void RefreshSelectedPeakGraph()
{
Part_Plotter.Children.Remove(m_selectedPeakGraph);
m_selectedPeakGraph = null;
var peakInfo = this.ViewModel.CurrentDataItem?.SelectedPeakInfo;
if (peakInfo != null)
{
PeakInfo[] point = new PeakInfo[] { peakInfo.PeakInfo };
EnumerableDataSource <PeakInfo> locatedPeaksDS = new EnumerableDataSource <PeakInfo>(point);
locatedPeaksDS.SetXMapping((item) => item.Pos.X);
locatedPeaksDS.SetYMapping((item) => item.Pos.Y);
locatedPeaksDS.AddMapping(PeaksMarker.DataContextProperty, (peakInfoItem) => peakInfoItem);
m_selectedPeakGraph = new ElementMarkerPointsGraph(locatedPeaksDS)
{
Marker = new SelectedPeaksMarker()
{
Size = 10, Pen = new Pen(Brushes.BlanchedAlmond, 1), Fill = Brushes.Transparent, ContextMenu = this.TryFindResource("PeakMarkerContextMenu") as ContextMenu
}
};
Part_Plotter.Children.Add(m_selectedPeakGraph);
OrderGraphs();
}
}
public PeakInfo[] getSampleArray(IPeakProvider peakProvider, int sampleCount)
{
PeakInfo[] samples = new PeakInfo[sampleCount];
for (int i = 0; i < sampleCount; i++)
{
samples[i] = peakProvider.GetNextPeak();
}
return(samples);
}
void generatePeaksSolver(string filename)
{
SortedDictionary <int, PeakInfo> thesePeaks = findPeaksSPAM(filename);
foreach (KeyValuePair <int, PeakInfo> peak in thesePeaks)
{
int centerPixel = peak.Key;
PeakInfo pi = peak.Value;
// grab one half-width's worth pixels to either side of centroid
if (centerPixel < gaussianHalfWidth || centerPixel + gaussianHalfWidth >= pixels)
{
logger.display("Warning: can't create {0}-pixel gaussian on peak centered at {1}", gaussianHalfWidth * 2 + 1, centerPixel);
continue; // leave SPAM resolution
}
// determine initial guesses
double guessIntensity = spectra[filename][centerPixel];
double guessWavelength = pi.wavelength;
double guessWidth = 1.0; // MZ: in Excel this converged fine (don't use zero)
double guessBaseline = 0.0; // MZ: in Excel this worked fine
GaussianSolver solver = new GaussianSolver(guessIntensity, guessWavelength, guessWidth, guessBaseline);
// Load the peak's local spectrum into the Solver.
//
// Note: the choice of which peaks to load into the Solver is significant in
// the Guassian curve generated, and therefore the calculated FWHM. We could:
//
// 1. Simply hard-code a half-width of 'n' pixels (fast, deterministic, simple, but may
// not reach all the way to the true baseline and therefore understates resolution).
// 2. Do something clever like stop where slope crosses 0.5 or 0.
//
// For now, just let user pick a half-width.
//
for (int i = 0; i < gaussianHalfWidth * 2 + 1; i++)
{
int pixel = centerPixel - gaussianHalfWidth + i;
solver.addPoint(wavelengths[pixel], spectra[filename][pixel]);
}
double resolution = solver.computeFWHM();
if (resolution < pi.fwhm * 2)
{
logger.display("replacing SPAM fwhm {0:f4} with gaussian {1:f4}", pi.fwhm, resolution);
pi.fwhm = resolution;
}
else
{
logger.display("NOT replacing SPAM fwhm {0:f4} with gaussian {1:f4} (something seems wonky)", pi.fwhm, resolution);
}
}
peaks.Add(filename, thesePeaks);
}
public PeakInfo[] getSamplePeakArray(string file, int desiredSamples)
{
PeakInfo[] samples = new PeakInfo[desiredSamples];
MaxPeakProvider mpp = new MaxPeakProvider();
using (var reader = new AudioFileReader(file))
{
int bytesPerSample = (reader.WaveFormat.BitsPerSample / 8);
var sc = reader.Length / (bytesPerSample);
var samplesPerPixel = (int)(sc / desiredSamples);
//var gapSize = settings.PixelsPerPeak + settings.SpacerPixels;
mpp.Init(reader, samplesPerPixel);
samples = getSampleArray(mpp, desiredSamples);
}
return(samples);
}
internal void RemovePeak(PeakInfo peakInfo)
{
if (peakInfo == null)
{
return;
}
if (!this.DataItem.IsAnalyzed || this.DataItem.LocatedPeaks == null)
{
return;
}
var locatedPeaks = this.DataItem.LocatedPeaks.ToList();
locatedPeaks.Remove(peakInfo);
this.DataItem.LocatedPeaks = locatedPeaks.ToArray();
}
private void AddPeak(object sender, EventArgs e)
{
if (string.IsNullOrEmpty(PPMShift.Text))
{
return;
}
PeakInfo peak = new PeakInfo();
peak.Shift = float.Parse(PPMShift.Text);
peak.Coupling = string.IsNullOrEmpty(Coupling.Text) ? "None" : Coupling.Text;
peak.Type = (PeakType)SignalType.SelectedIndex;
if ((int)peak.Type == -1)
{
peak.Type = (PeakType)SignalType.Items.IndexOf(SignalType.Text);
}
if ((int)peak.Type == -1)
{
return;
}
peak.HydrogenCount = int.Parse(HydrogenCount.Text);
peak.Description = Description.Text;
if (peak.Shift == 0.00f || peak.HydrogenCount == 0)
{
return;
}
PeakView.AddObject(peak);
PeakView.Sort(0);
SignalType.SelectedIndex = 0;
SignalType.Text = String.Empty;
PPMShift.Clear();
HydrogenCount.Clear();
Description.Clear();
Coupling.Clear();
}
internal int?GetNearestStimulusIndex(PeakInfo peakInfo)
{
int?nearestStimulusStart = null;
if (peakInfo == null || !this.DataItem.IsAnalyzed)
{
return(nearestStimulusStart);
}
int distMin = int.MaxValue;
for (int i = 0; i < this.DataItem.Sweeps.Length; i++)
{
var dist = Math.Abs(this.DataItem.Sweeps[i].StimulusInfo.StartSample - peakInfo.Sample);
if (dist < distMin)
{
distMin = dist;
nearestStimulusStart = i;
}
}
return(nearestStimulusStart);
}
internal void RemovePeak(PeakInfo peakInfo)
{
this.CurrentDataItem?.RemovePeak(peakInfo);
}
private void RemovePeakCommand_Executed(PeakInfo peakInfo)
{
this.ViewModel.RemovePeak(peakInfo);
}
internal int?GetNearestStimulusIndex(PeakInfo peakInfo)
{
return(peakInfo != null?GetNearestStimulusIndex(peakInfo.Pos.X) : null);
}
