public void ConstructAsymmetryShotNoiseTOF()
{
for (int i = 0; i < points.Count; i++)
{
EDMPoint point = (EDMPoint)points[i];
Shot shot = point.Shot;
TOF bottomScaled = (TOF)shot.TOFs[detectors.IndexOf("bottomProbeScaled")];
TOF top = (TOF)shot.TOFs[detectors.IndexOf("topProbeNoBackground")];
// Multiply TOFs by their calibrations
bottomScaled *= bottomScaled.Calibration;
top *= top.Calibration;
// Need the total signal TOF for later calculations
TOF total = bottomScaled + top;
// Get background counts
double topLaserBackground = (double)point.SinglePointData["TopDetectorBackground"] * bottomScaled.Calibration;
double bottomLaserBackground = (double)point.SinglePointData["BottomDetectorBackground"] * top.Calibration;
// Calculate the shot noise variance in the asymmetry detector
TOF asymmetryVariance =
bottomScaled * bottomScaled * top * 4.0
+ bottomScaled * top * top * 4.0
+ top * top * bottomLaserBackground * 8.0
+ bottomScaled * bottomScaled * topLaserBackground * 8.0;
asymmetryVariance /= total * total * total * total;
shot.TOFs.Add(asymmetryVariance);
}
detectors.Add("asymmetryShotNoiseVariance");
}
//slight variant which can be useful for debugging
public static Shot GetFakeShot(int gateStart, int gateLength, int clockPeriod, double intensity,
int numberOfDetectors, double scanParameter)
{
Random rng = new Random();
// generate some fake data
double[] detectorOnData = new double[gateLength];
double newRand = rng.NextDouble();
double centre = gateLength / 2 + 10 * scanParameter;
for (int i = 0; i < gateLength; i++)
{
detectorOnData[i] = (5 * rng.NextDouble()) + 5 * intensity *
Math.Exp(-Math.Pow((i - centre), 2) / (0.9 * gateLength));
}
TOF tofOn = new TOF();
tofOn.Data = detectorOnData;
tofOn.GateStartTime = gateStart;
tofOn.ClockPeriod = clockPeriod;
tofOn.Calibration = 1;
Shot sOn = new Shot();
for (int j = 0; j < numberOfDetectors; j++)
{
sOn.TOFs.Add(tofOn);
}
return(sOn);
}
public void GotPoint(int point, EDMPoint p)
{
// store the leakage measurements ready for the graph update
northLeakages[leakageIndex] = (double)p.SinglePointData["NorthCurrent"];
southLeakages[leakageIndex] = (double)p.SinglePointData["SouthCurrent"];
leakageIndex++;
if ((point % UPDATE_EVERY) == 0)
{
Shot data = p.Shot;
mainWindow.TankLevel = point;
TOF tof = (TOF)data.TOFs[0];
mainWindow.PlotTOF(0, tof.Data, tof.GateStartTime, tof.ClockPeriod);
tof = (TOF)data.TOFs[1];
mainWindow.PlotTOF(1, tof.Data, tof.GateStartTime, tof.ClockPeriod);
tof = (TOF)data.TOFs[2];
mainWindow.PlotTOF(2, tof.Data, tof.GateStartTime, tof.ClockPeriod);
tof = (TOF)data.TOFs[5];
mainWindow.PlotTOF(3, tof.Data, tof.GateStartTime, tof.ClockPeriod);
// update the leakage graphs
mainWindow.AppendLeakageMeasurement(new double[] { northLeakages[0] }, new double[] { southLeakages[0] });
leakageIndex = 0;
}
}
public void Add(TOF t)
{
if (!initialised)
{
// the first TOF to be added defines the parameters
gateStartTime = t.GateStartTime;
clockPeriod = t.ClockPeriod;
calibration = t.Calibration;
stats = new RunningStatistics[t.Length];
for (int i = 0; i < Length; i++)
{
stats[i] = new RunningStatistics();
}
initialised = true;
}
// add the TOF data - very minimal error checking: just check the lengths
if (t.Length == Length)
{
for (int i = 0; i < Length; i++)
{
stats[i].Push(t.Data[i]);
}
}
else
{
throw new TOFAccumulatorException();
}
}
public TOF GetAverageTOF(int index)
{
TOF temp = new TOF();
for (int i = 0 ; i < points.Count ; i++) temp += (TOF)((EDMPoint)points[i]).Shot.TOFs[index];
return temp /(points.Count);
}
public void NewScanLoaded()
{
window.ClearAll();
Scan averageScan = Controller.GetController().DataStore.AverageScan;
if (averageScan.Points.Count == 0)
{
return;
}
startSpectrumGate = averageScan.MinimumScanParameter;
endSpectrumGate = averageScan.MaximumScanParameter;
TOF tof = ((TOF)((Shot)((ScanPoint)averageScan.Points[0]).OnShots[0]).TOFs[0]);
startTOFGate = tof.GateStartTime;
endTOFGate = tof.GateStartTime + tof.ClockPeriod * tof.Length;
UpdateTOFAveragePlots();
UpdatePMTAveragePlots();
window.SpectrumGate = new PlotParameters(startSpectrumGate, endSpectrumGate /*, averageScan.Points.Count*/);
window.TOFGate = new PlotParameters(startTOFGate, endTOFGate);
if (spectrumFitMode == FitMode.Average)
{
FitAndPlotSpectrum(averageScan);
}
if (tofFitMode == FitMode.Average)
{
FitAverageTOF();
}
}
// NOTE: this function is rendered somewhat obsolete by the BlockTOFDemodulator.
// This function takes a list of switches, defining an analysis channel, and gives the
// average TOF for that analysis channel's positively contributing TOFs and the same for
// the negative contributors. Note that this definition may or may not line up with how
// the analysis channels are defined (they may differ by a sign, which might depend on
// the number of switches in the channel).
public TOF[] GetSwitchTOFs(string[] switches, int index)
{
TOF[] tofs = new TOF[2];
// calculate the state of the channel for each point in the block
int numSwitches = switches.Length;
int waveformLength = config.GetModulationByName(switches[0]).Waveform.Length;
List<bool[]> switchBits = new List<bool[]>();
foreach (string s in switches)
switchBits.Add(config.GetModulationByName(s).Waveform.Bits);
List<bool> channelStates = new List<bool>();
for (int point = 0; point < waveformLength; point++)
{
bool channelState = false;
for (int i = 0; i < numSwitches; i++)
{
channelState = channelState ^ switchBits[i][point];
}
channelStates.Add(channelState);
}
// build the "on" and "off" average TOFs
TOF tOn = new TOF();
TOF tOff = new TOF();
for (int i = 0; i < waveformLength; i++)
{
if (channelStates[i]) tOn += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]);
else tOff += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]);
}
tOn /= (waveformLength / 2);
tOff /= (waveformLength / 2);
tofs[0] = tOn;
tofs[1] = tOff;
return tofs;
}
private TOF[] GetTOFDetectorData(Block b, string detector)
{
int detectorIndex = b.detectors.IndexOf(detector);
TOF[] tofList = new TOF[b.Points.Count];
for (int i = 0; i < b.Points.Count; i++)
{
tofList[i] = (TOF)((EDMPoint)b.Points[i]).Shot.TOFs[detectorIndex];
}
return(tofList);
}
public TOF GetAverageTOF(int index)
{
TOF temp = new TOF();
for (int i = 0; i < points.Count; i++)
{
temp += (TOF)((EDMPoint)points[i]).Shot.TOFs[index];
}
return(temp / (points.Count));
}
// this function subtracts the background off a TOF signal
// the background is taken as the mean of a background array of points
public void SubtractBackgroundFromProbeDetectorTOFs()
{
for (int i = 0; i < points.Count; i++)
{
EDMPoint point = (EDMPoint)points[i];
Shot shot = point.Shot;
TOF t = (TOF)shot.TOFs[0];
double bg = t.GatedMeanAndUncertainty(2800, 2900)[0];
TOF bgSubtracted = t - bg;
// if value if negative, set to zero
for (int j = 0; j < bgSubtracted.Length; j++)
{
if (bgSubtracted.Data[j] < 0)
{
bgSubtracted.Data[j] = 0.0;
}
}
bgSubtracted.Calibration = t.Calibration;
shot.TOFs.Add(bgSubtracted);
point.SinglePointData.Add("BottomDetectorBackground", bg);
}
// give these data a name
detectors.Add("bottomProbeNoBackground");
for (int i = 0; i < points.Count; i++)
{
EDMPoint point = (EDMPoint)points[i];
Shot shot = point.Shot;
TOF t = (TOF)shot.TOFs[1];
double bg = t.GatedMeanAndUncertainty(3200, 3300)[0];
TOF bgSubtracted = t - bg;
// if value if negative, set to zero
for (int j = 0; j < bgSubtracted.Length; j++)
{
if (bgSubtracted.Data[j] < 0)
{
bgSubtracted.Data[j] = 0.0;
}
}
bgSubtracted.Calibration = t.Calibration;
shot.TOFs.Add(bgSubtracted);
point.SinglePointData.Add("TopDetectorBackground", bg);
}
// give these data a name
detectors.Add("topProbeNoBackground");
}
// this function adds a new set of detector data to the block, constructed
// by calculating the asymmetry of the top and bottom detectors (which must
// be scaled first)
public void ConstructAsymmetryTOF()
{
for (int i = 0; i < points.Count; i++)
{
Shot shot = ((EDMPoint)points[i]).Shot;
int bottomScaledIndex = detectors.IndexOf("bottomProbeScaled");
int topIndex = detectors.IndexOf("topProbeNoBackground");
TOF asymmetry = ((TOF)shot.TOFs[bottomScaledIndex] - (TOF)shot.TOFs[topIndex]) / ((TOF)shot.TOFs[bottomScaledIndex] + (TOF)shot.TOFs[topIndex]);
asymmetry.Calibration = 1;
shot.TOFs.Add(asymmetry);
}
// give these data a name
detectors.Add("asymmetry");
}
// this function adds a new set of detector data to the block, constructed
// by normalising the PMT data to the norm data. The normalisation is done
// by dividing the PMT tofs through by the integrated norm data. The integration
// is done according to the provided GatedDetectorExtractSpec.
//public void Normalise(GatedDetectorExtractSpec normGate)
//{
// GatedDetectorData normData = GatedDetectorData.ExtractFromBlock(this, normGate);
// double averageNorm = 0;
// foreach (double val in normData.PointValues) averageNorm += val;
// averageNorm /= normData.PointValues.Count;
// for (int i = 0; i < points.Count; i++)
// {
// Shot shot = ((EDMPoint)points[i]).Shot;
// TOF normedTOF = ((TOF)shot.TOFs[0]) / (normData.PointValues[i] * (1 / averageNorm));
// shot.TOFs.Add(normedTOF);
// }
// // give these data a name
// detectors.Add("topNormed");
//}
//// this function adds a new set of detector data to the block, constructed
//// by calculating the asymmetry of the top and bottom detectors The integration
//// is done according to the provided GatedDetectorExtractSpec.
//public void Normalise(GatedDetectorExtractSpec normGate)
//{
// GatedDetectorData normData = GatedDetectorData.ExtractFromBlock(this, normGate);
// for (int i = 0; i < points.Count; i++)
// {
// Shot shot = ((EDMPoint)points[i]).Shot;
// TOF normedTOF = ((TOF)shot.TOFs[0]) / (normData.PointValues[i] );
// shot.TOFs.Add(normedTOF);
// }
// // give these data a name
// detectors.Add("topNormed");
//}
// this function takes some of the single point data and adds it to the block shots as TOFs
// with one data point in them. This allows us to use the same code to break all of the data
// into channels.
public void TOFuliseSinglePointData(string[] channelsToTOFulise)
{
foreach (string spv in channelsToTOFulise)
{
for (int i = 0; i < points.Count; i++)
{
EDMPoint point = (EDMPoint)points[i];
Shot shot = point.Shot;
TOF spvTOF = new TOF((double)point.SinglePointData[spv]);
shot.TOFs.Add(spvTOF);
}
// give these data a name
detectors.Add(spv);
}
}
// This method is called by the GUI thread once the form has
// loaded and the UI is ready.
internal void UIInitialise()
{
// put the version number in the title bar to avoid confusion!
Version version = Assembly.GetEntryAssembly().GetName().Version;
mainWindow.Text += " " + version.ToString();
// This will load the shared code assembly so that we can get its
// version number and display that as well.
TOF t = new TOF();
Version sharedCodeVersion = Assembly.GetAssembly(t.GetType()).GetName().Version;
mainWindow.Text += " (" + sharedCodeVersion.ToString() + ")";
// start the status monitor
statusMonitorTimer = new System.Threading.Timer(new TimerCallback(UpdateStatusMonitor), null, 500, 500);
}
// this function scales up the bottom detector to match the top
public void CreateScaledBottomProbe()
{
for (int i = 0; i < points.Count; i++)
{
Shot shot = ((EDMPoint)points[i]).Shot;
int bottomIndex = detectors.IndexOf("bottomProbeNoBackground");
int topIndex = detectors.IndexOf("topProbeNoBackground");
TOF bottomTOF = (TOF)shot.TOFs[bottomIndex];
TOF topTOF = (TOF)shot.TOFs[topIndex];
TOF bottomScaled = TOF.ScaleTOFInTimeToMatchAnotherTOF(bottomTOF, topTOF, kDetectorDistanceRatio);
bottomScaled.Calibration = bottomTOF.Calibration;
shot.TOFs.Add(bottomScaled);
}
// give these data a name
detectors.Add("bottomProbeScaled");
}
// NOTE: this function is rendered somewhat obsolete by the BlockTOFDemodulator.
// This function takes a list of switches, defining an analysis channel, and gives the
// average TOF for that analysis channel's positively contributing TOFs and the same for
// the negative contributors. Note that this definition may or may not line up with how
// the analysis channels are defined (they may differ by a sign, which might depend on
// the number of switches in the channel).
public TOF[] GetSwitchTOFs(string[] switches, int index)
{
TOF[] tofs = new TOF[2];
// calculate the state of the channel for each point in the block
int numSwitches = switches.Length;
int waveformLength = config.GetModulationByName(switches[0]).Waveform.Length;
List <bool[]> switchBits = new List <bool[]>();
foreach (string s in switches)
{
switchBits.Add(config.GetModulationByName(s).Waveform.Bits);
}
List <bool> channelStates = new List <bool>();
for (int point = 0; point < waveformLength; point++)
{
bool channelState = false;
for (int i = 0; i < numSwitches; i++)
{
channelState = channelState ^ switchBits[i][point];
}
channelStates.Add(channelState);
}
// build the "on" and "off" average TOFs
TOF tOn = new TOF();
TOF tOff = new TOF();
for (int i = 0; i < waveformLength; i++)
{
if (channelStates[i])
{
tOn += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]);
}
else
{
tOff += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]);
}
}
tOn /= (waveformLength / 2);
tOff /= (waveformLength / 2);
tofs[0] = tOn;
tofs[1] = tOff;
return(tofs);
}
private void UpdateTOFAveragePlots()
{
Scan averageScan = Controller.GetController().DataStore.AverageScan;
if (averageScan.Points.Count == 0)
{
return;
}
TOF tof =
(TOF)((ArrayList)averageScan.GetGatedAverageOnShot(startSpectrumGate, endSpectrumGate).TOFs)[0];
window.PlotAverageOnTOF(tof);
Profile p = Controller.GetController().ProfileManager.CurrentProfile;
if (p != null && (bool)p.AcquisitorConfig.switchPlugin.Settings["switchActive"])
{
window.PlotAverageOffTOF(
(TOF)averageScan.GetGatedAverageOffShot(startSpectrumGate, endSpectrumGate).TOFs[0]);
}
}
// this function adds a new set of detector data to the block, constructed
// by normalising the PMT data to the norm data. The normalisation is done
// by dividing the PMT tofs through by the integrated norm data. The integration
// is done according to the provided GatedDetectorExtractSpec.
public void Normalise(GatedDetectorExtractSpec normGate)
{
GatedDetectorData normData = GatedDetectorData.ExtractFromBlock(this, normGate);
double averageNorm = 0;
foreach (double val in normData.PointValues)
{
averageNorm += val;
}
averageNorm /= normData.PointValues.Count;
for (int i = 0; i < points.Count; i++)
{
Shot shot = ((EDMPoint)points[i]).Shot;
TOF normedTOF = ((TOF)shot.TOFs[0]) / (normData.PointValues[i] * (1 / averageNorm));
shot.TOFs.Add(normedTOF);
}
// give these data a name
detectors.Add("topNormed");
}
// TOF-ulise all the single point detectors
public void TOFuliseSinglePointData()
{
EDMPoint point = (EDMPoint)points[0];
string[] pointDetectors = new string[point.SinglePointData.Keys.Count];
point.SinglePointData.Keys.CopyTo(pointDetectors, 0);
foreach (string spv in pointDetectors)
{
if (spv != "dummy") // the hashtable has "dummy" as the default entry, but we don't want it
{
for (int i = 0; i < points.Count; i++)
{
EDMPoint pt = (EDMPoint)points[i];
Shot shot = pt.Shot;
TOF spvTOF = new TOF((double)pt.SinglePointData[spv]);
shot.TOFs.Add(spvTOF);
}
// give these data a name
detectors.Add(spv);
}
}
}
private double[] FitSpectrum(Scan s)
{
double[] xDat = s.ScanParameterArray;
double scanStart = xDat[0];
double scanEnd = xDat[xDat.Length - 1];
TOF avTof = (TOF)s.GetGatedAverageOnShot(scanStart, scanEnd).TOFs[0];
double gateStart = avTof.GateStartTime;
double gateEnd = avTof.GateStartTime + avTof.Length * avTof.ClockPeriod;
double[] yDat = s.GetTOFOnIntegralArray(0, gateStart, gateEnd);
fitter.Fit(xDat, yDat, fitter.SuggestParameters(xDat, yDat, scanStart, scanEnd));
string report = fitter.ParameterReport;
string[] tokens = report.Split(' ');
double[] fitresult = new double[4];
for (int i = 0; i < fitresult.Length; i++)
{
fitresult[i] = Convert.ToDouble(tokens[2 * i + 1]);
}
return(fitresult);
}
public void HandleDataPoint(DataEventArgs e)
{
Profile currentProfile = Controller.GetController().ProfileManager.CurrentProfile;
// update the TOF graphs
if (currentProfile.GUIConfig.average)
{
if (shotCounter % currentProfile.GUIConfig.updateTOFsEvery == 0)
{
if (avOnTof != null)
{
window.PlotOnTOF(avOnTof / onAverages);
}
avOnTof = (TOF)e.point.AverageOnShot.TOFs[0];
onAverages = 1;
if ((bool)currentProfile.AcquisitorConfig.switchPlugin.Settings["switchActive"])
{
if (avOffTof != null)
{
window.PlotOffTOF(avOffTof / offAverages);
}
avOffTof = (TOF)e.point.AverageOffShot.TOFs[0];
offAverages = 1;
}
}
else // do the averaging
{
if (avOnTof != null)
{
avOnTof = avOnTof + ((TOF)e.point.AverageOnShot.TOFs[0]);
onAverages++;
}
if ((bool)currentProfile.AcquisitorConfig.switchPlugin.Settings["switchActive"] && avOffTof != null)
{
avOffTof = avOffTof + ((TOF)e.point.AverageOffShot.TOFs[0]);
offAverages++;
}
}
}
else // if not averaging
{
if (shotCounter % currentProfile.GUIConfig.updateTOFsEvery == 0)
{
window.PlotOnTOF((TOF)e.point.AverageOnShot.TOFs[0]);
if ((bool)currentProfile.AcquisitorConfig.switchPlugin.Settings["switchActive"])
{
window.PlotOffTOF((TOF)e.point.AverageOffShot.TOFs[0]);
}
}
}
// update the spectra
pointsToPlot.Points.Add(e.point);
if (shotCounter % currentProfile.GUIConfig.updateSpectraEvery == 0)
{
double[] onPoints = pointsToPlot.GetTOFOnIntegralArray(0,
startTOFGate, endTOFGate);
window.AppendToPMTOn(pointsToPlot.ScanParameterArray,
onPoints);
if ((bool)currentProfile.AcquisitorConfig.switchPlugin.Settings["switchActive"])
{
double[] offPoints = pointsToPlot.GetTOFOffIntegralArray(0,
startTOFGate, endTOFGate);
window.AppendToPMTOff(pointsToPlot.ScanParameterArray,
offPoints);
window.AppendToDifference(pointsToPlot.ScanParameterArray,
pointsToPlot.GetDifferenceIntegralArray(0,
startTOFGate, endTOFGate));
calculateNewGatedAverages(offPoints[offPoints.Length - 1], onPoints[onPoints.Length - 1]);
updateGatedAverageTextBoxes();
}
// update the spectrum fit if in shot mode.
if (spectrumFitMode == FitMode.Shot)
{
Scan currentScan = Controller.GetController().DataStore.CurrentScan;
if (currentScan.Points.Count > 10)
{
FitAndPlotSpectrum(currentScan);
}
}
pointsToPlot.Points.Clear();
}
shotCounter++;
}
public void PlotOnTOF(TOF t)
{
PlotY(tofGraph, tofOnPlot, t.GateStartTime, t.ClockPeriod, t.Data);
}
// this is the method that actually takes the data. It is called by Start() and shouldn't
// be called directly
public void Acquire()
{
// lock onto something that the front end can see
Monitor.Enter(MonitorLockObject);
scanMaster = new ScanMaster.Controller();
phaseLock = new EDMPhaseLock.MainForm();
hardwareController = new EDMHardwareControl.Controller();
// map modulations to physical channels
MapChannels();
// map the analog inputs
MapAnalogInputs();
Block b = new Block();
b.Config = config;
b.SetTimeStamp();
foreach (ScannedAnalogInput channel in inputs.Channels)
{
b.detectors.Add(channel.Channel.Name);
}
try
{
// get things going
AcquisitionStarting();
// enter the main loop
for (int point = 0; point < (int)config.Settings["numberOfPoints"]; point++)
{
// set the switch states and impose the appropriate wait times
ThrowSwitches(point);
// take a point
Shot s;
EDMPoint p;
if (Environs.Debug)
{
// just stuff a made up shot in
//Thread.Sleep(10);
s = DataFaker.GetFakeShot(1900, 50, 10, 3, 3);
((TOF)s.TOFs[0]).Calibration = ((ScannedAnalogInput)inputs.Channels[0]).Calibration;
p = new EDMPoint();
p.Shot = s;
//Thread.Sleep(20);
}
else
{
// everything should be ready now so start the analog
// input task (it will wait for a trigger)
inputTask.Start();
// get the raw data
double[,] analogData = inputReader.ReadMultiSample(inputs.GateLength);
inputTask.Stop();
// extract the data for each scanned channel and put it in a TOF
s = new Shot();
for (int i = 0; i < inputs.Channels.Count; i++)
{
// extract the raw data
double[] rawData = new double[inputs.GateLength];
for (int q = 0; q < inputs.GateLength; q++)
{
rawData[q] = analogData[i, q];
}
ScannedAnalogInput ipt = (ScannedAnalogInput)inputs.Channels[i];
// reduce the data
double[] data = ipt.Reduce(rawData);
TOF t = new TOF();
t.Calibration = ipt.Calibration;
// the 1000000 is because clock period is in microseconds;
t.ClockPeriod = 1000000 / ipt.CalculateClockRate(inputs.RawSampleRate);
t.GateStartTime = inputs.GateStartTime;
// this is a bit confusing. The chop is measured in points, so the gate
// has to be adjusted by the number of points times the clock period!
if (ipt.ReductionMode == DataReductionMode.Chop)
{
t.GateStartTime += (ipt.ChopStart * t.ClockPeriod);
}
t.Data = data;
// the 1000000 is because clock period is in microseconds;
t.ClockPeriod = 1000000 / ipt.CalculateClockRate(inputs.RawSampleRate);
s.TOFs.Add(t);
}
p = new EDMPoint();
p.Shot = s;
}
// do the "SinglePointData" (i.e. things that are measured once per point)
// We'll save the leakage monitor until right at the end.
// keep an eye on what the phase lock is doing
p.SinglePointData.Add("PhaseLockFrequency", phaseLock.OutputFrequency);
p.SinglePointData.Add("PhaseLockError", phaseLock.PhaseError);
// scan the analog inputs
double[] spd;
// fake some data if we're in debug mode
if (Environs.Debug)
{
spd = new double[7];
spd[0] = 1;
spd[1] = 2;
spd[2] = 3;
spd[3] = 4;
spd[4] = 5;
spd[5] = 6;
spd[6] = 7;
}
else
{
singlePointInputTask.Start();
spd = singlePointInputReader.ReadSingleSample();
singlePointInputTask.Stop();
}
p.SinglePointData.Add("ProbePD", spd[0]);
p.SinglePointData.Add("PumpPD", spd[1]);
p.SinglePointData.Add("MiniFlux1", spd[2]);
p.SinglePointData.Add("MiniFlux2", spd[3]);
p.SinglePointData.Add("MiniFlux3", spd[4]);
//p.SinglePointData.Add("CplusV", spd[5]);
//p.SinglePointData.Add("CminusV", spd[6]);
//hardwareController.UpdateVMonitor();
//p.SinglePointData.Add("CplusV", hardwareController.CPlusMonitorVoltage);
//hardwareController.UpdateLaserPhotodiodes();
//p.SinglePointData.Add("ProbePD", hardwareController.ProbePDVoltage);
//p.SinglePointData.Add("PumpPD", hardwareController.PumpPDVoltage);
//hardwareController.UpdateMiniFluxgates();
//p.SinglePointData.Add("MiniFlux1", hardwareController.MiniFlux1Voltage);
//p.SinglePointData.Add("MiniFlux2", hardwareController.MiniFlux2Voltage);
//p.SinglePointData.Add("MiniFlux3", hardwareController.MiniFlux3Voltage);
hardwareController.ReadIMonitor();
p.SinglePointData.Add("NorthCurrent", hardwareController.NorthCurrent);
p.SinglePointData.Add("SouthCurrent", hardwareController.SouthCurrent);
//hardwareController.UpdatePiMonitor();
//p.SinglePointData.Add("piMonitor", hardwareController.PiFlipMonVoltage);
//p.SinglePointData.Add("CminusV", hardwareController.CMinusMonitorVoltage);
// Hopefully the leakage monitors will have finished reading by now.
// We join them, read out the data, and then launch another asynchronous
// acquisition. [If this is the first shot of the block, the leakage monitor
// measurement will have been launched in AcquisitionStarting() ].
//hardwareController.WaitForIMonitorAsync();
//p.SinglePointData.Add("NorthCurrent", hardwareController.NorthCurrent);
//p.SinglePointData.Add("SouthCurrent", hardwareController.SouthCurrent);
//hardwareController.UpdateIMonitorAsync();
// randomise the Ramsey phase
// TODO: check whether the .NET rng is good enough
// TODO: reference where this number comes from
//double d = 2.3814 * (new Random().NextDouble());
//hardwareController.SetScramblerVoltage(d);
b.Points.Add(p);
// update the front end
Controller.GetController().GotPoint(point, p);
if (CheckIfStopping())
{
// release hardware
AcquisitionStopping();
// signal anybody waiting on the lock that we're done
Monitor.Pulse(MonitorLockObject);
Monitor.Exit(MonitorLockObject);
return;
}
}
}
catch (Exception e)
{
// try and stop the experiment gracefully
try
{
AcquisitionStopping();
}
catch (Exception) {} // about the best that can be done at this stage
Monitor.Pulse(MonitorLockObject);
Monitor.Exit(MonitorLockObject);
throw e;
}
AcquisitionStopping();
// hand the new block back to the controller
Controller.GetController().AcquisitionFinished(b);
// signal anybody waiting on the lock that we're done
Monitor.Pulse(MonitorLockObject);
Monitor.Exit(MonitorLockObject);
}
public void AcquireAndStepTarget()
{
// lock onto something that the front end can see
Monitor.Enter(MonitorLockObject);
scanMaster = new ScanMaster.Controller();
phaseLock = new EDMPhaseLock.MainForm();
hardwareController = new EDMHardwareControl.Controller();
// map modulations to physical channels
MapChannels();
// map the analog inputs
MapAnalogInputs();
Block b = new Block();
b.Config = config;
b.SetTimeStamp();
foreach (ScannedAnalogInput channel in inputs.Channels)
{
b.detectors.Add(channel.Channel.Name);
}
try
{
// get things going
AcquisitionStarting();
int point = 0;
// enter the main loop
for (point = 0; point < (int)config.Settings["maximumNumberOfTimesToStepTarget"]; point++)
{
// take a point
Shot s;
EDMPoint p;
if (Environs.Debug)
{
// just stuff a made up shot in
//Thread.Sleep(10);
s = DataFaker.GetFakeShot(1900, 50, 10, 3, 3);
((TOF)s.TOFs[0]).Calibration = ((ScannedAnalogInput)inputs.Channels[0]).Calibration;
p = new EDMPoint();
p.Shot = s;
//Thread.Sleep(20);
}
else
{
// everything should be ready now so start the analog
// input task (it will wait for a trigger)
inputTask.Start();
// get the raw data
double[,] analogData = inputReader.ReadMultiSample(inputs.GateLength);
inputTask.Stop();
// extract the data for each scanned channel and put it in a TOF
s = new Shot();
for (int i = 0; i < inputs.Channels.Count; i++)
{
// extract the raw data
double[] rawData = new double[inputs.GateLength];
for (int q = 0; q < inputs.GateLength; q++)
{
rawData[q] = analogData[i, q];
}
ScannedAnalogInput ipt = (ScannedAnalogInput)inputs.Channels[i];
// reduce the data
double[] data = ipt.Reduce(rawData);
TOF t = new TOF();
t.Calibration = ipt.Calibration;
// the 1000000 is because clock period is in microseconds;
t.ClockPeriod = 1000000 / ipt.CalculateClockRate(inputs.RawSampleRate);
t.GateStartTime = inputs.GateStartTime;
// this is a bit confusing. The chop is measured in points, so the gate
// has to be adjusted by the number of points times the clock period!
if (ipt.ReductionMode == DataReductionMode.Chop)
{
t.GateStartTime += (ipt.ChopStart * t.ClockPeriod);
}
t.Data = data;
// the 1000000 is because clock period is in microseconds;
t.ClockPeriod = 1000000 / ipt.CalculateClockRate(inputs.RawSampleRate);
s.TOFs.Add(t);
}
p = new EDMPoint();
p.Shot = s;
}
// do the "SinglePointData" (i.e. things that are measured once per point)
// We'll save the leakage monitor until right at the end.
// keep an eye on what the phase lock is doing
p.SinglePointData.Add("PhaseLockFrequency", phaseLock.OutputFrequency);
p.SinglePointData.Add("PhaseLockError", phaseLock.PhaseError);
// scan the analog inputs
double[] spd;
// fake some data if we're in debug mode
if (Environs.Debug)
{
spd = new double[7];
spd[0] = 1;
spd[1] = 2;
spd[2] = 3;
spd[3] = 4;
spd[4] = 5;
spd[5] = 6;
spd[6] = 7;
}
else
{
singlePointInputTask.Start();
spd = singlePointInputReader.ReadSingleSample();
singlePointInputTask.Stop();
}
p.SinglePointData.Add("ProbePD", spd[0]);
p.SinglePointData.Add("PumpPD", spd[1]);
p.SinglePointData.Add("MiniFlux1", spd[2]);
p.SinglePointData.Add("MiniFlux2", spd[3]);
p.SinglePointData.Add("MiniFlux3", spd[4]);
//p.SinglePointData.Add("CplusV", spd[5]);
//p.SinglePointData.Add("CminusV", spd[6]);
//hardwareController.UpdateVMonitor();
//p.SinglePointData.Add("CplusV", hardwareController.CPlusMonitorVoltage);
//hardwareController.UpdateLaserPhotodiodes();
//p.SinglePointData.Add("ProbePD", hardwareController.ProbePDVoltage);
//p.SinglePointData.Add("PumpPD", hardwareController.PumpPDVoltage);
//hardwareController.UpdateMiniFluxgates();
//p.SinglePointData.Add("MiniFlux1", hardwareController.MiniFlux1Voltage);
//p.SinglePointData.Add("MiniFlux2", hardwareController.MiniFlux2Voltage);
//p.SinglePointData.Add("MiniFlux3", hardwareController.MiniFlux3Voltage);
hardwareController.ReadIMonitor();
p.SinglePointData.Add("NorthCurrent", hardwareController.NorthCurrent);
p.SinglePointData.Add("SouthCurrent", hardwareController.SouthCurrent);
b.Points.Add(p);
// update the front end
Controller.GetController().GotPoint(point, p);
// Integrate the first toff and stop the sequence if the signal is sufficiently high
TOF detectorATOF = new TOF();
detectorATOF = (TOF)s.TOFs[0];
double sig = detectorATOF.Integrate((double)config.Settings["targetStepperGateStartTime"], (double)config.Settings["targetStepperGateEndTime"]);
if (sig > (double)config.Settings["minimumSignalToRun"])
{
Controller.GetController().TargetHealthy = true;
Stop();
point = (int)config.Settings["maximumNumberOfTimesToStepTarget"] + 1;
}
else
{
Controller.GetController().TargetHealthy = false;
hardwareController.StepTarget(2);
}
//if (CheckIfStopping())
//{
// release hardware
// AcquisitionStopping();
// signal anybody waiting on the lock that we're done
// Monitor.Pulse(MonitorLockObject);
// Monitor.Exit(MonitorLockObject);
// point = (int)config.Settings["maximumNumberOfTimesToStepTarget"];
// return;
//}
}
AcquisitionStopping();
// hand the new block back to the controller
Controller.GetController().IntelligentAcquisitionFinished();
// signal anybody waiting on the lock that we're done
Monitor.Pulse(MonitorLockObject);
Monitor.Exit(MonitorLockObject);
}
catch (Exception e)
{
// try and stop the experiment gracefully
try
{
AcquisitionStopping();
}
catch (Exception) { } // about the best that can be done at this stage
Monitor.Pulse(MonitorLockObject);
Monitor.Exit(MonitorLockObject);
throw e;
}
}
public DemodulatedBlock DemodulateBlock(Block b, DemodulationConfig demodulationConfig, int[] tofChannelsToAnalyse)
{
if (!b.detectors.Contains("asymmetry"))
{
b.AddDetectorsToBlock();
}
int blockLength = b.Points.Count;
DemodulatedBlock db = new DemodulatedBlock(b.TimeStamp, b.Config, demodulationConfig);
Dictionary <string, double[]> pointDetectorData = new Dictionary <string, double[]>();
foreach (string d in demodulationConfig.GatedDetectors)
{
pointDetectorData.Add(d, GetGatedDetectorData(b, d, demodulationConfig.Gates.GetGate(d)));
}
foreach (string d in demodulationConfig.PointDetectors)
{
pointDetectorData.Add(d, GetPointDetectorData(b, d));
}
Dictionary <string, TOF[]> tofDetectorData = new Dictionary <string, TOF[]>();
foreach (string d in demodulationConfig.TOFDetectors)
{
tofDetectorData.Add(d, GetTOFDetectorData(b, d));
}
// ----Demodulate channels----
// --Build list of modulations--
List <Modulation> modulations = GetModulations(b);
// --Work out switch state for each point--
List <uint> switchStates = GetSwitchStates(modulations);
// --Calculate state signs for each analysis channel--
// The first index selects the analysis channel, the second the switchState
int numStates = (int)Math.Pow(2, modulations.Count);
int[,] stateSigns = GetStateSigns(numStates);
// --This is done for each point/gated detector--
foreach (string d in pointDetectorData.Keys)
{
int detectorIndex = b.detectors.IndexOf(d);
// We obtain one Channel Set for each detector
ChannelSet <PointWithError> channelSet = new ChannelSet <PointWithError>();
// Detector calibration
double calibration = ((TOF)((EDMPoint)b.Points[0]).Shot.TOFs[detectorIndex]).Calibration;
// Divide points into bins depending on switch state
List <List <double> > statePoints = new List <List <double> >(numStates);
for (int i = 0; i < numStates; i++)
{
statePoints.Add(new List <double>(blockLength / numStates));
}
for (int i = 0; i < blockLength; i++)
{
statePoints[(int)switchStates[i]].Add(pointDetectorData[b.detectors[detectorIndex]][i]);
}
int subLength = blockLength / numStates;
// For each analysis channel, calculate the mean and standard error, then add to ChannelSet
for (int channel = 0; channel < numStates; channel++)
{
RunningStatistics stats = new RunningStatistics();
for (int subIndex = 0; subIndex < subLength; subIndex++)
{
double onVal = 0.0;
double offVal = 0.0;
for (int i = 0; i < numStates; i++)
{
if (stateSigns[channel, i] == 1)
{
onVal += statePoints[i][subIndex];
}
else
{
offVal += statePoints[i][subIndex];
}
}
onVal /= numStates;
offVal /= numStates;
stats.Push(onVal - offVal);
}
PointWithError pointWithError = new PointWithError()
{
Value = stats.Mean, Error = stats.StandardErrorOfSampleMean
};
// add the channel to the ChannelSet
List <string> usedSwitches = new List <string>();
for (int i = 0; i < modulations.Count; i++)
{
if ((channel & (1 << i)) != 0)
{
usedSwitches.Add(modulations[i].Name);
}
}
string[] channelName = usedSwitches.ToArray();
// the SIG channel has a special name
if (channel == 0)
{
channelName = new string[] { "SIG" }
}
;
channelSet.AddChannel(channelName, pointWithError);
}
// Add the ChannelSet to the demodulated block
db.AddDetector(b.detectors[detectorIndex], calibration, channelSet);
}
// --This is done for each TOF detector--
foreach (string d in tofDetectorData.Keys)
{
int detectorIndex = b.detectors.IndexOf(d);
// We obtain one Channel Set for each detector
ChannelSet <TOFWithError> channelSet = new ChannelSet <TOFWithError>();
// Detector calibration
double calibration = ((TOF)((EDMPoint)b.Points[0]).Shot.TOFs[detectorIndex]).Calibration;
// Divide TOFs into bins depending on switch state
List <List <TOF> > statePoints = new List <List <TOF> >(numStates);
for (int i = 0; i < numStates; i++)
{
statePoints.Add(new List <TOF>(blockLength / numStates));
}
for (int i = 0; i < blockLength; i++)
{
statePoints[(int)switchStates[i]].Add(tofDetectorData[b.detectors[detectorIndex]][i]);
}
int subLength = blockLength / numStates;
// For each analysis channel, calculate the mean and standard error, then add to ChannelSet
foreach (int channel in tofChannelsToAnalyse)
{
TOFAccumulator tofAccumulator = new TOFAccumulator();
for (int subIndex = 0; subIndex < subLength; subIndex++)
{
TOF onTOF = new TOF();
TOF offTOF = new TOF();
for (int i = 0; i < numStates; i++)
{
if (stateSigns[channel, i] == 1)
{
onTOF += statePoints[i][subIndex];
}
else
{
offTOF += statePoints[i][subIndex];
}
}
onTOF /= numStates;
offTOF /= numStates;
tofAccumulator.Add(onTOF - offTOF);
}
// add the channel to the ChannelSet
List <string> usedSwitches = new List <string>();
for (int i = 0; i < modulations.Count; i++)
{
if ((channel & (1 << i)) != 0)
{
usedSwitches.Add(modulations[i].Name);
}
}
string[] channelName = usedSwitches.ToArray();
// the SIG channel has a special name
if (channel == 0)
{
channelName = new string[] { "SIG" }
}
;
channelSet.AddChannel(channelName, tofAccumulator.GetResult());
}
// If the detector is a molecule detector, add the special channels
if (MOLECULE_DETECTORS.Contains(d))
{
channelSet = AppendChannelSetWithSpecialValues(channelSet);
}
// Add the ChannelSet to the demodulated block
db.AddDetector(d, calibration, channelSet);
}
return(db);
}
public TOFChannelSet TOFDemodulateBlock(Block b, int detectorIndex, bool allChannels)
{
// *** demodulate channels ***
// ** build the list of modulations **
List <string> modNames = new List <string>();
List <Waveform> modWaveforms = new List <Waveform>();
foreach (AnalogModulation mod in b.Config.AnalogModulations)
{
modNames.Add(mod.Name);
modWaveforms.Add(mod.Waveform);
}
foreach (DigitalModulation mod in b.Config.DigitalModulations)
{
modNames.Add(mod.Name);
modWaveforms.Add(mod.Waveform);
}
foreach (TimingModulation mod in b.Config.TimingModulations)
{
modNames.Add(mod.Name);
modWaveforms.Add(mod.Waveform);
}
// ** work out the switch state for each point **
int blockLength = modWaveforms[0].Length;
List <bool[]> wfBits = new List <bool[]>();
foreach (Waveform wf in modWaveforms)
{
wfBits.Add(wf.Bits);
}
List <uint> switchStates = new List <uint>(blockLength);
for (int i = 0; i < blockLength; i++)
{
uint switchState = 0;
for (int j = 0; j < wfBits.Count; j++)
{
if (wfBits[j][i])
{
switchState += (uint)Math.Pow(2, j);
}
}
switchStates.Add(switchState);
}
// pre-calculate the state signs for each analysis channel
// the first index selects the analysis channel, the second the switchState
int numStates = (int)Math.Pow(2, modWaveforms.Count);
bool[,] stateSigns = new bool[numStates, numStates];
// make a BlockDemodulator just to use its stateSign code
// They should probably share a base class.
BlockDemodulator bd = new BlockDemodulator();
for (uint i = 0; i < numStates; i++)
{
for (uint j = 0; j < numStates; j++)
{
stateSigns[i, j] = (bd.stateSign(j, i) == 1);
}
}
TOFChannelSet tcs = new TOFChannelSet();
// By setting all channels to false only a limited number of channels are analysed,
// namely those required to extract the edm (and the correction term). This speeds
// up the execution enormously when the BlockTOFDemodulator is used by the
// BlockDemodulator for calculating the non-linear channel combinations.
//int[] channelsToAnalyse;
List <int> channelsToAnalyse;
if (allChannels)
{
//channelsToAnalyse = new int[numStates];
channelsToAnalyse = new List <int>();
//for (int i = 0; i < numStates; i++) channelsToAnalyse[i] = i;
for (int i = 0; i < numStates; i++)
{
channelsToAnalyse.Add(i);
}
}
else
{
// just the essential channels - this code is a little awkward because, like
// so many bits of the analysis code, it was added long after the original
// code was written, and goes against some assumptions that were made back then!
int bIndex = modNames.IndexOf("B");
int dbIndex = modNames.IndexOf("DB");
int eIndex = modNames.IndexOf("E");
int rf1fIndex = modNames.IndexOf("RF1F");
int rf2fIndex = modNames.IndexOf("RF2F");
int rf1aIndex = modNames.IndexOf("RF1A");
int rf2aIndex = modNames.IndexOf("RF2A");
int lf1Index = modNames.IndexOf("LF1");
int lf2Index = modNames.IndexOf("LF2");
int bChannel = (1 << bIndex);
int dbChannel = (1 << dbIndex);
int ebChannel = (1 << eIndex) + (1 << bIndex);
int edbChannel = (1 << eIndex) + (1 << dbIndex);
int dbrf1fChannel = (1 << dbIndex) + (1 << rf1fIndex);
int dbrf2fChannel = (1 << dbIndex) + (1 << rf2fIndex);
int brf1fChannel = (1 << bIndex) + (1 << rf1fIndex);
int brf2fChannel = (1 << bIndex) + (1 << rf2fIndex);
int edbrf1fChannel = (1 << eIndex) + (1 << dbIndex) + (1 << rf1fIndex);
int edbrf2fChannel = (1 << eIndex) + (1 << dbIndex) + (1 << rf2fIndex);
int ebdbChannel = (1 << eIndex) + (1 << bIndex) + (1 << dbIndex);
int rf1fChannel = (1 << rf1fIndex);
int rf2fChannel = (1 << rf2fIndex);
int erf1fChannel = (1 << eIndex) + (1 << rf1fIndex);
int erf2fChannel = (1 << eIndex) + (1 << rf2fIndex);
int rf1aChannel = (1 << rf1aIndex);
int rf2aChannel = (1 << rf2aIndex);
int dbrf1aChannel = (1 << dbIndex) + (1 << rf1aIndex);
int dbrf2aChannel = (1 << dbIndex) + (1 << rf2aIndex);
int lf1Channel = (1 << lf1Index);
int dblf1Channel = (1 << dbIndex) + (1 << lf1Index);
channelsToAnalyse = new List <int>()
{
bChannel, dbChannel, ebChannel, edbChannel, dbrf1fChannel,
dbrf2fChannel, brf1fChannel, brf2fChannel, edbrf1fChannel, edbrf2fChannel, ebdbChannel,
rf1fChannel, rf2fChannel, erf1fChannel, erf2fChannel, rf1aChannel, rf2aChannel, dbrf1aChannel,
dbrf2aChannel, lf1Channel, dblf1Channel,
};
if (lf2Index != -1) // Index = -1 if "LF2" not found
{
int lf2Channel = (1 << lf2Index);
channelsToAnalyse.Add(lf2Channel);
int dblf2Channel = (1 << dbIndex) + (1 << lf2Index);
channelsToAnalyse.Add(dblf2Channel);
}
//channelsToAnalyse = new int[] { bChannel, dbChannel, ebChannel, edbChannel, dbrf1fChannel,
// dbrf2fChannel, brf1fChannel, brf2fChannel, edbrf1fChannel, edbrf2fChannel, ebdbChannel,
// rf1fChannel, rf2fChannel, erf1fChannel, erf2fChannel, rf1aChannel, rf2aChannel, dbrf1aChannel,
// dbrf2aChannel, lf1Channel, dblf1Channel, lf2Channel, dblf2Channel
//};
}
foreach (int channel in channelsToAnalyse)
{
// generate the Channel
TOFChannel tc = new TOFChannel();
TOF tOn = new TOF();
TOF tOff = new TOF();
for (int i = 0; i < blockLength; i++)
{
if (stateSigns[channel, switchStates[i]])
{
tOn += ((TOF)((EDMPoint)(b.Points[i])).Shot.TOFs[detectorIndex]);
}
else
{
tOff += ((TOF)((EDMPoint)(b.Points[i])).Shot.TOFs[detectorIndex]);
}
}
tOn /= (blockLength / 2);
tOff /= (blockLength / 2);
tc.On = tOn;
tc.Off = tOff;
// This "if" is to take care of the case of the "SIG" channel, for which there
// is no off TOF.
if (tc.Off.Length != 0)
{
tc.Difference = tc.On - tc.Off;
}
else
{
tc.Difference = tc.On;
}
// add the Channel to the ChannelSet
List <string> usedSwitches = new List <string>();
for (int i = 0; i < modNames.Count; i++)
{
if ((channel & (1 << i)) != 0)
{
usedSwitches.Add(modNames[i]);
}
}
string[] channelName = usedSwitches.ToArray();
// the SIG channel has a special name
if (channel == 0)
{
channelName = new string[] { "SIG" }
}
;
tcs.AddChannel(channelName, tc);
}
// ** add the special channels **
// extract the TOFChannels that we need.
TOFChannel c_eb = (TOFChannel)tcs.GetChannel(new string[] { "E", "B" });
TOFChannel c_edb = (TOFChannel)tcs.GetChannel(new string[] { "E", "DB" });
TOFChannel c_dbrf1f = (TOFChannel)tcs.GetChannel(new string[] { "DB", "RF1F" });
TOFChannel c_dbrf2f = (TOFChannel)tcs.GetChannel(new string[] { "DB", "RF2F" });
TOFChannel c_b = (TOFChannel)tcs.GetChannel(new string[] { "B" });
TOFChannel c_db = (TOFChannel)tcs.GetChannel(new string[] { "DB" });
TOFChannel c_brf1f = (TOFChannel)tcs.GetChannel(new string[] { "B", "RF1F" });
TOFChannel c_brf2f = (TOFChannel)tcs.GetChannel(new string[] { "B", "RF2F" });
TOFChannel c_edbrf1f = (TOFChannel)tcs.GetChannel(new string[] { "E", "DB", "RF1F" });
TOFChannel c_edbrf2f = (TOFChannel)tcs.GetChannel(new string[] { "E", "DB", "RF2F" });
TOFChannel c_ebdb = (TOFChannel)tcs.GetChannel(new string[] { "E", "B", "DB" });
TOFChannel c_rf1f = (TOFChannel)tcs.GetChannel(new string[] { "RF1F" });
TOFChannel c_rf2f = (TOFChannel)tcs.GetChannel(new string[] { "RF2F" });
TOFChannel c_erf1f = (TOFChannel)tcs.GetChannel(new string[] { "E", "RF1F" });
TOFChannel c_erf2f = (TOFChannel)tcs.GetChannel(new string[] { "E", "RF2F" });
TOFChannel c_rf1a = (TOFChannel)tcs.GetChannel(new string[] { "RF1A" });
TOFChannel c_rf2a = (TOFChannel)tcs.GetChannel(new string[] { "RF2A" });
TOFChannel c_dbrf1a = (TOFChannel)tcs.GetChannel(new string[] { "DB", "RF1A" });
TOFChannel c_dbrf2a = (TOFChannel)tcs.GetChannel(new string[] { "DB", "RF2A" });
TOFChannel c_lf1 = (TOFChannel)tcs.GetChannel(new string[] { "LF1" });
TOFChannel c_dblf1 = (TOFChannel)tcs.GetChannel(new string[] { "DB", "LF1" });
TOFChannel c_lf2;
TOFChannel c_dblf2;
if (modNames.IndexOf("LF2") == -1) // Index = -1 if "LF2" not found
{
TOF tofTemp = new TOF();
TOFChannel tcTemp = new TOFChannel();
// For many blocks there is no LF2 channel (and hence switch states).
// To get around this problem I will populate the TOFChannel with "SIG"
// It will then be obvious in the analysis when LF2 takes on real values.
for (int i = 0; i < blockLength; i++)
{
tofTemp += ((TOF)((EDMPoint)(b.Points[i])).Shot.TOFs[detectorIndex]);
}
tofTemp /= (blockLength / 2);
tcTemp.On = tofTemp;
tcTemp.Off = tofTemp;
tcTemp.Difference = tofTemp;
c_lf2 = tcTemp;
c_dblf2 = tcTemp;
}
else
{
c_lf2 = (TOFChannel)tcs.GetChannel(new string[] { "LF2" });
c_dblf2 = (TOFChannel)tcs.GetChannel(new string[] { "DB", "LF2" });
}
// work out some intermediate terms for the full, corrected edm. The names
// refer to the joint power of c_db and c_b in the term.
TOFChannel squaredTerms = (((c_db * c_db) - (c_dbrf1f * c_dbrf1f) - (c_dbrf2f * c_dbrf2f)) * c_eb)
- (c_b * c_db * c_edb);
// this is missing the term /beta c_db c_ebdb at the moment, mainly because
// I've no idea what beta should be.
TOFChannel linearTerms = (c_b * c_dbrf1f * c_edbrf1f) + (c_b * c_dbrf2f * c_edbrf2f)
- (c_db * c_brf1f * c_edbrf1f) - (c_db * c_brf2f * c_edbrf2f);
TOFChannel preDenominator = (c_db * c_db * c_db)
+ (c_dbrf1f * c_edb * c_edbrf1f) + (c_dbrf1f * c_edb * c_edbrf1f)
+ (c_dbrf2f * c_edb * c_edbrf2f) + (c_dbrf2f * c_edb * c_edbrf2f)
- c_db * (
(c_dbrf1f * c_dbrf1f) + (c_dbrf2f * c_dbrf2f) + (c_edb * c_edb)
+ (c_edbrf1f * c_edbrf1f) + (c_edbrf2f * c_edbrf2f)
);
// it's important when working out the non-linear channel
// combinations to always keep them dimensionless. If you
// don't you'll run into trouble with integral vs. average
// signal.
TOFChannel edmDB = c_eb / c_db;
tcs.AddChannel(new string[] { "EDMDB" }, edmDB);
// The corrected edm channel. This should be proportional to the edm phase.
TOFChannel edmCorrDB = (squaredTerms + linearTerms) / preDenominator;
tcs.AddChannel(new string[] { "EDMCORRDB" }, edmCorrDB);
// It's useful to have an estimate of the size of the correction. Here
// we return the difference between the corrected edm channel and the
// naive guess, edmDB.
TOFChannel correctionDB = edmCorrDB - edmDB;
tcs.AddChannel(new string[] { "CORRDB" }, correctionDB);
// The "old" correction that just corrects for the E-correlated amplitude change.
// This is included in the dblocks for debugging purposes.
TOFChannel correctionDB_old = (c_edb * c_b) / (c_db * c_db);
tcs.AddChannel(new string[] { "CORRDB_OLD" }, correctionDB_old);
TOFChannel edmCorrDB_old = edmDB - correctionDB_old;
tcs.AddChannel(new string[] { "EDMCORRDB_OLD" }, edmCorrDB_old);
// Normalised RFxF channels.
TOFChannel rf1fDB = c_rf1f / c_db;
tcs.AddChannel(new string[] { "RF1FDB" }, rf1fDB);
TOFChannel rf2fDB = c_rf2f / c_db;
tcs.AddChannel(new string[] { "RF2FDB" }, rf2fDB);
// And RFxF.DB channels, again normalised to DB. The naming of these channels is quite
// unfortunate, but it's just tough.
TOFChannel rf1fDBDB = c_dbrf1f / c_db;
tcs.AddChannel(new string[] { "RF1FDBDB" }, rf1fDBDB);
TOFChannel rf2fDBDB = c_dbrf2f / c_db;
tcs.AddChannel(new string[] { "RF2FDBDB" }, rf2fDBDB);
// Normalised RFxAchannels.
TOFChannel rf1aDB = c_rf1a / c_db;
tcs.AddChannel(new string[] { "RF1ADB" }, rf1aDB);
TOFChannel rf2aDB = c_rf2a / c_db;
tcs.AddChannel(new string[] { "RF2ADB" }, rf2aDB);
// And RFxA.DB channels, again normalised to DB. The naming of these channels is quite
// unfortunate, but it's just tough.
TOFChannel rf1aDBDB = c_dbrf1a / c_db;
tcs.AddChannel(new string[] { "RF1ADBDB" }, rf1aDBDB);
TOFChannel rf2aDBDB = c_dbrf2a / c_db;
tcs.AddChannel(new string[] { "RF2ADBDB" }, rf2aDBDB);
// the E.RFxF channels, normalized to DB
TOFChannel erf1fDB = c_erf1f / c_db;
tcs.AddChannel(new string[] { "ERF1FDB" }, erf1fDB);
TOFChannel erf2fDB = c_erf2f / c_db;
tcs.AddChannel(new string[] { "ERF2FDB" }, erf2fDB);
// the E.RFxF.DB channels, normalized to DB, again dodgy naming convention.
TOFChannel erf1fDBDB = c_edbrf1f / c_db;
tcs.AddChannel(new string[] { "ERF1FDBDB" }, erf1fDBDB);
TOFChannel erf2fDBDB = c_edbrf2f / c_db;
tcs.AddChannel(new string[] { "ERF2FDBDB" }, erf2fDBDB);
// the LF1 channel, normalized to DB
TOFChannel lf1DB = c_lf1 / c_db;
tcs.AddChannel(new string[] { "LF1DB" }, lf1DB);
TOFChannel lf1DBDB = c_dblf1 / c_db;
tcs.AddChannel(new string[] { "LF1DBDB" }, lf1DBDB);
// the LF2 channel, normalized to DB
TOFChannel lf2DB = c_lf2 / c_db;
tcs.AddChannel(new string[] { "LF2DB" }, lf2DB);
TOFChannel lf2DBDB = c_dblf2 / c_db;
tcs.AddChannel(new string[] { "LF2DBDB" }, lf2DBDB);
TOFChannel bDB = c_b / c_db;
tcs.AddChannel(new string[] { "BDB" }, bDB);
// we also need to extract the rf-step induced phase shifts. These come out in the
// B.RFxF channels, but like the edm, need to be corrected. I'm going to use just the
// simplest level of correction for these.
TOFChannel brf1fCorrDB = (c_brf1f / c_db) - ((c_b * c_dbrf1f) / (c_db * c_db));
tcs.AddChannel(new string[] { "BRF1FCORRDB" }, brf1fCorrDB);
TOFChannel brf2fCorrDB = (c_brf2f / c_db) - ((c_b * c_dbrf2f) / (c_db * c_db));
tcs.AddChannel(new string[] { "BRF2FCORRDB" }, brf2fCorrDB);
return(tcs);
}
}
public void PlotAverageOffTOF(TOF t)
{
PlotY(tofGraph, tofOffAveragePlot, t.GateStartTime, t.ClockPeriod, t.Data);
}
// NOTE: this function is rendered somewhat obsolete by the BlockTOFDemodulator.
// This function takes a list of switches, defining an analysis channel, and gives the
// average TOF for that analysis channel's positively contributing TOFs and the same for
// the negative contributors. Note that this definition may or may not line up with how
// the analysis channels are defined (they may differ by a sign, which might depend on
// the number of switches in the channel).
public TOF[] GetSwitchTOFs(string[] switches, int index, bool normed)
{
TOF[] tofs = new TOF[2];
// calculate the state of the channel for each point in the block
int numSwitches = switches.Length;
int waveformLength = config.GetModulationByName(switches[0]).Waveform.Length;
List<bool[]> switchBits = new List<bool[]>();
foreach (string s in switches)
switchBits.Add(config.GetModulationByName(s).Waveform.Bits);
List<bool> channelStates = new List<bool>();
for (int point = 0; point < waveformLength; point++)
{
bool channelState = false;
for (int i = 0; i < numSwitches; i++)
{
channelState = channelState ^ switchBits[i][point];
}
channelStates.Add(channelState);
}
// build the "on" and "off" average TOFs
TOF tOn = new TOF();
TOF tOff = new TOF();
if (!normed)
{
// if no normalisation is requested then the TOFs are added directly
for (int i = 0; i < waveformLength; i++)
{
if (channelStates[i]) tOn += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]);
else tOff += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]);
}
}
else
{
// otherwise each point's TOF is normalised to the ratio of that points norm
// signal (integrated over the cgate11) to the average norm signal for the block
double[] normIntegrals = GetTOFIntegralArray(1, 0, 3000);
double normMean = 0;
for (int j = 0; j < normIntegrals.Length; j++) normMean += normIntegrals[j];
normMean /= normIntegrals.Length;
for (int j = 0; j < normIntegrals.Length; j++) normIntegrals[j] /= normMean;
for (int i = 0; i < waveformLength; i++)
{
if (channelStates[i]) tOn += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]) / normIntegrals[i];
else tOff += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]) / normIntegrals[i];
}
}
tOn /= (waveformLength / 2);
tOff /= (waveformLength / 2);
tofs[0] = tOn;
tofs[1] = tOff;
return tofs;
}
// this function takes some of the single point data and adds it to the block shots as TOFs
// with one data point in them. This allows us to use the same code to break all of the data
// into channels.
public void TOFuliseSinglePointData(string[] channelsToTOFulise)
{
foreach (string spv in channelsToTOFulise)
{
for (int i = 0; i < points.Count; i++)
{
EDMPoint point = (EDMPoint)points[i];
Shot shot = point.Shot;
TOF spvTOF = new TOF((double)point.SinglePointData[spv]);
shot.TOFs.Add(spvTOF);
}
// give these data a name
detectors.Add(spv);
}
}
/// <summary>
/// GenerateTOF
/// </summary>
public override void GenerateTOF(Wordprocessing.Position pos, string stylesSourceFile, bool addDefaultStyles)
{
TOF.Generate(pos);
Style.CreateTOFStyles(stylesSourceFile, addDefaultStyles);
}
// NOTE: this function is rendered somewhat obsolete by the BlockTOFDemodulator.
// This function takes a list of switches, defining an analysis channel, and gives the
// average TOF for that analysis channel's positively contributing TOFs and the same for
// the negative contributors. Note that this definition may or may not line up with how
// the analysis channels are defined (they may differ by a sign, which might depend on
// the number of switches in the channel).
public TOF[] GetSwitchTOFs(string[] switches, int index, bool normed)
{
TOF[] tofs = new TOF[2];
// calculate the state of the channel for each point in the block
int numSwitches = switches.Length;
int waveformLength = config.GetModulationByName(switches[0]).Waveform.Length;
List <bool[]> switchBits = new List <bool[]>();
foreach (string s in switches)
{
switchBits.Add(config.GetModulationByName(s).Waveform.Bits);
}
List <bool> channelStates = new List <bool>();
for (int point = 0; point < waveformLength; point++)
{
bool channelState = false;
for (int i = 0; i < numSwitches; i++)
{
channelState = channelState ^ switchBits[i][point];
}
channelStates.Add(channelState);
}
// build the "on" and "off" average TOFs
TOF tOn = new TOF();
TOF tOff = new TOF();
if (!normed)
{
// if no normalisation is requested then the TOFs are added directly
for (int i = 0; i < waveformLength; i++)
{
if (channelStates[i])
{
tOn += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]);
}
else
{
tOff += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]);
}
}
}
else
{
// otherwise each point's TOF is normalised to the ratio of that points norm
// signal (integrated over the cgate11) to the average norm signal for the block
double[] normIntegrals = GetTOFIntegralArray(1, 0, 3000);
double normMean = 0;
for (int j = 0; j < normIntegrals.Length; j++)
{
normMean += normIntegrals[j];
}
normMean /= normIntegrals.Length;
for (int j = 0; j < normIntegrals.Length; j++)
{
normIntegrals[j] /= normMean;
}
for (int i = 0; i < waveformLength; i++)
{
if (channelStates[i])
{
tOn += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]) / normIntegrals[i];
}
else
{
tOff += ((TOF)((EDMPoint)Points[i]).Shot.TOFs[index]) / normIntegrals[i];
}
}
}
tOn /= (waveformLength / 2);
tOff /= (waveformLength / 2);
tofs[0] = tOn;
tofs[1] = tOff;
return(tofs);
}
public void HandleDataPoint(DataEventArgs e)
{
Profile currentProfile = Controller.GetController().ProfileManager.CurrentProfile;
// update the TOF graphs
if (currentProfile.GUIConfig.average)
{
if (shotCounter % currentProfile.GUIConfig.updateTOFsEvery == 0)
{
if (avOnTof != null)
{
window.PlotOnTOF(avOnTof / onAverages);
}
avOnTof = (TOF)e.point.AverageOnShot.TOFs[0];
onAverages = 1;
if ((bool)currentProfile.AcquisitorConfig.switchPlugin.Settings["switchActive"])
{
if (avOffTof != null)
{
window.PlotOffTOF(avOffTof / offAverages);
}
avOffTof = (TOF)e.point.AverageOffShot.TOFs[0];
offAverages = 1;
}
}
else // do the averaging
{
if (avOnTof != null)
{
avOnTof = avOnTof + ((TOF)e.point.AverageOnShot.TOFs[0]);
onAverages++;
}
if ((bool)currentProfile.AcquisitorConfig.switchPlugin.Settings["switchActive"] && avOffTof != null)
{
avOffTof = avOffTof + ((TOF)e.point.AverageOffShot.TOFs[0]);
offAverages++;
}
}
}
else // if not averaging
{
if (shotCounter % currentProfile.GUIConfig.updateTOFsEvery == 0)
{
window.PlotOnTOF((TOF)e.point.AverageOnShot.TOFs[0]);
if ((bool)currentProfile.AcquisitorConfig.switchPlugin.Settings["switchActive"])
{
window.PlotOffTOF((TOF)e.point.AverageOffShot.TOFs[0]);
}
}
}
// update the spectra
pointsToPlot.Points.Add(e.point);
if (shotCounter % currentProfile.GUIConfig.updateSpectraEvery == 0)
{
if (pointsToPlot.AnalogChannelCount >= 1)
{
window.AppendToAnalog1(pointsToPlot.ScanParameterArray, pointsToPlot.GetAnalogArray(0));
}
if (pointsToPlot.AnalogChannelCount >= 2)
{
window.AppendToAnalog2(pointsToPlot.ScanParameterArray, pointsToPlot.GetAnalogArray(1));
}
if (sdisplayMode == ScanDisplayMode.Integral)
{
window.AppendToPMTOn(pointsToPlot.ScanParameterArray,
pointsToPlot.GetTOFOnIntegralArray(0,
startTOFGate, endTOFGate));
}
if (sdisplayMode == ScanDisplayMode.IofAbs)
{
window.AppendToPMTOn(pointsToPlot.ScanParameterArray,
pointsToPlot.GetTOFOnAbsValIntegralArray(0,
startTOFGate, endTOFGate));
}
if ((bool)currentProfile.AcquisitorConfig.switchPlugin.Settings["switchActive"])
{
if (sdisplayMode == ScanDisplayMode.Integral)
{
window.AppendToPMTOff(pointsToPlot.ScanParameterArray,
pointsToPlot.GetTOFOffIntegralArray(0,
startTOFGate, endTOFGate));
window.AppendToDifference(pointsToPlot.ScanParameterArray,
pointsToPlot.GetDifferenceIntegralArray(0,
startTOFGate, endTOFGate));
}
if (sdisplayMode == ScanDisplayMode.IofAbs)
{
window.AppendToPMTOff(pointsToPlot.ScanParameterArray,
pointsToPlot.GetTOFOffAbsValIntegralArray(0,
startTOFGate, endTOFGate));
window.AppendToDifference(pointsToPlot.ScanParameterArray,
pointsToPlot.GetDifferenceAbsValIntegralArray(0,
startTOFGate, endTOFGate));
}
}
// update the spectrum fit if in shot mode.
if (spectrumFitMode == FitMode.Shot)
{
Scan currentScan = Controller.GetController().DataStore.CurrentScan;
if (currentScan.Points.Count > 10)
{
FitAndPlotSpectrum(currentScan);
}
}
pointsToPlot.Points.Clear();
}
shotCounter++;
}
