def registration(self, grid_points_x=3, grid_points_y=3):
galvothread = DAQmission()
readinchan = []
x_coords = np.linspace(-10, 10, grid_points_x + 2)[1:-1]
y_coords = np.linspace(-10, 10, grid_points_y + 2)[1:-1]
xy_mesh = np.reshape(np.meshgrid(x_coords, y_coords), (2, -1),
order='F').transpose()
galvo_coordinates = xy_mesh
camera_coordinates = np.zeros((galvo_coordinates.shape))
for i in range(galvo_coordinates.shape[0]):
galvothread.sendSingleAnalog('galvosx', galvo_coordinates[i, 0])
galvothread.sendSingleAnalog('galvosy', galvo_coordinates[i, 1])
time.sleep(1)
image = self.cam.SnapImage(0.06)
plt.imsave(
os.getcwd() +
'/CoordinatesManager/Registration_Images/2P/image_' + str(i) +
'.png', image)
camera_coordinates[i, :] = readRegistrationImages.gaussian_fitting(
image)
print('Galvo Coordinate')
print(galvo_coordinates)
print('Camera coordinates')
print(camera_coordinates)
del galvothread
self.cam.Exit()
transformation = CoordinateTransformations.polynomial2DFit(
camera_coordinates, galvo_coordinates, order=1)
print('Transformation found for x:')
print(transformation[:, :, 0])
print('Transformation found for y:')
print(transformation[:, :, 1])
return transformation
def gather_reference_coordinates_galvos(self):
galvothread = DAQmission()
readinchan = []
camera_coordinates = np.zeros((3, 2))
galvo_coordinates = np.array([[0, 3], [3, -3], [-3, -3]])
for i in range(3):
pos_x = galvo_coordinates[i, 0]
pos_y = galvo_coordinates[i, 1]
galvothread.sendSingleAnalog('galvosx', pos_x)
galvothread.sendSingleAnalog('galvosy', pos_y)
image = self.cam.SnapImage(0.04)
camera_coordinates[i, :] = gaussian_fitting(image)
del galvothread
return np.array([camera_coordinates, galvo_coordinates])
def control_for_registration(self, wavelength, value):
value = int(value)
daq = DAQmission()
if value == 0:
switch = False
else:
switch = True
if wavelength == "640":
print(wavelength + ":" + str(value))
print(str(switch))
daq.sendSingleAnalog("640AO", value)
daq.sendSingleDigital("640blanking", switch)
elif wavelength == "532":
print(wavelength + ":" + str(value))
print(str(switch))
daq.sendSingleAnalog("532AO", value)
daq.sendSingleDigital("640blanking", switch)
else:
print(wavelength + ":" + str(value))
print(str(switch))
daq.sendSingleAnalog("488AO", value)
daq.sendSingleDigital("640blanking", switch)
def control_for_registration(self, wavelength, value):
value = int(value)
daq = DAQmission()
if value == 0:
switch = False
else:
switch = True
if wavelength == '640':
print(wavelength + ':' + str(value))
print(str(switch))
daq.sendSingleAnalog('640AO', value)
daq.sendSingleDigital('640blanking', switch)
elif wavelength == '532':
print(wavelength + ':' + str(value))
print(str(switch))
daq.sendSingleAnalog('532AO', value)
daq.sendSingleDigital('640blanking', switch)
else:
print(wavelength + ':' + str(value))
print(str(switch))
daq.sendSingleAnalog('488AO', value)
daq.sendSingleDigital('640blanking', switch)
def execute_tread_single_sample_analog(self, channel):
daq = DAQmission()
if channel == '640AO':
self.lasers_status['640'][1] = self.slider640.value()
daq.sendSingleAnalog(channel, self.slider640.value() / 100)
elif channel == '532AO':
self.lasers_status['532'][1] = self.slider532.value()
daq.sendSingleAnalog(channel, self.slider532.value() / 100)
elif channel == '488AO':
self.lasers_status['488'][1] = self.slider488.value()
daq.sendSingleAnalog(channel, self.slider488.value() / 100)
self.sig_lasers_status_changed.emit(self.lasers_status)
def control_for_registration(self, wavelength, value):
value = int(value)
daq = DAQmission()
if value == 0:
switch = False
else:
switch = True
if wavelength == '640':
print(wavelength + ':' + str(value))
print(str(switch))
daq.sendSingleAnalog('640AO', value)
# execute_tread_singlesample_AOTF_analog = execute_tread_singlesample_analog()
# execute_tread_singlesample_AOTF_analog.set_waves('640AO', value)
# execute_tread_singlesample_AOTF_analog.start()
daq.sendSingleDigital('640blanking', switch)
# execute_tread_singlesample_AOTF_digital = execute_tread_singlesample_digital()
# execute_tread_singlesample_AOTF_digital.set_waves('640blanking', switch)
# execute_tread_singlesample_AOTF_digital.start()
elif wavelength == '532':
print(wavelength + ':' + str(value))
print(str(switch))
daq.sendSingleAnalog('532AO', value)
daq.sendSingleDigital('640blanking', switch)
# execute_tread_singlesample_AOTF_analog = execute_tread_singlesample_analog()
# execute_tread_singlesample_AOTF_analog.set_waves('532AO', value)
# execute_tread_singlesample_AOTF_analog.start()
# execute_tread_singlesample_AOTF_digital = execute_tread_singlesample_digital()
# execute_tread_singlesample_AOTF_digital.set_waves('640blanking', switch)
# execute_tread_singlesample_AOTF_digital.start()
else:
print(wavelength + ':' + str(value))
print(str(switch))
daq.sendSingleAnalog('488AO', value)
daq.sendSingleDigital('640blanking', switch)
class PatchclampSealTestUI(QWidget):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.saving_dir = r'M:\tnw\ist\do\projects\Neurophotonics\Brinkslab\Data\Patch clamp\seal_test'
#------------------------Initiating patchclamp class-------------------
self.sealTest = PatchclampSealTest()
self.sealTest.measurementThread.measurement.connect(
self.handleMeasurement) #Connecting to the measurement signal
self.holdTest = PatchclampSealTest_hold()
self.holdTest.measurementThread_hold.measurement.connect(
self.handleMeasurement) #Connecting to the measurement signal
self.currentclampTest = PatchclampSealTest_currentclamp()
self.currentclampTest.measurementThread_currentclamp.measurement.connect(
self.handleMeasurement) #Connecting to the measurement signal
self.zapfunction = PatchclampSealTest_zap()
#----------------------------------------------------------------------
#----------------------------------GUI---------------------------------
#----------------------------------------------------------------------
self.setFixedHeight(700)
self.setWindowTitle("Patchclamp Seal Test")
self.ICON_RED_LED = "./Icons/off.png"
self.ICON_GREEN_LED = '/Icons/on.png'
self.is_sealtesting = False
#------------------------------Gains-----------------------------------
gainContainer = StylishQT.roundQGroupBox(title="Gains")
# gainContainer.setFixedWidth(320)
gainLayout = QGridLayout()
gainLayout.addWidget(QLabel("Input Voltage"), 0, 0)
self.inVolGainList = QComboBox()
self.inVolGainList.addItems(['1/10', '1', '1/50'])
gainLayout.addWidget(self.inVolGainList, 1, 0)
gainLayout.addWidget(QLabel("Output Voltage"), 0, 1)
self.outVolGainList = QComboBox()
self.outVolGainList.addItems(['10', '2', '5', '1', '20', '50', '100'])
gainLayout.addWidget(self.outVolGainList, 1, 1)
gainLayout.addWidget(QLabel("Output Current"), 0, 2)
self.outCurGainList = QComboBox()
self.outCurGainList.addItems(['1', '2', '5', '10', '20', '50', '100'])
gainLayout.addWidget(self.outCurGainList, 1, 2)
gainLayout.addWidget(QLabel("Probe"), 0, 3)
self.probeGainList = QComboBox()
self.probeGainList.addItems(['100M\u03A9', '10G\u03A9'])
gainLayout.addWidget(self.probeGainList, 1, 3)
gainContainer.setLayout(gainLayout)
#------------------------------Wavesettings-----------------------------------
WavesettingsContainer = StylishQT.roundQGroupBox(title="Wave settings")
# WavesettingsContainer.setFixedWidth(320)
WavesettingsContainerLayout = QGridLayout()
WavesettingsContainerLayout.addWidget(QLabel("Voltage step(mV)"), 0, 0)
self.DiffVoltagebox = QSpinBox(self)
self.DiffVoltagebox.setMaximum(2000)
self.DiffVoltagebox.setMinimum(-2000)
self.DiffVoltagebox.setValue(10)
self.DiffVoltagebox.setSingleStep(10)
WavesettingsContainerLayout.addWidget(self.DiffVoltagebox, 0, 1)
WavesettingsContainerLayout.addWidget(QLabel("Voltage baseline(mV)"),
0, 2)
self.LowerVoltagebox = QSpinBox(self)
self.LowerVoltagebox.setMaximum(2000)
self.LowerVoltagebox.setMinimum(-2000)
self.LowerVoltagebox.setValue(0)
self.LowerVoltagebox.setSingleStep(30)
WavesettingsContainerLayout.addWidget(self.LowerVoltagebox, 0, 3)
WavesettingsContainer.setLayout(WavesettingsContainerLayout)
#------------------------------Membrane potential-----------------------------------
Vm_measureContainer = StylishQT.roundQGroupBox(title="Vm measurement")
# Vm_measureContainer.setFixedWidth(320)
Vm_measureContainerLayout = QGridLayout()
Vm_measureContainerLayout.addWidget(QLabel("Clamping current(pA)"), 0,
0)
self.clampingcurrentbox = QSpinBox(self)
self.clampingcurrentbox.setMaximum(2000)
self.clampingcurrentbox.setMinimum(-2000)
self.clampingcurrentbox.setValue(0)
self.clampingcurrentbox.setSingleStep(100)
Vm_measureContainerLayout.addWidget(self.clampingcurrentbox, 0, 1)
self.membraneVoltLabel = QLabel("Vm: ")
Vm_measureContainerLayout.addWidget(self.membraneVoltLabel, 0, 2)
self.VmstartButton = StylishQT.runButton()
self.VmstartButton.clicked.connect(lambda: self.measure_currentclamp())
Vm_measureContainerLayout.addWidget(self.VmstartButton, 0, 3)
self.VmstopButton = StylishQT.stop_deleteButton()
self.VmstopButton.setEnabled(False)
self.VmstopButton.clicked.connect(
lambda: self.stopMeasurement_currentclamp())
Vm_measureContainerLayout.addWidget(self.VmstopButton, 0, 4)
Vm_measureContainer.setLayout(Vm_measureContainerLayout)
#------------------------------zap-----------------------------------
zapContainer = StylishQT.roundQGroupBox(title="ZAP")
# zapContainer.setFixedWidth(320)
zapContainerLayout = QGridLayout()
self.ICON_zap = './Icons/zap.jpg'
self.zapiconlabel = QLabel()
self.zapiconlabel.setPixmap(QPixmap(self.ICON_zap))
zapContainerLayout.addWidget(self.zapiconlabel, 0, 0)
self.zapButton = QPushButton("ZAP!")
self.zapButton.setStyleSheet(
"QPushButton {color:white;background-color: blue; border-style: outset;border-radius: 10px;border-width: 2px;font: bold 14px;padding: 6px}"
"QPushButton:pressed {color:black;background-color: red; border-style: outset;border-radius: 10px;border-width: 2px;font: bold 14px;padding: 6px}"
"QPushButton:hover:!pressed {color:blue;background-color: white; border-style: outset;border-radius: 10px;border-width: 2px;font: bold 14px;padding: 6px}"
)
self.zapButton.setShortcut('z')
zapContainerLayout.addWidget(self.zapButton, 0, 1)
self.zapButton.clicked.connect(self.zap)
zapContainerLayout.addWidget(QLabel("ZAP voltage(V)"), 0, 2)
self.zapVbox = QDoubleSpinBox(self)
self.zapVbox.setMaximum(1)
self.zapVbox.setMinimum(-2000)
self.zapVbox.setValue(1)
self.zapVbox.setSingleStep(0.1)
zapContainerLayout.addWidget(self.zapVbox, 0, 3)
zapContainerLayout.addWidget(QLabel("ZAP duration(us)"), 0, 4)
self.zaptimebox = QSpinBox(self)
self.zaptimebox.setMaximum(200000000)
self.zaptimebox.setMinimum(-200000000)
self.zaptimebox.setValue(200)
self.zaptimebox.setSingleStep(200)
zapContainerLayout.addWidget(self.zaptimebox, 0, 5)
zapContainer.setLayout(zapContainerLayout)
#----------------------------Control-----------------------------------
controlContainer = StylishQT.roundQGroupBox(title="Control")
controlContainer.setFixedWidth(350)
controlLayout = QGridLayout()
# controlLayout.addWidget(QLabel("Holding Vm:"), 1, 0)
# self.HoldingList = QComboBox()
# self.HoldingList.addItems(['000 mV', '-30 mV', '-50 mV', '-40 mV', '-60 mV'])
# controlLayout.addWidget(self.HoldingList, 2, 0)
#
# self.iconlabel = QLabel(self)
# self.iconlabel.setPixmap(QPixmap(self.ICON_RED_LED))
# controlLayout.addWidget(self.iconlabel, 1, 1)
#
# self.holdingbutton = QPushButton("Hold")
# self.holdingbutton.setCheckable(True)
# #self.holdingbutton.toggle()
#
# self.holdingbutton.clicked.connect(lambda: self.btnstate())
# #self.holdingbutton.clicked.connect(lambda: self.hold())
# #self.holdingbutton.clicked.connect(self.setGreenlight)
# controlLayout.addWidget(self.holdingbutton, 2, 1)
# self.stopandholdbutton = QPushButton("Stop and Hold")
# self.stopandholdbutton.clicked.connect(lambda: self.stopMeasurement())
# self.stopandholdbutton.clicked.connect(lambda: self.measure_hold())
# self.stopandholdbutton.clicked.connect(self.setGreenlight)
# controlLayout.addWidget(self.stopandholdbutton, 0, 2)
'''
self.stopholdingbutton = QPushButton("Stop holding")
self.stopholdingbutton.clicked.connect(lambda: self.stophold())
self.stopholdingbutton.clicked.connect(self.setRedlight)
controlLayout.addWidget(self.stopholdingbutton, 2, 2)
'''
controlLayout.addWidget(gainContainer, 0, 0, 1, 2)
controlLayout.addWidget(WavesettingsContainer, 1, 0, 1, 2)
controlLayout.addWidget(Vm_measureContainer, 2, 0, 1, 2)
controlLayout.addWidget(zapContainer, 3, 0, 1, 2)
self.startButton = StylishQT.runButton("Start seal-test")
self.startButton.clicked.connect(lambda: self.measure())
# self.startButton.setFixedWidth(120)
# self.startButton.clicked.connect(self.setRedlight)
# self.startButton.clicked.connect(self.startUpdatingGUIThread)
controlLayout.addWidget(self.startButton, 4, 0, 1, 1)
self.stopButton = StylishQT.stop_deleteButton()
self.stopButton.setEnabled(False)
# self.stopButton.setFixedWidth(120)
self.stopButton.clicked.connect(lambda: self.stopMeasurement())
controlLayout.addWidget(self.stopButton, 4, 1, 1, 1)
controlContainer.setLayout(controlLayout)
#-----------------------------Plots------------------------------------
plotContainer = StylishQT.roundQGroupBox(title="Output")
plotContainer.setFixedWidth(350)
self.plotLayout = QGridLayout(
) #We set the plotLayout as an attribute of the object (i.e. self.plotLayout instead of plotLayout)
#This is to prevent the garbage collector of the C++ wrapper from deleting the layout and thus triggering errors.
#Derived from: https://stackoverflow.com/questions/17914960/pyqt-runtimeerror-wrapped-c-c-object-has-been-deleted
# and http://enki-editor.org/2014/08/23/Pyqt_mem_mgmt.html
# self.outVolPlotWidget = SlidingWindow(200, title = "Voltage", unit = "V") #Should be bigger than the readvalue
self.outCurPlotWidget = SlidingWindow(
200, title="Current",
unit="A") #Should be bigger than the readvalue
self.display_tab_widget = QTabWidget()
# self.plotLayout.addWidget(QLabel('Voltage (mV):'), 0, 0)
self.display_tab_widget.addTab(self.outCurPlotWidget, "Current")
# self.plotLayout.addWidget(self.outVolPlotWidget, 1, 0)
# self.plotLayout.addWidget(QLabel('Current (pA):'), 0, 1)
# self.display_tab_widget.addTab(self.outVolPlotWidget, "Voltage")
# self.plotLayout.addWidget(self.outCurPlotWidget, 1, 1)
valueContainer = QGroupBox("Resistance/Capacitance")
self.valueLayout = QGridLayout()
self.resistanceLabel = QLabel("Resistance: ")
self.capacitanceLabel = QLabel("Capacitance: ")
self.ratioLabel = QLabel("Ratio: ")
self.valueLayout.addWidget(self.resistanceLabel, 0, 0)
self.valueLayout.addWidget(self.capacitanceLabel, 0, 1)
self.valueLayout.addWidget(self.ratioLabel, 0, 2)
self.pipette_resistance = QLineEdit(self)
self.pipette_resistance.setPlaceholderText('Pipette resistance')
self.pipette_resistance.setFixedWidth(100)
self.valueLayout.addWidget(self.pipette_resistance, 1, 0)
self.savedataButton = QPushButton("Save figure")
self.savedataButton.clicked.connect(lambda: self.savePatchfigure())
self.valueLayout.addWidget(self.savedataButton, 1, 1)
self.resetButton = QPushButton("Reset Iplot")
self.resetButton.clicked.connect(lambda: self.ResetCurrentImgView())
self.valueLayout.addWidget(self.resetButton, 1, 2)
valueContainer.setLayout(self.valueLayout)
self.plotLayout.addWidget(self.display_tab_widget, 0, 0, 1, 1)
self.plotLayout.addWidget(valueContainer, 2, 0, 1, 1)
plotContainer.setLayout(self.plotLayout)
#---------------------------Adding to master---------------------------
master = QVBoxLayout()
master.addWidget(controlContainer)
master.addWidget(plotContainer)
self.setLayout(master)
#--------------------------Setting variables---------------------------
self.changeVolInGain(self.inVolGainList.currentText())
self.changeVolOutGain(self.outVolGainList.currentText())
self.changeCurOutGain(self.outCurGainList.currentText())
self.changeProbeGain(self.probeGainList.currentText())
self.inVolGainList.currentIndexChanged.connect(
lambda: self.changeVolInGain(self.inVolGainList.currentText()))
self.outVolGainList.currentIndexChanged.connect(
lambda: self.changeVolOutGain(self.outVolGainList.currentText()))
self.outCurGainList.currentIndexChanged.connect(
lambda: self.changeCurOutGain(self.outCurGainList.currentText()))
self.probeGainList.currentIndexChanged.connect(
lambda: self.changeProbeGain(self.probeGainList.currentText()))
def ResetCurrentImgView(self):
"""Closes the widget nicely, making sure to clear the graphics scene and release memory."""
self.outCurPlotWidget.close()
# self.outVolPlotWidget.close()
# Replot the imageview
self.outCurPlotWidget = SlidingWindow(200, title="Current", unit="A")
self.display_tab_widget.addTab(self.outCurPlotWidget, "Current")
# self.display_tab_widget.addTab(self.outVolPlotWidget, "Voltage")
def measure(self):
"""Pop up window asking to check the gains.
Returns
True if the measurement can be done
and
False if not.
"""
#check = QMessageBox.question(self, 'GAINS!', "Are all the gains corresponding?",
#QMessageBox.Yes | QMessageBox.No)
#if check == QMessageBox.Yes:
"""Start the patchclamp measurement"""
self.stopButton.setEnabled(True)
self.startButton.setEnabled(False)
self.diffvoltage = self.DiffVoltagebox.value() / 1000
self.lowervoltage = self.LowerVoltagebox.value() / 1000
self.sealTest.setWave(self.inVolGain, self.diffvoltage,
self.lowervoltage)
self.sealTest.start()
self.is_sealtesting = True
self.startUpdatingGUIThread()
def measure_hold(self):
"""Pop up window asking to check the gains.
Returns
True if the measurement can be done
and
False if not.
"""
self.holdTest.setWave(self.inVolGain,
float(self.HoldingList.currentText()[0:3]))
self.holdTest.start()
self.is_sealtesting = True
def measure_currentclamp(self):
"""Pop up window asking to check the gains.
Returns
True if the measurement can be done
and
False if not.
"""
#check = QMessageBox.question(self, 'GAINS!', "Are all the gains corresponding?",
#QMessageBox.Yes | QMessageBox.No)
#if check == QMessageBox.Yes:
"""Start the patchclamp measurement"""
self.VmstartButton.setEnabled(False)
self.VmstopButton.setEnabled(True)
self.currentclamp_value = self.clampingcurrentbox.value()
self.currentclampTest.setWave(self.inVolGain, self.probeGain,
self.currentclamp_value)
self.currentclampTest.start()
self.is_sealtesting = True
def hold(self):
constant = float(self.HoldingList.currentText()[0:3])
self.executer = DAQmission()
self.executer.sendSingleAnalog('patchAO', constant / 1000 * 10)
print("Holding vm at " + str(constant) + ' mV')
def stophold(self):
self.executer.sendSingleAnalog('patchAO', 0)
print('Stop holding')
def btnstate(self):
#source = self.sender()
if self.holdingbutton.isChecked():
self.measure_hold()
self.setGreenlight()
else:
self.stop_hold_Measurement()
self.setRedlight()
def setRedlight(self):
self.iconlabel.setPixmap(QPixmap(self.ICON_RED_LED))
def setGreenlight(self):
self.iconlabel.setPixmap(QPixmap(self.ICON_GREEN_LED))
def startUpdatingGUIThread(self):
time.sleep(0.3)
StartGUIThread = threading.Thread(target=self.startUpdatingGUI)
StartGUIThread.start()
# else:
# .disconnect()
def handleMeasurement(self, voltOut, curOut):
"""Handle the measurement. Update the graph."""
#Rescaling using gains
self.voltOut = voltOut / self.outVolGain
self.curOut = curOut / self.outCurGain / self.probeGain
def startUpdatingGUI(self):
while self.is_sealtesting == True:
try:
# self.outVolPlotWidget.append_(self.voltOut)
self.outCurPlotWidget.append_(self.curOut)
self.updateGraphs()
self.updateLabels(self.curOut, self.voltOut)
time.sleep(0.05)
except:
pass
def updateGraphs(self):
"""Update graphs."""
self.outCurPlotWidget.updateWindow()
# self.outVolPlotWidget.updateWindow()
def updateLabels(self, curOut, voltOut):
"""Update the resistance and capacitance labels.
http://scipy-lectures.org/intro/scipy/auto_examples/plot_curve_fit.html
https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.curve_fit.html"""
constants = MeasurementConstants()
sampPerCyc = int(constants.patchSealSampRate / constants.patchSealFreq)
try:
curOutCyc = curOut.reshape(int(curOut.size / sampPerCyc),
sampPerCyc)
curData = np.mean(curOutCyc, axis=0)
except:
curData = curOut
voltData = voltOut
try:
#Computing resistance
tres = np.mean(voltData)
dV = np.mean(voltData[voltData > tres]) - np.mean(
voltData[voltData < tres]) #Computing the voltage difference
dIss = np.mean(
curData[math.floor(0.15 *
sampPerCyc):math.floor(sampPerCyc / 2) -
2]) - np.mean(
curData[math.floor(0.65 * sampPerCyc):sampPerCyc -
2]) #Computing the current distance
membraneResistance = dV / (dIss * 1000000) #Ohms law (MegaOhm)
self.resistanceLabel.setText("Resistance: %.4f M\u03A9" %
membraneResistance)
self.estimated_size_resistance = 10000 / (
membraneResistance * 1000000
) #The resistance of a typical patch of membrane, RM is 10000 Omega/{cm}^2
except:
self.resistanceLabel.setText("Resistance: %s" % 'NaN')
try:
measured_vlotage = np.mean(voltData) * 1000
self.membraneVoltLabel.setText("Vm: %.2f mV" % measured_vlotage)
self.membraneVoltLabel.setStyleSheet('color: red')
except:
self.membraneVoltLabel.setText("Vm: %s" % 'NaN')
try:
#Computing capacitance
points = 10
maxCur = np.amax(curData)
maxCurIndex = np.where(curData == maxCur)[0][0]
curFit = curData[int(maxCurIndex + 1):int(
maxCurIndex + 1 + points - 1)] - 0.5 * (np.mean(curData[
math.floor(0.15 * sampPerCyc):math.floor(sampPerCyc / 2) -
2]) + np.mean(
curData[math.floor(0.65 * sampPerCyc):sampPerCyc - 2]))
timepoints = 1000 * np.arange(
3, points - 1 + 3) / constants.patchSealSampRate
#Fitting the data to an exponential of the form y=a*exp(-b*x) where b = 1/tau and tau = RC
#I(t)=I0*e^−t/τ, y=a*exp(-b*x), get log of both sides:log y = -bx + log a
fit = np.polyfit(
timepoints, curFit, 1
) #Converting the exponential to a linear function and fitting it
#Extracting data
current = fit[0]
resistance = dV * 1000 / current / 2 #Getting the resistance
tau = -1 / fit[1]
capacitance = 1000 * tau / resistance
self.capacitanceLabel.setText("Capacitance: %.4f" % capacitance)
self.estimated_size_capacitance = capacitance * (10**-12) * (10**6)
if self.estimated_size_capacitance > self.estimated_size_resistance:
self.estimated_ratio = self.estimated_size_capacitance / self.estimated_size_resistance
else:
self.estimated_ratio = self.estimated_size_resistance / self.estimated_size_capacitance
self.ratioLabel.setText(
"Ratio: %.4f" % self.estimated_ratio
) #http://www.cnbc.cmu.edu/~bard/passive2/node5.html
except:
self.capacitanceLabel.setText("Capacitance: %s" % 'NaN')
self.ratioLabel.setText("Ratio: %s" % 'NaN')
self.patch_parameters = "R_{}_C_{}".format(
round(membraneResistance, 3), round(capacitance, 3))
def stopMeasurement(self):
"""Stop the seal test."""
self.stopButton.setEnabled(False)
self.startButton.setEnabled(True)
self.sealTest.aboutToQuitHandler()
self.is_sealtesting = False
#constant = float(self.HoldingList.currentText()[0:3])
#self.executer = execute_constant_vpatch(constant/1000*10)
#print("Holding vm at "+str(constant)+' mV')
'''
def closeEvent(self, event):
"""On closing the application we have to make sure that the measuremnt
stops and the device gets freed."""
self.stopMeasurement()
'''
def stop_hold_Measurement(self):
"""Stop the seal test."""
self.holdTest.aboutToQuitHandler()
self.is_sealtesting = False
def close_hold_Event(self, event):
"""On closing the application we have to make sure that the measuremnt
stops and the device gets freed."""
self.stop_hold_Measurement()
def stopMeasurement_currentclamp(self):
"""Stop the seal test."""
self.VmstartButton.setEnabled(True)
self.VmstopButton.setEnabled(False)
self.currentclampTest.aboutToQuitHandler()
self.is_sealtesting = False
#Change gain
def changeVolInGain(self, gain):
if gain == '1':
self.inVolGain = 1
elif gain == '1/10':
self.inVolGain = 0.1
elif gain == '1/50':
self.inVolGain = 1. / 50
def changeVolOutGain(self, gain):
self.outVolGain = float(gain)
def changeCurOutGain(self, gain):
self.outCurGain = float(gain)
def changeProbeGain(self, gain):
if gain == '100M\u03A9':
self.probeGain = 100 * 10**6
elif gain == '10G\u03A9':
self.probeGain = 10 * 10**9
def zap(self):
self.zap_v = self.zapVbox.value()
self.zap_time = self.zaptimebox.value()
self.sealTest.aboutToQuitHandler()
self.zapfunction.setWave(self.inVolGain, self.zap_v, self.zap_time)
self.zapfunction.start()
time.sleep(0.06)
self.zapfunction.aboutToQuitHandler()
"""Start the patchclamp measurement"""
self.diffvoltage = self.DiffVoltagebox.value() / 1000
self.lowervoltage = self.LowerVoltagebox.value() / 1000
self.sealTest.setWave(self.inVolGain, self.diffvoltage,
self.lowervoltage)
self.sealTest.start()
def savePatchfigure(self):
# create an exporter instance, as an argument give it
# the item you wish to export
exporter = pg.exporters.ImageExporter(
self.outCurPlotWidget.getPlotItem())
# set export parameters if needed
exporter.parameters(
)['width'] = 500 # (note this also affects height parameter)
# save to file
exporter.export(
os.path.join(
self.saving_dir,
'SealTest_' + "Rpip_" + self.pipette_resistance.text() +
"Mohm_" + self.patch_parameters + '.png'))
class FocusFinder():
def __init__(self, source_of_image = "PMT", init_search_range = 0.010, total_step_number = 5, imaging_conditions = {'edge_volt':5}, \
motor_handle = None, camera_handle = None, twophoton_handle = None, *args, **kwargs):
"""
Parameters
----------
source_of_image : string, optional
The input source of image. The default is PMT.
init_search_range : int, optional
The step size when first doing coarse searching. The default is 0.010.
total_step_number : int, optional
Number of steps in total to find optimal focus. The default is 5.
imaging_conditions : list
Parameters for imaging.
For PMT, it specifies the scanning voltage.
For camera, it specifies the AOTF voltage and exposure time.
motor_handle : TYPE, optional
Handle to control PI motor. The default is None.
twophoton_handle : TYPE, optional
Handle to control Insight X3. The default is None.
Returns
-------
None.
"""
super().__init__(*args, **kwargs)
# The step size when first doing coarse searching.
self.init_search_range = init_search_range
# Number of steps in total to find optimal focus.
self.total_step_number = total_step_number
# Parameters for imaging.
self.imaging_conditions = imaging_conditions
if motor_handle == None:
# Connect the objective if the handle is not provided.
self.pi_device_instance = PIMotor()
else:
self.pi_device_instance = motor_handle
# Current position of the focus.
self.current_pos = self.pi_device_instance.GetCurrentPos()
# Number of steps already tried.
self.steps_taken = 0
# The focus degree of previous position.
self.previous_degree_of_focus = 0
# Number of going backwards.
self.turning_point = 0
# The input source of image.
self.source_of_image = source_of_image
if source_of_image == "PMT":
self.galvo = RasterScan(Daq_sample_rate = 500000, edge_volt = self.imaging_conditions['edge_volt'])
elif source_of_image == "Camera":
if camera_handle == None:
# If no camera instance fed in, initialize camera.
self.HamamatsuCam_ins = CamActuator()
self.HamamatsuCam_ins.initializeCamera()
else:
self.HamamatsuCam_ins = camera_handle
def gaussian_fit(self, move_to_focus = True):
# The upper edge.
upper_position = self.current_pos + self.init_search_range
# The lower edge.
lower_position = self.current_pos - self.init_search_range
# Generate the sampling positions.
sample_positions = np.linspace(lower_position, upper_position, self.total_step_number)
degree_of_focus_list = []
for each_pos in sample_positions:
# Go through each position and write down the focus degree.
degree_of_focus = self.evaluate_focus(round(each_pos, 6))
degree_of_focus_list.append(degree_of_focus)
print(degree_of_focus_list)
try:
interpolated_fitted_curve = ProcessImage.gaussian_fit(degree_of_focus_list)
# Generate the inpterpolated new focus position axis.
x_axis_new = np.linspace(lower_position, upper_position, len(interpolated_fitted_curve))
# Generate a dictionary and find the position where has the highest focus degree.
max_focus_pos = dict(zip(interpolated_fitted_curve, x_axis_new))[np.amax(interpolated_fitted_curve)]
if True: # Plot the fitting.
plt.plot(sample_positions, np.asarray(degree_of_focus_list),'b+:',label='data')
plt.plot(x_axis_new, interpolated_fitted_curve,'ro:',label='fit')
plt.legend()
plt.title('Fig. Fit for focus degree')
plt.xlabel('Position')
plt.ylabel('Focus degree')
plt.show()
max_focus_pos = round(max_focus_pos, 6)
print(max_focus_pos)
self.pi_device_instance.move(max_focus_pos)
# max_focus_pos_focus_degree = self.evaluate_focus(round(max_focus_pos, 6))
except:
print("Fitting failed. Find max in the list.")
max_focus_pos = sample_positions[degree_of_focus_list.index(max(degree_of_focus_list))]
print(max_focus_pos)
if move_to_focus == True:
self.pi_device_instance.move(max_focus_pos)
return max_focus_pos
def bisection(self):
"""
Bisection way of finding focus.
Returns
-------
mid_position : float
DESCRIPTION.
"""
# The upper edge in which we run bisection.
upper_position = self.current_pos + self.init_search_range
# The lower edge in which we run bisection.
lower_position = self.current_pos - self.init_search_range
for step_index in range(1, self.total_step_number + 1):
# In each step of bisection finding.
# In the first round, get degree of focus at three positions.
if step_index == 1:
# Get degree of focus in the mid.
mid_position = (upper_position + lower_position)/2
degree_of_focus_mid = self.evaluate_focus(mid_position)
print("mid focus degree: {}".format(round(degree_of_focus_mid, 5)))
# Break the loop if focus degree is below threshold which means
# that there's no cell in image.
if not ProcessImage.if_theres_cell(self.galvo_image.astype('float32')):
print('no cell')
mid_position = False
break
# Move to top and evaluate.
degree_of_focus_up = self.evaluate_focus(obj_position = upper_position)
print("top focus degree: {}".format(round(degree_of_focus_up, 5)))
# Move to bottom and evaluate.
degree_of_focus_low = self.evaluate_focus(obj_position = lower_position)
print("bot focus degree: {}".format(round(degree_of_focus_low, 5)))
# Sorting dicitonary of degrees in ascending.
biesection_range_dic = {"top":[upper_position, degree_of_focus_up],
"bot":[lower_position, degree_of_focus_low]}
# In the next rounds, only need to go to center and update boundaries.
elif step_index > 1:
# The upper edge in which we run bisection.
upper_position = biesection_range_dic["top"][0]
# The lower edge in which we run bisection.
lower_position = biesection_range_dic["bot"][0]
# Get degree of focus in the mid.
mid_position = (upper_position + lower_position)/2
degree_of_focus_mid = self.evaluate_focus(mid_position)
print("Current focus degree: {}".format(round(degree_of_focus_mid, 5)))
# If sits in upper half, make the middle values new bottom.
if biesection_range_dic["top"][1] > biesection_range_dic["bot"][1]:
biesection_range_dic["bot"] = [mid_position, degree_of_focus_mid]
else:
biesection_range_dic["top"] = [mid_position, degree_of_focus_mid]
print("The upper pos: {}; The lower: {}".format(biesection_range_dic["top"][0], biesection_range_dic["bot"][0]))
return mid_position
def evaluate_focus(self, obj_position = None):
"""
Evaluate the focus degree of certain objective position.
Parameters
----------
obj_position : float, optional
The target objective position. The default is None.
Returns
-------
degree_of_focus : float
Degree of focus.
"""
if obj_position != None:
self.pi_device_instance.move(obj_position)
# Get the image.
if self.source_of_image == "PMT":
self.galvo_image = self.galvo.run()
plt.figure()
plt.imshow(self.galvo_image)
plt.show()
if False:
with skimtiff.TiffWriter(os.path.join(r'M:\tnw\ist\do\projects\Neurophotonics\Brinkslab\Data\Xin\2020-11-17 gaussian fit auto-focus cells\trial_11', str(obj_position).replace(".", "_")+ '.tif')) as tif:
tif.save(self.galvo_image.astype('float32'), compress=0)
degree_of_focus = ProcessImage.local_entropy(self.galvo_image.astype('float32'))
elif self.source_of_image == "Camera":
# First configure the AOTF.
self.AOTF_runner = DAQmission()
# Find the AOTF channel key
for key in self.imaging_conditions:
if 'AO' in key:
# like '488AO'
AOTF_channel_key = key
# Set the AOTF first.
self.AOTF_runner.sendSingleDigital('blankingall', True)
self.AOTF_runner.sendSingleAnalog(AOTF_channel_key, self.imaging_conditions[AOTF_channel_key])
# Snap an image from camera
self.camera_image = self.HamamatsuCam_ins.SnapImage(self.imaging_conditions['exposure_time'])
time.sleep(0.5)
# Set back AOTF
self.AOTF_runner.sendSingleDigital('blankingall', False)
self.AOTF_runner.sendSingleAnalog(AOTF_channel_key, 0)
plt.figure()
plt.imshow(self.camera_image)
plt.show()
if False:
with skimtiff.TiffWriter(os.path.join(r'M:\tnw\ist\do\projects\Neurophotonics\Brinkslab\Data\Xin\2021-03-06 Camera AF\beads', str(obj_position).replace(".", "_")+ '.tif')) as tif:
tif.save(self.camera_image.astype('float32'), compress=0)
degree_of_focus = ProcessImage.variance_of_laplacian(self.camera_image.astype('float32'))
time.sleep(0.2)
return degree_of_focus
def registration(self, grid_points_x=3, grid_points_y=3):
"""
By default, generate 9 galvo voltage coordinates from (-5,-5) to (5,5),
take the camera images of these points, return a function matrix that
transforms camera_coordinates into galvo_coordinates using polynomial transform.
Parameters
----------
grid_points_x : TYPE, optional
DESCRIPTION. The default is 3.
grid_points_y : TYPE, optional
DESCRIPTION. The default is 3.
Returns
-------
transformation : TYPE
DESCRIPTION.
"""
galvothread = DAQmission()
readinchan = []
x_coords = np.linspace(-10, 10, grid_points_x + 2)[1:-1]
y_coords = np.linspace(-10, 10, grid_points_y + 2)[1:-1]
xy_mesh = np.reshape(np.meshgrid(x_coords, y_coords), (2, -1),
order='F').transpose()
galvo_coordinates = xy_mesh
camera_coordinates = np.zeros((galvo_coordinates.shape))
for i in range(galvo_coordinates.shape[0]):
galvothread.sendSingleAnalog('galvosx', galvo_coordinates[i, 0])
galvothread.sendSingleAnalog('galvosy', galvo_coordinates[i, 1])
time.sleep(1)
image = self.cam.SnapImage(0.06)
plt.imsave(
os.getcwd() +
'/CoordinatesManager/Registration_Images/2P/image_' + str(i) +
'.png', image)
camera_coordinates[i, :] = readRegistrationImages.gaussian_fitting(
image)
print('Galvo Coordinate')
print(galvo_coordinates)
print('Camera coordinates')
print(camera_coordinates)
del galvothread
self.cam.Exit()
transformation_cam2galvo = CoordinateTransformations.polynomial2DFit(
camera_coordinates, galvo_coordinates, order=1)
transformation_galvo2cam = CoordinateTransformations.polynomial2DFit(
galvo_coordinates, camera_coordinates, order=1)
print('Transformation found for x:')
print(transformation_cam2galvo[:, :, 0])
print('Transformation found for y:')
print(transformation_cam2galvo[:, :, 1])
print('galvo2cam found for x:')
print(transformation_galvo2cam[:, :, 0])
print('galvo2cam found for y:')
print(transformation_galvo2cam[:, :, 1])
return transformation_cam2galvo