예제 #1
0
파일: GPU.cs 프로젝트: dtegunov/warp
 public static extern void CompareParticles(IntPtr d_particles,
                                            IntPtr d_masks,
                                            IntPtr d_projections,
                                            int2 dims,
                                            IntPtr d_ctfcoords,
                                            CTFStruct[] h_ctfparams,
                                            float highpass,
                                            float lowpass,
                                            IntPtr d_scores,
                                            uint nparticles);
예제 #2
0
 public static extern void ParticleCTFMakeAverage(IntPtr d_ps,
                                                  IntPtr d_pscoords,
                                                  uint length,
                                                  uint sidelength,
                                                  CTFStruct[] h_sourceparams,
                                                  CTFStruct targetparams,
                                                  uint minbin,
                                                  uint maxbin,
                                                  uint batch,
                                                  IntPtr d_output);
예제 #3
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        public void FromStruct(CTFStruct s)
        {
            _PixelSize      = (decimal)s.PixelSize * 1e10M;
            _PixelSizeDelta = (decimal)s.PixelSizeDelta * 1e10M;
            _PixelSizeAngle = (decimal)s.PixelSizeAngle * (180M / (decimal)Math.PI);

            _Cs        = (decimal)s.Cs * 1e3M;
            _Voltage   = (decimal)s.Voltage * 1e-3M;
            _Amplitude = (decimal)s.Amplitude;

            _Defocus      = (decimal) - s.Defocus * 1e6M;
            _DefocusDelta = (decimal) - s.DefocusDelta * 1e6M;
            _DefocusAngle = (decimal)s.AstigmatismAngle * (180M / (decimal)Math.PI);

            //_Bfactor = (decimal) s.Bfactor * 1e20M;
            _Scale = (decimal)s.Scale;

            _PhaseShift = (decimal)s.PhaseShift / (decimal)Math.PI;

            OnPropertyChanged("");
        }
예제 #4
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        public CTFStruct ToStruct()
        {
            CTFStruct Result = new CTFStruct();

            Result.PixelSize      = (float)(PixelSize * 1e-10M);
            Result.PixelSizeDelta = (float)(PixelSizeDelta * 1e-10M);
            Result.PixelSizeAngle = (float)PixelSizeAngle / (float)(180.0 / Math.PI);

            Result.Cs        = (float)(Cs * 1e-3M);
            Result.Voltage   = (float)(Voltage * 1e3M);
            Result.Amplitude = (float)Amplitude;

            Result.Defocus          = (float)(-Defocus * 1e-6M);
            Result.DefocusDelta     = (float)(-DefocusDelta * 1e-6M);
            Result.AstigmatismAngle = (float)DefocusAngle / (float)(180.0 / Math.PI);

            Result.Bfactor = (float)(Bfactor * 1e-20M);
            Result.Scale   = (float)Scale;

            Result.PhaseShift = (float)(PhaseShift * (decimal)Math.PI);

            return(Result);
        }
예제 #5
0
파일: TiltSeries.cs 프로젝트: dtegunov/warp
        public Image GetCTFsOneAngle(Image tiltStack, Image ctfCoords, float3[] particleOrigins, int angleID, bool weighted = true, bool weightsonly = false, bool useglobalweights = true)
        {
            int NParticles = particleOrigins.Length;
            float3[] ImagePositions = GetPositionsInOneAngle(particleOrigins, angleID);

            float GridStep = 1f / (NTilts - 1);
            CTFStruct[] Params = new CTFStruct[NParticles];
            for (int p = 0; p < NParticles; p++)
            {
                decimal Defocus = (decimal)ImagePositions[p].Z;
                decimal DefocusDelta = (decimal)GridCTFDefocusDelta.GetInterpolated(new float3(0.5f, 0.5f, angleID * GridStep));
                decimal DefocusAngle = (decimal)GridCTFDefocusAngle.GetInterpolated(new float3(0.5f, 0.5f, angleID * GridStep));

                CTF CurrCTF = CTF.GetCopy();
                if (!weightsonly)
                {
                    CurrCTF.Defocus = Defocus;
                    CurrCTF.DefocusDelta = DefocusDelta;
                    CurrCTF.DefocusAngle = DefocusAngle;
                }
                else
                {
                    CurrCTF.Defocus = 0;
                    CurrCTF.DefocusDelta = 0;
                    CurrCTF.Cs = 0;
                    CurrCTF.Amplitude = 1;
                }
                //CurrCTF.PixelSize *= 4;

                if (weighted)
                {
                    if (GridAngleWeights.Dimensions.Elements() <= 1)
                        CurrCTF.Scale = (decimal)Math.Cos(AnglesCorrect[angleID] * Helper.ToRad);
                    else
                        CurrCTF.Scale = (decimal)GridAngleWeights.GetInterpolated(new float3(0.5f, 0.5f, angleID * GridStep));

                    if (GridDoseBfacs.Dimensions.Elements() <= 1)
                        CurrCTF.Bfactor = (decimal)-Dose[angleID] * 8;
                    else
                        CurrCTF.Bfactor = (decimal)GridDoseBfacs.GetInterpolated(new float3(0.5f, 0.5f, angleID * GridStep));

                    if (useglobalweights)
                    {
                        CurrCTF.Scale *= (decimal)GlobalWeight;
                        CurrCTF.Bfactor += (decimal)GlobalBfactor;
                    }
                }

                Params[p] = CurrCTF.ToStruct();
            }

            Image Result = new Image(IntPtr.Zero, new int3(ctfCoords.Dims.X, ctfCoords.Dims.Y, NParticles), true);
            GPU.CreateCTF(Result.GetDevice(Intent.Write), ctfCoords.GetDevice(Intent.Read), (uint)Result.ElementsSliceReal, Params, false, (uint)NParticles);

            return Result;
        }
예제 #6
0
파일: Movie.cs 프로젝트: dtegunov/warp
        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();
        }
예제 #7
0
파일: CTF.cs 프로젝트: dtegunov/warp
        public void FromStruct(CTFStruct s)
        {
            _PixelSize = (decimal) s.PixelSize * 1e10M;
            _PixelSizeDelta = (decimal) s.PixelSizeDelta * 1e10M;
            _PixelSizeAngle = (decimal) s.PixelSizeAngle * (180M / (decimal) Math.PI);

            _Cs = (decimal) s.Cs * 1e3M;
            _Voltage = (decimal) s.Voltage * 1e-3M;
            _Amplitude = (decimal) s.Amplitude;

            _Defocus = (decimal) -s.Defocus * 1e6M;
            _DefocusDelta = (decimal) -s.DefocusDelta * 1e6M;
            _DefocusAngle = (decimal) s.AstigmatismAngle * (180M / (decimal)Math.PI);

            //_Bfactor = (decimal) s.Bfactor * 1e20M;
            _Scale = (decimal) s.Scale;

            _PhaseShift = (decimal) s.PhaseShift / (decimal) Math.PI;

            OnPropertyChanged("");
        }
예제 #8
0
파일: TiltSeries.cs 프로젝트: dtegunov/warp
        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
        }
예제 #9
0
파일: TiltSeries.cs 프로젝트: dtegunov/warp
        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();
        }
예제 #10
0
파일: GPU.cs 프로젝트: dtegunov/warp
 public static extern void CreateParticleShift(IntPtr d_frame,
                                               int2 dimsframe,
                                               int nframes,
                                               float[] h_positions,
                                               float[] h_shifts,
                                               int npositions,
                                               int2 dimsregion,
                                               long[] h_indices,
                                               uint indiceslength,
                                               IntPtr d_masks,
                                               IntPtr d_projections,
                                               CTFStruct[] h_ctfparams,
                                               IntPtr d_ctfcoords,
                                               IntPtr d_invsigma,
                                               float pixelmajor,
                                               float pixelminor,
                                               float pixelangle,
                                               IntPtr d_outputparticles,
                                               IntPtr d_outputprojections,
                                               IntPtr d_outputinvsigma);
예제 #11
0
파일: GPU.cs 프로젝트: dtegunov/warp
 public static extern void CreateCTF(IntPtr d_output,
                                     IntPtr d_coords,
                                     uint length,
                                     CTFStruct[] h_params,
                                     bool amplitudesquared,
                                     uint batch);
예제 #12
0
 public static extern CTFStruct CTFFitMean(IntPtr d_ps,
                                           IntPtr d_pscoords,
                                           int2 dims,
                                           CTFStruct startparams,
                                           CTFFitStruct fp,
                                           bool doastigmatism);
예제 #13
0
파일: Movie.cs 프로젝트: dtegunov/warp
        public virtual void ProcessCTF(MapHeader originalHeader, Image originalStack, bool doastigmatism, decimal scaleFactor)
        {
            if (!Directory.Exists(PowerSpectrumDir))
                Directory.CreateDirectory(PowerSpectrumDir);

            //CTF = new CTF();
            PS1D = null;
            _SimulatedBackground = null;
            _SimulatedScale = new Cubic1D(new[] { new float2(0, 1), new float2(1, 1) });

            #region Dimensions and grids

            int NFrames = originalHeader.Dimensions.Z;
            int2 DimsImage = new int2(originalHeader.Dimensions);
            int2 DimsRegion = new int2(MainWindow.Options.CTFWindow, MainWindow.Options.CTFWindow);

            float OverlapFraction = 0.5f;
            int2 DimsPositionGrid;
            int3[] PositionGrid = Helper.GetEqualGridSpacing(DimsImage, new int2(DimsRegion.X / 1, DimsRegion.Y / 1), OverlapFraction, out DimsPositionGrid);
            int NPositions = (int)DimsPositionGrid.Elements();

            int CTFGridX = Math.Min(DimsPositionGrid.X, MainWindow.Options.GridCTFX);
            int CTFGridY = Math.Min(DimsPositionGrid.Y, MainWindow.Options.GridCTFY);
            int CTFGridZ = Math.Min(NFrames, MainWindow.Options.GridCTFZ);
            GridCTF = new CubicGrid(new int3(CTFGridX, CTFGridY, CTFGridZ));
            GridCTFPhase = new CubicGrid(new int3(1, 1, CTFGridZ));

            bool CTFSpace = CTFGridX * CTFGridY > 1;
            bool CTFTime = CTFGridZ > 1;
            int3 CTFSpectraGrid = new int3(CTFSpace ? DimsPositionGrid.X : 1,
                                           CTFSpace ? DimsPositionGrid.Y : 1,
                                           CTFTime ? CTFGridZ : 1);

            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)(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 / 180f * (float)Math.PI;

            #endregion

            #region Allocate GPU memory

            Image CTFSpectra = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.X, (int)CTFSpectraGrid.Elements()), true);
            Image CTFMean = new Image(IntPtr.Zero, new int3(DimsRegion), true);
            Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true);
            Image CTFCoordsPolarTrimmed = new Image(new int3(NFreq, DimsRegion.X, 1), false, true);

            #endregion

            // Extract movie regions, create individual spectra in Cartesian coordinates and their mean.

            #region Create spectra

            GPU.CreateSpectra(originalStack.GetDevice(Intent.Read),
                              DimsImage,
                              NFrames,
                              PositionGrid,
                              NPositions,
                              DimsRegion,
                              CTFSpectraGrid,
                              CTFSpectra.GetDevice(Intent.Write),
                              CTFMean.GetDevice(Intent.Write));
            originalStack.FreeDevice(); // Won't need it in this method anymore.

            #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, a));
                CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData });

                CoordsData = new float2[NFreq * DimsRegion.X];
                Helper.ForEachElement(CTFCoordsPolarTrimmed.DimsSlice, (x, y) =>
                {
                    float Angle = ((float)y / DimsRegion.X + 0.5f) * (float)Math.PI;
                    float Ny = 1f / DimsRegion.X;
                    CoordsData[y * NFreq + x] = new float2((x + MinFreqInclusive) * Ny, Angle);
                });
                CTFCoordsPolarTrimmed.UpdateHostWithComplex(new[] { CoordsData });
            }

            #endregion

            // Retrieve average 1D spectrum from CTFMean (not corrected for astigmatism yet).

            #region Initial 1D spectrum

            {
                Image CTFAverage1D = new Image(IntPtr.Zero, new int3(DimsRegion.X / 2, 1, 1));

                GPU.CTFMakeAverage(CTFMean.GetDevice(Intent.Read),
                                   CTFCoordsCart.GetDevice(Intent.Read),
                                   (uint)CTFMean.ElementsSliceReal,
                                   (uint)DimsRegion.X,
                                   new[] { new CTF().ToStruct() },
                                   new CTF().ToStruct(),
                                   0,
                                   (uint)DimsRegion.X / 2,
                                   null,
                                   1,
                                   CTFAverage1D.GetDevice(Intent.Write));

                //CTFAverage1D.WriteMRC("CTFAverage1D.mrc");

                float[] CTFAverage1DData = CTFAverage1D.GetHost(Intent.Read)[0];
                float2[] ForPS1D = new float2[DimsRegion.X / 2];
                for (int i = 0; i < ForPS1D.Length; i++)
                    ForPS1D[i] = new float2((float)i / DimsRegion.X, (float)Math.Round(CTFAverage1DData[i], 4));
                _PS1D = ForPS1D;

                CTFAverage1D.Dispose();
            }

            #endregion

            #region Background fitting methods

            Action UpdateBackgroundFit = () =>
            {
                float2[] ForPS1D = PS1D.Skip(Math.Max(5, MinFreqInclusive / 2)).ToArray();
                Cubic1D.FitCTF(ForPS1D,
                               v => v.Select(x => CTF.Get1D(x / (float)CTF.PixelSize, true)).ToArray(),
                               CTF.GetZeros(),
                               CTF.GetPeaks(),
                               out _SimulatedBackground,
                               out _SimulatedScale);
            };

            Action<bool> UpdateRotationalAverage = keepbackground =>
            {
                float[] MeanData = CTFMean.GetHost(Intent.Read)[0];

                Image CTFMeanCorrected = new Image(new int3(DimsRegion), true);
                float[] MeanCorrectedData = CTFMeanCorrected.GetHost(Intent.Write)[0];

                // Subtract current background estimate from spectra, populate coords.
                Helper.ForEachElementFT(DimsRegion,
                                        (x, y, xx, yy, r, a) =>
                                        {
                                            int i = y * (DimsRegion.X / 2 + 1) + x;
                                            MeanCorrectedData[i] = MeanData[i] - _SimulatedBackground.Interp(r / DimsRegion.X);
                                        });

                Image CTFAverage1D = new Image(IntPtr.Zero, new int3(DimsRegion.X / 2, 1, 1));

                GPU.CTFMakeAverage(CTFMeanCorrected.GetDevice(Intent.Read),
                                   CTFCoordsCart.GetDevice(Intent.Read),
                                   (uint)CTFMeanCorrected.DimsEffective.ElementsSlice(),
                                   (uint)DimsRegion.X,
                                   new[] { CTF.ToStruct() },
                                   CTF.ToStruct(),
                                   0,
                                   (uint)DimsRegion.X / 2,
                                   null,
                                   1,
                                   CTFAverage1D.GetDevice(Intent.Write));

                //CTFAverage1D.WriteMRC("CTFAverage1D.mrc");

                float[] RotationalAverageData = CTFAverage1D.GetHost(Intent.Read)[0];
                float2[] ForPS1D = new float2[PS1D.Length];
                if (keepbackground)
                    for (int i = 0; i < ForPS1D.Length; i++)
                        ForPS1D[i] = new float2((float)i / DimsRegion.X, RotationalAverageData[i] + _SimulatedBackground.Interp((float)i / DimsRegion.X));
                else
                    for (int i = 0; i < ForPS1D.Length; i++)
                        ForPS1D[i] = new float2((float)i / DimsRegion.X, RotationalAverageData[i]);
                MathHelper.UnNaN(ForPS1D);

                _PS1D = ForPS1D;

                CTFMeanCorrected.Dispose();
                CTFAverage1D.Dispose();
            };

            #endregion

            // Fit background to currently best average (not corrected for astigmatism yet).
            {
                float2[] ForPS1D = PS1D.Skip(MinFreqInclusive).Take(Math.Max(2, NFreq / 2)).ToArray();

                int NumNodes = Math.Max(3, (int)((MainWindow.Options.CTFRangeMax - MainWindow.Options.CTFRangeMin) * 5M));
                _SimulatedBackground = Cubic1D.Fit(ForPS1D, NumNodes); // This won't fit falloff and scale, because approx function is 0

                float[] CurrentBackground = _SimulatedBackground.Interp(PS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq / 2).ToArray();
                float[] Subtracted1D = new float[ForPS1D.Length];
                for (int i = 0; i < ForPS1D.Length; i++)
                    Subtracted1D[i] = ForPS1D[i].Y - CurrentBackground[i];
                MathHelper.NormalizeInPlace(Subtracted1D);

                float ZMin = (float)MainWindow.Options.CTFZMin;
                float ZMax = (float)MainWindow.Options.CTFZMax;
                float ZStep = (ZMax - ZMin) / 100f;

                float BestZ = 0, BestPhase = 0, BestScore = -999;
                for (float z = ZMin; z <= ZMax + 1e-5f; z += ZStep)
                {
                    for (float p = 0; p <= (MainWindow.Options.CTFDoPhase ? 1f : 0f); p += 0.01f)
                    {
                        CTF CurrentParams = new CTF
                        {
                            PixelSize = (MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5M,

                            Defocus = (decimal)z,
                            PhaseShift = (decimal)p,

                            Cs = MainWindow.Options.CTFCs,
                            Voltage = MainWindow.Options.CTFVoltage,
                            Amplitude = MainWindow.Options.CTFAmplitude
                        };
                        float[] SimulatedCTF = CurrentParams.Get1D(PS1D.Length, true).Skip(MinFreqInclusive).Take(Math.Max(2, NFreq / 2)).ToArray();
                        MathHelper.NormalizeInPlace(SimulatedCTF);
                        float Score = MathHelper.CrossCorrelate(Subtracted1D, SimulatedCTF);
                        if (Score > BestScore)
                        {
                            BestScore = Score;
                            BestZ = z;
                            BestPhase = p;
                        }
                    }
                }

                CTF = new CTF
                {
                    PixelSize = (MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5M,

                    Defocus = (decimal)BestZ,
                    PhaseShift = (decimal)BestPhase,

                    Cs = MainWindow.Options.CTFCs,
                    Voltage = MainWindow.Options.CTFVoltage,
                    Amplitude = MainWindow.Options.CTFAmplitude
                };

                UpdateRotationalAverage(true); // This doesn't have a nice background yet.
                UpdateBackgroundFit(); // Now get a reasonably nice background.
            }

            

            // Fit defocus, (phase shift), (astigmatism) to average background-subtracted spectrum, 
            // which is in polar coords at this point (for equal weighting of all frequencies).

            #region Grid search

            {
                Image CTFMeanPolarTrimmed = CTFMean.AsPolar((uint)MinFreqInclusive, (uint)(MinFreqInclusive + NFreq / 1));

                // Subtract current background.
                Image CurrentBackground = new Image(_SimulatedBackground.Interp(PS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq / 1).ToArray());
                CTFMeanPolarTrimmed.SubtractFromLines(CurrentBackground);
                CurrentBackground.Dispose();

                /*Image WaterMask = new Image(new int3(NFreq, 1, 1));
                float[] WaterData = WaterMask.GetHost(Intent.Write)[0];
                for (int i = 0; i < NFreq; i++)
                {
                    float f = (i + MinFreqInclusive) / (float)DimsRegion.X * 2f;
                    WaterData[i] = f > 0.2f && f < 0.6f ? 0f : 1f;
                }
                //CTFMeanPolarTrimmed.MultiplyLines(WaterMask);
                WaterMask.Dispose();*/

                // Normalize for CC (not strictly needed, but it's converted for fp16 later, so let's be on the safe side of the fp16 range.
                GPU.Normalize(CTFMeanPolarTrimmed.GetDevice(Intent.Read), CTFMeanPolarTrimmed.GetDevice(Intent.Write), (uint)CTFMeanPolarTrimmed.ElementsReal, 1);
                //CTFMeanPolarTrimmed.WriteMRC("ctfmeanpolartrimmed.mrc");

                CTF StartParams = new CTF
                {
                    PixelSize = (MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5M,
                    PixelSizeDelta = Math.Abs(MainWindow.Options.CTFPixelMax - MainWindow.Options.CTFPixelMin),
                    PixelSizeAngle = MainWindow.Options.CTFPixelAngle,

                    Defocus = CTF.Defocus,// (MainWindow.Options.CTFZMin + MainWindow.Options.CTFZMax) * 0.5M,
                    DefocusDelta = doastigmatism ? 0 : MainWindow.Options.CTFAstigmatism,
                    DefocusAngle = doastigmatism ? 0 : MainWindow.Options.CTFAstigmatismAngle,

                    Cs = MainWindow.Options.CTFCs,
                    Voltage = MainWindow.Options.CTFVoltage,
                    Amplitude = MainWindow.Options.CTFAmplitude
                };

                CTFFitStruct FitParams = new CTFFitStruct
                {
                    //Pixelsize = new float3(-0.02e-10f, 0.02e-10f, 0.01e-10f),
                    //Pixeldelta = new float3(0.0f, 0.02e-10f, 0.01e-10f),
                    //Pixelangle = new float3(0, 2 * (float)Math.PI, 1 * (float)Math.PI / 18),

                    //Defocus = new float3((float)(MainWindow.Options.CTFZMin - StartParams.Defocus) * 1e-6f,
                    //                     (float)(MainWindow.Options.CTFZMax - StartParams.Defocus) * 1e-6f,
                    //                     0.025e-6f),
                    Defocus = new float3(-0.4e-6f,
                                         0.4e-6f,
                                         0.025e-6f),

                    Defocusdelta = doastigmatism ? new float3(0, 0.8e-6f, 0.02e-6f) : new float3(0, 0, 0),
                    Astigmatismangle = doastigmatism ? new float3(0, 2 * (float)Math.PI, 1 * (float)Math.PI / 18) : new float3(0, 0, 0),
                    Phaseshift = MainWindow.Options.CTFDoPhase ? new float3(0, (float)Math.PI, 0.025f * (float)Math.PI) : new float3(0, 0, 0)
                };

                CTFStruct ResultStruct = GPU.CTFFitMean(CTFMeanPolarTrimmed.GetDevice(Intent.Read),
                                                        CTFCoordsPolarTrimmed.GetDevice(Intent.Read),
                                                        CTFMeanPolarTrimmed.DimsSlice,
                                                        StartParams.ToStruct(),
                                                        FitParams,
                                                        doastigmatism);
                CTF.FromStruct(ResultStruct);
                CTF.Defocus = Math.Max(CTF.Defocus, MainWindow.Options.CTFZMin);

                CTFMeanPolarTrimmed.Dispose();

                UpdateRotationalAverage(true); // This doesn't have a nice background yet.
                UpdateBackgroundFit(); // Now get a reasonably nice background.

                UpdateRotationalAverage(true); // This time, with the nice background.
                UpdateBackgroundFit(); // Make the background even nicer!
            }

            #endregion

            /*for (int i = 0; i < PS1D.Length; i++)
                PS1D[i].Y -= SimulatedBackground.Interp(PS1D[i].X);
            SimulatedBackground = new Cubic1D(SimulatedBackground.Data.Select(v => new float2(v.X, 0f)).ToArray());
            OnPropertyChanged("PS1D");

            CTFSpectra.Dispose();
            CTFMean.Dispose();
            CTFCoordsCart.Dispose();
            CTFCoordsPolarTrimmed.Dispose();

            Simulated1D = GetSimulated1D();
            CTFQuality = GetCTFQuality();

            return;*/

            // Do BFGS optimization of defocus, astigmatism and phase shift,
            // using 2D simulation for comparison

            #region BFGS

            bool[] CTFSpectraConsider = new bool[CTFSpectraGrid.Elements()];
            for (int i = 0; i < CTFSpectraConsider.Length; i++)
                CTFSpectraConsider[i] = true;
            int NCTFSpectraConsider = CTFSpectraConsider.Length;

            GridCTF = new CubicGrid(GridCTF.Dimensions, (float)CTF.Defocus, (float)CTF.Defocus, Dimension.X);
            GridCTFPhase = new CubicGrid(GridCTFPhase.Dimensions, (float)CTF.PhaseShift, (float)CTF.PhaseShift, Dimension.X);

            for (int preciseFit = 2; preciseFit < 3; preciseFit++)
            {
                NFreq = (MaxFreqExclusive - MinFreqInclusive) * (preciseFit + 1) / 3;
                //if (preciseFit >= 2)
                //    NFreq = MaxFreqExclusive - MinFreqInclusive;

                Image CTFSpectraPolarTrimmed = CTFSpectra.AsPolar((uint)MinFreqInclusive, (uint)(MinFreqInclusive + NFreq));
                CTFSpectra.FreeDevice(); // This will only be needed again for the final PS1D.

                #region Create background and scale

                float[] CurrentScale = _SimulatedScale.Interp(PS1D.Select(p => p.X).ToArray());

                Image CTFSpectraScale = new Image(new int3(NFreq, DimsRegion.X, 1));
                float[] CTFSpectraScaleData = CTFSpectraScale.GetHost(Intent.Write)[0];

                // Trim polar to relevant frequencies, and populate coordinates.
                Parallel.For(0, DimsRegion.X, y =>
                {
                    float Angle = ((float)y / DimsRegion.X + 0.5f) * (float)Math.PI;
                    for (int x = 0; x < NFreq; x++)
                        CTFSpectraScaleData[y * NFreq + x] = CurrentScale[x + MinFreqInclusive];
                });
                //CTFSpectraScale.WriteMRC("ctfspectrascale.mrc");

                // Background is just 1 line since we're in polar.
                Image CurrentBackground = new Image(_SimulatedBackground.Interp(PS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq).ToArray());

                #endregion

                CTFSpectraPolarTrimmed.SubtractFromLines(CurrentBackground);
                CurrentBackground.Dispose();

                // Normalize background-subtracted spectra.
                GPU.Normalize(CTFSpectraPolarTrimmed.GetDevice(Intent.Read),
                              CTFSpectraPolarTrimmed.GetDevice(Intent.Write),
                              (uint)CTFSpectraPolarTrimmed.ElementsSliceReal,
                              (uint)CTFSpectraGrid.Elements());
                //CTFSpectraPolarTrimmed.WriteMRC("ctfspectrapolartrimmed.mrc");

                #region Convert to fp16

                Image CTFSpectraPolarTrimmedHalf = CTFSpectraPolarTrimmed.AsHalf();
                CTFSpectraPolarTrimmed.Dispose();

                Image CTFSpectraScaleHalf = CTFSpectraScale.AsHalf();
                CTFSpectraScale.Dispose();
                Image CTFCoordsPolarTrimmedHalf = CTFCoordsPolarTrimmed.AsHalf();

                #endregion

                // 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(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 1f / (CTFGridZ + 1)));
                float[][] WiggleWeightsPhase = GridCTFPhase.GetWiggleWeights(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 1f / (CTFGridZ + 1)));

                // 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;

                    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

                float BorderZ = 0.5f / CTFGridZ;

                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(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));
                    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(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));

                    CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);

                    float[] Result = new float[LocalParams.Length];

                    GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
                                        CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
                                        CTFSpectraScaleHalf.GetDevice(Intent.Read),
                                        (uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
                                        LocalParams,
                                        Result,
                                        (uint)LocalParams.Length);

                    float Score = 0;
                    for (int i = 0; i < Result.Length; i++)
                        if (CTFSpectraConsider[i])
                            Score += Result[i];

                    Score /= NCTFSpectraConsider;

                    if (float.IsNaN(Score) || float.IsInfinity(Score))
                        throw new Exception("Bad score.");

                    return (1.0 - Score) * 1000.0;
                };

                Func<double[], double[]> Gradient = input =>
                {
                    const float Step = 0.005f;
                    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[CTFSpectraGrid.Elements()];
                    float[] ResultMinus = new float[CTFSpectraGrid.Elements()];

                    // ..., 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(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));

                        {
                            CubicGrid AlteredPlus = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v + Step).ToArray());
                            float[] DefocusValues = AlteredPlus.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));

                            CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);

                            GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFSpectraScaleHalf.GetDevice(Intent.Read),
                                                (uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
                                                LocalParams,
                                                ResultPlus,
                                                (uint)LocalParams.Length);
                        }
                        {
                            CubicGrid AlteredMinus = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v - Step).ToArray());
                            float[] DefocusValues = AlteredMinus.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));

                            CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);

                            GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFSpectraScaleHalf.GetDevice(Intent.Read),
                                                (uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
                                                LocalParams,
                                                ResultMinus,
                                                (uint)LocalParams.Length);
                        }
                        float[] LocalGradients = new float[ResultPlus.Length];
                        for (int i = 0; i < LocalGradients.Length; i++)
                            LocalGradients[i] = ResultMinus[i] - ResultPlus[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) * 1000f);
                    }

                    // ..., 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(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));

                        {
                            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(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));
                            CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);

                            GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFSpectraScaleHalf.GetDevice(Intent.Read),
                                                (uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
                                                LocalParams,
                                                ResultPlus,
                                                (uint)LocalParams.Length);
                        }
                        {
                            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(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));
                            CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);

                            GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFSpectraScaleHalf.GetDevice(Intent.Read),
                                                (uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
                                                LocalParams,
                                                ResultMinus,
                                                (uint)LocalParams.Length);
                        }
                        float[] LocalGradients = new float[ResultPlus.Length];
                        for (int i = 0; i < LocalGradients.Length; i++)
                            LocalGradients[i] = ResultMinus[i] - ResultPlus[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) * 1000f);
                    }

                    foreach (var i in Result)
                        if (double.IsNaN(i) || double.IsInfinity(i))
                            throw new Exception("Bad score.");

                    return Result;
                };

                #endregion

                #region Minimize first time with potential outpiers

                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);

                // Compute correlation for individual spectra, and throw away those that are >.75 sigma worse than mean.

                #region Discard outliers

                if (CTFSpace || CTFTime)
                {
                    CubicGrid Altered = new CubicGrid(GridCTF.Dimensions, StartParams.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v).ToArray());
                    float[] DefocusValues = Altered.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));
                    CubicGrid AlteredPhase = new CubicGrid(GridCTFPhase.Dimensions, StartParams.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v).ToArray());
                    float[] PhaseValues = AlteredPhase.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));

                    CTFStruct[] LocalParams = EvalGetCTF(StartParams, CTF, DefocusValues, PhaseValues);

                    float[] Result = new float[LocalParams.Length];

                    GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
                                        CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
                                        CTFSpectraScaleHalf.GetDevice(Intent.Read),
                                        (uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
                                        LocalParams,
                                        Result,
                                        (uint)LocalParams.Length);

                    float MeanResult = MathHelper.Mean(Result);
                    float StdResult = MathHelper.StdDev(Result);
                    CTFSpectraConsider = new bool[CTFSpectraGrid.Elements()];
                    Parallel.For(0, CTFSpectraConsider.Length, i =>
                    {
                        //if (Result[i] > MeanResult - StdResult * 1.5f)
                        CTFSpectraConsider[i] = true;
                        /*else
                        {
                            CTFSpectraConsider[i] = false;
                            for (int j = 0; j < WiggleWeights.Length; j++)
                                // Make sure the spectrum's gradient doesn't affect the overall gradient.
                                WiggleWeights[j][i] = 0;
                        }*/
                    });
                    NCTFSpectraConsider = CTFSpectraConsider.Where(v => v).Count();
                }

                #endregion

                BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Gradient)
                {
                    Past = 1,
                    Delta = 1e-6,
                    MaxLineSearch = 15,
                    Corrections = 20
                };
                Optimizer.Minimize(StartParams);

                #endregion

                #region Retrieve parameters

                CTF.Defocus = (decimal)MathHelper.Mean(Optimizer.Solution.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v));
                CTF.DefocusDelta = (decimal)Optimizer.Solution[StartParams.Length - 2];
                CTF.DefocusAngle = (decimal)(Optimizer.Solution[StartParams.Length - 1] * 20 / (Math.PI / 180));
                CTF.PhaseShift = (decimal)MathHelper.Mean(Optimizer.Solution.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v));

                if (CTF.DefocusDelta < 0)
                {
                    CTF.DefocusAngle += 90;
                    CTF.DefocusDelta *= -1;
                }
                CTF.DefocusAngle = ((int)CTF.DefocusAngle + 180 * 99) % 180;

                GridCTF = new CubicGrid(GridCTF.Dimensions, Optimizer.Solution.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v).ToArray());
                GridCTFPhase = new CubicGrid(GridCTFPhase.Dimensions, Optimizer.Solution.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v).ToArray());

                #endregion

                // Dispose GPU resources manually because GC can't be bothered to do it in time.
                CTFSpectraPolarTrimmedHalf.Dispose();
                CTFCoordsPolarTrimmedHalf.Dispose();
                CTFSpectraScaleHalf.Dispose();

                #region Get nicer envelope fit

                if (preciseFit >= 2)
                {
                    if (!CTFSpace && !CTFTime)
                    {
                        UpdateRotationalAverage(true);
                    }
                    else
                    {
                        Image CTFSpectraBackground = new Image(new int3(DimsRegion), true);
                        float[] CTFSpectraBackgroundData = CTFSpectraBackground.GetHost(Intent.Write)[0];

                        // Construct background in Cartesian coordinates.
                        Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) =>
                        {
                            CTFSpectraBackgroundData[y * CTFSpectraBackground.DimsEffective.X + x] = _SimulatedBackground.Interp(r / DimsRegion.X);
                        });

                        CTFSpectra.SubtractFromSlices(CTFSpectraBackground);

                        float[] DefocusValues = GridCTF.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, BorderZ));
                        CTFStruct[] LocalParams = DefocusValues.Select(v =>
                        {
                            CTF Local = CTF.GetCopy();
                            Local.Defocus = (decimal)v + 0.0M;

                            return Local.ToStruct();
                        }).ToArray();

                        Image CTFAverage1D = new Image(IntPtr.Zero, new int3(DimsRegion.X / 2, 1, 1));

                        CTF CTFAug = CTF.GetCopy();
                        CTFAug.Defocus += 0.0M;
                        GPU.CTFMakeAverage(CTFSpectra.GetDevice(Intent.Read),
                                           CTFCoordsCart.GetDevice(Intent.Read),
                                           (uint)CTFSpectra.ElementsSliceReal,
                                           (uint)DimsRegion.X,
                                           LocalParams,
                                           CTFAug.ToStruct(),
                                           0,
                                           (uint)DimsRegion.X / 2,
                                           CTFSpectraConsider.Select(v => v ? 1 : 0).ToArray(),
                                           (uint)CTFSpectraGrid.Elements(),
                                           CTFAverage1D.GetDevice(Intent.Write));

                        CTFSpectra.AddToSlices(CTFSpectraBackground);

                        float[] RotationalAverageData = CTFAverage1D.GetHost(Intent.Read)[0];
                        float2[] ForPS1D = new float2[PS1D.Length];
                        for (int i = 0; i < ForPS1D.Length; i++)
                            ForPS1D[i] = new float2((float)i / DimsRegion.X, (float)Math.Round(RotationalAverageData[i], 4) + _SimulatedBackground.Interp((float)i / DimsRegion.X));
                        MathHelper.UnNaN(ForPS1D);
                        _PS1D = ForPS1D;

                        CTFSpectraBackground.Dispose();
                        CTFAverage1D.Dispose();
                        CTFSpectra.FreeDevice();
                    }

                    CTF.Defocus = Math.Max(CTF.Defocus, MainWindow.Options.CTFZMin);
                    UpdateBackgroundFit();
                }

                #endregion
            }

            #endregion

            // Subtract background from 2D average and write it to disk. 
            // This image is used for quick visualization purposes only.

            #region PS2D update

            {
                int3 DimsAverage = new int3(DimsRegion.X, DimsRegion.X / 2, 1);
                float[] Average2DData = new float[DimsAverage.Elements()];
                float[] OriginalAverageData = CTFMean.GetHost(Intent.Read)[0];

                for (int y = 0; y < DimsAverage.Y; y++)
                {
                    int yy = y * y;
                    for (int x = 0; x < DimsAverage.Y; x++)
                    {
                        int xx = DimsRegion.X / 2 - x - 1;
                        xx *= xx;
                        float r = (float)Math.Sqrt(xx + yy) / DimsRegion.X;
                        Average2DData[y * DimsAverage.X + x] = OriginalAverageData[(y + DimsRegion.X / 2) * (DimsRegion.X / 2 + 1) + x] - SimulatedBackground.Interp(r);
                    }

                    for (int x = 0; x < DimsRegion.X / 2; x++)
                    {
                        int xx = x * x;
                        float r = (float)Math.Sqrt(xx + yy) / DimsRegion.X;
                        Average2DData[y * DimsAverage.X + x + DimsRegion.X / 2] = OriginalAverageData[(DimsRegion.X / 2 - y) * (DimsRegion.X / 2 + 1) + (DimsRegion.X / 2 - 1 - x)] - SimulatedBackground.Interp(r);
                    }
                }

                IOHelper.WriteMapFloat(PowerSpectrumPath,
                                       new HeaderMRC
                                       {
                                           Dimensions = DimsAverage,
                                           MinValue = MathHelper.Min(Average2DData),
                                           MaxValue = MathHelper.Max(Average2DData)
                                       },
                                       Average2DData);

                PS2DTemp = null;
                OnPropertyChanged("PS2D");
            }

            #endregion

            for (int i = 0; i < PS1D.Length; i++)
                PS1D[i].Y -= SimulatedBackground.Interp(PS1D[i].X);
            SimulatedBackground = new Cubic1D(SimulatedBackground.Data.Select(v => new float2(v.X, 0f)).ToArray());
            OnPropertyChanged("PS1D");

            CTFSpectra.Dispose();
            CTFMean.Dispose();
            CTFCoordsCart.Dispose();
            CTFCoordsPolarTrimmed.Dispose();

            Simulated1D = GetSimulated1D();
            CTFQuality = GetCTFQuality();

            SaveMeta();
        }
예제 #14
0
파일: Movie.cs 프로젝트: dtegunov/warp
        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());
        }
예제 #15
0
파일: TiltSeries.cs 프로젝트: dtegunov/warp
        public Image GetSubtomoCTFs(float3[] coords, Image ctfCoords, bool weighted = true, bool weightsonly = false, bool useglobalweights = true)
        {
            float3[] ImagePositions = GetPositionInImages(coords);

            float GridStep = 1f / (NTilts - 1);
            CTFStruct[] Params = new CTFStruct[NTilts];
            for (int t = 0; t < NTilts; t++)
            {
                decimal Defocus = (decimal)ImagePositions[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();
                if (!weightsonly)
                {
                    CurrCTF.Defocus = Defocus;
                    CurrCTF.DefocusDelta = DefocusDelta;
                    CurrCTF.DefocusAngle = DefocusAngle;
                }
                else
                {
                    CurrCTF.Defocus = 0;
                    CurrCTF.DefocusDelta = 0;
                    CurrCTF.Cs = 0;
                    CurrCTF.Amplitude = 1;
                }

                //CurrCTF.PixelSize *= 4;
                if (weighted)
                {
                    if (GridAngleWeights.Dimensions.Elements() <= 1)
                        CurrCTF.Scale = (decimal)Math.Cos(AnglesCorrect[t] * Helper.ToRad);
                    else
                        CurrCTF.Scale = (decimal)GridAngleWeights.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep));

                    if (GridDoseBfacs.Dimensions.Elements() <= 1)
                        CurrCTF.Bfactor = (decimal)-Dose[t] * 8;
                    else
                        CurrCTF.Bfactor = (decimal)GridDoseBfacs.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep));

                    if (useglobalweights)
                    {
                        CurrCTF.Scale *= (decimal)GlobalWeight;
                        CurrCTF.Bfactor += (decimal)GlobalBfactor;
                    }
                }

                Params[t] = CurrCTF.ToStruct();
            }

            Image Result = new Image(IntPtr.Zero, new int3(ctfCoords.Dims.X, ctfCoords.Dims.Y, NTilts), true);
            GPU.CreateCTF(Result.GetDevice(Intent.Write), ctfCoords.GetDevice(Intent.Read), (uint)Result.ElementsSliceReal, Params, false, (uint)NTilts);

            return Result;
        }
예제 #16
0
파일: TiltSeries.cs 프로젝트: dtegunov/warp
        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();
        }
예제 #17
0
파일: GPU.cs 프로젝트: dtegunov/warp
 public static extern void CTFCompareToSim(IntPtr d_ps, 
                                           IntPtr d_pscoords, 
                                           IntPtr d_scale, 
                                           uint length, 
                                           CTFStruct[] h_sourceparams, 
                                           float[] h_scores,
                                           uint batch);
예제 #18
0
파일: TiltSeries.cs 프로젝트: dtegunov/warp
        public void ProcessCTFOneAngle(Image angleImage,
                                       float angle,
                                       bool fromScratch,
                                       bool fixAstigmatism,
                                       float2 astigmatism,
                                       CTF previousCTF,
                                       CubicGrid previousGrid,
                                       Cubic1D previousBackground,
                                       Cubic1D previousScale,
                                       out CTF thisCTF,
                                       out CubicGrid thisGrid,
                                       out float2[] thisPS1D,
                                       out Cubic1D thisBackground,
                                       out Cubic1D thisScale,
                                       out Image thisPS2D)
        {
            CTF TempCTF = previousCTF != null ? previousCTF.GetCopy() : new CTF();
            float2[] TempPS1D = null;
            Cubic1D TempBackground = null, TempScale = null;
            CubicGrid TempGrid = null;

            #region Dimensions and grids

            int NFrames = angleImage.Dims.Z;
            int2 DimsImage = angleImage.DimsSlice;
            int2 DimsRegion = new int2(MainWindow.Options.CTFWindow, MainWindow.Options.CTFWindow);

            float OverlapFraction = 0.5f;
            int2 DimsPositionGrid;
            int3[] PositionGrid = Helper.GetEqualGridSpacing(DimsImage, new int2(DimsRegion.X, DimsRegion.Y), OverlapFraction, out DimsPositionGrid);
            int NPositions = (int)DimsPositionGrid.Elements();

            if (previousGrid == null)
                TempGrid = new CubicGrid(new int3(2, 2, 1));
            else
                TempGrid = new CubicGrid(new int3(2, 2, 1), previousGrid.FlatValues);

            bool CTFSpace = true;
            bool CTFTime = false;
            int3 CTFSpectraGrid = new int3(DimsPositionGrid.X, DimsPositionGrid.Y, 1);

            int MinFreqInclusive = (int)(MainWindow.Options.CTFRangeMin * DimsRegion.X / 2);
            int MaxFreqExclusive = (int)(MainWindow.Options.CTFRangeMax * DimsRegion.X / 2);
            int NFreq = MaxFreqExclusive - MinFreqInclusive;

            #endregion

            #region Allocate GPU memory

            Image CTFSpectra = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.X, (int)CTFSpectraGrid.Elements()), true);
            Image CTFMean = new Image(IntPtr.Zero, new int3(DimsRegion), true);
            Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true);
            Image CTFCoordsPolarTrimmed = new Image(new int3(NFreq, DimsRegion.X, 1), false, true);

            #endregion

            // Extract movie regions, create individual spectra in Cartesian coordinates and their mean.

            #region Create spectra

            GPU.CreateSpectra(angleImage.GetDevice(Intent.Read),
                              DimsImage,
                              NFrames,
                              PositionGrid,
                              NPositions,
                              DimsRegion,
                              CTFSpectraGrid,
                              CTFSpectra.GetDevice(Intent.Write),
                              CTFMean.GetDevice(Intent.Write));
            angleImage.FreeDevice(); // Won't need it in this method anymore.

            #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, a));
                CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData });

                CoordsData = new float2[NFreq * DimsRegion.X];
                Helper.ForEachElement(CTFCoordsPolarTrimmed.DimsSlice, (x, y) =>
                {
                    float Angle = ((float)y / DimsRegion.X + 0.5f) * (float)Math.PI;
                    float Ny = 1f / DimsRegion.X;
                    CoordsData[y * NFreq + x] = new float2((x + MinFreqInclusive) * Ny, Angle);
                });
                CTFCoordsPolarTrimmed.UpdateHostWithComplex(new[] { CoordsData });
            }

            #endregion

            // Retrieve average 1D spectrum from CTFMean (not corrected for astigmatism yet).

            #region Initial 1D spectrum

            {
                Image CTFAverage1D = new Image(IntPtr.Zero, new int3(DimsRegion.X / 2, 1, 1));

                GPU.CTFMakeAverage(CTFMean.GetDevice(Intent.Read),
                                   CTFCoordsCart.GetDevice(Intent.Read),
                                   (uint)CTFMean.ElementsSliceReal,
                                   (uint)DimsRegion.X,
                                   new[] { new CTF().ToStruct() },
                                   new CTF().ToStruct(),
                                   0,
                                   (uint)DimsRegion.X / 2,
                                   null,
                                   1,
                                   CTFAverage1D.GetDevice(Intent.Write));

                //CTFAverage1D.WriteMRC("CTFAverage1D.mrc");

                float[] CTFAverage1DData = CTFAverage1D.GetHost(Intent.Read)[0];
                float2[] ForPS1D = new float2[DimsRegion.X / 2];
                for (int i = 0; i < ForPS1D.Length; i++)
                    ForPS1D[i] = new float2((float)i / DimsRegion.X, (float)Math.Round(CTFAverage1DData[i], 4));
                TempPS1D = ForPS1D;

                CTFAverage1D.Dispose();
            }

            #endregion

            #region Background fitting methods

            Action UpdateBackgroundFit = () =>
            {
                float2[] ForPS1D = TempPS1D.Skip(Math.Max(5, MinFreqInclusive / 2)).ToArray();
                Cubic1D.FitCTF(ForPS1D,
                               v => v.Select(x => TempCTF.Get1D(x / (float)TempCTF.PixelSize, true)).ToArray(),
                               TempCTF.GetZeros(),
                               TempCTF.GetPeaks(),
                               out TempBackground,
                               out TempScale);
            };

            Action<bool> UpdateRotationalAverage = keepbackground =>
            {
                float[] MeanData = CTFMean.GetHost(Intent.Read)[0];

                Image CTFMeanCorrected = new Image(new int3(DimsRegion), true);
                float[] MeanCorrectedData = CTFMeanCorrected.GetHost(Intent.Write)[0];

                // Subtract current background estimate from spectra, populate coords.
                Helper.ForEachElementFT(DimsRegion,
                                        (x, y, xx, yy, r, a) =>
                                        {
                                            int i = y * (DimsRegion.X / 2 + 1) + x;
                                            MeanCorrectedData[i] = MeanData[i] - TempBackground.Interp(r / DimsRegion.X);
                                        });

                Image CTFAverage1D = new Image(IntPtr.Zero, new int3(DimsRegion.X / 2, 1, 1));

                GPU.CTFMakeAverage(CTFMeanCorrected.GetDevice(Intent.Read),
                                   CTFCoordsCart.GetDevice(Intent.Read),
                                   (uint)CTFMeanCorrected.DimsEffective.ElementsSlice(),
                                   (uint)DimsRegion.X,
                                   new[] { TempCTF.ToStruct() },
                                   TempCTF.ToStruct(),
                                   0,
                                   (uint)DimsRegion.X / 2,
                                   null,
                                   1,
                                   CTFAverage1D.GetDevice(Intent.Write));

                //CTFAverage1D.WriteMRC("CTFAverage1D.mrc");

                float[] RotationalAverageData = CTFAverage1D.GetHost(Intent.Read)[0];
                float2[] ForPS1D = new float2[TempPS1D.Length];
                if (keepbackground)
                    for (int i = 0; i < ForPS1D.Length; i++)
                        ForPS1D[i] = new float2((float)i / DimsRegion.X, RotationalAverageData[i] + TempBackground.Interp((float)i / DimsRegion.X));
                else
                    for (int i = 0; i < ForPS1D.Length; i++)
                        ForPS1D[i] = new float2((float)i / DimsRegion.X, RotationalAverageData[i]);
                MathHelper.UnNaN(ForPS1D);

                TempPS1D = ForPS1D;

                CTFMeanCorrected.Dispose();
                CTFAverage1D.Dispose();
            };

            #endregion

            // Fit background to currently best average (not corrected for astigmatism yet).
            {
                float2[] ForPS1D = TempPS1D.Skip(MinFreqInclusive).Take(Math.Max(2, NFreq / 2)).ToArray();

                float[] CurrentBackground;
                //if (previousBackground == null)
                {
                    int NumNodes = Math.Max(3, (int)((MainWindow.Options.CTFRangeMax - MainWindow.Options.CTFRangeMin) * 5M));
                    TempBackground = Cubic1D.Fit(ForPS1D, NumNodes); // This won't fit falloff and scale, because approx function is 0

                    CurrentBackground = TempBackground.Interp(TempPS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq / 2).ToArray();
                }
                /*else
                {
                    CurrentBackground = previousBackground.Interp(TempPS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq / 2).ToArray();
                    TempBackground = new Cubic1D(previousBackground.Data);
                }*/

                float[] Subtracted1D = new float[ForPS1D.Length];
                for (int i = 0; i < ForPS1D.Length; i++)
                    Subtracted1D[i] = ForPS1D[i].Y - CurrentBackground[i];
                MathHelper.NormalizeInPlace(Subtracted1D);

                float ZMin = (float)MainWindow.Options.CTFZMin;
                float ZMax = (float)MainWindow.Options.CTFZMax;
                float PhaseMin = 0f;
                float PhaseMax = MainWindow.Options.CTFDoPhase ? 1f : 0f;

                if (previousCTF != null)
                {
                    ZMin = (float)previousCTF.Defocus - 0.5f;
                    ZMax = (float)previousCTF.Defocus + 0.5f;
                    if (PhaseMax > 0)
                    {
                        PhaseMin = (float)previousCTF.PhaseShift - 0.3f;
                        PhaseMax = (float)previousCTF.PhaseShift + 0.3f;
                    }
                }

                float ZStep = (ZMax - ZMin) / 100f;

                float BestZ = 0, BestPhase = 0, BestScore = -999;
                for (float z = ZMin; z <= ZMax + 1e-5f; z += ZStep)
                {
                    for (float p = PhaseMin; p <= PhaseMax; p += 0.01f)
                    {
                        CTF CurrentParams = new CTF
                        {
                            PixelSize = (MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5M,

                            Defocus = (decimal)z,
                            PhaseShift = (decimal)p,

                            Cs = MainWindow.Options.CTFCs,
                            Voltage = MainWindow.Options.CTFVoltage,
                            Amplitude = MainWindow.Options.CTFAmplitude
                        };
                        float[] SimulatedCTF = CurrentParams.Get1D(TempPS1D.Length, true).Skip(MinFreqInclusive).Take(Math.Max(2, NFreq / 2)).ToArray();
                        MathHelper.NormalizeInPlace(SimulatedCTF);
                        float Score = MathHelper.CrossCorrelate(Subtracted1D, SimulatedCTF);
                        if (Score > BestScore)
                        {
                            BestScore = Score;
                            BestZ = z;
                            BestPhase = p;
                        }
                    }
                }

                TempCTF = new CTF
                {
                    PixelSize = (MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5M,

                    Defocus = (decimal)BestZ,
                    PhaseShift = (decimal)BestPhase,

                    Cs = MainWindow.Options.CTFCs,
                    Voltage = MainWindow.Options.CTFVoltage,
                    Amplitude = MainWindow.Options.CTFAmplitude
                };

                UpdateRotationalAverage(true); // This doesn't have a nice background yet.
                UpdateBackgroundFit(); // Now get a reasonably nice background.
            }

            // Fit defocus, (phase shift), (astigmatism) to average background-subtracted spectrum,
            // which is in polar coords at this point (for equal weighting of all frequencies).

            #region Grid search

            if (fromScratch)
            {
                Image CTFMeanPolarTrimmed = CTFMean.AsPolar((uint)MinFreqInclusive, (uint)(MinFreqInclusive + NFreq / 1));

                // Subtract current background.
                Image CurrentBackground = new Image(TempBackground.Interp(TempPS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq / 1).ToArray());
                CTFMeanPolarTrimmed.SubtractFromLines(CurrentBackground);
                CurrentBackground.Dispose();

                // Normalize for CC (not strictly needed, but it's converted for fp16 later, so let's be on the safe side of the fp16 range.
                GPU.Normalize(CTFMeanPolarTrimmed.GetDevice(Intent.Read), CTFMeanPolarTrimmed.GetDevice(Intent.Write), (uint)CTFMeanPolarTrimmed.ElementsReal, 1);
                //CTFMeanPolarTrimmed.WriteMRC("ctfmeanpolartrimmed.mrc");

                CTF StartParams = new CTF
                {
                    PixelSize = (MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5M,
                    PixelSizeDelta = Math.Abs(MainWindow.Options.CTFPixelMax - MainWindow.Options.CTFPixelMin),
                    PixelSizeAngle = MainWindow.Options.CTFPixelAngle,

                    Defocus = TempCTF.Defocus, // (MainWindow.Options.CTFZMin + MainWindow.Options.CTFZMax) * 0.5M,
                    DefocusDelta = 0,
                    DefocusAngle = 0,

                    PhaseShift = TempCTF.PhaseShift,

                    Cs = MainWindow.Options.CTFCs,
                    Voltage = MainWindow.Options.CTFVoltage,
                    Amplitude = MainWindow.Options.CTFAmplitude
                };

                CTFFitStruct FitParams = new CTFFitStruct
                {
                    Defocus = new float3(-0.4e-6f,
                                         0.4e-6f,
                                         0.025e-6f),

                    Defocusdelta = new float3(0, 0.8e-6f, 0.02e-6f),
                    Astigmatismangle = new float3(0, 2 * (float)Math.PI, 1 * (float)Math.PI / 18),
                    Phaseshift = MainWindow.Options.CTFDoPhase ? new float3(-0.2f * (float)Math.PI, 0.2f * (float)Math.PI, 0.025f * (float)Math.PI) : new float3(0, 0, 0)
                };

                CTFStruct ResultStruct = GPU.CTFFitMean(CTFMeanPolarTrimmed.GetDevice(Intent.Read),
                                                        CTFCoordsPolarTrimmed.GetDevice(Intent.Read),
                                                        CTFMeanPolarTrimmed.DimsSlice,
                                                        StartParams.ToStruct(),
                                                        FitParams,
                                                        true);
                TempCTF.FromStruct(ResultStruct);
                TempCTF.Defocus = Math.Max(TempCTF.Defocus, MainWindow.Options.CTFZMin);

                CTFMeanPolarTrimmed.Dispose();

                UpdateRotationalAverage(true); // This doesn't have a nice background yet.
                UpdateBackgroundFit(); // Now get a reasonably nice background.

                UpdateRotationalAverage(true); // This time, with the nice background.
                UpdateBackgroundFit(); // Make the background even nicer!
            }
            else if (previousCTF != null)
            {
                TempCTF.DefocusDelta = previousCTF.DefocusDelta;
                TempCTF.DefocusAngle = previousCTF.DefocusAngle;
            }

            if (fixAstigmatism)
            {
                TempCTF.DefocusDelta = (decimal)astigmatism.X;
                TempCTF.DefocusAngle = (decimal)astigmatism.Y;
            }

            #endregion

            if (previousGrid == null)
                TempGrid = new CubicGrid(TempGrid.Dimensions, (float)TempCTF.Defocus, (float)TempCTF.Defocus, Dimension.X);

            // Do BFGS optimization of defocus, astigmatism and phase shift,
            // using 2D simulation for comparison

            #region BFGS

            bool[] CTFSpectraConsider = new bool[CTFSpectraGrid.Elements()];
            for (int i = 0; i < CTFSpectraConsider.Length; i++)
                CTFSpectraConsider[i] = true;
            int NCTFSpectraConsider = CTFSpectraConsider.Length;

            {
                Image CTFSpectraPolarTrimmed = CTFSpectra.AsPolar((uint)MinFreqInclusive, (uint)(MinFreqInclusive + NFreq));
                CTFSpectra.FreeDevice(); // This will only be needed again for the final PS1D.

                #region Create background and scale

                float[] CurrentScale = TempScale.Interp(TempPS1D.Select(p => p.X).ToArray());

                Image CTFSpectraScale = new Image(new int3(NFreq, DimsRegion.X, 1));
                float[] CTFSpectraScaleData = CTFSpectraScale.GetHost(Intent.Write)[0];

                // Trim polar to relevant frequencies, and populate coordinates.
                Parallel.For(0, DimsRegion.X, y =>
                {
                    for (int x = 0; x < NFreq; x++)
                        CTFSpectraScaleData[y * NFreq + x] = CurrentScale[x + MinFreqInclusive];
                });
                //CTFSpectraScale.WriteMRC("ctfspectrascale.mrc");

                // Background is just 1 line since we're in polar.
                Image CurrentBackground = new Image(TempBackground.Interp(TempPS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq).ToArray());

                #endregion

                CTFSpectraPolarTrimmed.SubtractFromLines(CurrentBackground);
                CurrentBackground.Dispose();

                // Normalize background-subtracted spectra.
                GPU.Normalize(CTFSpectraPolarTrimmed.GetDevice(Intent.Read),
                              CTFSpectraPolarTrimmed.GetDevice(Intent.Write),
                              (uint)CTFSpectraPolarTrimmed.ElementsSliceReal,
                              (uint)CTFSpectraGrid.Elements());
                //CTFSpectraPolarTrimmed.WriteMRC("ctfspectrapolartrimmed.mrc");

                #region Convert to fp16

                Image CTFSpectraPolarTrimmedHalf = CTFSpectraPolarTrimmed.AsHalf();
                CTFSpectraPolarTrimmed.Dispose();

                Image CTFSpectraScaleHalf = CTFSpectraScale.AsHalf();
                CTFSpectraScale.Dispose();
                Image CTFCoordsPolarTrimmedHalf = CTFCoordsPolarTrimmed.AsHalf();

                #endregion

                // 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 = TempGrid.GetWiggleWeights(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));

                // Helper method for getting CTFStructs for the entire spectra grid.
                Func<double[], CTF, float[], CTFStruct[]> EvalGetCTF = (input, ctf, defocusValues) =>
                {
                    decimal AlteredPhase = MainWindow.Options.CTFDoPhase ? (decimal)input[input.Length - 3] : 0;
                    decimal AlteredDelta = (decimal)input[input.Length - 2];
                    decimal AlteredAngle = (decimal)(input[input.Length - 1] * 20 / (Math.PI / 180));

                    CTF Local = ctf.GetCopy();
                    Local.PhaseShift = AlteredPhase;
                    Local.DefocusDelta = AlteredDelta;
                    Local.DefocusAngle = AlteredAngle;

                    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;
                    }

                    return LocalParams;
                };

                // Simulate with adjusted CTF, compare to originals

                #region Eval and Gradient methods

                Func<double[], double> Eval = input =>
                {
                    CubicGrid Altered = new CubicGrid(TempGrid.Dimensions, input.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v).ToArray());
                    float[] DefocusValues = Altered.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));

                    CTFStruct[] LocalParams = EvalGetCTF(input, TempCTF, DefocusValues);

                    float[] Result = new float[LocalParams.Length];

                    GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
                                        CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
                                        CTFSpectraScaleHalf.GetDevice(Intent.Read),
                                        (uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
                                        LocalParams,
                                        Result,
                                        (uint)LocalParams.Length);

                    float Score = 0;
                    for (int i = 0; i < Result.Length; i++)
                        if (CTFSpectraConsider[i])
                            Score += Result[i];

                    Score /= NCTFSpectraConsider;

                    if (float.IsNaN(Score) || float.IsInfinity(Score))
                        throw new Exception("Bad score.");

                    return (1.0 - Score) * 1000.0;
                };

                Func<double[], double[]> Gradient = input =>
                {
                    const float Step = 0.005f;
                    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 - 3;
                    //int StartComponent = 0;
                    for (int i = StartComponent; i < input.Length; i++)
                    {
                        if (fixAstigmatism && i > StartComponent)
                            continue;

                        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[CTFSpectraGrid.Elements()];
                    float[] ResultMinus = new float[CTFSpectraGrid.Elements()];

                    // ..., take shortcut for defoci...
                    {
                        {
                            CubicGrid AlteredPlus = new CubicGrid(TempGrid.Dimensions, input.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v + Step).ToArray());
                            float[] DefocusValues = AlteredPlus.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));

                            CTFStruct[] LocalParams = EvalGetCTF(input, TempCTF, DefocusValues);

                            GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFSpectraScaleHalf.GetDevice(Intent.Read),
                                                (uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
                                                LocalParams,
                                                ResultPlus,
                                                (uint)LocalParams.Length);
                        }
                        {
                            CubicGrid AlteredMinus = new CubicGrid(TempGrid.Dimensions, input.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v - Step).ToArray());
                            float[] DefocusValues = AlteredMinus.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));

                            CTFStruct[] LocalParams = EvalGetCTF(input, TempCTF, DefocusValues);

                            GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
                                                CTFSpectraScaleHalf.GetDevice(Intent.Read),
                                                (uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
                                                LocalParams,
                                                ResultMinus,
                                                (uint)LocalParams.Length);
                        }
                        float[] LocalGradients = new float[ResultPlus.Length];
                        for (int i = 0; i < LocalGradients.Length; i++)
                            LocalGradients[i] = ResultMinus[i] - ResultPlus[i];

                        // Now compute gradients per grid anchor point using the precomputed individual gradients and wiggle factors.
                        Parallel.For(0, TempGrid.Dimensions.Elements(), i => Result[i] = MathHelper.ReduceWeighted(LocalGradients, WiggleWeights[i]) / LocalGradients.Length / (2f * Step) * 1000f);
                    }

                    foreach (var i in Result)
                        if (double.IsNaN(i) || double.IsInfinity(i))
                            throw new Exception("Bad score.");

                    return Result;
                };

                #endregion

                #region Minimize first time with potential outpiers

                double[] StartParams = new double[TempGrid.Dimensions.Elements() + 3];
                for (int i = 0; i < TempGrid.Dimensions.Elements(); i++)
                    StartParams[i] = TempGrid.FlatValues[i];
                StartParams[StartParams.Length - 3] = (double)TempCTF.PhaseShift;
                StartParams[StartParams.Length - 2] = (double)TempCTF.DefocusDelta;
                StartParams[StartParams.Length - 1] = (double)TempCTF.DefocusAngle / 20 * (Math.PI / 180);

                // Compute correlation for individual spectra, and throw away those that are >.75 sigma worse than mean.

                BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Gradient)
                {
                    Past = 1,
                    Delta = 1e-6,
                    MaxLineSearch = 15,
                    Corrections = 20
                };
                Optimizer.Minimize(StartParams);

                #endregion

                #region Retrieve parameters

                TempCTF.Defocus = (decimal)MathHelper.Mean(Optimizer.Solution.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v));
                TempCTF.PhaseShift = (decimal)Optimizer.Solution[StartParams.Length - 3];
                TempCTF.DefocusDelta = (decimal)Optimizer.Solution[StartParams.Length - 2];
                TempCTF.DefocusAngle = (decimal)(Optimizer.Solution[StartParams.Length - 1] * 20 / (Math.PI / 180));

                if (TempCTF.DefocusDelta < 0)
                {
                    TempCTF.DefocusAngle += 90;
                    TempCTF.DefocusDelta *= -1;
                }
                TempCTF.DefocusAngle = ((int)TempCTF.DefocusAngle + 180 * 99) % 180;

                TempGrid = new CubicGrid(TempGrid.Dimensions, Optimizer.Solution.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v).ToArray());

                #endregion

                // Dispose GPU resources manually because GC can't be bothered to do it in time.
                CTFSpectraPolarTrimmedHalf.Dispose();
                CTFCoordsPolarTrimmedHalf.Dispose();
                CTFSpectraScaleHalf.Dispose();

                #region Get nicer envelope fit

                {
                    {
                        Image CTFSpectraBackground = new Image(new int3(DimsRegion), true);
                        float[] CTFSpectraBackgroundData = CTFSpectraBackground.GetHost(Intent.Write)[0];

                        // Construct background in Cartesian coordinates.
                        Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) =>
                        {
                            CTFSpectraBackgroundData[y * CTFSpectraBackground.DimsEffective.X + x] = TempBackground.Interp(r / DimsRegion.X);
                        });

                        CTFSpectra.SubtractFromSlices(CTFSpectraBackground);

                        float[] DefocusValues = TempGrid.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));
                        CTFStruct[] LocalParams = DefocusValues.Select(v =>
                        {
                            CTF Local = TempCTF.GetCopy();
                            Local.Defocus = (decimal)v + 0.0M;

                            return Local.ToStruct();
                        }).ToArray();

                        Image CTFAverage1D = new Image(IntPtr.Zero, new int3(DimsRegion.X / 2, 1, 1));

                        CTF CTFAug = TempCTF.GetCopy();
                        CTFAug.Defocus += 0.0M;
                        GPU.CTFMakeAverage(CTFSpectra.GetDevice(Intent.Read),
                                           CTFCoordsCart.GetDevice(Intent.Read),
                                           (uint)CTFSpectra.ElementsSliceReal,
                                           (uint)DimsRegion.X,
                                           LocalParams,
                                           CTFAug.ToStruct(),
                                           0,
                                           (uint)DimsRegion.X / 2,
                                           CTFSpectraConsider.Select(v => v ? 1 : 0).ToArray(),
                                           (uint)CTFSpectraGrid.Elements(),
                                           CTFAverage1D.GetDevice(Intent.Write));

                        CTFSpectra.AddToSlices(CTFSpectraBackground);

                        float[] RotationalAverageData = CTFAverage1D.GetHost(Intent.Read)[0];
                        float2[] ForPS1D = new float2[TempPS1D.Length];
                        for (int i = 0; i < ForPS1D.Length; i++)
                            ForPS1D[i] = new float2((float)i / DimsRegion.X, (float)Math.Round(RotationalAverageData[i], 4) + TempBackground.Interp((float)i / DimsRegion.X));
                        MathHelper.UnNaN(ForPS1D);
                        TempPS1D = ForPS1D;

                        CTFSpectraBackground.Dispose();
                        CTFAverage1D.Dispose();
                        CTFSpectra.FreeDevice();
                    }

                    TempCTF.Defocus = Math.Max(TempCTF.Defocus, MainWindow.Options.CTFZMin);
                    UpdateBackgroundFit();
                }

                #endregion
            }

            #endregion

            // Subtract background from 2D average and write it to disk.
            // This image is used for quick visualization purposes only.

            #region PS2D update

            {
                int3 DimsAverage = new int3(DimsRegion.X, DimsRegion.X / 2, 1);
                float[] Average2DData = new float[DimsAverage.Elements()];
                float[] OriginalAverageData = CTFMean.GetHost(Intent.Read)[0];

                for (int y = 0; y < DimsAverage.Y; y++)
                {
                    int yy = y * y;
                    for (int x = 0; x < DimsAverage.Y; x++)
                    {
                        int xx = DimsRegion.X / 2 - x - 1;
                        xx *= xx;
                        float r = (float)Math.Sqrt(xx + yy) / DimsRegion.X;
                        Average2DData[y * DimsAverage.X + x] = OriginalAverageData[(y + DimsRegion.X / 2) * (DimsRegion.X / 2 + 1) + x] - TempBackground.Interp(r);
                    }

                    for (int x = 0; x < DimsRegion.X / 2; x++)
                    {
                        int xx = x * x;
                        float r = (float)Math.Sqrt(xx + yy) / DimsRegion.X;
                        Average2DData[y * DimsAverage.X + x + DimsRegion.X / 2] = OriginalAverageData[(DimsRegion.X / 2 - y) * (DimsRegion.X / 2 + 1) + (DimsRegion.X / 2 - 1 - x)] - TempBackground.Interp(r);
                    }
                }

                thisPS2D = new Image(Average2DData, DimsAverage);
            }

            #endregion

            for (int i = 0; i < TempPS1D.Length; i++)
                TempPS1D[i].Y -= TempBackground.Interp(TempPS1D[i].X);

            CTFSpectra.Dispose();
            CTFMean.Dispose();
            CTFCoordsCart.Dispose();
            CTFCoordsPolarTrimmed.Dispose();

            thisPS1D = TempPS1D;
            thisBackground = TempBackground;
            thisScale = TempScale;
            thisCTF = TempCTF;
            thisGrid = TempGrid;
        }
예제 #19
0
파일: GPU.cs 프로젝트: dtegunov/warp
 public static extern CTFStruct CTFFitMean(IntPtr d_ps, 
                                           IntPtr d_pscoords, 
                                           int2 dims, 
                                           CTFStruct startparams, 
                                           CTFFitStruct fp, 
                                           bool doastigmatism);
예제 #20
0
파일: TiltSeries.cs 프로젝트: dtegunov/warp
        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;
        }
예제 #21
0
파일: GPU.cs 프로젝트: dtegunov/warp
 public static extern void ParticleCTFCompareToSim(IntPtr d_ps,
                                                   IntPtr d_pscoords,
                                                   IntPtr d_ref,
                                                   IntPtr d_invsigma,
                                                   uint length,
                                                   CTFStruct[] h_sourceparams,
                                                   float[] h_scores,
                                                   uint nframes,
                                                   uint batch);
예제 #22
0
파일: GPU.cs 프로젝트: dtegunov/warp
 public static extern void ParticleCTFMakeAverage(IntPtr d_ps,
                                                  IntPtr d_pscoords,
                                                  uint length,
                                                  uint sidelength,
                                                  CTFStruct[] h_sourceparams,
                                                  CTFStruct targetparams,
                                                  uint minbin,
                                                  uint maxbin,
                                                  uint batch,
                                                  IntPtr d_output);
예제 #23
0
파일: GPU.cs 프로젝트: dtegunov/warp
 public static extern void PolishingGetDiff(IntPtr d_phase,
                                            IntPtr d_average,
                                            IntPtr d_shiftfactors,
                                            IntPtr d_ctfcoords,
                                            CTFStruct[] h_ctfparams,
                                            IntPtr d_invsigma,
                                            int2 dims,
                                            IntPtr d_shifts,
                                            float[] h_diff,
                                            float[] h_diffall,
                                            uint npositions,
                                            uint nframes);
예제 #24
0
파일: CTF.cs 프로젝트: dtegunov/warp
        public CTFStruct ToStruct()
        {
            CTFStruct Result = new CTFStruct();

            Result.PixelSize = (float)(PixelSize * 1e-10M);
            Result.PixelSizeDelta = (float)(PixelSizeDelta * 1e-10M);
            Result.PixelSizeAngle = (float)PixelSizeAngle / (float)(180.0 / Math.PI);

            Result.Cs = (float)(Cs * 1e-3M);
            Result.Voltage = (float)(Voltage * 1e3M);
            Result.Amplitude = (float)Amplitude;

            Result.Defocus = (float)(-Defocus * 1e-6M);
            Result.DefocusDelta = (float)(-DefocusDelta * 1e-6M);
            Result.AstigmatismAngle = (float)DefocusAngle / (float)(180.0 / Math.PI);

            Result.Bfactor = (float)(Bfactor * 1e-20M);
            Result.Scale = (float)Scale;

            Result.PhaseShift = (float)(PhaseShift * (decimal)Math.PI);

            return Result;
        }
예제 #25
0
파일: Movie.cs 프로젝트: dtegunov/warp
        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();
        }