def print_element_info(self,
pre_class,
post_class,
element,
field_name=None):
if field_name is not None:
fn = field_name.split('_all')[0] if field_name.endswith(
'all') else field_name.split('_first_pulse')[0]
units = [
field[1].get('units', '') for field in self.fields
if field[0] == field_name
][0]
print("Connection type: %s -> %s" % (pre_class, post_class))
print("\t Grand Average %s = %s" %
(field_name,
pg.siFormat(element[field_name].mean(), suffix=units)))
print("Connected Pairs:")
no_qc_data = []
for pair, value in element[field_name].iteritems():
if pair.synapse is not True:
continue
if np.isnan(value):
no_qc_data.append(pair)
else:
print("\t %s" % (pair))
print("\t\t Average %s: %s" %
(field_name, pg.siFormat(value, suffix=units)))
print("\t No QC Data:")
for pair in no_qc_data:
print("\t\t %s" % (pair))
def CAP(self, row):
actual = float(self.tbl.item(row, 0).text())
cap1 = self.get_capacitance(1)
self.I.__charge_cap__(0, 50000)
cap2 = self.get_capacitance(2)
if cap1 and cap2:
item = self.tbl.item(row, 1)
item.setText(
'%s,%s' %
(pg.siFormat(cap1, precision=4, suffix='F', space=True),
pg.siFormat(cap2, precision=3, suffix='F', space=True)))
self.CR1 = cap1 / actual
self.CR2 = cap2 / actual
else:
QtGui.QMessageBox.about(
self, 'Cap error',
"Capacitance invalid. \nIf a %sF capacitor is plugged correctly into CAP socket, this may be an issue."
% actual)
if abs(cap1 - actual) < self.CAPACITANCE_ERROR:
self.setSuccess(item, 1) #capacitance within error margins
else:
self.setSuccess(item, 0)
QtGui.QMessageBox.about(
self, 'Cap error',
"Capacitance invalid. \nIf a %sF capacitor is plugged correctly into CAP socket, this may be an issue."
% actual)
def mouseMoved(evt):
"""
Handle the event from the mouse.
Mainly updates the crosshair and top right values.
"""
if len(dataFrame.index):
pos = evt[
0] # using signal proxy turns original arguments into a tuple
mousePoint = vb.mapSceneToView(pos)
# Needed to round the values to multiple of 5,
# otherwise the index may not be defined for accessing values in the dataframe.
# Change according to the sampling rate.
index = int(mousePoint.x())
if index < lastIndex:
try:
val = pg.siFormat(mousePoint.y() / 1000, 3, 'A')
time = pg.siFormat(mousePoint.x(), 3, 's')
label.setText(
"<span style='font-size: 12pt'>time=%s, <span style='color: red'>y1=%s</span>"
% (time, val))
except KeyError:
pass
vLine.setPos(mousePoint.x())
hLine.setPos(mousePoint.y())
def generate_warnings(self):
self.warnings = []
latency_mode = []
for mode in modes:
latency_holding = []
for holding in holdings:
initial_latency = self.fit_params['initial'][mode][str(
holding)].get('xoffset')
fit_latency = self.fit_params['fit'][mode][str(holding)].get(
'xoffset')
if fit_latency is None or initial_latency is None:
continue
if abs(np.diff([fit_latency, initial_latency])) > 0.1e-3:
warning = 'Initial latency and fit latency differ by %s' % pg.siFormat(
abs(np.diff([fit_latency, initial_latency])),
suffix='s')
latency_holding.append(fit_latency)
if len(latency_holding) == 2 and abs(
np.diff(latency_holding)) > 0.01e-3:
warning = 'Fit latencies for %s mode do not match' % mode
self.warnings.append(warning)
latency_mode.append(np.mean(latency_holding))
latency_diff = np.diff(latency_mode)[0]
if abs(latency_diff) > 0.2e-3:
warning = 'Latency across modes differs by %s' % pg.siFormat(
latency_diff, suffix='s')
self.warnings.append(warning)
if np.min(latency_mode) < 0.4e-3 and self.ctrl_panel.user_params[
'Gap junction call'] is False:
self.warnings.append("Short latency; is this a gap junction?")
guess_sign = []
guess = None
for mode, fits1 in self.output_fit_parameters.items():
for holding, fit in fits1.items():
if 'amp' not in fit:
continue
if mode == 'ic':
guess = 1 if fit['amp'] > 0 else -1
elif mode == 'vc':
guess = -1 if fit['amp'] > 0 else 1
guess_sign.append(guess)
if np.all(np.array(guess) == 1):
guess = "ex"
elif np.all(np.array(guess) == -1):
guess = "in"
if guess is None:
self.warnings.append(
"Mixed amplitude signs; pick ex/in carefully.")
elif guess != self.ctrl_panel.user_params['Synapse call']:
self.warnings.append("Looks like an %s synapse??" % guess)
print_warning = '\n'.join(self.warnings)
self.ctrl_panel.output_params.child('Warnings').setValue(print_warning)
def plotClicked(self, plot, points):
if self.top_plot is not None:
self.plot.removeItem(self.top_plot)
# for pt, style in self.selected_points:
# brush, pen, size = style
# try:
# pt.setBrush(brush)
# pt.setPen(pen)
# pt.setSize(size)
# except AttributeError:
# pass
selected_points = [[], []]
for pt in points:
# style = (pt.brush(), pt.pen(), pt.size())
x, y = pt.pos()
selected_points[0].append(x)
selected_points[1].append(y)
data = pt.data()
pair = data.index
print('Clicked:' '%s' % pair)
fields = self.fieldList.selectedItems()
for field in fields:
field_name = field.text()
value = data[field_name]
print('%s: %s' % (field_name, pg.siFormat(value)))
# pt.setBrush(pg.mkBrush('y'))
# pt.setSize(15)
self.top_plot = self.plot.plot(selected_points[0], selected_points[1], pen=None, symbol='o', symbolBrush='y', symbolSize=15)
self.sigScatterPlotClicked.emit(self, points)
def plotClicked(self, plot, points):
if len(self.selected_points) > 0:
for pt, style in self.selected_points:
brush, pen, size = style
try:
pt.setBrush(brush)
pt.setPen(pen)
pt.setSize(size)
except AttributeError:
pass
self.selected_points = []
for pt in points:
style = (pt.brush(), pt.pen(), pt.size())
self.selected_points.append([pt, style])
data = pt.data()
element = ('%s -> %s ' %
(data.pre_class.name, data.post_class.name))
print('Clicked:' '%s' % element)
fields = self.fieldList.selectedItems()
for field in fields:
field_name = field.text()
value = data[field_name]
print('%s: %s' % (field_name, pg.siFormat(value)))
pt.setBrush(pg.mkBrush('y'))
pt.setSize(15)
self.sigScatterPlotClicked.emit(self, points)
def print_info(self):
# update instrument panel
self.instNameLabel.setText(self.parent.liaInfo.instName)
self.instInterfaceLabel.setText(self.parent.liaInfo.instInterface)
self.instInterfaceNumLabel.setText(
str(self.parent.liaInfo.instInterfaceNum))
# update ref group
self.refSrcLabel.setText(self.parent.liaInfo.refSrcText)
self.refFreqLabel.setText(
siFormat(self.parent.liaInfo.refFreq, suffix='Hz'))
self.refHarmLabel.setText('{:d}'.format(self.parent.liaInfo.refHarm))
self.refPhaseLabel.setText('{:.2f} deg'.format(
self.parent.liaInfo.refPhase))
# update input group
self.inputConfigLabel.setText(self.parent.liaInfo.configText)
self.inputGroundingLabel.setText(self.parent.liaInfo.groundingText)
self.inputCoupleLabel.setText(self.parent.liaInfo.coupleText)
self.inputFilterLabel.setText(self.parent.liaInfo.inputFilterText)
# update gain group
self.gainSensLabel.setText(self.parent.liaInfo.sensText)
self.gainTCLabel.setText(self.parent.liaInfo.tcText)
self.gainReserveLabel.setText(self.parent.liaInfo.reserveText)
self.lpSlopeLabel.setText(self.parent.liaInfo.lpSlopeText)
# update output group
self.outputDisp1Label.setText(self.parent.liaInfo.disp1Text)
self.outputDisp2Label.setText(self.parent.liaInfo.disp2Text)
self.outputFront1Label.setText(self.parent.liaInfo.front1Text)
self.outputFront2Label.setText(self.parent.liaInfo.front2Text)
self.outputSRateLabel.setText(self.parent.liaInfo.sampleRateText)
def plotClicked(self, plot, points):
if len(self.selected_points) > 0:
for pt, style in self.selected_points:
brush, pen, size = style
try:
pt.setBrush(brush)
pt.setPen(pen)
pt.setSize(size)
except AttributeError:
pass
self.selected_points = []
for pt in points:
style = (pt.brush(), pt.pen(), pt.size())
self.selected_points.append([pt, style])
data = pt.data()
print('Clicked:' '%s' % data.index)
# fields = self.fieldList.selectedItems()
for field, options in self.fields.items():
value = data[field]
if value is not None:
if options.get('mode') == 'range':
print('%s: %s' % (field, pg.siFormat(value)))
elif options.get('mode') == 'enum':
print('%s: %s' % (field, value))
pt.setBrush(pg.mkBrush('y'))
pt.setSize(15)
self.sigScatterPlotClicked.emit(self, plot, points)
def CCS(self, row):
self.I.set_state(CCS=1)
time.sleep(0.1)
V = self.I.get_voltage('CCS')
if V < 2.5:
item = self.tbl.item(row, 1)
res = V / 1.1e-3 #assume 1.1mA
print(V, res)
item.setText(
pg.siFormat(res,
precision=3,
suffix=u"\u03A9",
space=True,
error=None,
minVal=1e-25,
allowUnicode=True))
actual = float(self.tbl.item(row, 0).text())
if abs(res - actual) < self.CCS_ERROR:
self.setSuccess(item, 1) #resistance within error margins
self.CCS_SCALING = actual / res
else:
self.setSuccess(item, 0)
else:
item.setText('Open')
self.setSuccess(item, 0)
def generateText(self):
if len(self.values) == 0:
return ''
avg = self.averageValue()
val = self.values[-1][1]
if self.siPrefix:
return pg.siFormat(avg, suffix=self.suffix)
else:
return self.formatStr.format(value=val, avgValue=avg, suffix=self.suffix)
def print_element_info(self, pre_class, post_class, element, field_name=None):
if field_name is not None:
fn = field_name.split('_all')[0] if field_name.endswith('all') else field_name.split('_first_pulse')[0]
units = [field[1].get('units', '') for field in self.fields if field[0] == field_name][0]
print ("Connection type: %s -> %s" % (pre_class, post_class))
print ("\t Grand Average %s = %s" % (field_name, pg.siFormat(element[field_name].mean(), suffix=units)))
print ("Connected Pairs:")
no_qc_data = []
for pair, value in element[field_name].iteritems():
if pair.synapse is not True:
continue
if np.isnan(value):
no_qc_data.append(pair)
else:
print ("\t %s" % (pair))
print ("\t\t Average %s: %s" % (field_name, pg.siFormat(value, suffix=units)))
print("\t No QC Data:")
for pair in no_qc_data:
print ("\t\t %s" % (pair))
def generateText(self):
if len(self.values) == 0:
return ''
avg = self.averageValue()
val = self.values[-1][1]
if self.siPrefix:
return pg.siFormat(avg, suffix=self.suffix)
else:
return self.formatStr.format(value=val,
avgValue=avg,
suffix=self.suffix)
def __WA__(self, ADC, row):
self.I.set_wave(1e3) #1KHz test
x, y = self.I.capture1(ADC, 1000, 5) #get about five cycles
self.WCurve.setData(x, y)
self.tbl.item(row, 0).setText('1 KHz')
try:
amp, frq, ph, off = self.sineFit(x, y)
self.tbl.item(row, 1).setText(
pg.siFormat(frq, precision=3, suffix='Hz', space=True) + ',' +
pg.siFormat(amp, precision=3, suffix='V', space=True))
if abs(frq - 1e3) > 2:
self.setSuccess(self.tbl.item(row, 1), 0)
print(frq)
else:
self.setSuccess(self.tbl.item(row, 1), 1)
except:
self.tbl.item(row, 1).setText('Check Connections')
self.setSuccess(self.tbl.item(row, 1), 0)
def format_fit_output(self, values, name, suffix):
format_list = []
for p in zip(name, suffix):
if values.get(p[0]) is None:
format_list.append('nan')
else:
value = values[p[0]]
if p[0] == 'nrmse':
p_format = ('%0.2f' % value)
else:
p_format = pg.siFormat(value, suffix=p[1])
format_list.append(p_format)
output = ", ".join(format_list)
return output
def __init__(self, nsamples, initRange=[0, 30000], maxNSamples=90000):
QtGui.QLabel.__init__(self)
self.nsamples = nsamples
self.time_total = nsamples / SAMPLE_RATE # in seconds
# some drawing parameters
self.margin = 40
self.tickLength = 30
self.pen_timeline = QtGui.QPen(QtGui.QColor('gray'))
self.brush_scrubber = QtGui.QBrush(QtGui.QColor(200, 200, 200, 64))
self.pen_scrubber = QtGui.QPen()
self.pen_scrubber.setStyle(QtCore.Qt.NoPen)
# widget properties
self.setFrameStyle(QtGui.QFrame.StyledPanel)
self.setStyleSheet('background-color: #0F0F0F')
self.setMouseTracking(True)
# mouse state variables
self.edgeDetect = 0
self.edgeDetectMargin = 3
self.centerHold = 0
self.leftHold = 0
self.rightHold = 0
# scrubber state variables: to preserve state across resizings, it makes
# sense to track state as sample indices rather than pixels. however,
# we can set them from pixel values using setStateLeft(), setStateRight(),
# and setStateCenter(). these functions also implement limit-checking.
self.totalsamp = maxNSamples
if (initRange[1] - initRange[0]) > maxNSamples:
raise ValueError(
"Exceeding maximum number of samples to represent! initRange must be less than maxSamples!!"
)
self.minsamp = initRange[0]
self.maxsamp = initRange[1]
[timespan, suffix] = pg.siFormat(self.time_total,
suffix='s').split(' ')
self.leftLabel = QtGui.QLabel('sample 0 \n (0 %s)' % suffix)
self.rightLabel = QtGui.QLabel('sample %d' % self.nsamples + \
'\n (%s %s)' % (timespan, suffix))
for label in [self.leftLabel, self.rightLabel]:
label.setStyleSheet('color:gray; background:transparent')
label.setAlignment(QtCore.Qt.AlignCenter)
label.setParent(self)
label.show()
def compute():
"""
Function used to compute the info shown in the right side panel
from tjhe selected region.
"""
if len(dataFrame.index):
u = ualimSpin.value()
bounds = region.getRegion()
slicedDf = dataFrame.loc[bounds[0]:bounds[1]]
computeResult.setText(
pg.siFormat(
np.trapz(slicedDf.current.values / 1000 * u,
slicedDf.time.values), 3, 'J'))
# Info computations
delta = (region.getRegion()[1] - region.getRegion()[0])
integ = np.trapz(slicedDf.current.values / 1000,
slicedDf.time.values) / delta
avgCurr = pg.siFormat(integ, 3, 'A')
labAvgCurrent.setText(f"Average current: {avgCurr}")
avgPow = pg.siFormat(integ * u, 3, 'W')
labAvgPower.setText(f"Average power: {avgPow}")
delta = pg.siFormat(delta, 3, 's')
labBoxDelta.setText(f"\u0394t: {delta}")
def CAP1uF(self, row):
actual = float(self.tbl.item(row, 0).text())
cap = self.I.capacitance_via_RC_discharge()
if cap:
item = self.tbl.item(row, 1)
item.setText(
'%s' % (pg.siFormat(cap, precision=4, suffix='F', space=True)))
self.CRRC = actual / cap
else:
QtGui.QMessageBox.about(
self, 'Cap error',
"Capacitance invalid. \nIf a 1uF capacitor is plugged correctly into CAP socket, this may be an issue."
)
if abs(cap - actual) < 0.1e-6:
self.setSuccess(item, 1) #capacitance within error margins
else:
self.setSuccess(item, 0)
def paint(self, p, *args):
pg.ROI.paint(self, p, *args)
h1 = self.handles[0]['item'].pos()
h2 = self.handles[1]['item'].pos()
h4 = self.handles[3]['item']
h5 = self.handles[4]['item']
h4.setVisible(False)
h5.setVisible(False)
p1 = p.transform().map(h1)
p2 = p.transform().map(h2)
vec = pg.Point(h2) - pg.Point(h1)
length = vec.length()
pvec = p2 - p1
pvecT = pg.Point(pvec.y(), -pvec.x())
pos = 0.5 * (p1 + p2) + pvecT * 40 / pvecT.length()
angle = pg.Point(1, 0).angle(pg.Point(pvec))
self.ab_angle = angle
# Overlay a line to signal which side of the ROI is the back.
if self.ac_angle > 0:
self.newRoi.setVisible(True)
self.newRoi.setPos(h5.pos())
elif self.ac_angle < 0:
self.newRoi.setVisible(True)
self.newRoi.setPos(h4.pos())
else:
self.newRoi.setVisible(False)
self.newRoi.setSize(pg.Point(self.size()[0], 0))
p.resetTransform()
txt = pg.siFormat(
length,
suffix='m') + '\n%0.1f deg' % angle + '\n%0.1f deg' % self.ac_angle
p.drawText(QtCore.QRectF(pos.x() - 50,
pos.y() - 50, 100, 100),
QtCore.Qt.AlignCenter | QtCore.Qt.AlignVCenter, txt)
def SEN(self, row):
res = self.I.get_resistance()
item = self.tbl.item(row, 1)
if res != np.inf:
item.setText(
pg.siFormat(res,
precision=3,
suffix=u"\u03A9",
space=True,
error=None,
minVal=1e-25,
allowUnicode=True))
actual = float(self.tbl.item(row, 0).text())
if abs(res - actual) < self.RESISTANCE_ERROR:
self.setSuccess(item, 1) #resistance within error margins
self.RESISTANCE_SCALING = actual / res
else:
self.setSuccess(item, 0)
else:
item.setText('Open')
self.setSuccess(item, 0)
def CAP_SOCK(self, row):
#cap = self.I.get_capacitance()
V = self.I.__get_capacitance_voltage__(1, 0, 180)
Charge_Current = self.I.currents[1]
cap = (Charge_Current * 180 * 1e-6 / V) / self.I.currentScalers[1]
self.I.SOCKET_CAPACITANCE = cap
print(V, cap)
item = self.tbl.item(row, 1)
item.setText(
pg.siFormat(cap,
precision=3,
suffix='F',
space=True,
minVal=1e-25,
allowUnicode=True))
if abs(cap -
float(self.tbl.item(row, 0).text())) < self.CAPACITANCE_ERROR:
self.setSuccess(item, 1) #capacitance within error margins
self.socket_cap = cap
else:
self.setSuccess(item, 0)
def paint(self, p, *args):
pg.ROI.paint(self, p, *args)
h1 = self.handles[0]['item'].pos()
h2 = self.handles[1]['item'].pos()
h4 = self.handles[3]['item']
h5 = self.handles[4]['item']
h4.setVisible(False)
h5.setVisible(False)
p1 = p.transform().map(h1)
p2 = p.transform().map(h2)
vec = pg.Point(h2) - pg.Point(h1)
length = vec.length()
pvec = p2 - p1
pvecT = pg.Point(pvec.y(), -pvec.x())
pos = 0.5 * (p1 + p2) + pvecT * 40 / pvecT.length()
angle = pg.Point(1, 0).angle(pg.Point(pvec))
self.ab_angle = angle
# Overlay a line to signal which side of the ROI is the back.
if self.ac_angle > 0:
self.newRoi.setVisible(True)
self.newRoi.setPos(h5.pos())
elif self.ac_angle < 0:
self.newRoi.setVisible(True)
self.newRoi.setPos(h4.pos())
else:
self.newRoi.setVisible(False)
self.newRoi.setSize(pg.Point(self.size()[0], 0))
p.resetTransform()
txt = pg.siFormat(length, suffix='m') + '\n%0.1f deg' % angle + '\n%0.1f deg' % self.ac_angle
p.drawText(QtCore.QRectF(pos.x() - 50, pos.y() - 50, 100, 100), QtCore.Qt.AlignCenter | QtCore.Qt.AlignVCenter, txt)
def __init__(self, parent, entry_setting=()):
QtGui.QWidget.__init__(self, parent=None)
self.parent = parent
# add labels
self.scanNumLabel = QtGui.QCheckBox()
self.commentLabel = QtGui.QLabel()
self.dateLabel = QtGui.QLabel()
self.timeLabel = QtGui.QLabel()
self.itLabel = QtGui.QLabel()
self.sensLabel = QtGui.QLabel()
self.tcLabel = QtGui.QLabel()
self.modModeLabel = QtGui.QLabel()
self.modFreqLabel = QtGui.QLabel()
self.modAmpLabel = QtGui.QLabel()
self.startFreqLabel = QtGui.QLabel()
self.stopFreqLabel = QtGui.QLabel()
self.stepLabel = QtGui.QLabel()
self.ptsLabel = QtGui.QLabel()
self.avgLabel = QtGui.QLabel()
self.harmLabel = QtGui.QLabel()
self.phaseLabel = QtGui.QLabel()
# set label text
self.scanNumLabel.setText(str(entry_setting[0]))
self.commentLabel.setText(entry_setting[1])
self.dateLabel.setText(entry_setting[2])
self.timeLabel.setText(entry_setting[3])
self.itLabel.setText(siFormat(entry_setting[4]*1e-3, suffix='s'))
self.sensLabel.setText(siFormat(entry_setting[5], suffix='V'))
self.tcLabel.setText(siFormat(entry_setting[6], suffix='s'))
self.modModeLabel.setText(entry_setting[7])
self.modFreqLabel.setText(siFormat(entry_setting[8]*1e3, suffix='Hz'))
self.modAmpLabel.setText(siFormat(entry_setting[9]*1e3, suffix='Hz'))
self.startFreqLabel.setText('{:.3f}'.format(entry_setting[10]))
self.stopFreqLabel.setText('{:.3f}'.format(entry_setting[11]))
self.stepLabel.setText(siFormat(entry_setting[12]*1e6, suffix='Hz'))
self.ptsLabel.setText(str(entry_setting[13]))
self.avgLabel.setText(str(entry_setting[14]))
self.harmLabel.setText(str(entry_setting[15]))
self.phaseLabel.setText('{:.2f} deg'.format(entry_setting[16]))
def print_info(self):
# update instrument panel
self.instNameLabel.setText(self.parent.synInfo.instName)
self.instInterfaceLabel.setText(self.parent.synInfo.instInterface)
self.instInterfaceNumLabel.setText(
str(self.parent.synInfo.instInterfaceNum))
self.instRemoteDispLabel.setText(
'ON' if self.parent.synInfo.instRemoteDisp else 'OFF')
# update RF setting panel
self.rfOutputLabel.setText(
'ON' if self.parent.synInfo.rfToggle else 'OFF')
self.modOutputLabel.setText(
'ON' if self.parent.synInfo.modToggle else 'OFF')
self.synFreqLabel.setText('{:.9f} MHz'.format(
self.parent.synInfo.synFreq * 1e-6))
# update modulation setting panel
self.am1StateLabel.setText(
'ON' if self.parent.synInfo.AM1Toggle else 'OFF')
self.am1SrcLabel.setText(self.parent.synInfo.AM1Src)
self.am1DepthLabel.setText('{:.1f}% ({:.0f} dB)'.format(
self.parent.synInfo.AM1DepthPercent,
self.parent.synInfo.AM1DepthDbm))
self.am1FreqLabel.setText(
siFormat(self.parent.synInfo.AM1Freq, suffix='Hz'))
self.am1WaveLabel.setText(self.parent.synInfo.AM1Wave)
self.am2StateLabel.setText(
'ON' if self.parent.synInfo.AM2Toggle else 'OFF')
self.am2SrcLabel.setText(self.parent.synInfo.AM2Src)
self.am2DepthLabel.setText('{:.1f}% ({:.0f} dB)'.format(
self.parent.synInfo.AM2DepthPercent,
self.parent.synInfo.AM2DepthDbm))
self.am2FreqLabel.setText(
siFormat(self.parent.synInfo.AM2Freq, suffix='Hz'))
self.am2WaveLabel.setText(self.parent.synInfo.AM2Wave)
self.fm1StateLabel.setText(
'ON' if self.parent.synInfo.FM1Toggle else 'OFF')
self.fm1SrcLabel.setText(self.parent.synInfo.FM1Src)
self.fm1DevLabel.setText(
siFormat(self.parent.synInfo.FM1Dev, suffix='Hz'))
self.fm1FreqLabel.setText(
siFormat(self.parent.synInfo.FM1Freq, suffix='Hz'))
self.fm1WaveLabel.setText(self.parent.synInfo.FM1Wave)
self.fm2StateLabel.setText(
'ON' if self.parent.synInfo.FM2Toggle else 'OFF')
self.fm2SrcLabel.setText(self.parent.synInfo.FM2Src)
self.fm2DevLabel.setText(
siFormat(self.parent.synInfo.FM2Dev, suffix='Hz'))
self.fm2FreqLabel.setText(
siFormat(self.parent.synInfo.FM2Freq, suffix='Hz'))
self.fm2WaveLabel.setText(self.parent.synInfo.FM2Wave)
self.pm1StateLabel.setText(
'ON' if self.parent.synInfo.PM1Toggle else 'OFF')
self.pm1SrcLabel.setText(self.parent.synInfo.PM1Src)
self.pm1DevLabel.setText(
siFormat(self.parent.synInfo.PM1Dev, suffix='rad'))
self.pm1FreqLabel.setText(
siFormat(self.parent.synInfo.PM1Freq, suffix='Hz'))
self.pm1WaveLabel.setText(self.parent.synInfo.PM1Wave)
self.pm2StateLabel.setText(
'ON' if self.parent.synInfo.PM2Toggle else 'OFF')
self.pm2SrcLabel.setText(self.parent.synInfo.PM2Src)
self.pm2DevLabel.setText(
siFormat(self.parent.synInfo.PM2Dev, suffix='rad'))
self.pm2FreqLabel.setText(
siFormat(self.parent.synInfo.PM2Freq, suffix='Hz'))
self.pm2WaveLabel.setText(self.parent.synInfo.PM2Wave)
self.lfStateLabel.setText(
'ON' if self.parent.synInfo.LFToggle else 'OFF')
self.lfSrcLabel.setText(self.parent.synInfo.LFSrc)
self.lfVolLabel.setText(
siFormat(self.parent.synInfo.LFVoltage, suffix='V'))
def si_format(self):
return pg.siFormat(self)
def describe(self):
return "%s < %s < %s" % (pg.siFormat(self['Min'], suffix=self.units), self.fieldName, pg.siFormat(self['Max'], suffix=self.units))
def si_format(self):
return pg.siFormat(self)
def calc_rho(field,
data_xx,
data_xy,
curr=1e-9,
width=50e-6,
length=100e-6,
field_center=1,
name="Analyzed_Field_Sweep"):
"""
Calculate rho_xx, rho_xy from given data sweeps:
Parameters:
- field: field setpoints
- data_xx: V_xx DataArray
- data_xy: V_xy DataArray
- curr: Either the current as a number or as a DataArray. If a DataArray is given,
the trace will be averaged to extract a mean current.
- width/length: Width of the hall bar/distance between V_xx probes to extract
a sheet resistance
- field_center:
- name: Name to save output data
"""
path = "data" / Path(name)
np_field = field.ndarray.copy()
np_xx = data_xx.ndarray.copy()
np_xy = data_xy.ndarray.copy()
if isinstance(curr, qc.DataArray):
curr = np.average(-1 * (curr.ndarray.copy()) / 1e6)
print(curr)
# Calculate resistances
rho_xy = np_xy / curr
# rho_xx is scaled by the width+length of the hall bar to get a sheet resistivity
rho_xx = (np_xx / curr) * (width / length)
# Calculate density
# We want to do a fit between (field_center, -field_center) tesla as there is some extra structure
# above these values
min_ind = np.where(np.abs(np_field + field_center) < 0.01)[0][0]
max_ind = np.where(np.abs(np_field - field_center) < 0.01)[0][0]
min_ind, max_ind = np.min((min_ind, max_ind)), np.max((min_ind, max_ind))
res = np.polyfit(np_field[min_ind:max_ind], rho_xy[min_ind:max_ind], 1)
poly = np.poly1d(res)
# Then the density is given by 1/(|e| dp/dB), in cm^2
density = 1 / (const.e * res[0])
density *= 1e-4
print("Density is: {:.2e} cm^-2".format(density))
# And the calculated mobility is given by mu=1/(rho_xx |e| ns)
mu = 1 / (rho_xx * const.e * density)
# And let's quote the density slightly offset from 0, at 0.1T
mob_ind = np.where(np.abs(np_field - 0.1) < 0.005)[0][0]
mobility = mu[mob_ind]
print("Mobility is: {:.2e} cm^2/V s".format(mobility))
# And finally, let's create a new dataset. Leave location unset for now...
dataset = qc.DataSet(location=str(path))
da_field = qc.DataArray(array_id="Field",
label="Field",
unit="T",
is_setpoint=True,
preset_data=np_field)
da_reduced_field = qc.DataArray(array_id="Reduced_Field",
label="Field",
unit="T",
is_setpoint=True,
preset_data=np_field[min_ind:max_ind])
da_poly = qc.DataArray(array_id="Poly_Deg",
label="Polynomial Degree",
is_setpoint=True,
preset_data=list(range(2))[::-1])
da_rho_xy = qc.DataArray(array_id="Rho_XY",
label="Rho XY",
unit="Ohms",
set_arrays=(da_field, ),
preset_data=rho_xy)
da_rho_xy_fit = qc.DataArray(array_id="fit_Rho_XY",
label="Rho XY",
unit="Ohms",
set_arrays=(da_reduced_field, ),
preset_data=poly(np_field[min_ind:max_ind]))
da_rho_xy_coef = qc.DataArray(array_id="coef_Rho_XY",
label="Poly Coefficients",
set_arrays=(da_poly, ),
preset_data=res)
da_rho_xx = qc.DataArray(array_id="Rho_XX",
label="Rho XX",
unit="Ohms",
set_arrays=(da_field, ),
preset_data=rho_xx)
da_mu = qc.DataArray(array_id="mu",
label="Mobility",
unit="cm<sup>2</sup> (V s)<sup>-1</sup>",
set_arrays=(da_field, ),
preset_data=mu)
dataset.add_array(da_field)
dataset.add_array(da_reduced_field)
dataset.add_array(da_poly)
dataset.add_array(da_rho_xy)
dataset.add_array(da_rho_xy_fit)
dataset.add_array(da_rho_xy_coef)
dataset.add_array(da_rho_xx)
dataset.add_array(da_mu)
# Save the data
dataset.finalize()
# Make some nice plots
# Showing Density (Rho_XY) analysis
fig, ax = plt.subplots()
ax.plot(dataset.Field, dataset.Rho_XY, 'r')
ax.plot(dataset.Field, dataset.fit_Rho_XY, 'k')
ax.set_xlabel(format_ax(dataset.Field))
ax.set_ylabel(format_ax(dataset.Rho_XY))
ax.text(
0.05,
0.95,
"Using {} current<br>".format(qtplot.siFormat(curr, suffix="A")) +
"From a linear fit:<br>" +
"dρ/dB = {}<br>".format(qtplot.siFormat(res[0], suffix="Ω")) +
"n<sub>s</sub> = 1/(|e| dρ/dB) = {:e} cm<sup>-2</sup>".format(density),
transform=ax.transAxes)
fig.savefig(path / "rho_xy.png")
# Showing Mobility analysis
fig, ax = plt.subplots()
ax.plot(dataset.Field, dataset.mu, c=color_cycle[5])
ax.set_xlabel(format_ax(dataset.Field))
ax.set_ylabel(format_ax(dataset.mu))
ax.text(
0.05,
0.95,
"Mobility extracted from:<br>" +
"μ = 1/ρ<sub>xx</sub> |e| n<sub>s</sub>, with n<sub>s</sub>= {:.2e} cm<sup>-2</sup><br>"
.format(density) +
"And using W = {}, L = {}".format(qtplot.siFormat(width, suffix="m"),
qtplot.siFormat(length, suffix="m")),
transform=ax.transAxes)
fig.savefig(path / "mobility.png")
return dataset
def describe(self):
return "%s < %s < %s" % (pg.siFormat(
self['Min'], suffix=self.units), self.fieldName,
pg.siFormat(self['Max'], suffix=self.units))
fr, Pxx_den = scipy.signal.periodogram(inp['i1'], inp['samplerate'])
#f, Pxx_den = scipy.signal.welch(input, samplerate, nperseg=10*256, scaling='spectrum')
ax.set_ylabel('PSD [pA^2/Hz]')
ax.set_xlabel('Frequency')
ax.set_yscale('log')
ax.set_xscale('log')
ax.xaxis.set_major_formatter(EngFormatter(unit='Hz'))
ax.plot(fr, Pxx_den*1e24, 'b')
ax.grid(1)
ax.autoscale()
if inp['graphene']:
fr, Pxx_den = scipy.signal.periodogram(inp['i2'], inp['samplerate'])
ax.plot(fr, Pxx_den * 1e24, 'r')
ax.legend(['Ion', 'Transverse'])
textstr = 'STD ionic: {}\nSTD trans: {}'.format(pg.siFormat(np.std(inp['i1'])), pg.siFormat(np.std(inp['i2'])))
else:
textstr = 'STD ionic: {}'.format(pg.siFormat(np.std(inp['i1'])))
ax.text(0.75, 0.1, textstr, transform=ax.transAxes, fontsize=8,
verticalalignment='top', bbox=props)
if SaveAsPDF:
pp.savefig(fig1)
else:
fig1.savefig(directory + os.sep + str(os.path.split(filename)[1][:-4]) + '_PSD.png')
fig1.clear()
ax.clear()
plt.close(fig1)