public void AppendToZip(Scan scan, String name)
{
lock (this)
{
ZipEntry entry = new ZipEntry(name);
runningZipStream.PutNextEntry(entry);
xmls.Serialize(runningZipStream, scan);
}
}
// Note: this only really makes sense for sorted scans!
public static Scan operator +(Scan s1, Scan s2)
{
if (s1.Points.Count == s2.Points.Count)
{
Scan temp = new Scan();
for (int i = 0 ; i < s1.Points.Count ; i++)
temp.Points.Add((ScanPoint)s1.Points[i] + (ScanPoint)s2.Points[i]);
temp.ScanSettings = s1.ScanSettings;
return temp;
}
else
{
if (s1.Points.Count == 0) return s2;
if (s2.Points.Count == 0) return s1;
return null;
}
}
private void FitScan(Scan s, double gateStart, double gateEnd)
{
double scanStart = SpectrumGateLow;
double scanEnd = SpectrumGateHigh;
double[] xDat = s.ScanParameterArray;
double[] yDat = s.GetTOFOnIntegralArray(0, gateStart, gateEnd);
spectrumFitter.Fit(
xDat,
yDat,
spectrumFitter.SuggestParameters(xDat, yDat, scanStart, scanEnd)
);
}
private void FitAndPlotSpectrum(Scan scan)
{
FitScan(scan, startTOFGate, endTOFGate);
// plot the fit
window.ClearSpectrumFit();
window.PlotSpectrumFit(scan.ScanParameterArray, spectrumFitter.FittedValues);
// update the parameter report
window.SetLabel(window.spectrumFitResultsLabel, spectrumFitter.ParameterReport);
}
private void AnalyseScanNoise(Scan s, double gateStart, double gateEnd, double spectrumGateStart, double spectrumGateEnd)
{
double detectorRatio = (double)Environs.Hardware.GetInfo("machineLengthRatio");
string channelList = (string)s.GetSetting("shot","channel");
string[] channels = channelList.Split(new char[] { ',' });
double[] probedat;
double[] pumpdat;
double[] normedDat;
if (channels.Length == 2)
{
int[] detectors = { 0, 1 };
probedat = s.GetTOFOnOverShotNoiseArray(0, gateStart, gateEnd);
pumpdat = s.GetTOFOnOverShotNoiseArray(1, gateStart / detectorRatio, gateEnd / detectorRatio);
normedDat = s.GetTOFOnOverShotNoiseNormedArray(detectors, gateStart, gateEnd, gateStart / detectorRatio, gateEnd / detectorRatio);
}
else
{
probedat = s.GetTOFOnOverShotNoiseArray(0, gateStart, gateEnd);
pumpdat = probedat;
normedDat = probedat;
}
double tempP = 0;
double tempN = 0;
double tempTN = 0;
double scanStart = s.ScanParameterArray[0];
double scanEnd = s.ScanParameterArray[s.ScanParameterArray.Length - 1];
int pointStart = (int)Math.Round((spectrumGateStart * (probedat.Length - 1)) / (scanEnd - scanStart));
int pointEnd = (int)Math.Round((spectrumGateEnd * (probedat.Length - 1)) / (scanEnd - scanStart));
int pointLength = pointEnd - pointStart;
for (int i = pointStart; i < pointEnd; i++)
{
tempP += probedat[i];
tempN += pumpdat[i];
tempTN += normedDat[i];
}
OverShotNoise0 = tempP/pointLength;
OverShotNoise1 = tempN/pointLength;
OverShotNoise01 = tempTN/pointLength;
}
private void AnalyseNoise(Scan scan)
{
AnalyseScanNoise(scan, startTOFGate, endTOFGate, startSpectrumGate, endSpectrumGate);
// update the noise report
string[] info = {"top:", OverShotNoise0.ToString("G3"), "norm:",OverShotNoise1.ToString("G3"), "Normed:", OverShotNoise01.ToString("G3")};
window.SetLabel(window.noiseResultsLabel, String.Join(" ", info));
}
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 UpdateTotal()
{
totalScan += currentScan.GetSortedScan();
scansInTotal++;
}
public void ClearCurrentScan()
{
currentScan = new Scan();
}
public void ClearAll()
{
currentScan = new Scan();
totalScan = new Scan();
scansInTotal = 0;
}
// a method for saving the acquisitior settings into the scan
private void WriteScanSettings(Scan scan)
{
PluginSettings st;
ICollection keys;
scan.ScanSettings.Add("out:pluginName", acquisitor.Configuration.outputPlugin.GetType().ToString());
scan.ScanSettings.Add("switch:pluginName", acquisitor.Configuration.switchPlugin.GetType().ToString());
scan.ScanSettings.Add("shot:pluginName", acquisitor.Configuration.shotGathererPlugin.GetType().ToString());
scan.ScanSettings.Add("pg:pluginName", acquisitor.Configuration.pgPlugin.GetType().ToString());
scan.ScanSettings.Add("yag:pluginName", acquisitor.Configuration.yagPlugin.GetType().ToString());
scan.ScanSettings.Add("analog:pluginName", acquisitor.Configuration.analogPlugin.GetType().ToString());
// settings from the output plugin
st = acquisitor.Configuration.outputPlugin.Settings;
keys = st.Keys;
foreach (String key in keys) scan.ScanSettings.Add("out:" + key, st[key]);
// settings from the switch plugin
st = acquisitor.Configuration.switchPlugin.Settings;
keys = st.Keys;
foreach (String key in keys) scan.ScanSettings.Add("switch:" + key, st[key]);
// settings from the shot gatherer plugin
st = acquisitor.Configuration.shotGathererPlugin.Settings;
keys = st.Keys;
foreach (String key in keys) scan.ScanSettings.Add("shot:" + key, st[key]);
// settings from the pattern plugin
st = acquisitor.Configuration.pgPlugin.Settings;
keys = st.Keys;
foreach (String key in keys) scan.ScanSettings.Add("pg:" + key, st[key]);
// settings from the yag plugin
st = acquisitor.Configuration.yagPlugin.Settings;
keys = st.Keys;
foreach (String key in keys) scan.ScanSettings.Add("yag:" + key, st[key]);
// settings from the analog plugin
st = acquisitor.Configuration.analogPlugin.Settings;
keys = st.Keys;
foreach (String key in keys) scan.ScanSettings.Add("analog:" + key, st[key]);
}
public void SerializeScanAsZippedXML(Stream stream, Scan scan, String name)
{
ZipOutputStream zippedStream = new ZipOutputStream(stream);
zippedStream.SetLevel(5);
ZipEntry entry = new ZipEntry(name);
zippedStream.PutNextEntry(entry);
xmls.Serialize(zippedStream, scan);
zippedStream.Finish();
zippedStream.Close();
stream.Close();
}
public void SerializeScanAsBinary(String filePath, Scan scan)
{
Stream scanStream = new FileStream(filePath, FileMode.Create);
(new BinaryFormatter()).Serialize(scanStream, scan);
scanStream.Close();
}
public static Scan operator /(Scan s, int n)
{
Scan temp = new Scan();
foreach (ScanPoint sp in s.Points) temp.Points.Add(sp/n);
temp.ScanSettings = s.ScanSettings;
return temp;
}
public Scan GetSortedScan()
{
double[] spa = ScanParameterArray;
ScanPoint[] pts = (ScanPoint[])points.ToArray(typeof(ScanPoint));
Array.Sort(spa, pts);
Scan ss = new Scan();
ss.points.AddRange(pts);
ss.ScanSettings = ScanSettings;
return ss;
}
