public Microfacet(Spectrum reflectance, IFresnel fresnel, IMicrofacetDistribution distribution)
: base(BxDFType.BSDF_REFLECTION | BxDFType.BSDF_GLOSSY)
{
R = new Spectrum (reflectance.c[0], reflectance.c[1], reflectance.c[2]);
Fresnel = fresnel;
Distribution = distribution;
}
// DensityRegion Public Methods
public DensityRegion(Spectrum sa, Spectrum ss, float gg, Spectrum emit, AABB b) {
sig_a = sa;
sig_s = ss;
le = emit;
g = gg;
worldBound = b;
}
public DiffuseAreaLight(Transform lightToWorld, Spectrum Le, int ns, IShape shape)
: base(lightToWorld, ns)
{
Lemit = Le;
ShapeSet = new ShapeSet (shape);
area = ShapeSet.Area;
}
public static Spectrum SpecularReflect(RayDifferential ray, BSDF bsdf, Intersection isect, IRenderer renderer, Scene scene, Sample sample)
{
Vector wo = -ray.Direction, wi = new Vector ();
double pdf = 0.0;
Point p = bsdf.dgShading.p;
Normal n = bsdf.dgShading.n;
Spectrum f = bsdf.SampleF (wo, ref wi, new BSDFSample (), ref pdf, BxDFType.BSDF_REFLECTION | BxDFType.BSDF_SPECULAR);
Spectrum L = new Spectrum ();
if (pdf > 0.0 && !f.IsBlack && Util.AbsDot (wi, n) != 0.0)
{
RayDifferential rd = new RayDifferential (p, wi, ray, isect.RayEpsilon);
if (ray.HasDifferentials)
{
rd.HasDifferentials = true;
rd.RxOrigin = p + isect.dg.dpdx;
rd.RyOrigin = p + isect.dg.dpdy;
Normal dndx = bsdf.dgShading.dndu * bsdf.dgShading.dudx + bsdf.dgShading.dndv * bsdf.dgShading.dvdx;
Normal dndy = bsdf.dgShading.dndu * bsdf.dgShading.dudy + bsdf.dgShading.dndv * bsdf.dgShading.dvdy;
Vector dwodx = -ray.RxDirection - wo, dwody = -ray.Direction - wo;
double dDNdx = (dwodx ^ n) + (wo ^ dndx);
double dDNdy = (dwody ^ n) + (wo ^ dndy);
rd.RxDirection = wi - dwodx + 2 * new Vector ((wo ^ n) * dndx + dDNdx * n);
rd.RyDirection = wi - dwody + 2 * new Vector ((wo ^ n) * dndy + dDNdy * n);
}
Spectrum Li = renderer.Li (scene, rd, sample);
L = f * Li * Util.AbsDot (wi, n) / pdf;
}
return L;
}
public SpecularTransmission(Spectrum t, double ei, double et)
: base(BxDFType.BSDF_TRANSMISSION | BxDFType.BSDF_SPECULAR)
{
T = t;
EtaI = ei;
EtaT = et;
Fresnel = new FresnelDielectric (ei, et);
}
public OrenNayar(Spectrum reflectance, double sig)
: base(BxDFType.BSDF_REFLECTION | BxDFType.BSDF_DIFFUSE)
{
double sigma = Util.Radians (sig);
double sigma2 = sigma * sigma;
A = 1.0 - (sigma2 / (2.0 * (sigma2 + 0.33)));
B = 0.45 * sigma2 / (sigma2 + 0.09);
}
public static Spectrum FrCond(double cosi, Spectrum eta, Spectrum k)
{
Spectrum tmp = (eta * eta + k * k) * cosi * cosi;
Spectrum Rparl2 = (tmp - (2.0 * eta * cosi) + new Spectrum (1.0)) / (tmp + (2.0 * eta * cosi) + new Spectrum (1.0));
Spectrum tmp_f = eta * eta + k * k;
Spectrum Rperp2 = (tmp_f - (2.0 * eta * cosi) + new Spectrum (cosi * cosi)) / (tmp_f + (2.0 * eta * cosi) + new Spectrum (cosi * cosi));
return (Rparl2 + Rperp2) / 2.0;
}
public FresnelBlend(Spectrum rs, Spectrum rd, float e)
{
distribution =
//new Anisotropic(10,10);
//new Anisotropic(e*rs.Average, e*rd.Average);
new BlinnDistribution(e);
Rd = rd;
Rs = rs;
}
public Graph(CommonOptions commonOpts, params double[] coeffs)
{
Collectors = new Spectrum(commonOpts, coeffs);
int length = coeffs.Length;
_all = new int[length];
for (int i = 0; i < length; ++i) {
_all[i] = i + 1;
}
}
public OrenNayar(Spectrum reflectance, float sig)
: base(BxdfType.Reflection | BxdfType.Diffuse)
{
_reflectance = reflectance;
float sigma = MathUtility.ToRadians(sig);
float sigma2 = sigma * sigma;
_a = 1.0f - (sigma2 / (2.0f * (sigma2 + 0.33f)));
_b = 0.45f * sigma2 / (sigma2 + 0.09f);
}
public void Run()
{
ISampler sampler = MainSampler.GetSubSampler (TaskNumber, TaskCount);
if (sampler == null)
{
return;
}
int maxSamples = sampler.MaximumSampleCount;
Sample[] samples = OrigSample.Duplicate (maxSamples);
RayDifferential[] rays = new RayDifferential[maxSamples];
Spectrum[] Ls = new Spectrum[maxSamples];
Spectrum[] Ts = new Spectrum[maxSamples];
Intersection[] isects = new Intersection[maxSamples];
for (int i = 0; i < maxSamples; ++i)
{
samples[i] = new Sample ();
rays[i] = new RayDifferential ();
Ls[i] = new Spectrum ();
Ts[i] = new Spectrum ();
isects[i] = new Intersection ();
}
int sampleCount;
while ((sampleCount = sampler.GetMoreSamples (samples)) > 0)
{
for (int i = 0; i < sampleCount; ++i)
{
double rayWeight = Camera.GenerateRayDifferential (samples[i], ref rays[i]);
rays[i].ScaleDifferentials (1.0 / Math.Sqrt (sampler.SamplesPerPixel));
if (rayWeight > 0.0)
Ls[i] = rayWeight * Renderer.Li (Scene, rays[i], samples[i], ref isects[i], ref Ts[i]);
else
{
Ls[i] = new Spectrum ();
Ts[i] = new Spectrum (1.0);
}
// WARNINGS
}
if (sampler.ReportResults (samples, rays, Ls, isects, sampleCount))
{
for (int i = 0; i < sampleCount; ++i)
Camera.Film.AddSample (samples[i], Ls[i]);
}
}
Camera.Film.UpdateDisplay (sampler.xPixelStart, sampler.yPixelStart, sampler.xPixelEnd + 1, sampler.yPixelEnd + 1);
Reporter.Update ();
}
public PreprocessedCoefficients([NotNull] Element element, [NotNull] Func<double, double> getValue,
Region region, int n)
{
if (element == null) throw new ArgumentNullException("element");
if (getValue == null) throw new ArgumentNullException("getValue");
if (region.Width.IsZero()) throw new ArgumentException("region");
if (n <= 0) throw new ArgumentOutOfRangeException("n");
values = Spectrum.ByFunc(getValue, region, n);
Element = element;
}
public Spectrum F(Vector woW, Vector wiW, BxDFType flags)
{
Vector wi = WorldToLocal (wiW), wo = WorldToLocal (woW);
if ((wiW ^ ng) * (woW ^ ng) > 0)
flags &= ~BxDFType.BSDF_TRANSMISSION;
else
flags &= ~BxDFType.BSDF_REFLECTION;
Spectrum f = new Spectrum ();
for (int i = 0; i < nBxDFs; ++i)
if (bxdfs[i].MatchesFlags (flags))
f += bxdfs[i].F (wo, wi);
return f;
}
public virtual Spectrum Rho(Vector wo, int nSamples, double[] samples)
{
Spectrum r = new Spectrum ();
for (int i = 0; i < nSamples; ++i)
{
Vector wi = new Vector ();
double pdf = 0.0;
Spectrum f = SampleF (wo, ref wi, samples[2 * i], samples[2 * i + 1], ref pdf);
if (pdf > 0.0)
r += f * Util.AbsCosTheta (wi) / pdf;
}
return r / (double)nSamples;
}
/// <summary>
/// データの特性を取得。
/// </summary>
/// <param name="spectrum">スペクトル</param>
/// <param name="type">特性の種類</param>
/// <returns>特性</returns>
public static double[] GetData(Spectrum spectrum, Property type)
{
switch(type)
{
case Property.Amplitude:
{
double[] tmp = spectrum.GetPower();
Spectrum.Smooth(tmp);
return tmp;
}
case Property.Phase:
{
double[] tmp = spectrum.GetPhase();
Spectrum.Unwrap(tmp);
Spectrum.Smooth(tmp);
return tmp;
}
case Property.MinimumPhase:
{
double[] tmp = spectrum.GetMinimumPhase();
Spectrum.Smooth(tmp);
return tmp;
}
case Property.AllPassPhase:
{
double[] tmp = spectrum.GetPhase();
double[] tmp2 = spectrum.GetMinimumPhase();
for(int i=0; i<tmp.Length; ++i) tmp[i] += tmp2[i];
Spectrum.Unwrap(tmp);
Spectrum.Smooth(tmp);
return tmp;
}
case Property.PhaseDelay:
{
double[] tmp = spectrum.GetPhase();
Spectrum.Unwrap(tmp);
Spectrum.Smooth(tmp);
return Spectrum.GetPhaseDalay(tmp, 48000);
}
case Property.GroupDelay:
{
double[] tmp = spectrum.GetPhase();
Spectrum.Unwrap(tmp);
Spectrum.Smooth(tmp);
return Spectrum.GetGroupDalay(tmp, 48000);
}
default:
return spectrum.TimeSequence;
}
}//GetData
public Texture<Spectrum> GetSpectrumTexture(string n, Spectrum defaultValue)
{
var name = _geomParams.FindTexture(n);
if (string.IsNullOrEmpty(name))
name = _materialParams.FindTexture(n);
if (!string.IsNullOrEmpty(name))
{
if (_spectrumTextures.ContainsKey(name))
return _spectrumTextures[name];
throw new InvalidOperationException(string.Format("Couldn't find spectrum texture named '{0}' for parameter '{1}'", name, n));
}
var value = _geomParams.FindSpectrum(n, _materialParams.FindSpectrum(n, defaultValue));
return new ConstantTexture<Spectrum>(value);
}
public virtual Spectrum Rho(int nSamples, double[] samples1, double[] samples2)
{
Spectrum r = new Spectrum ();
for (int i = 0; i < nSamples; ++i)
{
Vector wo, wi = new Vector ();
wo = MonteCarlo.UniformSampleHemisphere (samples1[2 * i], samples1[2 * i + 1]);
double pdf_o = Util.InvTwoPi, pdf_i = 0.0;
Spectrum f = SampleF (wo, ref wi, samples2[2 * i], samples2[2 * i + 1], ref pdf_i);
if (pdf_i > 0.0)
r += f * Util.AbsCosTheta (wi) * Util.AbsCosTheta (wo) / (pdf_o * pdf_i);
}
return r / (Util.Pi * nSamples);
}
public static Spectrum SpecularTransmit(RayDifferential ray, BSDF bsdf, Intersection isect, IRenderer renderer, Scene scene, Sample sample)
{
Vector wo = -ray.Direction, wi = new Vector ();
double pdf = 0.0;
Point p = bsdf.dgShading.p;
Normal n = bsdf.dgShading.n;
Spectrum f = bsdf.SampleF (wo, ref wi, new BSDFSample (), ref pdf, BxDFType.BSDF_TRANSMISSION | BxDFType.BSDF_SPECULAR);
Spectrum L = new Spectrum ();
if (pdf > 0.0 && !f.IsBlack && Util.AbsDot (wi, n) != 0.0)
{
RayDifferential rd = new RayDifferential (p, wi, ray, isect.RayEpsilon);
if (ray.HasDifferentials)
{
rd.HasDifferentials = true;
rd.RxOrigin = p + isect.dg.dpdx;
rd.RyOrigin = p + isect.dg.dpdy;
double eta = bsdf.Eta;
Vector w = -wo;
if ((wo ^ n) < 0.0)
eta = 1.0 / eta;
Normal dndx = bsdf.dgShading.dndu * bsdf.dgShading.dudx + bsdf.dgShading.dndv * bsdf.dgShading.dvdx;
Normal dndy = bsdf.dgShading.dndu * bsdf.dgShading.dudy + bsdf.dgShading.dndv * bsdf.dgShading.dvdy;
Vector dwodx = -ray.RxDirection - wo, dwody = -ray.RyDirection - wo;
double dDNdx = (dwodx ^ n) + (wo ^ dndx);
double dDNdy = (dwody ^ n) + (wo ^ dndy);
double mu = eta * (w ^ n) - (wi ^ n);
double dmudx = (eta - (eta * eta * (w ^ n)) / (wi ^ n)) * dDNdx;
double dmudy = (eta - (eta * eta * (w ^ n)) / (wi ^ n)) * dDNdy;
rd.RxDirection = wi + eta * dwodx - new Vector (mu * dndx + dmudx * n);
rd.RyDirection = wi + eta * dwody - new Vector (mu * dndy + dmudy * n);
}
Spectrum Li = renderer.Li (scene, rd, sample);
L = f * Li * Util.AbsDot (wi, n) / pdf;
}
return L;
}
public static Spectrum[] ReadImage(string name, out int xSize, out int ySize)
{
Bitmap bitmap = new Bitmap (name);
Spectrum[] pixels = new Spectrum[bitmap.Width * bitmap.Height];
for (int y = 0; y < bitmap.Height; ++y)
{
for (int x = 0; x < bitmap.Width; ++x)
{
Color pixel = bitmap.GetPixel (x, y);
double[] c = new double[3];
c[0] = pixel.R / 255.0;
c[1] = pixel.G / 255.0;
c[2] = pixel.B / 255.0;
pixels[y * bitmap.Width + x] = new Spectrum (c[0], c[1], c[2]);
}
}
xSize = bitmap.Width;
ySize = bitmap.Height;
return pixels;
}
public AudioEngine()
{
Path = @"http://psv4.vk.me/c613621/u23628424/audios/45049760ad7c.mp3?extra=xy8j8Fwc0OnSqJcxvITYLiX-D4akkd_Rkl8cvuVgLlLvD9G133yv-_MAqCspCcmxxUdw9OMZGdrq702KUJ2PdO1oGDkTRvw&/Scratch%20Bandits%20Crew%20-%20Surround%20Me.mp3";
//Path = @"D:\Documents and Settings\Admin\Рабочий стол\C#\Music Primer\6ddb8171688e23.mp3";
// Path = @"http://www.sky.fm/mp3/the80s.pls";
//Path = @"http://download.wavetlan.com/SVV/Media/HTTP/WMA/WMALossless/Coldplay_StrawberrySwing_WMALossless.wma";
//Path = @"http://yp.shoutcast.com/sbin/tunein-station.pls?id=193174";
//+Path = @"http://yp.shoutcast.com/sbin/tunein-station.pls?id=193174";
//Path = @"http://radiocaroline259.nl/winamp_rc259_320.pls";
//Path = @"http://yp.shoutcast.com/sbin/tunein-station.pls?id=94181";
//Path = @"http://yp.shoutcast.com/sbin/tunein-station.pls?id=256410";
//Path = @"http://flacradio.esy.es/playlist/AI-Radio.m3u";
//Path = @"http://a.files.bbci.co.uk/media/live/manifesto/audio/simulcast/hls/uk/sbr_high/llnw/bbc_1xtra.m3u8";
ListSongs = new List<string>(
Directory.GetFiles(@"D:\Documents and Settings\Admin\Рабочий стол\C#\Music Primer"));
/* ListSongs = new List<string>();
ListSongs.Add(@"http://cs1-34v4.vk-cdn.net/p6/d1483bd42febd1.mp3?extra=vi0VwGa9y_QGmZqu8zXS2NNAuPHuBuHM-yChSaH3-vezjVEJMN7tvO6WDQq3CRsOk0SJw9apaTVSamib5nHTPROhCr8kCz3n&/CunninLynguists%20-%20Darkness%20(Dream%20On)%20(Instrumental).mp3");
ListSongs.Add(@"http://psv4.vk.me/c613231/u23628424/audios/bca9f0bb9989.mp3?extra=c7lN4T5gQC3FOQPpHCgWnmtCTk2F89a-HjouOB5qAPoKePRg_0OSR7nbm8tsFqS1ypEXhrV5khECX449brMq9qzqtiYNOfq1&/Mr.%20Moods%20-%20Rainbow.mp3");
ListSongs.Add(@"http://psv4.vk.me/c613924/u64887148/audios/73b365664dbb.mp3?extra=qbIEMne5L7HEkwI8l57HvsJbjpHEap8WEapQ5BVETzm-bo_6lpu3UPJ4gDnGJyc-G4-7cWHb_gqO9fDT9Ly87XQPYfwcEcaO&/PhybaOptikz%20-%20Chronicles.mp3");
ListSongs.Add(@"http://psv4.vk.me/c521100/u4594424/audios/0277415e656d.mp3?extra=tUmU_lLbAdXrMsDon27ayCWW3l6soR7fHTiQ0-6Qj6xuim7tQLXcEBXS0lq9uJ1TxuFkG-4xyQyWR004b_BL7nkaLcKZqMbd&/Roger%20Molls%20-%20You.mp3");
ListSongs.Add(@"http://psv4.vk.me/c613126/u247179947/audios/5b4259f1d5c3.mp3?extra=Fo_qX0TC-RHoozxSTQQZBedY9vxIlLk1VcPyRMziMarqYxCBZqIhX7cCPCPfB4XvYy2Gbnz9Zdl34KXdNtXu0ovlSeG_B86E&/Keizan%20-%20Keizan%20-%20Damn%20feat%20Dj%20Meloman.mp3");
ListSongs.Add(@"http://psv4.vk.me/c611427/u221922242/audios/d196c39b7b28.mp3?extra=OgcU7H3jJrRB94KkUdGFxqXRlGwh7ttN3sIB0LGRqYUIxFpXfm48v6FQWyHWHge3DDI5U02KBoSRHOJTQX9Pdwj31aeoWBFw&/Billa%20Qause%20-%20Slow%20Down.mp3");
ListSongs.Add(@"http://psv4.vk.me/c611324/u1444216/audios/36a640799476.mp3?extra=sr0Y8gulc4N5Wr4wEPavdJ98vK3FRAFX6pQbCC6JeDypyPoT8RGLsR4618C8CpZE1YaLlUfGmFMAyJCsXsnjSo4sg-lH87qq&/GRiZ%20-%20Love%20Will%20Follow%20You%20(feat.%20Russ%20Liquid).mp3");
ListSongs.Add(@"http://psv4.vk.me/c613327/u23628424/audios/fb86d3ceae8f.mp3?extra=q7-2v9Jh_Cq0V4QlhgEz7E4pvf3NxS9yPCE5MIdu_0NQsdQ13572JElzEgZt9Kj7VafbWfxb-vq2IP1BvLLqCE6MSD7MZRA6&/Kinack%20-%20Shine.mp3");
ListSongs.Add(@"http://cs1-42v4.vk-cdn.net/p23/7ffb834f38273a.mp3?extra=-mJYId08Rdph4HddpqC6noOAFcs6jvCw0hauKmXWQkREoEUclM-MMSstShqEYPguWrAemIoc5zA57nx89XmbnkHGh-E_5WgD&/Frameworks%20-%20Music%20Box.mp3");
ListSongs.Add(@"http://psv4.vk.me/c613121/u23628424/audios/659402091c6c.mp3?extra=ZfCP0UugdWy6oapnqKBTnvwtC2vXa_WQXZsE648_vkKMgn2e-3nP1E1fREEgJnUsSka0pMvOHvOlBwU6oyjird1po-WO0J8W&/Travelers%20Of%20Tyme%20-%20Raining%20Castanets%20(The%20Rains%20of%20Castamere).mp3");
*/
WahWahEffect = new WahWahService();
PitchShiftEffect = new PitchShiftService();
PhaserEffect = new PhaserService();
ChorusEffect = new ChorusService();
DistortionEffect = new DistortionService();
DynamicAmplificationEffect = new DynamicAmplificationService();
ReverberationEffect = new ReverberationService();
EchoEffect = new EchoService();
CompressorEffect = new CompressorService();
BiQuadFilterEffect = new BiQuadFilterService();
DSPEffect = new DSP();
WaveFormClass = new WaveFormService();
Spectrum = new Spectrum();
MemoryPlay = true;
_timer = new BASSTimer();
_timer.Tick += MusicTrackTick;
_timer.Start();
CurrentVolume = 1;
Crossfade = new CrossfadeService(CurrentVolume);
EqualizerEffect = new EqualizerService();
CrossfadeActive = true;
SoundOutProvider = new SoundOutProviderBASS();
_myUserAgentPtr = Marshal.StringToHGlobalAnsi(_myUserAgent);
_positionEventAggregator = new EventAggregator();
_waveFormEventAggregator = new EventAggregator();
DownloadMode = DownloadTypes.NoDownload;
_syncProcPos = SyncMethodPos;
Bass.BASS_SetConfigPtr(BASSConfig.BASS_CONFIG_NET_AGENT, _myUserAgentPtr);
SoundOutProvider.SetConfig(BASSConfig.BASS_CONFIG_FLOATDSP, true);
SoundOutProvider.SetConfig(BASSConfig.BASS_CONFIG_NET_TIMEOUT, 5000);
SoundOutProvider.SetConfig(BASSConfig.BASS_CONFIG_WMA_PREBUF, 0);
SoundOutProvider.SetConfig(BASSConfig.BASS_CONFIG_NET_PREBUF, 0);
SoundOutProvider.SetConfig(BASSConfig.BASS_CONFIG_NET_PLAYLIST, 2);
}
public Spectrum GetDeconvolutedSpectrum(Spectrum spec, int minCharge, int maxCharge, Tolerance tolerance, double corrThreshold)
{
return(GetDeconvolutedSpectrum(spec, minCharge, maxCharge, tolerance, corrThreshold, IsotopeOffsetTolerance, FilteringWindowSize));
}
public SnaSerializer(Spectrum spec)
: base(spec)
{
}
public void updateRow(SpectrumDataSet.SpectrumTableRow row, MassSpectrum spectrum)
{
spectrumList[spectrum.Index] = spectrum;
Spectrum s = spectrum.Element; //GetElement(false);
DataProcessing dp = spectrum.DataProcessing;
Scan scan = null;
InstrumentConfiguration ic = null;
if (s.scanList.scans.Count > 0)
{
scan = s.scanList.scans[0];
ic = scan.instrumentConfiguration;
}
if (dp == null)
{
dp = s.dataProcessing;
}
CVParam param;
param = s.cvParam(CVID.MS_ms_level);
row.MsLevel = !param.empty() ? (int)param.value : 0;
param = scan != null?scan.cvParam(CVID.MS_scan_start_time) : new CVParam();
row.ScanTime = !param.empty() ? param.timeInSeconds() : 0;
if (Properties.Settings.Default.TimeInMinutes)
{
row.ScanTime /= 60;
}
param = s.cvParam(CVID.MS_base_peak_m_z);
row.BasePeakMz = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_base_peak_intensity);
row.BasePeakIntensity = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_total_ion_current);
row.TotalIonCurrent = !param.empty() ? (double)param.value : 0;
var precursorInfo = new StringBuilder();
var isolationWindows = new StringBuilder();
if (row.MsLevel == 1 || s.precursors.Count == 0)
{
precursorInfo.Append("n/a");
isolationWindows.Append("n/a");
}
else
{
foreach (Precursor p in s.precursors)
{
foreach (SelectedIon si in p.selectedIons)
{
if (precursorInfo.Length > 0)
{
precursorInfo.Append(",");
}
precursorInfo.AppendFormat("{0:G8}", (double)si.cvParam(CVID.MS_selected_ion_m_z).value);
}
var iw = p.isolationWindow;
CVParam isolationTarget = iw.cvParam(CVID.MS_isolation_window_target_m_z);
if (!isolationTarget.empty())
{
double iwMz = (double)isolationTarget.value;
if (isolationWindows.Length > 0)
{
isolationWindows.Append(",");
}
CVParam lowerOffset = iw.cvParam(CVID.MS_isolation_window_lower_offset);
CVParam upperOffset = iw.cvParam(CVID.MS_isolation_window_upper_offset);
if (lowerOffset.empty() || upperOffset.empty())
{
isolationWindows.AppendFormat("{0:G8}", iwMz);
}
else
{
isolationWindows.AppendFormat("[{0:G8}-{1:G8}]", iwMz - (double)lowerOffset.value, iwMz + (double)upperOffset.value);
}
}
}
}
if (precursorInfo.Length == 0)
{
precursorInfo.Append("unknown");
}
row.PrecursorInfo = precursorInfo.ToString();
if (isolationWindows.Length == 0)
{
isolationWindows.Append("unknown");
}
row.IsolationWindows = isolationWindows.ToString();
StringBuilder scanInfo = new StringBuilder();
foreach (Scan scan2 in s.scanList.scans)
{
if (scan2.scanWindows.Count > 0)
{
foreach (ScanWindow sw in scan2.scanWindows)
{
if (scanInfo.Length > 0)
{
scanInfo.Append(",");
}
scanInfo.AppendFormat("[{0:G8}-{1:G8}]",
(double)sw.cvParam(CVID.MS_scan_window_lower_limit).value,
(double)sw.cvParam(CVID.MS_scan_window_upper_limit).value);
}
}
}
if (scanInfo.Length == 0)
{
scanInfo.Append("unknown");
}
row.ScanInfo = scanInfo.ToString();
row.IonMobility = scan != null ? (double)scan.cvParam(CVID.MS_ion_mobility_drift_time).value : 0;
if (row.IonMobility == 0 && scan != null)
{
row.IonMobility = (double)scan.cvParam(CVID.MS_inverse_reduced_ion_mobility).value;
if (row.IonMobility == 0)
{
// Early version of drift time info, before official CV params
var userparam = scan.userParam("drift time");
if (!userparam.empty())
{
row.IonMobility = userparam.timeInSeconds() * 1000.0;
}
}
}
row.SpotId = s.spotID;
row.SpectrumType = s.cvParamChild(CVID.MS_spectrum_type).name;
row.DataPoints = s.defaultArrayLength;
row.IcId = (ic == null || ic.id.Length == 0 ? "unknown" : ic.id);
row.DpId = (dp == null || dp.id.Length == 0 ? "unknown" : dp.id);
}
public LambertianReflection(Spectrum r)
: base(BxDFType.Reflection | BxDFType.Diffuse)
{
this.r = r;
}
static void _Main(string[] args)
{
const int N = 1024;
double[] x = new double[N];
IFilter filter = new ShelvingEqualizer(Common.Normalize(1000), 1);
// インパルス応答取得
filter.Clear();
/*
* filter.GetValue(1);
* for(int i=0; i<16; ++i)
* filter.GetValue(0);
*/
filter.GetValue(1);
for (int i = 1; i < N; ++i)
{
x[i] = filter.GetValue(0);
}
#if TIME_SEQUENCE
int n = N;
double[] t = new double[n];
for (int i = 0; i < n; ++i)
{
t[i] = i;
}
Graph.GraphForm gf = new Graph.GraphForm();
gf.Graph.AddEntry(t, x, new Pen(Color.Crimson));
gf.Graph.SetXAxis(0, n, 5, new Font(FontFamily.GenericSerif, 12), new SolidBrush(Color.Black));
gf.Graph.SetYAxis(0, 2, 5, new Font(FontFamily.GenericSerif, 12), new SolidBrush(Color.Black));
gf.Size = new Size(640, 480);
gf.ShowDialog();
#elif PHASE
Spectrum spec = Spectrum.FromTimeSequence(x, 1);
int n = spec.Count;
double[] t = new double[n];
for (int i = 0; i < n; ++i)
{
t[i] = i;
}
double[] y = spec.GetPhase();
Spectrum.Unwrap(y);
Graph.GraphForm gf = new Graph.GraphForm();
gf.Graph.AddEntry(t, y, new Pen(Color.Crimson));
gf.Graph.SetXAxis(0, n, 4, new Font(FontFamily.GenericSerif, 12), new SolidBrush(Color.Black));
gf.Graph.SetYAxis(-50, 0, 4, new Font(FontFamily.GenericSerif, 12), new SolidBrush(Color.Black));
gf.Size = new Size(640, 480);
gf.ShowDialog();
#elif GAIN
Spectrum spec = Spectrum.FromTimeSequence(x, 1);
int n = spec.Count;
double[] t = new double[n];
for (int i = 0; i < n; ++i)
{
t[i] = i;
}
double[] y = spec.GetAmplitude();
Graph.GraphForm gf = new Graph.GraphForm();
gf.Graph.AddEntry(t, y, new Pen(Color.Crimson));
gf.Graph.SetXAxis(0, n, 4, new Font(FontFamily.GenericSerif, 12), new SolidBrush(Color.Black));
gf.Graph.SetYAxis(0, 4, 4, new Font(FontFamily.GenericSerif, 12), new SolidBrush(Color.Black));
gf.Size = new Size(640, 480);
gf.ShowDialog();
#endif
#if false
const int N = 512;
double[] x = new double[N];
double[] x0 = new double[N];
double[] y0 = new double[N];
/*
* Random rnd = new Random();
* x0[0] = 1;
* x0[1] = 1;
* y0[0] = 0;
* y0[1] = 0;
* for(int i=1; i<N/2; ++i)
* {
* x0[2*i] = rnd.NextDouble();
* x0[2*i+1] = rnd.NextDouble();
* y0[2*i] = -x0[2*i+1];
* y0[2*i+1] = x0[2*i];
* }
* Fft fft = new Fft(N);
* fft.Invert(x0);
* fft.Invert(y0);
* for(int i=0; i<N; ++i)
* x[i] = x0[i];
* //*/
//*
for (int i = 0; i < N; ++i)
{
x[i] = 100;
for (int k = 1; k < 200; ++k)
{
x[i] += short.MaxValue / 4 / k * Math.Cos(Math.PI / 512 * 32 * i * k);
}
x0[i] = x[i];
y0[i] = 0;
for (int k = 1; k < 200; ++k)
{
y0[i] += short.MaxValue / 4 / k * Math.Sin(Math.PI / 512 * 32 * i * k);
}
}
//*/
double[] y = Spectrum.HilbertTransform(x);
using (StreamWriter writer = new StreamWriter("z.csv", false, Encoding.Default))
{
/*
* for(int i=0; i<x.Length; ++i)
* writer.Write("{0},{1},{2},{3},{4}\n", i, x0[i], x[i], y0[i], y[i]);
* //*/
//*
Spectrum a0 = Spectrum.FromTimeSequence(x0);
Spectrum a = Spectrum.FromTimeSequence(x);
Spectrum b0 = Spectrum.FromTimeSequence(y0);
Spectrum b = Spectrum.FromTimeSequence(y);
for (int i = 0; i < a.Count; ++i)
{
writer.Write("{0},{1},{2},{3},{4}\n", i, a0[i].Abs, a[i].Abs, b0[i].Abs, b[i].Abs);
// writer.Write("{0},{1},{2},{3},{4}\n", i, a0[i].Arg, a[i].Arg, b0[i].Arg, b[i].Arg);
}
//*/
}
#elif false
const int N = 1024;
double[] lp = new double[N];
IFilter lpf = new LowPassFir(16, Common.Normalize(2000));
lp[0] = lpf.GetValue(1);
for (int i = 1; i < N; ++i)
{
lp[i] = lpf.GetValue(0);
}
double[] bp = new double[N];
IFilter bpf = new BandPassFir(16, Common.Normalize(2000), Common.Normalize(8000));
lp[0] = bpf.GetValue(1);
for (int i = 1; i < N; ++i)
{
bp[i] = bpf.GetValue(0);
}
double[] hp = new double[N];
IFilter hpf = new HighPassFir(16, Common.Normalize(8000));
lp[0] = hpf.GetValue(1);
for (int i = 1; i < N; ++i)
{
hp[i] = hpf.GetValue(0);
}
Fft fft = new Fft(N);
fft.Transform(1, lp);
fft.Transform(1, bp);
fft.Transform(1, hp);
using (StreamWriter writer = new StreamWriter("z.csv", false, Encoding.Default))
{
double la = Common.Amp(lp[0]);
double ba = Common.Amp(bp[0]);
double ha = Common.Amp(hp[0]);
writer.Write("{0},{1},{2},{3}\n", 0, la, ba, ha);
for (int i = 1; i < N / 2; ++i)
{
la = Common.Amp(lp[2 * i] * lp[2 * i] + lp[2 * i + 1] * lp[2 * i + 1]);
ba = Common.Amp(bp[2 * i] * bp[2 * i] + bp[2 * i + 1] * bp[2 * i + 1]);
ha = Common.Amp(hp[2 * i] * hp[2 * i] + hp[2 * i + 1] * hp[2 * i + 1]);
writer.Write("{0},{1},{2},{3}\n", i, la, ba, ha);
}
la = Common.Amp(lp[1]);
ba = Common.Amp(bp[1]);
ha = Common.Amp(hp[1]);
writer.Write("{0},{1},{2},{3}\n", N / 2, la, ba, ha);
}
#elif false
uint length;
double[] l;
double[] r;
FormatHeader header;
using (WaveReader reader = new WaveReader(@"TD100V00H030.wav"))
{
header = reader.Header;
length = reader.Length;
int tmp = reader.Read(length, out l, out r);
}
IFilter lpf = new LowPassFir(16, Common.Normalize(4500));
IFilter bpf = new BandPassFir(16, Common.Normalize(4500), Common.Normalize(10000));
IFilter hpf = new HighPassFir(16, Common.Normalize(10000));
for (int i = 0; i < l.Length; ++i)
{
double lp = lpf.GetValue(l[i]);
double bp = bpf.GetValue(l[i]);
double hp = hpf.GetValue(l[i]);
l[i] = lp + bp + hp;
}
if (r != null)
{
for (int i = 0; i < l.Length; ++i)
{
double lp = lpf.GetValue(r[i]);
double bp = bpf.GetValue(r[i]);
double hp = hpf.GetValue(r[i]);
r[i] = lp + bp + hp;
}
}
using (WaveWriter writer = new WaveWriter("z.wav", header))
{
writer.Write(l, r);
}
#elif false
using (StreamWriter writer = new StreamWriter("z.csv", false, Encoding.Default))
{
for (int i = 0; i < l.Length; ++i)
{
writer.Write("{0},{1},{2}\n", i, l[i], r[i]);
}
}
#endif
}
public StraightLine(Spectrum spec)
{
_spectrum = new Spectrum(spec.SpectrumData);
}
public ScaledBxDF(BxDF b, Spectrum sc)
: base(b.Type)
{
bxdf = b;
s = sc;
}
public DialogResult ShowData(IntegrateResultItem item, List <IntegrateResultItem> results, Spectrum spec = null, int idMaxNum = 5)
{
if (item == null || results == null)
{
return(System.Windows.Forms.DialogResult.Cancel);
}
this._item = item;
this.lblName.Text = item.ToString();
//找出使用相同识别库和相同拟合库的性质
var lst = results.Where(d => d.GroupFitID == item.GroupFitID && d.GroupIDID == item.GroupIDID && ((double.IsNaN(d.IdWeight) && double.IsNaN(item.IdWeight)) || d.IdWeight == item.IdWeight) && ((double.IsNaN(d.FitWeight) && double.IsNaN(item.FitWeight)) || d.FitWeight == item.FitWeight)).ToList();
//识别
this.panelId.Title = "识别、拟合结果";
//添加第一行，显示最终预测结果
this.gridId.Rows.Add("");
this.gridId.Rows[0].Frozen = true;
if (spec != null)
{
this.gridId[0, 0].Value = spec.Name;
this.gridId[1, 0].Value = spec.UUID;
}
foreach (var idc in lst)
{
//添加性质列
this.gridId.Columns.Add(new DataGridViewTextBoxColumn()
{
Width = 80,
HeaderText = idc.Comp.Name,
SortMode = DataGridViewColumnSortMode.NotSortable
});
this.gridId[this.gridId.Columns.Count - 1, 0].Value = idc.Comp.PredictedValue.ToString(idc.Comp.EpsFormatString);
}
int k = 1;
if (item.IdResult != null)
{
//添加识别行
this.gridId.Rows.Add(
"识别结果",
"",
item.IDTQ.ToString("F4"),
item.IDSQ.ToString("F4"),
"",
item.ConfidenceId.ToString("F2"),
string.Format("{0}%/{1}%", item.PrimalWID, double.IsNaN(item.IdWeight) ? 0 : item.IdWeight));
for (int i = 0; i < lst.Count; i++)
{
this.gridId[7 + i, this.gridId.Rows.Count - 1].Value = lst[i].IdValue.ToString(lst[i].Comp.EpsFormatString);
}
this.gridId.Rows[this.gridId.Rows.Count - 1].DefaultCellStyle.BackColor = Color.FromArgb(221, 217, 195);
int idcounter = 0;
foreach (var r in item.IdResult)
{
if (idcounter >= idMaxNum)
{
break;
}
idcounter++;
var cell = new DataGridViewRowHeaderCell()
{
Value = k.ToString()
};
var row = new nodeIdRow(r)
{
HeaderCell = cell
};
var cells = new List <string>();
cells.AddRange(new string[] {
r.Spec.Name,
r.Spec.UUID,
r.TQ.ToString("F4"),
r.SQ.ToString("F4"),
r.Result.ToString(),
"",
""
});
foreach (var iditem in lst)
{
var c = r.Spec.Components.Contains(iditem.Comp) ? r.Spec.Components[iditem.Comp.Name] : null;
cells.Add(c != null ? c.ActualValue.ToString(c.EpsFormatString) : "");
}
row.CreateCells(this.gridId, cells.ToArray());
row.DefaultCellStyle.BackColor = Color.FromArgb(221, 217, 195);
this.gridId.Rows.Add(row);
k++;
}
}
//拟合
if (item.FitResult != null && item.FitResult.Specs != null)
{
var fitrow = new nodeFitRow(item.FitResult);
fitrow.CreateCells(this.gridId, "拟合结果",
"",
item.FitTQ.ToString("F4"),
item.FitSQ.ToString("F4"),
item.FitResult.Result.ToString(),
item.ConfidenceFit.ToString("F2"),
string.Format("{0}%/{1}%", item.PrimalWFit, double.IsNaN(item.FitWeight) ? 0 : item.FitWeight));
this.gridId.Rows.Add(fitrow);
for (int i = 0; i < lst.Count; i++)
{
this.gridId[7 + i, this.gridId.Rows.Count - 1].Value = lst[i].FitValue.ToString(lst[i].Comp.EpsFormatString);
}
this.gridId.Rows[this.gridId.Rows.Count - 1].DefaultCellStyle.BackColor = Color.FromArgb(217, 151, 149);
k = 1;
foreach (var d in item.FitResult.Specs)
{
var cell = new DataGridViewRowHeaderCell()
{
Value = k.ToString()
};
var row = new DataGridViewRow()
{
HeaderCell = cell
};
var cells = new List <string>();
if (k == 1)
{
cells.AddRange(new string[] {
d.Spec.Name,
d.Spec.UUID,
item.FitResult.TQ.ToString("F4"),
item.FitResult.SQ.ToString("F4"),
d.Rate.ToString("F4"),
"",
""
});
}
else
{
cells.AddRange(new string[] {
d.Spec.Name,
d.Spec.UUID,
"",
"",
d.Rate.ToString("F4"),
"",
""
});
}
//添加性质
foreach (var fititem in lst)
{
var c = d.Spec.Components.Contains(fititem.Comp) ? d.Spec.Components[fititem.Comp.Name] : null;
cells.Add(c != null ? c.ActualValue.ToString(c.EpsFormatString) : "");
}
row.CreateCells(this.gridId, cells.ToArray());
row.DefaultCellStyle.BackColor = Color.FromArgb(217, 151, 149);
this.gridId.Rows.Add(row);
k++;
}
}
//PLS
if (lst.Select(d => d.Pls1Result != null || d.AnnResult != null).Count() > 0)
{
//洗添加PLS-ANN的行
var plsrowP = new DataGridViewRow();
plsrowP.CreateCells(this.gridId, "PLS1预测结果");
plsrowP.DefaultCellStyle.BackColor = Color.FromArgb(117, 146, 60);
this.gridId.Rows.Add(plsrowP);
var plsrowW = new DataGridViewRow();
plsrowW.CreateCells(this.gridId, "PLS1比例");
plsrowW.DefaultCellStyle.BackColor = Color.FromArgb(117, 146, 60);
this.gridId.Rows.Add(plsrowW);
var plsrowMash = new DataGridViewRow();
plsrowMash.CreateCells(this.gridId, "马氏距离");
plsrowMash.DefaultCellStyle.BackColor = Color.FromArgb(117, 146, 60);
this.gridId.Rows.Add(plsrowMash);
var plsrowSec = new DataGridViewRow();
plsrowSec.CreateCells(this.gridId, "光谱残差");
plsrowSec.DefaultCellStyle.BackColor = Color.FromArgb(117, 146, 60);
this.gridId.Rows.Add(plsrowSec);
var plsrowND = new DataGridViewRow();
plsrowND.CreateCells(this.gridId, "最邻近距离");
plsrowND.DefaultCellStyle.BackColor = Color.FromArgb(117, 146, 60);
this.gridId.Rows.Add(plsrowND);
var annrowP = new DataGridViewRow();
annrowP.CreateCells(this.gridId, "ANN预测结果");
annrowP.DefaultCellStyle.BackColor = Color.FromArgb(83, 142, 213);
this.gridId.Rows.Add(annrowP);
var annrowW = new DataGridViewRow();
annrowW.CreateCells(this.gridId, "ANN比例");
annrowW.DefaultCellStyle.BackColor = Color.FromArgb(83, 142, 213);
this.gridId.Rows.Add(annrowW);
var annrowMash = new DataGridViewRow();
annrowMash.CreateCells(this.gridId, "马氏距离");
annrowMash.DefaultCellStyle.BackColor = Color.FromArgb(83, 142, 213);
this.gridId.Rows.Add(annrowMash);
var annrowSec = new DataGridViewRow();
annrowSec.CreateCells(this.gridId, "光谱残差");
annrowSec.DefaultCellStyle.BackColor = Color.FromArgb(83, 142, 213);
this.gridId.Rows.Add(annrowSec);
var annrowND = new DataGridViewRow();
annrowND.CreateCells(this.gridId, "最邻近距离");
annrowND.DefaultCellStyle.BackColor = Color.FromArgb(83, 142, 213);
this.gridId.Rows.Add(annrowND);
foreach (var r in lst)
{
if (r.Pls1Result != null)
{
var idx = this.findColumnIndex(r.Pls1Result.Comp.Name);
if (idx >= 0)
{
var factor = r.Pls1Result.Factor - 1;
plsrowP.Cells[idx].Value = r.Pls1Result.Comp.PredictedValue.ToString(r.Pls1Result.Comp.EpsFormatString);
plsrowP.Cells[idx].Style = r.Pls1Result.Comp.Style;
plsrowW.Cells[idx].Value = string.Format("{0}%/{1}%", this.doubleToString(r.PrimalWPLS1, 1), this.doubleToString(r.Pls1Weight, 1));
plsrowMash.Cells[idx].Value = string.Format("{0}/{1}", this.doubleToString(r.Pls1Result.MDMin), this.doubleToString(r.Pls1Result.MahDist[factor]));
plsrowSec.Cells[idx].Value = string.Format("{0}/{1}", this.doubleToString(r.Pls1Result.SRMin), this.doubleToString(r.Pls1Result.SR[factor]));
plsrowND.Cells[idx].Value = string.Format("{0}/{1}", this.doubleToString(r.Pls1Result.NDMin), this.doubleToString(r.Pls1Result.ND[factor]));
}
}
if (r.AnnResult != null)
{
var idx = this.findColumnIndex(r.AnnResult.Comp.Name);
if (idx >= 0)
{
var factor = r.AnnResult.Factor - 1;
annrowP.Cells[idx].Value = r.AnnResult.Comp.PredictedValue.ToString(r.AnnResult.Comp.EpsFormatString);
annrowP.Cells[idx].Style = r.AnnResult.Comp.Style;
annrowW.Cells[idx].Value = string.Format("{0}/{1}", this.doubleToString(r.PrimalWPLS1), this.doubleToString(r.Pls1Weight));
annrowMash.Cells[idx].Value = string.Format("{0}/{1}", this.doubleToString(r.AnnResult.MDMin), this.doubleToString(r.AnnResult.MahDist[factor]));
annrowSec.Cells[idx].Value = string.Format("{0}/{1}", this.doubleToString(r.AnnResult.SRMin), this.doubleToString(r.AnnResult.SR[factor]));
annrowND.Cells[idx].Value = string.Format("{0}/{1}", this.doubleToString(r.AnnResult.NDMin), this.doubleToString(r.AnnResult.ND[factor]));
}
}
}
}
return(this.ShowDialog());
}
public IAnalysisResult Analyze(Spectrum data, IMeasurementSettings settings)
{
var imdSettings = settings as IImdSettings;
if (imdSettings == null)
{
throw new InvalidOperationException();
}
var result = new ImdAnalysisResult();
result.Data = data;
var maxFrequency = imdSettings.LimitMaxFrequency ? imdSettings.MaxFrequency : data.MaxFrequency;
var f1 = imdSettings.F1Frequency;
var f2 = imdSettings.F2Frequency;
var f1i = data.GetFrequencyIndices(f1, imdSettings.WindowHalfSize);
var f2i = data.GetFrequencyIndices(f2, imdSettings.WindowHalfSize);
var f1rss = data.ValueAtFrequency(f1, x => x.Mean, imdSettings.WindowHalfSize);
var f2rss = data.ValueAtFrequency(f2, x => x.Mean, imdSettings.WindowHalfSize);
/* Total IMD+Noise is full bandwidth except F1 and F2 frequencies */
double totalImd = 0.0;
double total = 0.0;
var right = data.GetFrequencyIndices(maxFrequency, 0).First();
for (var f = 0; f < right; f++)
{
total += Math.Pow(data.Statistics[f].Mean, 2.0);
if (!f1i.Contains(f) && !f2i.Contains(f))
{
totalImd += Math.Pow(data.Statistics[f].Mean, 2.0);
}
}
totalImd = Math.Sqrt(totalImd) / Math.Sqrt(total);
result.TotalImdPlusNoisePercentage = 100.0 * totalImd;
result.TotalImdPlusNoiseDb = -totalImd.ToDbTp();
var orders = new Dictionary <int, double>();
var order = imdSettings.MaxOrder;
for (var n = -order + 1; n < order; n++)
{
for (var m = -order + 1; m < order; m++)
{
if (n == 0 || m == 0)
{
continue;
}
var o = Math.Max(Math.Abs(n), Math.Abs(m)) + 1;
var f = n * f1 + m * f2;
if (f > 0 && f < maxFrequency)
{
var imd = data.ValueAtFrequency(f, x => x.Mean, imdSettings.WindowHalfSize);
if (!orders.ContainsKey(o))
{
orders.Add(o, imd);
}
else
{
orders[o] += imd;
}
}
}
}
result.F1Db = -f1rss.ToDbTp();
result.F2Db = -f2rss.ToDbTp();
result.F1Frequency = f1;
result.F2Frequency = f2;
result.MaxOrder = imdSettings.MaxOrder;
result.Bandwidth = maxFrequency;
var sumOfOrders = 0.0;
for (var i = 2; i <= order; i++)
{
sumOfOrders += Math.Pow(orders[i], 2.0);
orders[i] = -orders[i].ToDbTp();
}
sumOfOrders = Math.Sqrt(sumOfOrders);
result.OrderedImd = orders.OrderBy(o => o.Key).ToDictionary(k => k.Key, v => v.Value);
result.ImdF2ForGivenOrderPercentage = (sumOfOrders / f1rss) * 100.0;
result.ImdF2ForGivenOrderDb = -(sumOfOrders / f1rss).ToDbTp();
result.ImdF1F2ForGivenOrderPercentage = (sumOfOrders / (f1rss + f2rss)) * 100.0;
result.ImdF1F2ForGivenOrderDb = -(sumOfOrders / (f1rss + f2rss)).ToDbTp();
return(result);
}
public Spectrum SampleF(Vector woW, out Vector wiW, BsdfSample bsdfSample,
out float pdf, out BxdfType sampledType, BxdfType flags = BxdfType.All)
{
// Choose which _BxDF_ to sample
int matchingComps = NumComponents(flags);
if (matchingComps == 0)
{
wiW = Vector.Zero;
pdf = 0.0f;
sampledType = 0;
return(Spectrum.CreateBlack());
}
int which = Math.Min(
MathUtility.Floor(bsdfSample.UComponent * matchingComps),
matchingComps - 1);
Bxdf bxdf = null;
int count = which;
foreach (var eachBxdf in _bxdfs)
{
if (eachBxdf.MatchesFlags(flags) && count-- == 0)
{
bxdf = eachBxdf;
break;
}
}
Debug.Assert(bxdf != null);
// Sample chosen _BxDF_
Vector wo = WorldToLocal(woW);
Vector wi;
pdf = 0.0f;
Spectrum f = bxdf.SampleF(wo, out wi, bsdfSample.UDir0, bsdfSample.UDir1, out pdf);
if (pdf == 0.0f)
{
wiW = Vector.Zero;
sampledType = 0;
return(Spectrum.CreateBlack());
}
sampledType = bxdf.Type;
wiW = LocalToWorld(wi);
// Compute overall PDF with all matching _BxDF_s
if (!bxdf.Type.HasFlag(BxdfType.Specular) && matchingComps > 1)
{
foreach (var eachBxdf in _bxdfs)
{
if (eachBxdf != bxdf && eachBxdf.MatchesFlags(flags))
{
pdf += bxdf.Pdf(wo, wi);
}
}
}
if (matchingComps > 1)
{
pdf /= matchingComps;
}
// Compute value of BSDF for sampled direction
if (!bxdf.Type.HasFlag(BxdfType.Specular))
{
f = Spectrum.CreateBlack();
if (Vector.Dot(wiW, _ng) * Vector.Dot(woW, _ng) > 0) // ignore BTDFs
{
flags &= ~BxdfType.Transmission;
}
else // ignore BRDFs
{
flags &= ~BxdfType.Reflection;
}
foreach (var eachBxdf in _bxdfs)
{
if (eachBxdf.MatchesFlags(flags))
{
f += eachBxdf.F(wo, wi);
}
}
}
return(f);
}
public Z80Serializer(Spectrum spec)
: base(spec)
{
}
public SpecularReflection(Spectrum r, Fresnel fresnel)
: base(BxDFType.Reflection | BxDFType.Specular)
{
this.reflectance = r;
this.fresnel = fresnel;
}
public FresnelConductor(Spectrum e, Spectrum k)
{
Eta = e;
K = k;
}
private static IScene Build()
{
var white =
new MatteMaterial(
new ConstantTexture <Spectrum>(Spectrum.FromRGB(new[] { 0.6f, 0f, 0.9f }, SpectrumType.Illuminant)),
new ConstantTexture <float>(0), null);
var sss = new DisneyMaterial(
new ConstantTexture <Spectrum>(Spectrum.FromRGB(new[] { 0.9f, 0.9f, 0.9f }, SpectrumType.Reflectance)),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1.5f),
new ConstantTexture <float>(0.5f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(0.5f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(0f),
new ConstantTexture <Spectrum>(new Spectrum(40f)),
false,
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0.5f),
null);
var red =
new DisneyMaterial(
new ConstantTexture <Spectrum>(Spectrum.FromRGB(new[] { 0.9f, 0f, 0f }, SpectrumType.Reflectance)),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1.5f),
new ConstantTexture <float>(0.8f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0.9f),
new ConstantTexture <float>(0f),
new ConstantTexture <Spectrum>(Spectrum.Zero),
false,
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0.5f),
null);
var yellow =
new DisneyMaterial(
new ConstantTexture <Spectrum>(Spectrum.FromRGB(new[] { 1f, 1f, 0f }, SpectrumType.Reflectance)),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1.5f),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0.9f),
new ConstantTexture <float>(0f),
new ConstantTexture <Spectrum>(Spectrum.Zero),
false,
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0.5f),
null);
var cyan =
new DisneyMaterial(
new ConstantTexture <Spectrum>(Spectrum.FromRGB(new[] { 0f, 1f, 1f }, SpectrumType.Reflectance)),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1.8f),
new ConstantTexture <float>(0.1f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(0.9f),
new ConstantTexture <float>(0f),
new ConstantTexture <Spectrum>(Spectrum.Zero),
false,
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0.5f),
null);
var metal = new DisneyMaterial(
new ConstantTexture <Spectrum>(Spectrum.FromRGB(new[] { 0.5f, 0.5f, 0.5f }, SpectrumType.Reflectance)),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(1.5f),
new ConstantTexture <float>(0.4f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(0f),
new ConstantTexture <Spectrum>(Spectrum.Zero),
false,
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0.5f),
null);
var mirror = new DisneyMaterial(
new ConstantTexture <Spectrum>(Spectrum.FromRGB(new[] { 0.7f, 0.7f, 0.8f }, SpectrumType.Reflectance)),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(1.5f),
new ConstantTexture <float>(0.1f),
new ConstantTexture <float>(0.5f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(0f),
new ConstantTexture <Spectrum>(Spectrum.Zero),
false,
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0.5f),
null);
var trans = new DisneyMaterial(
new ConstantTexture <Spectrum>(Spectrum.FromRGB(new[] { 0.0f, 0.8f, 0.0f }, SpectrumType.Illuminant)),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(2.5f),
new ConstantTexture <float>(0.01f),
new ConstantTexture <float>(0.5f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
new ConstantTexture <float>(1f),
new ConstantTexture <float>(0f),
new ConstantTexture <Spectrum>(new Spectrum(0f)),
false,
new ConstantTexture <float>(0f),
new ConstantTexture <float>(0f),
null);
var px = 3000;
var pz = 3000;
var tr = Transform.Translate(-500, 178, -600);
var tris = TriangleMesh.CreateTriangleMesh(
tr,
Transform.Invert(tr),
false,
2,
new[] { 0, 1, 2, 3, 2, 1 },
4,
new[]
{
new Point(0, 0, 0),
new Point(0, 0, pz),
new Point(px, 0, 0),
new Point(px, 0, pz)
},
null,
null, null, null, null, null);
var prims = new List <IPrimitive>();
foreach (var tri in tris)
{
prims.Add(new GeometricPrimitive(tri, red, null));
}
var s1t = Transform.Translate(278, 278, 100);
var s1 = new Sphere(s1t, Transform.Invert(s1t), false, 100f, -100, 100, 360);
var s1g = new GeometricPrimitive(s1, sss, null);
prims.Add(s1g);
var s2t = Transform.Translate(390, 228, 30);
var s2 = new Sphere(s2t, Transform.Invert(s2t), false, 50f, -50, 50, 360);
var s2g = new GeometricPrimitive(s2, cyan, null);
prims.Add(s2g);
var s3t = Transform.Translate(50, 328, 200);
var s3 = new Sphere(s3t, Transform.Invert(s3t), false, 150f, -150, 150, 360);
var s3g = new GeometricPrimitive(s3, yellow, null);
prims.Add(s3g);
var s4t = Transform.Translate(480, 238, -50);
var s4 = new Sphere(s4t, Transform.Invert(s4t), false, 60f, -60, 60, 360);
var s4g = new GeometricPrimitive(s4, metal, null);
prims.Add(s4g);
var s5t = Transform.Translate(490, 255, 250);
var s5 = new Sphere(s5t, Transform.Invert(s5t), false, 80f, -80, 80, 360);
var s5g = new GeometricPrimitive(s5, white, null);
prims.Add(s5g);
var s7t = Transform.Translate(150, 248, -120);
var s7 = new Sphere(s7t, Transform.Invert(s7t), false, 70f, -70, 70, 360);
var s7g = new GeometricPrimitive(s7, trans, null);
prims.Add(s7g);
//var temp = 5000f;
//var lightMatte =
// new MatteMaterial(
// new ConstantTexture<Spectrum>(Spectrum.FromBlackbodyT(temp)),
// new ConstantTexture<float>(0), null);
//var s6t = Transform.Translate(400, 188, -230);
//var s6 = new Sphere(s6t, Transform.Invert(s6t), false, 10f, -10, 10, 360);
//var dl = new DiffuseAreaLight(s6t, null, Spectrum.FromBlackbodyT(temp) * 60f, 12, s6);
//var s6g = new GeometricPrimitive(s6, lightMatte, dl);
//prims.Add(s6g);
var bvh = new BVH(prims.ToArray(), SplitMethod.HLBVH);
var lt = Transform.RotateX(MathF.Rad(75)).Translate(278, 600, -120);
var s = Spectrum.FromBlackbodyT(4500) * 400000f;
var spot = new SpotLight(lt, null, s, 120, 20);
lt = Transform.RotateX(MathF.Rad(75)).Translate(278, 300, -300);
s = Spectrum.FromBlackbodyT(6500) * 55000f;
var point = new PointLight(lt, null, s);
return(new Scene(bvh, new ILight[] { spot, point }));
}
public override void AddSample(CameraSample sample, Spectrum l)
{
// Compute sample's raster extent
float dimageX = sample.ImageX - 0.5f;
float dimageY = sample.ImageY - 0.5f;
int x0 = MathUtility.Ceiling(dimageX - _filter.XWidth);
int x1 = MathUtility.Floor(dimageX + _filter.XWidth);
int y0 = MathUtility.Ceiling(dimageY - _filter.YWidth);
int y1 = MathUtility.Floor(dimageY + _filter.YWidth);
x0 = Math.Max(x0, _xPixelStart);
x1 = Math.Min(x1, _xPixelStart + _xPixelCount - 1);
y0 = Math.Max(y0, _yPixelStart);
y1 = Math.Min(y1, _yPixelStart + _yPixelCount - 1);
if ((x1 - x0) < 0 || (y1 - y0) < 0)
return;
// Loop over filter support and add sample to pixel arrays
var xyz = l.ToXyz();
// Precompute $x$ and $y$ filter table offsets
var ifx = new int[x1 - x0 + 1];
for (int x = x0; x <= x1; ++x)
{
float fx = Math.Abs((x - dimageX) * _filter.InverseXWidth * FilterTableSize);
ifx[x - x0] = Math.Min(MathUtility.Floor(fx), FilterTableSize - 1);
}
var ify = new int[y1 - y0 + 1];
for (int y = y0; y <= y1; ++y)
{
float fy = Math.Abs((y - dimageY) * _filter.InverseYWidth * FilterTableSize);
ify[y - y0] = Math.Min(MathUtility.Floor(fy), FilterTableSize - 1);
}
bool syncNeeded = (_filter.XWidth > 0.5f || _filter.YWidth > 0.5f);
for (int y = y0; y <= y1; ++y)
{
for (int x = x0; x <= x1; ++x)
{
// Evaluate filter value at $(x,y)$ pixel
int offset = ify[y - y0] * FilterTableSize + ifx[x - x0];
float filterWt = _filterTable[offset];
// Update pixel values with filtered sample contribution
var pixel = _pixels[x - _xPixelStart, y - _yPixelStart];
if (!syncNeeded)
{
pixel.Lxyz[0] += filterWt * xyz[0];
pixel.Lxyz[1] += filterWt * xyz[1];
pixel.Lxyz[2] += filterWt * xyz[2];
pixel.WeightSum += filterWt;
}
else
{
// Safely update _Lxyz_ and _weightSum_ even with concurrency
AtomicAdd(ref pixel.Lxyz[0], filterWt * xyz[0]);
AtomicAdd(ref pixel.Lxyz[1], filterWt * xyz[1]);
AtomicAdd(ref pixel.Lxyz[2], filterWt * xyz[2]);
AtomicAdd(ref pixel.WeightSum, filterWt);
}
}
}
}
private void HandleSpectrum(
ref SpectrumTrackingInfo trackingInfo,
Dictionary <int, List <int> > isolationMzBinToScanNums,
Spectrum spec)
{
trackingInfo.SpecRead += 1;
//Console.WriteLine("Reading Scan {0}; {1} peaks", spec.ScanNum, spec.Peaks.Length);
ScanNumToMsLevel[spec.ScanNum] = spec.MsLevel;
ScanNumElutionTimeMap[spec.ScanNum] = spec.ElutionTime;
if (spec.MsLevel == 1)
{
if (trackingInfo.PrecursorSignalToNoiseRatioThreshold > 0.0)
{
spec.FilterNoise(trackingInfo.PrecursorSignalToNoiseRatioThreshold);
}
//foreach (var peak in spec.Peaks)
//{
// _ms1PeakList.Add(new LcMsPeak(peak.Mz, peak.Intensity, spec.ScanNum));
//}
_ms1PeakList.AddRange(spec.Peaks.Select(peak => new LcMsPeak(peak.Mz, peak.Intensity, spec.ScanNum)));
_scanNumSpecMap.Add(spec.ScanNum, spec);
}
else if (spec.MsLevel == 2)
{
var productSpec = spec as ProductSpectrum;
if (productSpec != null)
{
if (trackingInfo.ProductSignalToNoiseRatioThreshold > 0.0)
{
productSpec.FilterNoise(trackingInfo.ProductSignalToNoiseRatioThreshold);
}
var isolationWindow = productSpec.IsolationWindow;
var minBinNum = (int)Math.Round(isolationWindow.MinMz * IsolationWindowBinningFactor);
var maxBinNum = (int)Math.Round(isolationWindow.MaxMz * IsolationWindowBinningFactor);
for (var binNum = minBinNum; binNum <= maxBinNum; binNum++)
{
if (!isolationMzBinToScanNums.TryGetValue(binNum, out var scanNumList))
{
scanNumList = new List <int>();
isolationMzBinToScanNums[binNum] = scanNumList;
}
scanNumList.Add(productSpec.ScanNum);
}
_scanNumSpecMap.Add(spec.ScanNum, productSpec);
}
}
if (spec.ScanNum < trackingInfo.MinScanNum)
{
trackingInfo.MinScanNum = spec.ScanNum;
}
if (spec.ScanNum > trackingInfo.MaxScanNum)
{
trackingInfo.MaxScanNum = spec.ScanNum;
}
if (spec.MsLevel < trackingInfo.MinMsLevel)
{
trackingInfo.MinMsLevel = spec.MsLevel;
}
if (spec.MsLevel > trackingInfo.MaxMsLevel)
{
trackingInfo.MaxMsLevel = spec.MsLevel;
}
}
public static Spectrum FrDiel(double cosi, double cost, Spectrum etai, Spectrum etat)
{
Spectrum Rparl = ((etat * cosi) - (etai * cost)) / ((etat * cosi) + (etai * cost));
Spectrum Rperp = ((etai * cosi) - (etat * cost)) / ((etai * cosi) + (etat * cost));
return (Rparl * Rparl + Rperp * Rperp) / 2.0;
}
public DiffuseAreaLight(Transform lightToWorld, Spectrum lemit, int numSamples, Shape shape)
: base(lightToWorld, numSamples)
{
}
public RectangleLightFakeForSobolev(Point3D position, float length, float width, Spectrum illuminance, IMaterial material, int samples = 32)
: base(position, length, width, illuminance, material, samples)
{
}
public RankedPeaks(Spectrum spectrum)
: base(spectrum.Peaks, spectrum.ScanNum)
{
_spectrum = spectrum;
Array.Sort(Peaks, new IntensityComparer());
}
private void btnPredict_Click(object sender, EventArgs e)
{
if (this._model == null)
{
return;
}
OpenFileDialog myOpenFileDialog = new OpenFileDialog();
myOpenFileDialog.InitialDirectory = Busi.Common.Configuration.FolderSpectrum;
myOpenFileDialog.Multiselect = true;
myOpenFileDialog.Filter = Spectrum.GetDialogFilterString();
if (myOpenFileDialog.ShowDialog() == DialogResult.OK)
{
this.progressBar1.Visible = true;
this.toolStrip1.Enabled = false;
var flst = myOpenFileDialog.FileNames.ToList();
Action a = () =>
{
foreach (var f in flst)
{
var sp = new Spectrum(f);
var pr = this._model.Predict(sp);
if (this.dataGridView1.InvokeRequired)
{
ThreadStart s = () =>
{
if (!this._inited)
{
this.init(this._model);
}
this.addRow(pr, sp);
};
this.dataGridView1.Invoke(s);
}
else
{
if (!this._inited)
{
this.init(this._model);
}
this.addRow(pr, sp);
}
}
if (this.toolStrip1.InvokeRequired)
{
ThreadStart s = () =>
{
this.progressBar1.Visible = false;
this.toolStrip1.Enabled = true;
};
this.toolStrip1.Invoke(s);
}
else
{
this.progressBar1.Visible = false;
this.toolStrip1.Enabled = true;
}
};
a.BeginInvoke(null, null);
}
}
private void gridView_ShowCellToolTip(DataGridViewCell cell)
{
MassSpectrum spectrum = cell.OwningRow.Tag as MassSpectrum;
Spectrum s = spectrum.Element;
TreeViewForm treeViewForm = new TreeViewForm(spectrum);
TreeView tv = treeViewForm.TreeView;
if (gridView.Columns[cell.ColumnIndex].Name == "PrecursorInfo")
{
treeViewForm.Text = "Precursor Details";
if (s.precursors.Count == 0)
{
tv.Nodes.Add("No precursor information available.");
}
else
{
foreach (Precursor p in s.precursors)
{
string pNodeText = "Precursor scan";
if (p.sourceFile != null && p.externalSpectrumID.Length > 0)
{
pNodeText += String.Format(": {0}:{1}", p.sourceFile.name, p.externalSpectrumID);
}
else if (p.spectrumID.Length > 0)
{
pNodeText += String.Format(": {0}", p.spectrumID);
}
TreeNode pNode = tv.Nodes.Add(pNodeText);
addParamsToTreeNode(p as ParamContainer, pNode);
if (p.selectedIons.Count == 0)
{
pNode.Nodes.Add("No selected ion list available.");
}
else
{
foreach (SelectedIon si in p.selectedIons)
{
TreeNode siNode = pNode.Nodes.Add("Selected ion");
//siNode.ToolTipText = new CVTermInfo(CVID.MS_selected_ion); // not yet in CV
addParamsToTreeNode(si as ParamContainer, siNode);
}
}
if (p.activation.empty())
{
pNode.Nodes.Add("No activation details available.");
}
else
{
TreeNode actNode = pNode.Nodes.Add("Activation");
addParamsToTreeNode(p.activation as ParamContainer, actNode);
}
if (p.isolationWindow.empty())
{
pNode.Nodes.Add("No isolation window details available.");
}
else
{
TreeNode iwNode = pNode.Nodes.Add("Isolation Window");
addParamsToTreeNode(p.isolationWindow as ParamContainer, iwNode);
}
}
}
}
else if (gridView.Columns[cell.ColumnIndex].Name == "ScanInfo")
{
treeViewForm.Text = "Scan Configuration Details";
if (s.scanList.empty())
{
tv.Nodes.Add("No scan details available.");
}
else
{
TreeNode slNode = tv.Nodes.Add("Scan List");
addParamsToTreeNode(s.scanList as ParamContainer, slNode);
foreach (Scan scan in s.scanList.scans)
{
TreeNode scanNode = slNode.Nodes.Add("Acquisition");
addParamsToTreeNode(scan as ParamContainer, scanNode);
foreach (ScanWindow sw in scan.scanWindows)
{
TreeNode swNode = scanNode.Nodes.Add("Scan Window");
addParamsToTreeNode(sw as ParamContainer, swNode);
}
}
}
}
else if (gridView.Columns[cell.ColumnIndex].Name == "InstrumentConfigurationID")
{
treeViewForm.Text = "Instrument Configuration Details";
InstrumentConfiguration ic = s.scanList.scans[0].instrumentConfiguration;
if (ic == null || ic.empty())
{
tv.Nodes.Add("No instrument configuration details available.");
}
else
{
TreeNode icNode = tv.Nodes.Add(String.Format("Instrument Configuration ({0})", ic.id));
addParamsToTreeNode(ic as ParamContainer, icNode);
if (ic.componentList.Count == 0)
{
icNode.Nodes.Add("No component list available.");
}
else
{
TreeNode clNode = icNode.Nodes.Add("Component List");
foreach (pwiz.CLI.msdata.Component c in ic.componentList)
{
string cNodeText;
switch (c.type)
{
case ComponentType.ComponentType_Source:
cNodeText = "Source";
break;
case ComponentType.ComponentType_Analyzer:
cNodeText = "Analyzer";
break;
default:
case ComponentType.ComponentType_Detector:
cNodeText = "Detector";
break;
}
TreeNode cNode = clNode.Nodes.Add(cNodeText);
addParamsToTreeNode(c as ParamContainer, cNode);
}
}
Software sw = ic.software;
if (sw == null || sw.empty())
{
icNode.Nodes.Add("No software details available.");
}
else
{
TreeNode swNode = icNode.Nodes.Add(String.Format("Software ({0})", sw.id));
CVParam softwareParam = sw.cvParamChild(CVID.MS_software);
TreeNode swNameNode = swNode.Nodes.Add("Name: " + softwareParam.name);
swNameNode.ToolTipText = new CVTermInfo(softwareParam.cvid).def;
swNode.Nodes.Add("Version: " + sw.version);
}
}
}
else if (gridView.Columns[cell.ColumnIndex].Name == "DataProcessing")
{
treeViewForm.Text = "Data Processing Details";
DataProcessing dp = s.dataProcessing;
if (dp == null || dp.empty())
{
tv.Nodes.Add("No data processing details available.");
}
else
{
TreeNode dpNode = tv.Nodes.Add(String.Format("Data Processing ({0})", dp.id));
if (dp.processingMethods.Count == 0)
{
dpNode.Nodes.Add("No component list available.");
}
else
{
TreeNode pmNode = dpNode.Nodes.Add("Processing Methods");
foreach (ProcessingMethod pm in dp.processingMethods)
{
addParamsToTreeNode(pm as ParamContainer, pmNode);
}
}
}
}
else
{
return;
}
tv.ExpandAll();
treeViewForm.StartPosition = FormStartPosition.CenterParent;
treeViewForm.AutoSize = true;
//treeViewForm.DoAutoSize();
treeViewForm.Show(this.DockPanel);
//leaveTimer.Start();
this.Focus();
}
public Spectrum Li(Scene scene, RayDifferential ray, Sample sample, ref Intersection isect)
{
Spectrum T = new Spectrum ();
return Li (scene, ray, sample, ref isect, ref T);
}
public PeptideIsoform(Peptide peptide, Spectrum spectrum, int charge)
: base(peptide)
{
Spectrum = spectrum;
Charge = charge;
}
public virtual bool ReportResults(Sample[] samples, RayDifferential[] rays,
Spectrum[] ls, Intersection[] intersections, int count)
{
return true;
}
public ZxSerializer(Spectrum spec)
{
this._spec = spec;
}
public PlasticMaterial(Spectrum d, Spectrum s, float r)
{
diffuse = d;
specular = s;
roughness = r;
}
public dbgWD1793(Spectrum spectrum)
{
this._betaDiskDevice = (spectrum as IBetaDiskDevice);
this.InitializeComponent();
}
/// <summary>
/// Called on first instantiation (and subsequent core reboots)
/// </summary>
/// <param name="files"></param>
protected void InitializeMedia(List <byte[]> files)
{
mediaImages = files;
LoadAllMedia();
Spectrum.OSD_TapeInit();
}
/// <summary>
/// Write the supplied spectrum to the current position in <paramref name="writer"/>
/// </summary>
/// <param name="specIn"></param>
/// <param name="writer"></param>
protected internal override void WriteSpectrum(Spectrum specIn, BinaryWriter writer)
{
// All changes made here must be duplicated to ReadSpectrum() and GetPeakMetadataForSpectrum()
if (!(specIn is DeconvolutedSpectrum spec))
{
throw new ArgumentException("Input spectrum must be DeconvolutedSpectrum!", nameof(specIn));
}
// scan number: 4
writer.Write(spec.ScanNum);
// NativeID: 50
// pad or truncate to keep in limit (may have to change in future...)
writer.Write(spec.NativeId.PadRight(NativeIdLength).ToCharArray(0, NativeIdLength), 0, NativeIdLength);
// ms level: 1
writer.Write(Convert.ToByte(spec.MsLevel));
// elution time: 4
writer.Write(spec.ElutionTime);
// Total Ion Current: 4
writer.Write(Convert.ToSingle(spec.TotalIonCurrent));
var isolationWindow = spec.IsolationWindow;
// precursor mass: 8
writer.Write(isolationWindow.MonoisotopicMz ?? 0.0);
// precursor charge: 4
writer.Write(isolationWindow.Charge ?? 0);
// Activation method: 1
writer.Write((byte)spec.ActivationMethod);
// Isolation window target m/z: 8
writer.Write(isolationWindow.IsolationWindowTargetMz);
// Isolation window lower offset: 8
writer.Write(isolationWindow.IsolationWindowLowerOffset);
// Isolation window upper offset: 8
writer.Write(isolationWindow.IsolationWindowUpperOffset);
// Guarantee sorted peaks.
//var peaks = spec.Peaks.ToList();
Array.Sort(spec.Peaks);
//peaks.Sort();
// Number of peaks: 4
writer.Write(spec.Peaks.Length);
//writer.Write(peaks.Count);
foreach (var peakIn in spec.Peaks)
//foreach (var peak in peaks)
{
var peak = peakIn as DeconvolutedPeak;
if (peak == null)
{
throw new ArgumentException("Input spectrum peaks array must contain only DeconvolutedPeaks!");
}
// m/z: 8
writer.Write(peak.Mz);
// intensity: 4
writer.Write(Convert.ToSingle(peak.Intensity));
// charge: 4
writer.Write(peak.Charge);
// correlation: 4
writer.Write(Convert.ToSingle(peak.Corr));
// distance: 4
writer.Write(Convert.ToSingle(peak.Dist));
// Output indices of isotope peaks where index (in PbfLcMsRun) is < 65535
var isotopePeaksInRange = peak.ObservedPeakIndices.Where(x => x >= ushort.MinValue && x <= ushort.MaxValue).ToList();
if (isotopePeaksInRange.Count != peak.ObservedPeakIndices.Count)
{
WarnOnce(WriteWarnings.PeakIndexCannotBeStored, "Cannot output all observed peaks for some peaks - more than 65535 peaks in observed spectrum");
}
// Count of isotope peaks, as byte: 1
writer.Write((byte)isotopePeaksInRange.Count);
// Output indices, as unsigned shorts
foreach (var index in isotopePeaksInRange)
{
writer.Write((ushort)index);
}
}
}
public override void Splat(CameraSample sample, Spectrum l)
{
var xyz = l.ToXyz();
int x = MathUtility.Floor(sample.ImageX), y = MathUtility.Floor(sample.ImageY);
if (x < _xPixelStart || x - _xPixelStart >= _xPixelCount ||
y < _yPixelStart || y - _yPixelStart >= _yPixelCount) return;
var pixel = _pixels[x - _xPixelStart, y - _yPixelStart];
AtomicAdd(ref pixel.SplatXyz[0], xyz[0]);
AtomicAdd(ref pixel.SplatXyz[1], xyz[1]);
AtomicAdd(ref pixel.SplatXyz[2], xyz[2]);
}
private FilesStatus upload(Stream inputStream, string fileName, HttpContext context)
{
var statu = new FilesStatus();
var filename = RIPP.Web.Chem.Tools.Common.GetRnd(10, true, true, false) + Path.GetExtension(fileName);
var tempfullName = Path.Combine(StorageRoot, filename);
statu.progress = "1.0";
statu.size = (int)inputStream.Length;
statu.name = fileName;
try
{
//先保存在服务器一个临时文件
using (var fs = new FileStream(tempfullName, FileMode.Append, FileAccess.Write))
{
var buffer = new byte[1024];
var l = inputStream.Read(buffer, 0, 1024);
while (l > 0)
{
fs.Write(buffer, 0, l);
l = inputStream.Read(buffer, 0, 1024);
}
fs.Flush();
fs.Close();
}
}
catch
{
statu.error = "服务器错误，上传文件失败!";
return(statu);
}
//根据文件后缀尝试打开文件
var ftype = BindModel.CheckType(tempfullName);
model dbmodel = new model();
spec sp = new spec();
try
{
statu.type = ftype.GetDescription();
dbmodel.path = Path.Combine(RIPP.Web.Chem.Tools.Common.GetUploadPath(), filename);
sp.path = dbmodel.path;
switch (ftype)
{
case FileExtensionEnum.Allmethods:
var mBind = BindModel.ReadModel <BindModel>(tempfullName);
statu.description = mBind.ToString();
dbmodel.createtime = mBind.CreateTime;
dbmodel.name = mBind.Name;
// ;
// dbmodel.type = (int)ftype;
// dbmodel.
break;
case FileExtensionEnum.PLSBind:
var mPLS = BindModel.ReadModel <PLSModel>(tempfullName);
statu.description = mPLS.ToString();
dbmodel.createtime = mPLS.CreateTime;
dbmodel.name = mPLS.Name;
break;
case FileExtensionEnum.IdLib:
var mId = BindModel.ReadModel <IdentifyModel>(tempfullName);
statu.description = mId.ToString();
dbmodel.createtime = mId.CreateTime;
dbmodel.name = mId.Name;
break;
case FileExtensionEnum.FitLib:
var mFitting = BindModel.ReadModel <FittingModel>(tempfullName);
statu.description = mFitting.ToString();
dbmodel.createtime = mFitting.CreateTime;
dbmodel.name = mFitting.Name;
break;
case FileExtensionEnum.PLS1:
case FileExtensionEnum.PLSANN:
var mPLS1 = BindModel.ReadModel <PLSSubModel>(tempfullName);
statu.description = mPLS1.ToString();
dbmodel.createtime = mPLS1.CreateTime;
dbmodel.name = mPLS1.Name;
break;
case FileExtensionEnum.ItgBind:
var itgSub = BindModel.ReadModel <IntegrateModel>(tempfullName);
statu.description = itgSub.ToString();
dbmodel.createtime = itgSub.CreateTime;
dbmodel.name = itgSub.Name;
break;
case FileExtensionEnum.Spec:
default:
var s = new Spectrum(tempfullName);
ftype = FileExtensionEnum.Spec;
sp.Spec = s;
sp.name = Path.GetFileName(fileName);
statu.description = "光谱文件";
break;
}
}
catch (Exception ex)//读取文件失败
{
statu.error = "上传的文件类型有误，服务器无法识别，上传文件失败!";
if (File.Exists(tempfullName))
{
File.Delete(tempfullName);
}
return(statu);
}
//根据文件类型保存数据库
using (var db = new RIPPWebEntities())
{
if (ftype != FileExtensionEnum.Unkown)
{
var user = RIPP.Web.Chem.Tools.Common.Get_User;
if (user == null)
{
var uid = Convert.ToInt32(context.Request["uid"]);
user = db.S_User.Where(d => d.ID == uid).FirstOrDefault();
}
if (ftype == FileExtensionEnum.Spec)//光谱
{
if (RIPP.Web.Chem.Tools.Common.UserCanPredict(user))
{
sp.addtime = DateTime.Now;
sp.ext = Path.GetExtension(fileName).Substring(1);
sp.uid = user.ID;
sp.gid = user.GroupID;
db.spec.Add(sp);
db.SaveChanges();
statu.deleteType = "DELETE";
statu.deleteUrl = "/upload/UploadHandler.ashx?t=s&id=" + sp.id;
statu.url = "/admin/spec/detail/" + sp.id;
statu.id = sp.id;
File.Move(tempfullName, Path.Combine(HttpContext.Current.Server.MapPath("~/"), sp.path));//移动刚才上传的临时文件
}
else
{
statu.error = "您无权上传光谱文件，请与管理员联系。";
if (File.Exists(tempfullName))
{
File.Delete(tempfullName);
}
}
}
else//模型
{
if (user.HasRole(RoleEnum.Administrator) || user.HasRole(RoleEnum.Engineer))
{
dbmodel.addtime = DateTime.Now;
dbmodel.type = (int)ftype;
dbmodel.uid = user.ID;
dbmodel.gid = user.GroupID;
db.model.Add(dbmodel);
db.SaveChanges();
statu.deleteType = "DELETE";
statu.deleteUrl = "/upload/UploadHandler.ashx?t=m&id=" + dbmodel.id;
statu.url = "/admin/model/detail/" + dbmodel.id;
statu.id = dbmodel.id;
File.Move(tempfullName, Path.Combine(HttpContext.Current.Server.MapPath("~/"), dbmodel.path));//移动刚才上传的临时文件
}
else
{
statu.error = "您无权上传模型文件，请与管理员联系。";
if (File.Exists(tempfullName))
{
File.Delete(tempfullName);
}
}
}
}
}
return(statu);
}
//The DisplayColor method displays the name of a color.
private void DisplayColor(Spectrum color)
{
colorLabel.Text = color.ToString();
}
/// <summary>
/// Cycles through all the input callbacks
/// This should be done once per frame
/// </summary>
public void PollInput()
{
Spectrum.InputCallbacks.Call();
lock (this)
{
// parse single keyboard matrix keys
for (var i = 0; i < KeyboardDevice.KeyboardMatrix.Length; i++)
{
string key = KeyboardDevice.KeyboardMatrix[i];
bool prevState = KeyboardDevice.GetKeyStatus(key);
bool currState = Spectrum._controller.IsPressed(key);
if (currState != prevState)
{
KeyboardDevice.SetKeyStatus(key, currState);
}
}
// non matrix keys
foreach (string k in KeyboardDevice.NonMatrixKeys)
{
if (!k.StartsWith("Key"))
{
continue;
}
bool currState = Spectrum._controller.IsPressed(k);
KeyboardDevice.SetKeyStatus(k, currState);
}
// J1
foreach (string j in JoystickCollection[0].ButtonCollection)
{
bool prevState = JoystickCollection[0].GetJoyInput(j);
bool currState = Spectrum._controller.IsPressed(j);
if (currState != prevState)
{
JoystickCollection[0].SetJoyInput(j, currState);
}
}
// J2
foreach (string j in JoystickCollection[1].ButtonCollection)
{
bool prevState = JoystickCollection[1].GetJoyInput(j);
bool currState = Spectrum._controller.IsPressed(j);
if (currState != prevState)
{
JoystickCollection[1].SetJoyInput(j, currState);
}
}
// J3
foreach (string j in JoystickCollection[2].ButtonCollection)
{
bool prevState = JoystickCollection[2].GetJoyInput(j);
bool currState = Spectrum._controller.IsPressed(j);
if (currState != prevState)
{
JoystickCollection[2].SetJoyInput(j, currState);
}
}
}
// Tape control
if (Spectrum._controller.IsPressed(Play))
{
if (!pressed_Play)
{
Spectrum.OSD_FireInputMessage(Play);
TapeDevice.Play();
pressed_Play = true;
}
}
else
{
pressed_Play = false;
}
if (Spectrum._controller.IsPressed(Stop))
{
if (!pressed_Stop)
{
Spectrum.OSD_FireInputMessage(Stop);
TapeDevice.Stop();
pressed_Stop = true;
}
}
else
{
pressed_Stop = false;
}
if (Spectrum._controller.IsPressed(RTZ))
{
if (!pressed_RTZ)
{
Spectrum.OSD_FireInputMessage(RTZ);
TapeDevice.RTZ();
pressed_RTZ = true;
}
}
else
{
pressed_RTZ = false;
}
if (Spectrum._controller.IsPressed(Record))
{
}
if (Spectrum._controller.IsPressed(NextTape))
{
if (!pressed_NextTape)
{
Spectrum.OSD_FireInputMessage(NextTape);
TapeMediaIndex++;
pressed_NextTape = true;
}
}
else
{
pressed_NextTape = false;
}
if (Spectrum._controller.IsPressed(PrevTape))
{
if (!pressed_PrevTape)
{
Spectrum.OSD_FireInputMessage(PrevTape);
TapeMediaIndex--;
pressed_PrevTape = true;
}
}
else
{
pressed_PrevTape = false;
}
if (Spectrum._controller.IsPressed(NextBlock))
{
if (!pressed_NextBlock)
{
Spectrum.OSD_FireInputMessage(NextBlock);
TapeDevice.SkipBlock(true);
pressed_NextBlock = true;
}
}
else
{
pressed_NextBlock = false;
}
if (Spectrum._controller.IsPressed(PrevBlock))
{
if (!pressed_PrevBlock)
{
Spectrum.OSD_FireInputMessage(PrevBlock);
TapeDevice.SkipBlock(false);
pressed_PrevBlock = true;
}
}
else
{
pressed_PrevBlock = false;
}
if (Spectrum._controller.IsPressed(TapeStatus))
{
if (!pressed_TapeStatus)
{
Spectrum.OSD_ShowTapeStatus();
pressed_TapeStatus = true;
}
}
else
{
pressed_TapeStatus = false;
}
if (Spectrum._controller.IsPressed(HardResetStr))
{
if (!pressed_HardReset)
{
HardReset();
pressed_HardReset = true;
}
}
else
{
pressed_HardReset = false;
}
if (Spectrum._controller.IsPressed(SoftResetStr))
{
if (!pressed_SoftReset)
{
SoftReset();
pressed_SoftReset = true;
}
}
else
{
pressed_SoftReset = false;
}
// disk control
if (Spectrum._controller.IsPressed(NextDisk))
{
if (!pressed_NextDisk)
{
Spectrum.OSD_FireInputMessage(NextDisk);
DiskMediaIndex++;
pressed_NextDisk = true;
}
}
else
{
pressed_NextDisk = false;
}
if (Spectrum._controller.IsPressed(PrevDisk))
{
if (!pressed_PrevDisk)
{
Spectrum.OSD_FireInputMessage(PrevDisk);
DiskMediaIndex--;
pressed_PrevDisk = true;
}
}
else
{
pressed_PrevDisk = false;
}
if (Spectrum._controller.IsPressed(EjectDisk))
{
if (!pressed_EjectDisk)
{
Spectrum.OSD_FireInputMessage(EjectDisk);
if (UPDDiskDevice != null)
{
UPDDiskDevice.FDD_EjectDisk();
}
}
}
else
{
pressed_EjectDisk = false;
}
if (Spectrum._controller.IsPressed(DiskStatus))
{
if (!pressed_DiskStatus)
{
Spectrum.OSD_ShowDiskStatus();
pressed_DiskStatus = true;
}
}
else
{
pressed_DiskStatus = false;
}
}
public CompositeScorer(Spectrum ms2Spec, Tolerance tol, double relativeIsotopeIntensityThreshold = 0.1)
: base(ms2Spec, tol, 1, 20, relativeIsotopeIntensityThreshold)
{
}
private bool lessThan(Spectrum lhs, Spectrum rhs)
{
return((double)lhs.cvParam(CVID.MS_TIC).value < (double)rhs.cvParam(CVID.MS_TIC).value);
}
protected virtual bool IsCorrectionApplicable(Spectrum data, int index)
{
return(true);
}
// The DisplayColor method displays the
// name of a color.
private void DisplayColor(Spectrum color)
{
colorLabel.Text = color.ToString();
}
public abstract Spectrum Li(Scene scene, Renderer renderer, RayDifferential ray,
Sample sample, Random rng, out Spectrum transmittance);
public void updateRow(SpectrumDataSet.SpectrumTableRow row, MassSpectrum spectrum)
{
spectrumList[spectrum.Index] = spectrum;
Spectrum s = spectrum.Element; //GetElement(false);
DataProcessing dp = spectrum.DataProcessing;
Scan scan = null;
InstrumentConfiguration ic = null;
if (s.scanList.scans.Count > 0)
{
scan = s.scanList.scans[0];
ic = scan.instrumentConfiguration;
}
if (dp == null)
{
dp = s.dataProcessing;
}
CVParam param;
param = s.cvParam(CVID.MS_ms_level);
row.MsLevel = !param.empty() ? (int)param.value : 0;
param = scan != null?scan.cvParam(CVID.MS_scan_start_time) : new CVParam();
row.ScanTime = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_base_peak_m_z);
row.BasePeakMz = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_base_peak_intensity);
row.BasePeakIntensity = !param.empty() ? (double)param.value : 0;
param = s.cvParam(CVID.MS_total_ion_current);
row.TotalIonCurrent = !param.empty() ? (double)param.value : 0;
StringBuilder precursorInfo = new StringBuilder();
if (row.MsLevel == 1 || s.precursors.Count == 0)
{
precursorInfo.Append("n/a");
}
else
{
foreach (Precursor p in s.precursors)
{
foreach (SelectedIon si in p.selectedIons)
{
if (precursorInfo.Length > 0)
{
precursorInfo.Append(",");
}
precursorInfo.Append((double)si.cvParam(CVID.MS_selected_ion_m_z).value);
}
}
}
if (precursorInfo.Length == 0)
{
precursorInfo.Append("unknown");
}
row.PrecursorInfo = precursorInfo.ToString();
StringBuilder scanInfo = new StringBuilder();
foreach (Scan scan2 in s.scanList.scans)
{
if (scan2.scanWindows.Count > 0)
{
foreach (ScanWindow sw in scan2.scanWindows)
{
if (scanInfo.Length > 0)
{
scanInfo.Append(",");
}
scanInfo.AppendFormat("[{0}-{1}]",
(double)sw.cvParam(CVID.MS_scan_window_lower_limit).value,
(double)sw.cvParam(CVID.MS_scan_window_upper_limit).value);
}
}
}
if (scanInfo.Length == 0)
{
scanInfo.Append("unknown");
}
row.ScanInfo = scanInfo.ToString();
row.SpotId = s.spotID;
row.SpectrumType = s.cvParamChild(CVID.MS_spectrum_type).name;
row.DataPoints = s.defaultArrayLength;
row.IcId = (ic == null || ic.id.Length == 0 ? "unknown" : ic.id);
row.DpId = (dp == null || dp.id.Length == 0 ? "unknown" : dp.id);
}
