def GenStartMetadata(self, mdh):
if self.active: #we are active -> write metadata
self.GetStatus()
mdh.setEntry('Camera.Name', 'Andor IXon DV97')
mdh.setEntry('Camera.Model', self.GetHeadModel())
mdh.setEntry('Camera.SerialNumber', self.GetSerialNumber())
mdh.setEntry('Camera.IntegrationTime', self.tExp)
mdh.setEntry('Camera.CycleTime', self.tKin)
mdh.setEntry('Camera.EMGain', self.GetEMGain())
mdh.setEntry('Camera.ROIPosX', self.GetROIX1())
mdh.setEntry('Camera.ROIPosY', self.GetROIY1())
mdh.setEntry('Camera.ROIWidth', self.GetROIX2() - self.GetROIX1())
mdh.setEntry('Camera.ROIHeight', self.GetROIY2() - self.GetROIY1())
mdh.setEntry('Camera.StartCCDTemp', self.GetCCDTemp())
#these should really be read from a configuration file
#hard code them here until I get around to it
#current values are at 10Mhz using e.m. amplifier
np = noiseProperties[self.GetSerialNumber()]
mdh.setEntry('Camera.ReadNoise', np['ReadNoise'])
mdh.setEntry('Camera.NoiseFactor', 1.41)
mdh.setEntry('Camera.ElectronsPerCount', np['ElectronsPerCount'])
realEMGain = ccdCalibrator.getCalibratedCCDGain(
self.GetEMGain(), self.GetCCDTempSetPoint())
if not realEMGain == None:
mdh.setEntry('Camera.TrueEMGain', realEMGain)
def GenStartMetadata(self, mdh):
self.GetStatus()
mdh.setEntry('Camera.Name', 'Simulated EM CCD Camera')
mdh.setEntry('Camera.IntegrationTime', self.GetIntegTime())
mdh.setEntry('Camera.CycleTime', self.GetIntegTime())
mdh.setEntry('Camera.EMGain', self.GetEMGain())
mdh.setEntry('Camera.ROIPosX', self.GetROIX1())
mdh.setEntry('Camera.ROIPosY', self.GetROIY1())
mdh.setEntry('Camera.ROIWidth', self.GetROIX2() - self.GetROIX1())
mdh.setEntry('Camera.ROIHeight', self.GetROIY2() - self.GetROIY1())
#mdh.setEntry('Camera.StartCCDTemp', self.GetCCDTemp())
mdh.setEntry('Camera.ReadNoise', self.noiseMaker.ReadoutNoise)
mdh.setEntry('Camera.NoiseFactor', 1.41)
mdh.setEntry('Camera.ElectronsPerCount',
self.noiseMaker.ElectronsPerCount)
mdh.setEntry('Camera.ADOffset', self.noiseMaker.ADOffset)
#mdh.setEntry('Simulation.Fluorophores', self.fluors.fl)
#mdh.setEntry('Simulation.LaserPowers', self.laserPowers)
realEMGain = ccdCalibrator.getCalibratedCCDGain(
self.GetEMGain(), self.GetCCDTempSetPoint())
if not realEMGain == None:
mdh.setEntry('Camera.TrueEMGain', realEMGain)
#if 'spec' in self.fluors.fl.dtype.fields.keys(): #set the splitter parameters
if self.fluors and 'spec' in self.fluors.fl.dtype.fields.keys():
mdh['Splitter.Channel0ROI'] = [0, 0, 128, 256]
mdh['Splitter.Channel1ROI'] = [128, 0, 128, 256]
mdh['Splitter.Flip'] = False
def GenStartMetadata(self, mdh):
self.GetStatus()
mdh.setEntry('Camera.Name', 'Simulated EM CCD Camera')
mdh.setEntry('Camera.IntegrationTime', self.GetIntegTime())
mdh.setEntry('Camera.CycleTime', self.GetIntegTime())
mdh.setEntry('Camera.EMGain', self.GetEMGain())
mdh.setEntry('Camera.ROIPosX', self.GetROIX1())
mdh.setEntry('Camera.ROIPosY', self.GetROIY1())
mdh.setEntry('Camera.ROIWidth', self.GetROIX2() - self.GetROIX1())
mdh.setEntry('Camera.ROIHeight', self.GetROIY2() - self.GetROIY1())
#mdh.setEntry('Camera.StartCCDTemp', self.GetCCDTemp())
mdh.setEntry('Camera.ReadNoise', self.noiseMaker.ReadoutNoise)
mdh.setEntry('Camera.NoiseFactor', 1.41)
mdh.setEntry('Camera.ElectronsPerCount', self.noiseMaker.ElectronsPerCount)
mdh.setEntry('Camera.ADOffset', self.noiseMaker.ADOffset)
#mdh.setEntry('Simulation.Fluorophores', self.fluors.fl)
#mdh.setEntry('Simulation.LaserPowers', self.laserPowers)
realEMGain = ccdCalibrator.getCalibratedCCDGain(self.GetEMGain(), self.GetCCDTempSetPoint())
if not realEMGain == None:
mdh.setEntry('Camera.TrueEMGain', realEMGain)
#if 'spec' in self.fluors.fl.dtype.fields.keys(): #set the splitter parameters
if self.fluors and 'spec' in self.fluors.fl.dtype.fields.keys():
mdh['Splitter.Channel0ROI'] = [0,0,128, 256]
mdh['Splitter.Channel1ROI'] = [128,0,128, 256]
mdh['Splitter.Flip'] = False
def GenStartMetadata(self, mdh):
if self.active: #we are active -> write metadata
self.GetStatus()
mdh.setEntry('Camera.Name', 'Andor IXon DV97')
mdh.setEntry('Camera.Model', self.GetHeadModel())
mdh.setEntry('Camera.SerialNumber', self.GetSerialNumber())
mdh.setEntry('Camera.IntegrationTime', self.tExp)
mdh.setEntry('Camera.CycleTime', self.tKin)
mdh.setEntry('Camera.EMGain', self.GetEMGain())
mdh.setEntry('Camera.ROIPosX', self.GetROIX1())
mdh.setEntry('Camera.ROIPosY', self.GetROIY1())
mdh.setEntry('Camera.ROIWidth', self.GetROIX2() - self.GetROIX1())
mdh.setEntry('Camera.ROIHeight', self.GetROIY2() - self.GetROIY1())
mdh.setEntry('Camera.StartCCDTemp', self.GetCCDTemp())
#these should really be read from a configuration file
#hard code them here until I get around to it
#current values are at 10Mhz using e.m. amplifier
np = noiseProperties[self.GetSerialNumber()]
mdh.setEntry('Camera.ReadNoise', np['ReadNoise'])
mdh.setEntry('Camera.NoiseFactor', 1.41)
mdh.setEntry('Camera.ElectronsPerCount', np['ElectronsPerCount'])
realEMGain = ccdCalibrator.getCalibratedCCDGain(self.GetEMGain(), self.GetCCDTempSetPoint())
if not realEMGain == None:
mdh.setEntry('Camera.TrueEMGain', realEMGain)
def OnEMGainTextChange(self, event):
calEMGain = ccdCalibrator.getCalibratedCCDGain(float(self.tEMGain.GetValue()), self.cam.GetCCDTempSetPoint())
if calEMGain == None:
self.stTrueEMGain.SetLabel('True Gain = ????')
self.stTrueEMGain.SetForegroundColour(wx.RED)
else:
self.stTrueEMGain.SetLabel('True Gain = %3.2f' % calEMGain)
self.stTrueEMGain.SetForegroundColour(wx.BLUE)
def GenStartMetadata(self, mdh):
self.GetStatus()
mdh.setEntry('Camera.Name', 'Simulated EM CCD Camera')
mdh.setEntry('Camera.IntegrationTime', self.GetIntegTime())
mdh.setEntry('Camera.CycleTime', self.GetIntegTime())
mdh.setEntry('Camera.EMGain', self.GetEMGain())
#mdh.setEntry('Camera.ROIPosX', self.GetROIX1())
#mdh.setEntry('Camera.ROIPosY', self.GetROIY1())
x1, y1, x2, y2 = self.GetROI()
mdh.setEntry('Camera.ROIOriginX', x1)
mdh.setEntry('Camera.ROIOriginY', y1)
mdh.setEntry('Camera.ROIWidth', x2 - x1)
mdh.setEntry('Camera.ROIHeight', y2 - y1)
#mdh.setEntry('Camera.StartCCDTemp', self.GetCCDTemp())
mdh.setEntry('Camera.ReadNoise', self.noiseMaker.ReadoutNoise)
mdh.setEntry('Camera.NoiseFactor', 1.41)
mdh.setEntry('Camera.ElectronsPerCount',
self.noiseMaker.ElectronsPerCount)
mdh.setEntry('Camera.ADOffset', np.mean(self.noiseMaker.ADOffset))
#mdh.setEntry('Simulation.Fluorophores', self.fluors.fl)
#mdh.setEntry('Simulation.LaserPowers', self.laserPowers)
realEMGain = ccdCalibrator.getCalibratedCCDGain(
self.GetEMGain(), self.GetCCDTempSetPoint())
if not realEMGain is None:
mdh.setEntry('Camera.TrueEMGain', realEMGain)
if self.fluors and 'spec' in self.fluors.fl.dtype.fields.keys(
): #set the splitter parameters
mdh['Splitter.Channel0ROI'] = [0, 0, 128, 256]
mdh['Splitter.Channel1ROI'] = [128, 0, 128, 256]
mdh['Splitter.Flip'] = False
chan_specs = getattr(self, '_chan_specs', None)
if not chan_specs is None:
nChans = len(chan_specs)
x_pixels = len(self.XVals)
x_chan_pixels = x_pixels / nChans
y_pixels = len(self.YVals)
mdh['Multiview.NumROIs'] = nChans
mdh['Multiview.ROISize'] = [x_chan_pixels, y_pixels]
mdh['Multiview.ChannelColor'] = list(chan_specs)
for i in range(nChans):
mdh['Multiview.ROI%dOrigin' % i] = [i * x_chan_pixels, 0]
mdh['Splitter.Channel%dROI' %
i] = [i * x_chan_pixels, 0, x_chan_pixels, y_pixels]
def draw( self ):
"""Draw data."""
#matplotlib.interactive(False)
if not 'vsp' in dir(self.scope): # can't do anything
#self.figure.show()
#matplotlib.interactive(True)
return
emGainSettings = np.arange(0, 220, 5)
emGains = ccdCalibrator.getCalibratedCCDGain(emGainSettings, self.scope.cam.GetCCDTempSetPoint())
if emGains == None: # can't do anything
#self.figure.show()
#matplotlib.interactive(True)
return
matplotlib.interactive(False)
if not hasattr( self, 'spEMGain' ):
self.spEMSNR = self.figure.add_axes([.15,.55,.7,.3])
self.spEMHeadroom = self.figure.add_axes([.15,.55,.7,.3], axisbg=None, frameon=False, label='headroom')
self.spIntSNR = self.figure.add_axes([.15,.1,.7,.3])
self.spIntFrameRate = self.spIntSNR.twinx()#self.figure.add_axes([.15,.1,.7,.3], axisbg=None, frameon=False, label='framerate')
#a, ed = numpy.histogram(self.fitResults['tIndex'], self.Size[0]/2)
self.spEMSNR.cla()
self.spEMHeadroom.cla()
self.spIntSNR.cla()
self.spIntFrameRate.cla()
currEMGain = ccdCalibrator.getCalibratedCCDGain(self.scope.cam.GetEMGain(), self.scope.cam.GetCCDTempSetPoint())
Imin = self.scope.vsp.dmin
Imax = self.scope.vsp.dmax
Imean = self.scope.vsp.dmean
off = self.scope.cam.ADOffset
#snrMin = EMCCDTheory.SNR((np.minimum(Imin - off, 1)/currEMGain)*self.scope.cam.ElectronsPerCount, self.scope.cam.ReadoutNoise, emGains, self.scope.cam.NGainElements)
snrMean = EMCCDTheory.SNR(((Imean - off)/currEMGain)*self.scope.cam.ElectronsPerCount, self.scope.cam.ReadoutNoise, emGains, self.scope.cam.NGainElements)
snrMax = EMCCDTheory.SNR(((Imax - off)/currEMGain)*self.scope.cam.ElectronsPerCount, self.scope.cam.ReadoutNoise, emGains, self.scope.cam.NGainElements)
#self.spEMSNR.plot(np.log10(emGains), 10*np.log10(snrMin), color='b')
self.spEMSNR.plot(np.log10(emGains), 10*np.log10(snrMean), color='b', lw=2)
self.spEMSNR.plot(np.log10(emGains), 10*np.log10(snrMax), color='b', lw=2)
xticks = [1, 10, 100, 1000]
self.spEMSNR.set_xticks(np.log10(xticks))
self.spEMSNR.set_xticklabels([str(t) for t in xticks])
self.spEMSNR.set_xlim(np.log10(emGains).min(), np.log10(emGains).max())
self.spEMSNR.set_xlabel('True EM Gain')
self.spEMSNR.set_ylabel('SNR [dB]', color = 'b')
for t in self.spEMSNR.get_yticklabels():
t.set_color('b')
self.spEMHeadroom.yaxis.tick_right()
self.spEMHeadroom.yaxis.set_label_position('right')
self.spEMHeadroom.xaxis.tick_top()
self.spEMHeadroom.xaxis.set_label_position('top')
self.spEMHeadroom.semilogy(np.log10(emGains), np.maximum((self.scope.cam.SaturationThreshold - off)/((Imax - off)*emGains/currEMGain), 1), color='r', lw=2)
#self.spEMHeadroom.xaxis.tick_top()
xticks = [0, 50, 100, 150, 200]
self.spEMHeadroom.set_xticks(np.log10(ccdCalibrator.getCalibratedCCDGain(xticks, self.scope.cam.GetCCDTempSetPoint())))
self.spEMHeadroom.set_xticklabels([str(t) for t in xticks])
self.spEMHeadroom.set_xlim(np.log10(emGains).min(), np.log10(emGains).max())
self.spEMHeadroom.set_xlabel('EM Gain Setting')
self.spEMHeadroom.set_ylabel('Headroom - Isat/Imax', color = 'r')
self.spEMHeadroom.set_ylim(ymin=1)
for t in self.spEMHeadroom.get_yticklabels():
t.set_color('r')
iTimes = np.logspace(-3, 0, 50)
iScale = iTimes/self.scope.cam.GetIntegTime()
#snrMeanI = EMCCDTheory.SNR((iScale*(Imean - off)/currEMGain)*self.scope.cam.ElectronsPerCount, self.scope.cam.ReadoutNoise, currEMGain, self.scope.cam.NGainElements)
snrMaxI = EMCCDTheory.SNR((iScale*(Imax - off)/currEMGain)*self.scope.cam.ElectronsPerCount, self.scope.cam.ReadoutNoise, currEMGain, self.scope.cam.NGainElements,(iScale*(Imean - off)/currEMGain)*self.scope.cam.ElectronsPerCount)
evtI = (Imax - Imean)/scipy.special.gammainc(1, self.scope.cam.GetIntegTime()/self.eventDuration)
snrFlash = EMCCDTheory.SNR(((scipy.special.gammainc(1, iTimes/self.eventDuration)*evtI + iScale*(Imean - off))/currEMGain)*self.scope.cam.ElectronsPerCount, self.scope.cam.ReadoutNoise, currEMGain, self.scope.cam.NGainElements,(iScale*(Imean - off)/currEMGain)*self.scope.cam.ElectronsPerCount)
evtI = (Imax - Imean)/scipy.special.gammainc(1, self.scope.cam.GetIntegTime()*5/self.eventDuration)
snrFlash02 = EMCCDTheory.SNR(((scipy.special.gammainc(1, iTimes*5/self.eventDuration)*evtI + iScale*(Imean - off))/currEMGain)*self.scope.cam.ElectronsPerCount, self.scope.cam.ReadoutNoise, currEMGain, self.scope.cam.NGainElements,(iScale*(Imean - off)/currEMGain)*self.scope.cam.ElectronsPerCount)
evtI = (Imax - Imean)/scipy.special.gammainc(1, self.scope.cam.GetIntegTime()/(self.eventDuration*5))
snrFlash5 = EMCCDTheory.SNR(((scipy.special.gammainc(1, iTimes/(self.eventDuration*5))*evtI + iScale*(Imean - off))/currEMGain)*self.scope.cam.ElectronsPerCount, self.scope.cam.ReadoutNoise, currEMGain, self.scope.cam.NGainElements,(iScale*(Imean - off)/currEMGain)*self.scope.cam.ElectronsPerCount)
#self.spIntSNR.plot(np.log10(iTimes), 10*np.log10(snrMeanI), color='b', lw=2)
#self.spIntSNR.plot(np.log10(iTimes), 10*np.log10(snrMaxI), color='b', lw=2)
self.spIntSNR.plot(np.log10(iTimes), 10*np.log10(snrFlash), color='b', lw=2)
self.spIntSNR.plot(np.log10(iTimes), 10*np.log10(snrFlash02), color='b', lw=2, ls=';')
self.spIntSNR.plot(np.log10(iTimes), 10*np.log10(snrFlash5), color='b', lw=2, ls='--')
xticks = [1, 10, 100, 1000]
self.spIntSNR.set_xticks(np.log10(np.array(xticks)*1e-3))
self.spIntSNR.set_xticklabels([str(t) for t in xticks])
self.spIntSNR.set_xlim(np.log10(iTimes).min(), np.log10(iTimes).max())
self.spIntSNR.set_xlabel('Integration Time [ms]')
self.spIntSNR.set_ylabel('SNR [dB]', color = 'b')
for t in self.spIntSNR.get_yticklabels():
t.set_color('b')
self.spIntFrameRate.yaxis.tick_right()
self.spIntFrameRate.yaxis.set_label_position('right')
tFrame = np.maximum(iTimes, (1e-6/self.scope.cam.HorizShiftSpeeds[0][0][self.scope.cam.HSSpeed]*self.scope.cam.GetPicWidth()*self.scope.cam.GetPicHeight()))
tFrame += self.scope.cam.GetCCDHeight()*self.scope.cam.vertShiftSpeeds[self.scope.cam.VSSpeed]*1e-6
self.spIntFrameRate.plot(np.log10(iTimes), 1./tFrame, color='g', lw=2)
xticks = [1, 10, 100, 1000]
#self.spIntSNR.set_xticks(np.log10(np.array(xticks)*1e-3))
#self.spIntSNR.set_xticklabels([str(t) for t in xticks])
#self.spIntSNR.set_xlim(np.log10(iTimes).min(), np.log10(iTimes).max())
#self.spIntSNR.set_xlabel('Integration Time [ms]')
self.spIntFrameRate.set_ylabel('FPS', color = 'g')
for t in self.spIntFrameRate.get_yticklabels():
t.set_color('g')
#self.subplot1.set_yticks([0, a.max()])
#self.subplot2.plot(ed[:-1], numpy.cumsum(a), color='g' )
#self.subplot2.set_xticks([0, ed.max()])
#self.subplot2.set_yticks([0, a.sum()])
#self.figure.show()
matplotlib.interactive(True)
