def saveMA(self, fileName=None):
if self.imgData is None:
raise HelpfulException("There is no processed data to save.")
if fileName is None:
dh = self.getElement("File Loader").baseDir().name()
self.fileDialog = FileDialog(None, "Save image data", dh, '*.ma')
self.fileDialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
self.fileDialog.show()
self.fileDialog.fileSelected.connect(self.saveMA)
return
table = self.dbquery.table()
x = table['xPos'].min()
y = table['yPos'].min()
#print "params:", self.imgData.dtype.names
#print "shape:", self.imgData.shape
#arr = MetaArray(self.currentData) ### need to format this with axes and info
arr = MetaArray([self.imgData[p] for p in self.imgData.dtype.names], info=[
{'name':'vals', 'cols':[{'name':p} for p in self.imgData.dtype.names]},
{'name':'xPos', 'units':'m', 'values':np.arange(self.imgData.shape[0])*self.spacing+x},
{'name':'yPos', 'units':'m', 'values':np.arange(self.imgData.shape[1])*self.spacing+y},
{'spacing':self.spacing}
])
arr.write(fileName)
def saveMA(self, fileName=None):
if fileName is None:
dh = self.getElement("File Loader").baseDir().name()
self.fileDialog = FileDialog(None, "Save traces", dh, '*.ma')
self.fileDialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
self.fileDialog.show()
self.fileDialog.fileSelected.connect(self.saveMA)
return
#arr = MetaArray(self.currentData) ### need to format this with axes and info
arr = MetaArray([
self.currentData['Rs'], self.currentData['Rm'],
self.currentData['Ih']
],
info=[{
'name':
'vals',
'cols': [{
'name': 'Rs',
'units': 'Ohms'
}, {
'name': 'Rm',
'units': 'Ohms'
}, {
'name': 'Ih',
'units': 'A'
}]
}, {
'name': 'time',
'units': 's',
'values': self.currentData['time']
}])
arr.write(fileName)
def saveMA(self, fileName=None):
if fileName is None:
dh = self.getElement("File Loader").baseDir().name()
self.fileDialog = FileDialog(None, "Save traces", dh, '*.ma')
self.fileDialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
self.fileDialog.show()
self.fileDialog.fileSelected.connect(self.saveMA)
return
#arr = MetaArray(self.currentData) ### need to format this with axes and info
arr = MetaArray([self.currentData['Rs'], self.currentData['Rm'], self.currentData['Ih']], info=[
{'name':'vals', 'cols':[
{'name':'Rs', 'units':'Ohms'},
{'name':'Rm', 'units':'Ohms'},
{'name':'Ih', 'units':'A'}]},
{'name':'time', 'units':'s', 'values':self.currentData['time']}])
arr.write(fileName)
class MapImager(AnalysisModule):
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.dbIdentity = 'MapImager' ## how we identify to the database; this determines which tables we own
modPath = os.path.abspath(os.path.split(__file__)[0])
self._elements_ = OrderedDict([
('Database Query', {'type':'ctrl', 'object': DatabaseQueryWidget(self.dataManager()), 'size':(300,200), 'host':self}),
('File Loader', {'type':'fileInput', 'pos':('below', 'Database Query'), 'host':self, 'showFileTree':False}),
('Color Mapper', {'type':'ctrl', 'object': MapImagerColorMapper(filePath=os.path.join(modPath, "colorMaps"), host=self), 'size': (200,300), 'pos':('right', 'Database Query')}),
('Contour Plotter', {'type':'ctrl', 'object':ContourPlotter(host=self), 'pos':('below', 'Color Mapper')}),
('Canvas', {'type': 'canvas', 'pos': ('bottom', 'Color Mapper'), 'size': (700,600), 'allowTransforms': False, 'hideCtrl': True, 'args': {'name': 'MapImager'}}),
('Map Convolver', {'type':'ctrl', 'object': MapConvolver(), 'size': (200, 200), 'pos':('bottom', 'File Loader')}),
('Spatial Correlator', {'type':'ctrl', 'object':SpatialCorrelator(), 'size':(100,100), 'pos': ('bottom', 'Map Convolver')})
#('File Loader', {'type': 'fileInput', 'size': (100, 300), 'host': self, 'args': {'showFileTree': True}}),
#('ctrl', {'type': 'ctrl', 'object': self.ctrlWidget, 'pos': ('bottom', 'File Loader'), 'size': (100, 100)}),
#('Rs Plot', {'type': 'plot', 'pos':('right', 'File Loader'), 'size':(200, 600), 'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
#('Rm Plot', {'type': 'plot', 'pos':('bottom', 'Rs Plot'), 'size':(200, 600),'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
#('Ih Plot', {'type': 'plot', 'pos':('bottom', 'Rm Plot'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None, 's')}}),
#('Traces Plot', {'type': 'plot', 'pos':('right', 'ctrl'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None,'s')}}),
])
self.initializeElements()
for el in self.getAllElements():
self.getElement(el, create=True)
## reserve variables that will get set later
self.imgItem = None
self.spacing = None
self.imgData = None
self.dbquery = self.getElement("Database Query")
self.canvas = self.getElement("Canvas")
self.mapConvolver = self.getElement("Map Convolver")
self.colorMapper = self.getElement("Color Mapper")
self.spatialCorrelator = self.getElement("Spatial Correlator")
self.contourPlotter = self.getElement("Contour Plotter")
self.contourPlotter.setCanvas(self.canvas)
#self.outline = self.spatialCorrelator.getOutline()
#self.canvas.addGraphicsItem(self.outline)
self.dbquery.sigTableChanged.connect(self.setData)
self.mapConvolver.sigOutputChanged.connect(self.convolverOutputChanged)
self.mapConvolver.sigFieldsChanged.connect(self.convolverFieldsChanged)
self.spatialCorrelator.sigOutputChanged.connect(self.correlatorOutputChanged)
self.colorMapper.sigChanged.connect(self.computeColors)
def getFields(self):
return self.mapConvolver.getFields()
def setData(self):
data = self.dbquery.table()
self.data = data
self.getElement("Spatial Correlator").setData(data)
#self.getElement("Map Convolver").setData(data)
def convolverOutputChanged(self, data, spacing):
self.spacing = spacing
self.imgData = data
self.recolorMap(self.colorMapper.getColorArray(data))
self.adjustContours(data, self.imgItem)
def computeColors(self):
if self.imgData is not None:
try:
self.recolorMap(self.colorMapper.getColorArray(self.imgData))
except ValueError:
self.mapConvolver.process()
def correlatorOutputChanged(self, data):
#newFields= [f for f in data.dtype.descr if f not in self.data.dtype.descr]
#if len(newFields) > 0:
#arr = np.zeros(len(data), dtype=self.data.dtype.descr+newFields)
#arr[:] = self.data
#arr[:] = data
#self.data = arr
self.data = data
self.mapConvolver.setData(self.data)
def adjustContours(self, data, parentItem=None):
if data is None:
return
self.contourPlotter.adjustContours(data, parentItem=self.imgItem)
def recolorMap(self, data):
if self.imgItem is None:
if data is None:
return
table = self.dbquery.table()
x = table['xPos'].min()
y = table['yPos'].min()
self.imgItem = ImageCanvasItem(data, pos=(x, y), scale=self.spacing, movable=False, scalable=False, name="ConvolvedMap")
self.canvas.addItem(self.imgItem)
return
self.imgItem.updateImage(data)
def convolverFieldsChanged(self, fields):
self.giveOptsToCM(fields)
def giveOptsToCM(self, fields):
self.colorMapper.setArgList(fields)
self.contourPlotter.setArgList(fields)
def saveMA(self, fileName=None):
if self.imgData is None:
raise HelpfulException("There is no processed data to save.")
if fileName is None:
dh = self.getElement("File Loader").baseDir().name()
self.fileDialog = FileDialog(None, "Save image data", dh, '*.ma')
self.fileDialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
self.fileDialog.show()
self.fileDialog.fileSelected.connect(self.saveMA)
return
table = self.dbquery.table()
x = table['xPos'].min()
y = table['yPos'].min()
#print "params:", self.imgData.dtype.names
#print "shape:", self.imgData.shape
#arr = MetaArray(self.currentData) ### need to format this with axes and info
arr = MetaArray([self.imgData[p] for p in self.imgData.dtype.names], info=[
{'name':'vals', 'cols':[{'name':p} for p in self.imgData.dtype.names]},
{'name':'xPos', 'units':'m', 'values':np.arange(self.imgData.shape[0])*self.spacing+x},
{'name':'yPos', 'units':'m', 'values':np.arange(self.imgData.shape[1])*self.spacing+y},
{'spacing':self.spacing}
])
arr.write(fileName)
def loadFileRequested(self, fhList):
canvas = self.getElement('Canvas')
model = self.dataModel
for fh in fhList:
try:
## TODO: use more clever detection of Scan data here.
if fh.isFile() or model.dirType(fh) == 'Cell':
canvas.addFile(fh)
else:
#self.loadScan(fh)
debug.printExc("MapAnalyzer does not yet support loading scans")
return False
return True
except:
debug.printExc("Error loading file %s" % fh.name())
return False
class CellHealthTracker(AnalysisModule):
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrlWidget = QtGui.QWidget()
self.ctrl = CellHealthCtrlTemplate.Ui_widget()
self.ctrl.setupUi(self.ctrlWidget)
self.ctrlStateGroup = pg.WidgetGroup(self.ctrlWidget)
self.ctrl.startSpin.setOpts(step=0.05, suffix='s', siPrefix=True, value=0.35, dec=False)
self.ctrl.stopSpin.setOpts(step=0.05, suffix='s', siPrefix=True, value=0.5, dec=False)
## Setup basic GUI
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (100, 300), 'host': self, 'args': {'showFileTree': True}}),
('ctrl', {'type': 'ctrl', 'object': self.ctrlWidget, 'pos': ('bottom', 'File Loader'), 'size': (100, 100)}),
('Rs Plot', {'type': 'plot', 'pos':('right', 'File Loader'), 'size':(200, 600), 'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
('Rm Plot', {'type': 'plot', 'pos':('bottom', 'Rs Plot'), 'size':(200, 600),'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
('Ih Plot', {'type': 'plot', 'pos':('bottom', 'Rm Plot'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None, 's')}}),
('Traces Plot', {'type': 'plot', 'pos':('right', 'ctrl'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None,'s')}}),
])
self.initializeElements()
for el in self.getAllElements():
self.getElement(el, create=True)
self.tracesPlot = self.getElement('Traces Plot')
self.measurementArray = np.zeros(1000, dtype=[
('unixtime', float),
('time', float),
('Rs', float),
('Rm', float),
('Ih', float)
])
self.files = {} ## keys are dhs, values are {'data': array of time/Rs/Rm/Ih, 'ctrlState': state, 'traces': clampData}
self.ctrl.processBtn.clicked.connect(self.processClicked)
self.ctrl.saveBtn.clicked.connect(self.saveClicked)
def loadFileRequested(self, dhList):
"""Called by file loader when a file load is requested."""
## return True if file loads successfully, else return False
try:
for dh in dhList:
#if dh.name is "Patch":
#pass
if dh is None:
continue
if dh.isDir():
self.files[dh] = {}
#self.files[dh]['traces']=[]
#traces = []
self.tracesPlot.clear()
i = 0
limitTraces=False
if len(dh.subDirs()) > 80:
limitTraces=True
for f in dh.subDirs():
if i==0 or i%20==0 or not limitTraces:
fh = self.dataModel.getClampFile(dh[f])
if fh is not None:
self.loadClampData(fh, dh, plot=True)
else:
break ## assume that once we get one empty protocolDir, all the following ones will be empty too
i+=1
return True
except:
raise
def processClicked(self):
## read all the traces from the selected file
dh = self.getElement("File Loader").selectedFile()
if dh.isDir():
traces = []
for f in dh.subDirs():
fh = self.dataModel.getClampFile(dh[f])
if fh is not None:
trace = self.loadClampData(fh, dh, plot=False)
traces.append(trace)
## hand list of traces to self.process sequence
self.processSequence(traces, dh)
def loadClampData(self, f, dh, plot=True):
try:
data = f.read()
except:
print f
raise
#print f.info()
time = f.info()['__timestamp__']
#self.files[dh]['traces'].append((data, time))
if plot:
self.tracesPlot.plot(data['Channel':'primary'])
return (data, time)
def processSequence(self, traces, dh=None):
if dh is None:
dh = self.getElement("File Loader").selectedFile()
#self.files[dh]['data'] = np.zeros(len(self.files[dh]['traces']), dtype=self.measurementArray.dtype)
self.files[dh]['data'] = np.zeros(len(traces), dtype=self.measurementArray.dtype)
#for i, (data, time) in enumerate(self.files[dh]['traces']):
for i, (data, time) in enumerate(traces):
stats = self.measureParams(data)
stats['unixtime'] = time
self.files[dh]['data'][i] = stats
self.updatePlots()
def updatePlots(self):
i = len(self.measurementArray)
dtype = self.measurementArray.dtype
self.measurementArray = np.zeros(i, dtype=dtype)
count = 0
for dh in self.files:
data = self.files[dh].get('data', np.zeros(0, dtype=dtype))
if len(data) > len(self.measurementArray)-count:
self.extendMeasurementArray()
self.measurementArray[count:count+len(data)] = data
count += len(data)
self.measurementArray.sort(order='unixtime')
self.measurementArray['time'] = self.measurementArray['unixtime']-self.measurementArray[self.measurementArray['unixtime'] != 0]['unixtime'].min()
arr = self.measurementArray[self.measurementArray['unixtime'] != 0]
for x in ['Rs', 'Rm', 'Ih']:
p = self.getElement(x+' Plot')
p.clear()
p.plot(arr['time'], arr[x])
self.currentData = arr
def extendMeasurementArray(self):
i = len(self.measurementArray)
arr = np.zeros(i+1000, dtype=self.measurementArray.dtype)
arr[0:i] = self.measurementArray
self.measurementArray = arr
def saveClicked(self):
self.saveMA()
def saveMA(self, fileName=None):
if fileName is None:
dh = self.getElement("File Loader").baseDir().name()
self.fileDialog = FileDialog(None, "Save traces", dh, '*.ma')
self.fileDialog.setAcceptMode(QtGui.QFileDialog.AcceptSave)
self.fileDialog.show()
self.fileDialog.fileSelected.connect(self.saveMA)
return
#arr = MetaArray(self.currentData) ### need to format this with axes and info
arr = MetaArray([self.currentData['Rs'], self.currentData['Rm'], self.currentData['Ih']], info=[
{'name':'vals', 'cols':[
{'name':'Rs', 'units':'Ohms'},
{'name':'Rm', 'units':'Ohms'},
{'name':'Ih', 'units':'A'}]},
{'name':'time', 'units':'s', 'values':self.currentData['time']}])
arr.write(fileName)
def measureParams(self, data, display=None):
cmd = data['command']['Time':self.ctrl.startSpin.value():self.ctrl.stopSpin.value()]
#data = waveform['primary']['Time':self.ctrls['start'].value():self.ctrls['stop'].value()]
#print np.argwhere(cmd != cmd[0])
pulseStart = cmd.axisValues('Time')[np.argwhere(cmd != cmd[0])[0][0]]
pulseStop = cmd.axisValues('Time')[np.argwhere(cmd != cmd[0])[-1][0]]
#print "\n\nAnalysis parameters:", params
## Extract specific time segments
nudge = 0.1e-3
base = data['Time': :(pulseStart-nudge)]
pulse = data['Time': (pulseStart+nudge):(pulseStop-nudge)]
pulseEnd = data['Time': pulseStart+((pulseStop-pulseStart)*2./3.):pulseStop-nudge]
end = data['Time': (pulseStop+nudge): ]
#print "time ranges:", pulse.xvals('Time').min(),pulse.xvals('Time').max(),end.xvals('Time').min(),end.xvals('Time').max()
pulseAmp = pulse['command'].mean() - base['command'].mean()
method = str(self.ctrl.methodCombo.currentText())
#print method
if method == "Simple Ohm's law":
print 'using simple method'
if pulseAmp < 0:
RsPeak = data['primary'].min()
else:
RsPeak = data['primary'].max()
aRes = pulseAmp/(RsPeak-base['primary'].mean())
iRes = pulseAmp/(pulseEnd['primary'].mean() - base['primary'].mean())
rmc = base['primary'].mean()
elif method in ['Santos-Sacchi raw', 'Santos-Sacchi fit']:
### Exponential fit
## v[0] is offset to start of exp
## v[1] is amplitude of exp
## v[2] is tau
def expFn(v, t):
return (v[0]-v[1]) + v[1] * np.exp(-t / v[2])
## predictions
ar = 10e6
ir = 200e6
#if self.ctrls['mode'].currentText() == 'VC':
if True: ## Always want it to use VC settings for now
ari = pulseAmp / ar
iri = pulseAmp / ir
pred1 = [ari, ari-iri, 1e-3]
pred2 = [iri-ari, iri-ari, 1e-3]
else:
#clamp = self.manager.getDevice(self.clampName)
try:
bridge = data._info[-1]['ClampState']['ClampParams']['BridgeBalResist']
bridgeOn = data._info[-1]['ClampState']['ClampParams']['BridgeBalEnabled']
#bridge = float(clamp.getParam('BridgeBalResist')) ## pull this from the data instead.
#bridgeOn = clamp.getParam('BridgeBalEnable')
if not bridgeOn:
bridge = 0.0
except:
bridge = 0.0
#print "bridge:", bridge
arv = pulseAmp * ar - bridge
irv = pulseAmp * ir
pred1 = [arv, -irv, 10e-3]
pred2 = [irv, irv, 50e-3]
## Fit exponential to pulse and post-pulse traces
tVals1 = pulse.xvals('Time')-pulse.xvals('Time').min()
tVals2 = end.xvals('Time')-end.xvals('Time').min()
baseMean = base['primary'].mean()
fit1 = scipy.optimize.leastsq(
lambda v, t, y: y - expFn(v, t), pred1,
args=(tVals1, pulse['primary'] - baseMean),
maxfev=200, full_output=1)
#fit2 = scipy.optimize.leastsq(
#lambda v, t, y: y - expFn(v, t), pred2,
#args=(tVals2, end['primary'] - baseMean),
#maxfev=200, full_output=1, warning=False)
#err = max(abs(fit1[2]['fvec']).sum(), abs(fit2[2]['fvec']).sum())
err = abs(fit1[2]['fvec']).sum()
## Average fit1 with fit2 (needs massaging since fits have different starting points)
#print fit1
fit1 = fit1[0]
#fit2 = fit2[0]
#fitAvg = [ ## Let's just not do this.
#0.5 * (fit1[0] - (fit2[0] - (fit1[0] - fit1[1]))),
#0.5 * (fit1[1] - fit2[1]),
#0.5 * (fit1[2] + fit2[2])
#]
fitAvg = fit1
(fitOffset, fitAmp, fitTau) = fit1
#print fit1
fitTrace = np.empty(len(data))
## Handle analysis differently depending on clamp mode
#if self.ctrls['mode'].currentText() == 'VC':
if True: ## Always use VC mode for now
iBase = base['Channel': 'primary']
iPulse = pulse['Channel': 'primary']
iPulseEnd = pulseEnd['Channel': 'primary']
vBase = base['Channel': 'command']
vPulse = pulse['Channel': 'command']
vStep = vPulse.mean() - vBase.mean()
sign = [-1, 1][vStep > 0]
iStep = sign * max(1e-15, sign * (iPulseEnd.mean() - iBase.mean()))
iRes = vStep / iStep
#### From Santos-Sacchi 1993:
## 1. compute charge transfered during the charging phase
pTimes = pulse.xvals('Time')
iCapEnd = pTimes[-1]
iCap = iPulse['Time':pTimes[0]:iCapEnd] - iPulseEnd.mean()
## Instead, we will use the fit to guess how much charge transfer there would have been
## if the charging curve had gone all the way back to the beginning of the pulse
if method == "Santos-Sacchi fit":
iCap = expFn((fit1[1],fit1[1],fit1[2]), np.linspace(0, iCapEnd-pTimes[0], iCap.shape[0]))
Q = sum(iCap) * (iCapEnd - pTimes[0]) / iCap.shape[0]
Rin = iRes
Vc = vStep
Rs_denom = (Q * Rin + fitTau * Vc)
if Rs_denom != 0.0:
Rs = (Rin * fitTau * Vc) / Rs_denom
Rm = Rin - Rs
Cm = (Rin**2 * Q) / (Rm**2 * Vc)
else:
Rs = 0
Rm = 0
Cm = 0
aRes = Rs
cap = Cm
#if self.ctrls['mode'].currentText() == 'IC':
if False: ## ic measurements not yet supported in ui
iBase = base['Channel': 'command']
iPulse = pulse['Channel': 'command']
vBase = base['Channel': 'primary']
vPulse = pulse['Channel': 'primary']
vPulseEnd = pulseEnd['Channel': 'primary']
iStep = iPulse.mean() - iBase.mean()
if iStep >= 0:
vStep = max(1e-5, -fitAmp)
else:
vStep = min(-1e-5, -fitAmp)
if iStep == 0:
iStep = 1e-14
iRes = (vStep / iStep)
aRes = (fitOffset / iStep) + bridge
cap = fitTau / iRes
rmp = vBase.mean()
rmps = vBase.std()
rmc = iBase.mean()
rmcs = iBase.std()
##print rmp, rmc
## use ui to determine which stats to return
stats = np.zeros((1,), dtype=self.measurementArray.dtype)
if self.ctrl.RsCheck.isChecked():
stats['Rs'] = aRes
if self.ctrl.RmCheck.isChecked():
stats['Rm'] = iRes
#if self.ctrls['Capacitance'].isChecked():
#stats['Capacitance'] = cap
if self.ctrl.IhCheck.isChecked():
stats['Ih'] = rmc
#if self.ctrls['FitError'].isChecked():
#stats['FitError'] = err
#if self.ctrls['RestingPotential'].isChecked():
#stats['RestingPotential'] = rmp
return stats
class CellHealthTracker(AnalysisModule):
def __init__(self, host):
AnalysisModule.__init__(self, host)
self.ctrlWidget = Qt.QWidget()
self.ctrl = CellHealthCtrlTemplate.Ui_widget()
self.ctrl.setupUi(self.ctrlWidget)
self.ctrlStateGroup = pg.WidgetGroup(self.ctrlWidget)
self.ctrl.startSpin.setOpts(step=0.05, suffix='s', siPrefix=True, value=0.35, dec=False)
self.ctrl.stopSpin.setOpts(step=0.05, suffix='s', siPrefix=True, value=0.5, dec=False)
## Setup basic GUI
self._elements_ = OrderedDict([
('File Loader', {'type': 'fileInput', 'size': (100, 300), 'host': self, 'args': {'showFileTree': True}}),
('ctrl', {'type': 'ctrl', 'object': self.ctrlWidget, 'pos': ('bottom', 'File Loader'), 'size': (100, 100)}),
('Rs Plot', {'type': 'plot', 'pos':('right', 'File Loader'), 'size':(200, 600), 'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
('Rm Plot', {'type': 'plot', 'pos':('bottom', 'Rs Plot'), 'size':(200, 600),'labels':{'left':(None,'Ohms'), 'bottom':(None,'s')}}),
('Ih Plot', {'type': 'plot', 'pos':('bottom', 'Rm Plot'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None, 's')}}),
('Traces Plot', {'type': 'plot', 'pos':('right', 'ctrl'), 'size':(200, 600), 'labels':{'left':(None,'A'), 'bottom':(None,'s')}}),
])
self.initializeElements()
for el in self.getAllElements():
self.getElement(el, create=True)
self.tracesPlot = self.getElement('Traces Plot')
self.measurementArray = np.zeros(1000, dtype=[
('unixtime', float),
('time', float),
('Rs', float),
('Rm', float),
('Ih', float)
])
self.files = {} ## keys are dhs, values are {'data': array of time/Rs/Rm/Ih, 'ctrlState': state, 'traces': clampData}
self.ctrl.processBtn.clicked.connect(self.processClicked)
self.ctrl.saveBtn.clicked.connect(self.saveClicked)
def loadFileRequested(self, dhList):
"""Called by file loader when a file load is requested."""
## return True if file loads successfully, else return False
try:
for dh in dhList:
#if dh.name is "Patch":
#pass
if dh is None:
continue
if dh.isDir():
self.files[dh] = {}
#self.files[dh]['traces']=[]
#traces = []
self.tracesPlot.clear()
i = 0
limitTraces=False
if len(dh.subDirs()) > 80:
limitTraces=True
for f in dh.subDirs():
if i==0 or i%20==0 or not limitTraces:
fh = self.dataModel.getClampFile(dh[f])
if fh is not None:
self.loadClampData(fh, dh, plot=True)
else:
break ## assume that once we get one empty protocolDir, all the following ones will be empty too
i+=1
return True
except:
raise
def processClicked(self):
## read all the traces from the selected file
dh = self.getElement("File Loader").selectedFile()
if dh.isDir():
traces = []
for f in dh.subDirs():
fh = self.dataModel.getClampFile(dh[f])
if fh is not None:
trace = self.loadClampData(fh, dh, plot=False)
traces.append(trace)
## hand list of traces to self.process sequence
self.processSequence(traces, dh)
def loadClampData(self, f, dh, plot=True):
try:
data = f.read()
except:
print(f)
raise
#print f.info()
time = f.info()['__timestamp__']
#self.files[dh]['traces'].append((data, time))
if plot:
self.tracesPlot.plot(data['Channel':'primary'])
return (data, time)
def processSequence(self, traces, dh=None):
if dh is None:
dh = self.getElement("File Loader").selectedFile()
#self.files[dh]['data'] = np.zeros(len(self.files[dh]['traces']), dtype=self.measurementArray.dtype)
self.files[dh]['data'] = np.zeros(len(traces), dtype=self.measurementArray.dtype)
#for i, (data, time) in enumerate(self.files[dh]['traces']):
for i, (data, time) in enumerate(traces):
stats = self.measureParams(data)
stats['unixtime'] = time
self.files[dh]['data'][i] = stats
self.updatePlots()
def updatePlots(self):
i = len(self.measurementArray)
dtype = self.measurementArray.dtype
self.measurementArray = np.zeros(i, dtype=dtype)
count = 0
for dh in self.files:
data = self.files[dh].get('data', np.zeros(0, dtype=dtype))
if len(data) > len(self.measurementArray)-count:
self.extendMeasurementArray()
self.measurementArray[count:count+len(data)] = data
count += len(data)
self.measurementArray.sort(order='unixtime')
self.measurementArray['time'] = self.measurementArray['unixtime']-self.measurementArray[self.measurementArray['unixtime'] != 0]['unixtime'].min()
arr = self.measurementArray[self.measurementArray['unixtime'] != 0]
for x in ['Rs', 'Rm', 'Ih']:
p = self.getElement(x+' Plot')
p.clear()
p.plot(arr['time'], arr[x])
self.currentData = arr
def extendMeasurementArray(self):
i = len(self.measurementArray)
arr = np.zeros(i+1000, dtype=self.measurementArray.dtype)
arr[0:i] = self.measurementArray
self.measurementArray = arr
def saveClicked(self):
self.saveMA()
def saveMA(self, fileName=None):
if fileName is None:
dh = self.getElement("File Loader").baseDir().name()
self.fileDialog = FileDialog(None, "Save traces", dh, '*.ma')
self.fileDialog.setAcceptMode(Qt.QFileDialog.AcceptSave)
self.fileDialog.show()
self.fileDialog.fileSelected.connect(self.saveMA)
return
#arr = MetaArray(self.currentData) ### need to format this with axes and info
arr = MetaArray([self.currentData['Rs'], self.currentData['Rm'], self.currentData['Ih']], info=[
{'name':'vals', 'cols':[
{'name':'Rs', 'units':'Ohms'},
{'name':'Rm', 'units':'Ohms'},
{'name':'Ih', 'units':'A'}]},
{'name':'time', 'units':'s', 'values':self.currentData['time']}])
arr.write(fileName)
def measureParams(self, data, display=None):
cmd = data['command']['Time':self.ctrl.startSpin.value():self.ctrl.stopSpin.value()]
#data = waveform['primary']['Time':self.ctrls['start'].value():self.ctrls['stop'].value()]
#print np.argwhere(cmd != cmd[0])
pulseStart = cmd.axisValues('Time')[np.argwhere(cmd != cmd[0])[0][0]]
pulseStop = cmd.axisValues('Time')[np.argwhere(cmd != cmd[0])[-1][0]]
#print "\n\nAnalysis parameters:", params
## Extract specific time segments
nudge = 0.1e-3
base = data['Time': :(pulseStart-nudge)]
pulse = data['Time': (pulseStart+nudge):(pulseStop-nudge)]
pulseEnd = data['Time': pulseStart+((pulseStop-pulseStart)*2./3.):pulseStop-nudge]
end = data['Time': (pulseStop+nudge): ]
#print "time ranges:", pulse.xvals('Time').min(),pulse.xvals('Time').max(),end.xvals('Time').min(),end.xvals('Time').max()
pulseAmp = pulse['command'].mean() - base['command'].mean()
method = str(self.ctrl.methodCombo.currentText())
#print method
if method == "Simple Ohm's law":
print('using simple method')
if pulseAmp < 0:
RsPeak = data['primary'].min()
else:
RsPeak = data['primary'].max()
aRes = pulseAmp/(RsPeak-base['primary'].mean())
iRes = pulseAmp/(pulseEnd['primary'].mean() - base['primary'].mean())
rmc = base['primary'].mean()
elif method in ['Santos-Sacchi raw', 'Santos-Sacchi fit']:
### Exponential fit
## v[0] is offset to start of exp
## v[1] is amplitude of exp
## v[2] is tau
def expFn(v, t):
return (v[0]-v[1]) + v[1] * np.exp(-t / v[2])
## predictions
ar = 10e6
ir = 200e6
#if self.ctrls['mode'].currentText() == 'VC':
if True: ## Always want it to use VC settings for now
ari = pulseAmp / ar
iri = pulseAmp / ir
pred1 = [ari, ari-iri, 1e-3]
pred2 = [iri-ari, iri-ari, 1e-3]
else:
#clamp = self.manager.getDevice(self.clampName)
try:
bridge = data._info[-1]['ClampState']['ClampParams']['BridgeBalResist']
bridgeOn = data._info[-1]['ClampState']['ClampParams']['BridgeBalEnabled']
#bridge = float(clamp.getParam('BridgeBalResist')) ## pull this from the data instead.
#bridgeOn = clamp.getParam('BridgeBalEnable')
if not bridgeOn:
bridge = 0.0
except:
bridge = 0.0
#print "bridge:", bridge
arv = pulseAmp * ar - bridge
irv = pulseAmp * ir
pred1 = [arv, -irv, 10e-3]
pred2 = [irv, irv, 50e-3]
## Fit exponential to pulse and post-pulse traces
tVals1 = pulse.xvals('Time')-pulse.xvals('Time').min()
tVals2 = end.xvals('Time')-end.xvals('Time').min()
baseMean = base['primary'].mean()
fit1 = scipy.optimize.leastsq(
lambda v, t, y: y - expFn(v, t), pred1,
args=(tVals1, pulse['primary'] - baseMean),
maxfev=200, full_output=1)
#fit2 = scipy.optimize.leastsq(
#lambda v, t, y: y - expFn(v, t), pred2,
#args=(tVals2, end['primary'] - baseMean),
#maxfev=200, full_output=1, warning=False)
#err = max(abs(fit1[2]['fvec']).sum(), abs(fit2[2]['fvec']).sum())
err = abs(fit1[2]['fvec']).sum()
## Average fit1 with fit2 (needs massaging since fits have different starting points)
#print fit1
fit1 = fit1[0]
#fit2 = fit2[0]
#fitAvg = [ ## Let's just not do this.
#0.5 * (fit1[0] - (fit2[0] - (fit1[0] - fit1[1]))),
#0.5 * (fit1[1] - fit2[1]),
#0.5 * (fit1[2] + fit2[2])
#]
fitAvg = fit1
(fitOffset, fitAmp, fitTau) = fit1
#print fit1
fitTrace = np.empty(len(data))
## Handle analysis differently depending on clamp mode
#if self.ctrls['mode'].currentText() == 'VC':
if True: ## Always use VC mode for now
iBase = base['Channel': 'primary']
iPulse = pulse['Channel': 'primary']
iPulseEnd = pulseEnd['Channel': 'primary']
vBase = base['Channel': 'command']
vPulse = pulse['Channel': 'command']
vStep = vPulse.mean() - vBase.mean()
sign = [-1, 1][vStep > 0]
iStep = sign * max(1e-15, sign * (iPulseEnd.mean() - iBase.mean()))
iRes = vStep / iStep
#### From Santos-Sacchi 1993:
## 1. compute charge transfered during the charging phase
pTimes = pulse.xvals('Time')
iCapEnd = pTimes[-1]
iCap = iPulse['Time':pTimes[0]:iCapEnd] - iPulseEnd.mean()
## Instead, we will use the fit to guess how much charge transfer there would have been
## if the charging curve had gone all the way back to the beginning of the pulse
if method == "Santos-Sacchi fit":
iCap = expFn((fit1[1],fit1[1],fit1[2]), np.linspace(0, iCapEnd-pTimes[0], iCap.shape[0]))
Q = sum(iCap) * (iCapEnd - pTimes[0]) / iCap.shape[0]
Rin = iRes
Vc = vStep
Rs_denom = (Q * Rin + fitTau * Vc)
if Rs_denom != 0.0:
Rs = (Rin * fitTau * Vc) / Rs_denom
Rm = Rin - Rs
Cm = (Rin**2 * Q) / (Rm**2 * Vc)
else:
Rs = 0
Rm = 0
Cm = 0
aRes = Rs
cap = Cm
#if self.ctrls['mode'].currentText() == 'IC':
if False: ## ic measurements not yet supported in ui
iBase = base['Channel': 'command']
iPulse = pulse['Channel': 'command']
vBase = base['Channel': 'primary']
vPulse = pulse['Channel': 'primary']
vPulseEnd = pulseEnd['Channel': 'primary']
iStep = iPulse.mean() - iBase.mean()
if iStep >= 0:
vStep = max(1e-5, -fitAmp)
else:
vStep = min(-1e-5, -fitAmp)
if iStep == 0:
iStep = 1e-14
iRes = (vStep / iStep)
aRes = (fitOffset / iStep) + bridge
cap = fitTau / iRes
rmp = vBase.mean()
rmps = vBase.std()
rmc = iBase.mean()
rmcs = iBase.std()
##print rmp, rmc
## use ui to determine which stats to return
stats = np.zeros((1,), dtype=self.measurementArray.dtype)
if self.ctrl.RsCheck.isChecked():
stats['Rs'] = aRes
if self.ctrl.RmCheck.isChecked():
stats['Rm'] = iRes
#if self.ctrls['Capacitance'].isChecked():
#stats['Capacitance'] = cap
if self.ctrl.IhCheck.isChecked():
stats['Ih'] = rmc
#if self.ctrls['FitError'].isChecked():
#stats['FitError'] = err
#if self.ctrls['RestingPotential'].isChecked():
#stats['RestingPotential'] = rmp
return stats
