public void ExportParticlesMovieOld(Star table, int size)
{
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = table.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName))
RowIndices.Add(i);
if (RowIndices.Count == 0)
return;
if (!Directory.Exists(ParticlesDir))
Directory.CreateDirectory(ParticlesDir);
if (!Directory.Exists(ParticleCTFDir))
Directory.CreateDirectory(ParticleCTFDir);
MapHeader OriginalHeader = MapHeader.ReadFromFile(Path,
new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight),
MainWindow.Options.InputDatOffset,
ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));
/*Image OriginalStack = StageDataLoad.LoadMap(Path,
new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight),
MainWindow.Options.InputDatOffset,
ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));*/
//OriginalStack.Xray(20f);
int3 Dims = OriginalHeader.Dimensions;
int3 DimsRegion = new int3(size, size, 1);
int NParticles = RowIndices.Count / Dimensions.Z;
float PixelSize = (float)(MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5f;
float PixelDelta = (float)(MainWindow.Options.CTFPixelMax - MainWindow.Options.CTFPixelMin) * 0.5f;
float PixelAngle = (float)MainWindow.Options.CTFPixelAngle / (float)(180.0 / Math.PI);
Image CTFCoords;
{
float2[] CTFCoordsData = new float2[DimsRegion.ElementsSlice()];
//Helper.ForEachElementFT(new int2(DimsRegion), (x, y, xx, yy) =>
for (int y = 0; y < DimsRegion.Y; y++)
for (int x = 0; x < DimsRegion.X / 2 + 1; x++)
{
int xx = x;
int yy = y < DimsRegion.Y / 2 + 1 ? y : y - DimsRegion.Y;
float xs = xx / (float)DimsRegion.X;
float ys = yy / (float)DimsRegion.Y;
float r = (float)Math.Sqrt(xs * xs + ys * ys);
float angle = (float)(Math.Atan2(yy, xx));
float CurrentPixelSize = PixelSize + PixelDelta * (float)Math.Cos(2f * (angle - PixelAngle));
CTFCoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / CurrentPixelSize, angle);
} //);
CTFCoords = new Image(CTFCoordsData, DimsRegion.Slice(), true);
//CTFCoords.RemapToFT();
}
Image CTFFreq = CTFCoords.AsReal();
Image CTFStack = new Image(new int3(size, size, NParticles * Dimensions.Z), true);
int CTFStackIndex = 0;
string[] ColumnPosX = table.GetColumn("rlnCoordinateX");
string[] ColumnPosY = table.GetColumn("rlnCoordinateY");
int3[] Origins = new int3[NParticles];
for (int i = 0; i < NParticles; i++)
Origins[i] = new int3((int)double.Parse(ColumnPosX[RowIndices[i]]) - DimsRegion.X * 2 / 2,
(int)double.Parse(ColumnPosY[RowIndices[i]]) - DimsRegion.Y * 2 / 2,
0);
int IndexOffset = RowIndices[0];
string[] ColumnOriginX = table.GetColumn("rlnOriginX");
string[] ColumnOriginY = table.GetColumn("rlnOriginY");
string[] ColumnPriorX = table.GetColumn("rlnOriginXPrior");
string[] ColumnPriorY = table.GetColumn("rlnOriginYPrior");
float2[] ShiftPriors = new float2[NParticles];
for (int i = 0; i < NParticles; i++)
ShiftPriors[i] = new float2(float.Parse(ColumnPriorX[IndexOffset + i]),
float.Parse(ColumnPriorY[IndexOffset + i]));
float2[][] ParticleTracks = new float2[NParticles][];
for (int i = 0; i < NParticles; i++)
{
ParticleTracks[i] = new float2[Dimensions.Z];
for (int z = 0; z < Dimensions.Z; z++)
ParticleTracks[i][z] = new float2(float.Parse(ColumnOriginX[IndexOffset + z * NParticles + i]) - ShiftPriors[i].X,
float.Parse(ColumnOriginY[IndexOffset + z * NParticles + i]) - ShiftPriors[i].Y);
}
Image AverageFT = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true, true);
Image AveragePS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Image Weights = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Weights.Fill(1e-6f);
Image FrameParticles = new Image(IntPtr.Zero, new int3(DimsRegion.X * 2, DimsRegion.Y * 2, NParticles));
float StepZ = 1f / Math.Max(Dims.Z - 1, 1);
for (int z = 0; z < Dims.Z; z++)
{
float CoordZ = z * StepZ;
/*GPU.Extract(OriginalStack.GetDeviceSlice(z, Intent.Read),
FrameParticles.GetDevice(Intent.Write),
Dims.Slice(),
new int3(DimsRegion.X * 2, DimsRegion.Y * 2, 1),
Helper.ToInterleaved(Origins),
(uint)NParticles);*/
// Shift particles
{
float3[] Shifts = new float3[NParticles];
for (int i = 0; i < NParticles; i++)
{
float NormX = Math.Max(0.15f, Math.Min((float)Origins[i].X / Dims.X, 0.85f));
float NormY = Math.Max(0.15f, Math.Min((float)Origins[i].Y / Dims.Y, 0.85f));
float3 Coords = new float3(NormX, NormY, CoordZ);
Shifts[i] = new float3(GridMovementX.GetInterpolated(Coords) + ParticleTracks[i][z].X,
GridMovementY.GetInterpolated(Coords) + ParticleTracks[i][z].Y,
0f);
}
FrameParticles.ShiftSlices(Shifts);
}
Image FrameParticlesCropped = FrameParticles.AsPadded(new int2(DimsRegion));
Image FrameParticlesFT = FrameParticlesCropped.AsFFT();
FrameParticlesCropped.Dispose();
Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
PS.Fill(1f);
// Apply motion blur filter.
{
const int Samples = 11;
float StartZ = (z - 0.75f) * StepZ;
float StopZ = (z + 0.75f) * StepZ;
float2[] Shifts = new float2[Samples * NParticles];
for (int p = 0; p < NParticles; p++)
{
float NormX = Math.Max(0.15f, Math.Min((float)Origins[p].X / Dims.X, 0.85f));
float NormY = Math.Max(0.15f, Math.Min((float)Origins[p].Y / Dims.Y, 0.85f));
for (int zz = 0; zz < Samples; zz++)
{
float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz;
float3 Coords = new float3(NormX, NormY, zp);
Shifts[p * Samples + zz] = new float2(GridMovementX.GetInterpolated(Coords),
GridMovementY.GetInterpolated(Coords));
}
}
Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write),
DimsRegion,
Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()),
Samples,
(uint)NParticles);
PS.Multiply(MotionFilter);
//MotionFilter.WriteMRC("motion.mrc");
MotionFilter.Dispose();
}
// Apply CTF.
if (CTF != null)
{
CTFStruct[] Structs = new CTFStruct[NParticles];
for (int p = 0; p < NParticles; p++)
{
CTF Altered = CTF.GetCopy();
Altered.Defocus = (decimal)GridCTF.GetInterpolated(new float3(float.Parse(ColumnPosX[RowIndices[p]]) / Dims.X,
float.Parse(ColumnPosY[RowIndices[p]]) / Dims.Y,
z * StepZ));
Structs[p] = Altered.ToStruct();
}
Image CTFImage = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateCTF(CTFImage.GetDevice(Intent.Write),
CTFCoords.GetDevice(Intent.Read),
(uint)CTFCoords.ElementsSliceComplex,
Structs,
false,
(uint)NParticles);
//CTFImage.Abs();
PS.Multiply(CTFImage);
//CTFImage.WriteMRC("ctf.mrc");
CTFImage.Dispose();
}
// Apply dose weighting.
/*{
float3 NikoConst = new float3(0.245f, -1.665f, 2.81f);
// Niko's formula expects e-/A2/frame, we've got e-/px/frame -- convert!
float FrameDose = (float)MainWindow.Options.CorrectDosePerFrame * (z + 0.5f) / (PixelSize * PixelSize);
Image DoseImage = new Image(IntPtr.Zero, DimsRegion, true);
GPU.DoseWeighting(CTFFreq.GetDevice(Intent.Read),
DoseImage.GetDevice(Intent.Write),
(uint)DoseImage.ElementsSliceComplex,
new[] { FrameDose },
NikoConst,
1);
PS.MultiplySlices(DoseImage);
//DoseImage.WriteMRC("dose.mrc");
DoseImage.Dispose();
}*/
// Copy custom CTF into the CTF stack
GPU.CopyDeviceToDevice(PS.GetDevice(Intent.Read),
new IntPtr((long)CTFStack.GetDevice(Intent.Write) + CTFStack.ElementsSliceReal * NParticles * z * sizeof (float)),
CTFStack.ElementsSliceReal * NParticles);
Image PSAbs = new Image(PS.GetDevice(Intent.Read), new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
PSAbs.Abs();
FrameParticlesFT.Multiply(PSAbs);
AverageFT.Add(FrameParticlesFT);
Weights.Add(PSAbs);
PS.Multiply(PSAbs);
AveragePS.Add(PS);
PS.Dispose();
FrameParticlesFT.Dispose();
PSAbs.Dispose();
// Write paths to custom CTFs into the .star
for (int i = 0; i < NParticles; i++)
{
string ParticleCTFPath = (CTFStackIndex + 1).ToString("D6") + "@particlectf/" + RootName + ".mrcs";
table.SetRowValue(RowIndices[NParticles * z + i], "rlnCtfImage", ParticleCTFPath);
CTFStackIndex++;
}
}
FrameParticles.Dispose();
CTFCoords.Dispose();
CTFFreq.Dispose();
AverageFT.Divide(Weights);
AveragePS.Divide(Weights);
Weights.Dispose();
Image AverageParticles = AverageFT.AsIFFT();
AverageFT.Dispose();
GPU.NormParticles(AverageParticles.GetDevice(Intent.Read), AverageParticles.GetDevice(Intent.Write), DimsRegion, (uint)(90f / PixelSize), true, (uint)NParticles);
HeaderMRC ParticlesHeader = new HeaderMRC
{
Pixelsize = new float3(PixelSize, PixelSize, PixelSize)
};
AverageParticles.WriteMRC(ParticlesPath, ParticlesHeader);
AverageParticles.Dispose();
//OriginalStack.Dispose();
CTFStack.WriteMRC(DirectoryName + "particlectf/" + RootName + ".mrcs");
CTFStack.Dispose();
/*for (int i = 0; i < NParticles; i++)
{
string ParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs";
table.SetRowValue(RowIndices[i], "rlnImageName", ParticlePath);
}*/
AveragePS.Dispose();
//table.RemoveRows(RowIndices.Skip(NParticles).ToArray());
}
public void 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);
}