public Cubic1D(float2[] data) { // Sort points to go strictly from left to right. List<float2> DataList = data.ToList(); DataList.Sort((p1, p2) => p1.X.CompareTo(p2.X)); data = DataList.ToArray(); Data = data; Breaks = data.Select(i => i.X).ToArray(); Coefficients = new float4[data.Length - 1]; float[] h = MathHelper.Diff(data.Select(i => i.X).ToArray()); float[] del = MathHelper.Div(MathHelper.Diff(data.Select(i => i.Y).ToArray()), h); float[] slopes = GetPCHIPSlopes(data, del); float[] dzzdx = new float[del.Length]; for (int i = 0; i < dzzdx.Length; i++) dzzdx[i] = (del[i] - slopes[i]) / h[i]; float[] dzdxdx = new float[del.Length]; for (int i = 0; i < dzdxdx.Length; i++) dzdxdx[i] = (slopes[i + 1] - del[i]) / h[i]; for (int i = 0; i < Coefficients.Length; i++) Coefficients[i] = new float4((dzdxdx[i] - dzzdx[i]) / h[i], 2f * dzzdx[i] - dzdxdx[i], slopes[i], data[i].Y); }
private static float[] GetPCHIPSlopes(float2[] data, float[] del) { if (data.Length == 2) return new[] { del[0], del[0] }; // Do only linear float[] d = new float[data.Length]; float[] h = MathHelper.Diff(data.Select(i => i.X).ToArray()); for (int k = 0; k < del.Length - 1; k++) { if (del[k] * del[k + 1] <= 0f) continue; float hs = h[k] + h[k + 1]; float w1 = (h[k] + hs) / (3f * hs); float w2 = (hs + h[k + 1]) / (3f * hs); float dmax = Math.Max(Math.Abs(del[k]), Math.Abs(del[k + 1])); float dmin = Math.Min(Math.Abs(del[k]), Math.Abs(del[k + 1])); d[k + 1] = dmin / (w1 * (del[k] / dmax) + w2 * (del[k + 1] / dmax)); } d[0] = ((2f * h[0] + h[1]) * del[0] - h[0] * del[1]) / (h[0] + h[1]); if (Math.Sign(d[0]) != Math.Sign(del[0])) d[0] = 0; else if (Math.Sign(del[0]) != Math.Sign(del[1]) && Math.Abs(d[0]) > Math.Abs(3f * del[0])) d[0] = 3f * del[0]; int n = d.Length - 1; d[n] = ((2 * h[n - 1] + h[n - 2]) * del[n - 1] - h[n - 1] * del[n - 2]) / (h[n - 1] + h[n - 2]); if (Math.Sign(d[n]) != Math.Sign(del[n - 1])) d[n] = 0; else if (Math.Sign(del[n - 1]) != Math.Sign(del[n - 2]) && Math.Abs(d[n]) > Math.Abs(3f * del[n - 1])) d[n] = 3f * del[n - 1]; return d; }
public static void FitCTF(float2[] data, Func<float[], float[]> approximation, float[] zeros, float[] peaks, out Cubic1D background, out Cubic1D scale) { float MinX = MathHelper.Min(data.Select(p => p.X)), MaxX = MathHelper.Max(data.Select(p => p.X)), ScaleX = 1f / (MaxX - MinX); float MinY = MathHelper.Min(data.Select(p => p.Y)), MaxY = MathHelper.Max(data.Select(p => p.Y)), ScaleY = 1f / (MaxY - MinY); if (float.IsNaN(ScaleY)) ScaleY = 1f; peaks = peaks.Where(v => v >= MinX && v <= MaxX).Where((v, i) => i % 1 == 0).ToArray(); zeros = zeros.Where(v => v >= MinX && v <= MaxX).Where((v, i) => i % 1 == 0).ToArray(); float2[] ScaledData = data.Select(p => new float2((p.X - MinX) * ScaleX, (p.Y - MinY) * ScaleY)).ToArray(); float StdY = MathHelper.StdDev(data.Select(p => p.Y).ToArray()); double[] Start = new double[zeros.Length + peaks.Length]; double[] NodeX = new double[zeros.Length + peaks.Length]; Cubic1D DataSpline = new Cubic1D(data); for (int i = 0; i < zeros.Length; i++) { NodeX[i] = (zeros[i] - MinX) * ScaleX; Start[i] = DataSpline.Interp(zeros[i]) - MinY; } { Cubic1D PreliminaryBackground = new Cubic1D(Helper.Zip(NodeX.Take(zeros.Length).Select(v => (float)v).ToArray(), Start.Take(zeros.Length).Select(v => (float)v).ToArray())); float[] PreliminaryInterpolated = PreliminaryBackground.Interp(data.Select(v => (v.X - MinX) * ScaleX).ToArray()); float2[] BackgroundSubtracted = data.Select((v, i) => new float2(v.X, v.Y - MinY - PreliminaryInterpolated[i])).ToArray(); Cubic1D BackgroundSpline = new Cubic1D(BackgroundSubtracted); for (int i = 0; i < peaks.Length; i++) { NodeX[i + zeros.Length] = (peaks[i] - MinX) * ScaleX; float PeakValue = BackgroundSpline.Interp(peaks[i]); Start[i + zeros.Length] = Math.Max(0.0001f, PeakValue); } } float[] DataX = ScaledData.Select(p => p.X).ToArray(); float[] OriginalDataX = data.Select(p => p.X).ToArray(); float[] SimulatedCTF = approximation(OriginalDataX); float2[] NodesBackground = new float2[zeros.Length]; for (int i = 0; i < NodesBackground.Length; i++) NodesBackground[i] = new float2((float)NodeX[i], 0f); float2[] NodesScale = new float2[peaks.Length]; for (int i = 0; i < NodesScale.Length; i++) NodesScale[i] = new float2((float)NodeX[i + zeros.Length], 0f); Func<double[], double> Eval = input => { float2[] NodesBackgroundCopy = new float2[NodesBackground.Length]; for (int i = 0; i < zeros.Length; i++) NodesBackgroundCopy[i] = new float2(NodesBackground[i].X, (float)input[i]); float2[] NodesScaleCopy = new float2[NodesScale.Length]; for (int i = 0; i < peaks.Length; i++) NodesScaleCopy[i] = new float2(NodesScale[i].X, (float)input[i + zeros.Length]); float[] InterpolatedBackground = new Cubic1D(NodesBackgroundCopy).Interp(DataX); float[] InterpolatedScale = new Cubic1D(NodesScaleCopy).Interp(DataX); double Sum = 0f; for (int i = 0; i < ScaledData.Length; i++) { double Diff = ScaledData[i].Y - (InterpolatedBackground[i] + SimulatedCTF[i] * (double)InterpolatedScale[i]) * ScaleY; Sum += Diff * Diff; if (InterpolatedScale[i] < 0.0005f) Sum += (0.0005 - InterpolatedScale[i]) * 10; } //return Math.Sqrt(Sum / data.Length) * 10; return 0; }; Func<double[], double[]> Gradient = input => { double[] Result = new double[input.Length]; //Parallel.For(0, input.Length, i => for (int i = 0; i < input.Length; i++) { double[] UpperInput = new double[input.Length]; input.CopyTo(UpperInput, 0); UpperInput[i] += 0.0001; double UpperValue = Eval(UpperInput); double[] LowerInput = new double[input.Length]; input.CopyTo(LowerInput, 0); LowerInput[i] -= 0.0001; double LowerValue = Eval(LowerInput); Result[i] = (UpperValue - LowerValue) / 0.0002; }//); return Result; }; BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(Start.Length, Eval, Gradient); Optimizer.Minimize(Start); { for (int i = 0; i < zeros.Length; i++) NodesBackground[i] = new float2((float) NodeX[i] / ScaleX + MinX, (float) Optimizer.Solution[i] + MinY); for (int i = 0; i < peaks.Length; i++) NodesScale[i] = new float2((float)NodeX[i + zeros.Length] / ScaleX + MinX, Math.Max(0.001f, (float)Optimizer.Solution[i + zeros.Length])); background = new Cubic1D(NodesBackground); scale = new Cubic1D(NodesScale); } }
protected float2[] GetCTFQuality() { // Calculate the correlation between experimental and simulated peaks. // If there is no single complete peak (i. e. <=1 zeros), just take the entire // fitted range and treat it as one peak. if (PS1D == null || CTF == null || Simulated1D == null) return null; float[] Zeros = CTF.GetZeros(); float MinX = (float)MainWindow.Options.CTFRangeMin * 0.5f; float MaxX = MathHelper.Max(PS1D.Select(v => v.X)); Zeros = Zeros.Where(v => v >= MinX && v <= MaxX).ToArray(); if (Zeros.Length <= 1) Zeros = new[] { MinX, MaxX }; int[] Offsets = Zeros.Select(v => (int)(v / 0.5f * (PS1D.Length - 1))).ToArray(); float2[] Result = new float2[Zeros.Length - 1]; float[] Experimental = PS1D.Select(v => v.Y).ToArray(); float[] Simulated = Simulated1D.Select(v => v.Y).ToArray(); for (int i = 0; i < Zeros.Length - 1; i++) { float[] PeakExperimental = Experimental.Skip(Offsets[i]).Take(Offsets[i + 1] - Offsets[i] + 1).ToArray(); float[] PeakSimulated = Simulated.Skip(Offsets[i]).Take(Offsets[i + 1] - Offsets[i] + 1).ToArray(); float Correlation = MathHelper.CrossCorrelateNormalized(PeakExperimental, PeakSimulated); Result[i] = new float2((Zeros[i] + Zeros[i + 1]) * 0.5f, Math.Max(0.0f, Correlation)); } // Sanitation Result = Result.Select(v => float.IsNaN(v.Y) ? new float2(v.X, 0f) : v).ToArray(); return Result; }
public void ExportParticlesMovieOld(Star table, int size) { List<int> RowIndices = new List<int>(); string[] ColumnMicrographName = table.GetColumn("rlnMicrographName"); for (int i = 0; i < ColumnMicrographName.Length; i++) if (ColumnMicrographName[i].Contains(RootName)) RowIndices.Add(i); if (RowIndices.Count == 0) return; if (!Directory.Exists(ParticlesDir)) Directory.CreateDirectory(ParticlesDir); if (!Directory.Exists(ParticleCTFDir)) Directory.CreateDirectory(ParticleCTFDir); MapHeader OriginalHeader = MapHeader.ReadFromFile(Path, new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight), MainWindow.Options.InputDatOffset, ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType)); /*Image OriginalStack = StageDataLoad.LoadMap(Path, new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight), MainWindow.Options.InputDatOffset, ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));*/ //OriginalStack.Xray(20f); int3 Dims = OriginalHeader.Dimensions; int3 DimsRegion = new int3(size, size, 1); int NParticles = RowIndices.Count / Dimensions.Z; float PixelSize = (float)(MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5f; float PixelDelta = (float)(MainWindow.Options.CTFPixelMax - MainWindow.Options.CTFPixelMin) * 0.5f; float PixelAngle = (float)MainWindow.Options.CTFPixelAngle / (float)(180.0 / Math.PI); Image CTFCoords; { float2[] CTFCoordsData = new float2[DimsRegion.ElementsSlice()]; //Helper.ForEachElementFT(new int2(DimsRegion), (x, y, xx, yy) => for (int y = 0; y < DimsRegion.Y; y++) for (int x = 0; x < DimsRegion.X / 2 + 1; x++) { int xx = x; int yy = y < DimsRegion.Y / 2 + 1 ? y : y - DimsRegion.Y; float xs = xx / (float)DimsRegion.X; float ys = yy / (float)DimsRegion.Y; float r = (float)Math.Sqrt(xs * xs + ys * ys); float angle = (float)(Math.Atan2(yy, xx)); float CurrentPixelSize = PixelSize + PixelDelta * (float)Math.Cos(2f * (angle - PixelAngle)); CTFCoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / CurrentPixelSize, angle); } //); CTFCoords = new Image(CTFCoordsData, DimsRegion.Slice(), true); //CTFCoords.RemapToFT(); } Image CTFFreq = CTFCoords.AsReal(); Image CTFStack = new Image(new int3(size, size, NParticles * Dimensions.Z), true); int CTFStackIndex = 0; string[] ColumnPosX = table.GetColumn("rlnCoordinateX"); string[] ColumnPosY = table.GetColumn("rlnCoordinateY"); int3[] Origins = new int3[NParticles]; for (int i = 0; i < NParticles; i++) Origins[i] = new int3((int)double.Parse(ColumnPosX[RowIndices[i]]) - DimsRegion.X * 2 / 2, (int)double.Parse(ColumnPosY[RowIndices[i]]) - DimsRegion.Y * 2 / 2, 0); int IndexOffset = RowIndices[0]; string[] ColumnOriginX = table.GetColumn("rlnOriginX"); string[] ColumnOriginY = table.GetColumn("rlnOriginY"); string[] ColumnPriorX = table.GetColumn("rlnOriginXPrior"); string[] ColumnPriorY = table.GetColumn("rlnOriginYPrior"); float2[] ShiftPriors = new float2[NParticles]; for (int i = 0; i < NParticles; i++) ShiftPriors[i] = new float2(float.Parse(ColumnPriorX[IndexOffset + i]), float.Parse(ColumnPriorY[IndexOffset + i])); float2[][] ParticleTracks = new float2[NParticles][]; for (int i = 0; i < NParticles; i++) { ParticleTracks[i] = new float2[Dimensions.Z]; for (int z = 0; z < Dimensions.Z; z++) ParticleTracks[i][z] = new float2(float.Parse(ColumnOriginX[IndexOffset + z * NParticles + i]) - ShiftPriors[i].X, float.Parse(ColumnOriginY[IndexOffset + z * NParticles + i]) - ShiftPriors[i].Y); } Image AverageFT = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true, true); Image AveragePS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); Image Weights = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); Weights.Fill(1e-6f); Image FrameParticles = new Image(IntPtr.Zero, new int3(DimsRegion.X * 2, DimsRegion.Y * 2, NParticles)); float StepZ = 1f / Math.Max(Dims.Z - 1, 1); for (int z = 0; z < Dims.Z; z++) { float CoordZ = z * StepZ; /*GPU.Extract(OriginalStack.GetDeviceSlice(z, Intent.Read), FrameParticles.GetDevice(Intent.Write), Dims.Slice(), new int3(DimsRegion.X * 2, DimsRegion.Y * 2, 1), Helper.ToInterleaved(Origins), (uint)NParticles);*/ // Shift particles { float3[] Shifts = new float3[NParticles]; for (int i = 0; i < NParticles; i++) { float NormX = Math.Max(0.15f, Math.Min((float)Origins[i].X / Dims.X, 0.85f)); float NormY = Math.Max(0.15f, Math.Min((float)Origins[i].Y / Dims.Y, 0.85f)); float3 Coords = new float3(NormX, NormY, CoordZ); Shifts[i] = new float3(GridMovementX.GetInterpolated(Coords) + ParticleTracks[i][z].X, GridMovementY.GetInterpolated(Coords) + ParticleTracks[i][z].Y, 0f); } FrameParticles.ShiftSlices(Shifts); } Image FrameParticlesCropped = FrameParticles.AsPadded(new int2(DimsRegion)); Image FrameParticlesFT = FrameParticlesCropped.AsFFT(); FrameParticlesCropped.Dispose(); Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); PS.Fill(1f); // Apply motion blur filter. { const int Samples = 11; float StartZ = (z - 0.75f) * StepZ; float StopZ = (z + 0.75f) * StepZ; float2[] Shifts = new float2[Samples * NParticles]; for (int p = 0; p < NParticles; p++) { float NormX = Math.Max(0.15f, Math.Min((float)Origins[p].X / Dims.X, 0.85f)); float NormY = Math.Max(0.15f, Math.Min((float)Origins[p].Y / Dims.Y, 0.85f)); for (int zz = 0; zz < Samples; zz++) { float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz; float3 Coords = new float3(NormX, NormY, zp); Shifts[p * Samples + zz] = new float2(GridMovementX.GetInterpolated(Coords), GridMovementY.GetInterpolated(Coords)); } } Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write), DimsRegion, Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()), Samples, (uint)NParticles); PS.Multiply(MotionFilter); //MotionFilter.WriteMRC("motion.mrc"); MotionFilter.Dispose(); } // Apply CTF. if (CTF != null) { CTFStruct[] Structs = new CTFStruct[NParticles]; for (int p = 0; p < NParticles; p++) { CTF Altered = CTF.GetCopy(); Altered.Defocus = (decimal)GridCTF.GetInterpolated(new float3(float.Parse(ColumnPosX[RowIndices[p]]) / Dims.X, float.Parse(ColumnPosY[RowIndices[p]]) / Dims.Y, z * StepZ)); Structs[p] = Altered.ToStruct(); } Image CTFImage = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); GPU.CreateCTF(CTFImage.GetDevice(Intent.Write), CTFCoords.GetDevice(Intent.Read), (uint)CTFCoords.ElementsSliceComplex, Structs, false, (uint)NParticles); //CTFImage.Abs(); PS.Multiply(CTFImage); //CTFImage.WriteMRC("ctf.mrc"); CTFImage.Dispose(); } // Apply dose weighting. /*{ float3 NikoConst = new float3(0.245f, -1.665f, 2.81f); // Niko's formula expects e-/A2/frame, we've got e-/px/frame -- convert! float FrameDose = (float)MainWindow.Options.CorrectDosePerFrame * (z + 0.5f) / (PixelSize * PixelSize); Image DoseImage = new Image(IntPtr.Zero, DimsRegion, true); GPU.DoseWeighting(CTFFreq.GetDevice(Intent.Read), DoseImage.GetDevice(Intent.Write), (uint)DoseImage.ElementsSliceComplex, new[] { FrameDose }, NikoConst, 1); PS.MultiplySlices(DoseImage); //DoseImage.WriteMRC("dose.mrc"); DoseImage.Dispose(); }*/ // Copy custom CTF into the CTF stack GPU.CopyDeviceToDevice(PS.GetDevice(Intent.Read), new IntPtr((long)CTFStack.GetDevice(Intent.Write) + CTFStack.ElementsSliceReal * NParticles * z * sizeof (float)), CTFStack.ElementsSliceReal * NParticles); Image PSAbs = new Image(PS.GetDevice(Intent.Read), new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); PSAbs.Abs(); FrameParticlesFT.Multiply(PSAbs); AverageFT.Add(FrameParticlesFT); Weights.Add(PSAbs); PS.Multiply(PSAbs); AveragePS.Add(PS); PS.Dispose(); FrameParticlesFT.Dispose(); PSAbs.Dispose(); // Write paths to custom CTFs into the .star for (int i = 0; i < NParticles; i++) { string ParticleCTFPath = (CTFStackIndex + 1).ToString("D6") + "@particlectf/" + RootName + ".mrcs"; table.SetRowValue(RowIndices[NParticles * z + i], "rlnCtfImage", ParticleCTFPath); CTFStackIndex++; } } FrameParticles.Dispose(); CTFCoords.Dispose(); CTFFreq.Dispose(); AverageFT.Divide(Weights); AveragePS.Divide(Weights); Weights.Dispose(); Image AverageParticles = AverageFT.AsIFFT(); AverageFT.Dispose(); GPU.NormParticles(AverageParticles.GetDevice(Intent.Read), AverageParticles.GetDevice(Intent.Write), DimsRegion, (uint)(90f / PixelSize), true, (uint)NParticles); HeaderMRC ParticlesHeader = new HeaderMRC { Pixelsize = new float3(PixelSize, PixelSize, PixelSize) }; AverageParticles.WriteMRC(ParticlesPath, ParticlesHeader); AverageParticles.Dispose(); //OriginalStack.Dispose(); CTFStack.WriteMRC(DirectoryName + "particlectf/" + RootName + ".mrcs"); CTFStack.Dispose(); /*for (int i = 0; i < NParticles; i++) { string ParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs"; table.SetRowValue(RowIndices[i], "rlnImageName", ParticlePath); }*/ AveragePS.Dispose(); //table.RemoveRows(RowIndices.Skip(NParticles).ToArray()); }
public void ExportParticlesMovie(Star tableIn, Star tableOut, MapHeader originalHeader, Image originalStack, int size, float particleradius, decimal scaleFactor) { int CurrentDevice = GPU.GetDevice(); #region Make sure directories exist. lock (tableIn) { if (!Directory.Exists(ParticleMoviesDir)) Directory.CreateDirectory(ParticleMoviesDir); if (!Directory.Exists(ParticleCTFMoviesDir)) Directory.CreateDirectory(ParticleCTFMoviesDir); } #endregion #region Get row indices for all, and individual halves List<int> RowIndices = new List<int>(); string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName"); for (int i = 0; i < ColumnMicrographName.Length; i++) if (ColumnMicrographName[i].Contains(RootName)) RowIndices.Add(i); //RowIndices = RowIndices.Take(13).ToList(); List<int> RowIndices1 = new List<int>(); List<int> RowIndices2 = new List<int>(); for (int i = 0; i < RowIndices.Count; i++) if (tableIn.GetRowValue(RowIndices[i], "rlnRandomSubset") == "1") RowIndices1.Add(RowIndices[i]); else RowIndices2.Add(RowIndices[i]); #endregion if (RowIndices.Count == 0) return; #region Auxiliary variables List<int> TableOutIndices = new List<int>(); int3 Dims = originalHeader.Dimensions; Dims.Z = 36; int3 DimsRegion = new int3(size, size, 1); int3 DimsPadded = new int3(size * 2, size * 2, 1); int NParticles = RowIndices.Count; int NParticles1 = RowIndices1.Count; int NParticles2 = RowIndices2.Count; float PixelSize = (float)CTF.PixelSize / 1.00f; float PixelDelta = (float)CTF.PixelSizeDelta / 1.00f; float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad; #endregion #region Prepare initial coordinates and shifts string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); int3[] Origins1 = new int3[NParticles1]; int3[] Origins2 = new int3[NParticles2]; float3[] ResidualShifts1 = new float3[NParticles1]; float3[] ResidualShifts2 = new float3[NParticles2]; lock (tableIn) // Writing to the table, better be on the safe side { // Half1: Add translational shifts to coordinates, sans the fractional part for (int i = 0; i < NParticles1; i++) { float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices1[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices1[i]], CultureInfo.InvariantCulture)) * 1.00f; float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices1[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices1[i]], CultureInfo.InvariantCulture)) * 1.00f; Origins1[i] = new int3((int)(Pos.X - Shift.X), (int)(Pos.Y - Shift.Y), 0); ResidualShifts1[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X), -MathHelper.ResidualFraction(Pos.Y - Shift.Y), 0f); tableIn.SetRowValue(RowIndices1[i], "rlnCoordinateX", Origins1[i].X.ToString()); tableIn.SetRowValue(RowIndices1[i], "rlnCoordinateY", Origins1[i].Y.ToString()); tableIn.SetRowValue(RowIndices1[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices1[i], "rlnOriginY", "0.0"); } // Half2: Add translational shifts to coordinates, sans the fractional part for (int i = 0; i < NParticles2; i++) { float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices2[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices2[i]], CultureInfo.InvariantCulture)) * 1.00f; float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices2[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices2[i]], CultureInfo.InvariantCulture)) * 1.00f; Origins2[i] = new int3((int)(Pos.X - Shift.X), (int)(Pos.Y - Shift.Y), 0); ResidualShifts2[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X), -MathHelper.ResidualFraction(Pos.Y - Shift.Y), 0f); tableIn.SetRowValue(RowIndices2[i], "rlnCoordinateX", Origins2[i].X.ToString()); tableIn.SetRowValue(RowIndices2[i], "rlnCoordinateY", Origins2[i].Y.ToString()); tableIn.SetRowValue(RowIndices2[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices2[i], "rlnOriginY", "0.0"); } } #endregion #region Allocate memory for particle and PS stacks Image ParticleStackAll = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles * Dims.Z)); Image ParticleStack1 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1 * Dims.Z)); Image ParticleStack2 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2 * Dims.Z)); Image PSStackAll = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles * Dims.Z), true); Image PSStack1 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1 * Dims.Z), true); Image PSStack2 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2 * Dims.Z), true); Image FrameParticles1 = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles1)); Image FrameParticles2 = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles2)); float[][] ParticleStackData = ParticleStackAll.GetHost(Intent.Write); float[][] ParticleStackData1 = ParticleStack1.GetHost(Intent.Write); float[][] ParticleStackData2 = ParticleStack2.GetHost(Intent.Write); float[][] PSStackData = PSStackAll.GetHost(Intent.Write); float[][] PSStackData1 = PSStack1.GetHost(Intent.Write); float[][] PSStackData2 = PSStack2.GetHost(Intent.Write); #endregion #region Create rows in outTable lock (tableOut) // Creating rows in outTable, this absolutely needs to be staged sequentially { for (int z = 0; z < Dims.Z; z++) { for (int i = 0; i < NParticles; i++) { int Index = i < NParticles1 ? RowIndices1[i] : RowIndices2[i - NParticles1]; string OriParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs"; string ParticleName = (z * NParticles + i + 1).ToString("D6") + "@particlemovies/" + RootName + "_particles.mrcs"; string ParticleCTFName = (z * NParticles + i + 1).ToString("D6") + "@particlectfmovies/" + RootName + "_particlectf.mrcs"; List<string> NewRow = tableIn.GetRow(Index).Select(v => v).ToList(); // Get copy of original row. NewRow[tableOut.GetColumnIndex("rlnOriginalParticleName")] = OriParticlePath; NewRow[tableOut.GetColumnIndex("rlnAngleRotPrior")] = tableIn.GetRowValue(Index, "rlnAngleRot"); NewRow[tableOut.GetColumnIndex("rlnAngleTiltPrior")] = tableIn.GetRowValue(Index, "rlnAngleTilt"); NewRow[tableOut.GetColumnIndex("rlnAnglePsiPrior")] = tableIn.GetRowValue(Index, "rlnAnglePsi"); NewRow[tableOut.GetColumnIndex("rlnOriginXPrior")] = "0.0"; NewRow[tableOut.GetColumnIndex("rlnOriginYPrior")] = "0.0"; NewRow[tableOut.GetColumnIndex("rlnImageName")] = ParticleName; NewRow[tableOut.GetColumnIndex("rlnCtfImage")] = ParticleCTFName; NewRow[tableOut.GetColumnIndex("rlnMicrographName")] = (z + 1).ToString("D6") + "@stack/" + RootName + "_movie.mrcs"; TableOutIndices.Add(tableOut.RowCount); tableOut.AddRow(NewRow); } } } #endregion #region For every frame, extract particles from each half; shift, correct, and norm them float StepZ = 1f / Math.Max(Dims.Z - 1, 1); for (int z = 0; z < Dims.Z; z++) { float CoordZ = z * StepZ; #region Extract, correct, and norm particles #region Half 1 { if (originalStack != null) GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read), FrameParticles1.GetDevice(Intent.Write), Dims.Slice(), DimsPadded, Helper.ToInterleaved(Origins1.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()), (uint)NParticles1); // Shift particles { float3[] Shifts = new float3[NParticles1]; for (int i = 0; i < NParticles1; i++) { float3 Coords = new float3((float)Origins1[i].X / Dims.X, (float)Origins1[i].Y / Dims.Y, CoordZ); Shifts[i] = ResidualShifts1[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f; } FrameParticles1.ShiftSlices(Shifts); } Image FrameParticlesCropped = FrameParticles1.AsPadded(new int2(DimsRegion)); Image FrameParticlesCorrected = FrameParticlesCropped.AsAnisotropyCorrected(new int2(DimsRegion), PixelSize + PixelDelta / 2f, PixelSize - PixelDelta / 2f, PixelAngle, 6); FrameParticlesCropped.Dispose(); GPU.NormParticles(FrameParticlesCorrected.GetDevice(Intent.Read), FrameParticlesCorrected.GetDevice(Intent.Write), DimsRegion, (uint)(particleradius / PixelSize), true, (uint)NParticles1); float[][] FrameParticlesCorrectedData = FrameParticlesCorrected.GetHost(Intent.Read); for (int n = 0; n < NParticles1; n++) { ParticleStackData[z * NParticles + n] = FrameParticlesCorrectedData[n]; ParticleStackData1[z * NParticles1 + n] = FrameParticlesCorrectedData[n]; } //FrameParticlesCorrected.WriteMRC("intermediate_particles1.mrc"); FrameParticlesCorrected.Dispose(); } #endregion #region Half 2 { if (originalStack != null) GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read), FrameParticles2.GetDevice(Intent.Write), Dims.Slice(), DimsPadded, Helper.ToInterleaved(Origins2.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()), (uint)NParticles2); // Shift particles { float3[] Shifts = new float3[NParticles2]; for (int i = 0; i < NParticles2; i++) { float3 Coords = new float3((float)Origins2[i].X / Dims.X, (float)Origins2[i].Y / Dims.Y, CoordZ); Shifts[i] = ResidualShifts2[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f; } FrameParticles2.ShiftSlices(Shifts); } Image FrameParticlesCropped = FrameParticles2.AsPadded(new int2(DimsRegion)); Image FrameParticlesCorrected = FrameParticlesCropped.AsAnisotropyCorrected(new int2(DimsRegion), PixelSize + PixelDelta / 2f, PixelSize - PixelDelta / 2f, PixelAngle, 6); FrameParticlesCropped.Dispose(); GPU.NormParticles(FrameParticlesCorrected.GetDevice(Intent.Read), FrameParticlesCorrected.GetDevice(Intent.Write), DimsRegion, (uint)(particleradius / PixelSize), true, (uint)NParticles2); float[][] FrameParticlesCorrectedData = FrameParticlesCorrected.GetHost(Intent.Read); for (int n = 0; n < NParticles2; n++) { ParticleStackData[z * NParticles + NParticles1 + n] = FrameParticlesCorrectedData[n]; ParticleStackData2[z * NParticles2 + n] = FrameParticlesCorrectedData[n]; } //FrameParticlesCorrected.WriteMRC("intermediate_particles2.mrc"); FrameParticlesCorrected.Dispose(); } #endregion #endregion #region PS Half 1 { Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1), true); PS.Fill(1f); // Apply motion blur filter. #region Motion blur weighting { const int Samples = 11; float StartZ = (z - 0.5f) * StepZ; float StopZ = (z + 0.5f) * StepZ; float2[] Shifts = new float2[Samples * NParticles1]; for (int p = 0; p < NParticles1; p++) { float NormX = (float)Origins1[p].X / Dims.X; float NormY = (float)Origins1[p].Y / Dims.Y; for (int zz = 0; zz < Samples; zz++) { float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz; float3 Coords = new float3(NormX, NormY, zp); Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords) * 1.00f; } } Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles1), true); GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write), DimsRegion, Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()), Samples, (uint)NParticles1); PS.Multiply(MotionFilter); //MotionFilter.WriteMRC("motion.mrc"); MotionFilter.Dispose(); } #endregion float[][] PSData = PS.GetHost(Intent.Read); for (int n = 0; n < NParticles1; n++) PSStackData[z * NParticles + n] = PSData[n]; //PS.WriteMRC("intermediate_ps1.mrc"); PS.Dispose(); } #endregion #region PS Half 2 { Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2), true); PS.Fill(1f); // Apply motion blur filter. #region Motion blur weighting { const int Samples = 11; float StartZ = (z - 0.5f) * StepZ; float StopZ = (z + 0.5f) * StepZ; float2[] Shifts = new float2[Samples * NParticles2]; for (int p = 0; p < NParticles2; p++) { float NormX = (float)Origins2[p].X / Dims.X; float NormY = (float)Origins2[p].Y / Dims.Y; for (int zz = 0; zz < Samples; zz++) { float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz; float3 Coords = new float3(NormX, NormY, zp); Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords) * 1.00f; } } Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles2), true); GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write), DimsRegion, Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()), Samples, (uint)NParticles2); PS.Multiply(MotionFilter); //MotionFilter.WriteMRC("motion.mrc"); MotionFilter.Dispose(); } #endregion float[][] PSData = PS.GetHost(Intent.Read); for (int n = 0; n < NParticles2; n++) PSStackData[z * NParticles + NParticles1 + n] = PSData[n]; //PS.WriteMRC("intermediate_ps2.mrc"); PS.Dispose(); } #endregion } FrameParticles1.Dispose(); FrameParticles2.Dispose(); originalStack.FreeDevice(); #endregion HeaderMRC ParticlesHeader = new HeaderMRC { Pixelsize = new float3(PixelSize, PixelSize, PixelSize) }; // Do translation and rotation BFGS per particle { float MaxHigh = 2.6f; CubicGrid GridX = new CubicGrid(new int3(NParticles1, 1, 2)); CubicGrid GridY = new CubicGrid(new int3(NParticles1, 1, 2)); CubicGrid GridRot = new CubicGrid(new int3(NParticles1, 1, 2)); CubicGrid GridTilt = new CubicGrid(new int3(NParticles1, 1, 2)); CubicGrid GridPsi = new CubicGrid(new int3(NParticles1, 1, 2)); int2 DimsCropped = new int2(DimsRegion / (MaxHigh / PixelSize / 2f)) / 2 * 2; #region Get coordinates for CTF and Fourier-space shifts Image CTFCoords; Image ShiftFactors; { float2[] CTFCoordsData = new float2[(DimsCropped.X / 2 + 1) * DimsCropped.Y]; float2[] ShiftFactorsData = new float2[(DimsCropped.X / 2 + 1) * DimsCropped.Y]; for (int y = 0; y < DimsCropped.Y; y++) for (int x = 0; x < DimsCropped.X / 2 + 1; x++) { int xx = x; int yy = y < DimsCropped.Y / 2 + 1 ? y : y - DimsCropped.Y; float xs = xx / (float)DimsRegion.X; float ys = yy / (float)DimsRegion.Y; float r = (float)Math.Sqrt(xs * xs + ys * ys); float angle = (float)(Math.Atan2(yy, xx)); CTFCoordsData[y * (DimsCropped.X / 2 + 1) + x] = new float2(r / PixelSize, angle); ShiftFactorsData[y * (DimsCropped.X / 2 + 1) + x] = new float2((float)-xx / DimsRegion.X * 2f * (float)Math.PI, (float)-yy / DimsRegion.X * 2f * (float)Math.PI); } CTFCoords = new Image(CTFCoordsData, new int3(DimsCropped), true); ShiftFactors = new Image(ShiftFactorsData, new int3(DimsCropped), true); } #endregion #region Get inverse sigma2 spectrum for this micrograph from Relion's model.star Image Sigma2Noise = new Image(new int3(DimsCropped), true); { int GroupNumber = int.Parse(tableIn.GetRowValue(RowIndices[0], "rlnGroupNumber")); //Star SigmaTable = new Star("D:\\rado27\\Refine3D\\run1_ct5_it009_half1_model.star", "data_model_group_" + GroupNumber); Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber); float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray(); float[] Sigma2NoiseData = Sigma2Noise.GetHost(Intent.Write)[0]; Helper.ForEachElementFT(DimsCropped, (x, y, xx, yy, r, angle) => { int ir = (int)r; float val = 0; if (ir < SigmaValues.Length && ir >= size / (50f / PixelSize) && ir < DimsCropped.X / 2) { if (SigmaValues[ir] != 0f) val = 1f / SigmaValues[ir]; } Sigma2NoiseData[y * (DimsCropped.X / 2 + 1) + x] = val; }); float MaxSigma = MathHelper.Max(Sigma2NoiseData); for (int i = 0; i < Sigma2NoiseData.Length; i++) Sigma2NoiseData[i] /= MaxSigma; Sigma2Noise.RemapToFT(); } //Sigma2Noise.WriteMRC("d_sigma2noise.mrc"); #endregion #region Initialize particle angles for both halves float3[] ParticleAngles1 = new float3[NParticles1]; float3[] ParticleAngles2 = new float3[NParticles2]; for (int p = 0; p < NParticles1; p++) ParticleAngles1[p] = new float3(float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAngleRot")), float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAngleTilt")), float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAnglePsi"))); for (int p = 0; p < NParticles2; p++) ParticleAngles2[p] = new float3(float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAngleRot")), float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAngleTilt")), float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAnglePsi"))); #endregion #region Prepare masks Image Masks1, Masks2; { // Half 1 { Image Volume = StageDataLoad.LoadMap(MainWindow.Options.MaskPath, new int2(1, 1), 0, typeof (float)); Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); Image VolMaskFT = VolumePadded.AsFFT(true); VolumePadded.Dispose(); Image MasksFT = VolMaskFT.AsProjections(ParticleAngles1.Select(v => new float3(v.X * Helper.ToRad, v.Y * Helper.ToRad, v.Z * Helper.ToRad)).ToArray(), new int2(DimsRegion), MainWindow.Options.ProjectionOversample); VolMaskFT.Dispose(); Masks1 = MasksFT.AsIFFT(); MasksFT.Dispose(); Masks1.RemapFromFT(); Parallel.ForEach(Masks1.GetHost(Intent.ReadWrite), slice => { for (int i = 0; i < slice.Length; i++) slice[i] = (Math.Max(2f, Math.Min(50f, slice[i])) - 2) / 48f; }); } // Half 2 { Image Volume = StageDataLoad.LoadMap(MainWindow.Options.MaskPath, new int2(1, 1), 0, typeof(float)); Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); Image VolMaskFT = VolumePadded.AsFFT(true); VolumePadded.Dispose(); Image MasksFT = VolMaskFT.AsProjections(ParticleAngles2.Select(v => new float3(v.X * Helper.ToRad, v.Y * Helper.ToRad, v.Z * Helper.ToRad)).ToArray(), new int2(DimsRegion), MainWindow.Options.ProjectionOversample); VolMaskFT.Dispose(); Masks2 = MasksFT.AsIFFT(); MasksFT.Dispose(); Masks2.RemapFromFT(); Parallel.ForEach(Masks2.GetHost(Intent.ReadWrite), slice => { for (int i = 0; i < slice.Length; i++) slice[i] = (Math.Max(2f, Math.Min(50f, slice[i])) - 2) / 48f; }); } } //Masks1.WriteMRC("d_masks1.mrc"); //Masks2.WriteMRC("d_masks2.mrc"); #endregion #region Load and prepare references for both halves Image VolRefFT1; { Image Volume = StageDataLoad.LoadMap(MainWindow.Options.ReferencePath, new int2(1, 1), 0, typeof(float)); //GPU.Normalize(Volume.GetDevice(Intent.Read), Volume.GetDevice(Intent.Write), (uint)Volume.ElementsReal, 1); Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); VolRefFT1 = VolumePadded.AsFFT(true); VolumePadded.Dispose(); } VolRefFT1.FreeDevice(); Image VolRefFT2; { // Can't assume there is a second half, but certainly hope so string Half2Path = MainWindow.Options.ReferencePath; if (Half2Path.Contains("half1")) Half2Path = Half2Path.Replace("half1", "half2"); Image Volume = StageDataLoad.LoadMap(Half2Path, new int2(1, 1), 0, typeof(float)); //GPU.Normalize(Volume.GetDevice(Intent.Read), Volume.GetDevice(Intent.Write), (uint)Volume.ElementsReal, 1); Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); VolRefFT2 = VolumePadded.AsFFT(true); VolumePadded.Dispose(); } VolRefFT2.FreeDevice(); #endregion #region Prepare particles: group and resize to DimsCropped Image ParticleStackFT1 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles1 * Dims.Z / 3), true, true); { GPU.CreatePolishing(ParticleStack1.GetDevice(Intent.Read), ParticleStackFT1.GetDevice(Intent.Write), Masks1.GetDevice(Intent.Read), new int2(DimsRegion), DimsCropped, NParticles1, Dims.Z); ParticleStack1.FreeDevice(); Masks1.Dispose(); /*Image Amps = ParticleStackFT1.AsIFFT(); Amps.RemapFromFT(); Amps.WriteMRC("d_particlestackft1.mrc"); Amps.Dispose();*/ } Image ParticleStackFT2 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles2 * Dims.Z / 3), true, true); { GPU.CreatePolishing(ParticleStack2.GetDevice(Intent.Read), ParticleStackFT2.GetDevice(Intent.Write), Masks2.GetDevice(Intent.Read), new int2(DimsRegion), DimsCropped, NParticles2, Dims.Z); ParticleStack1.FreeDevice(); Masks2.Dispose(); /*Image Amps = ParticleStackFT2.AsIFFT(); Amps.RemapFromFT(); Amps.WriteMRC("d_particlestackft2.mrc"); Amps.Dispose();*/ } #endregion Image Projections1 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles1 * Dims.Z / 3), true, true); Image Projections2 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles2 * Dims.Z / 3), true, true); Image Shifts1 = new Image(new int3(NParticles1, Dims.Z / 3, 1), false, true); float3[] Angles1 = new float3[NParticles1 * Dims.Z / 3]; CTFStruct[] CTFParams1 = new CTFStruct[NParticles1 * Dims.Z / 3]; Image Shifts2 = new Image(new int3(NParticles2, Dims.Z / 3, 1), false, true); float3[] Angles2 = new float3[NParticles2 * Dims.Z / 3]; CTFStruct[] CTFParams2 = new CTFStruct[NParticles2 * Dims.Z / 3]; float[] BFacs = { -3.86f, 0.00f, -17.60f, -35.24f, -57.48f, -93.51f, -139.57f, -139.16f }; #region Initialize defocus and phase shift values float[] InitialDefoci1 = new float[NParticles1 * (Dims.Z / 3)]; float[] InitialPhaseShifts1 = new float[NParticles1 * (Dims.Z / 3)]; float[] InitialDefoci2 = new float[NParticles2 * (Dims.Z / 3)]; float[] InitialPhaseShifts2 = new float[NParticles2 * (Dims.Z / 3)]; for (int z = 0, i = 0; z < Dims.Z / 3; z++) { for (int p = 0; p < NParticles1; p++, i++) { InitialDefoci1[i] = GridCTF.GetInterpolated(new float3((float)Origins1[p].X / Dims.X, (float)Origins1[p].Y / Dims.Y, (float)(z * 3 + 1) / (Dims.Z - 1))); InitialPhaseShifts1[i] = GridCTFPhase.GetInterpolated(new float3((float)Origins1[p].X / Dims.X, (float)Origins1[p].Y / Dims.Y, (float)(z * 3 + 1) / (Dims.Z - 1))); CTF Alt = CTF.GetCopy(); Alt.PixelSize = (decimal)PixelSize; Alt.PixelSizeDelta = 0; Alt.Defocus = (decimal)InitialDefoci1[i]; Alt.PhaseShift = (decimal)InitialPhaseShifts1[i]; //Alt.Bfactor = (decimal)BFacs[z]; CTFParams1[i] = Alt.ToStruct(); } } for (int z = 0, i = 0; z < Dims.Z / 3; z++) { for (int p = 0; p < NParticles2; p++, i++) { InitialDefoci2[i] = GridCTF.GetInterpolated(new float3((float)Origins2[p].X / Dims.X, (float)Origins2[p].Y / Dims.Y, (float)(z * 3 + 1) / (Dims.Z - 1))); InitialPhaseShifts2[i] = GridCTFPhase.GetInterpolated(new float3((float)Origins2[p].X / Dims.X, (float)Origins2[p].Y / Dims.Y, (float)(z * 3 + 1) / (Dims.Z - 1))); CTF Alt = CTF.GetCopy(); Alt.PixelSize = (decimal)PixelSize; Alt.PixelSizeDelta = 0; Alt.Defocus = (decimal)InitialDefoci2[i]; Alt.PhaseShift = (decimal)InitialPhaseShifts2[i]; //Alt.Bfactor = (decimal)BFacs[z]; CTFParams2[i] = Alt.ToStruct(); } } #endregion #region SetPositions lambda Action<double[]> SetPositions = input => { float BorderZ = 0.5f / (Dims.Z / 3); GridX = new CubicGrid(new int3(NParticles, 1, 2), input.Take(NParticles * 2).Select(v => (float)v).ToArray()); GridY = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 1).Take(NParticles * 2).Select(v => (float)v).ToArray()); float[] AlteredX = GridX.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); float[] AlteredY = GridY.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); GridRot = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 2).Take(NParticles * 2).Select(v => (float)v).ToArray()); GridTilt = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 3).Take(NParticles * 2).Select(v => (float)v).ToArray()); GridPsi = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 4).Take(NParticles * 2).Select(v => (float)v).ToArray()); float[] AlteredRot = GridRot.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); float[] AlteredTilt = GridTilt.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); float[] AlteredPsi = GridPsi.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); float[] ShiftData1 = Shifts1.GetHost(Intent.Write)[0]; float[] ShiftData2 = Shifts2.GetHost(Intent.Write)[0]; for (int z = 0; z < Dims.Z / 3; z++) { // Half 1 for (int p = 0; p < NParticles1; p++) { int i1 = z * NParticles1 + p; int i = z * NParticles + p; ShiftData1[i1 * 2] = AlteredX[i]; ShiftData1[i1 * 2 + 1] = AlteredY[i]; Angles1[i1] = new float3(AlteredRot[i] * 1f * Helper.ToRad, AlteredTilt[i] * 1f * Helper.ToRad, AlteredPsi[i] * 1f * Helper.ToRad); } // Half 2 for (int p = 0; p < NParticles2; p++) { int i2 = z * NParticles2 + p; int i = z * NParticles + NParticles1 + p; ShiftData2[i2 * 2] = AlteredX[i]; ShiftData2[i2 * 2 + 1] = AlteredY[i]; Angles2[i2] = new float3(AlteredRot[i] * 1f * Helper.ToRad, AlteredTilt[i] * 1f * Helper.ToRad, AlteredPsi[i] * 1f * Helper.ToRad); } } }; #endregion #region EvalIndividuals lambda Func<double[], bool, double[]> EvalIndividuals = (input, redoProj) => { SetPositions(input); if (redoProj) { GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Write), VolRefFT1.Dims, DimsCropped, Helper.ToInterleaved(Angles1), MainWindow.Options.ProjectionOversample, (uint)(NParticles1 * Dims.Z / 3)); GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Write), VolRefFT2.Dims, DimsCropped, Helper.ToInterleaved(Angles2), MainWindow.Options.ProjectionOversample, (uint)(NParticles2 * Dims.Z / 3)); } /*{ Image ProjectionsAmps = Projections1.AsIFFT(); ProjectionsAmps.RemapFromFT(); ProjectionsAmps.WriteMRC("d_projectionsamps1.mrc"); ProjectionsAmps.Dispose(); } { Image ProjectionsAmps = Projections2.AsIFFT(); ProjectionsAmps.RemapFromFT(); ProjectionsAmps.WriteMRC("d_projectionsamps2.mrc"); ProjectionsAmps.Dispose(); }*/ float[] Diff1 = new float[NParticles1]; float[] DiffAll1 = new float[NParticles1 * (Dims.Z / 3)]; GPU.PolishingGetDiff(ParticleStackFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), CTFCoords.GetDevice(Intent.Read), CTFParams1, Sigma2Noise.GetDevice(Intent.Read), DimsCropped, Shifts1.GetDevice(Intent.Read), Diff1, DiffAll1, (uint)NParticles1, (uint)Dims.Z / 3); float[] Diff2 = new float[NParticles2]; float[] DiffAll2 = new float[NParticles2 * (Dims.Z / 3)]; GPU.PolishingGetDiff(ParticleStackFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), CTFCoords.GetDevice(Intent.Read), CTFParams2, Sigma2Noise.GetDevice(Intent.Read), DimsCropped, Shifts2.GetDevice(Intent.Read), Diff2, DiffAll2, (uint)NParticles2, (uint)Dims.Z / 3); double[] DiffBoth = new double[NParticles]; for (int p = 0; p < NParticles1; p++) DiffBoth[p] = Diff1[p]; for (int p = 0; p < NParticles2; p++) DiffBoth[NParticles1 + p] = Diff2[p]; return DiffBoth; }; #endregion Func<double[], double> Eval = input => { float Result = MathHelper.Mean(EvalIndividuals(input, true).Select(v => (float)v)) * NParticles; Debug.WriteLine(Result); return Result; }; Func<double[], double[]> Grad = input => { SetPositions(input); GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Write), VolRefFT1.Dims, DimsCropped, Helper.ToInterleaved(Angles1), MainWindow.Options.ProjectionOversample, (uint)(NParticles1 * Dims.Z / 3)); GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Write), VolRefFT2.Dims, DimsCropped, Helper.ToInterleaved(Angles2), MainWindow.Options.ProjectionOversample, (uint)(NParticles2 * Dims.Z / 3)); double[] Result = new double[input.Length]; double Step = 0.1; int NVariables = 10; // (Shift + Euler) * 2 for (int v = 0; v < NVariables; v++) { double[] InputPlus = new double[input.Length]; for (int i = 0; i < input.Length; i++) { int iv = i / NParticles; if (iv == v) InputPlus[i] = input[i] + Step; else InputPlus[i] = input[i]; } double[] ScorePlus = EvalIndividuals(InputPlus, v >= 4); double[] InputMinus = new double[input.Length]; for (int i = 0; i < input.Length; i++) { int iv = i / NParticles; if (iv == v) InputMinus[i] = input[i] - Step; else InputMinus[i] = input[i]; } double[] ScoreMinus = EvalIndividuals(InputMinus, v >= 4); for (int i = 0; i < NParticles; i++) Result[v * NParticles + i] = (ScorePlus[i] - ScoreMinus[i]) / (Step * 2.0); } return Result; }; double[] StartParams = new double[NParticles * 2 * 5]; for (int i = 0; i < NParticles * 2; i++) { int p = i % NParticles; StartParams[NParticles * 2 * 0 + i] = 0; StartParams[NParticles * 2 * 1 + i] = 0; if (p < NParticles1) { StartParams[NParticles * 2 * 2 + i] = ParticleAngles1[p].X / 1.0; StartParams[NParticles * 2 * 3 + i] = ParticleAngles1[p].Y / 1.0; StartParams[NParticles * 2 * 4 + i] = ParticleAngles1[p].Z / 1.0; } else { p -= NParticles1; StartParams[NParticles * 2 * 2 + i] = ParticleAngles2[p].X / 1.0; StartParams[NParticles * 2 * 3 + i] = ParticleAngles2[p].Y / 1.0; StartParams[NParticles * 2 * 4 + i] = ParticleAngles2[p].Z / 1.0; } } BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Grad); Optimizer.Epsilon = 3e-7; Optimizer.Maximize(StartParams); #region Calculate particle quality for high frequencies float[] ParticleQuality = new float[NParticles * (Dims.Z / 3)]; { Sigma2Noise.Dispose(); Sigma2Noise = new Image(new int3(DimsCropped), true); { int GroupNumber = int.Parse(tableIn.GetRowValue(RowIndices[0], "rlnGroupNumber")); //Star SigmaTable = new Star("D:\\rado27\\Refine3D\\run1_ct5_it009_half1_model.star", "data_model_group_" + GroupNumber); Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber); float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray(); float[] Sigma2NoiseData = Sigma2Noise.GetHost(Intent.Write)[0]; Helper.ForEachElementFT(DimsCropped, (x, y, xx, yy, r, angle) => { int ir = (int)r; float val = 0; if (ir < SigmaValues.Length && ir >= size / (4.0f / PixelSize) && ir < DimsCropped.X / 2) { if (SigmaValues[ir] != 0f) val = 1f / SigmaValues[ir] / (ir * 3.14f); } Sigma2NoiseData[y * (DimsCropped.X / 2 + 1) + x] = val; }); float MaxSigma = MathHelper.Max(Sigma2NoiseData); for (int i = 0; i < Sigma2NoiseData.Length; i++) Sigma2NoiseData[i] /= MaxSigma; Sigma2Noise.RemapToFT(); } //Sigma2Noise.WriteMRC("d_sigma2noiseScore.mrc"); SetPositions(StartParams); GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Write), VolRefFT1.Dims, DimsCropped, Helper.ToInterleaved(Angles1), MainWindow.Options.ProjectionOversample, (uint)(NParticles1 * Dims.Z / 3)); GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Write), VolRefFT2.Dims, DimsCropped, Helper.ToInterleaved(Angles2), MainWindow.Options.ProjectionOversample, (uint)(NParticles2 * Dims.Z / 3)); float[] Diff1 = new float[NParticles1]; float[] ParticleQuality1 = new float[NParticles1 * (Dims.Z / 3)]; GPU.PolishingGetDiff(ParticleStackFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), CTFCoords.GetDevice(Intent.Read), CTFParams1, Sigma2Noise.GetDevice(Intent.Read), DimsCropped, Shifts1.GetDevice(Intent.Read), Diff1, ParticleQuality1, (uint)NParticles1, (uint)Dims.Z / 3); float[] Diff2 = new float[NParticles2]; float[] ParticleQuality2 = new float[NParticles2 * (Dims.Z / 3)]; GPU.PolishingGetDiff(ParticleStackFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), CTFCoords.GetDevice(Intent.Read), CTFParams2, Sigma2Noise.GetDevice(Intent.Read), DimsCropped, Shifts2.GetDevice(Intent.Read), Diff2, ParticleQuality2, (uint)NParticles2, (uint)Dims.Z / 3); for (int z = 0; z < Dims.Z / 3; z++) { for (int p = 0; p < NParticles1; p++) ParticleQuality[z * NParticles + p] = ParticleQuality1[z * NParticles1 + p]; for (int p = 0; p < NParticles2; p++) ParticleQuality[z * NParticles + NParticles1 + p] = ParticleQuality2[z * NParticles2 + p]; } } #endregion lock (tableOut) // Only changing cell values, but better be safe in case table implementation changes later { GridX = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Take(NParticles * 2).Select(v => (float)v).ToArray()); GridY = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 1).Take(NParticles * 2).Select(v => (float)v).ToArray()); float[] AlteredX = GridX.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); float[] AlteredY = GridY.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); GridRot = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 2).Take(NParticles * 2).Select(v => (float)v).ToArray()); GridTilt = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 3).Take(NParticles * 2).Select(v => (float)v).ToArray()); GridPsi = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 4).Take(NParticles * 2).Select(v => (float)v).ToArray()); float[] AlteredRot = GridRot.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); float[] AlteredTilt = GridTilt.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); float[] AlteredPsi = GridPsi.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); for (int i = 0; i < TableOutIndices.Count; i++) { int p = i % NParticles; int z = i / NParticles; float Defocus = 0, PhaseShift = 0; if (p < NParticles1) { Defocus = GridCTF.GetInterpolated(new float3((float)Origins1[p].X / Dims.X, (float)Origins1[p].Y / Dims.Y, (float)z / (Dims.Z - 1))); PhaseShift = GridCTFPhase.GetInterpolated(new float3((float)Origins1[p].X / Dims.X, (float)Origins1[p].Y / Dims.Y, (float)z / (Dims.Z - 1))); } else { p -= NParticles1; Defocus = GridCTF.GetInterpolated(new float3((float)Origins2[p].X / Dims.X, (float)Origins2[p].Y / Dims.Y, (float)z / (Dims.Z - 1))); PhaseShift = GridCTFPhase.GetInterpolated(new float3((float)Origins2[p].X / Dims.X, (float)Origins2[p].Y / Dims.Y, (float)z / (Dims.Z - 1))); } tableOut.SetRowValue(TableOutIndices[i], "rlnOriginX", AlteredX[i].ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnOriginY", AlteredY[i].ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnAngleRot", (-AlteredRot[i]).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnAngleTilt", (-AlteredTilt[i]).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnAnglePsi", (-AlteredPsi[i]).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnDefocusU", ((Defocus + (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnDefocusV", ((Defocus - (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnPhaseShift", (PhaseShift * 180f).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnCtfFigureOfMerit", (ParticleQuality[(z / 3) * NParticles + (i % NParticles)]).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnMagnification", ((float)MainWindow.Options.CTFDetectorPixel * 10000f / PixelSize).ToString()); } } VolRefFT1.Dispose(); VolRefFT2.Dispose(); Projections1.Dispose(); Projections2.Dispose(); Sigma2Noise.Dispose(); ParticleStackFT1.Dispose(); ParticleStackFT2.Dispose(); Shifts1.Dispose(); Shifts2.Dispose(); CTFCoords.Dispose(); ShiftFactors.Dispose(); ParticleStack1.Dispose(); ParticleStack2.Dispose(); PSStack1.Dispose(); PSStack2.Dispose(); } // Write movies to disk asynchronously, so the next micrograph can load. Thread SaveThread = new Thread(() => { GPU.SetDevice(CurrentDevice); // It's a separate thread, make sure it's using the same device ParticleStackAll.WriteMRC(ParticleMoviesPath, ParticlesHeader); //ParticleStackAll.WriteMRC("D:\\gala\\particlemovies\\" + RootName + "_particles.mrcs", ParticlesHeader); ParticleStackAll.Dispose(); PSStackAll.WriteMRC(ParticleCTFMoviesPath); //PSStackAll.WriteMRC("D:\\rado27\\particlectfmovies\\" + RootName + "_particlectf.mrcs"); PSStackAll.Dispose(); }); SaveThread.Start(); }