class PatchWindow(QtGui.QMainWindow):
sigWindowClosed = QtCore.Signal(object)
def __init__(self, dm, clampName):
QtGui.QMainWindow.__init__(self)
self.setWindowTitle(clampName)
self.startTime = None
self.redrawCommand = 1
self.analysisItems = {
'inputResistance': u'Ω',
'accessResistance': u'Ω',
'capacitance': 'F',
'restingPotential': 'V',
'restingCurrent': 'A',
'fitError': ''
}
self.params = {
'mode': 'vc',
'rate': 400000,
'downsample': 10,
'cycleTime': .2,
'recordTime': 0.1,
'delayTime': 0.03,
'pulseTime': 0.05,
'icPulse': -30e-12,
'vcPulse': -10e-3,
'icHolding': 0,
'vcHolding': -65e-3,
'icHoldingEnabled': False,
'icPulseEnabled': True,
'vcHoldingEnabled': False,
'vcPulseEnabled': True,
'drawFit': True,
'average': 1,
}
self.paramLock = Mutex(QtCore.QMutex.Recursive)
self.manager = dm
self.clampName = clampName
self.thread = PatchThread(self)
self.cw = QtGui.QWidget()
self.setCentralWidget(self.cw)
self.ui = Ui_Form()
self.ui.setupUi(self.cw)
#self.logBtn = LogButton("Log")
#self.statusBar().addPermanentWidget(self.logBtn)
self.setStatusBar(StatusBar())
self.stateFile = os.path.join('modules', self.clampName + '_ui.cfg')
uiState = Manager.getManager().readConfigFile(self.stateFile)
if 'geometry' in uiState:
geom = QtCore.QRect(*uiState['geometry'])
self.setGeometry(geom)
if 'window' in uiState:
ws = QtCore.QByteArray.fromPercentEncoding(uiState['window'])
self.restoreState(ws)
self.ui.splitter_2.setSizes([self.width()/4, self.width()*3./4.])
self.plots = {}
for k in self.analysisItems:
p = PlotWidget()
p.setLabel('left', text=k, units=self.analysisItems[k])
self.ui.plotLayout.addWidget(p)
self.plots[k] = p
#irp = self.plots['inputResistance']
#irp.setManualYScale()
#irp.setYLog(True)
#irp.setYRange(1e6, 1e11)
self.ui.icPulseSpin.setOpts(dec=True, step=1, minStep=1e-12, bounds=[None,None], siPrefix=True, suffix='A')
self.ui.vcPulseSpin.setOpts(dec=True, step=1, minStep=1e-3, bounds=[None,None], siPrefix=True, suffix='V')
self.ui.icHoldSpin.setOpts(dec=True, step=1, minStep=1e-12, bounds=[None,None], siPrefix=True, suffix='A')
self.ui.vcHoldSpin.setOpts(dec=True, step=1, minStep=1e-3, bounds=[None,None], siPrefix=True, suffix='V')
self.ui.cycleTimeSpin.setOpts(dec=True, step=1, minStep=1e-6, bounds=[0,None], siPrefix=True, suffix='s')
self.ui.pulseTimeSpin.setOpts(dec=True, step=1, minStep=1e-6, bounds=[0,1.], siPrefix=True, suffix='s')
self.ui.delayTimeSpin.setOpts(dec=True, step=1, minStep=1e-6, bounds=[0,1.], siPrefix=True, suffix='s')
self.stateGroup = WidgetGroup([
(self.ui.icPulseSpin, 'icPulse'),
(self.ui.vcPulseSpin, 'vcPulse'),
(self.ui.icHoldSpin, 'icHolding'),
(self.ui.vcHoldSpin, 'vcHolding'),
(self.ui.icPulseCheck, 'icPulseEnabled'),
(self.ui.vcPulseCheck, 'vcPulseEnabled'),
(self.ui.icHoldCheck, 'icHoldingEnabled'),
(self.ui.vcHoldCheck, 'vcHoldingEnabled'),
(self.ui.cycleTimeSpin, 'cycleTime'),
(self.ui.pulseTimeSpin, 'pulseTime'),
(self.ui.delayTimeSpin, 'delayTime'),
(self.ui.drawFitCheck, 'drawFit'),
(self.ui.averageSpin, 'average'),
])
self.stateGroup.setState(self.params)
self.ui.patchPlot.setLabel('left', text='Primary', units='A')
self.patchCurve = self.ui.patchPlot.plot(pen=QtGui.QPen(QtGui.QColor(200, 200, 200)))
self.patchFitCurve = self.ui.patchPlot.plot(pen=QtGui.QPen(QtGui.QColor(0, 100, 200)))
self.ui.commandPlot.setLabel('left', text='Command', units='V')
self.commandCurve = self.ui.commandPlot.plot(pen=QtGui.QPen(QtGui.QColor(200, 200, 200)))
self.ui.startBtn.clicked.connect(self.startClicked)
self.ui.recordBtn.clicked.connect(self.recordClicked)
self.ui.bathModeBtn.clicked.connect(self.bathMode)
self.ui.patchModeBtn.clicked.connect(self.patchMode)
self.ui.cellModeBtn.clicked.connect(self.cellMode)
self.ui.monitorModeBtn.clicked.connect(self.monitorMode)
self.ui.resetBtn.clicked.connect(self.resetClicked)
self.thread.finished.connect(self.threadStopped)
self.thread.sigNewFrame.connect(self.handleNewFrame)
self.ui.vcModeRadio.toggled.connect(self.updateParams)
self.stateGroup.sigChanged.connect(self.updateParams)
## Configure analysis plots, curves, and data arrays
self.analysisCurves = {}
self.analysisData = {'time': []}
for n in self.analysisItems:
w = getattr(self.ui, n+'Check')
w.clicked.connect(self.showPlots)
p = self.plots[n]
self.analysisCurves[n] = p.plot(pen=QtGui.QPen(QtGui.QColor(200, 200, 200)))
for suf in ['', 'Std']:
self.analysisData[n+suf] = []
self.showPlots()
self.updateParams()
self.show()
self.bathMode()
def quit(self):
#print "Stopping patch thread.."
geom = self.geometry()
uiState = {'window': str(self.saveState().toPercentEncoding()), 'geometry': [geom.x(), geom.y(), geom.width(), geom.height()]}
Manager.getManager().writeConfigFile(uiState, self.stateFile)
self.thread.stop(block=True)
#print "Patch thread exited; module quitting."
def closeEvent(self, ev):
self.quit()
self.sigWindowClosed.emit(self)
def bathMode(self):
self.ui.vcPulseCheck.setChecked(True)
self.ui.vcHoldCheck.setChecked(False)
self.ui.vcModeRadio.setChecked(True)
self.ui.cycleTimeSpin.setValue(0.2)
self.ui.pulseTimeSpin.setValue(10e-3)
self.ui.delayTimeSpin.setValue(10e-3)
self.ui.averageSpin.setValue(1)
def patchMode(self):
self.ui.vcPulseCheck.setChecked(True)
self.ui.vcHoldCheck.setChecked(True)
self.ui.vcModeRadio.setChecked(True)
self.ui.cycleTimeSpin.setValue(0.2)
self.ui.pulseTimeSpin.setValue(10e-3)
self.ui.delayTimeSpin.setValue(10e-3)
self.ui.averageSpin.setValue(1)
def cellMode(self):
self.ui.icPulseCheck.setChecked(True)
self.ui.icModeRadio.setChecked(True)
self.ui.cycleTimeSpin.setValue(250e-3)
self.ui.pulseTimeSpin.setValue(150e-3)
self.ui.delayTimeSpin.setValue(30e-3)
self.ui.averageSpin.setValue(1)
def monitorMode(self):
self.ui.cycleTimeSpin.setValue(40)
self.ui.averageSpin.setValue(5)
def showPlots(self):
"""Show/hide analysis plot widgets"""
for n in self.analysisItems:
w = getattr(self.ui, n+'Check')
p = self.plots[n]
if w.isChecked():
p.show()
else:
p.hide()
self.updateAnalysisPlots()
def updateParams(self, *args):
with self.paramLock:
if self.ui.icModeRadio.isChecked():
mode = 'ic'
else:
mode = 'vc'
self.params['mode'] = mode
state = self.stateGroup.state()
for p in self.params:
if p in state:
self.params[p] = state[p]
self.params['recordTime'] = self.params['delayTime'] *2.0 + self.params['pulseTime']
self.thread.updateParams()
self.redrawCommand = 2 ## may need to redraw twice to make sure the update has gone through
def recordClicked(self):
if self.ui.recordBtn.isChecked():
data = self.makeAnalysisArray()
if data.shape[0] == 0: ## no data yet; don't start the file
self.storageFile = None
return
self.newFile(data)
else:
self.storageFile = None
def newFile(self, data):
sd = self.storageDir()
self.storageFile = sd.writeFile(data, self.clampName, autoIncrement=True, appendAxis='Time', newFile=True)
if self.startTime is not None:
self.storageFile.setInfo({'startTime': self.startTime})
def storageDir(self):
return self.manager.getCurrentDir().getDir('Patch', create=True)
#def storageFile(self):
#sd = self.storageDir()
#return sd.getFile(self.clampName, create=True)
def resetClicked(self):
self.ui.recordBtn.setChecked(False)
self.recordClicked()
for n in self.analysisData:
self.analysisData[n] = []
self.startTime = None
def handleNewFrame(self, frame):
prof = Profiler('PatchWindow.handleNewFrame', disabled=True)
with self.paramLock:
mode = self.params['mode']
data = frame['data'][self.clampName]
if mode == 'vc':
self.ui.patchPlot.setLabel('left', units='A')
else:
self.ui.patchPlot.setLabel('left', units='V')
prof.mark('1')
self.patchCurve.setData(data.xvals('Time'), data['primary'])
prof.mark('2')
if self.redrawCommand > 0:
self.redrawCommand -= 1
#print "set command curve"
self.commandCurve.setData(data.xvals('Time'), data['command'])
if mode == 'vc':
self.ui.commandPlot.setLabel('left', units='V')
else:
self.ui.commandPlot.setLabel('left', units='A')
prof.mark('3')
#self.ui.patchPlot.replot()
#self.ui.commandPlot.replot()
if frame['analysis']['fitTrace'] is not None:
self.patchFitCurve.show()
self.patchFitCurve.setData(data.xvals('Time'), frame['analysis']['fitTrace'])
else:
self.patchFitCurve.hide()
prof.mark('4')
for k in self.analysisItems:
if k in frame['analysis']:
self.analysisData[k].append(frame['analysis'][k])
prof.mark('5')
for r in ['input', 'access']:
res = r+'Resistance'
label = getattr(self.ui, res+'Label')
resistance = frame['analysis'][res]
label.setText(siFormat(resistance) + u'Ω')
prof.mark('6')
self.ui.restingPotentialLabel.setText(siFormat(frame['analysis']['restingPotential'], error=frame['analysis']['restingPotentialStd'], suffix='V'))
self.ui.restingCurrentLabel.setText(siFormat(frame['analysis']['restingCurrent'], error=frame['analysis']['restingCurrentStd'], suffix='A'))
self.ui.capacitanceLabel.setText('%sF' % siFormat(frame['analysis']['capacitance']))
self.ui.fitErrorLabel.setText('%7.2g' % frame['analysis']['fitError'])
prof.mark('7')
start = data._info[-1]['DAQ']['command']['startTime']
if self.startTime is None:
self.startTime = start
if self.ui.recordBtn.isChecked() and self.storageFile is not None:
self.storageFile.setInfo({'startTime': self.startTime})
self.analysisData['time'].append(start - self.startTime)
prof.mark('8')
self.updateAnalysisPlots()
prof.mark('9')
## Record to disk if requested.
if self.ui.recordBtn.isChecked():
arr = self.makeAnalysisArray(lastOnly=True)
#print "appending array", arr.shape
if self.storageFile is None:
self.newFile(arr)
else:
arr.write(self.storageFile.name(), appendAxis='Time')
prof.mark('10')
prof.finish()
def makeAnalysisArray(self, lastOnly=False):
## Determine how much of the data to include in this array
if lastOnly:
sl = slice(-1, None)
else:
sl = slice(None)
## Generate the meta-info structure
info = [
{'name': 'Time', 'values': self.analysisData['time'][sl], 'units': 's'},
{'name': 'Value', 'cols': []}
]
for k in self.analysisItems:
for s in ['', 'Std']:
if len(self.analysisData[k+s]) < 1:
continue
info[1]['cols'].append({'name': k+s, 'units': self.analysisItems[k]})
## Create the blank MetaArray
data = MetaArray(
(len(info[0]['values']), len(info[1]['cols'])),
dtype=float,
info=info
)
## Fill with data
for k in self.analysisItems:
for s in ['', 'Std']:
if len(self.analysisData[k+s]) < 1:
continue
try:
data[:, k+s] = self.analysisData[k+s][sl]
except:
print data.shape, data[:, k+s].shape, len(self.analysisData[k+s][sl])
raise
return data
def updateAnalysisPlots(self):
for n in self.analysisItems:
p = self.plots[n]
if p.isVisible():
self.analysisCurves[n].setData(self.analysisData['time'], self.analysisData[n])
#if len(self.analysisData[n+'Std']) > 0:
#self.analysisCurves[p+'Std'].setData(self.analysisData['time'], self.analysisData[n+'Std'])
#p.replot()
def startClicked(self):
if self.ui.startBtn.isChecked():
if not self.thread.isRunning():
self.thread.start()
Manager.logMsg("Patch module started.")
self.ui.startBtn.setText('Stop')
else:
self.ui.startBtn.setEnabled(False)
self.thread.stop()
Manager.logMsg("Patch module stopped.")
def threadStopped(self):
self.ui.startBtn.setText('Start')
self.ui.startBtn.setEnabled(True)
self.ui.startBtn.setChecked(False)
class DaqChannelGui(QtGui.QWidget):
def __init__(self,
parent,
name,
config,
plot,
dev,
taskRunner,
daqName=None):
QtGui.QWidget.__init__(self, parent)
## Name of this channel
self.name = name
## Parent taskGui object
self.taskGui = weakref.ref(parent)
## Configuration for this channel defined in the device configuration file
self.config = config
self.scale = 1.0
self.units = ''
## The device handle for this channel's DAQGeneric device
self.dev = dev
## The task GUI window which contains this object
self.taskRunner = weakref.ref(taskRunner)
## Make sure task interface includes our DAQ device
if daqName is None:
self.daqDev = self.dev.getDAQName(self.name)
else:
self.daqDev = daqName
self.daqUI = self.taskRunner().getDevice(self.daqDev)
## plot widget
self.plot = plot
self.plot.setDownsampling(ds=True, auto=True, mode='peak')
self.plot.setClipToView(True)
def postUiInit(self):
## Automatically locate all read/writable widgets and group them together for easy
## save/restore operations
self.stateGroup = WidgetGroup(self)
self.stateGroup.addWidget(self.plot, name='plot')
self.displayCheckChanged()
self.ui.displayCheck.stateChanged.connect(self.displayCheckChanged)
if 'units' in self.config:
self.setUnits(self.config['units'])
else:
self.setUnits('')
def updateTitle(self):
self.ui.groupBox.setTitle(self.name + " (%s)" % self.units)
def setUnits(self, units):
self.units = units
for s in self.getSpins():
if isinstance(s, SpinBox):
s.setOpts(suffix=units)
self.updateTitle()
def getSpins(self):
return []
def setChildrenVisible(self, obj, vis):
for c in obj.children():
if isinstance(c, QtGui.QWidget):
c.setVisible(vis)
else:
self.setChildrenVisible(c, vis)
def saveState(self):
return self.stateGroup.state()
def restoreState(self, state):
self.stateGroup.setState(state)
if hasattr(self.ui, 'waveGeneratorWidget'):
self.ui.waveGeneratorWidget.update()
def clearPlots(self):
self.plot.clear()
self.currentPlot = None
def displayCheckChanged(self):
if self.stateGroup.state()['displayCheck']:
self.plot.show()
else:
self.plot.hide()
def taskStarted(self, params):
pass
def taskSequenceStarted(self):
pass
def quit(self):
#print "quit DAQGeneric channel", self.name
self.plot.close()
class DaqChannelGui(QtGui.QWidget):
def __init__(self, parent, name, config, plot, dev, taskRunner, daqName=None):
QtGui.QWidget.__init__(self, parent)
## Name of this channel
self.name = name
## Parent taskGui object
self.taskGui = weakref.ref(parent)
## Configuration for this channel defined in the device configuration file
self.config = config
self.scale = 1.0
self.units = ''
## The device handle for this channel's DAQGeneric device
self.dev = dev
## The task GUI window which contains this object
self.taskRunner = weakref.ref(taskRunner)
## Make sure task interface includes our DAQ device
if daqName is None:
self.daqDev = self.dev.getDAQName(self.name)
else:
self.daqDev = daqName
self.daqUI = self.taskRunner().getDevice(self.daqDev)
## plot widget
self.plot = plot
self.plot.setDownsampling(ds=True, auto=True, mode='peak')
self.plot.setClipToView(True)
#plot.setCanvasBackground(QtGui.QColor(0,0,0))
#plot.replot()
## Curves displayed in self.plot
#self.plots = []
def postUiInit(self):
## Automatically locate all read/writable widgets and group them together for easy
## save/restore operations
self.stateGroup = WidgetGroup(self)
self.stateGroup.addWidget(self.plot, name='plot')
self.displayCheckChanged()
#QtCore.QObject.connect(self.ui.displayCheck, QtCore.SIGNAL('stateChanged(int)'), self.displayCheckChanged)
self.ui.displayCheck.stateChanged.connect(self.displayCheckChanged)
#QtCore.QObject.connect(self.ui.groupBox, QtCore.SIGNAL('toggled(bool)'), self.groupBoxClicked)
self.ui.groupBox.toggled.connect(self.groupBoxClicked)
#if 'userScale' in self.config:
#self.setScale(self.config['userScale'])
#else:
#self.setScale(1.0)
if 'units' in self.config:
self.setUnits(self.config['units'])
else:
self.setUnits('')
def updateTitle(self):
if self.ui.groupBox.isChecked():
plus = ""
else:
plus = "[+] "
#units = " (x%s)" % siFormat(self.scale, suffix=self.units)
self.ui.groupBox.setTitle(plus + self.name + " (%s)" %self.units)
def setUnits(self, units):
self.units = units
for s in self.getSpins():
if isinstance(s, SpinBox):
s.setOpts(suffix=units)
self.updateTitle()
def getSpins(self):
return []
#def setScale(self, scale):
#self.scale = scale
#self.updateTitle()
def groupBoxClicked(self, b):
self.setChildrenVisible(self.ui.groupBox, b)
self.updateTitle()
#if b:
# self.ui.groupBox.setTitle(unicode(self.ui.groupBox.title())[4:])
#else:
# self.ui.groupBox.setTitle("[+] " + unicode(self.ui.groupBox.title()))
def setChildrenVisible(self, obj, vis):
for c in obj.children():
if isinstance(c, QtGui.QWidget):
c.setVisible(vis)
else:
self.setChildrenVisible(c, vis)
def saveState(self):
return self.stateGroup.state()
def restoreState(self, state):
self.stateGroup.setState(state)
if hasattr(self.ui, 'waveGeneratorWidget'):
self.ui.waveGeneratorWidget.update()
def clearPlots(self):
#for i in self.plots:
#i.detach()
#self.plots = []
self.plot.clear()
self.currentPlot = None
def displayCheckChanged(self):
if self.stateGroup.state()['displayCheck']:
self.plot.show()
else:
self.plot.hide()
def taskStarted(self, params):
pass
def taskSequenceStarted(self):
pass
def quit(self):
#print "quit DAQGeneric channel", self.name
self.plot.close()
class PatchWindow(QtGui.QMainWindow):
sigWindowClosed = QtCore.Signal(object)
def __init__(self, dm, config):
clampName = config['clampDev']
QtGui.QMainWindow.__init__(self)
self.setWindowTitle(clampName)
self.startTime = None
self.redrawCommand = 1
self.analysisItems = {
'inputResistance': u'Ω',
'accessResistance': u'Ω',
'capacitance': 'F',
'restingPotential': 'V',
'restingCurrent': 'A',
'fitError': ''
}
self.params = {
'mode': 'vc',
'rate': config.get('sampleRate', 100000),
'downsample': config.get('downsample', 3),
'cycleTime': .2,
'recordTime': 0.1,
'delayTime': 0.03,
'pulseTime': 0.05,
'icPulse': -30e-12,
'vcPulse': -10e-3,
'icHolding': 0,
'vcHolding': -65e-3,
'icHoldingEnabled': False,
'icPulseEnabled': True,
'vcHoldingEnabled': False,
'vcPulseEnabled': True,
'drawFit': True,
'average': 1,
}
self.paramLock = Mutex(QtCore.QMutex.Recursive)
self.manager = dm
self.clampName = clampName
self.thread = PatchThread(self)
self.cw = QtGui.QWidget()
self.setCentralWidget(self.cw)
self.ui = Ui_Form()
self.ui.setupUi(self.cw)
#self.logBtn = LogButton("Log")
#self.statusBar().addPermanentWidget(self.logBtn)
self.setStatusBar(StatusBar())
self.stateFile = os.path.join('modules', self.clampName + '_ui.cfg')
uiState = Manager.getManager().readConfigFile(self.stateFile)
if 'geometry' in uiState:
geom = QtCore.QRect(*uiState['geometry'])
self.setGeometry(geom)
if 'window' in uiState:
ws = QtCore.QByteArray.fromPercentEncoding(uiState['window'])
self.restoreState(ws)
self.ui.splitter_2.setSizes([self.width() / 4, self.width() * 3. / 4.])
self.ui.splitter.setStretchFactor(0, 30)
self.ui.splitter.setStretchFactor(1, 10)
self.plots = {}
for k in self.analysisItems:
p = PlotWidget()
p.setLabel('left', text=k, units=self.analysisItems[k])
self.ui.plotLayout.addWidget(p)
self.plots[k] = p
irp = self.plots['inputResistance']
irp.setLogMode(y=True, x=False)
irp.setYRange(6, 11)
self.ui.icPulseSpin.setOpts(dec=True,
step=1,
minStep=1e-12,
bounds=[None, None],
siPrefix=True,
suffix='A')
self.ui.vcPulseSpin.setOpts(dec=True,
step=1,
minStep=1e-3,
bounds=[None, None],
siPrefix=True,
suffix='V')
self.ui.icHoldSpin.setOpts(dec=True,
step=1,
minStep=1e-12,
bounds=[None, None],
siPrefix=True,
suffix='A')
self.ui.vcHoldSpin.setOpts(dec=True,
step=1,
minStep=1e-3,
bounds=[None, None],
siPrefix=True,
suffix='V')
self.ui.cycleTimeSpin.setOpts(dec=True,
step=1,
minStep=1e-6,
bounds=[0, None],
siPrefix=True,
suffix='s')
self.ui.pulseTimeSpin.setOpts(dec=True,
step=1,
minStep=1e-6,
bounds=[0, 1.],
siPrefix=True,
suffix='s')
self.ui.delayTimeSpin.setOpts(dec=True,
step=1,
minStep=1e-6,
bounds=[0, 1.],
siPrefix=True,
suffix='s')
self.stateGroup = WidgetGroup([
(self.ui.icPulseSpin, 'icPulse'),
(self.ui.vcPulseSpin, 'vcPulse'),
(self.ui.icHoldSpin, 'icHolding'),
(self.ui.vcHoldSpin, 'vcHolding'),
(self.ui.icPulseCheck, 'icPulseEnabled'),
(self.ui.vcPulseCheck, 'vcPulseEnabled'),
(self.ui.icHoldCheck, 'icHoldingEnabled'),
(self.ui.vcHoldCheck, 'vcHoldingEnabled'),
(self.ui.cycleTimeSpin, 'cycleTime'),
(self.ui.pulseTimeSpin, 'pulseTime'),
(self.ui.delayTimeSpin, 'delayTime'),
(self.ui.drawFitCheck, 'drawFit'),
(self.ui.averageSpin, 'average'),
])
self.stateGroup.setState(self.params)
self.ui.patchPlot.setLabel('left', text='Primary', units='A')
self.patchCurve = self.ui.patchPlot.plot(
pen=QtGui.QPen(QtGui.QColor(200, 200, 200)))
self.patchFitCurve = self.ui.patchPlot.plot(
pen=QtGui.QPen(QtGui.QColor(0, 100, 200)))
self.ui.commandPlot.setLabel('left', text='Command', units='V')
self.commandCurve = self.ui.commandPlot.plot(
pen=QtGui.QPen(QtGui.QColor(200, 200, 200)))
self.ui.startBtn.clicked.connect(self.startClicked)
self.ui.recordBtn.clicked.connect(self.recordClicked)
self.ui.bathModeBtn.clicked.connect(self.bathMode)
self.ui.patchModeBtn.clicked.connect(self.patchMode)
self.ui.cellModeBtn.clicked.connect(self.cellMode)
self.ui.monitorModeBtn.clicked.connect(self.monitorMode)
self.ui.resetBtn.clicked.connect(self.resetClicked)
self.thread.finished.connect(self.threadStopped)
self.thread.sigNewFrame.connect(self.handleNewFrame)
self.ui.vcModeRadio.toggled.connect(self.updateParams)
self.stateGroup.sigChanged.connect(self.updateParams)
## Configure analysis plots, curves, and data arrays
self.analysisCurves = {}
self.analysisData = {'time': []}
for n in self.analysisItems:
w = getattr(self.ui, n + 'Check')
w.clicked.connect(self.showPlots)
p = self.plots[n]
self.analysisCurves[n] = p.plot(
pen=QtGui.QPen(QtGui.QColor(200, 200, 200)))
for suf in ['', 'Std']:
self.analysisData[n + suf] = []
self.showPlots()
self.updateParams()
self.show()
self.bathMode()
def quit(self):
#print "Stopping patch thread.."
geom = self.geometry()
uiState = {
'window': str(self.saveState().toPercentEncoding()),
'geometry': [geom.x(),
geom.y(),
geom.width(),
geom.height()]
}
Manager.getManager().writeConfigFile(uiState, self.stateFile)
self.thread.stop(block=True)
#print "Patch thread exited; module quitting."
def closeEvent(self, ev):
self.quit()
self.sigWindowClosed.emit(self)
def bathMode(self):
self.ui.vcPulseCheck.setChecked(True)
self.ui.vcHoldCheck.setChecked(False)
self.ui.vcModeRadio.setChecked(True)
self.ui.cycleTimeSpin.setValue(0.2)
self.ui.pulseTimeSpin.setValue(10e-3)
self.ui.delayTimeSpin.setValue(10e-3)
self.ui.averageSpin.setValue(1)
def patchMode(self):
self.ui.vcPulseCheck.setChecked(True)
self.ui.vcHoldCheck.setChecked(True)
self.ui.vcModeRadio.setChecked(True)
self.ui.cycleTimeSpin.setValue(0.2)
self.ui.pulseTimeSpin.setValue(10e-3)
self.ui.delayTimeSpin.setValue(10e-3)
self.ui.averageSpin.setValue(1)
def cellMode(self):
self.ui.icPulseCheck.setChecked(True)
self.ui.icModeRadio.setChecked(True)
self.ui.cycleTimeSpin.setValue(250e-3)
self.ui.pulseTimeSpin.setValue(150e-3)
self.ui.delayTimeSpin.setValue(30e-3)
self.ui.averageSpin.setValue(1)
def monitorMode(self):
self.ui.cycleTimeSpin.setValue(40)
self.ui.averageSpin.setValue(5)
def showPlots(self):
"""Show/hide analysis plot widgets"""
for n in self.analysisItems:
w = getattr(self.ui, n + 'Check')
p = self.plots[n]
if w.isChecked():
p.show()
else:
p.hide()
self.updateAnalysisPlots()
def updateParams(self, *args):
with self.paramLock:
if self.ui.icModeRadio.isChecked():
mode = 'ic'
else:
mode = 'vc'
self.params['mode'] = mode
state = self.stateGroup.state()
for p in self.params:
if p in state:
self.params[p] = state[p]
self.params['recordTime'] = self.params[
'delayTime'] * 2.0 + self.params['pulseTime']
self.thread.updateParams()
self.redrawCommand = 2 ## may need to redraw twice to make sure the update has gone through
def recordClicked(self):
if self.ui.recordBtn.isChecked():
data = self.makeAnalysisArray()
if data.shape[0] == 0: ## no data yet; don't start the file
self.storageFile = None
return
self.newFile(data)
else:
self.storageFile = None
def newFile(self, data):
sd = self.storageDir()
self.storageFile = sd.writeFile(data,
self.clampName,
autoIncrement=True,
appendAxis='Time',
newFile=True)
if self.startTime is not None:
self.storageFile.setInfo({'startTime': self.startTime})
def storageDir(self):
return self.manager.getCurrentDir().getDir('Patch', create=True)
#def storageFile(self):
#sd = self.storageDir()
#return sd.getFile(self.clampName, create=True)
def resetClicked(self):
self.ui.recordBtn.setChecked(False)
self.recordClicked()
for n in self.analysisData:
self.analysisData[n] = []
self.startTime = None
def handleNewFrame(self, frame):
prof = Profiler('PatchWindow.handleNewFrame', disabled=True)
with self.paramLock:
mode = self.params['mode']
data = frame['data'][self.clampName]
if mode == 'vc':
self.ui.patchPlot.setLabel('left', units='A')
else:
self.ui.patchPlot.setLabel('left', units='V')
prof.mark('1')
self.patchCurve.setData(data.xvals('Time'), data['primary'])
prof.mark('2')
if self.redrawCommand > 0:
self.redrawCommand -= 1
#print "set command curve"
self.commandCurve.setData(data.xvals('Time'), data['command'])
if mode == 'vc':
self.ui.commandPlot.setLabel('left', units='V')
else:
self.ui.commandPlot.setLabel('left', units='A')
prof.mark('3')
#self.ui.patchPlot.replot()
#self.ui.commandPlot.replot()
if frame['analysis']['fitTrace'] is not None:
self.patchFitCurve.show()
self.patchFitCurve.setData(data.xvals('Time'),
frame['analysis']['fitTrace'])
else:
self.patchFitCurve.hide()
prof.mark('4')
for k in self.analysisItems:
if k in frame['analysis']:
self.analysisData[k].append(frame['analysis'][k])
prof.mark('5')
for r in ['input', 'access']:
res = r + 'Resistance'
label = getattr(self.ui, res + 'Label')
resistance = frame['analysis'][res]
label.setText(siFormat(resistance) + u'Ω')
prof.mark('6')
self.ui.restingPotentialLabel.setText(
siFormat(frame['analysis']['restingPotential'],
error=frame['analysis']['restingPotentialStd'],
suffix='V'))
self.ui.restingCurrentLabel.setText(
siFormat(frame['analysis']['restingCurrent'],
error=frame['analysis']['restingCurrentStd'],
suffix='A'))
self.ui.capacitanceLabel.setText(
'%sF' % siFormat(frame['analysis']['capacitance']))
self.ui.fitErrorLabel.setText('%7.2g' % frame['analysis']['fitError'])
prof.mark('7')
start = data._info[-1]['DAQ']['command']['startTime']
if self.startTime is None:
self.startTime = start
if self.ui.recordBtn.isChecked() and self.storageFile is not None:
self.storageFile.setInfo({'startTime': self.startTime})
self.analysisData['time'].append(start - self.startTime)
prof.mark('8')
self.updateAnalysisPlots()
prof.mark('9')
## Record to disk if requested.
if self.ui.recordBtn.isChecked():
arr = self.makeAnalysisArray(lastOnly=True)
#print "appending array", arr.shape
if self.storageFile is None:
self.newFile(arr)
else:
arr.write(self.storageFile.name(), appendAxis='Time')
prof.mark('10')
prof.finish()
def makeAnalysisArray(self, lastOnly=False):
## Determine how much of the data to include in this array
if lastOnly:
sl = slice(-1, None)
else:
sl = slice(None)
## Generate the meta-info structure
info = [{
'name': 'Time',
'values': self.analysisData['time'][sl],
'units': 's'
}, {
'name': 'Value',
'cols': []
}]
for k in self.analysisItems:
for s in ['', 'Std']:
if len(self.analysisData[k + s]) < 1:
continue
info[1]['cols'].append({
'name': k + s,
'units': self.analysisItems[k]
})
## Create the blank MetaArray
data = MetaArray((len(info[0]['values']), len(info[1]['cols'])),
dtype=float,
info=info)
## Fill with data
for k in self.analysisItems:
for s in ['', 'Std']:
if len(self.analysisData[k + s]) < 1:
continue
try:
data[:, k + s] = self.analysisData[k + s][sl]
except:
print data.shape, data[:, k + s].shape, len(
self.analysisData[k + s][sl])
raise
return data
def updateAnalysisPlots(self):
for n in self.analysisItems:
p = self.plots[n]
if p.isVisible():
self.analysisCurves[n].setData(self.analysisData['time'],
self.analysisData[n])
#if len(self.analysisData[n+'Std']) > 0:
#self.analysisCurves[p+'Std'].setData(self.analysisData['time'], self.analysisData[n+'Std'])
#p.replot()
def startClicked(self):
if self.ui.startBtn.isChecked():
if not self.thread.isRunning():
self.thread.start()
Manager.logMsg("Patch module started.")
self.ui.startBtn.setText('Stop')
else:
self.ui.startBtn.setEnabled(False)
self.thread.stop()
Manager.logMsg("Patch module stopped.")
def threadStopped(self):
self.ui.startBtn.setText('Start')
self.ui.startBtn.setEnabled(True)
self.ui.startBtn.setChecked(False)