np.array(yan), 2)
yp[1::2] = yp[::2] + 0.6
c.setData(xp.flatten(),
yp.flatten(),
connect='pairs',
pen=pg.mkPen(pg.intColor(nr, self.nrep),
hues=self.nrep,
width=1.0))
p2.addItem(c)
p2.setXLink(p1)
p3 = self.win.addPlot(title='%s Spikes' % self.cell,
row=2,
col=0,
labels={
'bottom': 'T (ms)',
'left': 'Trial #'
})
xcn = []
ycn = []
xspks = []
for k in range(self.nrep):
bspk = PU.findspikes(self.time[k], self.vms[k], -35.)
xcn.extend(bspk)
yr = k + np.zeros_like(bspk) + 0.2
ycn.extend(yr)
d = pg.PlotCurveItem()
xp = np.repeat(np.array(xcn), 2)
yp = np.repeat(np.array(ycn), 2)
yp[1::2] = yp[::2] + 0.6
d.setData(xp.flatten(),
yp.flatten(),
connect='pairs',
pen=pg.mkPen('k', width=1.5))
p3.addItem(d)
p3.setXLink(p1)
p4 = self.win.addPlot(title='%s Vm' % self.cell,
row=3,
col=0,
labels={
'bottom': 'T (ms)',
'left': 'Vm (mV)'
})
for nr in range(self.nrep):
p4.plot(self.time[nr],
self.vms[nr],
pen=pg.mkPen(pg.intColor(nr, self.nrep),
hues=self.nrep,
width=1.0))
p4.setXLink(p1)
p5 = self.win.addPlot(title='xmtr',
row=0,
col=1,
labels={
'bottom': 'T (ms)',
'left': 'gSyn'
})
if synapseType == 'multisite':
for nr in [0]:
syn = self.synapses[nr]
j = 0
for k in range(self.n_sgc):
synapse = syn[k]
for i in range(synapse.terminal.n_rzones):
p5.plot(self.time[nr],
self.xmtrs[nr]['xmtr%04d' % j],
pen=pg.mkPen(pg.intColor(nr, self.nrep),
hues=self.nrep,
width=1.0))
j = j + 1
p5.setXLink(p1)
p6 = self.win.addPlot(title='AN PSTH',
row=1,
col=1,
labels={
'bottom': 'T (ms)',
'left': 'Sp/ms/trial'
})
bins = np.arange(0, 200, 1)
(hist, binedges) = np.histogram(xan, bins)
curve6 = p6.plot(binedges,
hist,
stepMode=True,
fillBrush=(0, 0, 0, 255),
brush=pg.mkBrush('k'),
fillLevel=0)
p7 = self.win.addPlot(title='%s PSTH' % self.cell,
row=2,
col=1,
labels={
'bottom': 'T (ms)',
'left': 'Sp/ms/trial'
})
bins = np.arange(0, 200, 1)
(hist, binedges) = np.histogram(xcn, bins)
curve7 = p7.plot(binedges,
hist,
stepMode=True,
fillBrush=(0, 0, 0, 255),
brush=pg.mkBrush('k'),
fillLevel=0)
self.win.show()
def makefigs(bounds:(int, int)=(1922, 2005), outdir:str='.'):
"Construit et enregistre les visualisations graphiques de la fonction Rollin"
makepath = lambda path: os.path.join(outdir, path)
if not os.path.isdir(outdir):
raise RuntimeError("Given output directory is not valid: " + str(outdir))
# Build the data
ANNEES = tuple(range(*bounds))
NOMBRES_ROLLIN = range(1, 10)
ROLLIN = tuple(rollin(annee) for annee in ANNEES)
assert min(ROLLIN) == 1 and max(ROLLIN) == 9, (min(ROLLIN), max(ROLLIN))
def evolution(nbs:[int], start:int) -> [int]:
prev = start
for nb in nbs:
nb, prev = nb - prev, nb
yield nb
EVOLUTION = tuple(evolution(ROLLIN, rollin(bounds[0] - 1)))
GREEN = (119,172,48)
RED = (200,12,48)
# Association nombre de Rollin -> années
ANNEE_PAR_NB = {} # nombre de rollin -> {années}
for annee, nb_rollin in zip(ANNEES, ROLLIN):
ANNEE_PAR_NB.setdefault(nb_rollin, []).append(annee)
COMPTAGE_ANNEES = tuple(len(ANNEE_PAR_NB[nb]) for nb in NOMBRES_ROLLIN)
# Simple plot de la fonction
plot = init("Nombre de Rollin et son évolution en fonction de l'année ({}-{})".format(*bounds))
# plot = win.addPlot(title="Plotting with symbols")
plot.addLegend()
plot.plot(ANNEES, ROLLIN, pen=GREEN, symbolBrush=GREEN, symbolPen='w', symbol='d', symbolSize=14, name="Nombre de Rollin")
# Plot de l'évolution du nombre de Rollin
plot.plot(ANNEES, EVOLUTION, pen=RED, symbolBrush=RED, symbolPen='w', symbol='t2', symbolSize=14, name="Évolution du nombre de Rollin")
# plot.setXRange(bounds[0]-10, bounds[1]+1)
plot.setYRange(min(EVOLUTION + ROLLIN), max(EVOLUTION + ROLLIN) + 2)
plot.show()
# Nombre d'années pour chaque nombre de Rollin
win = init_base("Dénombrement des années {}-{} selon leur nombre de Rollin".format(*bounds))
# help(pg.BarGraphItem)
win.addItem(pg.BarGraphItem(x=NOMBRES_ROLLIN, height=COMPTAGE_ANNEES, width=0.3))
# for nb_rollin in NOMBRES_ROLLIN:
# win.addItem(pg.BarGraphItem(x=[nb_rollin], height=[ANNEE_PAR_NB[nb_rollin]], width=0.3))
win.show()
# Boxplot, pour avoir une idée de la distribution des années
# does not exists in pyqtgraph ; building it myself…
win = init_base("Dénombrement des années {}-{} selon leur nombre de Rollin".format(*bounds))
for nb_rollin in NOMBRES_ROLLIN:
annees = ANNEE_PAR_NB[nb_rollin]
win.plot(x=[nb_rollin], y=annees, pen=None, symbol='o', symbolBrush=pg.intColor(nb_rollin,6))
mean, median, stdev = statistics.mean(annees), statistics.median(annees), statistics.stdev(annees)
maxi, mini = max(annees), min(annees)
limits_amplitude = (maxi - mini) / 2
middle = limits_amplitude + mini
boxes = (
(middle, limits_amplitude*2, 0.8, 'b', 1.2),
(mean, stdev, 0.5, 'w', 3),
(mean, 0, 0.5, 'w', 3),
(median, 0, 0.5, 'r', 4),
)
for center, amplitude, beam, color, width in boxes:
win.addItem(pg.ErrorBarItem(x=np.array([nb_rollin]), y=np.array([center]), height=np.array([amplitude]), beam=beam, pen={'color': color, 'width': width}))
win.show()
f = QtGui.QFont()
f.setPointSize(10)
symbol.addText(0, 0, f, label)
br = symbol.boundingRect()
scale = min(1. / br.width(), 1. / br.height())
tr = QtGui.QTransform()
tr.scale(scale, scale)
tr.rotate(angle)
tr.translate(-br.x() - br.width()/2., -br.y() - br.height()/2.)
return TextSymbol(label, tr.map(symbol), 0.1 / scale)
random_str = lambda : (''.join([chr(np.random.randint(ord('A'),ord('z'))) for i in range(np.random.randint(1,5))]), np.random.randint(0, 360))
s2 = pg.ScatterPlotItem(size=10, pen=pg.mkPen('w'), pxMode=True)
pos = np.random.normal(size=(2,n), scale=1e-5)
spots = [{'pos': pos[:,i], 'data': 1, 'brush':pg.intColor(i, n), 'symbol': i%5, 'size': 5+i/10.} for i in range(n)]
s2.addPoints(spots)
spots = [{'pos': pos[:,i], 'data': 1, 'brush':pg.intColor(i, n), 'symbol': label[1], 'size': label[2]*(5+i/10.)} for (i, label) in [(i, createLabel(*random_str())) for i in range(n)]]
s2.addPoints(spots)
w2.addItem(s2)
s2.sigClicked.connect(clicked)
## 3) Spots are not transform-invariant, not identical (bottom-left).
## This is the slowest case, since all spots must be completely re-drawn
## every time because their apparent transformation may have changed.
s3 = pg.ScatterPlotItem(pxMode=False) ## Set pxMode=False to allow spots to transform with the view
spots3 = []
for i in range(10):
for j in range(10):
import numpy as np
win = pg.plot()
win.setWindowTitle('pyqtgraph example: beeswarm')
data = np.random.normal(size=(4, 20))
data[0] += 5
data[1] += 7
data[2] += 5
data[3] = 10 + data[3] * 2
## Make bar graph
# bar = pg.BarGraphItem(x=range(4), height=data.mean(axis=1), width=0.5, brush=0.4)
# win.addItem(bar)
## add scatter plots on top
for i in range(4):
xvals = pg.pseudoScatter(data[i], spacing=0.4, bidir=True) * 0.2
win.plot(x=xvals + i, y=data[i], pen=None, symbol='o', symbolBrush=pg.intColor(i, 6, maxValue=128))
## Make error bars
err = pg.ErrorBarItem(x=np.arange(4), y=data.mean(axis=1), height=data.std(axis=1), beam=0.5,
pen={'color': 'w', 'width': 2})
win.addItem(err)
## Start Qt event loop unless running in interactive mode or using pyside.
if __name__ == '__main__':
import sys
if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
QtGui.QApplication.instance().exec_()
p.setPen('b', width=2)
lastClicked = points
s1.sigClicked.connect(clicked)
## 2) Spots are transform-invariant, but not identical (top-right plot).
## In this case, drawing is as fast as 1), but there is more startup overhead
## and memory usage since each spot generates its own pre-rendered image.
s2 = pg.ScatterPlotItem(size=10, pen=pg.mkPen('w'), pxMode=True)
pos = np.random.normal(size=(2, n), scale=1e-5)
spots = [{
'pos': pos[:, i],
'data': 1,
'brush': pg.intColor(i, n),
'symbol': i % 5,
'size': 5 + i / 10.
} for i in range(n)]
s2.addPoints(spots)
w2.addItem(s2)
s2.sigClicked.connect(clicked)
## 3) Spots are not transform-invariant, not identical (bottom-left).
## This is the slowest case, since all spots must be completely re-drawn
## every time because their apparent transformation may have changed.
s3 = pg.ScatterPlotItem(
pxMode=False
) ## Set pxMode=False to allow spots to transform with the view
spots3 = []
def plot_transform(transform, scales=None, multiview=False):
""" Display the different bands on the requested scales.
Parameters
----------
transform: WaveletTransformBase derived instance
a wavelet decomposition.
scales: list of int, default None
the desired scales, if None compute at all scales.
multiview: bool, default False
if True use a slider to select a specific band.
"""
# Set default scales
scales = scales or range(transform.nb_scale)
# Create application and tab widget
app = pyqtgraph.mkQApp()
tabs = QtGui.QTabWidget()
tabs.setWindowTitle("Wavelet Transform")
# Go through each scale
pen = pyqtgraph.intColor(2)
for scale in scales:
# Create the plots for this scales with scrolling possibilities
scroller = QtGui.QScrollArea()
tabs.addTab(scroller, "Scale {0}".format(scale))
# Go through each band of the current scale
# > using multiview
# TODO: update this code
if multiview:
raise NotImplementedError(
"Multiview transform view not yet implemented.")
window = pyqtgraph.image(numpy.asarray(transform[scale]))
scroller.setWidget(window)
# > using mosaic
else:
window = pyqtgraph.GraphicsWindow()
scroller.setWidget(window)
scale_data = transform[scale]
if not isinstance(scale_data, list):
scale_data = [scale_data]
for subband_data in scale_data:
# Deal with complex data
if numpy.iscomplex(subband_data).any():
subband_data = numpy.abs(subband_data)
subband_data = numpy.lib.pad(
subband_data, 1, "constant",
constant_values=subband_data.max())
# Select viewer
if subband_data.ndim == 1:
ax = window.addPlot()
ax.plot(subband_data, pen=pen)
elif subband_data.ndim == 2:
box = window.addViewBox()
box.setAspectLocked(True)
image = pyqtgraph.ImageItem(subband_data)
box.addItem(image)
else:
raise ValueError("This function currently support only "
"1D or 2D data.")
window.nextRow()
# Display the tab
tabs.show()
# Run application
app.exec_()
def __init__(self, rts, update_freq=50, z_ax='abs_pu', use_colors=False, rotating=False, *args, **kwargs):
super().__init__(*args, **kwargs)
self.rts = rts
self.ps = rts.ps
self.dt = self.rts.dt
ps = self.ps
self.z_ax = z_ax
# nx.draw(G)
self.scale = 10
if self.z_ax == 'angle':
self.scale_z = 10*np.ones(ps.n_bus)
self.offset_z = 3 # *np.ones(ps.n_bus)
elif self.z_ax == 'abs':
self.scale_z = 10 * ps.v_n / max(ps.v_n) * 0.3
self.offset_z = 0 # np.zeros(ps.n_bus)
elif self.z_ax == 'abs_pu':
self.scale_z = 10 * 0.3*(ps.v_n**0)
self.offset_z = 0 # np.zeros(ps.n_bus)
# elif self.z_ax == 'both':
# self.scale_z = 10*np.ones(ps.n_bus)
# self.offset_z = 12*np.ones(ps.n_bus)
line_admittances = np.zeros(len(ps.lines), dtype=[('Y', float)])
for i, line in enumerate(ps.lines):
line_admittances[i] = abs(ps.read_admittance_data('line', line)[2])
trafo_admittances = np.zeros(len(ps.transformers), dtype=[('Y', float)])
for i, trafo in enumerate(ps.transformers):
trafo_admittances[i] = abs(ps.read_admittance_data('transformer', trafo)[2])
self.G = nx.MultiGraph()
self.G.add_nodes_from(ps.buses['name'])
# G.add_edges_from(ps.lines[['from_bus', 'to_bus']])
# G.add_edges_from(ps.transformers[['from_bus', 'to_bus']])
self.G.add_weighted_edges_from(
dps_uf.combine_recarrays(ps.lines, line_admittances)[['from_bus', 'to_bus', 'Y']])
self.G.add_weighted_edges_from(
dps_uf.combine_recarrays(ps.transformers, trafo_admittances)[['from_bus', 'to_bus', 'Y']])
self.grid_layout()
self.n_edges = len(ps.lines) + len(ps.transformers)
self.edge_from_bus = np.concatenate([dps_uf.lookup_strings(type_['from_bus'], ps.buses['name']) for type_ in [ps.lines, ps.transformers]])
self.edge_to_bus = np.concatenate([dps_uf.lookup_strings(type_['to_bus'], ps.buses['name']) for type_ in [ps.lines, ps.transformers]])
self.edge_x = np.vstack([self.x[self.edge_from_bus], self.x[self.edge_to_bus]]).T
self.edge_y = np.vstack([self.y[self.edge_from_bus], self.y[self.edge_to_bus]]).T
self.edge_z = np.vstack([self.z[self.edge_from_bus], self.z[self.edge_to_bus]]).T
self.colors = lambda i: pg.intColor(i, hues=9, values=1, maxValue=255, minValue=150, maxHue=360, minHue=0, sat=255, alpha=255)
self.window = gl.GLViewWidget()
# self.window.setBackgroundColor('w')
self.window.setWindowTitle('Grid')
self.window.setGeometry(0, 110, 1920, 1080)
self.window.setCameraPosition(distance=30, elevation=12)
self.window.show()
self.rotating = rotating
self.gz = gl.GLGridItem()
self.gz.translate(dx=0, dy=0, dz=-self.offset_z)
self.window.addItem(self.gz)
color = np.ones((ps.n_bus, 4))
color[:, -1] = 0.5
if use_colors:
color[ps.gen_bus_idx, :] = np.array([self.colors(i).getRgb() for i in range(self.ps.n_gen_bus)]) / 255
else:
color[ps.gen_bus_idx, :] = np.array([1 / 3, 2 / 3, 1, 0.5])[None, :]
self.points = gl.GLScatterPlotItem(
pos=np.vstack([self.x, self.y, self.z]).T,
color=color,
size=15
)
self.edge_x_mod = np.append(self.edge_x, np.nan*np.ones((self.n_edges, 1)), axis=1)
self.edge_y_mod = np.append(self.edge_y, np.nan*np.ones((self.n_edges, 1)), axis=1)
self.edge_z_mod = np.append(self.edge_z, np.nan*np.ones((self.n_edges, 1)), axis=1)
# line_x_mod = line_x
# line_y_mod = line_y
edge_pos = np.vstack([self.edge_x_mod.flatten(), self.edge_y_mod.flatten(), self.edge_z_mod.flatten()]).T
line_color = np.ones((self.n_edges, 4))
line_color[:, -1] = 0.5
line_color[len(ps.lines):, :] = np.array([1 / 3, 2 / 3, 1, 0.5])[None, :]
# self.scale_branch_flows = 4
line_widths = np.ones((self.n_edges, 4))
self.lines = gl.GLLinePlotItem(pos=edge_pos, color=np.repeat(line_color, 3, axis=0), antialias=True, width=2)
self.window.addItem(self.points)
self.window.addItem(self.lines)
# self.axis = gl.GLAxisItem()
# self.graphWidget.show()
self.timer = QtCore.QTimer()
self.timer.timeout.connect(self.update)
self.timer.start(1000//update_freq)
self.t_prev = time.time()
for index in range(1, len(sPi)): # Build the plot series
if index == 1:
print('Decimal Point skipped')
else:
x.append(float(xDict[int(sPi[index])]) + x[index - 2])
y.append(float(yDict[int(sPi[index])]) + y[index - 2])
# create plot
pg.setConfigOption('background', 'w')
pg.intColor(index,
hues=9,
values=1,
maxValue=255,
minValue=150,
maxHue=360,
minHue=0,
sat=255,
alpha=255)
print()
plt = pg.plot(x,
y,
title=theTitle,
pen=pg.mkPen(cosmetic=True, width=1.2,
color='b')) #, symbol='.')
plt.showGrid(x=True, y=True)
plt.hideAxis('left')
plt.hideAxis('bottom')
## Start Qt event loop.
def _update_plots(self):
sweeps = self.sweeps
self.current_event_set = None
self.event_table.clear()
# clear all plots
self.pre_plot.clear()
self.post_plot.clear()
pre = self.params['pre']
post = self.params['post']
# If there are no selected sweeps or channels have not been set, return
if len(sweeps) == 0 or pre == post or pre not in self.channels or post not in self.channels:
return
pre_mode = sweeps[0][pre].clamp_mode
post_mode = sweeps[0][post].clamp_mode
for ch, mode, plot in [(pre, pre_mode, self.pre_plot), (post, post_mode, self.post_plot)]:
units = 'A' if mode == 'vc' else 'V'
plot.setLabels(left=("Channel %d" % ch, units), bottom=("Time", 's'))
# Iterate over selected channels of all sweeps, plotting traces one at a time
# Collect information about pulses and spikes
pulses = []
spikes = []
post_traces = []
for i,sweep in enumerate(sweeps):
pre_trace = sweep[pre]['primary']
post_trace = sweep[post]['primary']
# Detect pulse times
stim = sweep[pre]['command'].data
sdiff = np.diff(stim)
on_times = np.argwhere(sdiff > 0)[1:, 0] # 1: skips test pulse
off_times = np.argwhere(sdiff < 0)[1:, 0]
pulses.append(on_times)
# filter data
post_filt = self.artifact_remover.process(post_trace, list(on_times) + list(off_times))
post_filt = self.baseline_remover.process(post_filt)
post_filt = self.filter.process(post_filt)
post_traces.append(post_filt)
# plot raw data
color = pg.intColor(i, hues=len(sweeps)*1.3, sat=128)
color.setAlpha(128)
for trace, plot in [(pre_trace, self.pre_plot), (post_filt, self.post_plot)]:
plot.plot(trace.time_values, trace.data, pen=color, antialias=False)
# detect spike times
spike_times = []
spike_info = []
for on, off in zip(on_times, off_times):
spikes = detect_evoked_spikes(sweep[pre], [on, off])
spike_info.append(spikes)
for spike in spikes:
if spike['max_slope_time'] is None:
continue
spike_times.append(spike['max_slope_time'])
spikes.append(spike_info)
dt = pre_trace.dt
vticks = pg.VTickGroup(spike_times, yrange=[0.0, 0.2], pen=color)
self.pre_plot.addItem(vticks)
# Iterate over spikes, plotting average response
all_responses = []
avg_responses = []
fits = []
fit = None
npulses = max(map(len, pulses))
self.response_plots.clear()
self.response_plots.set_shape(1, npulses+1) # 1 extra for global average
self.response_plots.setYLink(self.response_plots[0,0])
for i in range(1, npulses+1):
self.response_plots[0,i].hideAxis('left')
units = 'A' if post_mode == 'vc' else 'V'
self.response_plots[0, 0].setLabels(left=("Averaged events (Channel %d)" % post, units))
fit_pen = {'color':(30, 30, 255), 'width':2, 'dash': [1, 1]}
for i in range(npulses):
# get the chunk of each sweep between spikes
responses = []
all_responses.append(responses)
for j, sweep in enumerate(sweeps):
# get the current spike
if i >= len(spikes[j]):
continue
spike = spikes[j][i]
if spike is None:
continue
# find next spike
next_spike = None
for sp in spikes[j][i+1:]:
if sp is not None:
next_spike = sp
break
# determine time range for response
max_len = int(40e-3 / dt) # don't take more than 50ms for any response
start = spike['rise_index']
if next_spike is not None:
stop = min(start + max_len, next_spike['rise_index'])
else:
stop = start + max_len
# collect data from this trace
trace = post_traces[j]
d = trace.data[start:stop].copy()
responses.append(d)
if len(responses) == 0:
continue
# extend all responses to the same length and take nanmean
avg = ragged_mean(responses, method='clip')
avg -= float_mode(avg[:int(1e-3/dt)])
avg_responses.append(avg)
# plot average response for this pulse
start = np.median([sp[i]['rise_index'] for sp in spikes if sp[i] is not None]) * dt
t = np.arange(len(avg)) * dt
self.response_plots[0,i].plot(t, avg, pen='w', antialias=True)
# fit!
fit = self.fit_psp(avg, t, dt, post_mode)
fits.append(fit)
# let the user mess with this fit
curve = self.response_plots[0,i].plot(t, fit.eval(), pen=fit_pen, antialias=True).curve
curve.setClickable(True)
curve.fit = fit
curve.sigClicked.connect(self.fit_curve_clicked)
# display global average
global_avg = ragged_mean(avg_responses, method='clip')
t = np.arange(len(global_avg)) * dt
self.response_plots[0,-1].plot(t, global_avg, pen='w', antialias=True)
global_fit = self.fit_psp(global_avg, t, dt, post_mode)
self.response_plots[0,-1].plot(t, global_fit.eval(), pen=fit_pen, antialias=True)
# display fit parameters in table
events = []
for i,f in enumerate(fits + [global_fit]):
if f is None:
continue
if i >= len(fits):
vals = OrderedDict([('id', 'avg'), ('spike_time', np.nan), ('spike_stdev', np.nan)])
else:
spt = [s[i]['peak_index'] * dt for s in spikes if s[i] is not None]
vals = OrderedDict([('id', i), ('spike_time', np.mean(spt)), ('spike_stdev', np.std(spt))])
vals.update(OrderedDict([(k,f.best_values[k]) for k in f.params.keys()]))
events.append(vals)
self.current_event_set = (pre, post, events, sweeps)
self.event_set_list.setCurrentRow(0)
self.event_set_selected()
def analyze(self):
if self.plotlist != [[], [], [], [], []]:
for x in self.plotlist:
self.p1.getRoiPlot().removeItem(x)
self.plotlist = [[], [], [], [], []]
dntpnames = ["dCTP", "dATP", "dGTP", "dTTP"]
dntps = [[], [], [], []]
zpro = [[], [], [], []]
n = len(dntps)
lz, lx, ly = self.stack.shape
seq = self.stack.reshape(lz, lx * ly)
for i, x in enumerate(dntpnames):
fn = [
filename for filename in os.listdir(self.direc)
if filename.startswith(x) and filename.endswith('.h5')
]
hfile = h5py.File(self.direc + os.sep + fn[-1])
# print self.direc + os.sep+ fn[-1]
dntps[i] = np.array(hfile["images"]).astype(float)
if self.roip1 != []:
dntps[i] = dntps[i][:, self.roip1[1]:self.roip2[1] + 1,
self.roip1[0]:self.roip2[0] + 1]
# if self.filtertype != []:
dntps[i] = dntps[i][100:900]
dntps[i] -= np.mean(dntps[i])
dntps[i] = (dntps[i] / dntps[i].std())
zpro[i] = np.median(dntps[i], 0)
zpro[0] -= np.mean(zpro[0])
zpro[1] -= np.mean(zpro[1])
zpro[1] -= np.mean(zpro[2])
zpro[2] -= np.mean(zpro[3])
cscore = ascore = gscore = tscore = np.array(())
scores = [cscore, ascore, gscore, tscore]
total = []
for i, x in enumerate(scores):
x = np.dot(seq, zpro[i].ravel())
x = (x - x.mean()) / x.std()
if i == 0:
total = x**2
else:
total = total + x**2
color = pg.intColor(i, hues=4)
scores[i] = x
self.plotlist[i] = self.p1.getRoiPlot().plot(x - np.median(x),
pen=color)
self.p1.getRoiPlot().setRange(yRange=[-4, 10])
scores = pd.DataFrame(np.transpose(scores))
tot = abs(scores[0] + scores[1] - scores[2] - scores[3])
predictedseq = np.zeros(len(tot))
predictedseq[np.array(scores.idxmax(axis=1) == 0)] = 1
predictedseq[np.array(scores.idxmax(axis=1) == 1)] = 2
predictedseq[np.array(scores.idxmax(axis=1) == 2)] = 3
predictedseq[np.array(scores.idxmax(axis=1) == 3)] = 4
predictedseq[np.array(
tot < np.median(predictedseq) + np.std(predictedseq))] = 0
self.plotlist[4] = self.p1.getRoiPlot().plot(predictedseq,
pen=pg.mkPen('w',
width=3))
expts = ExperimentList(cache='expts_cache.pkl')
dates = [(e.date - expts[0].date).days for e in expts]
ud = list(np.unique(dates))
days = [ud.index(d) for d in dates]
probed = np.array([e.n_connections_probed for e in expts])
found = np.array([e.n_connections for e in expts])
ctypes = [tuple(exp.cre_types) for exp in expts]
n_ctypes = len(set(ctypes))
ctype_colors = {}
for exp in expts:
ct = tuple(exp.cre_types)
color = pg.intColor(len(ctype_colors), hues=6, values=2, minValue=100)
ctype_colors.setdefault(ct, pg.mkBrush(color))
expt_colors = [ctype_colors[ct] for ct in ctypes]
p1 = pg.plot(
dates,
np.cumsum(probed),
symbol='o',
symbolBrush=expt_colors,
symbolPen=None,
title="Connections probed over time (including no-experiment days)")
p1 = pg.plot(days,
np.cumsum(probed),
symbol='o',
def myLayout(self):
self.layout = QtGui.QVBoxLayout(self) #the whole window, main layout
self.inputLayout = QtGui.QGridLayout()
self.plotLayout = QtGui.QGridLayout()
self.layout.addLayout(self.inputLayout)
self.layout.addLayout(self.plotLayout)
self.m_button = QtGui.QSpinBox()
self.m_button.setRange(-50, 50)
self.m_button.setValue(0)
self.inputLayout.addWidget(self.m_button, 1, 0)
self.inputLayout.addWidget(QtGui.QLabel("Zernike m"), 0, 0)
self.n_button = QtGui.QSpinBox()
self.n_button.setValue(2)
self.inputLayout.addWidget(self.n_button, 1, 1)
self.inputLayout.addWidget(QtGui.QLabel("Zernike n"), 0, 1)
self.m_button.editingFinished.connect(self.worker_calc_zernike)
self.n_button.editingFinished.connect(self.worker_calc_zernike)
self.scatterPlotItem1 = pg.ScatterPlotItem(size=30,
pen=pg.mkPen(None),
brush=pg.intColor(2))
ah = 0.5
hh = ah * np.sqrt(3) / 2.0
hpoint1 = QtCore.QPointF(0, -ah)
hpoint2 = QtCore.QPointF(hh, -ah / 2)
hpoint3 = QtCore.QPointF(hh, ah / 2)
hpoint4 = QtCore.QPointF(0, ah)
hpoint5 = QtCore.QPointF(-hh, ah / 2)
hpoint6 = QtCore.QPointF(-hh, -ah / 2)
hexagonShape = QtGui.QPolygonF(
[hpoint1, hpoint2, hpoint3, hpoint4, hpoint5, hpoint6])
spotShape = QtGui.QPainterPath()
spotShape.addPolygon(hexagonShape)
#self.scatterPlotItem1.Symbols['h'] = hexagonShape
self.scatterPlotItem1.setData(symbol=spotShape)
self.graphWindow1 = pg.GraphicsLayoutWidget()
self.graphWindow2 = pg.GraphicsLayoutWidget()
self.graphWindow3 = pg.GraphicsLayoutWidget()
self.graphWindow4 = pg.GraphicsLayoutWidget()
#self.graphWindow.setSizePolicy(QtGui.QSizePolicy.Expanding,QtGui.QSizePolicy.Expanding)
self.plotLayout.addWidget(self.graphWindow1, 0, 0)
self.plotLayout.addWidget(self.graphWindow2, 0, 1)
self.plotLayout.addWidget(self.graphWindow3, 1, 0)
self.plotLayout.addWidget(self.graphWindow4, 1, 1)
view1 = self.graphWindow1.addViewBox()
view1.setAspectLocked(True)
self.img1 = pg.ImageItem(border='w')
#self.scatterPlotItem1.addPoints(self.electrodeCoordinates[:,0]*self.x_points/2.0/self.laserSpotSizeScale+self.x_points/2, self.electrodeCoordinates[:,1]*self.y_points/2.0/self.laserSpotSizeScale+self.y_points/2)
view1.addItem(self.img1)
view1.addItem(self.scatterPlotItem1)
view2 = self.graphWindow2.addViewBox()
view2.setAspectLocked(True)
self.img2 = pg.ImageItem(border='w')
self.scatterPlotItem1.addPoints(
self.electrodeCoordinates[:, 0] * self.x_points /
self.laserSpotSizeScale + self.x_points / 2,
self.electrodeCoordinates[:, 1] * self.y_points /
self.laserSpotSizeScale + self.y_points / 2)
view2.addItem(self.img2)
view3 = self.graphWindow3.addViewBox()
view3.setAspectLocked(True)
self.img3 = pg.ImageItem(border='w')
self.scatterPlotItem1.addPoints(
self.electrodeCoordinates[:, 0] * self.x_points /
self.laserSpotSizeScale + self.x_points / 2,
self.electrodeCoordinates[:, 1] * self.y_points /
self.laserSpotSizeScale + self.y_points / 2)
view3.addItem(self.img3)
view4 = self.graphWindow4.addViewBox()
view4.setAspectLocked(True)
self.img4 = pg.ImageItem(border='w')
self.scatterPlotItem1.addPoints(
self.electrodeCoordinates[:, 0] * self.x_points /
self.laserSpotSizeScale + self.x_points / 2,
self.electrodeCoordinates[:, 1] * self.y_points /
self.laserSpotSizeScale + self.y_points / 2)
view4.addItem(self.img4)
#
#self.spots = QtGui.QGraphicsWidget()
#self.spots.data(0)
#self.graphWindow.addItem(self.spots,{'pos': self.electrodeCoordinates[1], 'data': 1, 'brush':pg.intColor(2), 'symbol': 'o', 'size': 50})
#=======================================================================
# spots = {'pos': self.electrodeCoordinates[1], 'data': 1, 'brush':pg.intColor(2), 'symbol': 'o', 'size': 50}
# #for i in range(0,3):
# # spots.append({'pos': self.electrodeCoordinates[i], 'data': 1, 'brush':pg.intColor(2), 'symbol': 'o', 'size': 50})
#
#=======================================================================
self.calc_zernike()
def show_pg(self, cell=None, rmponly=False):
print("rmpvalue : ")
print(rmponly)
"""
Plot results from run_iv()
Using pyqtgraph.
Parameters
----------
cell : cell object (default: None)
"""
#
# Generate figure with subplots
# note that some of the plot windows are not used... maybe later
#
app = pg.mkQApp()
win = pg.GraphicsWindow() #'%s %s (%s)' % (cell.status['name'], cell.status['modelType'], cell.status['species']))
self.win = win
win.resize(1000, 800)
Vplot = win.addPlot(labels={'left': 'Vm (mV)', 'bottom': 'Time (ms)'})
rightGrid = win.addLayout(rowspan=2)
win.nextRow()
PostCellPlot = win.addPlot(labels={'left': 'Ipost (nA)', 'bottom': 'Time (ms)'})
win.nextRow()
Iplot = win.addPlot(labels={'left': 'Iinj (nA)', 'bottom': 'Time (ms)'})
# right side:
IVplot = rightGrid.addPlot(labels={'left': 'Vm (mV)', 'bottom': 'Icmd (nA)'})
IVplot.showGrid(x=True, y=True)
rightGrid.nextRow()
spikePlot = rightGrid.addPlot(labels={'left': 'Iinj (nA)', 'bottom': 'Spike times (ms)'})
rightGrid.nextRow()
FIplot = rightGrid.addPlot(labels={'left': 'Spike count', 'bottom': 'Iinj (nA)'})
win.ci.layout.setRowStretchFactor(0, 10)
win.ci.layout.setRowStretchFactor(1, 5)
#
# Plot the simulation results
#
Vm = self.sgc_voltage_traces
Iinj = self.current_traces
# Icmd = self.current_cmd
DVm = self.axon_voltage_traces
post = self.post_cell_current_traces
calyxca = self.calyx_ca
t = self.time_values
steps = len(Iinj)
# plot I, V traces
colors = [(i, steps*3./2.) for i in range(steps)]
# plot all the stimuli
for i in range(steps):
Vplot.plot(t, Vm[i], pen='w')
#Iplot.plot(t, Iinj[i], pen=colors[i]) # that was the current pulses
Iplot.plot(t[:len(calyxca[i])], calyxca[i], pen='y') # calcium is more interesting
PostCellPlot.plot(t, post[i], pen=colors[i])
if len(DVm) == 0:
continue
nnodes = len(DVm[i])
axcolors = [pg.intColor(k, nnodes) for k in range(nnodes)]
for j in range(len(DVm[i])): # for each site
if j in range(nnodes): #[1, nnodes-1]:
ilen = len(DVm[i][j])
Vplot.plot(t[:ilen], DVm[i][j], pen=axcolors[j])
trange = [0,140]
xmin = trange[0]
xmax = trange[1]
Vplot.setXRange(xmin, xmax)
print("rescaled voltage")
Iplot.setXRange(xmin, xmax)
PostCellPlot.setXRange(xmin, xmax)
Iplot.setXLink(Vplot)
PostCellPlot.setXLink(Vplot)
if rmponly:
print("In this condition")
return
data[0] += 5
data[1] += 7
data[2] += 5
data[3] = 10 + data[3] * 2
## Make bar graph
#bar = pg.BarGraphItem(x=range(4), height=data.mean(axis=1), width=0.5, brush=0.4)
#win.addItem(bar)
## add scatter plots on top
for i in range(4):
xvals = pg.pseudoScatter(data[i], spacing=0.4, bidir=True) * 0.2
win.plot(x=xvals + i,
y=data[i],
pen=None,
symbol='o',
symbolBrush=pg.intColor(i, 6, maxValue=128))
## Make error bars
err = pg.ErrorBarItem(x=np.arange(4),
y=data.mean(axis=1),
height=data.std(axis=1),
beam=0.5,
pen={
'color': 'w',
'width': 2
})
#win.addItem(err)
## Start Qt event loop unless running in interactive mode or using pyside.
def get_color(i, j, data):
x = data.iloc[i][data.columns[j]]
return pg.intColor(int((x + 1) / 2 * 1000), 1000)
def __init__(self,
settings: Settings,
data_model: DataModel,
parent: Optional[QWidget] = None,
*args: Any) -> None:
super().__init__(parent, *args)
self.setObjectName('plot_dialog')
self.settings: Settings = settings
self.setModal(True)
self.setWindowTitle(self.tr('Plot'))
if parent is not None:
self.setWindowIcon(parent.windowIcon())
layout: QHBoxLayout = QHBoxLayout(self)
controls_panel: QWidget = QWidget(self)
layout.addWidget(controls_panel)
controls_layout: QFormLayout = QFormLayout(controls_panel)
plot: pg.PlotWidget = pg.PlotWidget(self)
canvas: pg.PlotItem = plot.getPlotItem()
canvas.setAxisItems({'bottom': pg.DateAxisItem()})
layout.addWidget(plot)
layout.setStretch(0, 0)
cursor_balloon: pg.TextItem = pg.TextItem()
plot.addItem(cursor_balloon, True) # ignore bounds
def on_mouse_moved(event: Tuple[QPointF]) -> None:
pos: QPointF = event[0]
if plot.sceneBoundingRect().contains(pos):
point: QPointF = canvas.vb.mapSceneToView(pos)
if plot.visibleRange().contains(point):
cursor_balloon.setPos(point)
cursor_balloon.setText(
f'{datetime.fromtimestamp(round(point.x()))}\n{point.y()}'
)
balloon_border: QRectF = cursor_balloon.boundingRect()
sx: float
sy: float
sx, sy = canvas.vb.viewPixelSize()
balloon_width: float = balloon_border.width() * sx
balloon_height: float = balloon_border.height() * sy
anchor_x: float = 0.0 if point.x() - plot.visibleRange(
).left() < balloon_width else 1.0
anchor_y: float = 0.0 if plot.visibleRange().bottom(
) - point.y() < balloon_height else 1.0
cursor_balloon.setAnchor((anchor_x, anchor_y))
cursor_balloon.setVisible(True)
else:
cursor_balloon.setVisible(False)
else:
cursor_balloon.setVisible(False)
self._mouse_moved_signal_proxy: pg.SignalProxy = pg.SignalProxy(
plot.scene().sigMouseMoved, rateLimit=10, slot=on_mouse_moved)
header: str
column: np.ndarray
visibility: bool
self.lines: List[pg.PlotDataItem] = []
self.color_buttons: List[pg.ColorButton] = []
visible_columns_count: int = 0
visible_headers: List[str] = []
for header, column, visibility in zip(
data_model.header, data_model.all_data,
self.settings.check_items_values):
if not (visibility and (self.settings.show_all_zero_columns
or not np.alltrue((column == 0.0) | np.isnan(column)))) \
or header.endswith(('(s)', '(sec)', '(secs)')):
continue
else:
visible_columns_count += 1
visible_headers.append(header)
def set_line_color(sender: pg.ColorButton) -> None:
index: int = self.color_buttons.index(sender)
self.lines[index].setPen(sender.color())
self.settings.line_colors[visible_headers[index]] = sender.color()
for header, column, visibility in zip(
data_model.header, data_model.all_data,
self.settings.check_items_values):
if not (visibility and (self.settings.show_all_zero_columns
or not np.alltrue((column == 0.0) | np.isnan(column)))) \
or header.endswith(('(s)', '(sec)', '(secs)')):
continue
color: QColor = self.settings.line_colors.get(
header, pg.intColor(len(self.lines),
hues=visible_columns_count))
self.color_buttons.append(pg.ColorButton(controls_panel, color))
controls_layout.addRow(header, self.color_buttons[-1])
self.lines.append(
canvas.plot(np.column_stack((data_model.all_data[0], column)),
name=header,
pen=color))
self.color_buttons[-1].sigColorChanged.connect(set_line_color)
self.settings.beginGroup('plot')
window_settings: bytes = self.settings.value('geometry')
if window_settings is not None:
self.restoreGeometry(window_settings)
self.settings.endGroup()
for p in lastClicked:
p.resetPen()
for p in points:
print('Pos: ', p.pos())
p.setPen('b', width=2)
lastClicked = points
n = 20
w = view.addViewBox()
s = pg.ScatterPlotItem(size=10, pen=pg.mkPen('w'))
pos = np.linspace(0, 100, n)
spots = [{
'pos': (0, pos[i]),
'data': 1,
'brush': pg.intColor(i),
'symbol': 1,
'size': 10
} for i in range(n)]
s.addPoints(spots)
w.addItem(s)
s.sigClicked.connect(clicked)
if __name__ == '__main__':
QtGui.QApplication.instance().exec_()
import pyqtgraph as pg
import pyqtgraph.opengl
class MyView(pg.opengl.GLViewWidget):
for p in points:
p.setPen('b', width=2)
lastClicked = points
s1.sigClicked.connect(clicked)
# 2) Spots are transform-invariant, but not identical (top-right plot).
# In this case, drawing is almsot as fast as 1), but there is more startup
# overhead and memory usage since each spot generates its own pre-rendered
# image.
s2 = pg.ScatterPlotItem(size=10, pen=pg.mkPen('w'), pxMode=True)
pos = np.random.normal(size=(2, n), scale=1e-5)
spots = [{'pos': pos[:, i], 'data': 1, 'brush':pg.intColor(
i, n), 'symbol': i % 5, 'size': 5+i/10.} for i in range(n)]
s2.addPoints(spots)
w2.addItem(s2)
s2.sigClicked.connect(clicked)
# 3) Spots are not transform-invariant, not identical (bottom-left).
# This is the slowest case, since all spots must be completely re-drawn
# every time because their apparent transformation may have changed.
# Set pxMode=False to allow spots to transform with the view
s3 = pg.ScatterPlotItem(pxMode=False)
spots3 = []
for i in range(10):
for j in range(10):
spots3.append({'pos': (1e-6*i, 1e-6*j), 'size': 1e-6,
def __init__(self, model_runner):
QtGui.QWidget.__init__(self)
self.layout = QtGui.QGridLayout()
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
self.slicer = NDSlicer(model_runner.param_space.axes())
self.slicer.selection_changed.connect(self.selection_changed)
self.layout.addWidget(self.slicer)
# set up a few default 2D slicer views
v1 = self.slicer.params.child('2D views').addNew()
v1['axis 0'] = 'n_release_sites'
v1['axis 1'] = 'base_release_probability'
v2 = self.slicer.params.child('2D views').addNew()
v2['axis 0'] = 'depression_amount'
v2['axis 1'] = 'base_release_probability'
self.slicer.dockarea.moveDock(v2.viewer.dock, 'bottom', v1.viewer.dock)
v3 = self.slicer.params.child('2D views').addNew()
v3['axis 0'] = 'depression_tau'
v3['axis 1'] = 'base_release_probability'
v4 = self.slicer.params.child('2D views').addNew()
v4['axis 0'] = 'facilitation_amount'
v4['axis 1'] = 'base_release_probability'
self.slicer.dockarea.moveDock(v4.viewer.dock, 'bottom', v3.viewer.dock)
self.result_widget = ModelSingleResultWidget()
self.result_dock = pg.dockarea.Dock('model results')
self.result_dock.addWidget(self.result_widget)
self.slicer.dockarea.addDock(self.result_dock, 'bottom')
# turn on max projection for all parameters by default
for ch in self.slicer.params.child('max project'):
if ch.name() == 'synapse':
continue
ch.setValue(True)
self.model_runner = model_runner
self.param_space = model_runner.param_space
# result_img = np.zeros(self.param_space.result.shape)
# for ind in np.ndindex(result_img.shape):
# result_img[ind] = self.param_space.result[ind].likelihood
result_img = self.param_space.result['likelihood']
self.slicer.set_data(result_img)
self.results = result_img
# select best result
best = np.unravel_index(np.argmax(result_img), result_img.shape)
self.select_result(best)
max_like = self.results.max()
# if results are combined across synapses, set up colors
if 'synapse' in self.param_space.params:
self.slicer.params['color axis', 'axis'] = 'synapse'
syn_axis = list(self.param_space.params.keys()).index('synapse')
max_img = np.array([result_img.take(i, axis=syn_axis).max() for i in range(result_img.shape[syn_axis])])
max_like = max_img.min()
max_img = max_img.min() / max_img
syns = self.param_space.params['synapse']
for i in syns:
c = pg.colorTuple(pg.intColor(i, len(syns)*1.2))
c = pg.mkColor(c[0]*max_img[i], c[1]*max_img[i], c[2]*max_img[i])
self.slicer.params['color axis', 'colors', str(i)] = c
# set histogram range
self.slicer.histlut.setLevels(max_like * 0.85, max_like)
def _get_color(self, index):
''' Returns incremental plot colors based on index '''
return pg.intColor(index, minValue=self.plot_min_value, maxValue=self.plot_max_value,
hues=self.distinct_plot_hues, minHue=self.plot_min_hue, maxHue=self.plot_max_hue)
def makeMultiplePlots():
## if (sys.flags.interactive != 1) or not hasattr(QtCore, 'PYQT_VERSION'):
## QtGui.QApplication.instance().exec_()
app = QtGui.QApplication([])
mw = QtGui.QMainWindow()
mw.resize(800,800)
view = pg.GraphicsLayoutWidget() ## GraphicsView with GraphicsLayout inserted by default
mw.setCentralWidget(view)
mw.show()
mw.setWindowTitle('pyqtgraph example: ScatterPlot')
## create four areas to add plots
w1 = view.addPlot()
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
s1.sigClicked.connect(clicked)
## 2) Spots are transform-invariant, but not identical (top-right plot).
## In this case, drawing is as fast as 1), but there is more startup overhead
## and memory usage since each spot generates its own pre-rendered image.
s2 = pg.ScatterPlotItem(size=10, pen=pg.mkPen('w'), pxMode=True)
pos = np.random.normal(size=(2,n), scale=1e-5)
spots = [{'pos': pos[:,i], 'data': 1, 'brush':pg.intColor(i, n), 'symbol': i%5, 'size': 5+i/10.} for i in range(n)]
s2.addPoints(spots)
w2.addItem(s2)
s2.sigClicked.connect(clicked)
## 3) Spots are not transform-invariant, not identical (bottom-left).
## This is the slowest case, since all spots must be completely re-drawn
## every time because their apparent transformation may have changed.
s3 = pg.ScatterPlotItem(pxMode=False) ## Set pxMode=False to allow spots to transform with the view
spots3 = []
for i in range(10):
for j in range(10):
spots3.append({'pos': (1e-6*i, 1e-6*j), 'size': 1e-6, 'pen': {'color': 'w', 'width': 2}, 'brush':pg.intColor(i*10+j, 100)})
s3.addPoints(spots3)
w3.addItem(s3)
s3.sigClicked.connect(clicked)
## Test performance of large scatterplots
s4 = pg.ScatterPlotItem(size=10, pen=pg.mkPen(None), brush=pg.mkBrush(255, 255, 255, 20))
pos = np.random.normal(size=(2,10000), scale=1e-9)
s4.addPoints(x=pos[0], y=pos[1])
w4.addItem(s4)
s4.sigClicked.connect(clicked)
def setup(self):
self.has_turbo = 'tc110_turbo' in self.app.hardware
if self.has_turbo:
self.turbo_names = []
for name in ['prep', 'ion', 'nano']:
for x in ['speed', 'power', 'temp']:
self.turbo_names.append(name + "_" + x)
self.settings.New('delta_t',
dtype=float,
unit='s',
vmin=0.0,
initial=1.0)
self.settings.New('save_h5', dtype=bool, initial=True)
#display
self.settings.New('show_last', dtype=int, initial=-1)
self.names = names = ('Prep', 'Nano')
for name in self.names:
self.settings.New(name + "_pressure",
dtype=float,
ro=True,
si=True,
unit="Bar")
#self.settings.New('start_time', dtype=str, ro=True, initial = datestring())
self.settings.New('ADC_channels', dtype=str, initial='9215A/ai0:1')
self.settings.New('TC_channels', dtype=str, initial='cDAQ1-9211/ai0:1')
#setup gui
self.ui = QtWidgets.QWidget()
self.layout = QtWidgets.QHBoxLayout()
self.ui.setLayout(self.layout)
self.control_widget = QtWidgets.QGroupBox(self.name)
self.layout.addWidget(self.control_widget, stretch=0)
self.control_widget.setLayout(QtWidgets.QVBoxLayout())
self.start_button = QtWidgets.QPushButton("Start")
self.control_widget.layout().addWidget(self.start_button)
self.stop_button = QtWidgets.QPushButton("Stop")
self.control_widget.layout().addWidget(self.stop_button)
self.start_button.clicked.connect(self.start)
self.stop_button.clicked.connect(self.interrupt)
self.control_widget.layout().addWidget(\
self.settings.New_UI(exclude=['activation','progress','profile']))
self.control_widget.layout().addWidget(\
self.app.settings.New_UI())
self.graph_layout = pg.GraphicsLayoutWidget(border=(100, 100, 100))
self.layout.addWidget(self.graph_layout, stretch=1)
self.ui.show()
self.ui.setWindowTitle("auger_pressure_history")
self.NUM_CHANS = 2
self.TC_CHAN_NAMES = ['oven_air', 'vac_system']
self.TC_CHANS = 2
self.plots = []
#ion gauge pressure display
axis = DateAxis(orientation='bottom')
self.pressure_plot = plot = self.graph_layout.addPlot(
title="Pressure", axisItems={'bottom': axis})
plot.setLogMode(y=True)
plot.setYRange(-11, -6)
plot.showGrid(y=True, x=True, alpha=1.0)
plot.addLegend()
self.plots.append(plot)
self.pressure_plot_lines = []
for i in range(self.NUM_CHANS):
color = pg.intColor(i)
plot_line = self.pressure_plot.plot(pen=pg.mkPen(color, width=4),
name=names[i],
autoDownsample=True)
self.pressure_plot_lines.append(plot_line)
self.graph_layout.nextRow()
#turbo status display
self.turbo_plot = self.graph_layout.addPlot(title="Turbo",
axisItems={'bottom': axis})
self.turbo_plot.showGrid(y=True, x=True, alpha=1.0)
self.turbo_plot.addLegend()
self.turbo_plot_lines = dict()
for name in self.turbo_names:
if 'prep' in name:
color = 'r'
elif 'ion' in name:
color = 'y'
else:
color = 'w'
if 'speed' in name:
width = 4
style = 1
elif 'power' in name:
style = 2
width = 2
else:
style = style = 3
width = 1
self.turbo_plot_lines[name] = self.turbo_plot.plot(
pen=pg.mkPen(color=color, width=width),
name=name,
autoDownsample=True)
def __init__(self,filename,env,parent=None):
super(overview,self).__init__(parent)
pg.setConfigOption('background', 'w')
pg.setConfigOption('foreground', 'k')
self.fileName=filename
self.setWindowTitle("Overview Signal")
self.showMaximized()
self.env=env
p1=self.addPlot(title='Current Big coils')
self.nextRow()
p2=self.addPlot(title='Pressure')
self.nextRow()
p3=self.addPlot(title='Helicon power')
self.nextRow()
p4=self.addPlot(title='ICRF power')
self.nextRow()
p5=self.addPlot(title='Density Langmuir probe')
self.nextRow()
p6=self.addPlot(title='Amplitude B-dot probes')
self.nextRow()
p7=self.addPlot(title='Phase B-dot probes')
indexColor=0
for x in self.fileName:
try:
timeCoils,dataCoils,sampling=readHdf5.getData(x,'S7/Big_coil_I [A]',env)
except:
pass
try:
timeP,dataP,sampling=readHdf5.getData(x,'S7/vacuum [mbar]',env)
except:
pass
try:
timeHF,dataHF,sampling=readHdf5.getData(x,'Generator/Fpower',env)
except:
pass
try:
timeHR,dataHR,sampling=readHdf5.getData(x,'Generator/Rpower',env)
except:
pass
try:
timeIF,dataIF,sampling=readHdf5.getData(x,'PXI M6251/IC_fwd',env)
except:
pass
try:
timeIR,dataIR,sampling=readHdf5.getData(x,'PXI M6251/IC_ref',env)
except:
pass
try:
dataL=np.array(readHdf5.getDataProcess(x,'Process/Langmuir_dens',env))
timeL=np.array(readHdf5.getDataProcess(x,'Process/Langmuir_time',env))
except:
pass
try:
timeFW,dataFW,sampling=readHdf5.getData(x,'PXI M6251/U_fast',env)
except:
pass
try:
timeSW,dataSW,sampling=readHdf5.getData(x,'PXI M6251/U_slow',env)
except:
pass
try:
timePhase1,dataPhase1,sampling=readHdf5.getData(x,'PXI M6251/Phi_fast',env)
except:
pass
try:
timePhase2,dataPhase2,sampling=readHdf5.getData(x,'PXI M6251/Phi_slow',env)
except:
pass
pencil=pg.mkPen(color=pg.intColor(indexColor))
try:
p1.plot(timeCoils,dataCoils,pen=pencil)
except:
pass
try:
p2.plot(timeP,dataP,pen=pencil)
except:
pass
try:
p3.plot(timeHF,dataHF,pen=pencil)
p3.plot(timeHR,dataHR,pen=pencil)
except:
pass
try:
p4.plot(timeIF,dataIF,pen=pencil)
p4.plot(timeIR,dataIR,pen=pencil)
except:
pass
try:
p5.plot(timeL,dataL,pen=pencil)
except:
pass
try:
p6.plot(timeFW,dataFW,pen=pencil)
p6.plot(timeSW,dataSW,pen=pencil)
except:
pass
try:
p7.plot(timePhase1,dataPhase1-dataPhase2,pen=pencil)
except:
pass
indexColor=indexColor+1
p7.setXLink(p1)
p6.setXLink(p1)
p5.setXLink(p1)
p4.setXLink(p1)
p3.setXLink(p1)
p2.setXLink(p1)
def init_UI(self):
"""Produce the widgets and buttons."""
self.centre_widget = QWidget()
self.tabs = QTabWidget() # make tabs for each main display
self.centre_widget.layout = QVBoxLayout()
self.centre_widget.layout.addWidget(self.tabs)
self.centre_widget.setLayout(self.centre_widget.layout)
self.setCentralWidget(self.centre_widget)
# change font size
font = QFont()
font.setPixelSize(18)
#### menubar at top gives options ####
menubar = self.menuBar()
# file menubar allows you to save/load data
file_menu = menubar.addMenu('File')
for label, function in [['Load Config', self.load_config],
['Save Config', self.save_config],
['Load Trace', self.load_trace],
['Save Trace', self.save_trace],
['Save Graph', self.save_graph]]:
action = QAction(label, self)
action.triggered.connect(function)
file_menu.addAction(action)
#### tab for settings ####
settings_tab = QWidget()
settings_grid = QGridLayout()
settings_tab.setLayout(settings_grid)
self.tabs.addTab(settings_tab, "Settings")
self.settings = QTableWidget(1, 6)
self.settings.setHorizontalHeaderLabels(['Duration (ms)',
'Sample Rate (kS/s)', 'Trigger Channel', 'Trigger Level (V)',
'Trigger Edge', 'Use Trigger?'])
settings_grid.addWidget(self.settings, 0,0, 1,1)
defaults = [str(self.stats['Duration (ms)']), str(self.stats['Sample Rate (kS/s)']),
self.stats['Trigger Channel'], str(self.stats['Trigger Level (V)']),
self.stats['Trigger Edge'], '1']
validators = [double_validator, double_validator, None, double_validator, None, bool_validator]
for i in range(6):
table_item = QLineEdit(defaults[i]) # user can edit text to change the setting
if defaults[i] == 'Sample Rate (kS/s)': table_item.setEnabled(False)
table_item.setValidator(validators[i]) # validator limits the values that can be entered
self.settings.setCellWidget(0,i, table_item)
self.settings.resizeColumnToContents(1)
self.settings.setFixedHeight(70) # make it take up less space
self.settings.cellWidget(0,0).textChanged.connect(self.check_slice_duration)
# start/stop: start waiting for a trigger or taking an acquisition
self.toggle = QPushButton('Start', self)
self.toggle.setCheckable(True)
self.toggle.clicked.connect(self.activate)
settings_grid.addWidget(self.toggle, 1,0, 1,1)
# channels
self.channels = QTableWidget(8, 7) # make table
self.channels.setHorizontalHeaderLabels(['Channel', 'Label',
'Scale (X/V)', 'Offset (V)', 'Range', 'Acquire?', 'Plot?'])
settings_grid.addWidget(self.channels, 2,0, 1,1)
validators = [None, double_validator, double_validator, None, bool_validator, bool_validator]
for i in range(8):
chan = 'Dev2/ai'+str(i) # name of virtual channel
table_item = QLabel(chan)
self.channels.setCellWidget(i,0, table_item)
if chan in self.stats['channels']: # load values from previous
defaults = self.stats['channels'][chan]
else: # default values when none are loaded
defaults = channel_stats("[dummy, "+str(i)+", 1.0, 0.0, 5.0, 0, 0]")['dummy']
for j, key in zip([0,1,2,4,5], ['label', 'scale', 'offset', 'acquire', 'plot']):
table_item = QLineEdit(str(defaults[key]))
if 'acquire' in key:
table_item.textChanged.connect(self.check_slice_channels)
elif 'plot' in key:
table_item.textChanged.connect(self.set_acquire)
table_item.setValidator(validators[j])
self.channels.setCellWidget(i,j+1, table_item)
vrange = QComboBox() # only allow certain values for voltage range
vrange.text = vrange.currentText # overload function so it's same as QLabel
vrange.addItems(['%.1f'%x for x in self.slave.vrs])
try: vrange.setCurrentIndex(self.slave.vrs.index(defaults['range']))
except Exception as e: logger.error('Invalid channel voltage range\n'+str(e))
self.channels.setCellWidget(i,4, vrange)
#### Plot for most recently acquired trace ####
trace_tab = QWidget()
trace_grid = QGridLayout()
trace_tab.setLayout(trace_grid)
self.tabs.addTab(trace_tab, "Trace")
# button activates horizontal line
self.hline_toggle = QPushButton('Horizontal line', self, checkable=True)
self.hline_toggle.clicked.connect(self.add_horizontal)
trace_grid.addWidget(self.hline_toggle, 0,0, 1,1)
self.hline_label = QLabel()
trace_grid.addWidget(self.hline_label, 0,1, 1,1)
fadeline_button = QPushButton('Persist', self)
fadeline_button.clicked.connect(self.set_fadelines)
trace_grid.addWidget(fadeline_button, 0,2, 1,1)
# plot the trace
self.trace_canvas = pg.PlotWidget()
self.trace_legend = self.trace_canvas.addLegend()
self.trace_canvas.getAxis('bottom').tickFont = font
self.trace_canvas.getAxis('left').tickFont = font
self.trace_canvas.setLabel('bottom', 'Time', 's', **{'font-size':'18pt'})
self.trace_canvas.setLabel('left', 'Voltage', 'V', **{'font-size':'18pt'})
self.lines = [] # handles for lines plotting the last measurement
self.fadelines = [] # handles for previous measurement lines
for i in range(8):
chan = self.channels.cellWidget(i,1).text()
self.lines.append(self.trace_canvas.plot([1], name=chan,
pen=pg.mkPen(pg.intColor(i), width=3)))
self.lines[i].hide()
self.fadelines.append(self.trace_canvas.plot([1],
pen=pg.mkPen(pg.intColor(i, alpha=50), width=2)))
self.fadelines[i].hide()
self.hline = pg.InfiniteLine(1., angle=0, pen='k', movable=True)
self.trace_canvas.addItem(self.hline)
self.hline.sigPositionChanged.connect(self.update_hline)
self.hline.hide()
trace_grid.addWidget(self.trace_canvas, 1,0, 1,3)
#### Settings for slices of the trace accumulating into the graph ####
slice_tab = QWidget()
slice_grid = QGridLayout()
slice_tab.setLayout(slice_grid)
self.tabs.addTab(slice_tab, "Slice")
# Buttons to add/remove slices and reset graph
for i, (label, func) in enumerate([['Add slice', self.add_slice],
['Remove slice', self.del_slice], ['Reset graph', self.reset_graph]]):
button = QPushButton(label, self)
button.clicked.connect(func)
slice_grid.addWidget(button, 0,i, 1,1)
# parameters for slices
self.slices = QTableWidget(0, 4) # make table
self.slices.setHorizontalHeaderLabels(['Slice name',
'Start (ms)', 'End (ms)', 'Channels'])
slice_grid.addWidget(self.slices, 1,0, 1,3)
#### Plot for graph of accumulated data ####
graph_tab = QWidget()
graph_grid = QGridLayout()
graph_tab.setLayout(graph_grid)
self.tabs.addTab(graph_tab, "Graph")
self.mean_graph = pg.PlotWidget() # for plotting means
self.stdv_graph = pg.PlotWidget() # for plotting standard deviations
self.graph_legends = []
for i, g in enumerate([self.mean_graph, self.stdv_graph]):
g.getAxis('bottom').tickFont = font
g.getAxis('bottom').setFont(font)
g.getAxis('left').tickFont = font
g.getAxis('left').setFont(font)
graph_grid.addWidget(g, i,0, 1,1)
self.reset_lines() # make a line for every slice channel
self.stdv_graph.setLabel('bottom', 'Shot', '', **{'font-size':'18pt'})
self.stdv_graph.setLabel('left', 'Standard Deviation', 'V', **{'font-size':'18pt'})
self.mean_graph.setLabel('left', 'Mean', 'V', **{'font-size':'18pt'})
#### tab for TCP message settings ####
tcp_tab = QWidget()
tcp_grid = QGridLayout()
tcp_tab.setLayout(tcp_grid)
self.tabs.addTab(tcp_tab, "Sync")
label = QLabel('Run number: ')
tcp_grid.addWidget(label, 0,0, 1,1)
self.n_edit = QLineEdit(str(self.stats['n']))
self.n_edit.setValidator(int_validator)
self.n_edit.textEdited[str].connect(self.set_n)
tcp_grid.addWidget(self.n_edit, 0,1, 1,1)
label = QLabel('Save directory: ')
tcp_grid.addWidget(label, 1,0, 1,1)
self.save_edit = QLineEdit(self.stats['save_dir'])
self.save_edit.textEdited[str].connect(self.set_save_dir)
tcp_grid.addWidget(self.save_edit, 1,1, 1,1)
label = QLabel('Trace file name: ')
tcp_grid.addWidget(label, 2,0, 1,1)
self.trace_edit = QLineEdit(self.stats['trace_file'])
self.trace_edit.textEdited[str].connect(self.set_trace_file)
tcp_grid.addWidget(self.trace_edit, 2,1, 1,1)
label = QLabel('Graph file name: ')
tcp_grid.addWidget(label, 3,0, 1,1)
self.graph_edit = QLineEdit(self.stats['graph_file'])
self.graph_edit.textEdited[str].connect(self.set_graph_file)
tcp_grid.addWidget(self.graph_edit, 3,1, 1,1)
reset = QPushButton('Reset TCP client', self)
reset.clicked.connect(self.reset_client)
tcp_grid.addWidget(reset, 4,0, 1,1)
#### Title and icon ####
self.setWindowTitle('- NI DAQ Controller -')
self.setWindowIcon(QIcon('docs/daqicon.png'))
self.setGeometry(200, 200, 800, 600)
def creategradient(self):
g = QtGui.QLinearGradient()
for i in range(17):
g.setColorAt(float(i)/17.0, pg.intColor(i, hues=17))
return g
def new_curve(self, results, color=None, **kwargs):
if color is None:
color = pg.intColor(self.browser.topLevelItemCount() % 8)
return self.plot_widget.new_curve(results, color=color, **kwargs)
view.nextRow()
w3 = view.addPlot(title="residual Sugar vs Density in red Wines")
w4 = view.addPlot(title="residual Sugar vs Density in white Wines")
print("Generating data, this takes a few seconds...")
# 1: pH vs Alcohol red wines (color = quality)
s1 = pg.ScatterPlotItem(size=10, pxMode=True)
spots1 = []
n = len(data['alcohol'])
x_var1 = data['alcohol']
y_var1 = data['pH']
scale = data['quality']
for i in range(n):
spots1.append({
'pos': (x_var1[i], y_var1[i]),
'brush': pg.intColor(scale[i] * 10, 100)
})
s1.addPoints(spots1)
w1.addItem(s1)
# 2: pH vs Alcohol white(color = quality)
s2 = pg.ScatterPlotItem(size=10, pxMode=True)
spots2 = []
n = len(data2['alcohol'])
x_var2 = data2['alcohol']
y_var2 = data2['pH']
scale2 = data2['quality']
for i in range(n):
spots2.append({
'pos': (x_var2[i], y_var2[i]),
'brush': pg.intColor(scale2[i] * 10, 100)
def updatePlot(self, *args):
rawIndex = self.rawCB.currentIndex()
trajIndex = self.trajCB.currentIndex()
# get current acquisition if data or trajectory plot enabled
if rawIndex != 0 or trajIndex != 0:
# get currently selected row from table view
row = self.tableView.currentIndex().row()
# read corresponding acquisiton from table model buffer
aq = ismrmrd.Acquisition(
self.tableModel.rbuffer.getCell(row)['head'])
# update raw data plot
if rawIndex != 0:
# get the data
data = self.tableModel.rbuffer.getCell(row)['data'].view(
np.complex64).reshape(
(aq.active_channels, aq.number_of_samples))[:]
# modifiy data depending on selected visualization
if self.rawCB.currentText() == 'Real':
dataOut = np.real(data)
elif self.rawCB.currentText() == 'Imag':
dataOut = np.imag(data)
elif self.rawCB.currentText() == 'FFT (magnitude)':
dataOut = abs(np.fft.fftshift(np.fft.fft(data)))
elif self.rawCB.currentText() == 'Phase':
dataOut = np.angle(data)
elif self.rawCB.currentText() == 'Phase (unwrapped)':
dataOut = np.unwrap(np.angle(data))
else:
dataOut = abs(data)
# remove old plots and legend entries
for item in self.rawPlot.items():
self.rawPlot.removeItem(item)
try:
self.rawPlot.legend.scene().removeItem(self.rawPlot.legend)
except Exception as e:
print(e)
#self.plotWidget.rawPlot.clear()
self.rawPlot.setTitle('Coil data')
self.rawPlot.legend = self.rawPlot.addLegend()
for ind in range(0, len(dataOut)):
color = pg.intColor(ind)
self.rawPlot.plot(dataOut[ind, :],
pen=pg.mkPen(color),
name=' Channel ' + str(ind))
self.rawPlot.show()
else:
self.rawPlot.hide()
# update trajectory plot
if self.trajCB.currentIndex() != 0 and aq.traj.size > 0:
# get the data
data = self.tableModel.rbuffer.getCell(row)['traj'].reshape(
(aq.number_of_samples, aq.trajectory_dimensions))[:]
# modifiy data depending on selected visualization
if self.trajCB.currentText() == 'FFT (magnitude)':
dataOut = abs(np.fft.fft(data))
else:
dataOut = data
# remove old plots and legend entries
for item in self.trajPlot.items():
self.trajPlot.removeItem(item)
try:
self.trajPlot.legend.scene().removeItem(self.trajPlot.legend)
except Exception as e:
print(e)
#self.plotWidget.trajPlot.clear()
self.trajPlot.setTitle('Trajectory data')
self.trajPlot.legend = self.trajPlot.addLegend()
for ind in range(0, dataOut.shape[1]):
color = pg.intColor(ind)
self.trajPlot.plot(dataOut[:, ind],
pen=pg.mkPen(color),
name=' Channel ' + str(ind))
self.trajPlot.show()
else:
self.trajPlot.hide()
def update_scater_plot():
global number_of_spikes
global tsne_spots
global spike_info
scatter_item.clear()
scatter_selected_item.clear()
number_of_spikes = len(spike_info)
progdialog = QtWidgets.QProgressDialog()
progdialog.setGeometry(500, 500, 400, 40)
progdialog.setWindowTitle('Loading t-sne plot')
progdialog.setMinimum(0)
progdialog.setMaximum(5)
progdialog.setWindowModality(QtCore.Qt.WindowModal)
progdialog.setLabelText(
'Generating colors _____________________________________')
progdialog.show()
progdialog.setValue(0)
QtWidgets.QApplication.processEvents()
color = [
pg.intColor(spike_info['template_after_sorting'].iloc[i],
hues=50,
values=1,
maxValue=255,
minValue=150,
maxHue=360,
minHue=0,
sat=255,
alpha=255) for i in range(number_of_spikes)
]
progdialog.setLabelText(
'Generating brushes ____________________________________')
progdialog.setValue(1)
brush = [pg.mkBrush(color[i]) for i in range(number_of_spikes)]
progdialog.setLabelText(
'Generating positions __________________________________')
progdialog.setValue(2)
tsne_spots = [{
'pos':
[spike_info['tsne_x'].iloc[i], spike_info['tsne_y'].iloc[i]],
'data':
1,
'brush':
brush[i]
} for i in range(number_of_spikes)]
progdialog.setLabelText(
'Adding points to plot __________________________________')
progdialog.setValue(3)
scatter_item.addPoints(tsne_spots)
progdialog.setLabelText(
'Generating symbols ... Almost done ______________________')
progdialog.setValue(4)
symbol = []
for i in range(number_of_spikes):
symbol.append(
hf.symbol_from_type(spike_info['type_after_sorting'].iloc[i]))
scatter_item.setSymbol(symbol)
progdialog.setValue(5)
progdialog.close()
def add_data(self,x,y,yerr=None,name=None,fit=False,color=None):
"""
Adds data into the plot where:
x=Array of x-values
y=Array of y-values
yerr=Array of yerr-values. If None yerr will be set to sqrt(y)
name=any string to be used for the key to put the data
fit= True if the data corresponds to a fit
"""
if not (isinstance(yerr,list) or isinstance(yerr,np.ndarray)):
yerr=np.ones_like(y)
x=np.array(x)
y=np.array(y)
if len(x)==len(y) and len(y)==len(yerr):
if name is None:
dname=str(self.data_num)
else:
dname=name
if np.all(yerr==1):
self.yerr[dname]=False
else:
self.yerr[dname]=True
self.fit[dname]=fit
if dname in self.data.keys():
if color is None:
color=self.data[dname].opts['symbolPen'].color()
pen=pg.mkPen(color=color,width=float(self.lineWidthLineEdit.text()))
symbol='o'
if self.fit[dname]:
symbol=None
self.data[dname].setData(x,y,pen=pen,symbol=symbol,symbolSize=float(self.pointSizeLineEdit.text()),symbolPen=pg.mkPen(color=color),symbolBrush=pg.mkBrush(color=color))
#self.data[dname].setPen(pg.mkPen(color=pg.intColor(np.random.choice(range(0,210),1)[0]),width=int(self.lineWidthLineEdit.text())))
#if self.errorbarCheckBox.isChecked():
# self.dataErrPos[dname].setData(x,np.where(y+yerr/2.0>0,y+yerr/2.0,y))
# self.dataErrNeg[dname].setData(x,np.where(y-yerr/2.0>0,y-yerr/2.0,y))
self.err[dname]= yerr
self.dataErr[dname].setData(x=x, y=y, top=self.err[dname], bottom=self.err[dname], pen='w')# beam=min(np.abs(x))*0.01*float(self.pointSizeLineEdit.text()),pen='w')
#self.dataErr[dname].setCurves(self.dataErrPos[dname],self.dataErrNeg[dname])
else:
if color is None:
color=pg.intColor(np.random.choice(range(0,210),1)[0])
#color=self.data[dname].opts['pen'].color()
pen=pg.mkPen(color=color,width=float(self.lineWidthLineEdit.text()))
symbol='o'
if self.fit[dname]:
symbol=None
self.data[dname]=pg.PlotDataItem(x,y,pen=pen,symbol=symbol,symbolSize=float(self.pointSizeLineEdit.text()),symbolPen=pg.mkPen(color=color),symbolBrush=pg.mkBrush(color=color))
self.dataErr[dname] = pg.ErrorBarItem()
self.err[dname]=yerr
self.dataErr[dname].setData(x=x,y=y,top=self.err[dname],bottom=self.err[dname], pen='w')# beam=min(np.abs(x))*0.01*float(self.pointSizeLineEdit.text()),pen='w')
self.data[dname].curve.setClickable(True,width=10)
self.data[dname].sigClicked.connect(self.colorChanged)
#if self.errorbarCheckBox.isChecked():
# self.dataErrPos[dname]=pg.PlotDataItem(x,np.where(y+yerr/2.0>0,y+yerr/2.0,y))
# self.dataErrNeg[dname]=pg.PlotDataItem(x,np.where(y-yerr/2.0>0,y-yerr/2.0,y))
#self.dataErr[dname]=pg.FillBetweenItem(curve1=self.dataErrPos[dname],curve2=self.dataErrNeg[dname],brush=pg.mkBrush(color=pg.hsvColor(1.0,sat=0.0,alpha=0.2)))
self.data_num+=1
#if len(x)>1:
self.Plot([dname])
return True
else:
QMessageBox.warning(self,'Data error','The dimensions of x, y or yerr are not matching',QMessageBox.Ok)
return False
def on_tsne_color_scheme_combo_box_change(index):
global number_of_spikes
global spike_info
progdialog = QtWidgets.QProgressDialog()
progdialog.setGeometry(500, 500, 400, 40)
progdialog.setWindowTitle('Changing spike color scheme')
progdialog.setMinimum(0)
progdialog.setMaximum(2)
progdialog.setWindowModality(QtCore.Qt.WindowModal)
progdialog.setLabelText(
'Generating colors and symbols ... ')
progdialog.show()
progdialog.setValue(0)
QtWidgets.QApplication.processEvents()
spikes_to_change = range(number_of_spikes)
if index == 0:
color_scheme = spike_info['template_after_sorting']
brush = [
pg.intColor(color_scheme.iloc[i],
hues=50,
values=1,
maxValue=255,
minValue=150,
maxHue=360,
minHue=0,
sat=255,
alpha=255) for i in spikes_to_change
]
symbol = []
for i in spikes_to_change:
symbol.append(
hf.symbol_from_type(
spike_info['type_after_sorting'].iloc[i]))
elif index == 1:
color_scheme = spike_info['template_after_cleaning']
brush = [
pg.intColor(color_scheme.iloc[i],
hues=50,
values=1,
maxValue=255,
minValue=150,
maxHue=360,
minHue=0,
sat=255,
alpha=255) for i in spikes_to_change
]
symbol = []
for i in spikes_to_change:
symbol.append(
hf.symbol_from_type(
spike_info['type_after_cleaning'].iloc[i]))
progdialog.setValue(1)
progdialog.setLabelText(
'Applying colors and symbols ... ')
QtWidgets.QApplication.processEvents()
scatter_item.setBrush(brush)
scatter_item.setSymbol(symbol)
progdialog.setValue(2)
progdialog.close()
def plotResults(self, res, runInfo, somasite=['postsynapticV', 'postsynapticI', 'dendriteV']):
clist={'axon': 'r', 'heminode': 'g', 'stalk':'y', 'branch': 'g', 'neck': 'b',
'swelling': 'm', 'tip': 'k', 'parentaxon': '', r'synapse': 'c', 'Soma': 'k',
'dendrite': 'c', 'dend': 'c'}
dx = np.array([x for k,x in res['distanceMap'].items()])
dlen = res['monitor']['postsynapticV'].shape[0]
dxmax = np.max(dx)
if self.plotmode == 'pg':
self.plots['Soma'].setLabel('left', 'V')
self.plots['Soma'].plot(res['monitor']['time'][:dlen], res['monitor']['postsynapticV'],
pen=pg.mkPen(clist['Soma'], width=0.5), )
if 'dendriteV' in somasite and self.plots['Dendrite'] is not None and len(res['monitor']['dendriteV']) > 0:
self.plots['Dendrite'].plot(res['monitor']['time'][:dlen],
res['monitor']['dendriteV'], pen=pg.mkPen(clist['dendrite'], width=0.5), )
self.plots['Dendrite'].setLabel('left', 'V (mV)')
if 'vec' in res.keys()and self.plots['p4'] is not None:
for v in res['vec']:
self.plots['p4'].plot(res['monitor']['time'], res['vec'][v],
pen=pg.mkPen(pg.intColor(int(255.*res['distanceMap'][v]/dxmax))),
width=1.5)
if 'postsynapticI' in somasite and self.plots['Iinj'] is not None:
vlen = len(res['monitor']['postsynapticI'])
self.plots['Iinj'].plot(res['monitor']['time'][0:vlen], res['monitor']['postsynapticI'],
pen = pg.mkPen('b', width=0.5))
self.plots['Iinj'].setLabel('left', 'I (inj, nA)')
if 'vec' in res.keys() and self.plots['p4'] is not None:
for v in res['vec']:
self.plots['p4'].plot(res['monitor']['time'], res['vec'][v],
pen=pg.mkPen(pg.intColor(int(255.*res['distanceMap'][v]/dxmax))),
width=0.5)
#for c in res['ICa']:
# self.plots['Dendrite'].plot(res['monitor']['time'], res['ICa'][c]*1e12, pen=pg.mkPen('b', width=1.5))
# self.plots['Iinj'].plot(res['vec']['time'], res['Cai'][c]*1e6, pen=pg.mkPen('g', width=1.5))
#p2.set_ylim(-5e-12, 1e-12)
self.plots['Soma'].setXRange(0., 120., padding=0.2)
self.plots['Dendrite'].setXRange(0., 120., padding=0.2)
if self.plots['Iinj'] is not None:
self.plots['Iinj'].setXRange(0., 120., padding=0.2)
pgPH.cleanAxes([self.plots['Soma'], self.plots['Dendrite'], self.plots['Iinj'], self.plots['p4']])
pgPH.nice_plot(self.plots['Soma'])
pgPH.calbar(self.plots['Soma'], [110, -50, 20, 50])
# pgPH.nice_plot(self.plots['Dendrite'])
# pgPH.calbar(self.plots['Dendrite'], [110, 0.1, 20, 1])
if self.plots['Iinj'] is not None:
pgPH.nice_plot(self.plots['Iinj'])
pgPH.calbar(self.plots['Iinj'], [110, -0.1, 20, 1])
elif self.plotmode == 'mpl':
self.plots['Soma'].set_ylabel('V')
self.plots['Soma'].plot(res['monitor']['time'][:dlen], res['monitor']['postsynapticV'],
color=clist['Soma'], linewidth=0.5)
if 'dendriteV' in somasite and self.plots['Dendrite'] is not None and len(res['monitor']['dendriteV']) > 0:
self.plots['Dendrite'].plot(res['monitor']['time'][:dlen],
res['monitor']['dendriteV'], color=clist['dendrite'], linewidth=0.5)
self.plots['Dendrite'].set_ylabel('V (mV)')
if 'vec' in res.keys()and self.plots['p4'] is not None:
for v in res['vec']:
self.plots['p4'].plot(res['monitor']['time'], res['vec'][v],
color=[[int(255.*res['distanceMap'][v]/dxmax)]*3],
linewidth=0.75)
if 'postsynapticI' in somasite and self.plots['Iinj'] is not None:
vlen = len(res['monitor']['postsynapticI'])
self.plots['Iinj'].plot(res['monitor']['time'][0:vlen], res['monitor']['postsynapticI'],
color='b', linewidth=0.5)
self.plots['Iinj'].set_ylabel('I (inj, nA)')
if 'vec' in res.keys() and self.plots['p4'] is not None:
for v in res['vec']:
self.plots['p4'].plot(res['monitor']['time'], res['vec'][v],
color=[[int(255.*res['distanceMap'][v]/dxmax)]*3],
linewidth=0.75)
#for c in res['ICa']:
# self.plots['Dendrite'].plot(res['monitor']['time'], res['ICa'][c]*1e12, pen=pg.mkPen('b', width=1.5))
# self.plots['Iinj'].plot(res['vec']['time'], res['Cai'][c]*1e6, pen=pg.mkPen('g', width=1.5))
#p2.set_ylim(-5e-12, 1e-12)
self.plots['Soma'].set_xlim(0., 120.)
self.plots['Dendrite'].set_xlim(0., 120.)
if self.plots['Iinj'] is not None:
self.plots['Iinj'].set_xlim(0., 120.)
PH.cleanAxes([self.plots['Soma'], self.plots['Dendrite'], self.plots['Iinj']])
PH.nice_plot(self.plots['Soma'])
PH.calbar(self.plots['Soma'], [110, -50, 20, 50])
PH.nice_plot(self.plots['Dendrite'])
PH.calbar(self.plots['Dendrite'], [110, -50, 20, 50])
# pgPH.nice_plot(self.plots['Dendrite'])
# pgPH.calbar(self.plots['Dendrite'], [110, 0.1, 20, 1])
if self.plots['Iinj'] is not None:
PH.nice_plot(self.plots['Iinj'])
PH.calbar(self.plots['Iinj'], [110, -0.1, 20, 1])
def define_pens(self, width=2, max_colors=10):
self._line_width = width
self._max_colors = max_colors
self._brightness_percentage = 90
self._pens = [pg.mkPen(pg.intColor(i, self._max_colors+1).lighter(self._brightness_percentage), width=self._line_width) for i in range(self._max_colors)]