public static MapHeader ReadFromFile(BinaryReader reader, FileInfo info, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType) { MapHeader Header = null; if (info.Extension.ToLower() == ".mrc" || info.Extension.ToLower() == ".mrcs" || info.Extension.ToLower() == ".ali" || info.Extension.ToLower() == ".rec" || info.Extension.ToLower() == ".st") { Header = new HeaderMRC(reader); } else if (info.Extension.ToLower() == ".em") { Header = new HeaderEM(reader); } else if (info.Extension.ToLower() == ".tif" || info.Extension.ToLower() == ".tiff") { Header = new HeaderTiff(info.FullName); } else if (info.Extension.ToLower() == ".dat") { long SliceElements = headerlessSliceDims.Elements() * ImageFormatsHelper.SizeOf(headerlessType); long Slices = (info.Length - headerlessOffset) / SliceElements; int3 Dims3 = new int3(headerlessSliceDims.X, headerlessSliceDims.Y, (int)Slices); Header = new HeaderRaw(Dims3, headerlessOffset, headerlessType); } else { throw new Exception("File type not supported."); } return(Header); }
public static MapHeader ReadFromFile(BinaryReader reader, string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, Stream stream = null) { MapHeader Header = null; string Extension = Helper.PathToExtension(path).ToLower(); if (Extension == ".mrc" || Extension == ".mrcs" || Extension == ".rec" || Extension == ".st") Header = new HeaderMRC(reader); else if (Extension == ".em") Header = new HeaderEM(reader); else if (Extension == ".dm4" || Extension == ".dm3") Header = new HeaderDM4(reader); else if (Extension == ".tif" || Extension == ".tiff") Header = new HeaderTiff(path, stream); else if (Extension == ".eer") Header = new HeaderEER(path, stream); else if (Extension == ".dat") { FileInfo info = new FileInfo(path); long SliceElements = headerlessSliceDims.Elements() * ImageFormatsHelper.SizeOf(headerlessType); long Slices = (info.Length - headerlessOffset) / SliceElements; int3 Dims3 = new int3(headerlessSliceDims.X, headerlessSliceDims.Y, (int)Slices); Header = new HeaderRaw(Dims3, headerlessOffset, headerlessType); } else throw new Exception("File type not supported."); return Header; }
public static MapHeader ReadFromFile(string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType) { MapHeader Header = null; FileInfo Info = new FileInfo(path); using (BinaryReader Reader = new BinaryReader(File.OpenRead(path))) { Header = ReadFromFile(Reader, Info, headerlessSliceDims, headerlessOffset, headerlessType); } return(Header); }
public static MapHeader ReadFromFile(string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, bool isBigEndian, Stream stream = null) { MapHeader Header = null; if (GetHeaderType(path) != typeof(HeaderTiff)) using (BinaryReader Reader = isBigEndian ? new BinaryReaderBE(File.OpenRead(path)) : new BinaryReader(File.OpenRead(path))) { Header = ReadFromFile(Reader, path, headerlessSliceDims, headerlessOffset, headerlessType); } else Header = ReadFromFile(null, path, headerlessSliceDims, headerlessOffset, headerlessType, stream); return Header; }
public static MapHeader ReadFromFile(string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType, Stream stream = null) { try { MapHeader Result = ReadFromFile(path, headerlessSliceDims, headerlessOffset, headerlessType, false, stream); if (Result.Dimensions.X < 0 || Result.Dimensions.Y < 0 || Result.Dimensions.Z < 0 || (Result.Dimensions.ElementsSlice() > 1 && Result.Dimensions.Z > 9999999)) throw new Exception(); return Result; } catch { return ReadFromFile(path, headerlessSliceDims, headerlessOffset, headerlessType, true, stream); } }
public static MapHeader ReadFromFilePatient(int attempts, int mswait, string path, int2 headerlessSliceDims, long headerlessOffset, Type headerlessType) { MapHeader Result = null; for (int a = 0; a < attempts; a++) { try { Result = ReadFromFile(path, headerlessSliceDims, headerlessOffset, headerlessType); break; } catch { Thread.Sleep(mswait); } } if (Result == null) throw new Exception("Could not successfully read file within the specified number of attempts."); return Result; }
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(); }
public void PerformComparison(MapHeader originalHeader, Star stardata, Image refft, Image maskft, decimal scaleFactor) { int NFrames = originalHeader.Dimensions.Z; int2 DimsImage = new int2(originalHeader.Dimensions); float3[] PositionsGrid; float3[] PositionsShift; float3[] ParticleAngles; List<int> RowIndices = new List<int>(); { string[] ColumnNames = stardata.GetColumn("rlnMicrographName"); for (int i = 0; i < ColumnNames.Length; i++) if (ColumnNames[i].Contains(RootName)) RowIndices.Add(i); string[] ColumnOriginX = stardata.GetColumn("rlnCoordinateX"); string[] ColumnOriginY = stardata.GetColumn("rlnCoordinateY"); string[] ColumnShiftX = stardata.GetColumn("rlnOriginX"); string[] ColumnShiftY = stardata.GetColumn("rlnOriginY"); string[] ColumnAngleRot = stardata.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = stardata.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = stardata.GetColumn("rlnAnglePsi"); PositionsGrid = new float3[RowIndices.Count]; PositionsShift = new float3[RowIndices.Count]; ParticleAngles = new float3[RowIndices.Count]; { int i = 0; foreach (var nameIndex in RowIndices) { float OriginX = float.Parse(ColumnOriginX[nameIndex]); float OriginY = float.Parse(ColumnOriginY[nameIndex]); float ShiftX = float.Parse(ColumnShiftX[nameIndex]); float ShiftY = float.Parse(ColumnShiftY[nameIndex]); PositionsGrid[i] = new float3((OriginX - ShiftX) / DimsImage.X, (OriginY - ShiftY) / DimsImage.Y, 0); PositionsShift[i] = new float3(ShiftX, ShiftY, 0f); ParticleAngles[i] = new float3(-float.Parse(ColumnAngleRot[nameIndex]) * Helper.ToRad, -float.Parse(ColumnAngleTilt[nameIndex]) * Helper.ToRad, -float.Parse(ColumnAnglePsi[nameIndex]) * Helper.ToRad); i++; } } } int NPositions = PositionsGrid.Length; if (NPositions == 0) return; Image Particles = StageDataLoad.LoadMap(ParticlesPath, new int2(1, 1), 0, typeof (float)); int2 DimsRegion = new int2(Particles.Dims.X, Particles.Dims.X); Particles.ShiftSlices(PositionsShift); int MinFreqInclusive = (int)(MainWindow.Options.MovementRangeMin * DimsRegion.X / 2); int MaxFreqExclusive = (int)(MainWindow.Options.MovementRangeMax * DimsRegion.X / 2); int NFreq = MaxFreqExclusive - MinFreqInclusive; Image ParticleMasksFT = maskft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); Image ParticleMasks = ParticleMasksFT.AsIFFT(); ParticleMasksFT.Dispose(); ParticleMasks.RemapFromFT(); Parallel.ForEach(ParticleMasks.GetHost(Intent.ReadWrite), slice => { for (int i = 0; i < slice.Length; i++) slice[i] = (Math.Max(2f, Math.Min(25f, slice[i])) - 2) / 23f; }); Image ProjectionsFT = refft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); Image Projections = ProjectionsFT.AsIFFT(); ProjectionsFT.Dispose(); // Addresses for CTF simulation Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true); { float2[] CoordsData = new float2[CTFCoordsCart.ElementsSliceComplex]; Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) => CoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, a)); CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData }); CTFCoordsCart.RemapToFT(); } float[] ValuesDefocus = GridCTF.GetInterpolatedNative(PositionsGrid); CTFStruct[] PositionsCTF = ValuesDefocus.Select(v => { CTF Altered = CTF.GetCopy(); Altered.Defocus = (decimal)v; //Altered.Bfactor = -MainWindow.Options.MovementBfactor; return Altered.ToStruct(); }).ToArray(); Image Scores = new Image(IntPtr.Zero, new int3(NPositions, 1, 1)); GPU.CompareParticles(Particles.GetDevice(Intent.Read), ParticleMasks.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), DimsRegion, CTFCoordsCart.GetDevice(Intent.Read), PositionsCTF, MinFreqInclusive, MaxFreqExclusive, Scores.GetDevice(Intent.Write), (uint)NPositions); float[] ScoresData = Scores.GetHost(Intent.Read)[0]; for (int p = 0; p < NPositions; p++) { stardata.SetRowValue(RowIndices[p], "rlnCtfFigureOfMerit", ScoresData[p].ToString(CultureInfo.InvariantCulture)); } Scores.Dispose(); Projections.Dispose(); ParticleMasks.Dispose(); CTFCoordsCart.Dispose(); Particles.Dispose(); }
public void ExportParticlesMovie(Star tableIn, Star tableOut, MapHeader originalHeader, Image originalStack, int size, float particleradius, decimal scaleFactor) { int CurrentDevice = GPU.GetDevice(); #region Make sure directories exist. lock (tableIn) { if (!Directory.Exists(ParticleMoviesDir)) Directory.CreateDirectory(ParticleMoviesDir); if (!Directory.Exists(ParticleCTFMoviesDir)) Directory.CreateDirectory(ParticleCTFMoviesDir); } #endregion #region Get row indices for all, and individual halves List<int> RowIndices = new List<int>(); string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName"); for (int i = 0; i < ColumnMicrographName.Length; i++) if (ColumnMicrographName[i].Contains(RootName)) RowIndices.Add(i); //RowIndices = RowIndices.Take(13).ToList(); List<int> RowIndices1 = new List<int>(); List<int> RowIndices2 = new List<int>(); for (int i = 0; i < RowIndices.Count; i++) if (tableIn.GetRowValue(RowIndices[i], "rlnRandomSubset") == "1") RowIndices1.Add(RowIndices[i]); else RowIndices2.Add(RowIndices[i]); #endregion if (RowIndices.Count == 0) return; #region Auxiliary variables List<int> TableOutIndices = new List<int>(); int3 Dims = originalHeader.Dimensions; Dims.Z = 36; int3 DimsRegion = new int3(size, size, 1); int3 DimsPadded = new int3(size * 2, size * 2, 1); int NParticles = RowIndices.Count; int NParticles1 = RowIndices1.Count; int NParticles2 = RowIndices2.Count; float PixelSize = (float)CTF.PixelSize / 1.00f; float PixelDelta = (float)CTF.PixelSizeDelta / 1.00f; float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad; #endregion #region Prepare initial coordinates and shifts string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); int3[] Origins1 = new int3[NParticles1]; int3[] Origins2 = new int3[NParticles2]; float3[] ResidualShifts1 = new float3[NParticles1]; float3[] ResidualShifts2 = new float3[NParticles2]; lock (tableIn) // Writing to the table, better be on the safe side { // Half1: Add translational shifts to coordinates, sans the fractional part for (int i = 0; i < NParticles1; i++) { float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices1[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices1[i]], CultureInfo.InvariantCulture)) * 1.00f; float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices1[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices1[i]], CultureInfo.InvariantCulture)) * 1.00f; Origins1[i] = new int3((int)(Pos.X - Shift.X), (int)(Pos.Y - Shift.Y), 0); ResidualShifts1[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X), -MathHelper.ResidualFraction(Pos.Y - Shift.Y), 0f); tableIn.SetRowValue(RowIndices1[i], "rlnCoordinateX", Origins1[i].X.ToString()); tableIn.SetRowValue(RowIndices1[i], "rlnCoordinateY", Origins1[i].Y.ToString()); tableIn.SetRowValue(RowIndices1[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices1[i], "rlnOriginY", "0.0"); } // Half2: Add translational shifts to coordinates, sans the fractional part for (int i = 0; i < NParticles2; i++) { float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices2[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices2[i]], CultureInfo.InvariantCulture)) * 1.00f; float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices2[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices2[i]], CultureInfo.InvariantCulture)) * 1.00f; Origins2[i] = new int3((int)(Pos.X - Shift.X), (int)(Pos.Y - Shift.Y), 0); ResidualShifts2[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X), -MathHelper.ResidualFraction(Pos.Y - Shift.Y), 0f); tableIn.SetRowValue(RowIndices2[i], "rlnCoordinateX", Origins2[i].X.ToString()); tableIn.SetRowValue(RowIndices2[i], "rlnCoordinateY", Origins2[i].Y.ToString()); tableIn.SetRowValue(RowIndices2[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices2[i], "rlnOriginY", "0.0"); } } #endregion #region Allocate memory for particle and PS stacks Image ParticleStackAll = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles * Dims.Z)); Image ParticleStack1 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1 * Dims.Z)); Image ParticleStack2 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2 * Dims.Z)); Image PSStackAll = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles * Dims.Z), true); Image PSStack1 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1 * Dims.Z), true); Image PSStack2 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2 * Dims.Z), true); Image FrameParticles1 = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles1)); Image FrameParticles2 = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles2)); float[][] ParticleStackData = ParticleStackAll.GetHost(Intent.Write); float[][] ParticleStackData1 = ParticleStack1.GetHost(Intent.Write); float[][] ParticleStackData2 = ParticleStack2.GetHost(Intent.Write); float[][] PSStackData = PSStackAll.GetHost(Intent.Write); float[][] PSStackData1 = PSStack1.GetHost(Intent.Write); float[][] PSStackData2 = PSStack2.GetHost(Intent.Write); #endregion #region Create rows in outTable lock (tableOut) // Creating rows in outTable, this absolutely needs to be staged sequentially { for (int z = 0; z < Dims.Z; z++) { for (int i = 0; i < NParticles; i++) { int Index = i < NParticles1 ? RowIndices1[i] : RowIndices2[i - NParticles1]; string OriParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs"; string ParticleName = (z * NParticles + i + 1).ToString("D6") + "@particlemovies/" + RootName + "_particles.mrcs"; string ParticleCTFName = (z * NParticles + i + 1).ToString("D6") + "@particlectfmovies/" + RootName + "_particlectf.mrcs"; List<string> NewRow = tableIn.GetRow(Index).Select(v => v).ToList(); // Get copy of original row. NewRow[tableOut.GetColumnIndex("rlnOriginalParticleName")] = OriParticlePath; NewRow[tableOut.GetColumnIndex("rlnAngleRotPrior")] = tableIn.GetRowValue(Index, "rlnAngleRot"); NewRow[tableOut.GetColumnIndex("rlnAngleTiltPrior")] = tableIn.GetRowValue(Index, "rlnAngleTilt"); NewRow[tableOut.GetColumnIndex("rlnAnglePsiPrior")] = tableIn.GetRowValue(Index, "rlnAnglePsi"); NewRow[tableOut.GetColumnIndex("rlnOriginXPrior")] = "0.0"; NewRow[tableOut.GetColumnIndex("rlnOriginYPrior")] = "0.0"; NewRow[tableOut.GetColumnIndex("rlnImageName")] = ParticleName; NewRow[tableOut.GetColumnIndex("rlnCtfImage")] = ParticleCTFName; NewRow[tableOut.GetColumnIndex("rlnMicrographName")] = (z + 1).ToString("D6") + "@stack/" + RootName + "_movie.mrcs"; TableOutIndices.Add(tableOut.RowCount); tableOut.AddRow(NewRow); } } } #endregion #region For every frame, extract particles from each half; shift, correct, and norm them float StepZ = 1f / Math.Max(Dims.Z - 1, 1); for (int z = 0; z < Dims.Z; z++) { float CoordZ = z * StepZ; #region Extract, correct, and norm particles #region Half 1 { if (originalStack != null) GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read), FrameParticles1.GetDevice(Intent.Write), Dims.Slice(), DimsPadded, Helper.ToInterleaved(Origins1.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()), (uint)NParticles1); // Shift particles { float3[] Shifts = new float3[NParticles1]; for (int i = 0; i < NParticles1; i++) { float3 Coords = new float3((float)Origins1[i].X / Dims.X, (float)Origins1[i].Y / Dims.Y, CoordZ); Shifts[i] = ResidualShifts1[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f; } FrameParticles1.ShiftSlices(Shifts); } Image FrameParticlesCropped = FrameParticles1.AsPadded(new int2(DimsRegion)); Image FrameParticlesCorrected = FrameParticlesCropped.AsAnisotropyCorrected(new int2(DimsRegion), PixelSize + PixelDelta / 2f, PixelSize - PixelDelta / 2f, PixelAngle, 6); FrameParticlesCropped.Dispose(); GPU.NormParticles(FrameParticlesCorrected.GetDevice(Intent.Read), FrameParticlesCorrected.GetDevice(Intent.Write), DimsRegion, (uint)(particleradius / PixelSize), true, (uint)NParticles1); float[][] FrameParticlesCorrectedData = FrameParticlesCorrected.GetHost(Intent.Read); for (int n = 0; n < NParticles1; n++) { ParticleStackData[z * NParticles + n] = FrameParticlesCorrectedData[n]; ParticleStackData1[z * NParticles1 + n] = FrameParticlesCorrectedData[n]; } //FrameParticlesCorrected.WriteMRC("intermediate_particles1.mrc"); FrameParticlesCorrected.Dispose(); } #endregion #region Half 2 { if (originalStack != null) GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read), FrameParticles2.GetDevice(Intent.Write), Dims.Slice(), DimsPadded, Helper.ToInterleaved(Origins2.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()), (uint)NParticles2); // Shift particles { float3[] Shifts = new float3[NParticles2]; for (int i = 0; i < NParticles2; i++) { float3 Coords = new float3((float)Origins2[i].X / Dims.X, (float)Origins2[i].Y / Dims.Y, CoordZ); Shifts[i] = ResidualShifts2[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f; } FrameParticles2.ShiftSlices(Shifts); } Image FrameParticlesCropped = FrameParticles2.AsPadded(new int2(DimsRegion)); Image FrameParticlesCorrected = FrameParticlesCropped.AsAnisotropyCorrected(new int2(DimsRegion), PixelSize + PixelDelta / 2f, PixelSize - PixelDelta / 2f, PixelAngle, 6); FrameParticlesCropped.Dispose(); GPU.NormParticles(FrameParticlesCorrected.GetDevice(Intent.Read), FrameParticlesCorrected.GetDevice(Intent.Write), DimsRegion, (uint)(particleradius / PixelSize), true, (uint)NParticles2); float[][] FrameParticlesCorrectedData = FrameParticlesCorrected.GetHost(Intent.Read); for (int n = 0; n < NParticles2; n++) { ParticleStackData[z * NParticles + NParticles1 + n] = FrameParticlesCorrectedData[n]; ParticleStackData2[z * NParticles2 + n] = FrameParticlesCorrectedData[n]; } //FrameParticlesCorrected.WriteMRC("intermediate_particles2.mrc"); FrameParticlesCorrected.Dispose(); } #endregion #endregion #region PS Half 1 { Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1), true); PS.Fill(1f); // Apply motion blur filter. #region Motion blur weighting { const int Samples = 11; float StartZ = (z - 0.5f) * StepZ; float StopZ = (z + 0.5f) * StepZ; float2[] Shifts = new float2[Samples * NParticles1]; for (int p = 0; p < NParticles1; p++) { float NormX = (float)Origins1[p].X / Dims.X; float NormY = (float)Origins1[p].Y / Dims.Y; for (int zz = 0; zz < Samples; zz++) { float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz; float3 Coords = new float3(NormX, NormY, zp); Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords) * 1.00f; } } Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles1), true); GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write), DimsRegion, Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()), Samples, (uint)NParticles1); PS.Multiply(MotionFilter); //MotionFilter.WriteMRC("motion.mrc"); MotionFilter.Dispose(); } #endregion float[][] PSData = PS.GetHost(Intent.Read); for (int n = 0; n < NParticles1; n++) PSStackData[z * NParticles + n] = PSData[n]; //PS.WriteMRC("intermediate_ps1.mrc"); PS.Dispose(); } #endregion #region PS Half 2 { Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2), true); PS.Fill(1f); // Apply motion blur filter. #region Motion blur weighting { const int Samples = 11; float StartZ = (z - 0.5f) * StepZ; float StopZ = (z + 0.5f) * StepZ; float2[] Shifts = new float2[Samples * NParticles2]; for (int p = 0; p < NParticles2; p++) { float NormX = (float)Origins2[p].X / Dims.X; float NormY = (float)Origins2[p].Y / Dims.Y; for (int zz = 0; zz < Samples; zz++) { float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz; float3 Coords = new float3(NormX, NormY, zp); Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords) * 1.00f; } } Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles2), true); GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write), DimsRegion, Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()), Samples, (uint)NParticles2); PS.Multiply(MotionFilter); //MotionFilter.WriteMRC("motion.mrc"); MotionFilter.Dispose(); } #endregion float[][] PSData = PS.GetHost(Intent.Read); for (int n = 0; n < NParticles2; n++) PSStackData[z * NParticles + NParticles1 + n] = PSData[n]; //PS.WriteMRC("intermediate_ps2.mrc"); PS.Dispose(); } #endregion } FrameParticles1.Dispose(); FrameParticles2.Dispose(); originalStack.FreeDevice(); #endregion HeaderMRC ParticlesHeader = new HeaderMRC { Pixelsize = new float3(PixelSize, PixelSize, PixelSize) }; // Do translation and rotation BFGS per particle { float MaxHigh = 2.6f; CubicGrid GridX = new CubicGrid(new int3(NParticles1, 1, 2)); CubicGrid GridY = new CubicGrid(new int3(NParticles1, 1, 2)); CubicGrid GridRot = new CubicGrid(new int3(NParticles1, 1, 2)); CubicGrid GridTilt = new CubicGrid(new int3(NParticles1, 1, 2)); CubicGrid GridPsi = new CubicGrid(new int3(NParticles1, 1, 2)); int2 DimsCropped = new int2(DimsRegion / (MaxHigh / PixelSize / 2f)) / 2 * 2; #region Get coordinates for CTF and Fourier-space shifts Image CTFCoords; Image ShiftFactors; { float2[] CTFCoordsData = new float2[(DimsCropped.X / 2 + 1) * DimsCropped.Y]; float2[] ShiftFactorsData = new float2[(DimsCropped.X / 2 + 1) * DimsCropped.Y]; for (int y = 0; y < DimsCropped.Y; y++) for (int x = 0; x < DimsCropped.X / 2 + 1; x++) { int xx = x; int yy = y < DimsCropped.Y / 2 + 1 ? y : y - DimsCropped.Y; float xs = xx / (float)DimsRegion.X; float ys = yy / (float)DimsRegion.Y; float r = (float)Math.Sqrt(xs * xs + ys * ys); float angle = (float)(Math.Atan2(yy, xx)); CTFCoordsData[y * (DimsCropped.X / 2 + 1) + x] = new float2(r / PixelSize, angle); ShiftFactorsData[y * (DimsCropped.X / 2 + 1) + x] = new float2((float)-xx / DimsRegion.X * 2f * (float)Math.PI, (float)-yy / DimsRegion.X * 2f * (float)Math.PI); } CTFCoords = new Image(CTFCoordsData, new int3(DimsCropped), true); ShiftFactors = new Image(ShiftFactorsData, new int3(DimsCropped), true); } #endregion #region Get inverse sigma2 spectrum for this micrograph from Relion's model.star Image Sigma2Noise = new Image(new int3(DimsCropped), true); { int GroupNumber = int.Parse(tableIn.GetRowValue(RowIndices[0], "rlnGroupNumber")); //Star SigmaTable = new Star("D:\\rado27\\Refine3D\\run1_ct5_it009_half1_model.star", "data_model_group_" + GroupNumber); Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber); float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray(); float[] Sigma2NoiseData = Sigma2Noise.GetHost(Intent.Write)[0]; Helper.ForEachElementFT(DimsCropped, (x, y, xx, yy, r, angle) => { int ir = (int)r; float val = 0; if (ir < SigmaValues.Length && ir >= size / (50f / PixelSize) && ir < DimsCropped.X / 2) { if (SigmaValues[ir] != 0f) val = 1f / SigmaValues[ir]; } Sigma2NoiseData[y * (DimsCropped.X / 2 + 1) + x] = val; }); float MaxSigma = MathHelper.Max(Sigma2NoiseData); for (int i = 0; i < Sigma2NoiseData.Length; i++) Sigma2NoiseData[i] /= MaxSigma; Sigma2Noise.RemapToFT(); } //Sigma2Noise.WriteMRC("d_sigma2noise.mrc"); #endregion #region Initialize particle angles for both halves float3[] ParticleAngles1 = new float3[NParticles1]; float3[] ParticleAngles2 = new float3[NParticles2]; for (int p = 0; p < NParticles1; p++) ParticleAngles1[p] = new float3(float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAngleRot")), float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAngleTilt")), float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAnglePsi"))); for (int p = 0; p < NParticles2; p++) ParticleAngles2[p] = new float3(float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAngleRot")), float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAngleTilt")), float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAnglePsi"))); #endregion #region Prepare masks Image Masks1, Masks2; { // Half 1 { Image Volume = StageDataLoad.LoadMap(MainWindow.Options.MaskPath, new int2(1, 1), 0, typeof (float)); Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); Image VolMaskFT = VolumePadded.AsFFT(true); VolumePadded.Dispose(); Image MasksFT = VolMaskFT.AsProjections(ParticleAngles1.Select(v => new float3(v.X * Helper.ToRad, v.Y * Helper.ToRad, v.Z * Helper.ToRad)).ToArray(), new int2(DimsRegion), MainWindow.Options.ProjectionOversample); VolMaskFT.Dispose(); Masks1 = MasksFT.AsIFFT(); MasksFT.Dispose(); Masks1.RemapFromFT(); Parallel.ForEach(Masks1.GetHost(Intent.ReadWrite), slice => { for (int i = 0; i < slice.Length; i++) slice[i] = (Math.Max(2f, Math.Min(50f, slice[i])) - 2) / 48f; }); } // Half 2 { Image Volume = StageDataLoad.LoadMap(MainWindow.Options.MaskPath, new int2(1, 1), 0, typeof(float)); Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); Image VolMaskFT = VolumePadded.AsFFT(true); VolumePadded.Dispose(); Image MasksFT = VolMaskFT.AsProjections(ParticleAngles2.Select(v => new float3(v.X * Helper.ToRad, v.Y * Helper.ToRad, v.Z * Helper.ToRad)).ToArray(), new int2(DimsRegion), MainWindow.Options.ProjectionOversample); VolMaskFT.Dispose(); Masks2 = MasksFT.AsIFFT(); MasksFT.Dispose(); Masks2.RemapFromFT(); Parallel.ForEach(Masks2.GetHost(Intent.ReadWrite), slice => { for (int i = 0; i < slice.Length; i++) slice[i] = (Math.Max(2f, Math.Min(50f, slice[i])) - 2) / 48f; }); } } //Masks1.WriteMRC("d_masks1.mrc"); //Masks2.WriteMRC("d_masks2.mrc"); #endregion #region Load and prepare references for both halves Image VolRefFT1; { Image Volume = StageDataLoad.LoadMap(MainWindow.Options.ReferencePath, new int2(1, 1), 0, typeof(float)); //GPU.Normalize(Volume.GetDevice(Intent.Read), Volume.GetDevice(Intent.Write), (uint)Volume.ElementsReal, 1); Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); VolRefFT1 = VolumePadded.AsFFT(true); VolumePadded.Dispose(); } VolRefFT1.FreeDevice(); Image VolRefFT2; { // Can't assume there is a second half, but certainly hope so string Half2Path = MainWindow.Options.ReferencePath; if (Half2Path.Contains("half1")) Half2Path = Half2Path.Replace("half1", "half2"); Image Volume = StageDataLoad.LoadMap(Half2Path, new int2(1, 1), 0, typeof(float)); //GPU.Normalize(Volume.GetDevice(Intent.Read), Volume.GetDevice(Intent.Write), (uint)Volume.ElementsReal, 1); Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample); Volume.Dispose(); VolumePadded.RemapToFT(true); VolRefFT2 = VolumePadded.AsFFT(true); VolumePadded.Dispose(); } VolRefFT2.FreeDevice(); #endregion #region Prepare particles: group and resize to DimsCropped Image ParticleStackFT1 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles1 * Dims.Z / 3), true, true); { GPU.CreatePolishing(ParticleStack1.GetDevice(Intent.Read), ParticleStackFT1.GetDevice(Intent.Write), Masks1.GetDevice(Intent.Read), new int2(DimsRegion), DimsCropped, NParticles1, Dims.Z); ParticleStack1.FreeDevice(); Masks1.Dispose(); /*Image Amps = ParticleStackFT1.AsIFFT(); Amps.RemapFromFT(); Amps.WriteMRC("d_particlestackft1.mrc"); Amps.Dispose();*/ } Image ParticleStackFT2 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles2 * Dims.Z / 3), true, true); { GPU.CreatePolishing(ParticleStack2.GetDevice(Intent.Read), ParticleStackFT2.GetDevice(Intent.Write), Masks2.GetDevice(Intent.Read), new int2(DimsRegion), DimsCropped, NParticles2, Dims.Z); ParticleStack1.FreeDevice(); Masks2.Dispose(); /*Image Amps = ParticleStackFT2.AsIFFT(); Amps.RemapFromFT(); Amps.WriteMRC("d_particlestackft2.mrc"); Amps.Dispose();*/ } #endregion Image Projections1 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles1 * Dims.Z / 3), true, true); Image Projections2 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles2 * Dims.Z / 3), true, true); Image Shifts1 = new Image(new int3(NParticles1, Dims.Z / 3, 1), false, true); float3[] Angles1 = new float3[NParticles1 * Dims.Z / 3]; CTFStruct[] CTFParams1 = new CTFStruct[NParticles1 * Dims.Z / 3]; Image Shifts2 = new Image(new int3(NParticles2, Dims.Z / 3, 1), false, true); float3[] Angles2 = new float3[NParticles2 * Dims.Z / 3]; CTFStruct[] CTFParams2 = new CTFStruct[NParticles2 * Dims.Z / 3]; float[] BFacs = { -3.86f, 0.00f, -17.60f, -35.24f, -57.48f, -93.51f, -139.57f, -139.16f }; #region Initialize defocus and phase shift values float[] InitialDefoci1 = new float[NParticles1 * (Dims.Z / 3)]; float[] InitialPhaseShifts1 = new float[NParticles1 * (Dims.Z / 3)]; float[] InitialDefoci2 = new float[NParticles2 * (Dims.Z / 3)]; float[] InitialPhaseShifts2 = new float[NParticles2 * (Dims.Z / 3)]; for (int z = 0, i = 0; z < Dims.Z / 3; z++) { for (int p = 0; p < NParticles1; p++, i++) { InitialDefoci1[i] = GridCTF.GetInterpolated(new float3((float)Origins1[p].X / Dims.X, (float)Origins1[p].Y / Dims.Y, (float)(z * 3 + 1) / (Dims.Z - 1))); InitialPhaseShifts1[i] = GridCTFPhase.GetInterpolated(new float3((float)Origins1[p].X / Dims.X, (float)Origins1[p].Y / Dims.Y, (float)(z * 3 + 1) / (Dims.Z - 1))); CTF Alt = CTF.GetCopy(); Alt.PixelSize = (decimal)PixelSize; Alt.PixelSizeDelta = 0; Alt.Defocus = (decimal)InitialDefoci1[i]; Alt.PhaseShift = (decimal)InitialPhaseShifts1[i]; //Alt.Bfactor = (decimal)BFacs[z]; CTFParams1[i] = Alt.ToStruct(); } } for (int z = 0, i = 0; z < Dims.Z / 3; z++) { for (int p = 0; p < NParticles2; p++, i++) { InitialDefoci2[i] = GridCTF.GetInterpolated(new float3((float)Origins2[p].X / Dims.X, (float)Origins2[p].Y / Dims.Y, (float)(z * 3 + 1) / (Dims.Z - 1))); InitialPhaseShifts2[i] = GridCTFPhase.GetInterpolated(new float3((float)Origins2[p].X / Dims.X, (float)Origins2[p].Y / Dims.Y, (float)(z * 3 + 1) / (Dims.Z - 1))); CTF Alt = CTF.GetCopy(); Alt.PixelSize = (decimal)PixelSize; Alt.PixelSizeDelta = 0; Alt.Defocus = (decimal)InitialDefoci2[i]; Alt.PhaseShift = (decimal)InitialPhaseShifts2[i]; //Alt.Bfactor = (decimal)BFacs[z]; CTFParams2[i] = Alt.ToStruct(); } } #endregion #region SetPositions lambda Action<double[]> SetPositions = input => { float BorderZ = 0.5f / (Dims.Z / 3); GridX = new CubicGrid(new int3(NParticles, 1, 2), input.Take(NParticles * 2).Select(v => (float)v).ToArray()); GridY = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 1).Take(NParticles * 2).Select(v => (float)v).ToArray()); float[] AlteredX = GridX.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); float[] AlteredY = GridY.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); GridRot = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 2).Take(NParticles * 2).Select(v => (float)v).ToArray()); GridTilt = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 3).Take(NParticles * 2).Select(v => (float)v).ToArray()); GridPsi = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 4).Take(NParticles * 2).Select(v => (float)v).ToArray()); float[] AlteredRot = GridRot.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); float[] AlteredTilt = GridTilt.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); float[] AlteredPsi = GridPsi.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ)); float[] ShiftData1 = Shifts1.GetHost(Intent.Write)[0]; float[] ShiftData2 = Shifts2.GetHost(Intent.Write)[0]; for (int z = 0; z < Dims.Z / 3; z++) { // Half 1 for (int p = 0; p < NParticles1; p++) { int i1 = z * NParticles1 + p; int i = z * NParticles + p; ShiftData1[i1 * 2] = AlteredX[i]; ShiftData1[i1 * 2 + 1] = AlteredY[i]; Angles1[i1] = new float3(AlteredRot[i] * 1f * Helper.ToRad, AlteredTilt[i] * 1f * Helper.ToRad, AlteredPsi[i] * 1f * Helper.ToRad); } // Half 2 for (int p = 0; p < NParticles2; p++) { int i2 = z * NParticles2 + p; int i = z * NParticles + NParticles1 + p; ShiftData2[i2 * 2] = AlteredX[i]; ShiftData2[i2 * 2 + 1] = AlteredY[i]; Angles2[i2] = new float3(AlteredRot[i] * 1f * Helper.ToRad, AlteredTilt[i] * 1f * Helper.ToRad, AlteredPsi[i] * 1f * Helper.ToRad); } } }; #endregion #region EvalIndividuals lambda Func<double[], bool, double[]> EvalIndividuals = (input, redoProj) => { SetPositions(input); if (redoProj) { GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Write), VolRefFT1.Dims, DimsCropped, Helper.ToInterleaved(Angles1), MainWindow.Options.ProjectionOversample, (uint)(NParticles1 * Dims.Z / 3)); GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Write), VolRefFT2.Dims, DimsCropped, Helper.ToInterleaved(Angles2), MainWindow.Options.ProjectionOversample, (uint)(NParticles2 * Dims.Z / 3)); } /*{ Image ProjectionsAmps = Projections1.AsIFFT(); ProjectionsAmps.RemapFromFT(); ProjectionsAmps.WriteMRC("d_projectionsamps1.mrc"); ProjectionsAmps.Dispose(); } { Image ProjectionsAmps = Projections2.AsIFFT(); ProjectionsAmps.RemapFromFT(); ProjectionsAmps.WriteMRC("d_projectionsamps2.mrc"); ProjectionsAmps.Dispose(); }*/ float[] Diff1 = new float[NParticles1]; float[] DiffAll1 = new float[NParticles1 * (Dims.Z / 3)]; GPU.PolishingGetDiff(ParticleStackFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), CTFCoords.GetDevice(Intent.Read), CTFParams1, Sigma2Noise.GetDevice(Intent.Read), DimsCropped, Shifts1.GetDevice(Intent.Read), Diff1, DiffAll1, (uint)NParticles1, (uint)Dims.Z / 3); float[] Diff2 = new float[NParticles2]; float[] DiffAll2 = new float[NParticles2 * (Dims.Z / 3)]; GPU.PolishingGetDiff(ParticleStackFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), CTFCoords.GetDevice(Intent.Read), CTFParams2, Sigma2Noise.GetDevice(Intent.Read), DimsCropped, Shifts2.GetDevice(Intent.Read), Diff2, DiffAll2, (uint)NParticles2, (uint)Dims.Z / 3); double[] DiffBoth = new double[NParticles]; for (int p = 0; p < NParticles1; p++) DiffBoth[p] = Diff1[p]; for (int p = 0; p < NParticles2; p++) DiffBoth[NParticles1 + p] = Diff2[p]; return DiffBoth; }; #endregion Func<double[], double> Eval = input => { float Result = MathHelper.Mean(EvalIndividuals(input, true).Select(v => (float)v)) * NParticles; Debug.WriteLine(Result); return Result; }; Func<double[], double[]> Grad = input => { SetPositions(input); GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Write), VolRefFT1.Dims, DimsCropped, Helper.ToInterleaved(Angles1), MainWindow.Options.ProjectionOversample, (uint)(NParticles1 * Dims.Z / 3)); GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Write), VolRefFT2.Dims, DimsCropped, Helper.ToInterleaved(Angles2), MainWindow.Options.ProjectionOversample, (uint)(NParticles2 * Dims.Z / 3)); double[] Result = new double[input.Length]; double Step = 0.1; int NVariables = 10; // (Shift + Euler) * 2 for (int v = 0; v < NVariables; v++) { double[] InputPlus = new double[input.Length]; for (int i = 0; i < input.Length; i++) { int iv = i / NParticles; if (iv == v) InputPlus[i] = input[i] + Step; else InputPlus[i] = input[i]; } double[] ScorePlus = EvalIndividuals(InputPlus, v >= 4); double[] InputMinus = new double[input.Length]; for (int i = 0; i < input.Length; i++) { int iv = i / NParticles; if (iv == v) InputMinus[i] = input[i] - Step; else InputMinus[i] = input[i]; } double[] ScoreMinus = EvalIndividuals(InputMinus, v >= 4); for (int i = 0; i < NParticles; i++) Result[v * NParticles + i] = (ScorePlus[i] - ScoreMinus[i]) / (Step * 2.0); } return Result; }; double[] StartParams = new double[NParticles * 2 * 5]; for (int i = 0; i < NParticles * 2; i++) { int p = i % NParticles; StartParams[NParticles * 2 * 0 + i] = 0; StartParams[NParticles * 2 * 1 + i] = 0; if (p < NParticles1) { StartParams[NParticles * 2 * 2 + i] = ParticleAngles1[p].X / 1.0; StartParams[NParticles * 2 * 3 + i] = ParticleAngles1[p].Y / 1.0; StartParams[NParticles * 2 * 4 + i] = ParticleAngles1[p].Z / 1.0; } else { p -= NParticles1; StartParams[NParticles * 2 * 2 + i] = ParticleAngles2[p].X / 1.0; StartParams[NParticles * 2 * 3 + i] = ParticleAngles2[p].Y / 1.0; StartParams[NParticles * 2 * 4 + i] = ParticleAngles2[p].Z / 1.0; } } BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Grad); Optimizer.Epsilon = 3e-7; Optimizer.Maximize(StartParams); #region Calculate particle quality for high frequencies float[] ParticleQuality = new float[NParticles * (Dims.Z / 3)]; { Sigma2Noise.Dispose(); Sigma2Noise = new Image(new int3(DimsCropped), true); { int GroupNumber = int.Parse(tableIn.GetRowValue(RowIndices[0], "rlnGroupNumber")); //Star SigmaTable = new Star("D:\\rado27\\Refine3D\\run1_ct5_it009_half1_model.star", "data_model_group_" + GroupNumber); Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber); float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray(); float[] Sigma2NoiseData = Sigma2Noise.GetHost(Intent.Write)[0]; Helper.ForEachElementFT(DimsCropped, (x, y, xx, yy, r, angle) => { int ir = (int)r; float val = 0; if (ir < SigmaValues.Length && ir >= size / (4.0f / PixelSize) && ir < DimsCropped.X / 2) { if (SigmaValues[ir] != 0f) val = 1f / SigmaValues[ir] / (ir * 3.14f); } Sigma2NoiseData[y * (DimsCropped.X / 2 + 1) + x] = val; }); float MaxSigma = MathHelper.Max(Sigma2NoiseData); for (int i = 0; i < Sigma2NoiseData.Length; i++) Sigma2NoiseData[i] /= MaxSigma; Sigma2Noise.RemapToFT(); } //Sigma2Noise.WriteMRC("d_sigma2noiseScore.mrc"); SetPositions(StartParams); GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Write), VolRefFT1.Dims, DimsCropped, Helper.ToInterleaved(Angles1), MainWindow.Options.ProjectionOversample, (uint)(NParticles1 * Dims.Z / 3)); GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Write), VolRefFT2.Dims, DimsCropped, Helper.ToInterleaved(Angles2), MainWindow.Options.ProjectionOversample, (uint)(NParticles2 * Dims.Z / 3)); float[] Diff1 = new float[NParticles1]; float[] ParticleQuality1 = new float[NParticles1 * (Dims.Z / 3)]; GPU.PolishingGetDiff(ParticleStackFT1.GetDevice(Intent.Read), Projections1.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), CTFCoords.GetDevice(Intent.Read), CTFParams1, Sigma2Noise.GetDevice(Intent.Read), DimsCropped, Shifts1.GetDevice(Intent.Read), Diff1, ParticleQuality1, (uint)NParticles1, (uint)Dims.Z / 3); float[] Diff2 = new float[NParticles2]; float[] ParticleQuality2 = new float[NParticles2 * (Dims.Z / 3)]; GPU.PolishingGetDiff(ParticleStackFT2.GetDevice(Intent.Read), Projections2.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), CTFCoords.GetDevice(Intent.Read), CTFParams2, Sigma2Noise.GetDevice(Intent.Read), DimsCropped, Shifts2.GetDevice(Intent.Read), Diff2, ParticleQuality2, (uint)NParticles2, (uint)Dims.Z / 3); for (int z = 0; z < Dims.Z / 3; z++) { for (int p = 0; p < NParticles1; p++) ParticleQuality[z * NParticles + p] = ParticleQuality1[z * NParticles1 + p]; for (int p = 0; p < NParticles2; p++) ParticleQuality[z * NParticles + NParticles1 + p] = ParticleQuality2[z * NParticles2 + p]; } } #endregion lock (tableOut) // Only changing cell values, but better be safe in case table implementation changes later { GridX = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Take(NParticles * 2).Select(v => (float)v).ToArray()); GridY = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 1).Take(NParticles * 2).Select(v => (float)v).ToArray()); float[] AlteredX = GridX.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); float[] AlteredY = GridY.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); GridRot = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 2).Take(NParticles * 2).Select(v => (float)v).ToArray()); GridTilt = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 3).Take(NParticles * 2).Select(v => (float)v).ToArray()); GridPsi = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 4).Take(NParticles * 2).Select(v => (float)v).ToArray()); float[] AlteredRot = GridRot.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); float[] AlteredTilt = GridTilt.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); float[] AlteredPsi = GridPsi.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0)); for (int i = 0; i < TableOutIndices.Count; i++) { int p = i % NParticles; int z = i / NParticles; float Defocus = 0, PhaseShift = 0; if (p < NParticles1) { Defocus = GridCTF.GetInterpolated(new float3((float)Origins1[p].X / Dims.X, (float)Origins1[p].Y / Dims.Y, (float)z / (Dims.Z - 1))); PhaseShift = GridCTFPhase.GetInterpolated(new float3((float)Origins1[p].X / Dims.X, (float)Origins1[p].Y / Dims.Y, (float)z / (Dims.Z - 1))); } else { p -= NParticles1; Defocus = GridCTF.GetInterpolated(new float3((float)Origins2[p].X / Dims.X, (float)Origins2[p].Y / Dims.Y, (float)z / (Dims.Z - 1))); PhaseShift = GridCTFPhase.GetInterpolated(new float3((float)Origins2[p].X / Dims.X, (float)Origins2[p].Y / Dims.Y, (float)z / (Dims.Z - 1))); } tableOut.SetRowValue(TableOutIndices[i], "rlnOriginX", AlteredX[i].ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnOriginY", AlteredY[i].ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnAngleRot", (-AlteredRot[i]).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnAngleTilt", (-AlteredTilt[i]).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnAnglePsi", (-AlteredPsi[i]).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnDefocusU", ((Defocus + (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnDefocusV", ((Defocus - (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnPhaseShift", (PhaseShift * 180f).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnCtfFigureOfMerit", (ParticleQuality[(z / 3) * NParticles + (i % NParticles)]).ToString(CultureInfo.InvariantCulture)); tableOut.SetRowValue(TableOutIndices[i], "rlnMagnification", ((float)MainWindow.Options.CTFDetectorPixel * 10000f / PixelSize).ToString()); } } VolRefFT1.Dispose(); VolRefFT2.Dispose(); Projections1.Dispose(); Projections2.Dispose(); Sigma2Noise.Dispose(); ParticleStackFT1.Dispose(); ParticleStackFT2.Dispose(); Shifts1.Dispose(); Shifts2.Dispose(); CTFCoords.Dispose(); ShiftFactors.Dispose(); ParticleStack1.Dispose(); ParticleStack2.Dispose(); PSStack1.Dispose(); PSStack2.Dispose(); } // Write movies to disk asynchronously, so the next micrograph can load. Thread SaveThread = new Thread(() => { GPU.SetDevice(CurrentDevice); // It's a separate thread, make sure it's using the same device ParticleStackAll.WriteMRC(ParticleMoviesPath, ParticlesHeader); //ParticleStackAll.WriteMRC("D:\\gala\\particlemovies\\" + RootName + "_particles.mrcs", ParticlesHeader); ParticleStackAll.Dispose(); PSStackAll.WriteMRC(ParticleCTFMoviesPath); //PSStackAll.WriteMRC("D:\\rado27\\particlectfmovies\\" + RootName + "_particlectf.mrcs"); PSStackAll.Dispose(); }); SaveThread.Start(); }
public void ExportParticles(Star tableIn, Star tableOut, MapHeader originalHeader, Image originalStack, int size, float particleradius, decimal scaleFactor) { if (!tableIn.HasColumn("rlnAutopickFigureOfMerit")) tableIn.AddColumn("rlnAutopickFigureOfMerit"); List<int> RowIndices = new List<int>(); string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName"); for (int i = 0; i < ColumnMicrographName.Length; i++) if (ColumnMicrographName[i].Contains(RootName)) RowIndices.Add(i); if (RowIndices.Count == 0) return; if (!Directory.Exists(ParticlesDir)) Directory.CreateDirectory(ParticlesDir); if (!Directory.Exists(ParticleCTFDir)) Directory.CreateDirectory(ParticleCTFDir); int3 Dims = originalHeader.Dimensions; int3 DimsRegion = new int3(size, size, 1); int3 DimsPadded = new int3(size * 2, size * 2, 1); int NParticles = RowIndices.Count; float PixelSize = (float)CTF.PixelSize; float PixelDelta = (float)CTF.PixelSizeDelta; float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad; /*Image CTFCoords; Image CTFFreq; { float2[] CTFCoordsData = new float2[(DimsRegion.X / 2 + 1) * DimsRegion.Y]; float[] CTFFreqData = new float[(DimsRegion.X / 2 + 1) * DimsRegion.Y]; for (int y = 0; y < DimsRegion.Y; y++) for (int x = 0; x < DimsRegion.X / 2 + 1; x++) { int xx = x; int yy = y < DimsRegion.Y / 2 + 1 ? y : y - DimsRegion.Y; float xs = xx / (float)DimsRegion.X; float ys = yy / (float)DimsRegion.Y; float r = (float)Math.Sqrt(xs * xs + ys * ys); float angle = (float)(Math.Atan2(yy, xx)); float CurrentPixelSize = PixelSize + PixelDelta * (float)Math.Cos(2f * (angle - PixelAngle)); CTFCoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, angle); CTFFreqData[y * (DimsRegion.X / 2 + 1) + x] = r / CurrentPixelSize; } CTFCoords = new Image(CTFCoordsData, DimsRegion.Slice(), true); CTFFreq = new Image(CTFFreqData, DimsRegion.Slice(), true); }*/ string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX"); string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY"); string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX"); string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY"); int3[] Origins = new int3[NParticles]; float3[] ResidualShifts = new float3[NParticles]; for (int i = 0; i < NParticles; i++) { float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture)) * 1.00f; float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture), float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture)) * 1.00f; Origins[i] = new int3((int)(Pos.X - Shift.X), (int)(Pos.Y - Shift.Y), 0); ResidualShifts[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X), -MathHelper.ResidualFraction(Pos.Y - Shift.Y), 0f); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", Origins[i].X.ToString()); tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", Origins[i].Y.ToString()); tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0"); tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0"); } Image AverageFT = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true, true); Image AveragePS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); Image Weights = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); Weights.Fill(1e-6f); Image FrameParticles = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles)); float StepZ = 1f / Math.Max(Dims.Z - 1, 1); for (int z = 0; z < Dims.Z; z++) { float CoordZ = z * StepZ; if (originalStack != null) GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read), FrameParticles.GetDevice(Intent.Write), Dims.Slice(), DimsPadded, Helper.ToInterleaved(Origins.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()), (uint)NParticles); // Shift particles { float3[] Shifts = new float3[NParticles]; for (int i = 0; i < NParticles; i++) { float3 Coords = new float3((float)Origins[i].X / Dims.X, (float)Origins[i].Y / Dims.Y, CoordZ); Shifts[i] = ResidualShifts[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f; } FrameParticles.ShiftSlices(Shifts); } Image FrameParticlesCropped = FrameParticles.AsPadded(new int2(DimsRegion)); Image FrameParticlesFT = FrameParticlesCropped.AsFFT(); FrameParticlesCropped.Dispose(); //Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); //PS.Fill(1f); // Apply motion blur filter. #region Motion blur weighting /*{ const int Samples = 11; float StartZ = (z - 0.5f) * StepZ; float StopZ = (z + 0.5f) * StepZ; float2[] Shifts = new float2[Samples * NParticles]; for (int p = 0; p < NParticles; p++) { float NormX = (float)Origins[p].X / Dims.X; float NormY = (float)Origins[p].Y / Dims.Y; for (int zz = 0; zz < Samples; zz++) { float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz; float3 Coords = new float3(NormX, NormY, zp); Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords); } } Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write), DimsRegion, Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()), Samples, (uint)NParticles); PS.Multiply(MotionFilter); //MotionFilter.WriteMRC("motion.mrc"); MotionFilter.Dispose(); }*/ #endregion // Apply CTF. #region CTF weighting /*if (CTF != null) { CTFStruct[] Structs = new CTFStruct[NParticles]; for (int p = 0; p < NParticles; p++) { CTF Altered = CTF.GetCopy(); Altered.Defocus = (decimal)GridCTF.GetInterpolated(new float3(Origins[p].X / Dims.X, Origins[p].Y / Dims.Y, z * StepZ)); Structs[p] = Altered.ToStruct(); } Image CTFImage = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); GPU.CreateCTF(CTFImage.GetDevice(Intent.Write), CTFCoords.GetDevice(Intent.Read), (uint)CTFCoords.ElementsSliceComplex, Structs, false, (uint)NParticles); //CTFImage.Abs(); PS.Multiply(CTFImage); //CTFImage.WriteMRC("ctf.mrc"); CTFImage.Dispose(); }*/ #endregion // Apply dose. #region Dose weighting /*{ float3 NikoConst = new float3(0.245f, -1.665f, 2.81f); // Niko's formula expects e-/A2/frame, we've got e-/px/frame -- convert! float FrameDose = (float)MainWindow.Options.CorrectDosePerFrame * (z + 0.5f) / (PixelSize * PixelSize); Image DoseImage = new Image(IntPtr.Zero, DimsRegion, true); GPU.DoseWeighting(CTFFreq.GetDevice(Intent.Read), DoseImage.GetDevice(Intent.Write), (uint)DoseImage.ElementsSliceComplex, new[] { FrameDose }, NikoConst, 1); PS.MultiplySlices(DoseImage); //DoseImage.WriteMRC("dose.mrc"); DoseImage.Dispose(); }*/ #endregion //Image PSAbs = new Image(PS.GetDevice(Intent.Read), new int3(DimsRegion.X, DimsRegion.Y, NParticles), true); //PSAbs.Abs(); //FrameParticlesFT.Multiply(PS); AverageFT.Add(FrameParticlesFT); //Weights.Add(PSAbs); //PS.Multiply(PS); //AveragePS.Add(PS); //PS.Dispose(); FrameParticlesFT.Dispose(); //PSAbs.Dispose(); } FrameParticles.Dispose(); //CTFCoords.Dispose(); //AverageFT.Divide(Weights); //AveragePS.Divide(Weights); //AverageFT.Multiply(AveragePS); Weights.Dispose(); Image AverageParticlesUncorrected = AverageFT.AsIFFT(); AverageFT.Dispose(); Image AverageParticles = AverageParticlesUncorrected.AsAnisotropyCorrected(new int2(DimsRegion), (float)(CTF.PixelSize + CTF.PixelSizeDelta / 2M), (float)(CTF.PixelSize - CTF.PixelSizeDelta / 2M), (float)CTF.PixelSizeAngle * Helper.ToRad, 8); AverageParticlesUncorrected.Dispose(); GPU.NormParticles(AverageParticles.GetDevice(Intent.Read), AverageParticles.GetDevice(Intent.Write), DimsRegion, (uint)(particleradius / (PixelSize / 1.00f)), true, (uint)NParticles); HeaderMRC ParticlesHeader = new HeaderMRC { Pixelsize = new float3(PixelSize, PixelSize, PixelSize) }; AverageParticles.WriteMRC(ParticlesPath, ParticlesHeader); AverageParticles.Dispose(); //AveragePS.WriteMRC(ParticleCTFPath, ParticlesHeader); AveragePS.Dispose(); float[] DistanceWeights = new float[NParticles]; for (int p1 = 0; p1 < NParticles - 1; p1++) { float2 Pos1 = new float2(Origins[p1].X, Origins[p1].Y); for (int p2 = p1 + 1; p2 < NParticles; p2++) { float2 Pos2 = new float2(Origins[p2].X, Origins[p2].Y); float2 Diff = Pos2 - Pos1; float Dist = Diff.X * Diff.X + Diff.Y * Diff.Y; Dist = 1f / Dist; DistanceWeights[p1] += Dist; DistanceWeights[p2] += Dist; } } for (int i = 0; i < NParticles; i++) { string ParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs"; tableIn.SetRowValue(RowIndices[i], "rlnImageName", ParticlePath); //string ParticleCTFsPath = (i + 1).ToString("D6") + "@particlectf/" + RootName + "_particlectf.mrcs"; //tableIn.SetRowValue(RowIndices[i], "rlnCtfImage", ParticleCTFsPath); tableIn.SetRowValue(RowIndices[i], "rlnAutopickFigureOfMerit", DistanceWeights[i].ToString(CultureInfo.InvariantCulture)); } }
public void ProcessParticleShift(MapHeader originalHeader, Image originalStack, Star stardata, Image refft, Image maskft, int dimbox, decimal scaleFactor) { // Deal with dimensions and grids. int NFrames = originalHeader.Dimensions.Z; int2 DimsImage = new int2(originalHeader.Dimensions); int2 DimsRegion = new int2(dimbox, dimbox); decimal SubdivisionRatio = 4M; List<int3> PyramidSizes = new List<int3>(); PyramidSizes.Add(new int3(MainWindow.Options.GridMoveX, MainWindow.Options.GridMoveX, Math.Min(NFrames, MainWindow.Options.GridMoveZ))); while (true) { int3 Previous = PyramidSizes.Last(); int NewZ = Math.Min((int)Math.Round(Previous.Z / SubdivisionRatio), Previous.Z - 1); if (NewZ < 2) break; PyramidSizes.Add(new int3(Previous.X * 2, Previous.Y * 2, NewZ)); } PyramidShiftX.Clear(); PyramidShiftY.Clear(); float3[] PositionsGrid, PositionsGridPerFrame; float2[] PositionsExtraction, PositionsShift; float3[] ParticleAngles; List<int> RowIndices = new List<int>(); { string[] ColumnNames = stardata.GetColumn("rlnMicrographName"); for (int i = 0; i < ColumnNames.Length; i++) if (ColumnNames[i].Contains(RootName)) RowIndices.Add(i); string[] ColumnOriginX = stardata.GetColumn("rlnCoordinateX"); string[] ColumnOriginY = stardata.GetColumn("rlnCoordinateY"); string[] ColumnShiftX = stardata.GetColumn("rlnOriginX"); string[] ColumnShiftY = stardata.GetColumn("rlnOriginY"); string[] ColumnAngleRot = stardata.GetColumn("rlnAngleRot"); string[] ColumnAngleTilt = stardata.GetColumn("rlnAngleTilt"); string[] ColumnAnglePsi = stardata.GetColumn("rlnAnglePsi"); PositionsGrid = new float3[RowIndices.Count]; PositionsGridPerFrame = new float3[RowIndices.Count * NFrames]; PositionsExtraction = new float2[RowIndices.Count]; PositionsShift = new float2[RowIndices.Count * NFrames]; ParticleAngles = new float3[RowIndices.Count]; { int i = 0; foreach (var nameIndex in RowIndices) { float OriginX = float.Parse(ColumnOriginX[nameIndex]); float OriginY = float.Parse(ColumnOriginY[nameIndex]); float ShiftX = float.Parse(ColumnShiftX[nameIndex]); float ShiftY = float.Parse(ColumnShiftY[nameIndex]); PositionsExtraction[i] = new float2(OriginX - ShiftX, OriginY - ShiftY); PositionsGrid[i] = new float3((OriginX - ShiftX) / DimsImage.X, (OriginY - ShiftY) / DimsImage.Y, 0.5f); for (int z = 0; z < NFrames; z++) { PositionsGridPerFrame[z * RowIndices.Count + i] = new float3(PositionsGrid[i].X, PositionsGrid[i].Y, (float)z / (NFrames - 1)); PositionsShift[z * RowIndices.Count + i] = GetShiftFromPyramid(PositionsGridPerFrame[z * RowIndices.Count + i]); } ParticleAngles[i] = new float3(float.Parse(ColumnAngleRot[nameIndex]) * Helper.ToRad, float.Parse(ColumnAngleTilt[nameIndex]) * Helper.ToRad, float.Parse(ColumnAnglePsi[nameIndex]) * Helper.ToRad); i++; } } } int NPositions = PositionsGrid.Length; if (NPositions == 0) return; int MinFreqInclusive = (int)(MainWindow.Options.MovementRangeMin * DimsRegion.X / 2); int MaxFreqExclusive = (int)(MainWindow.Options.MovementRangeMax * DimsRegion.X / 2); int NFreq = MaxFreqExclusive - MinFreqInclusive; int CentralFrame = NFrames / 2; int MaskExpansions = 4; // Math.Max(1, PyramidSizes[0].Z / 3); int[] MaskSizes = new int[MaskExpansions]; // Allocate memory and create all prerequisites: int MaskLength; Image ShiftFactors; Image Phases; Image Projections; Image Shifts; Image InvSigma; { List<long> Positions = new List<long>(); List<float2> Factors = new List<float2>(); List<float2> Freq = new List<float2>(); int Min2 = MinFreqInclusive * MinFreqInclusive; int Max2 = MaxFreqExclusive * MaxFreqExclusive; for (int y = 0; y < DimsRegion.Y; y++) { int yy = y - DimsRegion.X / 2; for (int x = 0; x < DimsRegion.X / 2 + 1; x++) { int xx = x - DimsRegion.X / 2; int r2 = xx * xx + yy * yy; if (r2 >= Min2 && r2 < Max2) { Positions.Add(y * (DimsRegion.X / 2 + 1) + x); Factors.Add(new float2((float)xx / DimsRegion.X * 2f * (float)Math.PI, (float)yy / DimsRegion.X * 2f * (float)Math.PI)); float Angle = (float)Math.Atan2(yy, xx); float r = (float)Math.Sqrt(r2); Freq.Add(new float2(r, Angle)); } } } // Addresses for CTF simulation Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true); { float2[] CoordsData = new float2[CTFCoordsCart.ElementsSliceComplex]; Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) => CoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, a)); CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData }); CTFCoordsCart.RemapToFT(); } float[] ValuesDefocus = GridCTF.GetInterpolatedNative(PositionsGrid); CTFStruct[] PositionsCTF = ValuesDefocus.Select(v => { CTF Altered = CTF.GetCopy(); Altered.PixelSizeDelta = 0; Altered.Defocus = (decimal)v; //Altered.Bfactor = -MainWindow.Options.MovementBfactor; return Altered.ToStruct(); }).ToArray(); // Sort everyone with ascending distance from center. List<KeyValuePair<float, int>> FreqIndices = Freq.Select((v, i) => new KeyValuePair<float, int>(v.X, i)).ToList(); FreqIndices.Sort((a, b) => a.Key.CompareTo(b.Key)); int[] SortedIndices = FreqIndices.Select(v => v.Value).ToArray(); Helper.Reorder(Positions, SortedIndices); Helper.Reorder(Factors, SortedIndices); Helper.Reorder(Freq, SortedIndices); long[] RelevantMask = Positions.ToArray(); ShiftFactors = new Image(Helper.ToInterleaved(Factors.ToArray())); MaskLength = RelevantMask.Length; // Get mask sizes for different expansion steps. for (int i = 0; i < MaskExpansions; i++) { float CurrentMaxFreq = MinFreqInclusive + (MaxFreqExclusive - MinFreqInclusive) / (float)MaskExpansions * (i + 1); MaskSizes[i] = Freq.Count(v => v.X * v.X < CurrentMaxFreq * CurrentMaxFreq); } Phases = new Image(IntPtr.Zero, new int3(MaskLength, NPositions, NFrames), false, true, false); Projections = new Image(IntPtr.Zero, new int3(MaskLength, NPositions, NFrames), false, true, false); InvSigma = new Image(IntPtr.Zero, new int3(MaskLength, 1, 1)); Image ParticleMasksFT = maskft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); Image ParticleMasks = ParticleMasksFT.AsIFFT(); ParticleMasksFT.Dispose(); ParticleMasks.RemapFromFT(); Parallel.ForEach(ParticleMasks.GetHost(Intent.ReadWrite), slice => { for (int i = 0; i < slice.Length; i++) slice[i] = (Math.Max(2f, Math.Min(25f, slice[i])) - 2) / 23f; }); Image ProjectionsSparse = refft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample); Image InvSigmaSparse = new Image(new int3(DimsRegion), true); { int GroupNumber = int.Parse(stardata.GetRowValue(RowIndices[0], "rlnGroupNumber")); //Star SigmaTable = new Star("D:\\rado27\\RefineWarppolish\\run1_model.star", "data_model_group_" + GroupNumber); Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber); float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray(); float[] Sigma2NoiseData = InvSigmaSparse.GetHost(Intent.Write)[0]; Helper.ForEachElementFT(new int2(DimsRegion.X, DimsRegion.Y), (x, y, xx, yy, r, angle) => { int ir = (int)r; float val = 0; if (ir < SigmaValues.Length) { if (SigmaValues[ir] != 0f) val = 1f / SigmaValues[ir]; } Sigma2NoiseData[y * (DimsRegion.X / 2 + 1) + x] = val; }); float MaxSigma = MathHelper.Max(Sigma2NoiseData); for (int i = 0; i < Sigma2NoiseData.Length; i++) Sigma2NoiseData[i] /= MaxSigma; InvSigmaSparse.RemapToFT(); } //InvSigmaSparse.WriteMRC("d_sigma2noise.mrc"); float PixelSize = (float)CTF.PixelSize; float PixelDelta = (float)CTF.PixelSizeDelta; float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad; GPU.CreateParticleShift(originalStack.GetDevice(Intent.Read), DimsImage, NFrames, Helper.ToInterleaved(PositionsExtraction), Helper.ToInterleaved(PositionsShift), NPositions, DimsRegion, RelevantMask, (uint)RelevantMask.Length, ParticleMasks.GetDevice(Intent.Read), ProjectionsSparse.GetDevice(Intent.Read), PositionsCTF, CTFCoordsCart.GetDevice(Intent.Read), InvSigmaSparse.GetDevice(Intent.Read), PixelSize + PixelDelta / 2, PixelSize - PixelDelta / 2, PixelAngle, Phases.GetDevice(Intent.Write), Projections.GetDevice(Intent.Write), InvSigma.GetDevice(Intent.Write)); InvSigmaSparse.Dispose(); ParticleMasks.Dispose(); ProjectionsSparse.Dispose(); CTFCoordsCart.Dispose(); originalStack.FreeDevice(); Shifts = new Image(new float[NPositions * NFrames * 2]); } #region Fit movement { int NPyramidPoints = 0; float[][][] WiggleWeights = new float[PyramidSizes.Count][][]; for (int p = 0; p < PyramidSizes.Count; p++) { CubicGrid WiggleGrid = new CubicGrid(PyramidSizes[p]); NPyramidPoints += (int)PyramidSizes[p].Elements(); WiggleWeights[p] = WiggleGrid.GetWiggleWeights(PositionsGridPerFrame); } double[] StartParams = new double[NPyramidPoints * 2]; for (int m = 3; m < MaskExpansions; m++) { for (int currentGrid = 0; currentGrid < PyramidSizes.Count; currentGrid++) { Action<double[]> SetPositions = input => { // Construct CubicGrids and get interpolated shift values. float[] AlteredX = new float[PositionsGridPerFrame.Length]; float[] AlteredY = new float[PositionsGridPerFrame.Length]; int Offset = 0; foreach (var size in PyramidSizes) { int Elements = (int)size.Elements(); CubicGrid GridX = new CubicGrid(size, input.Skip(Offset).Take(Elements).Select(v => (float)v).ToArray()); AlteredX = MathHelper.Plus(AlteredX, GridX.GetInterpolatedNative(PositionsGridPerFrame)); CubicGrid GridY = new CubicGrid(size, input.Skip(NPyramidPoints + Offset).Take(Elements).Select(v => (float)v).ToArray()); AlteredY = MathHelper.Plus(AlteredY, GridY.GetInterpolatedNative(PositionsGridPerFrame)); Offset += Elements; } // Finally, set the shift values in the device array. float[] ShiftData = Shifts.GetHost(Intent.Write)[0]; for (int i = 0; i < PositionsGridPerFrame.Length; i++) { ShiftData[i * 2] = AlteredX[i]; ShiftData[i * 2 + 1] = AlteredY[i]; } }; Func<double[], double> Eval = input => { SetPositions(input); float[] Diff = new float[NPositions * NFrames]; GPU.ParticleShiftGetDiff(Phases.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), InvSigma.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), Diff, (uint)NPositions, (uint)NFrames); //for (int i = 0; i < Diff.Length; i++) //Diff[i] = Diff[i] * 100f; double Score = Diff.Sum(); //Debug.WriteLine(Score); return Score; }; Func<double[], double[]> Grad = input => { SetPositions(input); float[] Diff = new float[NPositions * NFrames * 2]; GPU.ParticleShiftGetGrad(Phases.GetDevice(Intent.Read), Projections.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), InvSigma.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), Diff, (uint)NPositions, (uint)NFrames); //for (int i = 0; i < Diff.Length; i++) //Diff[i] = Diff[i] * 100f; float[] DiffX = new float[NPositions * NFrames], DiffY = new float[NPositions * NFrames]; for (int i = 0; i < DiffX.Length; i++) { DiffX[i] = Diff[i * 2]; DiffY[i] = Diff[i * 2 + 1]; } double[] Result = new double[input.Length]; int Offset = 0; for (int p = 0; p < PyramidSizes.Count; p++) { //if (p == currentGrid) Parallel.For(0, (int)PyramidSizes[p].Elements(), i => { Result[Offset + i] = MathHelper.ReduceWeighted(DiffX, WiggleWeights[p][i]); Result[NPyramidPoints + Offset + i] = MathHelper.ReduceWeighted(DiffY, WiggleWeights[p][i]); }); Offset += (int)PyramidSizes[p].Elements(); } return Result; }; BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Grad); //Optimizer.Corrections = 20; Optimizer.Minimize(StartParams); } { PyramidShiftX.Clear(); PyramidShiftY.Clear(); int Offset = 0; foreach (var size in PyramidSizes) { int Elements = (int)size.Elements(); CubicGrid GridX = new CubicGrid(size, StartParams.Skip(Offset).Take(Elements).Select(v => (float)v).ToArray()); PyramidShiftX.Add(GridX); CubicGrid GridY = new CubicGrid(size, StartParams.Skip(NPyramidPoints + Offset).Take(Elements).Select(v => (float)v).ToArray()); PyramidShiftY.Add(GridY); Offset += Elements; } } } } #endregion ShiftFactors.Dispose(); Phases.Dispose(); Projections.Dispose(); Shifts.Dispose(); InvSigma.Dispose(); SaveMeta(); }
public void ProcessShift(MapHeader originalHeader, Image originalStack, decimal scaleFactor) { // Deal with dimensions and grids. int NFrames = originalHeader.Dimensions.Z; int2 DimsImage = new int2(originalHeader.Dimensions); int2 DimsRegion = new int2(768, 768); float OverlapFraction = 0.0f; int2 DimsPositionGrid; int3[] PositionGrid = Helper.GetEqualGridSpacing(DimsImage, DimsRegion, OverlapFraction, out DimsPositionGrid); //PositionGrid = new[] { new int3(0, 0, 0) }; //DimsPositionGrid = new int2(1, 1); int NPositions = PositionGrid.Length; int ShiftGridX = 1; int ShiftGridY = 1; int ShiftGridZ = Math.Min(NFrames, MainWindow.Options.GridMoveZ); GridMovementX = new CubicGrid(new int3(ShiftGridX, ShiftGridY, ShiftGridZ)); GridMovementY = new CubicGrid(new int3(ShiftGridX, ShiftGridY, ShiftGridZ)); int LocalGridX = Math.Min(DimsPositionGrid.X, MainWindow.Options.GridMoveX); int LocalGridY = Math.Min(DimsPositionGrid.Y, MainWindow.Options.GridMoveY); int LocalGridZ = Math.Min(2, NFrames); GridLocalX = new CubicGrid(new int3(LocalGridX, LocalGridY, LocalGridZ)); GridLocalY = new CubicGrid(new int3(LocalGridX, LocalGridY, LocalGridZ)); int3 ShiftGrid = new int3(DimsPositionGrid.X, DimsPositionGrid.Y, NFrames); int MinFreqInclusive = (int)(MainWindow.Options.MovementRangeMin * DimsRegion.X / 2); int MaxFreqExclusive = (int)(MainWindow.Options.MovementRangeMax * DimsRegion.X / 2); int NFreq = MaxFreqExclusive - MinFreqInclusive; int CentralFrame = NFrames / 2; int MaskExpansions = Math.Max(1, ShiftGridZ / 3); int[] MaskSizes = new int[MaskExpansions]; // Allocate memory and create all prerequisites: int MaskLength; Image ShiftFactors; Image Phases; Image PhasesAverage; Image Shifts; { List<long> Positions = new List<long>(); List<float2> Factors = new List<float2>(); List<float2> Freq = new List<float2>(); int Min2 = MinFreqInclusive * MinFreqInclusive; int Max2 = MaxFreqExclusive * MaxFreqExclusive; 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; for (int y = 0; y < DimsRegion.Y; y++) { int yy = y - DimsRegion.X / 2; for (int x = 0; x < DimsRegion.X / 2 + 1; x++) { int xx = x - DimsRegion.X / 2; int r2 = xx * xx + yy * yy; if (r2 >= Min2 && r2 < Max2) { Positions.Add(y * (DimsRegion.X / 2 + 1) + x); Factors.Add(new float2((float)xx / DimsRegion.X * 2f * (float)Math.PI, (float)yy / DimsRegion.X * 2f * (float)Math.PI)); float Angle = (float)Math.Atan2(yy, xx); float r = (float)Math.Sqrt(r2); Freq.Add(new float2(r, Angle)); } } } // Sort everyone with ascending distance from center. List<KeyValuePair<float, int>> FreqIndices = Freq.Select((v, i) => new KeyValuePair<float, int>(v.X, i)).ToList(); FreqIndices.Sort((a, b) => a.Key.CompareTo(b.Key)); int[] SortedIndices = FreqIndices.Select(v => v.Value).ToArray(); Helper.Reorder(Positions, SortedIndices); Helper.Reorder(Factors, SortedIndices); Helper.Reorder(Freq, SortedIndices); float Bfac = (float)MainWindow.Options.MovementBfactor * 0.25f / PixelSize / DimsRegion.X; float2[] BfacWeightsData = Freq.Select(v => (float)Math.Exp(v.X * Bfac)).Select(v => new float2(v, v)).ToArray(); Image BfacWeights = new Image(Helper.ToInterleaved(BfacWeightsData), false, false, false); long[] RelevantMask = Positions.ToArray(); ShiftFactors = new Image(Helper.ToInterleaved(Factors.ToArray())); MaskLength = RelevantMask.Length; // Get mask sizes for different expansion steps. for (int i = 0; i < MaskExpansions; i++) { float CurrentMaxFreq = MinFreqInclusive + (MaxFreqExclusive - MinFreqInclusive) / (float)MaskExpansions * (i + 1); MaskSizes[i] = Freq.Count(v => v.X * v.X < CurrentMaxFreq * CurrentMaxFreq); } Phases = new Image(IntPtr.Zero, new int3(MaskLength * 2, DimsPositionGrid.X * DimsPositionGrid.Y, NFrames), false, false, false); GPU.CreateShift(originalStack.GetDevice(Intent.Read), new int2(originalHeader.Dimensions), originalHeader.Dimensions.Z, PositionGrid, PositionGrid.Length, DimsRegion, RelevantMask, (uint)MaskLength, Phases.GetDevice(Intent.Write)); Phases.MultiplyLines(BfacWeights); BfacWeights.Dispose(); originalStack.FreeDevice(); PhasesAverage = new Image(IntPtr.Zero, new int3(MaskLength, NPositions, 1), false, true, false); Shifts = new Image(new float[NPositions * NFrames * 2]); } #region Fit global movement { int MinXSteps = 1, MinYSteps = 1; int MinZSteps = Math.Min(NFrames, 3); int3 ExpansionGridSize = new int3(MinXSteps, MinYSteps, MinZSteps); float[][] WiggleWeights = new CubicGrid(ExpansionGridSize).GetWiggleWeights(ShiftGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); double[] StartParams = new double[ExpansionGridSize.Elements() * 2]; for (int m = 0; m < MaskExpansions; m++) { double[] LastAverage = null; Action<double[]> SetPositions = input => { // Construct CubicGrids and get interpolated shift values. CubicGrid AlteredGridX = new CubicGrid(ExpansionGridSize, input.Where((v, i) => i % 2 == 0).Select(v => (float)v).ToArray()); float[] AlteredX = AlteredGridX.GetInterpolatedNative(new int3(DimsPositionGrid.X, DimsPositionGrid.Y, NFrames), new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); CubicGrid AlteredGridY = new CubicGrid(ExpansionGridSize, input.Where((v, i) => i % 2 == 1).Select(v => (float)v).ToArray()); float[] AlteredY = AlteredGridY.GetInterpolatedNative(new int3(DimsPositionGrid.X, DimsPositionGrid.Y, NFrames), new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); // Let movement start at 0 in the central frame. /*float2[] CenterFrameOffsets = new float2[NPositions]; for (int i = 0; i < NPositions; i++) CenterFrameOffsets[i] = new float2(AlteredX[CentralFrame * NPositions + i], AlteredY[CentralFrame * NPositions + i]);*/ // Finally, set the shift values in the device array. float[] ShiftData = Shifts.GetHost(Intent.Write)[0]; Parallel.For(0, AlteredX.Length, i => { ShiftData[i * 2] = AlteredX[i];// - CenterFrameOffsets[i % NPositions].X; ShiftData[i * 2 + 1] = AlteredY[i];// - CenterFrameOffsets[i % NPositions].Y; }); }; Action<double[]> DoAverage = input => { if (LastAverage == null || input.Where((t, i) => t != LastAverage[i]).Any()) { SetPositions(input); GPU.ShiftGetAverage(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Write), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), (uint)NPositions, (uint)NFrames); if (LastAverage == null) LastAverage = new double[input.Length]; Array.Copy(input, LastAverage, input.Length); } }; Func<double[], double> Eval = input => { DoAverage(input); float[] Diff = new float[NPositions * NFrames]; GPU.ShiftGetDiff(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), Diff, (uint)NPositions, (uint)NFrames); for (int i = 0; i < Diff.Length; i++) Diff[i] = Diff[i];// * 100f; return Diff.Sum(); }; Func<double[], double[]> Grad = input => { DoAverage(input); float[] GradX = new float[NPositions * NFrames], GradY = new float[NPositions * NFrames]; float[] Diff = new float[NPositions * NFrames * 2]; GPU.ShiftGetGrad(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), Diff, (uint)NPositions, (uint)NFrames); //for (int i = 0; i < Diff.Length; i++) //Diff[i] = Diff[i] * 100f; for (int i = 0; i < GradX.Length; i++) { GradX[i] = Diff[i * 2]; GradY[i] = Diff[i * 2 + 1]; } double[] Result = new double[input.Length]; Parallel.For(0, input.Length / 2, i => { Result[i * 2] = MathHelper.ReduceWeighted(GradX, WiggleWeights[i]); Result[i * 2 + 1] = MathHelper.ReduceWeighted(GradY, WiggleWeights[i]); }); return Result; }; /*Func<double[], double[]> Grad = input => { DoAverage(input); float[] GradX = new float[NPositions * NFrames], GradY = new float[NPositions * NFrames]; float Step = 0.002f; { double[] InputXP = new double[input.Length]; for (int i = 0; i < input.Length; i++) if (i % 2 == 0) InputXP[i] = input[i] + Step; else InputXP[i] = input[i]; SetPositions(InputXP); float[] DiffXP = new float[NPositions * NFrames]; GPU.ShiftGetDiff(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), DiffXP, (uint)NPositions, (uint)NFrames); double[] InputXM = new double[input.Length]; for (int i = 0; i < input.Length; i++) if (i % 2 == 0) InputXM[i] = input[i] - Step; else InputXM[i] = input[i]; SetPositions(InputXM); float[] DiffXM = new float[NPositions * NFrames]; GPU.ShiftGetDiff(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), DiffXM, (uint)NPositions, (uint)NFrames); for (int i = 0; i < GradX.Length; i++) GradX[i] = (DiffXP[i] - DiffXM[i]) / (Step * 2); } { double[] InputYP = new double[input.Length]; for (int i = 0; i < input.Length; i++) if (i % 2 == 1) InputYP[i] = input[i] + Step; else InputYP[i] = input[i]; SetPositions(InputYP); float[] DiffYP = new float[NPositions * NFrames]; GPU.ShiftGetDiff(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), DiffYP, (uint)NPositions, (uint)NFrames); double[] InputYM = new double[input.Length]; for (int i = 0; i < input.Length; i++) if (i % 2 == 1) InputYM[i] = input[i] - Step; else InputYM[i] = input[i]; SetPositions(InputYM); float[] DiffYM = new float[NPositions * NFrames]; GPU.ShiftGetDiff(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), DiffYM, (uint)NPositions, (uint)NFrames); for (int i = 0; i < GradY.Length; i++) GradY[i] = (DiffYP[i] - DiffYM[i]) / (Step * 2); } double[] Result = new double[input.Length]; Parallel.For(0, input.Length / 2, i => { Result[i * 2] = MathHelper.ReduceWeighted(GradX, WiggleWeights[i]); Result[i * 2 + 1] = MathHelper.ReduceWeighted(GradY, WiggleWeights[i]); }); return Result; };*/ BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Grad); Optimizer.Corrections = 20; Optimizer.Minimize(StartParams); float MeanX = MathHelper.Mean(Optimizer.Solution.Where((v, i) => i % 2 == 0).Select(v => (float)v)); float MeanY = MathHelper.Mean(Optimizer.Solution.Where((v, i) => i % 2 == 1).Select(v => (float)v)); for (int i = 0; i < ExpansionGridSize.Elements(); i++) { Optimizer.Solution[i * 2] -= MeanX; Optimizer.Solution[i * 2 + 1] -= MeanY; } // Store coarse values in grids. GridMovementX = new CubicGrid(ExpansionGridSize, Optimizer.Solution.Where((v, i) => i % 2 == 0).Select(v => (float)v).ToArray()); GridMovementY = new CubicGrid(ExpansionGridSize, Optimizer.Solution.Where((v, i) => i % 2 == 1).Select(v => (float)v).ToArray()); if (m < MaskExpansions - 1) { // Refine sampling. ExpansionGridSize = new int3((int)Math.Round((float)(ShiftGridX - MinXSteps) / (MaskExpansions - 1) * (m + 1) + MinXSteps), (int)Math.Round((float)(ShiftGridY - MinYSteps) / (MaskExpansions - 1) * (m + 1) + MinYSteps), (int)Math.Round((float)(ShiftGridZ - MinZSteps) / (MaskExpansions - 1) * (m + 1) + MinZSteps)); WiggleWeights = new CubicGrid(ExpansionGridSize).GetWiggleWeights(ShiftGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); // Resize the grids to account for finer sampling. GridMovementX = GridMovementX.Resize(ExpansionGridSize); GridMovementY = GridMovementY.Resize(ExpansionGridSize); // Construct start parameters for next optimization iteration. StartParams = new double[ExpansionGridSize.Elements() * 2]; for (int i = 0; i < ExpansionGridSize.Elements(); i++) { StartParams[i * 2] = GridMovementX.FlatValues[i]; StartParams[i * 2 + 1] = GridMovementY.FlatValues[i]; } } } } #endregion // Center the global shifts /*{ float2[] AverageShifts = new float2[ShiftGridZ]; for (int i = 0; i < AverageShifts.Length; i++) AverageShifts[i] = new float2(MathHelper.Mean(GridMovementX.GetSliceXY(i)), MathHelper.Mean(GridMovementY.GetSliceXY(i))); float2 CenterShift = MathHelper.Mean(AverageShifts); GridMovementX = new CubicGrid(GridMovementX.Dimensions, GridMovementX.FlatValues.Select(v => v - CenterShift.X).ToArray()); GridMovementY = new CubicGrid(GridMovementY.Dimensions, GridMovementY.FlatValues.Select(v => v - CenterShift.Y).ToArray()); }*/ #region Fit local movement /*{ int MinXSteps = LocalGridX, MinYSteps = LocalGridY; int MinZSteps = LocalGridZ; int3 ExpansionGridSize = new int3(MinXSteps, MinYSteps, MinZSteps); float[][] WiggleWeights = new CubicGrid(ExpansionGridSize).GetWiggleWeights(ShiftGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); double[] StartParams = new double[ExpansionGridSize.Elements() * 2]; for (int m = MaskExpansions - 1; m < MaskExpansions; m++) { double[] LastAverage = null; Action<double[]> SetPositions = input => { // Construct CubicGrids and get interpolated shift values. float[] GlobalX = GridMovementX.GetInterpolatedNative(new int3(DimsPositionGrid.X, DimsPositionGrid.Y, NFrames), new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); CubicGrid AlteredGridX = new CubicGrid(ExpansionGridSize, input.Where((v, i) => i % 2 == 0).Select(v => (float)v).ToArray()); float[] AlteredX = AlteredGridX.GetInterpolatedNative(new int3(DimsPositionGrid.X, DimsPositionGrid.Y, NFrames), new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); AlteredX = MathHelper.Plus(GlobalX, AlteredX); float[] GlobalY = GridMovementY.GetInterpolatedNative(new int3(DimsPositionGrid.X, DimsPositionGrid.Y, NFrames), new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); CubicGrid AlteredGridY = new CubicGrid(ExpansionGridSize, input.Where((v, i) => i % 2 == 1).Select(v => (float)v).ToArray()); float[] AlteredY = AlteredGridY.GetInterpolatedNative(new int3(DimsPositionGrid.X, DimsPositionGrid.Y, NFrames), new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); AlteredY = MathHelper.Plus(GlobalY, AlteredY); // Let movement start at 0 in the central frame. float2[] CenterFrameOffsets = new float2[NPositions]; for (int i = 0; i < NPositions; i++) CenterFrameOffsets[i] = new float2(AlteredX[CentralFrame * NPositions + i], AlteredY[CentralFrame * NPositions + i]); // Finally, set the shift values in the device array. float[] ShiftData = Shifts.GetHost(Intent.Write)[0]; Parallel.For(0, AlteredX.Length, i => { ShiftData[i * 2] = AlteredX[i] - CenterFrameOffsets[i % NPositions].X; ShiftData[i * 2 + 1] = AlteredY[i] - CenterFrameOffsets[i % NPositions].Y; }); }; Action<double[]> DoAverage = input => { if (LastAverage == null || input.Where((t, i) => t != LastAverage[i]).Any()) { SetPositions(input); GPU.ShiftGetAverage(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Write), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), (uint)NPositions, (uint)NFrames); if (LastAverage == null) LastAverage = new double[input.Length]; Array.Copy(input, LastAverage, input.Length); } }; Func<double[], double> Eval = input => { DoAverage(input); float[] Diff = new float[NPositions * NFrames]; GPU.ShiftGetDiff(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), Diff, (uint)NPositions, (uint)NFrames); for (int i = 0; i < Diff.Length; i++) Diff[i] = Diff[i] * 100f; return MathHelper.Mean(Diff); }; Func<double[], double[]> Grad = input => { DoAverage(input); float[] Diff = new float[NPositions * NFrames * 2]; GPU.ShiftGetGrad(Phases.GetDevice(Intent.Read), PhasesAverage.GetDevice(Intent.Read), ShiftFactors.GetDevice(Intent.Read), (uint)MaskLength, (uint)MaskSizes[m], Shifts.GetDevice(Intent.Read), Diff, (uint)NPositions, (uint)NFrames); for (int i = 0; i < Diff.Length; i++) Diff[i] = Diff[i] * 100f; float[] DiffX = new float[NPositions * NFrames], DiffY = new float[NPositions * NFrames]; for (int i = 0; i < DiffX.Length; i++) { DiffX[i] = Diff[i * 2]; DiffY[i] = Diff[i * 2 + 1]; } double[] Result = new double[input.Length]; Parallel.For(0, input.Length / 2, i => { Result[i * 2] = MathHelper.ReduceWeighted(DiffX, WiggleWeights[i]); Result[i * 2 + 1] = MathHelper.ReduceWeighted(DiffY, WiggleWeights[i]); }); return Result; }; BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Grad); Optimizer.Corrections = 20; Optimizer.Minimize(StartParams); float MeanX = MathHelper.Mean(Optimizer.Solution.Where((v, i) => i % 2 == 0).Select(v => (float)v)); float MeanY = MathHelper.Mean(Optimizer.Solution.Where((v, i) => i % 2 == 1).Select(v => (float)v)); for (int i = 0; i < ExpansionGridSize.Elements(); i++) { Optimizer.Solution[i * 2] -= MeanX; Optimizer.Solution[i * 2 + 1] -= MeanY; } // Store coarse values in grids. GridLocalX = new CubicGrid(ExpansionGridSize, Optimizer.Solution.Where((v, i) => i % 2 == 0).Select(v => (float)v).ToArray()); GridLocalY = new CubicGrid(ExpansionGridSize, Optimizer.Solution.Where((v, i) => i % 2 == 1).Select(v => (float)v).ToArray()); if (m < MaskExpansions - 1) { // Refine sampling. ExpansionGridSize = new int3((int)Math.Round((float)(LocalGridX - MinXSteps) / (MaskExpansions - 1) * (m + 1) + MinXSteps), (int)Math.Round((float)(LocalGridY - MinYSteps) / (MaskExpansions - 1) * (m + 1) + MinYSteps), (int)Math.Round((float)(LocalGridZ - MinZSteps) / (MaskExpansions - 1) * (m + 1) + MinZSteps)); WiggleWeights = new CubicGrid(ExpansionGridSize).GetWiggleWeights(ShiftGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0f)); // Resize the grids to account for finer sampling. GridLocalX = GridLocalX.Resize(ExpansionGridSize); GridLocalY = GridLocalY.Resize(ExpansionGridSize); // Construct start parameters for next optimization iteration. StartParams = new double[ExpansionGridSize.Elements() * 2]; for (int i = 0; i < ExpansionGridSize.Elements(); i++) { StartParams[i * 2] = GridLocalX.FlatValues[i]; StartParams[i * 2 + 1] = GridLocalY.FlatValues[i]; } } } }*/ #endregion ShiftFactors.Dispose(); Phases.Dispose(); PhasesAverage.Dispose(); Shifts.Dispose(); // Center the local shifts /*{ float2[] AverageShifts = new float2[LocalGridZ]; for (int i = 0; i < AverageShifts.Length; i++) AverageShifts[i] = new float2(MathHelper.Mean(GridLocalX.GetSliceXY(i)), MathHelper.Mean(GridLocalY.GetSliceXY(i))); float2 CenterShift = MathHelper.Mean(AverageShifts); GridLocalX = new CubicGrid(GridLocalX.Dimensions, GridLocalX.FlatValues.Select(v => v - CenterShift.X).ToArray()); GridLocalY = new CubicGrid(GridLocalY.Dimensions, GridLocalY.FlatValues.Select(v => v - CenterShift.Y).ToArray()); }*/ SaveMeta(); }
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(); }
public static void WriteMapFloat(string path, MapHeader header, float[][] data) { Type ValueType = header.GetValueType(); using (BinaryWriter Writer = new BinaryWriter(CreateWithBigBuffer(path))) { header.Write(Writer); long Elements = header.Dimensions.ElementsSlice(); for (int z = 0; z < data.Length; z++) { byte[] Bytes = new byte[Elements * ImageFormatsHelper.SizeOf(ValueType)]; unsafe { fixed (float* DataPtr = data[z]) fixed (byte* BytesPtr = Bytes) { float* DataP = DataPtr; if (ValueType == typeof(byte)) { byte* BytesP = BytesPtr; for (long i = 0; i < Elements; i++) *BytesP++ = (byte)*DataP++; } else if (ValueType == typeof(short)) { short* BytesP = (short*)BytesPtr; for (long i = 0; i < Elements; i++) *BytesP++ = (short)*DataP++; } else if (ValueType == typeof(ushort)) { ushort* BytesP = (ushort*)BytesPtr; for (long i = 0; i < Elements; i++) *BytesP++ = (ushort)Math.Min(Math.Max(0f, *DataP++ * 16f), 65536f); } else if (ValueType == typeof(int)) { int* BytesP = (int*)BytesPtr; for (long i = 0; i < Elements; i++) *BytesP++ = (int)*DataP++; } else if (ValueType == typeof(float)) { float* BytesP = (float*)BytesPtr; for (long i = 0; i < Elements; i++) *BytesP++ = *DataP++; } else if (ValueType == typeof(double)) { double* BytesP = (double*)BytesPtr; for (long i = 0; i < Elements; i++) *BytesP++ = (double)*DataP++; } } } Writer.Write(Bytes); } } }
public override void ProcessCTF(MapHeader originalHeader, Image originalStack, bool doastigmatism, decimal scaleFactor) { if (!Directory.Exists(PowerSpectrumDir)) Directory.CreateDirectory(PowerSpectrumDir); AreAnglesInverted = false; float LastFittedAngle = 9999f; float AverageDose = Dose[IndicesSortedDose.Last()] / NTilts; List<int> ProcessedIndices = new List<int>(); CTF[] FitCTF = new CTF[NTilts]; CubicGrid[] FitGrids = new CubicGrid[NTilts]; float2[][] FitPS1D = new float2[NTilts][]; Cubic1D[] FitBackground = new Cubic1D[NTilts]; Cubic1D[] FitScale = new Cubic1D[NTilts]; Image[] FitPS2D = new Image[NTilts]; float[][] StackData = originalStack.GetHost(Intent.Read); #region Get astigmatism from lower tilts List<float> AstigmatismDeltas = new List<float>(); List<float> AstigmatismAngles = new List<float>(); for (int i = 0; i < Math.Min(NTilts, 6); i++) { int AngleID = IndicesSortedAbsoluteAngle[i]; Image UncroppedAngleImage = new Image(StackData[AngleID], originalStack.Dims.Slice()); Image AngleImage = UncroppedAngleImage.AsPadded(new int2(3500, 3500)); UncroppedAngleImage.Dispose(); int BestPrevious = -1; if (Math.Abs(LastFittedAngle - Angles[AngleID]) <= 5.1f) BestPrevious = IndicesSortedAbsoluteAngle[i - 1]; else if (ProcessedIndices.Count > 0) { List<int> SortedProcessed = new List<int>(ProcessedIndices); SortedProcessed.Sort((a, b) => Math.Abs(Angles[AngleID] - Angles[a]).CompareTo(Math.Abs(Angles[AngleID] - Angles[b]))); if (Math.Abs(Dose[SortedProcessed.First()] - Dose[AngleID]) < AverageDose * 5f) BestPrevious = SortedProcessed.First(); } CTF ThisCTF; CubicGrid ThisGrid; float2[] ThisPS1D; Cubic1D ThisBackground, ThisScale; Image ThisPS2D; CTF PrevCTF = BestPrevious >= 0 ? FitCTF[BestPrevious] : null; CubicGrid PrevGrid = BestPrevious >= 0 ? FitGrids[BestPrevious] : null; Cubic1D PrevBackground = BestPrevious >= 0 ? FitBackground[BestPrevious] : null; Cubic1D PrevScale = BestPrevious >= 0 ? FitScale[BestPrevious] : null; ProcessCTFOneAngle(AngleImage, Angles[AngleID], BestPrevious < 0, false, new float2(0, 0), PrevCTF, PrevGrid, PrevBackground, PrevScale, out ThisCTF, out ThisGrid, out ThisPS1D, out ThisBackground, out ThisScale, out ThisPS2D); AngleImage.Dispose(); FitCTF[AngleID] = ThisCTF; FitGrids[AngleID] = ThisGrid; FitPS1D[AngleID] = ThisPS1D; FitBackground[AngleID] = ThisBackground; FitScale[AngleID] = ThisScale; FitPS2D[AngleID] = ThisPS2D; LastFittedAngle = Angles[AngleID]; ProcessedIndices.Add(AngleID); AstigmatismDeltas.Add((float)ThisCTF.DefocusDelta); AstigmatismAngles.Add((float)ThisCTF.DefocusAngle); } ProcessedIndices.Clear(); LastFittedAngle = 9999; int[] GoodIndices = MathHelper.WithinNStdFromMedianIndices(AstigmatismDeltas.ToArray(), 1f); float MeanAstigmatismDelta = MathHelper.Mean(GoodIndices.Select(i => AstigmatismDeltas[i])); float2 MeanAstigmatismVector = MathHelper.Mean(GoodIndices.Select(i => new float2((float)Math.Cos(AstigmatismAngles[i] * Helper.ToRad), (float)Math.Sin(AstigmatismAngles[i] * Helper.ToRad)))); float MeanAstigmatismAngle = (float)Math.Atan2(MeanAstigmatismVector.Y, MeanAstigmatismVector.X) * Helper.ToDeg; #endregion #region Fit every tilt for (int i = 0; i < NTilts; i++) { int AngleID = IndicesSortedDose[i]; Image UncroppedAngleImage = new Image(StackData[AngleID], originalStack.Dims.Slice()); Image AngleImage = UncroppedAngleImage.AsPadded(new int2(3500, 3500)); UncroppedAngleImage.Dispose(); int BestPrevious = -1; if (Math.Abs(LastFittedAngle - Angles[AngleID]) <= 5.1f) BestPrevious = IndicesSortedDose[i - 1]; else if (ProcessedIndices.Count > 0) { List<int> SortedProcessed = new List<int>(ProcessedIndices); SortedProcessed.Sort((a, b) => Math.Abs(Angles[AngleID] - Angles[a]).CompareTo(Math.Abs(Angles[AngleID] - Angles[b]))); if (Math.Abs(Dose[SortedProcessed.First()] - Dose[AngleID]) < AverageDose * 5f) BestPrevious = SortedProcessed.First(); } CTF ThisCTF; CubicGrid ThisGrid; float2[] ThisPS1D; Cubic1D ThisBackground, ThisScale; Image ThisPS2D; CTF PrevCTF = BestPrevious >= 0 ? FitCTF[BestPrevious] : null; CubicGrid PrevGrid = BestPrevious >= 0 ? FitGrids[BestPrevious] : null; Cubic1D PrevBackground = BestPrevious >= 0 ? FitBackground[BestPrevious] : null; Cubic1D PrevScale = BestPrevious >= 0 ? FitScale[BestPrevious] : null; ProcessCTFOneAngle(AngleImage, Angles[AngleID], BestPrevious < 0, true, new float2(MeanAstigmatismDelta, MeanAstigmatismAngle), PrevCTF, PrevGrid, PrevBackground, PrevScale, out ThisCTF, out ThisGrid, out ThisPS1D, out ThisBackground, out ThisScale, out ThisPS2D); AngleImage.Dispose(); FitCTF[AngleID] = ThisCTF; FitGrids[AngleID] = ThisGrid; FitPS1D[AngleID] = ThisPS1D; FitBackground[AngleID] = ThisBackground; FitScale[AngleID] = ThisScale; FitPS2D[AngleID] = ThisPS2D; LastFittedAngle = Angles[AngleID]; ProcessedIndices.Add(AngleID); } #endregion CTF = FitCTF[IndicesSortedDose[0]]; #region Determine if angles are inverted compared to actual defocus { float[] UnbiasedAngles = FitGrids.Select(g => { float X1 = (g.FlatValues[0] + g.FlatValues[2]) * 0.5f; float X2 = (g.FlatValues[1] + g.FlatValues[3]) * 0.5f; float Delta = (X2 - X1) * 10000; float Distance = (float)MainWindow.Options.BinnedPixelSize * 3000;// originalHeader.Dimensions.X; return (float)Math.Atan2(Delta, Distance) * Helper.ToDeg; }).ToArray(); float Unbiased1 = 0, Unbiased2 = 0, Original1 = 0, Original2 = 0; for (int i = 0; i < NTilts; i++) { int ii = IndicesSortedAngle[i]; if (i < NTilts / 2) { Unbiased1 += UnbiasedAngles[ii]; Original1 += Angles[ii]; } else { Unbiased2 += UnbiasedAngles[ii]; Original2 += Angles[ii]; } } if ((Unbiased1 > Unbiased2) != (Original1 > Original2)) AreAnglesInverted = true; } #endregion // Create grids for fitted CTF params { float[] DefocusValues = new float[NTilts]; float[] DeltaValues = new float[NTilts]; float[] AngleValues = new float[NTilts]; for (int i = 0; i < NTilts; i++) { DefocusValues[i] = (float)FitCTF[i].Defocus; DeltaValues[i] = (float)FitCTF[i].DefocusDelta; AngleValues[i] = (float)FitCTF[i].DefocusAngle; } GridCTF = new CubicGrid(new int3(1, 1, NTilts), DefocusValues); GridCTFDefocusDelta = new CubicGrid(new int3(1, 1, NTilts), DeltaValues); GridCTFDefocusAngle = new CubicGrid(new int3(1, 1, NTilts), AngleValues); } // Put all 2D spectra into one stack and write it to disk for display purposes { Image AllPS2D = new Image(new int3(FitPS2D[0].Dims.X, FitPS2D[0].Dims.Y, NTilts)); float[][] AllPS2DData = AllPS2D.GetHost(Intent.Write); for (int i = 0; i < NTilts; i++) { AllPS2DData[i] = FitPS2D[i].GetHost(Intent.Read)[0]; FitPS2D[i].Dispose(); } AllPS2D.WriteMRC(PowerSpectrumPath); } // Store 1D spectrum data TiltPS1D.Clear(); TiltSimulatedBackground.Clear(); TiltSimulatedScale.Clear(); for (int i = 0; i < NTilts; i++) { TiltPS1D.Add(FitPS1D[i]); TiltSimulatedBackground.Add(new Cubic1D(FitBackground[i].Data.Select(v => new float2(v.X, 0)).ToArray())); TiltSimulatedScale.Add(FitScale[i]); } PS1D = FitPS1D[IndicesSortedDose[0]]; SimulatedBackground = TiltSimulatedBackground[IndicesSortedDose[0]]; SimulatedScale = FitScale[IndicesSortedDose[0]]; OnPropertyChanged("PS1D"); Simulated1D = GetSimulated1D(); CTFQuality = GetCTFQuality(); SaveMeta(); }
private void PrepareHeaderAndMap(string path, Image imageGain, decimal scaleFactor, out MapHeader header, out Image stack) { header = MapHeader.ReadFromFile(path, new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight), MainWindow.Options.InputDatOffset, ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType)); if (scaleFactor == 1M) { stack = StageDataLoad.LoadMap(path, new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight), MainWindow.Options.InputDatOffset, ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType)); if (imageGain != null) stack.MultiplySlices(imageGain); stack.Xray(20f); } else { int3 ScaledDims = new int3((int)Math.Round(header.Dimensions.X * scaleFactor), (int)Math.Round(header.Dimensions.Y * scaleFactor), header.Dimensions.Z); header.Dimensions = ScaledDims; stack = new Image(ScaledDims); float[][] OriginalStackData = stack.GetHost(Intent.Write); //Parallel.For(0, ScaledDims.Z, new ParallelOptions {MaxDegreeOfParallelism = 4}, z => for (int z = 0; z < ScaledDims.Z; z++) { Image Layer = StageDataLoad.LoadMap(path, new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight), MainWindow.Options.InputDatOffset, ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType), z); //lock (OriginalStackData) { if (imageGain != null) Layer.MultiplySlices(imageGain); Layer.Xray(20f); Image ScaledLayer = Layer.AsScaledMassive(new int2(ScaledDims)); Layer.Dispose(); OriginalStackData[z] = ScaledLayer.GetHost(Intent.Read)[0]; ScaledLayer.Dispose(); } }//); //stack.WriteMRC("d_stack.mrc"); } }
public void CreateCorrected(MapHeader originalHeader, Image originalStack) { if (!Directory.Exists(AverageDir)) Directory.CreateDirectory(AverageDir); if (!Directory.Exists(CTFDir)) Directory.CreateDirectory(CTFDir); if (MainWindow.Options.PostStack && !Directory.Exists(ShiftedStackDir)) Directory.CreateDirectory(ShiftedStackDir); int3 Dims = originalStack.Dims; Image ShiftedStack = null; if (MainWindow.Options.PostStack) ShiftedStack = new Image(Dims); 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[Dims.ElementsSlice()]; Helper.ForEachElementFT(new int2(Dims), (x, y, xx, yy) => { float xs = xx / (float)Dims.X; float ys = yy / (float)Dims.Y; float r = (float)Math.Sqrt(xs * xs + ys * ys); float angle = (float)(Math.Atan2(yy, xx) + Math.PI / 2.0); float CurrentPixelSize = PixelSize + PixelDelta * (float)Math.Cos(2f * (angle - PixelAngle)); CTFCoordsData[y * (Dims.X / 2 + 1) + x] = new float2(r / CurrentPixelSize, angle); }); CTFCoords = new Image(CTFCoordsData, Dims.Slice(), true); CTFCoords.RemapToFT(); } Image CTFFreq = CTFCoords.AsReal(); CubicGrid CollapsedMovementX = GridMovementX.CollapseXY(); CubicGrid CollapsedMovementY = GridMovementY.CollapseXY(); CubicGrid CollapsedCTF = GridCTF.CollapseXY(); Image AverageFT = new Image(Dims.Slice(), true, true); Image AveragePS = new Image(Dims.Slice(), true, false); Image Weights = new Image(Dims.Slice(), true, false); Weights.Fill(1e-6f); float StepZ = 1f / Math.Max(Dims.Z - 1, 1); for (int nframe = 0; nframe < Dims.Z; nframe++) { Image PS = new Image(Dims.Slice(), true); PS.Fill(1f); // Apply motion blur filter. /*{ float StartZ = (nframe - 0.5f) * StepZ; float StopZ = (nframe + 0.5f) * StepZ; float2[] Shifts = new float2[21]; for (int z = 0; z < Shifts.Length; z++) { float zp = StartZ + (StopZ - StartZ) / (Shifts.Length - 1) * z; Shifts[z] = new float2(CollapsedMovementX.GetInterpolated(new float3(0.5f, 0.5f, zp)), CollapsedMovementY.GetInterpolated(new float3(0.5f, 0.5f, zp))); } // Center the shifts around 0 float2 ShiftMean = MathHelper.Mean(Shifts); Shifts = Shifts.Select(v => v - ShiftMean).ToArray(); Image MotionFilter = new Image(IntPtr.Zero, Dims.Slice(), true); GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write), MotionFilter.Dims, Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()), (uint)Shifts.Length, 1); PS.Multiply(MotionFilter); //MotionFilter.WriteMRC("motion.mrc"); MotionFilter.Dispose(); }*/ // Apply CTF. /*if (CTF != null) { CTF Altered = CTF.GetCopy(); Altered.Defocus = (decimal)CollapsedCTF.GetInterpolated(new float3(0.5f, 0.5f, nframe * StepZ)); Image CTFImage = new Image(IntPtr.Zero, Dims.Slice(), true); GPU.CreateCTF(CTFImage.GetDevice(Intent.Write), CTFCoords.GetDevice(Intent.Read), (uint)CTFCoords.ElementsSliceComplex, new[] { Altered.ToStruct() }, false, 1); 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 * (nframe + 0.5f) / (PixelSize * PixelSize); Image DoseImage = new Image(IntPtr.Zero, Dims.Slice(), true); GPU.DoseWeighting(CTFFreq.GetDevice(Intent.Read), DoseImage.GetDevice(Intent.Write), (uint)DoseImage.ElementsSliceComplex, new[] { FrameDose }, NikoConst, 1); PS.Multiply(DoseImage); //DoseImage.WriteMRC("dose.mrc"); DoseImage.Dispose(); }*/ Image Frame = new Image(originalStack.GetHost(Intent.Read)[nframe], Dims.Slice()); Frame.ShiftSlicesMassive(new[] { new float3(CollapsedMovementX.GetInterpolated(new float3(0.5f, 0.5f, nframe * StepZ)), CollapsedMovementY.GetInterpolated(new float3(0.5f, 0.5f, nframe * StepZ)), 0f) }); if (MainWindow.Options.PostStack) ShiftedStack.GetHost(Intent.Write)[nframe] = Frame.GetHost(Intent.Read)[0]; Image FrameFT = Frame.AsFFT(); Frame.Dispose(); //Image PSSign = new Image(PS.GetDevice(Intent.Read), Dims.Slice(), true); //Image PSSign = new Image(Dims.Slice(), true); //PSSign.Fill(1f); //PSSign.Sign(); // Do phase flipping before averaging. //FrameFT.Multiply(PSSign); //PS.Multiply(PSSign); //PSSign.Dispose(); //FrameFT.Multiply(PS); AverageFT.Add(FrameFT); Weights.Add(PS); //PS.WriteMRC("ps.mrc"); PS.Multiply(PS); AveragePS.Add(PS); PS.Dispose(); FrameFT.Dispose(); } CTFCoords.Dispose(); CTFFreq.Dispose(); //AverageFT.Divide(Weights); //AverageFT.WriteMRC("averageft.mrc"); //Weights.WriteMRC("weights.mrc"); AveragePS.Divide(Weights); Weights.Dispose(); Image Average = AverageFT.AsIFFT(); AverageFT.Dispose(); MapHeader Header = originalHeader; Header.Dimensions = Dims.Slice(); Average.WriteMRC(AveragePath); Average.Dispose(); AveragePS.WriteMRC(CTFPath); AveragePS.Dispose(); TempAverageImage = null; OnPropertyChanged("AverageImage"); using (TextWriter Writer = File.CreateText(AverageDir + RootName + "_ctffind3.log")) { decimal Mag = (MainWindow.Options.CTFDetectorPixel * 10000M / CTF.PixelSize); Writer.WriteLine("CS[mm], HT[kV], AmpCnst, XMAG, DStep[um]"); Writer.WriteLine($"{CTF.Cs} {CTF.Voltage} {CTF.Amplitude} {Mag} {MainWindow.Options.CTFDetectorPixel}"); float BestQ = 0; float2[] Q = CTFQuality; if (Q != null) foreach (var q in Q) { if (q.Y < 0.3f) break; BestQ = q.X * 2f; } Writer.WriteLine($"{(CTF.Defocus + CTF.DefocusDelta / 2M) * 1e4M} {(CTF.Defocus - CTF.DefocusDelta / 2M) * 1e4M} {CTF.DefocusAngle} {BestQ} {CTF.PhaseShift * 180M} Final Values"); } if (MainWindow.Options.PostStack) ShiftedStack.WriteMRC(ShiftedStackPath); }