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);
}
