public static double[] Smooth([NotNull] double[] spectrum, double cutOff, IntRegion region)
{
if (spectrum == null) throw new ArgumentNullException("spectrum");
if (cutOff <= 0) throw new ArgumentException("cutOff");
var result = FFT_smoothing(spectrum, cutOff, region);
return result;
}
void build(CGVMesh vmesh, CGVolume vol, IntRegion subset)
{
// Because each Material ID forms a submesh
// Do we need to calculate localU?
if (GenerateUV)
{
System.Array.Resize <Vector2>(ref vmesh.UV, vmesh.Count);
}
// Prepare Submeshes
prepareSubMeshes(vmesh, groupsByMatID, subset.Length, ref m_Material);
//prepareSubMeshes(vmesh, groupsByMatID, vol.Count - 1, ref m_Material);
SamplePointsMaterialGroupCollection col;
SamplePointsMaterialGroup grp;
int vtIdx = 0;
int[] triIdx = new int[groupsByMatID.Count]; // triIdx for each submesh
// for all sample segments (except the last) along the path, create Triangles to the next segment
for (int sample = subset.From; sample < subset.To; sample++)
{
// for each submesh (collection)
for (int subMeshIdx = 0; subMeshIdx < groupsByMatID.Count; subMeshIdx++)
{
col = groupsByMatID[subMeshIdx];
// create UV and triangles for all groups in submesh
for (int g = 0; g < col.Count; g++)
{
grp = col[g];
if (GenerateUV)
{
createMaterialGroupUV(ref vmesh, ref vol, ref grp, col.MaterialID, col.AspectCorrection, sample, vtIdx);
}
for (int p = 0; p < grp.Patches.Count; p++)
{
createPatchTriangles(ref vmesh.SubMeshes[subMeshIdx].Triangles, ref triIdx[subMeshIdx], vtIdx + grp.Patches[p].Start, grp.Patches[p].Count, vol.CrossSize, ReverseTriOrder);
}
}
}
vtIdx += vol.CrossSize;
}
// UV for last path segment
if (GenerateUV)
{
// for each submesh (collection)
for (int subMeshIdx = 0; subMeshIdx < groupsByMatID.Count; subMeshIdx++)
{
col = groupsByMatID[subMeshIdx];
// create triangles
for (int g = 0; g < col.Count; g++)
{
grp = col[g];
createMaterialGroupUV(ref vmesh, ref vol, ref grp, col.MaterialID, col.AspectCorrection, subset.To, vtIdx);
}
}
}
}
public static double[] FFT_smoothing([NotNull] double[] x, double cutOff, IntRegion tr)
{
if (x == null) throw new ArgumentNullException("x");
var n = tr.Width;
var nn = GetNn(n);
var chH = tr.Max;
var chL = tr.Min;
var br = new double[8192];
var y = new double[x.Length];
var window = GetWindow(nn, n);
var offset = Convert.ToInt32((2*nn - chL - chH - 1)/2);
var chLo = chL + offset;
var chHo = chH + offset;
//Extend Left side
var points = from i in Enumerable.Range(chL, Convert.ToInt32(cutOff)) select new Point(i, x[i]);
var func = Statistics.GetLeastSquaresLine(points).Function;
for (var i = 0; i <= chLo - 1; i++)
br[i] = func(i - offset)*window[i];
//Spectrum Main Body
for (var i = chLo; i <= chHo; i++)
br[i] = x[i - offset]*window[i];
//Extend Right side
points = from i in Enumerable.Range(Convert.ToInt32(chH - cutOff + 1), Convert.ToInt32(cutOff))
select new Point(i, x[i]);
func = Statistics.GetLeastSquaresLine(points).Function;
for (var i = chHo; i <= nn*2 - 1; i++)
br[i] = func(i - offset)*window[i];
//FFT
var z = ArrayFactory.ByFunc(i => new Complex(br[i], 0), 4096);
z = CalcFft(z, false);
//High Frequency Cutoff
var fc = Convert.ToInt32(nn*2/cutOff);
var i0 = fc*2;
for (var i = 1; i <= nn; i++) {
var f = i > i0 ? 0 : (Math.Cos(Math.PI*i/fc/2) + 1)/2;
z[i] = f*z[i];
z[nn*2 - i] = f*z[nn*2 - i];
}
//IFFT
z = CalcFft(z, true);
var y1 = z.Select(Complex.Abs).ToArray();
foreach (var i in tr)
y[i] = y1[i + offset]/window[i + offset];
return y;
}
public static double[] Calculate([NotNull] double[] spectrum, [CanBeNull] double[] model, double param1,
double param2, IntRegion target)
{
if (spectrum == null) throw new ArgumentException("spectrum");
model = model ?? ArrayFactory.Repeat(1.0, spectrum.Length);
var background = ArrayFactory.Repeat(1.0, spectrum.Length);
Calculate(spectrum, model, ref background, param1, param2, target);
return background;
}
private static void Calculate([NotNull] double[] spectrumInCount, [NotNull] double[] model,
[NotNull] ref double[] backGround, double bgParm1, double bgParm2, IntRegion tr)
{
if (spectrumInCount == null) throw new ArgumentNullException("spectrumInCount");
if (backGround == null) throw new ArgumentNullException("backGround");
if (model == null) throw new ArgumentNullException("model");
var buffer = new double[4096];
var background0 = new double[4096];
var statisticalError = new double[4096];
//Initialization
double b1 = 0;
var ch0 = model.FirstIndex(d => d > 0);
for (var ch = ch0; ch <= Convert.ToInt32(ch0 + bgParm1); ch++) {
if (spectrumInCount[ch] > b1 & !model[ch].IsZero())
b1 = spectrumInCount[ch]/model[ch];
}
foreach (var ch in tr) {
if (model[ch].IsZero()) {
backGround[ch] = b1;
statisticalError[ch] = 0;
}
else {
backGround[ch] = spectrumInCount[ch]/model[ch];
statisticalError[ch] = Math.Sqrt(spectrumInCount[ch])/model[ch]*bgParm2;
}
}
var count = 0;
var stage = 1;
double multiplier = 3;
//Loop
do {
foreach (var ch in tr) background0[ch] = backGround[ch];
foreach (var ch in tr) {
var x = spectrumInCount[ch]/model[ch];
var b = backGround[ch];
if (model[ch].IsZero() | x > b + (statisticalError[ch]*multiplier))
buffer[ch] = b;
else
buffer[ch] = x;
}
backGround = Smoothing.FFT_smoothing(buffer, bgParm1, tr);
var isConverged = false;
foreach (var ch in tr.Where(ch => !background0[ch].IsZero())) {
if (backGround[ch].IsNear(background0[ch], background0[ch]*0.005))
isConverged = true;
}
count++;
switch (stage) {
case 1:
if (count == 100 || !isConverged) {
stage = 2;
multiplier = 1;
count = 0;
}
break;
case 2:
if (count == 100 || !isConverged)
stage = 0;
break;
}
} while (stage != 0);
foreach (var ch in tr) backGround[ch] *= model[ch];
}
public void DoPeakFitting(double liveTime)
{
if (Input == null) throw new InvalidOperationException();
var region = new IntRegion((int) DataProcessRegion.X1, (int) DataProcessRegion.X2);
Smoothed = Smoothing.Smooth(Input, SmoothingCutoffFrequency, region);
Background = PeakFitting.Background.Calculate(
Smoothed, null, BackgroundParameter0, BackgroundParameter1, region);
var pf = new PeakFitting.PeakFitting {Calibration = Calibration, LineInfo = LineInfo};
var result = pf.PeakFit(Input, Background, region, liveTime);
Calibration = pf.Calibration;
PeakFit = pf.PeakFitSpectrum;
FittingResult = result.ToArray();
}
private static bool PeakFittingMain(
[NotNull] IEnumerable<PeakCollection> peakGroups,
[NotNull] double[] spectrum1,
[NotNull] double[] spectrum2,
[NotNull] double[] netSpectrum,
IntRegion tr)
{
if (peakGroups == null) throw new ArgumentNullException("peakGroups");
if (spectrum1 == null) throw new ArgumentNullException("spectrum1");
if (spectrum2 == null) throw new ArgumentNullException("spectrum2");
if (netSpectrum == null) throw new ArgumentNullException("netSpectrum");
var pg = peakGroups.ToArray();
var paramCount = pg.Length;
if (paramCount >= tr.Width) return false;
try {
foreach (var i in Enumerable.Range(0, 20)) {
var a = new double[paramCount, paramCount];
var b = new double[paramCount];
foreach (var ch in tr) {
// ピークを重ねあわせて、スペクトルを作る。
spectrum2[ch] = 0;
var da = new double[paramCount];
foreach (var l in Enumerable.Range(0, paramCount)) {
da[l] = PeaksForSingleElement(ch, pg[l]);
//FDH
spectrum2[ch] += pg[l].Height*da[l];
}
foreach (var l in Enumerable.Range(0, paramCount)) {
for (var m = l; m <= paramCount - 1; m++)
a[l, m] += da[l]*da[m];
b[l] += da[l]*(netSpectrum[ch] - spectrum2[ch]);
}
}
a = a.Synmetric();
var ans = Matrix.GaussJordanMethod(a, b);
foreach (var l in Enumerable.Range(0, paramCount)) pg[l].Height += ans[l];
var canContinue = Enumerable.Range(0, paramCount).Any(l => Math.Abs(ans[l]) > pg[l].Height*0.0001);
if (!canContinue) break;
}
foreach (var ch in tr) spectrum2[ch] += spectrum1[ch];
return true;
}
catch (Exception) {
return false;
}
}
public IEnumerable<LineIntensity> PeakFit(
[NotNull] double[] input,
[NotNull] double[] background,
IntRegion targetRegion,
double liveTime)
{
if (input == null) throw new ArgumentNullException("input");
if (background == null) throw new ArgumentNullException("background");
if (Calibration == null) throw new InvalidOperationException("Calibration is null");
if (LineInfo == null) throw new InvalidOperationException("LineInfo is null");
var net = new double[input.Length];
foreach (var i in Enumerable.Range(0, Math.Min(input.Length, background.Length)))
net[i] = input[i] - background[i];
var peakCollections = ToPeakCollections(LineInfo, Calibration, net);
var result = PeakFittingMain(peakCollections, input, background, net, targetRegion);
var list = new List<LineIntensity>();
if (result) {
foreach (var p in peakCollections) {
var ph = p.Height > 0 ? p.Height : 0;
var pii = ph > 0 ? ph*Math.Sqrt(Math.PI/p.First().Height) : 0;
var lic = LineInfo.First(li => li.Name == p.Name);
list.Add(new LineIntensity(lic, pii/liveTime));
}
}
PeakFitSpectrum = background;
return list;
}
void build(CGVMesh vmesh, CGVolume vol, IntRegion subset)
{
// Because each Material ID forms a submesh
// Do we need to calculate localU?
if (GenerateUV)
{
System.Array.Resize<Vector2>(ref vmesh.UV, vmesh.Count);
}
// Prepare Submeshes
prepareSubMeshes(vmesh, groupsByMatID, subset.Length, ref m_Material);
//prepareSubMeshes(vmesh, groupsByMatID, vol.Count - 1, ref m_Material);
SamplePointsMaterialGroupCollection col;
SamplePointsMaterialGroup grp;
int vtIdx = 0;
int[] triIdx = new int[groupsByMatID.Count]; // triIdx for each submesh
// for all sample segments (except the last) along the path, create Triangles to the next segment
for (int sample = subset.From; sample < subset.To; sample++)
{
// for each submesh (collection)
for (int subMeshIdx = 0; subMeshIdx < groupsByMatID.Count; subMeshIdx++)
{
col = groupsByMatID[subMeshIdx];
// create UV and triangles for all groups in submesh
for (int g = 0; g < col.Count; g++)
{
grp = col[g];
if (GenerateUV)
createMaterialGroupUV(ref vmesh, ref vol, ref grp, col.MaterialID, col.AspectCorrection, sample, vtIdx);
for (int p = 0; p < grp.Patches.Count; p++)
createPatchTriangles(ref vmesh.SubMeshes[subMeshIdx].Triangles, ref triIdx[subMeshIdx], vtIdx+grp.Patches[p].Start, grp.Patches[p].Count, vol.CrossSize, ReverseTriOrder);
}
}
vtIdx += vol.CrossSize;
}
// UV for last path segment
if (GenerateUV)
{
// for each submesh (collection)
for (int subMeshIdx = 0; subMeshIdx < groupsByMatID.Count; subMeshIdx++)
{
col = groupsByMatID[subMeshIdx];
// create triangles
for (int g = 0; g < col.Count; g++)
{
grp = col[g];
createMaterialGroupUV(ref vmesh, ref vol, ref grp, col.MaterialID, col.AspectCorrection, subset.To, vtIdx);
}
}
}
}
