public TiltSeries(string path) : base(path) { if (Angles.Length < Dimensions.Z) // In case angles and dose haven't been read and stored in .xml yet. { if (File.Exists(DirectoryName + RootName + ".star")) { Star Table = new Star(DirectoryName + RootName + ".star"); if (!Table.HasColumn("wrpDose") || !Table.HasColumn("wrpAngleTilt")) throw new Exception("STAR file has no wrpDose or wrpTilt column."); List<float> TempAngles = new List<float>(); List<float> TempDose = new List<float>(); for (int i = 0; i < Table.RowCount; i++) { TempAngles.Add(float.Parse(Table.GetRowValue(i, "wrpAngleTilt"))); TempDose.Add(float.Parse(Table.GetRowValue(i, "wrpDose"))); } if (TempAngles.Count == 0) throw new Exception("Metadata must contain 2 values per tilt: angle, dose."); if (TempAngles.Count != Dimensions.Z) throw new Exception("Metadata must contain one line for each image in tilt series."); Angles = TempAngles.ToArray(); Dose = TempDose.ToArray(); } else { HeaderMRC Header = new HeaderMRC(new BinaryReader(File.OpenRead(Path))); if (Header.ImodTilt != null) { Angles = Header.ImodTilt; Dose = new float[Angles.Length]; } else throw new Exception("A .meta file with angles and accumulated dose, or at least tilt angle data in the .ali's header are needed to work with tilt series."); } } }
public Star(Star[] tables) { List<string> Common = new List<string>(tables[0].GetColumnNames()); foreach (var table in tables) Common.RemoveAll(c => !table.HasColumn(c)); foreach (string name in Common) NameMapping.Add(name, NameMapping.Count); foreach (var table in tables) { int[] ColumnIndices = Common.Select(c => table.GetColumnID(c)).ToArray(); for (int r = 0; r < table.RowCount; r++) { List<string> Row = new List<string>(Common.Count); for (int c = 0; c < ColumnIndices.Length; c++) Row.Add(table.GetRowValue(r, ColumnIndices[c])); AddRow(Row); } } }
public Image SimulateTiltSeries(Star tableIn, int3 stackDimensions, int size, int3 volumeDimensions, Dictionary<int, Projector> references, float resolution) { VolumeDimensions = volumeDimensions; Image SimulatedStack = new Image(stackDimensions); #region Get rows from table 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); if (RowIndices.Count == 0) return SimulatedStack; int NParticles = RowIndices.Count; #endregion #region Make sure all columns and directories are there if (!tableIn.HasColumn("rlnImageName")) tableIn.AddColumn("rlnImageName"); if (!tableIn.HasColumn("rlnCtfImage")) tableIn.AddColumn("rlnCtfImage"); if (!tableIn.HasColumn("rlnParticleSelectZScore")) tableIn.AddColumn("rlnParticleSelectZScore"); if (!Directory.Exists(ParticlesDir)) Directory.CreateDirectory(ParticlesDir); if (!Directory.Exists(ParticleCTFDir)) Directory.CreateDirectory(ParticleCTFDir); #endregion #region Get subtomo positions from table float3[] ParticleOrigins = new float3[NParticles]; float3[] ParticleAngles = new float3[NParticles]; int[] ParticleSubset = new int[NParticles]; { string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ"); string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi"); string[] ColumnSubset = tableIn.GetColumn("rlnRandomSubset"); for (int i = 0; i < NParticles; i++) { float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleOrigins[i] = Pos - Shift; //ParticleOrigins[i] /= new float3(3838f / 959f, 3710f / 927f, 4f); float3 Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleAngles[i] = Angle; ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", ParticleOrigins[i].X.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", ParticleOrigins[i].Y.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateZ", ParticleOrigins[i].Z.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginZ", "0.0"); } } #endregion #region Deal with subsets List<int> SubsetIDs = new List<int>(); foreach (var i in ParticleSubset) if (!SubsetIDs.Contains(i)) SubsetIDs.Add(i); SubsetIDs.Sort(); // For each subset, create a list of its particle IDs Dictionary<int, List<int>> SubsetParticleIDs = SubsetIDs.ToDictionary(subsetID => subsetID, subsetID => new List<int>()); for (int i = 0; i < ParticleSubset.Length; i++) SubsetParticleIDs[ParticleSubset[i]].Add(i); foreach (var list in SubsetParticleIDs.Values) list.Sort(); // Note where each subset starts and ends in a unified, sorted (by subset) particle ID list Dictionary<int, Tuple<int, int>> SubsetRanges = new Dictionary<int, Tuple<int, int>>(); { int Start = 0; foreach (var pair in SubsetParticleIDs) { SubsetRanges.Add(pair.Key, new Tuple<int, int>(Start, Start + pair.Value.Count)); Start += pair.Value.Count; } } List<int> SubsetContinuousIDs = new List<int>(); foreach (var pair in SubsetParticleIDs) SubsetContinuousIDs.AddRange(pair.Value); // Reorder particle information to match the order of SubsetContinuousIDs ParticleOrigins = SubsetContinuousIDs.Select(i => ParticleOrigins[i]).ToArray(); ParticleAngles = SubsetContinuousIDs.Select(i => ParticleAngles[i]).ToArray(); ParticleSubset = SubsetContinuousIDs.Select(i => ParticleSubset[i]).ToArray(); #endregion int CoarseSize = (int)Math.Round(size * ((float)CTF.PixelSize * 2 / resolution)) / 2 * 2; int3 CoarseDims = new int3(CoarseSize, CoarseSize, 1); // Positions the particles were extracted at/shifted to, to calculate effectively needed shifts later float3[] ExtractedAt = new float3[NParticles * NTilts]; // Extract images, mask and resize them, create CTFs #region Preflight { Image CTFCoords = GetCTFCoords(CoarseSize, size); #region Create mask with soft edge Image Mask; { Image MaskBig = new Image(new int3(size, size, 1)); float MaskRadius = MainWindow.Options.ExportParticleRadius / (float)CTF.PixelSize; float SoftEdge = 16f; float[] MaskBigData = MaskBig.GetHost(Intent.Write)[0]; for (int y = 0; y < size; y++) { int yy = y - size / 2; yy *= yy; for (int x = 0; x < size; x++) { int xx = x - size / 2; xx *= xx; float R = (float)Math.Sqrt(xx + yy); if (R <= MaskRadius) MaskBigData[y * size + x] = 1; else MaskBigData[y * size + x] = (float)(Math.Cos(Math.Min(1, (R - MaskRadius) / SoftEdge) * Math.PI) * 0.5 + 0.5); } } MaskBig.WriteMRC("d_maskbig.mrc"); Mask = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize)); MaskBig.Dispose(); } Mask.WriteMRC("d_masksmall.mrc"); #endregion #region Create Fourier space mask Image FourierMask = new Image(CoarseDims, true); { float[] FourierMaskData = FourierMask.GetHost(Intent.Write)[0]; int MaxR2 = CoarseSize * CoarseSize / 4; for (int y = 0; y < CoarseSize; y++) { int yy = y < CoarseSize / 2 + 1 ? y : y - CoarseSize; yy *= yy; for (int x = 0; x < CoarseSize / 2 + 1; x++) { int xx = x * x; int R2 = yy + xx; FourierMaskData[y * (CoarseSize / 2 + 1) + x] = R2 < MaxR2 ? 1 : 0; } } } #endregion #region For each particle, create CTFs and projections, and insert them into the simulated tilt series for (int p = 0; p < NParticles; p++) { Image ParticleImages; Image ParticleCTFs = new Image(new int3(CoarseSize, CoarseSize, NTilts), true); float3 ParticleCoords = ParticleOrigins[p]; float3[] Positions = GetPositionInImages(ParticleCoords); // Create CTFs { float GridStep = 1f / (NTilts - 1); CTFStruct[] Params = new CTFStruct[NTilts]; for (int t = 0; t < NTilts; t++) { decimal Defocus = (decimal)Positions[t].Z; decimal DefocusDelta = (decimal)GridCTFDefocusDelta.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); decimal DefocusAngle = (decimal)GridCTFDefocusAngle.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); CTF CurrCTF = CTF.GetCopy(); CurrCTF.Defocus = Defocus; CurrCTF.DefocusDelta = DefocusDelta; CurrCTF.DefocusAngle = DefocusAngle; CurrCTF.Scale = (decimal)Math.Cos(Angles[t] * Helper.ToRad); CurrCTF.Bfactor = (decimal)-Dose[t] * 8; Params[t] = CurrCTF.ToStruct(); } GPU.CreateCTF(ParticleCTFs.GetDevice(Intent.Write), CTFCoords.GetDevice(Intent.Read), (uint)CoarseDims.ElementsFFT(), Params, false, (uint)NTilts); ParticleCTFs.MultiplySlices(FourierMask); } // Make projections { float3[] ImageShifts = new float3[NTilts]; float3[] ImageAngles = new float3[NTilts]; float3[] CurrPositions = GetPositionInImages(ParticleOrigins[p]); float3[] CurrAngles = GetParticleAngleInImages(ParticleOrigins[p], ParticleAngles[p]); for (int t = 0; t < NTilts; t++) { ImageShifts[t] = new float3(CurrPositions[t].X - (int)CurrPositions[t].X, // +diff because we are shifting the projections into experimental data frame CurrPositions[t].Y - (int)CurrPositions[t].Y, CurrPositions[t].Z - (int)CurrPositions[t].Z); ImageAngles[t] = CurrAngles[t]; } Image ProjectionsFT = new Image(IntPtr.Zero, new int3(CoarseSize, CoarseSize, NTilts), true, true); Projector Reference = references[ParticleSubset[p]]; GPU.ProjectForward(Reference.Data.GetDevice(Intent.Read), ProjectionsFT.GetDevice(Intent.Write), Reference.Data.Dims, new int2(CoarseSize, CoarseSize), Helper.ToInterleaved(ImageAngles), Reference.Oversampling, (uint)NTilts); ProjectionsFT.Multiply(ParticleCTFs); Image Projections = ProjectionsFT.AsIFFT(); ProjectionsFT.Dispose(); Projections.RemapFromFT(); GPU.NormParticles(Projections.GetDevice(Intent.Read), Projections.GetDevice(Intent.Write), new int3(CoarseSize, CoarseSize, 1), (uint)(MainWindow.Options.ExportParticleRadius / CTF.PixelSize * (CTF.PixelSize * 2 / (decimal)resolution)), true, (uint)NTilts); Projections.MultiplySlices(Mask); ParticleImages = Projections.AsScaled(new int2(size, size)); Projections.Dispose(); ParticleImages.ShiftSlices(ImageShifts); } // Extract images { for (int t = 0; t < NTilts; t++) { Positions[t] -= size / 2; int2 IntPosition = new int2((int)Positions[t].X, (int)Positions[t].Y); float[] SimulatedData; lock (SimulatedStack) SimulatedData = SimulatedStack.GetHost(Intent.Write)[t]; float[] ImageData = ParticleImages.GetHost(Intent.Read)[t]; for (int y = 0; y < size; y++) { int PosY = (y + IntPosition.Y + SimulatedStack.Dims.Y) % SimulatedStack.Dims.Y; for (int x = 0; x < size; x++) { int PosX = (x + IntPosition.X + SimulatedStack.Dims.X) % SimulatedStack.Dims.X; SimulatedData[PosY * SimulatedStack.Dims.X + PosX] += ImageData[y * size + x]; } } } } ParticleImages.Dispose(); ParticleCTFs.Dispose(); } #endregion Mask.Dispose(); FourierMask.Dispose(); CTFCoords.Dispose(); } #endregion return SimulatedStack; }
public void RealspaceRefineGlobal(Star tableIn, Image tiltStack, int size, int3 volumeDimensions, Dictionary<int, Projector> references, float resolution, int healpixorder, string symmetry, Dictionary<int, Projector> outReconstructions) { VolumeDimensions = volumeDimensions; #region Get rows from table 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); if (RowIndices.Count == 0) return; int NParticles = RowIndices.Count; #endregion #region Make sure all columns and directories are there if (!tableIn.HasColumn("rlnImageName")) tableIn.AddColumn("rlnImageName"); if (!tableIn.HasColumn("rlnCtfImage")) tableIn.AddColumn("rlnCtfImage"); if (!tableIn.HasColumn("rlnParticleSelectZScore")) tableIn.AddColumn("rlnParticleSelectZScore"); if (!Directory.Exists(ParticlesDir)) Directory.CreateDirectory(ParticlesDir); if (!Directory.Exists(ParticleCTFDir)) Directory.CreateDirectory(ParticleCTFDir); #endregion #region Get subtomo positions from table float3[] ParticleOrigins = new float3[NParticles]; float3[] ParticleAngles = new float3[NParticles]; int[] ParticleSubset = new int[NParticles]; { string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ"); string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi"); string[] ColumnSubset = tableIn.GetColumn("rlnRandomSubset"); for (int i = 0; i < NParticles; i++) { float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleOrigins[i] = Pos - Shift; //ParticleOrigins[i] /= new float3(3838f / 959f, 3710f / 927f, 4f); float3 Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleAngles[i] = Angle; if (ColumnSubset != null) ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]); else ParticleSubset[i] = (i % 2) + 1; tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", ParticleOrigins[i].X.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", ParticleOrigins[i].Y.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateZ", ParticleOrigins[i].Z.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginZ", "0.0"); } } #endregion #region Deal with subsets List<int> SubsetIDs = new List<int>(); foreach (var i in ParticleSubset) if (!SubsetIDs.Contains(i)) SubsetIDs.Add(i); SubsetIDs.Sort(); // For each subset, create a list of its particle IDs Dictionary<int, List<int>> SubsetParticleIDs = SubsetIDs.ToDictionary(subsetID => subsetID, subsetID => new List<int>()); for (int i = 0; i < ParticleSubset.Length; i++) SubsetParticleIDs[ParticleSubset[i]].Add(i); foreach (var list in SubsetParticleIDs.Values) list.Sort(); // Note where each subset starts and ends in a unified, sorted (by subset) particle ID list Dictionary<int, Tuple<int, int>> SubsetRanges = new Dictionary<int, Tuple<int, int>>(); { int Start = 0; foreach (var pair in SubsetParticleIDs) { SubsetRanges.Add(pair.Key, new Tuple<int, int>(Start, Start + pair.Value.Count)); Start += pair.Value.Count; } } List<int> SubsetContinuousIDs = new List<int>(); foreach (var pair in SubsetParticleIDs) SubsetContinuousIDs.AddRange(pair.Value); // Reorder particle information to match the order of SubsetContinuousIDs ParticleOrigins = SubsetContinuousIDs.Select(i => ParticleOrigins[i]).ToArray(); ParticleAngles = SubsetContinuousIDs.Select(i => ParticleAngles[i]).ToArray(); ParticleSubset = SubsetContinuousIDs.Select(i => ParticleSubset[i]).ToArray(); #endregion int CoarseSize = (int)Math.Round(size * ((float)CTF.PixelSize * 2 / resolution)) / 2 * 2; int3 CoarseDims = new int3(CoarseSize, CoarseSize, 1); // Create mask, CTF coords, reference projections, shifts Image Mask; Image CTFCoords = GetCTFCoords(CoarseSize, size); Dictionary<int, Image> SubsetProjections = new Dictionary<int, Image>(); float3[] AnglesOri = Helper.GetHealpixAngles(healpixorder, symmetry); List<float3> Shifts = new List<float3>(); for (int z = -1; z <= 1; z++) for (int y = -1; y <= 1; y++) for (int x = -1; x <= 1; x++) if (x * x + y * y + z * z <= 1) Shifts.Add(new float3((float)x / CoarseSize * size * 0.5f, (float)y / CoarseSize * size * 0.5f, (float)z / CoarseSize * size * 0.5f)); #region Preflight { #region Create mask with soft edge { Image MaskBig = new Image(new int3(size, size, 1)); float MaskRadius = MainWindow.Options.ExportParticleRadius / (float)CTF.PixelSize; float SoftEdge = 16f; float[] MaskBigData = MaskBig.GetHost(Intent.Write)[0]; for (int y = 0; y < size; y++) { int yy = y - size / 2; yy *= yy; for (int x = 0; x < size; x++) { int xx = x - size / 2; xx *= xx; float R = (float)Math.Sqrt(xx + yy); if (R <= MaskRadius) MaskBigData[y * size + x] = 1; else MaskBigData[y * size + x] = (float)(Math.Cos(Math.Min(1, (R - MaskRadius) / SoftEdge) * Math.PI) * 0.5 + 0.5); } } MaskBig.WriteMRC("d_maskbig.mrc"); Mask = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize)); Mask.RemapToFT(); MaskBig.Dispose(); } Mask.WriteMRC("d_masksmall.mrc"); #endregion #region Create projections for each angular sample, adjusted for each tilt foreach (var subset in SubsetRanges) { float3[] AnglesAlt = new float3[AnglesOri.Length * NTilts]; for (int t = 0; t < NTilts; t++) { for (int a = 0; a < AnglesOri.Length; a++) { float GridStep = 1f / (NTilts - 1); float3 GridCoords = new float3(0.5f, 0.5f, t * GridStep); Matrix3 ParticleMatrix = Matrix3.Euler(AnglesOri[a].X * Helper.ToRad, AnglesOri[a].Y * Helper.ToRad, AnglesOri[a].Z * Helper.ToRad); Matrix3 TiltMatrix = Matrix3.Euler(0, -AnglesCorrect[t] * Helper.ToRad, 0); Matrix3 CorrectionMatrix = Matrix3.RotateZ(GridAngleZ.GetInterpolated(GridCoords) * Helper.ToRad) * Matrix3.RotateY(GridAngleY.GetInterpolated(GridCoords) * Helper.ToRad) * Matrix3.RotateX(GridAngleX.GetInterpolated(GridCoords) * Helper.ToRad); Matrix3 Rotation = CorrectionMatrix * TiltMatrix * ParticleMatrix; AnglesAlt[a * NTilts + t] = Matrix3.EulerFromMatrix(Rotation); } } Image ProjFT = references[subset.Key].Project(new int2(CoarseSize, CoarseSize), AnglesAlt, CoarseSize / 2); Image CheckProj = ProjFT.AsIFFT(); CheckProj.RemapFromFT(); CheckProj.WriteMRC("d_proj.mrc"); CheckProj.Dispose(); ProjFT.FreeDevice(); SubsetProjections[subset.Key] = ProjFT; } #endregion } #endregion float3[] OptimizedShifts = new float3[NParticles]; float3[] OptimizedAngles = new float3[NParticles]; #region Correlate each particle with all projections foreach (var subset in SubsetRanges) { Image Projections = SubsetProjections[subset.Key]; for (int p = subset.Value.Item1; p < subset.Value.Item2; p++) //Parallel.For(subset.Value.Item1, subset.Value.Item2, new ParallelOptions { MaxDegreeOfParallelism = 4 }, p => { Image ParticleImages; Image ParticleCTFs = new Image(new int3(CoarseSize, CoarseSize, NTilts), true); Image ParticleWeights; // Positions the particles were extracted at/shifted to, to calculate effectively needed shifts later float3[] ExtractedAt = new float3[NTilts]; float3 ParticleCoords = ParticleOrigins[p]; float3[] Positions = GetPositionInImages(ParticleCoords); #region Create CTFs { float GridStep = 1f / (NTilts - 1); CTFStruct[] Params = new CTFStruct[NTilts]; for (int t = 0; t < NTilts; t++) { decimal Defocus = (decimal)Positions[t].Z; decimal DefocusDelta = (decimal)GridCTFDefocusDelta.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); decimal DefocusAngle = (decimal)GridCTFDefocusAngle.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); CTF CurrCTF = CTF.GetCopy(); CurrCTF.Defocus = Defocus; CurrCTF.DefocusDelta = DefocusDelta; CurrCTF.DefocusAngle = DefocusAngle; CurrCTF.Scale = (decimal)Math.Cos(Angles[t] * Helper.ToRad); CurrCTF.Bfactor = (decimal)-Dose[t] * 8; Params[t] = CurrCTF.ToStruct(); } GPU.CreateCTF(ParticleCTFs.GetDevice(Intent.Write), CTFCoords.GetDevice(Intent.Read), (uint)CoarseDims.ElementsFFT(), Params, false, (uint)NTilts); } #endregion #region Weights are sums of the 2D CTFs { Image CTFAbs = new Image(ParticleCTFs.GetDevice(Intent.Read), ParticleCTFs.Dims, true); CTFAbs.Abs(); ParticleWeights = CTFAbs.AsSum2D(); CTFAbs.Dispose(); { float[] Weights = ParticleWeights.GetHost(Intent.ReadWrite)[0]; float Sum = Weights.Sum(); for (int i = 0; i < Weights.Length; i++) Weights[i] /= Sum; } } #endregion #region Extract images { Image Extracted = new Image(new int3(size, size, NTilts)); float[][] ExtractedData = Extracted.GetHost(Intent.Write); Parallel.For(0, NTilts, t => { ExtractedAt[t] = new float3((int)Positions[t].X, (int)Positions[t].Y, 0); Positions[t] -= size / 2; int2 IntPosition = new int2((int)Positions[t].X, (int)Positions[t].Y); float[] OriginalData; lock (tiltStack) OriginalData = tiltStack.GetHost(Intent.Read)[t]; float[] ImageData = ExtractedData[t]; for (int y = 0; y < size; y++) { int PosY = (y + IntPosition.Y + tiltStack.Dims.Y) % tiltStack.Dims.Y; for (int x = 0; x < size; x++) { int PosX = (x + IntPosition.X + tiltStack.Dims.X) % tiltStack.Dims.X; ImageData[y * size + x] = -OriginalData[PosY * tiltStack.Dims.X + PosX]; } } }); ParticleImages = Extracted.AsScaled(new int2(CoarseSize, CoarseSize)); ParticleImages.RemapToFT(); //Scaled.WriteMRC("d_particleimages.mrc"); Extracted.Dispose(); } #endregion Image ProjectionsConv = new Image(IntPtr.Zero, Projections.Dims, true, true); GPU.MultiplyComplexSlicesByScalar(Projections.GetDevice(Intent.Read), ParticleCTFs.GetDevice(Intent.Read), ProjectionsConv.GetDevice(Intent.Write), ParticleCTFs.ElementsComplex, (uint)AnglesOri.Length); Image ProjectionsReal = ProjectionsConv.AsIFFT(); GPU.NormalizeMasked(ProjectionsReal.GetDevice(Intent.Read), ProjectionsReal.GetDevice(Intent.Write), Mask.GetDevice(Intent.Read), (uint)ProjectionsReal.ElementsSliceReal, (uint)ProjectionsReal.Dims.Z); //ProjectionsReal.WriteMRC("d_projconv.mrc"); ProjectionsConv.Dispose(); #region For each particle offset, correlate each tilt image with all reference projection float[][] AllResults = new float[Shifts.Count][]; //for (int s = 0; s < Shifts.Count; s++) Parallel.For(0, Shifts.Count, new ParallelOptions { MaxDegreeOfParallelism = 2 }, s => { AllResults[s] = new float[AnglesOri.Length]; float3 ParticleCoordsAlt = ParticleOrigins[p] - Shifts[s]; float3[] PositionsAlt = GetPositionInImages(ParticleCoordsAlt); float3[] PositionDiff = new float3[NTilts]; for (int t = 0; t < NTilts; t++) PositionDiff[t] = (ExtractedAt[t] - PositionsAlt[t]) / size * CoarseSize; float[] ShiftResults = new float[AnglesOri.Length]; GPU.TomoRealspaceCorrelate(ProjectionsReal.GetDevice(Intent.Read), new int2(CoarseSize, CoarseSize), (uint)AnglesOri.Length, (uint)NTilts, ParticleImages.GetDevice(Intent.Read), ParticleCTFs.GetDevice(Intent.Read), Mask.GetDevice(Intent.Read), ParticleWeights.GetDevice(Intent.Read), Helper.ToInterleaved(PositionDiff), ShiftResults); AllResults[s] = ShiftResults; }); #endregion ProjectionsReal.Dispose(); ParticleImages.Dispose(); ParticleCTFs.Dispose(); ParticleWeights.Dispose(); #region Find best offset/angle combination and store it in table float3 BestShift = new float3(0, 0, 0); float3 BestAngle = new float3(0, 0, 0); float BestScore = -1e30f; for (int s = 0; s < Shifts.Count; s++) for (int a = 0; a < AnglesOri.Length; a++) if (AllResults[s][a] > BestScore) { BestScore = AllResults[s][a]; BestAngle = AnglesOri[a]; BestShift = Shifts[s]; } tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnOriginX", BestShift.X.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnOriginY", BestShift.Y.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnOriginZ", BestShift.Z.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnAngleRot", BestAngle.X.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnAngleTilt", BestAngle.Y.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnAnglePsi", BestAngle.Z.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnParticleSelectZScore", BestScore.ToString(CultureInfo.InvariantCulture)); OptimizedShifts[p] = BestShift; OptimizedAngles[p] = BestAngle; #endregion } // Dispose all projections for this subset, they won't be needed later SubsetProjections[subset.Key].Dispose(); } #endregion CTFCoords.Dispose(); #region Back-project with hopefully better parameters { CTFCoords = GetCTFCoords(size, size); foreach (var subsetRange in SubsetRanges) { for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++) { float3 ParticleCoords = ParticleOrigins[p] - OptimizedShifts[p]; Image FullParticleImages = GetSubtomoImages(tiltStack, size, ParticleCoords, true); Image FullParticleCTFs = GetSubtomoCTFs(ParticleCoords, CTFCoords); //Image FullParticleCTFWeights = GetSubtomoCTFs(ParticleCoords, CTFCoords, true, true); FullParticleImages.Multiply(FullParticleCTFs); //FullParticleImages.Multiply(FullParticleCTFWeights); FullParticleCTFs.Multiply(FullParticleCTFs); float3[] FullParticleAngles = GetParticleAngleInImages(ParticleCoords, OptimizedAngles[p]); outReconstructions[subsetRange.Key].BackProject(FullParticleImages, FullParticleCTFs, FullParticleAngles); FullParticleImages.Dispose(); FullParticleCTFs.Dispose(); //FullParticleCTFWeights.Dispose(); } } CTFCoords.Dispose(); } #endregion }
public void PerformOptimizationStep(Star tableIn, Image tiltStack, int size, int3 volumeDimensions, Dictionary<int, Projector> references, float resolution, Dictionary<int, Projector> outReconstructions, Dictionary<int, Projector> outCTFReconstructions) { VolumeDimensions = volumeDimensions; #region Get rows from table 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); if (RowIndices.Count == 0) return; int NParticles = RowIndices.Count; #endregion #region Make sure all columns and directories are there if (!tableIn.HasColumn("rlnImageName")) tableIn.AddColumn("rlnImageName"); if (!tableIn.HasColumn("rlnCtfImage")) tableIn.AddColumn("rlnCtfImage"); if (!tableIn.HasColumn("rlnParticleSelectZScore")) tableIn.AddColumn("rlnParticleSelectZScore"); if (!Directory.Exists(ParticlesDir)) Directory.CreateDirectory(ParticlesDir); if (!Directory.Exists(ParticleCTFDir)) Directory.CreateDirectory(ParticleCTFDir); #endregion #region Get subtomo positions from table float3[] ParticleOrigins = new float3[NParticles]; float3[] ParticleOrigins2 = new float3[NParticles]; float3[] ParticleAngles = new float3[NParticles]; float3[] ParticleAngles2 = new float3[NParticles]; int[] ParticleSubset = new int[NParticles]; { string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ"); string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi"); string[] ColumnSubset = tableIn.GetColumn("rlnRandomSubset"); string[] ColumnPosX2 = tableIn.GetColumn("rlnOriginXPrior"); string[] ColumnPosY2 = tableIn.GetColumn("rlnOriginYPrior"); string[] ColumnPosZ2 = tableIn.GetColumn("rlnOriginZPrior"); string[] ColumnAngleRot2 = tableIn.GetColumn("rlnAngleRotPrior"); string[] ColumnAngleTilt2 = tableIn.GetColumn("rlnAngleTiltPrior"); string[] ColumnAnglePsi2 = tableIn.GetColumn("rlnAnglePsiPrior"); for (int i = 0; i < NParticles; i++) { float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Pos2 = Pos; //if (ColumnPosX2 != null && ColumnPosY2 != null && ColumnPosZ2 != null) // Pos2 = new float3(float.Parse(ColumnPosX2[RowIndices[i]], CultureInfo.InvariantCulture), // float.Parse(ColumnPosY2[RowIndices[i]], CultureInfo.InvariantCulture), // float.Parse(ColumnPosZ2[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleOrigins[i] = Pos - Shift; ParticleOrigins2[i] = Pos2 - Shift; float3 Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Angle2 = Angle; //if (ColumnAngleRot2 != null && ColumnAngleTilt2 != null && ColumnAnglePsi2 != null) // Angle2 = new float3(float.Parse(ColumnAngleRot2[RowIndices[i]], CultureInfo.InvariantCulture), // float.Parse(ColumnAngleTilt2[RowIndices[i]], CultureInfo.InvariantCulture), // float.Parse(ColumnAnglePsi2[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleAngles[i] = Angle; ParticleAngles2[i] = Angle2; ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", ParticleOrigins[i].X.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", ParticleOrigins[i].Y.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateZ", ParticleOrigins[i].Z.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginZ", "0.0"); } } #endregion #region Deal with subsets List<int> SubsetIDs = new List<int>(); foreach (var i in ParticleSubset) if (!SubsetIDs.Contains(i)) SubsetIDs.Add(i); SubsetIDs.Sort(); // For each subset, create a list of its particle IDs Dictionary<int, List<int>> SubsetParticleIDs = SubsetIDs.ToDictionary(subsetID => subsetID, subsetID => new List<int>()); for (int i = 0; i < ParticleSubset.Length; i++) SubsetParticleIDs[ParticleSubset[i]].Add(i); foreach (var list in SubsetParticleIDs.Values) list.Sort(); // Note where each subset starts and ends in a unified, sorted (by subset) particle ID list Dictionary<int, Tuple<int, int>> SubsetRanges = new Dictionary<int, Tuple<int, int>>(); { int Start = 0; foreach (var pair in SubsetParticleIDs) { SubsetRanges.Add(pair.Key, new Tuple<int, int>(Start, Start + pair.Value.Count)); Start += pair.Value.Count; } } List<int> SubsetContinuousIDs = new List<int>(); foreach (var pair in SubsetParticleIDs) SubsetContinuousIDs.AddRange(pair.Value); // Reorder particle information to match the order of SubsetContinuousIDs ParticleOrigins = SubsetContinuousIDs.Select(i => ParticleOrigins[i]).ToArray(); ParticleOrigins2 = SubsetContinuousIDs.Select(i => ParticleOrigins2[i]).ToArray(); ParticleAngles = SubsetContinuousIDs.Select(i => ParticleAngles[i]).ToArray(); ParticleAngles2 = SubsetContinuousIDs.Select(i => ParticleAngles2[i]).ToArray(); ParticleSubset = SubsetContinuousIDs.Select(i => ParticleSubset[i]).ToArray(); #endregion if (GridMovementX.Dimensions.Elements() == 1) { int MaxSlice = SubsetRanges.Last().Value.Item2 > 100 ? 1 : 1; GridMovementX = new CubicGrid(new int3(MaxSlice, MaxSlice, NTilts)); GridMovementY = new CubicGrid(new int3(MaxSlice, MaxSlice, NTilts)); //GridLocalX = new CubicGrid(new int3(4, 4, 4)); //GridLocalY = new CubicGrid(new int3(4, 4, 4)); //GridLocalZ = new CubicGrid(new int3(4, 4, 4)); GridAngleX = new CubicGrid(new int3(1, 1, NTilts)); GridAngleY = new CubicGrid(new int3(1, 1, NTilts)); GridAngleZ = new CubicGrid(new int3(1, 1, NTilts)); } if (GridLocalX.Dimensions.Elements() == 1) { GridLocalX = new CubicGrid(new int3(4, 4, 4)); GridLocalY = new CubicGrid(new int3(4, 4, 4)); GridLocalZ = new CubicGrid(new int3(4, 4, 4)); } //else //{ // GridMovementX = GridMovementX.Resize(new int3(4, 4, NTilts)); // GridMovementY = GridMovementY.Resize(new int3(4, 4, NTilts)); //} int CoarseSize = (int)Math.Round(size * ((float)CTF.PixelSize * 2 / resolution)) / 2 * 2; int3 CoarseDims = new int3(CoarseSize, CoarseSize, 1); // Positions the particles were extracted at/shifted to, to calculate effectively needed shifts later float2[] ExtractedAt = new float2[NParticles * NTilts]; // Extract images, mask and resize them, create CTFs Image ParticleImages = new Image(new int3(CoarseSize, CoarseSize, NParticles * NTilts), true, true); Image ParticleCTFs = new Image(new int3(CoarseSize, CoarseSize, NParticles * NTilts), true); Image ParticleWeights = null; Image ShiftFactors = null; #region Preflight float KeepBFac = GlobalBfactor; GlobalBfactor = 0; { Image CTFCoords = GetCTFCoords(CoarseSize, size); #region Precalculate vectors for shifts in Fourier space { float2[] ShiftFactorsData = new float2[(CoarseSize / 2 + 1) * CoarseSize]; for (int y = 0; y < CoarseSize; y++) for (int x = 0; x < CoarseSize / 2 + 1; x++) { int xx = x; int yy = y < CoarseSize / 2 + 1 ? y : y - CoarseSize; ShiftFactorsData[y * (CoarseSize / 2 + 1) + x] = new float2((float)-xx / size * 2f * (float)Math.PI, (float)-yy / size * 2f * (float)Math.PI); } ShiftFactors = new Image(ShiftFactorsData, new int3(CoarseSize, CoarseSize, 1), true); } #endregion #region Create mask with soft edge Image Mask; Image MaskSubt; { Image MaskBig = new Image(new int3(size, size, 1)); float MaskRadius = MainWindow.Options.ExportParticleRadius / (float)CTF.PixelSize; float SoftEdge = 16f; float[] MaskBigData = MaskBig.GetHost(Intent.Write)[0]; for (int y = 0; y < size; y++) { int yy = y - size / 2; yy *= yy; for (int x = 0; x < size; x++) { int xx = x - size / 2; xx *= xx; float R = (float)Math.Sqrt(xx + yy); if (R <= MaskRadius) MaskBigData[y * size + x] = 1; else MaskBigData[y * size + x] = (float)(Math.Cos(Math.Min(1, (R - MaskRadius) / SoftEdge) * Math.PI) * 0.5 + 0.5); } } //MaskBig.WriteMRC("d_maskbig.mrc"); Mask = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize)); Mask.RemapToFT(); MaskBigData = MaskBig.GetHost(Intent.Write)[0]; for (int y = 0; y < size; y++) { int yy = y - size / 2; yy *= yy; for (int x = 0; x < size; x++) { int xx = x - size / 2; xx *= xx; float R = (float)Math.Sqrt(xx + yy); if (R <= 30) MaskBigData[y * size + x] = 1; else MaskBigData[y * size + x] = 0; } } MaskSubt = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize)); MaskSubt.RemapToFT(); MaskBig.Dispose(); } //Mask.WriteMRC("d_masksmall.mrc"); #endregion #region Create Fourier space mask Image FourierMask = new Image(CoarseDims, true); { float[] FourierMaskData = FourierMask.GetHost(Intent.Write)[0]; int MaxR2 = CoarseSize * CoarseSize / 4; for (int y = 0; y < CoarseSize; y++) { int yy = y < CoarseSize / 2 + 1 ? y : y - CoarseSize; yy *= yy; for (int x = 0; x < CoarseSize / 2 + 1; x++) { int xx = x * x; int R2 = yy + xx; FourierMaskData[y * (CoarseSize / 2 + 1) + x] = R2 < MaxR2 ? 1 : 0; } } } #endregion #region For each particle, create CTFs and extract & preprocess images for entire tilt series for (int p = 0; p < NParticles; p++) { float3 ParticleCoords = ParticleOrigins[p]; float3[] Positions = GetPositionInImages(ParticleCoords); float3[] ProjAngles = GetParticleAngleInImages(ParticleCoords, ParticleAngles[p]); Image Extracted = new Image(new int3(size, size, NTilts)); float[][] ExtractedData = Extracted.GetHost(Intent.Write); float3[] Residuals = new float3[NTilts]; Image SubtrahendsCTF = new Image(new int3(CoarseSize, CoarseSize, NTilts), true); // Create CTFs { CTFStruct[] CTFParams = new CTFStruct[NTilts]; float GridStep = 1f / (NTilts - 1); CTFStruct[] Params = new CTFStruct[NTilts]; for (int t = 0; t < NTilts; t++) { decimal Defocus = (decimal)Positions[t].Z; decimal DefocusDelta = (decimal)GridCTFDefocusDelta.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); decimal DefocusAngle = (decimal)GridCTFDefocusAngle.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); CTF CurrCTF = CTF.GetCopy(); CurrCTF.Defocus = Defocus; CurrCTF.DefocusDelta = DefocusDelta; CurrCTF.DefocusAngle = DefocusAngle; CurrCTF.Scale = (decimal)Math.Cos(Angles[t] * Helper.ToRad); CurrCTF.Bfactor = (decimal)-Dose[t] * 8; Params[t] = CurrCTF.ToStruct(); } GPU.CreateCTF(ParticleCTFs.GetDeviceSlice(NTilts * p, Intent.Write), CTFCoords.GetDevice(Intent.Read), (uint)CoarseDims.ElementsFFT(), Params, false, (uint)NTilts); } //{ // CTFStruct[] CTFParams = new CTFStruct[NTilts]; // float GridStep = 1f / (NTilts - 1); // CTFStruct[] Params = new CTFStruct[NTilts]; // for (int t = 0; t < NTilts; t++) // { // decimal Defocus = (decimal)Positions[t].Z; // decimal DefocusDelta = (decimal)GridCTFDefocusDelta.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); // decimal DefocusAngle = (decimal)GridCTFDefocusAngle.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); // CTF CurrCTF = CTF.GetCopy(); // CurrCTF.Defocus = Defocus; // CurrCTF.DefocusDelta = DefocusDelta; // CurrCTF.DefocusAngle = DefocusAngle; // CurrCTF.Scale = 1; // CurrCTF.Bfactor = 0; // Params[t] = CurrCTF.ToStruct(); // } // GPU.CreateCTF(SubtrahendsCTF.GetDevice(Intent.Write), // CTFCoords.GetDevice(Intent.Read), // (uint)CoarseDims.ElementsFFT(), // Params, // false, // (uint)NTilts); //} // Extract images { for (int t = 0; t < NTilts; t++) { ExtractedAt[p * NTilts + t] = new float2(Positions[t].X, Positions[t].Y); Positions[t] -= size / 2; int2 IntPosition = new int2((int)Positions[t].X, (int)Positions[t].Y); float2 Residual = new float2(-(Positions[t].X - IntPosition.X), -(Positions[t].Y - IntPosition.Y)); Residuals[t] = new float3(Residual / size * CoarseSize); float[] OriginalData; lock (tiltStack) OriginalData = tiltStack.GetHost(Intent.Read)[t]; float[] ImageData = ExtractedData[t]; for (int y = 0; y < size; y++) { int PosY = (y + IntPosition.Y + tiltStack.Dims.Y) % tiltStack.Dims.Y; for (int x = 0; x < size; x++) { int PosX = (x + IntPosition.X + tiltStack.Dims.X) % tiltStack.Dims.X; ImageData[y * size + x] = OriginalData[PosY * tiltStack.Dims.X + PosX]; } } } GPU.NormParticles(Extracted.GetDevice(Intent.Read), Extracted.GetDevice(Intent.Write), new int3(size, size, 1), (uint)(MainWindow.Options.ExportParticleRadius / CTF.PixelSize), true, (uint)NTilts); Image Scaled = Extracted.AsScaled(new int2(CoarseSize, CoarseSize)); //Scaled.WriteMRC("d_scaled.mrc"); Extracted.Dispose(); Scaled.ShiftSlices(Residuals); Scaled.RemapToFT(); //GPU.NormalizeMasked(Scaled.GetDevice(Intent.Read), // Scaled.GetDevice(Intent.Write), // MaskSubt.GetDevice(Intent.Read), // (uint)Scaled.ElementsSliceReal, // (uint)NTilts); //{ // //Image SubtrahendsFT = subtrahendReference.Project(new int2(CoarseSize, CoarseSize), ProjAngles, CoarseSize / 2); // //SubtrahendsFT.Multiply(SubtrahendsCTF); // //Image Subtrahends = SubtrahendsFT.AsIFFT(); // //SubtrahendsFT.Dispose(); // ////GPU.NormalizeMasked(Subtrahends.GetDevice(Intent.Read), // //// Subtrahends.GetDevice(Intent.Write), // //// MaskSubt.GetDevice(Intent.Read), // //// (uint)Subtrahends.ElementsSliceReal, // //// (uint)NTilts); // //Scaled.Subtract(Subtrahends); // //Subtrahends.Dispose(); // Image FocusMaskFT = maskReference.Project(new int2(CoarseSize, CoarseSize), ProjAngles, CoarseSize / 2); // Image FocusMask = FocusMaskFT.AsIFFT(); // FocusMaskFT.Dispose(); // Scaled.Multiply(FocusMask); // FocusMask.Dispose(); //} Scaled.MultiplySlices(Mask); GPU.FFT(Scaled.GetDevice(Intent.Read), ParticleImages.GetDeviceSlice(p * NTilts, Intent.Write), CoarseDims, (uint)NTilts); Scaled.Dispose(); SubtrahendsCTF.Dispose(); } } #endregion ParticleCTFs.MultiplySlices(FourierMask); Mask.Dispose(); FourierMask.Dispose(); MaskSubt.Dispose(); Image ParticleCTFsAbs = new Image(ParticleCTFs.GetDevice(Intent.Read), ParticleCTFs.Dims, true); ParticleCTFsAbs.Abs(); ParticleWeights = ParticleCTFsAbs.AsSum2D(); ParticleCTFsAbs.Dispose(); { float[] ParticleWeightsData = ParticleWeights.GetHost(Intent.ReadWrite)[0]; float Max = MathHelper.Max(ParticleWeightsData); for (int i = 0; i < ParticleWeightsData.Length; i++) ParticleWeightsData[i] /= Max; } CTFCoords.Dispose(); //Image CheckImages = ParticleImages.AsIFFT(); //CheckImages.WriteMRC("d_particleimages.mrc"); //CheckImages.Dispose(); //ParticleCTFs.WriteMRC("d_particlectfs.mrc"); } GlobalBfactor = KeepBFac; #endregion bool DoPerParticleMotion = true; bool DoImageAlignment = true; #region BFGS evaluation and gradient double[] StartParams; Func<double[], Tuple<float2[], float3[]>> GetImageShiftsAndAngles; Func<double[], float2[]> GetImageShifts; Func<float3[], Image> GetProjections; Func<double[], double[]> EvalIndividual; Func<double[], double> Eval; Func<double[], double[]> Gradient; { List<double> StartParamsList = new List<double>(); StartParamsList.AddRange(CreateVectorFromGrids(Dimensions.X)); StartParamsList.AddRange(CreateVectorFromParameters(ParticleOrigins, ParticleOrigins2, ParticleAngles, ParticleAngles2, size)); StartParams = StartParamsList.ToArray(); // Remember where the values for each grid are stored in the optimized vector List<Tuple<int, int>> VectorGridRanges = new List<Tuple<int, int>>(); List<int> GridElements = new List<int>(); List<int> GridSliceElements = new List<int>(); { int Start = 0; VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridMovementX.Dimensions.Elements())); Start += (int)GridMovementX.Dimensions.Elements(); VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridMovementY.Dimensions.Elements())); Start += (int)GridMovementY.Dimensions.Elements(); VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridAngleX.Dimensions.Elements())); Start += (int)GridAngleX.Dimensions.Elements(); VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridAngleY.Dimensions.Elements())); Start += (int)GridAngleY.Dimensions.Elements(); VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridAngleZ.Dimensions.Elements())); Start += (int)GridAngleZ.Dimensions.Elements(); VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridLocalX.Dimensions.Elements())); Start += (int)GridLocalX.Dimensions.Elements(); VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridLocalY.Dimensions.Elements())); Start += (int)GridLocalY.Dimensions.Elements(); VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridLocalZ.Dimensions.Elements())); GridElements.Add((int)GridMovementX.Dimensions.Elements()); GridElements.Add((int)GridMovementY.Dimensions.Elements()); GridElements.Add((int)GridAngleX.Dimensions.Elements()); GridElements.Add((int)GridAngleY.Dimensions.Elements()); GridElements.Add((int)GridAngleZ.Dimensions.Elements()); GridElements.Add((int)GridLocalX.Dimensions.Elements()); GridElements.Add((int)GridLocalY.Dimensions.Elements()); GridElements.Add((int)GridLocalZ.Dimensions.Elements()); GridSliceElements.Add((int)GridMovementX.Dimensions.ElementsSlice()); GridSliceElements.Add((int)GridMovementY.Dimensions.ElementsSlice()); GridSliceElements.Add((int)GridAngleX.Dimensions.ElementsSlice()); GridSliceElements.Add((int)GridAngleY.Dimensions.ElementsSlice()); GridSliceElements.Add((int)GridAngleZ.Dimensions.ElementsSlice()); GridSliceElements.Add((int)GridLocalX.Dimensions.ElementsSlice()); GridSliceElements.Add((int)GridLocalY.Dimensions.ElementsSlice()); GridSliceElements.Add((int)GridLocalZ.Dimensions.ElementsSlice()); } int NVectorGridParams = VectorGridRanges.Last().Item2; int NVectorParticleParams = NParticles * 12; GetImageShiftsAndAngles = input => { // Retrieve particle positions & angles, and grids from input vector float3[] NewPositions, NewPositions2, NewAngles, NewAngles2; GetParametersFromVector(input, NParticles, size, out NewPositions, out NewPositions2, out NewAngles, out NewAngles2); SetGridsFromVector(input, Dimensions.X); // Using current positions, angles and grids, get parameters for image shifts and reference projection angles float2[] ImageShifts = new float2[NParticles * NTilts]; float3[] ImageAngles = new float3[NParticles * NTilts]; float3[] PerTiltPositions = new float3[NParticles * NTilts]; float3[] PerTiltAngles = new float3[NParticles * NTilts]; int[] SortedDosePrecalc = IndicesSortedDose; for (int p = 0; p < NParticles; p++) { if (DoPerParticleMotion) { float3 CoordsDiff = NewPositions2[p] - NewPositions[p]; float3 AnglesDiff = NewAngles2[p] - NewAngles[p]; for (int t = 0; t < NTilts; t++) { float DoseID = SortedDosePrecalc[t] / (float)(NTilts - 1); PerTiltPositions[p * NTilts + t] = NewPositions[p] + CoordsDiff * DoseID; PerTiltAngles[p * NTilts + t] = NewAngles[p] + AnglesDiff * DoseID; } } else { for (int t = 0; t < NTilts; t++) { PerTiltPositions[p * NTilts + t] = NewPositions[p]; PerTiltAngles[p * NTilts + t] = NewAngles[p]; } } } float3[] CurrPositions = GetPositionInImages(PerTiltPositions); float3[] CurrAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles); for (int i = 0; i < ImageShifts.Length; i++) { ImageShifts[i] = new float2(ExtractedAt[i].X - CurrPositions[i].X, ExtractedAt[i].Y - CurrPositions[i].Y); // -diff because those are extraction positions, i. e. opposite direction of shifts ImageAngles[i] = CurrAngles[i]; } return new Tuple<float2[], float3[]>(ImageShifts, ImageAngles); }; GetImageShifts = input => { // Retrieve particle positions & angles, and grids from input vector float3[] NewPositions, NewPositions2, NewAngles, NewAngles2; GetParametersFromVector(input, NParticles, size, out NewPositions, out NewPositions2, out NewAngles, out NewAngles2); SetGridsFromVector(input, Dimensions.X); // Using current positions, angles and grids, get parameters for image shifts and reference projection angles float2[] ImageShifts = new float2[NParticles * NTilts]; float3[] PerTiltPositions = new float3[NParticles * NTilts]; int[] SortedDosePrecalc = IndicesSortedDose; for (int p = 0; p < NParticles; p++) { if (DoPerParticleMotion) { float3 CoordsDiff = NewPositions2[p] - NewPositions[p]; float3 AnglesDiff = NewAngles2[p] - NewAngles[p]; for (int t = 0; t < NTilts; t++) { float DoseID = SortedDosePrecalc[t] / (float)(NTilts - 1); PerTiltPositions[p * NTilts + t] = NewPositions[p] + CoordsDiff * DoseID; } } else { for (int t = 0; t < NTilts; t++) PerTiltPositions[p * NTilts + t] = NewPositions[p]; } } float3[] CurrPositions = GetPositionInImages(PerTiltPositions); for (int i = 0; i < ImageShifts.Length; i++) ImageShifts[i] = new float2(ExtractedAt[i].X - CurrPositions[i].X, ExtractedAt[i].Y - CurrPositions[i].Y); // -diff because those are extraction positions, i. e. opposite direction of shifts return ImageShifts; }; GetProjections = imageAngles => { Image Projections = new Image(IntPtr.Zero, new int3(CoarseSize, CoarseSize, NParticles * NTilts), true, true); foreach (var subset in SubsetRanges) { Projector Reference = references[subset.Key]; int SubsetStart = subset.Value.Item1 * NTilts; int SubsetEnd = subset.Value.Item2 * NTilts; float3[] SubsetAngles = imageAngles.Skip(SubsetStart).Take(SubsetEnd - SubsetStart).ToArray(); GPU.ProjectForward(Reference.Data.GetDevice(Intent.Read), Projections.GetDeviceSlice(SubsetStart, Intent.Write), Reference.Data.Dims, new int2(CoarseSize, CoarseSize), Helper.ToInterleaved(SubsetAngles), Reference.Oversampling, (uint)(SubsetEnd - SubsetStart)); } /*Image CheckProjections = Projections.AsIFFT(); //CheckProjections.RemapFromFT(); CheckProjections.WriteMRC("d_projections.mrc"); CheckProjections.Dispose();*/ return Projections; }; EvalIndividual = input => { Tuple<float2[], float3[]> ShiftsAndAngles = GetImageShiftsAndAngles(input); Image Projections = GetProjections(ShiftsAndAngles.Item2); float[] Results = new float[NParticles * NTilts]; GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), ParticleCTFs.GetDevice(Intent.Read), ParticleWeights.GetDevice(Intent.Read), new int2(CoarseSize, CoarseSize), Helper.ToInterleaved(ShiftsAndAngles.Item1), Results, (uint)(NParticles * NTilts)); Projections.Dispose(); return Results.Select(i => (double)i).ToArray(); }; int OptimizationIterations = 0; bool GetOut = false; double Delta = 0.1; float Delta2 = 2 * (float)Delta; int[] WarpGridIDs = { 5, 6, 7 }; Dictionary<int, float2[][]> WiggleWeightsWarp = new Dictionary<int, float2[][]>(); foreach (var gridID in WarpGridIDs) { int NElements = GridElements[gridID]; WiggleWeightsWarp.Add(gridID, new float2[NElements][]); for (int ge = 0; ge < NElements; ge++) { double[] InputMinus = new double[StartParams.Length], InputPlus = new double[StartParams.Length]; for (int i = 0; i < StartParams.Length; i++) { InputMinus[i] = StartParams[i]; InputPlus[i] = StartParams[i]; } InputMinus[VectorGridRanges[gridID].Item1 + ge] -= Delta; InputPlus[VectorGridRanges[gridID].Item1 + ge] += Delta; float2[] ImageShiftsPlus = GetImageShifts(InputPlus); float2[] ImageShiftsMinus = GetImageShifts(InputMinus); float2[] Weights = new float2[ImageShiftsPlus.Length]; for (int i = 0; i < ImageShiftsPlus.Length; i++) Weights[i] = (ImageShiftsPlus[i] - ImageShiftsMinus[i]) / Delta2; WiggleWeightsWarp[gridID][ge] = Weights; } } Eval = input => { double Result = EvalIndividual(input).Sum(); lock (tableIn) Debug.WriteLine(GPU.GetDevice() + ", " + RootName + ": " + Result); OptimizationIterations++; return Result; }; Func<double[], double[], double, double[]> GradientParticles = (inputMinus, inputPlus, delta) => { double[] EvalMinus = EvalIndividual(inputMinus); double[] EvalPlus = EvalIndividual(inputPlus); double[] Diff = new double[EvalMinus.Length]; for (int i = 0; i < Diff.Length; i++) Diff[i] = (EvalPlus[i] - EvalMinus[i]) / (2 * delta); return Diff; }; Gradient = input => { double[] Result = new double[input.Length]; if (OptimizationIterations > 60) return Result; float2[] ImageShiftGradients = new float2[NParticles * NTilts]; #region Compute gradient for individual image shifts { Tuple<float2[], float3[]> ShiftsAndAngles = GetImageShiftsAndAngles(input); Image Projections = GetProjections(ShiftsAndAngles.Item2); float2[] ShiftsXPlus = new float2[NParticles * NTilts]; float2[] ShiftsXMinus = new float2[NParticles * NTilts]; float2[] ShiftsYPlus = new float2[NParticles * NTilts]; float2[] ShiftsYMinus = new float2[NParticles * NTilts]; float2 DeltaX = new float2((float)Delta, 0); float2 DeltaY = new float2(0, (float)Delta); for (int i = 0; i < ShiftsXPlus.Length; i++) { ShiftsXPlus[i] = ShiftsAndAngles.Item1[i] + DeltaX; ShiftsXMinus[i] = ShiftsAndAngles.Item1[i] - DeltaX; ShiftsYPlus[i] = ShiftsAndAngles.Item1[i] + DeltaY; ShiftsYMinus[i] = ShiftsAndAngles.Item1[i] - DeltaY; } float[] ScoresXPlus = new float[NParticles * NTilts]; float[] ScoresXMinus = new float[NParticles * NTilts]; float[] ScoresYPlus = new float[NParticles * NTilts]; float[] ScoresYMinus = new float[NParticles * NTilts]; GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), ParticleCTFs.GetDevice(Intent.Read), ParticleWeights.GetDevice(Intent.Read), new int2(CoarseSize, CoarseSize), Helper.ToInterleaved(ShiftsXPlus), ScoresXPlus, (uint)(NParticles * NTilts)); GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), ParticleCTFs.GetDevice(Intent.Read), ParticleWeights.GetDevice(Intent.Read), new int2(CoarseSize, CoarseSize), Helper.ToInterleaved(ShiftsXMinus), ScoresXMinus, (uint)(NParticles * NTilts)); GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), ParticleCTFs.GetDevice(Intent.Read), ParticleWeights.GetDevice(Intent.Read), new int2(CoarseSize, CoarseSize), Helper.ToInterleaved(ShiftsYPlus), ScoresYPlus, (uint)(NParticles * NTilts)); GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), ParticleCTFs.GetDevice(Intent.Read), ParticleWeights.GetDevice(Intent.Read), new int2(CoarseSize, CoarseSize), Helper.ToInterleaved(ShiftsYMinus), ScoresYMinus, (uint)(NParticles * NTilts)); Projections.Dispose(); for (int i = 0; i < ImageShiftGradients.Length; i++) { ImageShiftGradients[i] = new float2((ScoresXPlus[i] - ScoresXMinus[i]) / Delta2, (ScoresYPlus[i] - ScoresYMinus[i]) / Delta2); } } #endregion // First, do particle parameters, i. e. 3D position within tomogram, rotation, across 2 points in time // Altering each particle's parameters results in a change in its NTilts images, but nothing else { int[] TranslationIDs = DoPerParticleMotion ? new[] { 0, 1, 2, 3, 4, 5 } : new[] { 0, 1, 2 }; int[] RotationIDs = DoPerParticleMotion ? new [] {6, 7, 8, 9, 10, 11} : new [] { 6, 7, 8}; foreach (var paramID in RotationIDs) { double[] InputMinus = new double[input.Length], InputPlus = new double[input.Length]; for (int i = 0; i < input.Length; i++) { InputMinus[i] = input[i]; InputPlus[i] = input[i]; } for (int p = 0; p < NParticles; p++) { InputMinus[NVectorGridParams + p * 12 + paramID] -= Delta; InputPlus[NVectorGridParams + p * 12 + paramID] += Delta; } double[] ResultParticles = GradientParticles(InputMinus, InputPlus, Delta); for (int p = 0; p < NParticles; p++) { double ParticleSum = 0; for (int t = 0; t < NTilts; t++) ParticleSum += ResultParticles[p * NTilts + t]; Result[NVectorGridParams + p * 12 + paramID] = ParticleSum; } } // Translation-related gradients can all be computed efficiently from previously retrieved per-image gradients foreach (var paramID in TranslationIDs) { double[] InputMinus = new double[input.Length], InputPlus = new double[input.Length]; for (int i = 0; i < input.Length; i++) { InputMinus[i] = input[i]; InputPlus[i] = input[i]; } for (int p = 0; p < NParticles; p++) { InputMinus[NVectorGridParams + p * 12 + paramID] -= Delta; InputPlus[NVectorGridParams + p * 12 + paramID] += Delta; } float2[] ImageShiftsPlus = GetImageShifts(InputPlus); float2[] ImageShiftsMinus = GetImageShifts(InputMinus); for (int p = 0; p < NParticles; p++) { double ParticleSum = 0; for (int t = 0; t < NTilts; t++) { int i = p * NTilts + t; float2 ShiftDelta = (ImageShiftsPlus[i] - ImageShiftsMinus[i]) / Delta2; float ShiftGradient = ShiftDelta.X * ImageShiftGradients[i].X + ShiftDelta.Y * ImageShiftGradients[i].Y; ParticleSum += ShiftGradient; } Result[NVectorGridParams + p * 12 + paramID] = ParticleSum; } } // If there is no per-particle motion, just copy the gradients for these parameters from parameterIDs 0-5 if (!DoPerParticleMotion) { int[] RedundantIDs = { 3, 4, 5, 9, 10, 11 }; foreach (var paramID in RedundantIDs) for (int p = 0; p < NParticles; p++) Result[NVectorGridParams + p * 12 + paramID] = Result[NVectorGridParams + p * 12 + paramID - 3]; } } // Now deal with grids. Each grid slice (i. e. temporal point) will correspond to one tilt only, thus the gradient // for each slice is the (weighted, in case of spatial resolution) sum of NParticles images in the corresponding tilt. if (DoImageAlignment) { int[] RotationGridIDs = { 2, 3, 4 }; foreach (var gridID in RotationGridIDs) { int SliceElements = GridSliceElements[gridID]; for (int se = 0; se < SliceElements; se++) { double[] InputMinus = new double[input.Length], InputPlus = new double[input.Length]; for (int i = 0; i < input.Length; i++) { InputMinus[i] = input[i]; InputPlus[i] = input[i]; } for (int gp = VectorGridRanges[gridID].Item1 + se; gp < VectorGridRanges[gridID].Item2; gp += SliceElements) { InputMinus[gp] -= Delta; InputPlus[gp] += Delta; } double[] ResultParticles = GradientParticles(InputMinus, InputPlus, Delta); for (int i = 0; i < ResultParticles.Length; i++) { int GridTime = i % NTilts; Result[VectorGridRanges[gridID].Item1 + GridTime * SliceElements + se] += ResultParticles[i]; } } } // Translation-related gradients can all be computed efficiently from previously retrieved per-image gradients int[] TranslationGridIDs = { 0, 1 }; foreach (var gridID in TranslationGridIDs) { int SliceElements = GridSliceElements[gridID]; for (int se = 0; se < SliceElements; se++) { double[] InputMinus = new double[input.Length], InputPlus = new double[input.Length]; for (int i = 0; i < input.Length; i++) { InputMinus[i] = input[i]; InputPlus[i] = input[i]; } for (int gp = VectorGridRanges[gridID].Item1 + se; gp < VectorGridRanges[gridID].Item2; gp += SliceElements) { InputMinus[gp] -= Delta; InputPlus[gp] += Delta; } float2[] ImageShiftsPlus = GetImageShifts(InputPlus); float2[] ImageShiftsMinus = GetImageShifts(InputMinus); for (int i = 0; i < ImageShiftsPlus.Length; i++) { float2 ShiftDelta = (ImageShiftsPlus[i] - ImageShiftsMinus[i]) / Delta2; float ShiftGradient = ShiftDelta.X * ImageShiftGradients[i].X + ShiftDelta.Y * ImageShiftGradients[i].Y; int GridSlice = i % NTilts; Result[VectorGridRanges[gridID].Item1 + GridSlice * SliceElements + se] += ShiftGradient; } } } // Warp grids don't have any shortcuts for getting multiple gradients at once, so they use pre-calculated wiggle weights foreach (var gridID in WarpGridIDs) { int NElements = GridElements[gridID]; for (int ge = 0; ge < NElements; ge++) { float2[] Weights = WiggleWeightsWarp[gridID][ge]; for (int i = 0; i < Weights.Length; i++) { float2 ShiftDelta = Weights[i]; float ShiftGradient = ShiftDelta.X * ImageShiftGradients[i].X + ShiftDelta.Y * ImageShiftGradients[i].Y; Result[VectorGridRanges[gridID].Item1 + ge] += ShiftGradient; } } } } return Result; }; } #endregion BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Gradient); Optimizer.Epsilon = 3e-7; Optimizer.Maximize(StartParams); float3[] OptimizedOrigins, OptimizedOrigins2, OptimizedAngles, OptimizedAngles2; GetParametersFromVector(StartParams, NParticles, size, out OptimizedOrigins, out OptimizedOrigins2, out OptimizedAngles, out OptimizedAngles2); SetGridsFromVector(StartParams, Dimensions.X); #region Calculate correlation scores, update table with new positions and angles { double[] ImageScores = EvalIndividual(StartParams); float[] ParticleScores = new float[NParticles]; for (int i = 0; i < ImageScores.Length; i++) ParticleScores[i / NTilts] += (float)ImageScores[i]; //if (!tableIn.HasColumn("rlnOriginXPrior")) // tableIn.AddColumn("rlnOriginXPrior"); //if (!tableIn.HasColumn("rlnOriginYPrior")) // tableIn.AddColumn("rlnOriginYPrior"); //if (!tableIn.HasColumn("rlnOriginZPrior")) // tableIn.AddColumn("rlnOriginZPrior"); //if (!tableIn.HasColumn("rlnAngleRotPrior")) // tableIn.AddColumn("rlnAngleRotPrior"); //if (!tableIn.HasColumn("rlnAngleTiltPrior")) // tableIn.AddColumn("rlnAngleTiltPrior"); //if (!tableIn.HasColumn("rlnAnglePsiPrior")) // tableIn.AddColumn("rlnAnglePsiPrior"); lock (tableIn) for (int p = 0; p < NParticles; p++) { int Row = RowIndices[SubsetContinuousIDs[p]]; tableIn.SetRowValue(Row, "rlnCoordinateX", OptimizedOrigins[p].X.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(Row, "rlnCoordinateY", OptimizedOrigins[p].Y.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(Row, "rlnCoordinateZ", OptimizedOrigins[p].Z.ToString(CultureInfo.InvariantCulture)); //tableIn.SetRowValue(Row, "rlnOriginXPrior", OptimizedOrigins2[p].X.ToString(CultureInfo.InvariantCulture)); //tableIn.SetRowValue(Row, "rlnOriginYPrior", OptimizedOrigins2[p].Y.ToString(CultureInfo.InvariantCulture)); //tableIn.SetRowValue(Row, "rlnOriginZPrior", OptimizedOrigins2[p].Z.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(Row, "rlnAngleRot", OptimizedAngles[p].X.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(Row, "rlnAngleTilt", OptimizedAngles[p].Y.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(Row, "rlnAnglePsi", OptimizedAngles[p].Z.ToString(CultureInfo.InvariantCulture)); //tableIn.SetRowValue(Row, "rlnAngleRotPrior", OptimizedAngles2[p].X.ToString(CultureInfo.InvariantCulture)); //tableIn.SetRowValue(Row, "rlnAngleTiltPrior", OptimizedAngles2[p].Y.ToString(CultureInfo.InvariantCulture)); //tableIn.SetRowValue(Row, "rlnAnglePsiPrior", OptimizedAngles2[p].Z.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(Row, "rlnParticleSelectZScore", ParticleScores[p].ToString(CultureInfo.InvariantCulture)); } } #endregion ParticleImages?.Dispose(); ParticleCTFs?.Dispose(); ParticleWeights?.Dispose(); ShiftFactors?.Dispose(); #region Extract particles at full resolution and back-project them into the reconstruction volumes { GPU.SetDevice(0); Image CTFCoords = GetCTFCoords(size, size); int[] SortedDosePrecalc = IndicesSortedDose; foreach (var subsetRange in SubsetRanges) { lock (outReconstructions[subsetRange.Key]) { for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++) { float3[] PerTiltPositions = new float3[NTilts]; float3[] PerTiltAngles = new float3[NTilts]; float3 CoordsDiff = OptimizedOrigins2[p] - OptimizedOrigins[p]; float3 AnglesDiff = OptimizedAngles2[p] - OptimizedAngles[p]; for (int t = 0; t < NTilts; t++) { float DoseID = SortedDosePrecalc[t] / (float)(NTilts - 1); PerTiltPositions[t] = OptimizedOrigins[p] + CoordsDiff * DoseID; PerTiltAngles[t] = OptimizedAngles[p] + AnglesDiff * DoseID; } Image FullParticleImages = GetSubtomoImages(tiltStack, size, PerTiltPositions, true); Image FullParticleCTFs = GetSubtomoCTFs(PerTiltPositions, CTFCoords); FullParticleImages.Multiply(FullParticleCTFs); FullParticleCTFs.Abs(); float3[] FullParticleAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles); outReconstructions[subsetRange.Key].BackProject(FullParticleImages, FullParticleCTFs, FullParticleAngles); FullParticleImages.Dispose(); FullParticleCTFs.Dispose(); } for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++) { float3[] PerTiltPositions = new float3[NTilts]; float3[] PerTiltAngles = new float3[NTilts]; float3 CoordsDiff = OptimizedOrigins2[p] - OptimizedOrigins[p]; float3 AnglesDiff = OptimizedAngles2[p] - OptimizedAngles[p]; for (int t = 0; t < NTilts; t++) { float DoseID = SortedDosePrecalc[t] / (float)(NTilts - 1); PerTiltPositions[t] = OptimizedOrigins[p] + CoordsDiff * DoseID; PerTiltAngles[t] = OptimizedAngles[p] + AnglesDiff * DoseID; } float3[] FullParticleAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles); Image FullParticleCTFs = GetSubtomoCTFs(PerTiltPositions, CTFCoords, false); Image FullParticleCTFWeights = GetSubtomoCTFs(PerTiltPositions, CTFCoords, true); // CTF has to be converted to complex numbers with imag = 0 float2[] CTFsComplexData = new float2[FullParticleCTFs.ElementsComplex]; float[] CTFWeightsData = new float[FullParticleCTFs.ElementsComplex]; float[] CTFsContinuousData = FullParticleCTFs.GetHostContinuousCopy(); float[] CTFWeightsContinuousData = FullParticleCTFWeights.GetHostContinuousCopy(); for (int i = 0; i < CTFsComplexData.Length; i++) { CTFsComplexData[i] = new float2(Math.Abs(CTFsContinuousData[i] * CTFWeightsContinuousData[i]), 0); CTFWeightsData[i] = Math.Abs(CTFWeightsContinuousData[i]); } Image CTFsComplex = new Image(CTFsComplexData, FullParticleCTFs.Dims, true); Image CTFWeights = new Image(CTFWeightsData, FullParticleCTFs.Dims, true); outCTFReconstructions[subsetRange.Key].BackProject(CTFsComplex, CTFWeights, FullParticleAngles); FullParticleCTFs.Dispose(); FullParticleCTFWeights.Dispose(); CTFsComplex.Dispose(); CTFWeights.Dispose(); } outReconstructions[subsetRange.Key].FreeDevice(); outCTFReconstructions[subsetRange.Key].FreeDevice(); } } CTFCoords.Dispose(); } #endregion SaveMeta(); }
public void AddToPerAngleReconstructions(Star tableIn, Image tiltStack, int size, int3 volumeDimensions, Dictionary<int, Projector[]> perAngleReconstructions, Dictionary<int, Projector[]> perAngleWeights) { VolumeDimensions = volumeDimensions; #region Get rows from table 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); if (RowIndices.Count == 0) return; int NParticles = RowIndices.Count; #endregion #region Make sure all columns and directories are there if (!Directory.Exists(WeightOptimizationDir)) Directory.CreateDirectory(WeightOptimizationDir); #endregion #region Get subtomo positions from table float3[] ParticleOrigins = new float3[NParticles]; float3[] ParticleOrigins2 = new float3[NParticles]; float3[] ParticleAngles = new float3[NParticles]; float3[] ParticleAngles2 = new float3[NParticles]; int[] ParticleSubset = new int[NParticles]; { string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ"); string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi"); string[] ColumnSubset = tableIn.GetColumn("rlnRandomSubset"); string[] ColumnPosX2 = tableIn.GetColumn("rlnOriginXPrior"); string[] ColumnPosY2 = tableIn.GetColumn("rlnOriginYPrior"); string[] ColumnPosZ2 = tableIn.GetColumn("rlnOriginZPrior"); string[] ColumnAngleRot2 = tableIn.GetColumn("rlnAngleRotPrior"); string[] ColumnAngleTilt2 = tableIn.GetColumn("rlnAngleTiltPrior"); string[] ColumnAnglePsi2 = tableIn.GetColumn("rlnAnglePsiPrior"); for (int i = 0; i < NParticles; i++) { float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Pos2 = Pos; if (ColumnPosX2 != null && ColumnPosY2 != null && ColumnPosZ2 != null) Pos2 = new float3(float.Parse(ColumnPosX2[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY2[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosZ2[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleOrigins[i] = Pos - Shift; ParticleOrigins2[i] = Pos2 - Shift; float3 Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Angle2 = Angle; if (ColumnAngleRot2 != null && ColumnAngleTilt2 != null && ColumnAnglePsi2 != null) Angle2 = new float3(float.Parse(ColumnAngleRot2[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAngleTilt2[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAnglePsi2[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleAngles[i] = Angle; ParticleAngles2[i] = Angle2; ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]); } } #endregion List<int> SubsetIDs = new List<int>(); foreach (var i in ParticleSubset) if (!SubsetIDs.Contains(i)) SubsetIDs.Add(i); SubsetIDs.Sort(); SubsetIDs.Remove(1); SubsetIDs.Remove(2); foreach (int subsetID in SubsetIDs) { for (int t = 0; t < NTilts; t++) { int AngleID = t; lock (perAngleReconstructions[subsetID][t]) { AddToReconstructionOneAngle(tiltStack, subsetID, size, ParticleOrigins, ParticleOrigins2, ParticleAngles, ParticleAngles2, ParticleSubset, AngleID, perAngleReconstructions[subsetID][t], perAngleWeights[subsetID][t]); perAngleReconstructions[subsetID][t].FreeDevice(); perAngleWeights[subsetID][t].FreeDevice(); } } } }
public void ProcessParticleShift(MapHeader originalHeader, Image originalStack, Star stardata, Image refft, Image maskft, int dimbox, decimal scaleFactor) { // Deal with dimensions and grids. int NFrames = originalHeader.Dimensions.Z; int2 DimsImage = new int2(originalHeader.Dimensions); int2 DimsRegion = new int2(dimbox, dimbox); decimal SubdivisionRatio = 4M; List<int3> PyramidSizes = new List<int3>(); PyramidSizes.Add(new int3(MainWindow.Options.GridMoveX, MainWindow.Options.GridMoveX, Math.Min(NFrames, MainWindow.Options.GridMoveZ))); while (true) { int3 Previous = PyramidSizes.Last(); int NewZ = Math.Min((int)Math.Round(Previous.Z / SubdivisionRatio), Previous.Z - 1); if (NewZ < 2) break; PyramidSizes.Add(new int3(Previous.X * 2, Previous.Y * 2, NewZ)); } PyramidShiftX.Clear(); PyramidShiftY.Clear(); float3[] PositionsGrid, PositionsGridPerFrame; float2[] PositionsExtraction, PositionsShift; float3[] ParticleAngles; List<int> RowIndices = new List<int>(); { string[] ColumnNames = stardata.GetColumn("rlnMicrographName"); for (int i = 0; i < ColumnNames.Length; i++) if (ColumnNames[i].Contains(RootName)) RowIndices.Add(i); string[] ColumnOriginX = stardata.GetColumn("rlnCoordinateX"); string[] ColumnOriginY = stardata.GetColumn("rlnCoordinateY"); string[] ColumnShiftX = stardata.GetColumn("rlnOriginX"); string[] ColumnShiftY = stardata.GetColumn("rlnOriginY"); string[] ColumnAngleRot = stardata.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = stardata.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = stardata.GetColumn("rlnAnglePsi"); PositionsGrid = new float3[RowIndices.Count]; PositionsGridPerFrame = new float3[RowIndices.Count * NFrames]; PositionsExtraction = new float2[RowIndices.Count]; PositionsShift = new float2[RowIndices.Count * NFrames]; ParticleAngles = new float3[RowIndices.Count]; { int i = 0; foreach (var nameIndex in RowIndices) { float OriginX = float.Parse(ColumnOriginX[nameIndex]); float OriginY = float.Parse(ColumnOriginY[nameIndex]); float ShiftX = float.Parse(ColumnShiftX[nameIndex]); float ShiftY = float.Parse(ColumnShiftY[nameIndex]); PositionsExtraction[i] = new float2(OriginX - ShiftX, OriginY - ShiftY); PositionsGrid[i] = new float3((OriginX - ShiftX) / DimsImage.X, (OriginY - ShiftY) / DimsImage.Y, 0.5f); for (int z = 0; z < NFrames; z++) { PositionsGridPerFrame[z * RowIndices.Count + i] = new float3(PositionsGrid[i].X, PositionsGrid[i].Y, (float)z / (NFrames - 1)); PositionsShift[z * RowIndices.Count + i] = GetShiftFromPyramid(PositionsGridPerFrame[z * RowIndices.Count + i]); } ParticleAngles[i] = new float3(float.Parse(ColumnAngleRot[nameIndex]) * Helper.ToRad, float.Parse(ColumnAngleTilt[nameIndex]) * Helper.ToRad, float.Parse(ColumnAnglePsi[nameIndex]) * Helper.ToRad); i++; } } } int NPositions = PositionsGrid.Length; if (NPositions == 0) return; int MinFreqInclusive = (int)(MainWindow.Options.MovementRangeMin * DimsRegion.X / 2); int MaxFreqExclusive = (int)(MainWindow.Options.MovementRangeMax * DimsRegion.X / 2); int NFreq = MaxFreqExclusive - MinFreqInclusive; int CentralFrame = NFrames / 2; int MaskExpansions = 4; // Math.Max(1, PyramidSizes[0].Z / 3); int[] MaskSizes = new int[MaskExpansions]; // Allocate memory and create all prerequisites: int MaskLength; Image ShiftFactors; Image Phases; Image Projections; Image Shifts; Image InvSigma; { List<long> Positions = new List<long>(); List<float2> Factors = new List<float2>(); List<float2> Freq = new List<float2>(); int Min2 = MinFreqInclusive * MinFreqInclusive; int Max2 = MaxFreqExclusive * MaxFreqExclusive; for (int y = 0; y < DimsRegion.Y; y++) { int yy = y - DimsRegion.X / 2; for (int x = 0; x < DimsRegion.X / 2 + 1; x++) { int xx = x - DimsRegion.X / 2; int r2 = xx * xx + yy * yy; if (r2 >= Min2 && r2 < Max2) { Positions.Add(y * (DimsRegion.X / 2 + 1) + x); Factors.Add(new float2((float)xx / DimsRegion.X * 2f * (float)Math.PI, (float)yy / DimsRegion.X * 2f * (float)Math.PI)); float Angle = (float)Math.Atan2(yy, xx); float r = (float)Math.Sqrt(r2); Freq.Add(new float2(r, Angle)); } } } // Addresses for CTF simulation Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true); { float2[] CoordsData = new float2[CTFCoordsCart.ElementsSliceComplex]; Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) => CoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, a)); CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData }); CTFCoordsCart.RemapToFT(); } float[] ValuesDefocus = GridCTF.GetInterpolatedNative(PositionsGrid); CTFStruct[] PositionsCTF = ValuesDefocus.Select(v => { CTF Altered = CTF.GetCopy(); Altered.PixelSizeDelta = 0; Altered.Defocus = (decimal)v; //Altered.Bfactor = -MainWindow.Options.MovementBfactor; return Altered.ToStruct(); }).ToArray(); // Sort everyone with ascending distance from center. List<KeyValuePair<float, int>> FreqIndices = Freq.Select((v, i) => new KeyValuePair<float, int>(v.X, i)).ToList(); FreqIndices.Sort((a, b) => a.Key.CompareTo(b.Key)); int[] SortedIndices = FreqIndices.Select(v => v.Value).ToArray(); Helper.Reorder(Positions, SortedIndices); Helper.Reorder(Factors, SortedIndices); Helper.Reorder(Freq, SortedIndices); long[] RelevantMask = Positions.ToArray(); ShiftFactors = new Image(Helper.ToInterleaved(Factors.ToArray())); MaskLength = RelevantMask.Length; // Get mask sizes for different expansion steps. for (int i = 0; i < MaskExpansions; i++) { float CurrentMaxFreq = MinFreqInclusive + (MaxFreqExclusive - MinFreqInclusive) / (float)MaskExpansions * (i + 1); MaskSizes[i] = Freq.Count(v => v.X * v.X < CurrentMaxFreq * CurrentMaxFreq); } Phases = new Image(IntPtr.Zero, new int3(MaskLength, NPositions, NFrames), false, true, false); Projections = new Image(IntPtr.Zero, new int3(MaskLength, NPositions, NFrames), false, true, false); InvSigma = new Image(IntPtr.Zero, new int3(MaskLength, 1, 1)); Image ParticleMasksFT = maskft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); Image ParticleMasks = ParticleMasksFT.AsIFFT(); ParticleMasksFT.Dispose(); ParticleMasks.RemapFromFT(); Parallel.ForEach(ParticleMasks.GetHost(Intent.ReadWrite), slice => { for (int i = 0; i < slice.Length; i++) slice[i] = (Math.Max(2f, Math.Min(25f, slice[i])) - 2) / 23f; }); Image ProjectionsSparse = refft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); Image InvSigmaSparse = new Image(new int3(DimsRegion), true); { int GroupNumber = int.Parse(stardata.GetRowValue(RowIndices[0], "rlnGroupNumber")); //Star SigmaTable = new Star("D:\\rado27\\RefineWarppolish\\run1_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 = InvSigmaSparse.GetHost(Intent.Write)[0]; Helper.ForEachElementFT(new int2(DimsRegion.X, DimsRegion.Y), (x, y, xx, yy, r, angle) => { int ir = (int)r; float val = 0; if (ir < SigmaValues.Length) { if (SigmaValues[ir] != 0f) val = 1f / SigmaValues[ir]; } Sigma2NoiseData[y * (DimsRegion.X / 2 + 1) + x] = val; }); float MaxSigma = MathHelper.Max(Sigma2NoiseData); for (int i = 0; i < Sigma2NoiseData.Length; i++) Sigma2NoiseData[i] /= MaxSigma; InvSigmaSparse.RemapToFT(); } //InvSigmaSparse.WriteMRC("d_sigma2noise.mrc"); float PixelSize = (float)CTF.PixelSize; float PixelDelta = (float)CTF.PixelSizeDelta; float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad; GPU.CreateParticleShift(originalStack.GetDevice(Intent.Read), DimsImage, NFrames, Helper.ToInterleaved(PositionsExtraction), Helper.ToInterleaved(PositionsShift), NPositions, DimsRegion, RelevantMask, (uint)RelevantMask.Length, ParticleMasks.GetDevice(Intent.Read), ProjectionsSparse.GetDevice(Intent.Read), PositionsCTF, CTFCoordsCart.GetDevice(Intent.Read), InvSigmaSparse.GetDevice(Intent.Read), PixelSize + PixelDelta / 2, PixelSize - PixelDelta / 2, PixelAngle, Phases.GetDevice(Intent.Write), Projections.GetDevice(Intent.Write), InvSigma.GetDevice(Intent.Write)); InvSigmaSparse.Dispose(); ParticleMasks.Dispose(); ProjectionsSparse.Dispose(); CTFCoordsCart.Dispose(); originalStack.FreeDevice(); Shifts = new Image(new float[NPositions * NFrames * 2]); } #region Fit movement { int NPyramidPoints = 0; float[][][] WiggleWeights = new float[PyramidSizes.Count][][]; for (int p = 0; p < PyramidSizes.Count; p++) { CubicGrid WiggleGrid = new CubicGrid(PyramidSizes[p]); NPyramidPoints += (int)PyramidSizes[p].Elements(); WiggleWeights[p] = WiggleGrid.GetWiggleWeights(PositionsGridPerFrame); } double[] StartParams = new double[NPyramidPoints * 2]; for (int m = 3; m < MaskExpansions; m++) { for (int currentGrid = 0; currentGrid < PyramidSizes.Count; currentGrid++) { Action<double[]> SetPositions = input => { // Construct CubicGrids and get interpolated shift values. float[] AlteredX = new float[PositionsGridPerFrame.Length]; float[] AlteredY = new float[PositionsGridPerFrame.Length]; int Offset = 0; foreach (var size in PyramidSizes) { int Elements = (int)size.Elements(); CubicGrid GridX = new CubicGrid(size, input.Skip(Offset).Take(Elements).Select(v => (float)v).ToArray()); AlteredX = MathHelper.Plus(AlteredX, GridX.GetInterpolatedNative(PositionsGridPerFrame)); CubicGrid GridY = new CubicGrid(size, input.Skip(NPyramidPoints + Offset).Take(Elements).Select(v => (float)v).ToArray()); AlteredY = MathHelper.Plus(AlteredY, GridY.GetInterpolatedNative(PositionsGridPerFrame)); Offset += Elements; } // Finally, set the shift values in the device array. float[] ShiftData = Shifts.GetHost(Intent.Write)[0]; for (int i = 0; i < PositionsGridPerFrame.Length; i++) { ShiftData[i * 2] = AlteredX[i]; ShiftData[i * 2 + 1] = AlteredY[i]; } }; Func<double[], double> Eval = input => { SetPositions(input); float[] Diff = new float[NPositions * NFrames]; GPU.ParticleShiftGetDiff(Phases.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), InvSigma.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), Diff, (uint)NPositions, (uint)NFrames); //for (int i = 0; i < Diff.Length; i++) //Diff[i] = Diff[i] * 100f; double Score = Diff.Sum(); //Debug.WriteLine(Score); return Score; }; Func<double[], double[]> Grad = input => { SetPositions(input); float[] Diff = new float[NPositions * NFrames * 2]; GPU.ParticleShiftGetGrad(Phases.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), InvSigma.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), Diff, (uint)NPositions, (uint)NFrames); //for (int i = 0; i < Diff.Length; i++) //Diff[i] = Diff[i] * 100f; float[] DiffX = new float[NPositions * NFrames], DiffY = new float[NPositions * NFrames]; for (int i = 0; i < DiffX.Length; i++) { DiffX[i] = Diff[i * 2]; DiffY[i] = Diff[i * 2 + 1]; } double[] Result = new double[input.Length]; int Offset = 0; for (int p = 0; p < PyramidSizes.Count; p++) { //if (p == currentGrid) Parallel.For(0, (int)PyramidSizes[p].Elements(), i => { Result[Offset + i] = MathHelper.ReduceWeighted(DiffX, WiggleWeights[p][i]); Result[NPyramidPoints + Offset + i] = MathHelper.ReduceWeighted(DiffY, WiggleWeights[p][i]); }); Offset += (int)PyramidSizes[p].Elements(); } return Result; }; BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Grad); //Optimizer.Corrections = 20; Optimizer.Minimize(StartParams); } { PyramidShiftX.Clear(); PyramidShiftY.Clear(); int Offset = 0; foreach (var size in PyramidSizes) { int Elements = (int)size.Elements(); CubicGrid GridX = new CubicGrid(size, StartParams.Skip(Offset).Take(Elements).Select(v => (float)v).ToArray()); PyramidShiftX.Add(GridX); CubicGrid GridY = new CubicGrid(size, StartParams.Skip(NPyramidPoints + Offset).Take(Elements).Select(v => (float)v).ToArray()); PyramidShiftY.Add(GridY); Offset += Elements; } } } } #endregion ShiftFactors.Dispose(); Phases.Dispose(); Projections.Dispose(); Shifts.Dispose(); InvSigma.Dispose(); SaveMeta(); }
private void ButtonPolishParticles_OnClick(object sender, RoutedEventArgs e) { System.Windows.Forms.OpenFileDialog Dialog = new System.Windows.Forms.OpenFileDialog { Filter = "STAR Files|*.star", Multiselect = false }; System.Windows.Forms.DialogResult Result = Dialog.ShowDialog(); if (Result == System.Windows.Forms.DialogResult.OK) { System.Windows.Forms.SaveFileDialog SaveDialog = new System.Windows.Forms.SaveFileDialog { Filter = "STAR Files|*.star" }; System.Windows.Forms.DialogResult SaveResult = SaveDialog.ShowDialog(); if (SaveResult == System.Windows.Forms.DialogResult.OK) { Thread ProcessThread = new Thread(() => { Star TableIn = new Star(Dialog.FileName); if (TableIn.GetColumn("rlnCtfImage") == null) TableIn.AddColumn("rlnCtfImage"); string[] ColumnNames = TableIn.GetColumn("rlnMicrographName"); string[] ColumnCoordsX = TableIn.GetColumn("rlnCoordinateX"); string[] ColumnCoordsY = TableIn.GetColumn("rlnCoordinateY"); Star TableOut = new Star(TableIn.GetColumnNames()); Image ImageGain = null; if (!string.IsNullOrEmpty(Options.GainPath) && Options.CorrectGain) try { ImageGain = StageDataLoad.LoadMap(Options.GainPath, new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight), MainWindow.Options.InputDatOffset, ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType)); } catch { return; } foreach (var movie in Options.Movies) if (movie.DoProcess) { MapHeader OriginalHeader = null; Image OriginalStack = null; decimal ScaleFactor = 1M / (decimal)Math.Pow(2, (double)Options.PostBinTimes); PrepareHeaderAndMap(movie.Path, ImageGain, ScaleFactor, out OriginalHeader, out OriginalStack); //OriginalStack.WriteMRC("d_stack.mrc"); movie.UpdateStarDefocus(TableIn, ColumnNames, ColumnCoordsX, ColumnCoordsY); movie.ExportParticlesMovie(TableIn, TableOut, OriginalHeader, OriginalStack, Options.ExportParticleSize, Options.ExportParticleRadius, ScaleFactor); OriginalStack?.Dispose(); //Debug.WriteLine(movie.Path); TableOut.Save(SaveDialog.FileName); } TableOut.Save(SaveDialog.FileName); ImageGain?.Dispose(); }); ProcessThread.Start(); } } }
public void ExportSubtomos(Star tableIn, Image tiltStack, int size, int3 volumeDimensions) { VolumeDimensions = volumeDimensions; #region Get rows from table 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); //if (RowIndices.Count == 0) // return; int NParticles = RowIndices.Count; #endregion #region Make sure all columns and directories are there if (!tableIn.HasColumn("rlnImageName")) tableIn.AddColumn("rlnImageName"); if (!tableIn.HasColumn("rlnCtfImage")) tableIn.AddColumn("rlnCtfImage"); if (!Directory.Exists(ParticlesDir)) Directory.CreateDirectory(ParticlesDir); if (!Directory.Exists(ParticleCTFDir)) Directory.CreateDirectory(ParticleCTFDir); #endregion #region Get subtomo positions from table float3[] Origins = new float3[NParticles]; float3[] ParticleAngles = new float3[NParticles]; { string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ"); string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi"); for (int i = 0; i < NParticles; i++) { float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture)); //Origins[i] *= new float3(3838f / 959f, 3710f / 927f, 4f); Origins[i] = Pos - Shift; float3 Angle = new float3(0, 0, 0); if (ColumnAngleRot != null && ColumnAngleTilt != null && ColumnAnglePsi != null) Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleAngles[i] = Angle; tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", Origins[i].X.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", Origins[i].Y.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateZ", Origins[i].Z.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginZ", "0.0"); //tableIn.SetRowValue(RowIndices[i], "rlnAngleRot", "0.0"); //tableIn.SetRowValue(RowIndices[i], "rlnAngleTilt", "0.0"); //tableIn.SetRowValue(RowIndices[i], "rlnAnglePsi", "0.0"); } } #endregion tiltStack.FreeDevice(); /*int SizeCropped = 50;//size / 2; int3 Grid = (VolumeDimensions + SizeCropped - 1) / SizeCropped; List<float3> GridCoords = new List<float3>(); for (int z = 0; z < Grid.Z; z++) for (int y = 0; y < Grid.Y; y++) for (int x = 0; x < Grid.X; x++) GridCoords.Add(new float3(x * SizeCropped + SizeCropped / 2, y * SizeCropped + SizeCropped / 2, z * SizeCropped + SizeCropped / 2)); Origins = GridCoords.ToArray(); NParticles = Origins.Length;*/ if (NParticles == 0) return; Image CTFCoords = GetCTFCoords(size, size); int PlanForw, PlanBack, PlanForwCTF; Projector.GetPlans(new int3(size, size, size), 2, out PlanForw, out PlanBack, out PlanForwCTF); //Parallel.For(0, NParticles, new ParallelOptions() { MaxDegreeOfParallelism = 1 }, p => for (int p = 0; p < NParticles; p++) { lock (tableIn) { tableIn.SetRowValue(RowIndices[p], "rlnImageName", "particles/" + RootName + "_" + p.ToString("D5") + ".mrc"); tableIn.SetRowValue(RowIndices[p], "rlnCtfImage", "particlectf/" + RootName + "_" + p.ToString("D5") + ".mrc"); //tableIn.Save("D:\\rubisco\\luisexported.star"); } if (File.Exists(ParticlesDir + RootName + "_" + p.ToString("D5") + ".mrc")) return; Image Subtomo, SubtomoCTF; GetSubtomo(tiltStack, Origins[p], ParticleAngles[p], CTFCoords, out Subtomo, out SubtomoCTF, PlanForw, PlanBack, PlanForwCTF); //Image SubtomoCropped = Subtomo.AsPadded(new int3(SizeCropped, SizeCropped, SizeCropped)); Subtomo.WriteMRC(ParticlesDir + RootName + "_" + p.ToString("D5") + ".mrc"); SubtomoCTF.WriteMRC(ParticleCTFDir + RootName + "_" + p.ToString("D5") + ".mrc"); //SubtomoCropped.Dispose(); Subtomo?.Dispose(); SubtomoCTF?.Dispose(); }//); GPU.DestroyFFTPlan(PlanForw); GPU.DestroyFFTPlan(PlanBack); GPU.DestroyFFTPlan(PlanForwCTF); CTFCoords.Dispose(); }
public static float[] LoadFloat(string path, string name1 = null) { Star TableIn = new Star(path); return (name1 == null ? TableIn.GetColumn(0) : TableIn.GetColumn(name1)).Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray(); }
public void PerformComparison(MapHeader originalHeader, Star stardata, Image refft, Image maskft, decimal scaleFactor) { int NFrames = originalHeader.Dimensions.Z; int2 DimsImage = new int2(originalHeader.Dimensions); float3[] PositionsGrid; float3[] PositionsShift; float3[] ParticleAngles; List<int> RowIndices = new List<int>(); { string[] ColumnNames = stardata.GetColumn("rlnMicrographName"); for (int i = 0; i < ColumnNames.Length; i++) if (ColumnNames[i].Contains(RootName)) RowIndices.Add(i); string[] ColumnOriginX = stardata.GetColumn("rlnCoordinateX"); string[] ColumnOriginY = stardata.GetColumn("rlnCoordinateY"); string[] ColumnShiftX = stardata.GetColumn("rlnOriginX"); string[] ColumnShiftY = stardata.GetColumn("rlnOriginY"); string[] ColumnAngleRot = stardata.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = stardata.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = stardata.GetColumn("rlnAnglePsi"); PositionsGrid = new float3[RowIndices.Count]; PositionsShift = new float3[RowIndices.Count]; ParticleAngles = new float3[RowIndices.Count]; { int i = 0; foreach (var nameIndex in RowIndices) { float OriginX = float.Parse(ColumnOriginX[nameIndex]); float OriginY = float.Parse(ColumnOriginY[nameIndex]); float ShiftX = float.Parse(ColumnShiftX[nameIndex]); float ShiftY = float.Parse(ColumnShiftY[nameIndex]); PositionsGrid[i] = new float3((OriginX - ShiftX) / DimsImage.X, (OriginY - ShiftY) / DimsImage.Y, 0); PositionsShift[i] = new float3(ShiftX, ShiftY, 0f); ParticleAngles[i] = new float3(-float.Parse(ColumnAngleRot[nameIndex]) * Helper.ToRad, -float.Parse(ColumnAngleTilt[nameIndex]) * Helper.ToRad, -float.Parse(ColumnAnglePsi[nameIndex]) * Helper.ToRad); i++; } } } int NPositions = PositionsGrid.Length; if (NPositions == 0) return; Image Particles = StageDataLoad.LoadMap(ParticlesPath, new int2(1, 1), 0, typeof (float)); int2 DimsRegion = new int2(Particles.Dims.X, Particles.Dims.X); Particles.ShiftSlices(PositionsShift); int MinFreqInclusive = (int)(MainWindow.Options.MovementRangeMin * DimsRegion.X / 2); int MaxFreqExclusive = (int)(MainWindow.Options.MovementRangeMax * DimsRegion.X / 2); int NFreq = MaxFreqExclusive - MinFreqInclusive; Image ParticleMasksFT = maskft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); Image ParticleMasks = ParticleMasksFT.AsIFFT(); ParticleMasksFT.Dispose(); ParticleMasks.RemapFromFT(); Parallel.ForEach(ParticleMasks.GetHost(Intent.ReadWrite), slice => { for (int i = 0; i < slice.Length; i++) slice[i] = (Math.Max(2f, Math.Min(25f, slice[i])) - 2) / 23f; }); Image ProjectionsFT = refft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); Image Projections = ProjectionsFT.AsIFFT(); ProjectionsFT.Dispose(); // Addresses for CTF simulation Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true); { float2[] CoordsData = new float2[CTFCoordsCart.ElementsSliceComplex]; Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) => CoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, a)); CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData }); CTFCoordsCart.RemapToFT(); } float[] ValuesDefocus = GridCTF.GetInterpolatedNative(PositionsGrid); CTFStruct[] PositionsCTF = ValuesDefocus.Select(v => { CTF Altered = CTF.GetCopy(); Altered.Defocus = (decimal)v; //Altered.Bfactor = -MainWindow.Options.MovementBfactor; return Altered.ToStruct(); }).ToArray(); Image Scores = new Image(IntPtr.Zero, new int3(NPositions, 1, 1)); GPU.CompareParticles(Particles.GetDevice(Intent.Read), ParticleMasks.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), DimsRegion, CTFCoordsCart.GetDevice(Intent.Read), PositionsCTF, MinFreqInclusive, MaxFreqExclusive, Scores.GetDevice(Intent.Write), (uint)NPositions); float[] ScoresData = Scores.GetHost(Intent.Read)[0]; for (int p = 0; p < NPositions; p++) { stardata.SetRowValue(RowIndices[p], "rlnCtfFigureOfMerit", ScoresData[p].ToString(CultureInfo.InvariantCulture)); } Scores.Dispose(); Projections.Dispose(); ParticleMasks.Dispose(); CTFCoordsCart.Dispose(); Particles.Dispose(); }
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(); }
public void ExportParticles(Star tableIn, Star tableOut, MapHeader originalHeader, Image originalStack, int size, float particleradius, decimal scaleFactor) { if (!tableIn.HasColumn("rlnAutopickFigureOfMerit")) tableIn.AddColumn("rlnAutopickFigureOfMerit"); 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); if (RowIndices.Count == 0) return; if (!Directory.Exists(ParticlesDir)) Directory.CreateDirectory(ParticlesDir); if (!Directory.Exists(ParticleCTFDir)) Directory.CreateDirectory(ParticleCTFDir); int3 Dims = originalHeader.Dimensions; int3 DimsRegion = new int3(size, size, 1); int3 DimsPadded = new int3(size * 2, size * 2, 1); int NParticles = RowIndices.Count; float PixelSize = (float)CTF.PixelSize; float PixelDelta = (float)CTF.PixelSizeDelta; float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad; /*Image CTFCoords; Image CTFFreq; { float2[] CTFCoordsData = new float2[(DimsRegion.X / 2 + 1) * DimsRegion.Y]; float[] CTFFreqData = new float[(DimsRegion.X / 2 + 1) * DimsRegion.Y]; 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 / DimsRegion.X, angle); CTFFreqData[y * (DimsRegion.X / 2 + 1) + x] = r / CurrentPixelSize; } CTFCoords = new Image(CTFCoordsData, DimsRegion.Slice(), true); CTFFreq = new Image(CTFFreqData, DimsRegion.Slice(), true); }*/ string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); int3[] Origins = new int3[NParticles]; float3[] ResidualShifts = new float3[NParticles]; for (int i = 0; i < NParticles; i++) { float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture)) * 1.00f; float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture)) * 1.00f; Origins[i] = new int3((int)(Pos.X - Shift.X), (int)(Pos.Y - Shift.Y), 0); ResidualShifts[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X), -MathHelper.ResidualFraction(Pos.Y - Shift.Y), 0f); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", Origins[i].X.ToString()); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", Origins[i].Y.ToString()); tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0"); } 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(DimsPadded.X, DimsPadded.Y, NParticles)); float StepZ = 1f / Math.Max(Dims.Z - 1, 1); for (int z = 0; z < Dims.Z; z++) { float CoordZ = z * StepZ; if (originalStack != null) GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read), FrameParticles.GetDevice(Intent.Write), Dims.Slice(), DimsPadded, Helper.ToInterleaved(Origins.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()), (uint)NParticles); // Shift particles { float3[] Shifts = new float3[NParticles]; for (int i = 0; i < NParticles; i++) { float3 Coords = new float3((float)Origins[i].X / Dims.X, (float)Origins[i].Y / Dims.Y, CoordZ); Shifts[i] = ResidualShifts[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f; } 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. #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 * NParticles]; for (int p = 0; p < NParticles; p++) { float NormX = (float)Origins[p].X / Dims.X; float NormY = (float)Origins[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); } } 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(); }*/ #endregion // Apply CTF. #region CTF weighting /*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(Origins[p].X / Dims.X, Origins[p].Y / 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(); }*/ #endregion // Apply dose. #region 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(); }*/ #endregion //Image PSAbs = new Image(PS.GetDevice(Intent.Read), new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); //PSAbs.Abs(); //FrameParticlesFT.Multiply(PS); AverageFT.Add(FrameParticlesFT); //Weights.Add(PSAbs); //PS.Multiply(PS); //AveragePS.Add(PS); //PS.Dispose(); FrameParticlesFT.Dispose(); //PSAbs.Dispose(); } FrameParticles.Dispose(); //CTFCoords.Dispose(); //AverageFT.Divide(Weights); //AveragePS.Divide(Weights); //AverageFT.Multiply(AveragePS); Weights.Dispose(); Image AverageParticlesUncorrected = AverageFT.AsIFFT(); AverageFT.Dispose(); Image AverageParticles = AverageParticlesUncorrected.AsAnisotropyCorrected(new int2(DimsRegion), (float)(CTF.PixelSize + CTF.PixelSizeDelta / 2M), (float)(CTF.PixelSize - CTF.PixelSizeDelta / 2M), (float)CTF.PixelSizeAngle * Helper.ToRad, 8); AverageParticlesUncorrected.Dispose(); GPU.NormParticles(AverageParticles.GetDevice(Intent.Read), AverageParticles.GetDevice(Intent.Write), DimsRegion, (uint)(particleradius / (PixelSize / 1.00f)), true, (uint)NParticles); HeaderMRC ParticlesHeader = new HeaderMRC { Pixelsize = new float3(PixelSize, PixelSize, PixelSize) }; AverageParticles.WriteMRC(ParticlesPath, ParticlesHeader); AverageParticles.Dispose(); //AveragePS.WriteMRC(ParticleCTFPath, ParticlesHeader); AveragePS.Dispose(); float[] DistanceWeights = new float[NParticles]; for (int p1 = 0; p1 < NParticles - 1; p1++) { float2 Pos1 = new float2(Origins[p1].X, Origins[p1].Y); for (int p2 = p1 + 1; p2 < NParticles; p2++) { float2 Pos2 = new float2(Origins[p2].X, Origins[p2].Y); float2 Diff = Pos2 - Pos1; float Dist = Diff.X * Diff.X + Diff.Y * Diff.Y; Dist = 1f / Dist; DistanceWeights[p1] += Dist; DistanceWeights[p2] += Dist; } } for (int i = 0; i < NParticles; i++) { string ParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs"; tableIn.SetRowValue(RowIndices[i], "rlnImageName", ParticlePath); //string ParticleCTFsPath = (i + 1).ToString("D6") + "@particlectf/" + RootName + "_particlectf.mrcs"; //tableIn.SetRowValue(RowIndices[i], "rlnCtfImage", ParticleCTFsPath); tableIn.SetRowValue(RowIndices[i], "rlnAutopickFigureOfMerit", DistanceWeights[i].ToString(CultureInfo.InvariantCulture)); } }
public void UpdateStarDefocus(Star table, string[] columnNames, string[] columnCoordsX, string[] columnCoordsY) { List<int> NameIndices = new List<int>(); string InvariantRoot = RootName; for (int i = 0; i < columnNames.Length; i++) if (columnNames[i].Contains(InvariantRoot)) NameIndices.Add(i); //if (NameIndices.Count == 0) //Debug.WriteLine(RootName + ": " + NameIndices.Count); foreach (var nameIndex in NameIndices) { float CoordX = float.Parse(columnCoordsX[nameIndex], CultureInfo.InvariantCulture); float CoordY = float.Parse(columnCoordsY[nameIndex], CultureInfo.InvariantCulture); float LocalDefocus = GridCTF.GetInterpolated(new float3(CoordX / (Dimensions.X * 0.5f), CoordY / (Dimensions.Y * 0.5f), 4f / 37f)); table.SetRowValue(nameIndex, "rlnDefocusU", ((LocalDefocus + (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture)); table.SetRowValue(nameIndex, "rlnDefocusV", ((LocalDefocus - (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture)); table.SetRowValue(nameIndex, "rlnDefocusAngle", ((float)CTF.DefocusAngle).ToString(CultureInfo.InvariantCulture)); // Go from pixel size to magnification float Mag = (float)(MainWindow.Options.CTFDetectorPixel * 10000M / (CTF.PixelSize / 1.00M)); table.SetRowValue(nameIndex, "rlnMagnification", Mag.ToString(CultureInfo.InvariantCulture)); //table.SetRowValue(nameIndex, "rlnSphericalAberration", ((float)CTF.Cs).ToString(CultureInfo.InvariantCulture)); //float LocalPhaseShift = GridCTFPhase.GetInterpolated(new float3(0.5f, 0.5f, 4f / 37f)); //table.SetRowValue(nameIndex, "rlnPhaseShift", (LocalPhaseShift * 180f).ToString(CultureInfo.InvariantCulture)); } }
public void AlignTiltMovies(Star tableIn, int3 stackDimensions, int size, int3 volumeDimensions, Dictionary<int, Projector> references, float resolution) { Star TableSeries = new Star(DirectoryName + RootName + ".star"); Image SimulatedSeries = StageDataLoad.LoadMap("d_simulatedseries.mrc", new int2(1, 1), 0, typeof (float)); //Image SimulatedSeries = StageDataLoad.LoadMap(DirectoryName + RootName + ".ali", new int2(1, 1), 0, typeof(float)); Image AlignedSeries = new Image(SimulatedSeries.Dims); for (int t = 26; t < NTilts; t++) { Image TiltMovie = StageDataLoad.LoadMap(DirectoryName + TableSeries.GetRowValue(t, "wrpMovieName"), new int2(1, 1), 0, typeof (float)); Image Template = new Image(SimulatedSeries.GetHost(Intent.Read)[t], SimulatedSeries.Dims.Slice()); float MovieAngle = float.Parse(TableSeries.GetRowValue(t, "wrpAnglePsi"), CultureInfo.InvariantCulture); //float2 MovieShift = new float2(-float.Parse(TableSeries.GetRowValue(t, "wrpShiftX"), CultureInfo.InvariantCulture), // -float.Parse(TableSeries.GetRowValue(t, "wrpShiftY"), CultureInfo.InvariantCulture)); float2 MovieShift = new float2(5.64f, -21f); Image Aligned = AlignOneTiltMovie(TiltMovie, Template, MovieAngle, MovieShift, resolution); AlignedSeries.GetHost(Intent.Write)[t] = Aligned.GetHost(Intent.Read)[0]; Aligned.Dispose(); TiltMovie.Dispose(); Template.Dispose(); } SimulatedSeries.Dispose(); AlignedSeries.WriteMRC(DirectoryName + RootName + ".aligned"); AlignedSeries.Dispose(); }
public void MakePerTomogramReconstructions(Star tableIn, Image tiltStack, int size, int3 volumeDimensions) { VolumeDimensions = volumeDimensions; #region Get rows from table 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); if (RowIndices.Count == 0) return; int NParticles = RowIndices.Count; #endregion #region Make sure all columns and directories are there if (!Directory.Exists(WeightOptimizationDir)) Directory.CreateDirectory(WeightOptimizationDir); #endregion #region Get subtomo positions from table float3[] ParticleOrigins = new float3[NParticles]; float3[] ParticleOrigins2 = new float3[NParticles]; float3[] ParticleAngles = new float3[NParticles]; float3[] ParticleAngles2 = new float3[NParticles]; int[] ParticleSubset = new int[NParticles]; { string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ"); string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi"); string[] ColumnSubset = tableIn.GetColumn("rlnRandomSubset"); string[] ColumnPosX2 = tableIn.GetColumn("rlnOriginXPrior"); string[] ColumnPosY2 = tableIn.GetColumn("rlnOriginYPrior"); string[] ColumnPosZ2 = tableIn.GetColumn("rlnOriginZPrior"); string[] ColumnAngleRot2 = tableIn.GetColumn("rlnAngleRotPrior"); string[] ColumnAngleTilt2 = tableIn.GetColumn("rlnAngleTiltPrior"); string[] ColumnAnglePsi2 = tableIn.GetColumn("rlnAnglePsiPrior"); for (int i = 0; i < NParticles; i++) { float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Pos2 = Pos; if (ColumnPosX2 != null && ColumnPosY2 != null && ColumnPosZ2 != null) Pos2 = new float3(float.Parse(ColumnPosX2[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY2[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosZ2[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleOrigins[i] = Pos - Shift; ParticleOrigins2[i] = Pos2 - Shift; //ParticleOrigins[i] /= new float3(3838f / 959f, 3710f / 927f, 4f); float3 Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Angle2 = Angle; if (ColumnAngleRot2 != null && ColumnAngleTilt2 != null && ColumnAnglePsi2 != null) Angle2 = new float3(float.Parse(ColumnAngleRot2[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAngleTilt2[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAnglePsi2[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleAngles[i] = Angle; ParticleAngles2[i] = Angle2; ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]); } } #endregion List<int> SubsetIDs = new List<int>(); foreach (var i in ParticleSubset) if (!SubsetIDs.Contains(i)) SubsetIDs.Add(i); SubsetIDs.Sort(); for (int subset = 0; subset < SubsetIDs.Count; subset++) { if (File.Exists(WeightOptimizationDir + $"{RootName}_subset{SubsetIDs[subset]}.mrc")) continue; Tuple<Image, Image> Reconstruction = MakeReconstructionOneTomogram(tiltStack, SubsetIDs[subset], size, ParticleOrigins, ParticleOrigins2, ParticleAngles, ParticleAngles2, ParticleSubset); Reconstruction.Item1.WriteMRC(WeightOptimizationDir + $"{RootName}_subset{SubsetIDs[subset]}.mrc"); Reconstruction.Item1.Dispose(); Reconstruction.Item2.WriteMRC(WeightOptimizationDir + $"{RootName}_subset{SubsetIDs[subset]}.weight.mrc"); Reconstruction.Item2.Dispose(); } }
private void ButtonExportParticles_OnClick(object sender, RoutedEventArgs e) { System.Windows.Forms.OpenFileDialog Dialog = new System.Windows.Forms.OpenFileDialog { Filter = "STAR Files|*.star", Multiselect = false }; System.Windows.Forms.DialogResult Result = Dialog.ShowDialog(); if (Result == System.Windows.Forms.DialogResult.OK) { System.Windows.Forms.SaveFileDialog SaveDialog = new System.Windows.Forms.SaveFileDialog { Filter = "STAR Files|*.star" }; System.Windows.Forms.DialogResult SaveResult = SaveDialog.ShowDialog(); if (SaveResult == System.Windows.Forms.DialogResult.OK) { Thread ProcessThread = new Thread(() => { Star TableIn = new Star(Dialog.FileName); //if (TableIn.GetColumn("rlnCtfImage") == null) // TableIn.AddColumn("rlnCtfImage"); string[] ColumnNames = TableIn.GetColumn("rlnMicrographName"); string[] Excluded = Options.Movies.Where(m => m.Status == ProcessingStatus.Skip).Select(m => m.RootName).ToArray(); List<int> ForDelete = new List<int>(); for (int r = 0; r < TableIn.RowCount; r++) for (int ex = 0; ex < Excluded.Length; ex++) if (ColumnNames[r].Contains(Excluded[ex])) ForDelete.Add(r); TableIn.RemoveRows(ForDelete.ToArray()); ColumnNames = TableIn.GetColumn("rlnMicrographName"); string[] ColumnCoordsX = TableIn.GetColumn("rlnCoordinateX"); string[] ColumnCoordsY = TableIn.GetColumn("rlnCoordinateY"); Star TableOut = new Star(TableIn.GetColumnNames()); int MaxDevices = 999; int UsedDevices = Math.Min(MaxDevices, GPU.GetDeviceCount()); Queue<DeviceToken> Devices = new Queue<DeviceToken>(); for (int d = 0; d < UsedDevices; d++) Devices.Enqueue(new DeviceToken(d)); //for (int d = 0; d < UsedDevices; d++) // Devices.Enqueue(new DeviceToken(d)); int NTokens = Devices.Count; DeviceToken[] IOSync = new DeviceToken[UsedDevices]; for (int d = 0; d < UsedDevices; d++) IOSync[d] = new DeviceToken(d); Image[] ImageGain = new Image[UsedDevices]; if (!string.IsNullOrEmpty(Options.GainPath) && Options.CorrectGain && File.Exists(Options.GainPath)) for (int d = 0; d < UsedDevices; d++) try { GPU.SetDevice(d); ImageGain[d] = StageDataLoad.LoadMap(Options.GainPath, new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight), MainWindow.Options.InputDatOffset, ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType)); } catch { return; } //Dictionary<int, Projector>[] DeviceReferences = new Dictionary<int, Projector>[GPU.GetDeviceCount()]; //Dictionary<int, Projector>[] DeviceReconstructions = new Dictionary<int, Projector>[GPU.GetDeviceCount()]; //Dictionary<int, Projector>[] DeviceCTFReconstructions = new Dictionary<int, Projector>[GPU.GetDeviceCount()]; //for (int d = 0; d < GPU.GetDeviceCount(); d++) //{ // GPU.SetDevice(d); // Dictionary<int, Projector> References = new Dictionary<int, Projector>(); // { // Image Ref1 = StageDataLoad.LoadMap("F:\\badaben\\vlion123\\warp_ref1.mrc", new int2(1, 1), 0, typeof(float)); // Image Ref2 = StageDataLoad.LoadMap("F:\\badaben\\vlion123\\warp_ref2.mrc", new int2(1, 1), 0, typeof(float)); // Image Ref3 = StageDataLoad.LoadMap("F:\\badaben\\vlion123\\warp_ref3.mrc", new int2(1, 1), 0, typeof(float)); // Image Ref4 = StageDataLoad.LoadMap("F:\\badaben\\vlion123\\warp_ref4.mrc", new int2(1, 1), 0, typeof(float)); // //Image Ref5 = StageDataLoad.LoadMap("F:\\badaben\\vlion12\\warp_ref5.mrc", new int2(1, 1), 0, typeof(float)); // //Image Ref6 = StageDataLoad.LoadMap("F:\\badaben\\vlion12\\warp_ref6.mrc", new int2(1, 1), 0, typeof(float)); // //Image Ref1 = StageDataLoad.LoadMap("F:\\badaben\\chloro\\warp_ref1.mrc", new int2(1, 1), 0, typeof(float)); // //Image Ref2 = StageDataLoad.LoadMap("F:\\badaben\\chloro\\warp_ref2.mrc", new int2(1, 1), 0, typeof(float)); // //Image Ref3 = StageDataLoad.LoadMap("F:\\stefanribo\\vlion\\mini_warp_ref3.mrc", new int2(1, 1), 0, typeof(float)); // //Image Ref4 = StageDataLoad.LoadMap("F:\\stefanribo\\vlion\\mini_warp_ref4.mrc", new int2(1, 1), 0, typeof(float)); // References.Add(1, new Projector(Ref1, 2)); // References.Add(2, new Projector(Ref2, 2)); // References.Add(3, new Projector(Ref3, 2)); // References.Add(4, new Projector(Ref4, 2)); // //References.Add(5, new Projector(Ref5, 2)); // //References.Add(6, new Projector(Ref6, 2)); // //References.Add(3, new Projector(Ref3, 2)); // Ref1.Dispose(); // Ref2.Dispose(); // Ref3.Dispose(); // Ref4.Dispose(); // //Ref5.Dispose(); // //Ref6.Dispose(); // } // DeviceReferences[d] = References; // Dictionary<int, Projector> Reconstructions = new Dictionary<int, Projector>(); // foreach (var reference in References) // { // Reconstructions.Add(reference.Key, new Projector(reference.Value.Dims, reference.Value.Oversampling)); // Reconstructions[reference.Key].FreeDevice(); // } // DeviceReconstructions[d] = Reconstructions; // Dictionary<int, Projector> CTFReconstructions = new Dictionary<int, Projector>(); // foreach (var reference in References) // { // CTFReconstructions.Add(reference.Key, new Projector(reference.Value.Dims, reference.Value.Oversampling)); // CTFReconstructions[reference.Key].FreeDevice(); // } // DeviceCTFReconstructions[d] = CTFReconstructions; //} int NTilts = (int)MathHelper.Max(Options.Movies.Select(m => (float)((TiltSeries)m).NTilts)); Dictionary<int, Projector[]> PerAngleReconstructions = new Dictionary<int, Projector[]>(); Dictionary<int, Projector[]> PerAngleWeightReconstructions = new Dictionary<int, Projector[]>(); //{ // int[] ColumnSubset = TableIn.GetColumn("rlnRandomSubset").Select(s => int.Parse(s)).ToArray(); // List<int> SubsetIDs = new List<int>(); // foreach (var subset in ColumnSubset) // if (!SubsetIDs.Contains(subset)) // SubsetIDs.Add(subset); // SubsetIDs.Sort(); // SubsetIDs.Remove(1); // SubsetIDs.Remove(2); // int Size = Options.ExportParticleSize; // //foreach (var subsetID in SubsetIDs) // //{ // // PerAngleReconstructions.Add(subsetID, new Projector[NTilts]); // // PerAngleWeightReconstructions.Add(subsetID, new Projector[NTilts]); // // for (int t = 0; t < NTilts; t++) // // { // // PerAngleReconstructions[subsetID][t] = new Projector(new int3(Size, Size, Size), 2); // // PerAngleReconstructions[subsetID][t].FreeDevice(); // // PerAngleWeightReconstructions[subsetID][t] = new Projector(new int3(Size, Size, Size), 2); // // PerAngleWeightReconstructions[subsetID][t].FreeDevice(); // // } // //} //} foreach (var movie in Options.Movies) if (movie.DoProcess) { //if (((TiltSeries)movie).GlobalBfactor < -200) // continue; while (Devices.Count <= 0) Thread.Sleep(20); DeviceToken CurrentDevice; lock (Devices) CurrentDevice = Devices.Dequeue(); Thread DeviceThread = new Thread(() => { GPU.SetDevice(CurrentDevice.ID); MapHeader OriginalHeader = null; Image OriginalStack = null; decimal ScaleFactor = 1M / (decimal)Math.Pow(2, (double)Options.PostBinTimes); lock (IOSync[CurrentDevice.ID]) PrepareHeaderAndMap(movie.Path, ImageGain[CurrentDevice.ID], ScaleFactor, out OriginalHeader, out OriginalStack); if (movie.GetType() == typeof (Movie)) { movie.UpdateStarDefocus(TableIn, ColumnNames, ColumnCoordsX, ColumnCoordsY); //movie.ExportParticles(TableIn, TableOut, OriginalHeader, OriginalStack, Options.ExportParticleSize, Options.ExportParticleRadius, ScaleFactor); } else if (movie.GetType() == typeof (TiltSeries)) { //((TiltSeries)movie).ExportSubtomos(TableIn, OriginalStack, Options.ExportParticleSize, new int3(928, 928, 300)); //((TiltSeries)movie).ExportSubtomos(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3712, 3712, 1400)); //((TiltSeries)movie).Reconstruct(OriginalStack, 128, 3.42f * 4 * 2, new int3(3712, 3712, 1400)); /*for (int refinement = 0; refinement < 20; refinement++) {*/ //OriginalStack.FreeDevice(); //((TiltSeries)movie).PerformOptimizationStep(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3712, 3712, 1400), DeviceReferences[CurrentDevice.ID], 22f, DeviceReconstructions[0], DeviceCTFReconstructions[0]); //((TiltSeries)movie).RealspaceRefineGlobal(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3838, 3710, 1200), References, 30, 2, "D4", Reconstructions); //Image Simulated = ((TiltSeries)movie).SimulateTiltSeries(TableIn, OriginalStack.Dims, Options.ExportParticleSize, new int3(3712, 3712, 1200), References, 15); //Simulated.WriteMRC("d_simulatedseries.mrc"); //((TiltSeries)movie).AlignTiltMovies(TableIn, OriginalStack.Dims, Options.ExportParticleSize, new int3(3712, 3712, 1200), References, 100); /*TableIn.Save(SaveDialog.FileName + $".it{refinement:D2}.star"); }*/ //((TiltSeries)movie).ExportSubtomos(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3712, 3712, 1400)); //Image Reference = StageDataLoad.LoadMap("F:\\chloroplastribo\\vlion\\warp_ref3.mrc", new int2(1, 1), 0, typeof (float)); //((TiltSeries)movie).Correlate(OriginalStack, Reference, 128, 40, 400, new int3(3712, 3712, 1400), 2, "C1"); //Reference.Dispose(); //GPU.SetDevice(0); //((TiltSeries)movie).MakePerTomogramReconstructions(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3712, 3712, 1400)); //((TiltSeries)movie).AddToPerAngleReconstructions(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3710, 3710, 1400), PerAngleReconstructions, PerAngleWeightReconstructions); } OriginalStack?.Dispose(); //Debug.WriteLine(movie.Path); //TableIn.Save(SaveDialog.FileName); lock (Devices) Devices.Enqueue(CurrentDevice); Debug.WriteLine("Done: " + movie.RootName); }); DeviceThread.Start(); } while (Devices.Count != NTokens) Thread.Sleep(20); for (int d = 0; d < UsedDevices; d++) { ImageGain[d]?.Dispose(); } //for (int d = 0; d < DeviceReferences.Length; d++) //{ // GPU.SetDevice(d); // foreach (var reconstruction in DeviceReconstructions[d]) // { // if (d == 0) // { // Image ReconstructedMap = reconstruction.Value.Reconstruct(false); // //ReconstructedMap.WriteMRC($"F:\\chloroplastribo\\vlion\\warped_{reconstruction.Key}_nodeconv.mrc"); // Image ReconstructedCTF = DeviceCTFReconstructions[d][reconstruction.Key].Reconstruct(true); // Image ReconstructedMapFT = ReconstructedMap.AsFFT(true); // ReconstructedMap.Dispose(); // int Dim = ReconstructedMap.Dims.Y; // int DimFT = Dim / 2 + 1; // int R2 = Dim / 2 - 2; // R2 *= R2; // foreach (var slice in ReconstructedCTF.GetHost(Intent.ReadWrite)) // { // for (int y = 0; y < Dim; y++) // { // int yy = y < Dim / 2 + 1 ? y : y - Dim; // yy *= yy; // for (int x = 0; x < DimFT; x++) // { // int xx = x * x; // slice[y * DimFT + x] = xx + yy < R2 ? Math.Max(1e-2f, slice[y * DimFT + x]) : 1f; // } // } // } // ReconstructedMapFT.Divide(ReconstructedCTF); // ReconstructedMap = ReconstructedMapFT.AsIFFT(true); // ReconstructedMapFT.Dispose(); // //GPU.SphereMask(ReconstructedMap.GetDevice(Intent.Read), // // ReconstructedMap.GetDevice(Intent.Write), // // ReconstructedMap.Dims, // // (float)(ReconstructedMap.Dims.X / 2 - 8), // // 8, // // 1); // ReconstructedMap.WriteMRC($"F:\\badaben\\vlion123\\warped_{reconstruction.Key}.mrc"); // ReconstructedMap.Dispose(); // } // reconstruction.Value.Dispose(); // DeviceReferences[d][reconstruction.Key].Dispose(); // DeviceCTFReconstructions[d][reconstruction.Key].Dispose(); // } //} //string WeightOptimizationDir = ((TiltSeries)Options.Movies[0]).WeightOptimizationDir; //foreach (var subset in PerAngleReconstructions) //{ // for (int t = 0; t < NTilts; t++) // { // Image Reconstruction = PerAngleReconstructions[subset.Key][t].Reconstruct(false); // PerAngleReconstructions[subset.Key][t].Dispose(); // Reconstruction.WriteMRC(WeightOptimizationDir + $"subset{subset.Key}_tilt{t.ToString("D3")}.mrc"); // Reconstruction.Dispose(); // foreach (var slice in PerAngleWeightReconstructions[subset.Key][t].Weights.GetHost(Intent.ReadWrite)) // for (int i = 0; i < slice.Length; i++) // slice[i] = Math.Min(1, slice[i]); // Image WeightReconstruction = PerAngleWeightReconstructions[subset.Key][t].Reconstruct(true); // PerAngleWeightReconstructions[subset.Key][t].Dispose(); // WeightReconstruction.WriteMRC(WeightOptimizationDir + $"subset{subset.Key}_tilt{t.ToString("D3")}.weight.mrc"); // WeightReconstruction.Dispose(); // } //} TableIn.Save(SaveDialog.FileName); }); ProcessThread.Start(); } } }
public void PerformGlobalParticleAlignment(Star tableIn, Image tiltStack, int size, int3 volumeDimensions, Dictionary<int, Projector> references, float resolution, int healpixOrder, string symmetry, float offsetRange, float offsetStep, Dictionary<int, Projector> outReconstructions, Dictionary<int, Projector> outCTFReconstructions) { VolumeDimensions = volumeDimensions; #region Get rows from table 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); if (RowIndices.Count == 0) return; int NParticles = RowIndices.Count; #endregion #region Make sure all columns and directories are there if (!tableIn.HasColumn("rlnImageName")) tableIn.AddColumn("rlnImageName"); if (!tableIn.HasColumn("rlnCtfImage")) tableIn.AddColumn("rlnCtfImage"); if (!tableIn.HasColumn("rlnParticleSelectZScore")) tableIn.AddColumn("rlnParticleSelectZScore"); if (!Directory.Exists(ParticlesDir)) Directory.CreateDirectory(ParticlesDir); if (!Directory.Exists(ParticleCTFDir)) Directory.CreateDirectory(ParticleCTFDir); #endregion #region Get subtomo positions from table float3[] ParticleOrigins = new float3[NParticles]; float3[] ParticleOrigins2 = new float3[NParticles]; float3[] ParticleAngles = new float3[NParticles]; float3[] ParticleAngles2 = new float3[NParticles]; int[] ParticleSubset = new int[NParticles]; { string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ"); string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi"); string[] ColumnSubset = tableIn.GetColumn("rlnRandomSubset"); for (int i = 0; i < NParticles; i++) { float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Pos2 = Pos; float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture)); ParticleOrigins[i] = Pos - Shift; ParticleOrigins2[i] = Pos2 - Shift; float3 Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture)); float3 Angle2 = Angle; ParticleAngles[i] = Angle; ParticleAngles2[i] = Angle2; ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", ParticleOrigins[i].X.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", ParticleOrigins[i].Y.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateZ", ParticleOrigins[i].Z.ToString(CultureInfo.InvariantCulture)); tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginZ", "0.0"); } } #endregion #region Deal with subsets List<int> SubsetIDs = new List<int>(); foreach (var i in ParticleSubset) if (!SubsetIDs.Contains(i)) SubsetIDs.Add(i); SubsetIDs.Sort(); // For each subset, create a list of its particle IDs Dictionary<int, List<int>> SubsetParticleIDs = SubsetIDs.ToDictionary(subsetID => subsetID, subsetID => new List<int>()); for (int i = 0; i < ParticleSubset.Length; i++) SubsetParticleIDs[ParticleSubset[i]].Add(i); foreach (var list in SubsetParticleIDs.Values) list.Sort(); // Note where each subset starts and ends in a unified, sorted (by subset) particle ID list Dictionary<int, Tuple<int, int>> SubsetRanges = new Dictionary<int, Tuple<int, int>>(); { int Start = 0; foreach (var pair in SubsetParticleIDs) { SubsetRanges.Add(pair.Key, new Tuple<int, int>(Start, Start + pair.Value.Count)); Start += pair.Value.Count; } } List<int> SubsetContinuousIDs = new List<int>(); foreach (var pair in SubsetParticleIDs) SubsetContinuousIDs.AddRange(pair.Value); // Reorder particle information to match the order of SubsetContinuousIDs ParticleOrigins = SubsetContinuousIDs.Select(i => ParticleOrigins[i]).ToArray(); ParticleOrigins2 = SubsetContinuousIDs.Select(i => ParticleOrigins2[i]).ToArray(); ParticleAngles = SubsetContinuousIDs.Select(i => ParticleAngles[i]).ToArray(); ParticleAngles2 = SubsetContinuousIDs.Select(i => ParticleAngles2[i]).ToArray(); ParticleSubset = SubsetContinuousIDs.Select(i => ParticleSubset[i]).ToArray(); #endregion int CoarseSize = (int)Math.Round(size * ((float)CTF.PixelSize * 2 / resolution)) / 2 * 2; int3 CoarseDims = new int3(CoarseSize, CoarseSize, 1); // Positions the particles were extracted at/shifted to, to calculate effectively needed shifts later float2[] ExtractedAt = new float2[NParticles * NTilts]; // Extract images, mask and resize them, create CTFs Image ParticleImages = new Image(new int3(CoarseSize, CoarseSize, NParticles * NTilts), true, true); Image ParticleCTFs = new Image(new int3(CoarseSize, CoarseSize, NParticles * NTilts), true); Image ParticleWeights = null; Image ShiftFactors = null; #region Preflight float KeepBFac = GlobalBfactor; GlobalBfactor = 0; { Image CTFCoords = GetCTFCoords(CoarseSize, size); #region Precalculate vectors for shifts in Fourier space { float2[] ShiftFactorsData = new float2[(CoarseSize / 2 + 1) * CoarseSize]; for (int y = 0; y < CoarseSize; y++) for (int x = 0; x < CoarseSize / 2 + 1; x++) { int xx = x; int yy = y < CoarseSize / 2 + 1 ? y : y - CoarseSize; ShiftFactorsData[y * (CoarseSize / 2 + 1) + x] = new float2((float)-xx / size * 2f * (float)Math.PI, (float)-yy / size * 2f * (float)Math.PI); } ShiftFactors = new Image(ShiftFactorsData, new int3(CoarseSize, CoarseSize, 1), true); } #endregion #region Create mask with soft edge Image Mask; Image MaskSubt; { Image MaskBig = new Image(new int3(size, size, 1)); float MaskRadius = MainWindow.Options.ExportParticleRadius / (float)CTF.PixelSize; float SoftEdge = 16f; float[] MaskBigData = MaskBig.GetHost(Intent.Write)[0]; for (int y = 0; y < size; y++) { int yy = y - size / 2; yy *= yy; for (int x = 0; x < size; x++) { int xx = x - size / 2; xx *= xx; float R = (float)Math.Sqrt(xx + yy); if (R <= MaskRadius) MaskBigData[y * size + x] = 1; else MaskBigData[y * size + x] = (float)(Math.Cos(Math.Min(1, (R - MaskRadius) / SoftEdge) * Math.PI) * 0.5 + 0.5); } } //MaskBig.WriteMRC("d_maskbig.mrc"); Mask = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize)); Mask.RemapToFT(); MaskBigData = MaskBig.GetHost(Intent.Write)[0]; for (int y = 0; y < size; y++) { int yy = y - size / 2; yy *= yy; for (int x = 0; x < size; x++) { int xx = x - size / 2; xx *= xx; float R = (float)Math.Sqrt(xx + yy); if (R <= 30) MaskBigData[y * size + x] = 1; else MaskBigData[y * size + x] = 0; } } MaskSubt = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize)); MaskSubt.RemapToFT(); MaskBig.Dispose(); } //Mask.WriteMRC("d_masksmall.mrc"); #endregion #region Create Fourier space mask Image FourierMask = new Image(CoarseDims, true); { float[] FourierMaskData = FourierMask.GetHost(Intent.Write)[0]; int MaxR2 = CoarseSize * CoarseSize / 4; for (int y = 0; y < CoarseSize; y++) { int yy = y < CoarseSize / 2 + 1 ? y : y - CoarseSize; yy *= yy; for (int x = 0; x < CoarseSize / 2 + 1; x++) { int xx = x * x; int R2 = yy + xx; FourierMaskData[y * (CoarseSize / 2 + 1) + x] = R2 < MaxR2 ? 1 : 0; } } } #endregion #region For each particle, create CTFs and extract & preprocess images for entire tilt series for (int p = 0; p < NParticles; p++) { float3 ParticleCoords = ParticleOrigins[p]; float3[] Positions = GetPositionInImages(ParticleCoords); float3[] ProjAngles = GetParticleAngleInImages(ParticleCoords, ParticleAngles[p]); Image Extracted = new Image(new int3(size, size, NTilts)); float[][] ExtractedData = Extracted.GetHost(Intent.Write); float3[] Residuals = new float3[NTilts]; Image SubtrahendsCTF = new Image(new int3(CoarseSize, CoarseSize, NTilts), true); // Create CTFs { CTFStruct[] CTFParams = new CTFStruct[NTilts]; float GridStep = 1f / (NTilts - 1); CTFStruct[] Params = new CTFStruct[NTilts]; for (int t = 0; t < NTilts; t++) { decimal Defocus = (decimal)Positions[t].Z; decimal DefocusDelta = (decimal)GridCTFDefocusDelta.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); decimal DefocusAngle = (decimal)GridCTFDefocusAngle.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep)); CTF CurrCTF = CTF.GetCopy(); CurrCTF.Defocus = Defocus; CurrCTF.DefocusDelta = DefocusDelta; CurrCTF.DefocusAngle = DefocusAngle; CurrCTF.Scale = (decimal)Math.Cos(Angles[t] * Helper.ToRad); CurrCTF.Bfactor = (decimal)-Dose[t] * 8; Params[t] = CurrCTF.ToStruct(); } GPU.CreateCTF(ParticleCTFs.GetDeviceSlice(NTilts * p, Intent.Write), CTFCoords.GetDevice(Intent.Read), (uint)CoarseDims.ElementsFFT(), Params, false, (uint)NTilts); } // Extract images { for (int t = 0; t < NTilts; t++) { ExtractedAt[p * NTilts + t] = new float2(Positions[t].X, Positions[t].Y); Positions[t] -= size / 2; int2 IntPosition = new int2((int)Positions[t].X, (int)Positions[t].Y); float2 Residual = new float2(-(Positions[t].X - IntPosition.X), -(Positions[t].Y - IntPosition.Y)); Residuals[t] = new float3(Residual / size * CoarseSize); float[] OriginalData; lock (tiltStack) OriginalData = tiltStack.GetHost(Intent.Read)[t]; float[] ImageData = ExtractedData[t]; for (int y = 0; y < size; y++) { int PosY = (y + IntPosition.Y + tiltStack.Dims.Y) % tiltStack.Dims.Y; for (int x = 0; x < size; x++) { int PosX = (x + IntPosition.X + tiltStack.Dims.X) % tiltStack.Dims.X; ImageData[y * size + x] = OriginalData[PosY * tiltStack.Dims.X + PosX]; } } } GPU.NormParticles(Extracted.GetDevice(Intent.Read), Extracted.GetDevice(Intent.Write), new int3(size, size, 1), (uint)(MainWindow.Options.ExportParticleRadius / CTF.PixelSize), true, (uint)NTilts); Image Scaled = Extracted.AsScaled(new int2(CoarseSize, CoarseSize)); //Scaled.WriteMRC("d_scaled.mrc"); Extracted.Dispose(); Scaled.ShiftSlices(Residuals); Scaled.RemapToFT(); //GPU.NormalizeMasked(Scaled.GetDevice(Intent.Read), // Scaled.GetDevice(Intent.Write), // MaskSubt.GetDevice(Intent.Read), // (uint)Scaled.ElementsSliceReal, // (uint)NTilts); //{ // //Image SubtrahendsFT = subtrahendReference.Project(new int2(CoarseSize, CoarseSize), ProjAngles, CoarseSize / 2); // //SubtrahendsFT.Multiply(SubtrahendsCTF); // //Image Subtrahends = SubtrahendsFT.AsIFFT(); // //SubtrahendsFT.Dispose(); // ////GPU.NormalizeMasked(Subtrahends.GetDevice(Intent.Read), // //// Subtrahends.GetDevice(Intent.Write), // //// MaskSubt.GetDevice(Intent.Read), // //// (uint)Subtrahends.ElementsSliceReal, // //// (uint)NTilts); // //Scaled.Subtract(Subtrahends); // //Subtrahends.Dispose(); // Image FocusMaskFT = maskReference.Project(new int2(CoarseSize, CoarseSize), ProjAngles, CoarseSize / 2); // Image FocusMask = FocusMaskFT.AsIFFT(); // FocusMaskFT.Dispose(); // Scaled.Multiply(FocusMask); // FocusMask.Dispose(); //} Scaled.MultiplySlices(Mask); GPU.FFT(Scaled.GetDevice(Intent.Read), ParticleImages.GetDeviceSlice(p * NTilts, Intent.Write), CoarseDims, (uint)NTilts); Scaled.Dispose(); SubtrahendsCTF.Dispose(); } } #endregion ParticleCTFs.MultiplySlices(FourierMask); Mask.Dispose(); FourierMask.Dispose(); MaskSubt.Dispose(); Image ParticleCTFsAbs = new Image(ParticleCTFs.GetDevice(Intent.Read), ParticleCTFs.Dims, true); ParticleCTFsAbs.Abs(); ParticleWeights = ParticleCTFsAbs.AsSum2D(); ParticleCTFsAbs.Dispose(); { float[] ParticleWeightsData = ParticleWeights.GetHost(Intent.ReadWrite)[0]; float Max = MathHelper.Max(ParticleWeightsData); for (int i = 0; i < ParticleWeightsData.Length; i++) ParticleWeightsData[i] /= Max; } CTFCoords.Dispose(); //Image CheckImages = ParticleImages.AsIFFT(); //CheckImages.WriteMRC("d_particleimages.mrc"); //CheckImages.Dispose(); //ParticleCTFs.WriteMRC("d_particlectfs.mrc"); } GlobalBfactor = KeepBFac; #endregion #region Global alignment Func<float3[], float2[]> GetImageShifts = input => { // Using current positions, angles and grids, get parameters for image shifts float2[] ImageShifts = new float2[NParticles * NTilts]; float3[] PerTiltPositions = new float3[NParticles * NTilts]; for (int p = 0; p < NParticles; p++) for (int t = 0; t < NTilts; t++) PerTiltPositions[p * NTilts + t] = input[p]; float3[] CurrPositions = GetPositionInImages(PerTiltPositions); for (int i = 0; i < ImageShifts.Length; i++) ImageShifts[i] = new float2(ExtractedAt[i].X - CurrPositions[i].X, ExtractedAt[i].Y - CurrPositions[i].Y); // -diff because those are extraction positions, i. e. opposite direction of shifts return ImageShifts; }; Func<float3[], float3[]> GetImageAngles = input => { int NAngles = input.Length; float3 VolumeCenter = new float3(VolumeDimensions.X / 2, VolumeDimensions.Y / 2, VolumeDimensions.Z / 2); float3[] PerTiltPositions = new float3[NAngles * NTilts]; float3[] PerTiltAngles = new float3[NAngles * NTilts]; for (int a = 0; a < NAngles; a++) for (int t = 0; t < NTilts; t++) { PerTiltPositions[a * NTilts + t] = VolumeCenter; PerTiltAngles[a * NTilts + t] = input[a]; } float3[] ImageAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles); return ImageAngles; }; float3[] RelativeOffsets; { List<float3> RelativeOffsetList = new List<float3>(); int NSteps = (int)Math.Ceiling(offsetRange / offsetStep); for (int z = -NSteps; z <= NSteps; z++) for (int y = -NSteps; y <= NSteps; y++) for (int x = -NSteps; x <= NSteps; x++) { float R = (float)Math.Sqrt(x * x + y * y + z * z) * offsetStep; if (R > offsetRange + 1e-6f) continue; RelativeOffsetList.Add(new float3(x * offsetStep, y * offsetStep, z * offsetStep)); } RelativeOffsets = RelativeOffsetList.ToArray(); } float3[] HealpixAngles = Helper.GetHealpixAngles(healpixOrder, symmetry).Select(a => a * Helper.ToRad).ToArray(); float3[] ProjectionAngles = GetImageAngles(HealpixAngles); float3[] OptimizedOrigins = new float3[NParticles]; float3[] OptimizedAngles = new float3[NParticles]; float[] BestScores = new float[NParticles].Select(v => -float.MaxValue).ToArray(); int BatchAngles = 128; Image Projections = new Image(new int3(CoarseSize, CoarseSize, BatchAngles * NTilts), true, true); foreach (var subset in SubsetRanges) { int NSubset = subset.Value.Item2 - subset.Value.Item1; float[] ImageOffsets = new float[NSubset * NTilts * RelativeOffsets.Length * 2]; for (int o = 0; o < RelativeOffsets.Length; o++) { float3[] OffsetOrigins = new float3[NSubset]; for (int p = 0; p < NSubset; p++) OffsetOrigins[p] = ParticleOrigins[subset.Value.Item1 + p] + RelativeOffsets[o]; float[] TheseOffsets = Helper.ToInterleaved(GetImageShifts(OffsetOrigins)); Array.Copy(TheseOffsets, 0, ImageOffsets, TheseOffsets.Length * o, TheseOffsets.Length); } int[] ShiftIDs = new int[NSubset]; int[] AngleIDs = new int[NSubset]; float[] SubsetScores = new float[NSubset]; GPU.TomoGlobalAlign(ParticleImages.GetDeviceSlice(subset.Value.Item1 * NTilts, Intent.Read), ShiftFactors.GetDevice(Intent.Read), ParticleCTFs.GetDeviceSlice(subset.Value.Item1 * NTilts, Intent.Read), ParticleWeights.GetDeviceSlice(subset.Value.Item1 * NTilts, Intent.Read), new int2(CoarseDims), references[subset.Key].Data.GetDevice(Intent.Read), references[subset.Key].Data.Dims, references[subset.Key].Oversampling, Helper.ToInterleaved(ProjectionAngles), (uint)HealpixAngles.Length, ImageOffsets, (uint)RelativeOffsets.Length, (uint)NSubset, (uint)NTilts, AngleIDs, ShiftIDs, SubsetScores); for (int i = 0; i < NSubset; i++) { OptimizedOrigins[subset.Value.Item1 + i] = ParticleOrigins[subset.Value.Item1 + i] + RelativeOffsets[ShiftIDs[i]]; OptimizedAngles[subset.Value.Item1 + i] = HealpixAngles[AngleIDs[i]]; BestScores[subset.Value.Item1 + i] = SubsetScores[i]; } } Projections.Dispose(); #endregion ParticleImages?.Dispose(); ParticleCTFs?.Dispose(); ParticleWeights?.Dispose(); ShiftFactors?.Dispose(); #region Extract particles at full resolution and back-project them into the reconstruction volumes { GPU.SetDevice(0); Image CTFCoords = GetCTFCoords(size, size); int[] SortedDosePrecalc = IndicesSortedDose; foreach (var subsetRange in SubsetRanges) { lock (outReconstructions[subsetRange.Key]) { for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++) { float3[] PerTiltPositions = new float3[NTilts]; float3[] PerTiltAngles = new float3[NTilts]; for (int t = 0; t < NTilts; t++) { PerTiltPositions[t] = OptimizedOrigins[p]; PerTiltAngles[t] = OptimizedAngles[p]; } Image FullParticleImages = GetSubtomoImages(tiltStack, size, PerTiltPositions, true); Image FullParticleCTFs = GetSubtomoCTFs(PerTiltPositions, CTFCoords); FullParticleImages.Multiply(FullParticleCTFs); FullParticleCTFs.Abs(); float3[] FullParticleAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles); outReconstructions[subsetRange.Key].BackProject(FullParticleImages, FullParticleCTFs, FullParticleAngles); FullParticleImages.Dispose(); FullParticleCTFs.Dispose(); } for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++) { float3[] PerTiltPositions = new float3[NTilts]; float3[] PerTiltAngles = new float3[NTilts]; for (int t = 0; t < NTilts; t++) { PerTiltPositions[t] = OptimizedOrigins[p]; PerTiltAngles[t] = OptimizedAngles[p]; } float3[] FullParticleAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles); Image FullParticleCTFs = GetSubtomoCTFs(PerTiltPositions, CTFCoords, false); Image FullParticleCTFWeights = GetSubtomoCTFs(PerTiltPositions, CTFCoords, true); // CTF has to be converted to complex numbers with imag = 0 float2[] CTFsComplexData = new float2[FullParticleCTFs.ElementsComplex]; float[] CTFWeightsData = new float[FullParticleCTFs.ElementsComplex]; float[] CTFsContinuousData = FullParticleCTFs.GetHostContinuousCopy(); float[] CTFWeightsContinuousData = FullParticleCTFWeights.GetHostContinuousCopy(); for (int i = 0; i < CTFsComplexData.Length; i++) { CTFsComplexData[i] = new float2(Math.Abs(CTFsContinuousData[i] * CTFWeightsContinuousData[i]), 0); CTFWeightsData[i] = Math.Abs(CTFWeightsContinuousData[i]); } Image CTFsComplex = new Image(CTFsComplexData, FullParticleCTFs.Dims, true); Image CTFWeights = new Image(CTFWeightsData, FullParticleCTFs.Dims, true); outCTFReconstructions[subsetRange.Key].BackProject(CTFsComplex, CTFWeights, FullParticleAngles); FullParticleCTFs.Dispose(); FullParticleCTFWeights.Dispose(); CTFsComplex.Dispose(); CTFWeights.Dispose(); } outReconstructions[subsetRange.Key].FreeDevice(); outCTFReconstructions[subsetRange.Key].FreeDevice(); } } CTFCoords.Dispose(); } #endregion SaveMeta(); }
private void ButtonStartProcessing_OnClick(object sender, RoutedEventArgs e) { if (!IsProcessing) { foreach (var item in DisableWhenRunning) item.IsEnabled = false; ButtonStartProcessing.Content = "STOP PROCESSING"; IsProcessing = true; Thread ProcessThread = new Thread(() => { int MaxDevices = 999; int UsedDevices = Math.Min(MaxDevices, GPU.GetDeviceCount()); Image[] ImageGain = new Image[UsedDevices]; if (!string.IsNullOrEmpty(Options.GainPath) && Options.CorrectGain && File.Exists(Options.GainPath)) for (int d = 0; d < UsedDevices; d++) try { GPU.SetDevice(d); ImageGain[d] = StageDataLoad.LoadMap(Options.GainPath, new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight), MainWindow.Options.InputDatOffset, ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType)); } catch { return; } Image[] VolRefFT = new Image[UsedDevices], VolMaskFT = new Image[UsedDevices]; if ((Options.ProcessCTF && Options.ProcessParticleCTF) || (Options.ProcessMovement && Options.ProcessParticleShift)) if (File.Exists(Options.ReferencePath) && File.Exists(Options.MaskPath)) { for (int d = 0; d < UsedDevices; d++) { GPU.SetDevice(d); { Image Volume = StageDataLoad.LoadMap(Options.ReferencePath, new int2(1, 1), 0, typeof (float)); Image VolumePadded = Volume.AsPadded(Volume.Dims * Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); VolRefFT[d] = VolumePadded.AsFFT(true); VolumePadded.Dispose(); } { Image Volume = StageDataLoad.LoadMap(Options.MaskPath, new int2(1, 1), 0, typeof (float)); Image VolumePadded = Volume.AsPadded(Volume.Dims * Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); VolMaskFT[d] = VolumePadded.AsFFT(true); VolumePadded.Dispose(); } } } Star ParticlesStar = null; if (File.Exists(Options.DataStarPath)) ParticlesStar = new Star(Options.DataStarPath); Queue<DeviceToken> Devices = new Queue<DeviceToken>(); for (int d = 0; d < UsedDevices; d++) Devices.Enqueue(new DeviceToken(d)); //for (int d = 0; d < UsedDevices; d++) // Devices.Enqueue(new DeviceToken(d)); int NTokens = Devices.Count; DeviceToken[] IOSync = new DeviceToken[UsedDevices]; for (int d = 0; d < UsedDevices; d++) IOSync[d] = new DeviceToken(d); foreach (var Movie in Options.Movies) { if (!IsProcessing) break; if (Movie.Status != ProcessingStatus.Skip && Movie.Status != ProcessingStatus.Processed) { while (Devices.Count <= 0) Thread.Sleep(20); if (!IsProcessing) break; DeviceToken CurrentDevice; lock (Devices) CurrentDevice = Devices.Dequeue(); Thread DeviceThread = new Thread(() => { GPU.SetDevice(CurrentDevice.ID); MapHeader OriginalHeader = null; Image OriginalStack = null; decimal ScaleFactor = 1M / (decimal)Math.Pow(2, (double)Options.PostBinTimes); lock (IOSync[CurrentDevice.ID]) PrepareHeaderAndMap(Movie.Path, ImageGain[CurrentDevice.ID], ScaleFactor, out OriginalHeader, out OriginalStack); /*OriginalHeader = MapHeader.ReadFromFile(Movie.Path, new int2(Options.InputDatWidth, Options.InputDatHeight), Options.InputDatOffset, ImageFormatsHelper.StringToType(Options.InputDatType));*/ //try { if (Options.ProcessMovement) { if (!Options.ProcessParticleShift) Movie.ProcessShift(OriginalHeader, OriginalStack, ScaleFactor); else Movie.ProcessParticleShift(OriginalHeader, OriginalStack, ParticlesStar, VolRefFT[CurrentDevice.ID], VolMaskFT[CurrentDevice.ID], VolRefFT[CurrentDevice.ID].Dims.X / Options.ProjectionOversample, ScaleFactor); } if (Options.ProcessCTF) { if (!Options.ProcessParticleCTF) Movie.ProcessCTF(OriginalHeader, OriginalStack, true, ScaleFactor); else Movie.ProcessParticleCTF(OriginalHeader, OriginalStack, ParticlesStar, VolRefFT[CurrentDevice.ID], VolMaskFT[CurrentDevice.ID], VolRefFT[CurrentDevice.ID].Dims.X / Options.ProjectionOversample, ScaleFactor); } if (Options.PostAverage || Options.PostStack) Movie.CreateCorrected(OriginalHeader, OriginalStack); //Movie.PerformComparison(OriginalHeader, ParticlesStar, VolRefFT, VolMaskFT, ScaleFactor); //((TiltSeries)Movie).Reconstruct(OriginalStack, 128, 3.42f * 4 * 2, new int3(3712, 3712, 1400)); //Image Reference = StageDataLoad.LoadMap("F:\\badaben\\ref.mrc", new int2(1, 1), 0, typeof(float)); //((TiltSeries)Movie).Correlate(OriginalStack, Reference, 128, 80, 400, new int3(3712, 3712, 1400), 2, "C1"); //Reference.Dispose(); Movie.Status = ProcessingStatus.Processed; } /*catch { Movie.Status = ProcessingStatus.Unprocessed; }*/ OriginalStack?.Dispose(); lock (Devices) Devices.Enqueue(CurrentDevice); }); DeviceThread.Start(); } } while (Devices.Count != NTokens) Thread.Sleep(20); //ParticlesStar.Save("F:\\rado27\\20S_defocused_dataset_part1\\warpmaps2\\run1_it017_data_everything.star"); //MoviesStar.Save("D:\\rado27\\Refine3D\\run1_ct5_data_movies.star"); for (int d = 0; d < UsedDevices; d++) { ImageGain[d]?.Dispose(); VolRefFT[d]?.Dispose(); VolMaskFT[d]?.Dispose(); } }); ProcessThread.Start(); } else { foreach (var item in DisableWhenRunning) item.IsEnabled = true; ButtonStartProcessing.Content = "START PROCESSING"; IsProcessing = false; } }
public void ProcessParticleCTF(MapHeader originalHeader, Image originalStack, Star stardata, Image refft, Image maskft, int dimbox, decimal scaleFactor) { //CTF.Cs = MainWindow.Options.CTFCs; #region Dimensions and grids int NFrames = originalHeader.Dimensions.Z; int2 DimsImage = new int2(originalHeader.Dimensions); int2 DimsRegion = new int2(dimbox, dimbox); float3[] PositionsGrid; float3[] PositionsExtraction; float3[] ParticleAngles; List<int> RowIndices = new List<int>(); { string[] ColumnNames = stardata.GetColumn("rlnMicrographName"); for (int i = 0; i < ColumnNames.Length; i++) if (ColumnNames[i].Contains(RootName)) RowIndices.Add(i); string[] ColumnOriginX = stardata.GetColumn("rlnCoordinateX"); string[] ColumnOriginY = stardata.GetColumn("rlnCoordinateY"); string[] ColumnShiftX = stardata.GetColumn("rlnOriginX"); string[] ColumnShiftY = stardata.GetColumn("rlnOriginY"); string[] ColumnAngleRot = stardata.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = stardata.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = stardata.GetColumn("rlnAnglePsi"); PositionsGrid = new float3[RowIndices.Count]; PositionsExtraction = new float3[RowIndices.Count]; ParticleAngles = new float3[RowIndices.Count]; { int i = 0; foreach (var nameIndex in RowIndices) { float OriginX = float.Parse(ColumnOriginX[nameIndex]); float OriginY = float.Parse(ColumnOriginY[nameIndex]); float ShiftX = float.Parse(ColumnShiftX[nameIndex]); float ShiftY = float.Parse(ColumnShiftY[nameIndex]); PositionsExtraction[i] = new float3(OriginX - ShiftX - dimbox / 2, OriginY - ShiftY - dimbox / 2, 0f); PositionsGrid[i] = new float3((OriginX - ShiftX) / DimsImage.X, (OriginY - ShiftY) / DimsImage.Y, 0); ParticleAngles[i] = new float3(float.Parse(ColumnAngleRot[nameIndex]) * Helper.ToRad, float.Parse(ColumnAngleTilt[nameIndex]) * Helper.ToRad, float.Parse(ColumnAnglePsi[nameIndex]) * Helper.ToRad); i++; } } } int NPositions = PositionsGrid.Length; if (NPositions == 0) return; int CTFGridX = MainWindow.Options.GridCTFX; int CTFGridY = MainWindow.Options.GridCTFY; int CTFGridZ = Math.Min(NFrames, MainWindow.Options.GridCTFZ); int FrameGroupSize = CTFGridZ > 1 ? 12 : 1; int NFrameGroups = CTFGridZ > 1 ? NFrames / FrameGroupSize : 1; GridCTF = GridCTF.Resize(new int3(CTFGridX, CTFGridY, CTFGridZ)); GridCTFPhase = GridCTFPhase.Resize(new int3(1, 1, CTFGridZ)); int NSpectra = NFrameGroups * NPositions; int MinFreqInclusive = (int)(MainWindow.Options.CTFRangeMin * DimsRegion.X / 2); int MaxFreqExclusive = (int)(MainWindow.Options.CTFRangeMax * DimsRegion.X / 2); int NFreq = MaxFreqExclusive - MinFreqInclusive; float PixelSize = (float)CTF.PixelSize; float PixelDelta = (float)CTF.PixelSizeDelta; float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad; #endregion #region Allocate GPU memory Image CTFSpectra = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.X, NSpectra), true, true); Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true); Image ParticleRefs = refft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); /*Image ParticleRefsIFT = ParticleRefs.AsIFFT(); ParticleRefsIFT.WriteMRC("d_particlerefs.mrc"); ParticleRefsIFT.Dispose();*/ #endregion // Extract movie regions, create individual spectra in Cartesian coordinates. #region Create spectra Image ParticleMasksFT = maskft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); Image ParticleMasks = ParticleMasksFT.AsIFFT(); ParticleMasksFT.Dispose(); Parallel.ForEach(ParticleMasks.GetHost(Intent.ReadWrite), slice => { for (int i = 0; i < slice.Length; i++) slice[i] = (Math.Max(2f, Math.Min(25f, slice[i])) - 2) / 23f; }); int3[] PositionsExtractionPerFrame = new int3[PositionsExtraction.Length * NFrames]; for (int z = 0; z < NFrames; z++) { for (int p = 0; p < NPositions; p++) { float3 Coords = new float3(PositionsGrid[p].X, PositionsGrid[p].Y, z / (float)(NFrames - 1)); float2 Offset = GetShiftFromPyramid(Coords); PositionsExtractionPerFrame[z * NPositions + p] = new int3((int)Math.Round(PositionsExtraction[p].X - Offset.X), (int)Math.Round(PositionsExtraction[p].Y - Offset.Y), 0); } } float3[] PositionsGridPerFrame = new float3[NSpectra]; for (int z = 0; z < NFrameGroups; z++) { for (int p = 0; p < NPositions; p++) { float3 Coords = new float3(PositionsGrid[p].X, PositionsGrid[p].Y, (z * FrameGroupSize + FrameGroupSize / 2) / (float)(NFrames - 1)); PositionsGridPerFrame[z * NPositions + p] = Coords; } } GPU.CreateParticleSpectra(originalStack.GetDevice(Intent.Read), DimsImage, NFrames, PositionsExtractionPerFrame, NPositions, ParticleMasks.GetDevice(Intent.Read), DimsRegion, CTFGridZ > 1, FrameGroupSize, PixelSize + PixelDelta / 2f, PixelSize - PixelDelta / 2f, PixelAngle, CTFSpectra.GetDevice(Intent.Write)); originalStack.FreeDevice(); // Won't need it in this method anymore. ParticleMasks.Dispose(); /*Image CTFSpectraIFT = CTFSpectra.AsIFFT(); CTFSpectraIFT.RemapFromFT(); CTFSpectraIFT.WriteMRC("d_ctfspectra.mrc"); CTFSpectraIFT.Dispose();*/ #endregion // Populate address arrays for later. #region Init addresses { float2[] CoordsData = new float2[CTFCoordsCart.ElementsSliceComplex]; Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) => CoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, a)); CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData }); CTFCoordsCart.RemapToFT(); } #endregion // Band-pass filter reference projections { Image BandMask = new Image(new int3(DimsRegion.X, DimsRegion.Y, 1), true); float[] BandMaskData = BandMask.GetHost(Intent.Write)[0]; float[] CTFCoordsData = CTFCoordsCart.GetHost(Intent.Read)[0]; for (int i = 0; i < BandMaskData.Length; i++) BandMaskData[i] = (CTFCoordsData[i * 2] >= MinFreqInclusive / (float)DimsRegion.X && CTFCoordsData[i * 2] < MaxFreqExclusive / (float)DimsRegion.X) ? 1 : 0; ParticleRefs.MultiplySlices(BandMask); BandMask.Dispose(); } Image Sigma2Noise = new Image(new int3(DimsRegion), true); { int GroupNumber = int.Parse(stardata.GetRowValue(RowIndices[0], "rlnGroupNumber")); 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(new int2(DimsRegion.X, DimsRegion.Y), (x, y, xx, yy, r, angle) => { int ir = (int)r; float val = 0; if (ir < SigmaValues.Length) { if (SigmaValues[ir] != 0f) val = 1f / SigmaValues[ir]; } Sigma2NoiseData[y * (DimsRegion.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"); // Do BFGS optimization of defocus, astigmatism and phase shift, // using 2D simulation for comparison #region BFGS { // Wiggle weights show how the defocus on the spectra grid is altered // by changes in individual anchor points of the spline grid. // They are used later to compute the dScore/dDefocus values for each spectrum // only once, and derive the values for each anchor point from them. float[][] WiggleWeights = GridCTF.GetWiggleWeights(PositionsGridPerFrame); float[][] WiggleWeightsPhase = GridCTFPhase.GetWiggleWeights(PositionsGridPerFrame); // Helper method for getting CTFStructs for the entire spectra grid. Func<double[], CTF, float[], float[], CTFStruct[]> EvalGetCTF = (input, ctf, defocusValues, phaseValues) => { decimal AlteredDelta = (decimal)input[input.Length - 2]; decimal AlteredAngle = (decimal)(input[input.Length - 1] * 20 / (Math.PI / 180)); CTF Local = ctf.GetCopy(); Local.DefocusDelta = AlteredDelta; Local.DefocusAngle = AlteredAngle; Local.PixelSizeDelta = 0; CTFStruct LocalStruct = Local.ToStruct(); CTFStruct[] LocalParams = new CTFStruct[defocusValues.Length]; for (int i = 0; i < LocalParams.Length; i++) { LocalParams[i] = LocalStruct; LocalParams[i].Defocus = defocusValues[i] * -1e-6f; LocalParams[i].PhaseShift = phaseValues[i] * (float)Math.PI; } return LocalParams; }; // Simulate with adjusted CTF, compare to originals #region Eval and Gradient methods Func<double[], double> Eval = input => { CubicGrid Altered = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v).ToArray()); float[] DefocusValues = Altered.GetInterpolatedNative(PositionsGridPerFrame); CubicGrid AlteredPhase = new CubicGrid(GridCTFPhase.Dimensions, input.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v).ToArray()); float[] PhaseValues = AlteredPhase.GetInterpolatedNative(PositionsGridPerFrame); CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues); float[] Result = new float[LocalParams.Length]; GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read), CTFCoordsCart.GetDevice(Intent.Read), ParticleRefs.GetDevice(Intent.Read), Sigma2Noise.GetDevice(Intent.Read), (uint)CTFSpectra.ElementsSliceComplex, LocalParams, Result, (uint)NFrameGroups, (uint)NPositions); float Score = 0; for (int i = 0; i < Result.Length; i++) Score += Result[i]; Score /= NSpectra; if (float.IsNaN(Score) || float.IsInfinity(Score)) throw new Exception("Bad score."); return Score * 1.0; }; Func<double[], double[]> Gradient = input => { const float Step = 0.001f; double[] Result = new double[input.Length]; // In 0D grid case, just get gradient for all 4 parameters. // In 1+D grid case, do simple gradient for astigmatism and phase... int StartComponent = input.Length - 2; //int StartComponent = 0; /*for (int i = StartComponent; i < input.Length; i++) { double[] UpperInput = new double[input.Length]; input.CopyTo(UpperInput, 0); UpperInput[i] += Step; double UpperValue = Eval(UpperInput); double[] LowerInput = new double[input.Length]; input.CopyTo(LowerInput, 0); LowerInput[i] -= Step; double LowerValue = Eval(LowerInput); Result[i] = (UpperValue - LowerValue) / (2f * Step); }*/ float[] ResultPlus = new float[NSpectra]; float[] ResultMinus = new float[NSpectra]; // ..., take shortcut for defoci... { CubicGrid AlteredPhase = new CubicGrid(GridCTFPhase.Dimensions, input.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v).ToArray()); float[] PhaseValues = AlteredPhase.GetInterpolatedNative(PositionsGridPerFrame); { CubicGrid AlteredPlus = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v + Step).ToArray()); float[] DefocusValues = AlteredPlus.GetInterpolatedNative(PositionsGridPerFrame); CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues); GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read), CTFCoordsCart.GetDevice(Intent.Read), ParticleRefs.GetDevice(Intent.Read), Sigma2Noise.GetDevice(Intent.Read), (uint)CTFSpectra.ElementsSliceComplex, LocalParams, ResultPlus, (uint)NFrameGroups, (uint)NPositions); } { CubicGrid AlteredMinus = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v - Step).ToArray()); float[] DefocusValues = AlteredMinus.GetInterpolatedNative(PositionsGridPerFrame); CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues); GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read), CTFCoordsCart.GetDevice(Intent.Read), ParticleRefs.GetDevice(Intent.Read), Sigma2Noise.GetDevice(Intent.Read), (uint)CTFSpectra.ElementsSliceComplex, LocalParams, ResultMinus, (uint)NFrameGroups, (uint)NPositions); } float[] LocalGradients = new float[ResultPlus.Length]; for (int i = 0; i < LocalGradients.Length; i++) LocalGradients[i] = ResultPlus[i] - ResultMinus[i]; // Now compute gradients per grid anchor point using the precomputed individual gradients and wiggle factors. Parallel.For(0, GridCTF.Dimensions.Elements(), i => Result[i] = MathHelper.ReduceWeighted(LocalGradients, WiggleWeights[i]) / LocalGradients.Length / (2f * Step) * 1f); } // ..., and take shortcut for phases. if (MainWindow.Options.CTFDoPhase) { CubicGrid AlteredPlus = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v).ToArray()); float[] DefocusValues = AlteredPlus.GetInterpolatedNative(PositionsGridPerFrame); { CubicGrid AlteredPhasePlus = new CubicGrid(GridCTFPhase.Dimensions, input.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v + Step).ToArray()); float[] PhaseValues = AlteredPhasePlus.GetInterpolatedNative(PositionsGridPerFrame); CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues); GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read), CTFCoordsCart.GetDevice(Intent.Read), ParticleRefs.GetDevice(Intent.Read), Sigma2Noise.GetDevice(Intent.Read), (uint)CTFSpectra.ElementsSliceComplex, LocalParams, ResultPlus, (uint)NFrameGroups, (uint)NPositions); } { CubicGrid AlteredPhaseMinus = new CubicGrid(GridCTFPhase.Dimensions, input.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v - Step).ToArray()); float[] PhaseValues = AlteredPhaseMinus.GetInterpolatedNative(PositionsGridPerFrame); CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues); GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read), CTFCoordsCart.GetDevice(Intent.Read), ParticleRefs.GetDevice(Intent.Read), Sigma2Noise.GetDevice(Intent.Read), (uint)CTFSpectra.ElementsSliceComplex, LocalParams, ResultMinus, (uint)NFrameGroups, (uint)NPositions); } float[] LocalGradients = new float[ResultPlus.Length]; for (int i = 0; i < LocalGradients.Length; i++) LocalGradients[i] = ResultPlus[i] - ResultMinus[i]; // Now compute gradients per grid anchor point using the precomputed individual gradients and wiggle factors. Parallel.For(0, GridCTFPhase.Dimensions.Elements(), i => Result[i + GridCTF.Dimensions.Elements()] = MathHelper.ReduceWeighted(LocalGradients, WiggleWeightsPhase[i]) / LocalGradients.Length / (2f * Step) * 1f); } foreach (var i in Result) if (double.IsNaN(i) || double.IsInfinity(i)) throw new Exception("Bad score."); return Result; }; #endregion #region Maximize normalized cross-correlation double[] StartParams = new double[GridCTF.Dimensions.Elements() + GridCTFPhase.Dimensions.Elements() + 2]; for (int i = 0; i < GridCTF.Dimensions.Elements(); i++) StartParams[i] = GridCTF.FlatValues[i]; for (int i = 0; i < GridCTFPhase.Dimensions.Elements(); i++) StartParams[i + GridCTF.Dimensions.Elements()] = GridCTFPhase.FlatValues[i]; StartParams[StartParams.Length - 2] = (double)CTF.DefocusDelta; StartParams[StartParams.Length - 1] = (double)CTF.DefocusAngle / 20 * (Math.PI / 180); BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Gradient); /*{ Past = 1, Delta = 1e-6, MaxLineSearch = 15, Corrections = 20 };*/ double[] BestStart = new double[StartParams.Length]; for (int i = 0; i < BestStart.Length; i++) BestStart[i] = StartParams[i]; double BestValue = Eval(StartParams); for (int o = 0; o < 1; o++) { /*for (int step = 0; step < 150; step++) { float Adjustment = (step - 75) / 75f * 0.075f; double[] Adjusted = new double[StartParams.Length]; for (int j = 0; j < Adjusted.Length; j++) if (j < GridCTF.Dimensions.Elements()) Adjusted[j] = StartParams[j] + Adjustment; else Adjusted[j] = StartParams[j]; double NewValue = Eval(Adjusted); if (NewValue > BestValue) { BestValue = NewValue; for (int j = 0; j < GridCTF.Dimensions.Elements(); j++) BestStart[j] = StartParams[j] + Adjustment; } } for (int i = 0; i < GridCTF.Dimensions.Elements(); i++) StartParams[i] = BestStart[i];*/ Optimizer.Maximize(StartParams); } #endregion #region Retrieve parameters decimal NewDefocus = (decimal)MathHelper.Mean(StartParams.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v)); Debug.WriteLine(CTF.Defocus - NewDefocus); CTF.Defocus = (decimal)MathHelper.Mean(StartParams.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v)); CTF.DefocusDelta = (decimal)StartParams[StartParams.Length - 2]; CTF.DefocusAngle = (decimal)(StartParams[StartParams.Length - 1] * 20 / (Math.PI / 180)); CTF.PhaseShift = (decimal)MathHelper.Mean(StartParams.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v)); GridCTF = new CubicGrid(GridCTF.Dimensions, StartParams.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v).ToArray()); GridCTFPhase = new CubicGrid(GridCTFPhase.Dimensions, StartParams.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v).ToArray()); #endregion Sigma2Noise.Dispose(); } #endregion ParticleRefs.Dispose(); //ParticleAmps.Dispose(); CTFSpectra.Dispose(); CTFCoordsCart.Dispose(); Simulated1D = GetSimulated1D(); CTFQuality = GetCTFQuality(); SaveMeta(); }