async void UpdateMask()
{
if (!IsInitialized)
{
return;
}
bool DoNew = (bool)RadioMaskNew.IsChecked;
bool UseHalfmap2 = (bool)RadioHalfmap2File.IsChecked && Halfmap2 != null;
float Threshold = (float)MaskThreshold;
float LowpassNyquist = (float)HalfmapPixelSize * 2 / (float)MaskLowpass;
ProgressMask.Visibility = Visibility.Visible;
await Task.Run(() =>
{
MaskFinal?.Dispose();
MaskFinal = null;
if (!DoNew && Mask != null)
{
MaskFinal = Mask.GetCopyGPU();
MaskFinal.Binarize(Threshold);
}
else if (DoNew)
{
MaskFinal = Halfmap1.GetCopyGPU();
if (UseHalfmap2)
{
MaskFinal.Add(Halfmap2);
MaskFinal.Multiply(0.5f);
}
MaskFinal.Bandpass(0, LowpassNyquist, true);
MaskFinal.Binarize(Threshold);
}
Dispatcher.Invoke(() =>
{
RendererMask.Volume = MaskFinal;
});
});
ProgressMask.Visibility = Visibility.Hidden;
RevalidateTab();
}
public static (Image[] Halves1, Image[] Halves2, float2[] Stats) TrainOnVolumes(NoiseNet3D network,
Image[] halves1,
Image[] halves2,
Image[] masks,
float angpix,
float lowpass,
float upsample,
bool dontFlatten,
bool performTraining,
int niterations,
float startFrom,
int batchsize,
int gpuprocess,
Action <string> progressCallback)
{
if (batchsize != 4)
{
niterations = niterations * 4 / batchsize;
Debug.WriteLine($"Adjusting the number of iterations to {niterations} to match different batch size.\n");
}
GPU.SetDevice(gpuprocess);
#region Mask
Debug.Write("Preparing mask... ");
progressCallback?.Invoke("Preparing mask... ");
int3[] BoundingBox = Helper.ArrayOfFunction(i => new int3(-1), halves1.Length);
if (masks != null)
{
for (int i = 0; i < masks.Length; i++)
{
Image Mask = masks[i];
Mask.TransformValues((x, y, z, v) =>
{
if (v > 0.5f)
{
BoundingBox[i].X = Math.Max(BoundingBox[i].X, Math.Abs(x - Mask.Dims.X / 2) * 2);
BoundingBox[i].Y = Math.Max(BoundingBox[i].Y, Math.Abs(y - Mask.Dims.Y / 2) * 2);
BoundingBox[i].Z = Math.Max(BoundingBox[i].Z, Math.Abs(z - Mask.Dims.Z / 2) * 2);
}
return(v);
});
if (BoundingBox[i].X < 2)
{
throw new Exception("Mask does not seem to contain any non-zero values.");
}
BoundingBox[i] += 64;
BoundingBox[i].X = Math.Min(BoundingBox[i].X, Mask.Dims.X);
BoundingBox[i].Y = Math.Min(BoundingBox[i].Y, Mask.Dims.Y);
BoundingBox[i].Z = Math.Min(BoundingBox[i].Z, Mask.Dims.Z);
}
}
Console.WriteLine("done.\n");
#endregion
#region Load and prepare data
Console.WriteLine("Preparing data:");
List <Image> Maps1 = new List <Image>();
List <Image> Maps2 = new List <Image>();
List <Image> HalvesForDenoising1 = new List <Image>();
List <Image> HalvesForDenoising2 = new List <Image>();
List <float2> StatsForDenoising = new List <float2>();
for (int imap = 0; imap < halves1.Length; imap++)
{
Debug.Write($"Preparing map {imap}... ");
progressCallback?.Invoke($"Preparing map {imap}... ");
Image Map1 = halves1[imap];
Image Map2 = halves2[imap];
float MapPixelSize = Map1.PixelSize / upsample;
if (!dontFlatten)
{
Image Average = Map1.GetCopy();
Average.Add(Map2);
if (masks != null)
{
Average.Multiply(masks[imap]);
}
float[] Spectrum = Average.AsAmplitudes1D(true, 1, (Average.Dims.X + Average.Dims.Y + Average.Dims.Z) / 6);
Average.Dispose();
int i10A = Math.Min((int)(angpix * 2 / 10 * Spectrum.Length), Spectrum.Length - 1);
float Amp10A = Spectrum[i10A];
for (int i = 0; i < Spectrum.Length; i++)
{
Spectrum[i] = i < i10A ? 1 : (Amp10A / Math.Max(1e-10f, Spectrum[i]));
}
Image Map1Flat = Map1.AsSpectrumMultiplied(true, Spectrum);
Map1.FreeDevice();
Map1 = Map1Flat;
Map1.FreeDevice();
Image Map2Flat = Map2.AsSpectrumMultiplied(true, Spectrum);
Map2.FreeDevice();
Map2 = Map2Flat;
Map2.FreeDevice();
}
if (lowpass > 0)
{
Map1.Bandpass(0, angpix * 2 / lowpass, true, 0.01f);
Map2.Bandpass(0, angpix * 2 / lowpass, true, 0.01f);
}
if (upsample != 1f)
{
Image Map1Scaled = Map1.AsScaled(Map1.Dims * upsample / 2 * 2);
Map1.FreeDevice();
Map1 = Map1Scaled;
Map1.FreeDevice();
Image Map2Scaled = Map2.AsScaled(Map2.Dims * upsample / 2 * 2);
Map2.FreeDevice();
Map2 = Map2Scaled;
Map2.FreeDevice();
}
Image ForDenoising1 = Map1.GetCopy();
Image ForDenoising2 = Map2.GetCopy();
if (BoundingBox[imap].X > 0)
{
Image Map1Cropped = Map1.AsPadded(BoundingBox[imap]);
Map1.FreeDevice();
Map1 = Map1Cropped;
Map1.FreeDevice();
Image Map2Cropped = Map2.AsPadded(BoundingBox[imap]);
Map2.FreeDevice();
Map2 = Map2Cropped;
Map2.FreeDevice();
}
float2 MeanStd = MathHelper.MeanAndStd(Helper.Combine(Map1.GetHostContinuousCopy(), Map2.GetHostContinuousCopy()));
Map1.TransformValues(v => (v - MeanStd.X) / MeanStd.Y);
Map2.TransformValues(v => (v - MeanStd.X) / MeanStd.Y);
ForDenoising1.TransformValues(v => (v - MeanStd.X) / MeanStd.Y);
ForDenoising2.TransformValues(v => (v - MeanStd.X) / MeanStd.Y);
HalvesForDenoising1.Add(ForDenoising1);
HalvesForDenoising2.Add(ForDenoising2);
StatsForDenoising.Add(MeanStd);
GPU.PrefilterForCubic(Map1.GetDevice(Intent.ReadWrite), Map1.Dims);
Map1.FreeDevice();
Maps1.Add(Map1);
GPU.PrefilterForCubic(Map2.GetDevice(Intent.ReadWrite), Map2.Dims);
Map2.FreeDevice();
Maps2.Add(Map2);
Debug.WriteLine(" Done.");
}
if (masks != null)
{
foreach (var mask in masks)
{
mask.FreeDevice();
}
}
#endregion
int Dim = network.BoxDimensions.X;
progressCallback?.Invoke($"0/{niterations}");
if (performTraining)
{
GPU.SetDevice(gpuprocess);
#region Training
Random Rand = new Random(123);
int NMaps = Maps1.Count;
int NMapsPerBatch = Math.Min(128, NMaps);
int MapSamples = batchsize;
Image[] ExtractedSource = Helper.ArrayOfFunction(i => new Image(new int3(Dim, Dim, Dim * MapSamples)), NMapsPerBatch);
Image[] ExtractedTarget = Helper.ArrayOfFunction(i => new Image(new int3(Dim, Dim, Dim * MapSamples)), NMapsPerBatch);
for (int iter = (int)(startFrom * niterations); iter < niterations; iter++)
{
int[] ShuffledMapIDs = Helper.RandomSubset(Helper.ArrayOfSequence(0, NMaps, 1), NMapsPerBatch, Rand.Next(9999));
for (int m = 0; m < NMapsPerBatch; m++)
{
int MapID = ShuffledMapIDs[m];
Image Map1 = Maps1[MapID];
Image Map2 = Maps2[MapID];
int3 DimsMap = Map1.Dims;
int3 Margin = new int3((int)(Dim / 2 * 1.5f));
//Margin.Z = 0;
float3[] Position = Helper.ArrayOfFunction(i => new float3((float)Rand.NextDouble() * (DimsMap.X - Margin.X * 2) + Margin.X,
(float)Rand.NextDouble() * (DimsMap.Y - Margin.Y * 2) + Margin.Y,
(float)Rand.NextDouble() * (DimsMap.Z - Margin.Z * 2) + Margin.Z), MapSamples);
float3[] Angle = Helper.ArrayOfFunction(i => new float3((float)Rand.NextDouble() * 360,
(float)Rand.NextDouble() * 360,
(float)Rand.NextDouble() * 360) * Helper.ToRad, MapSamples);
{
ulong[] Texture = new ulong[1], TextureArray = new ulong[1];
GPU.CreateTexture3D(Map1.GetDevice(Intent.Read), Map1.Dims, Texture, TextureArray, true);
//Map1.FreeDevice();
GPU.Rotate3DExtractAt(Texture[0],
Map1.Dims,
ExtractedSource[m].GetDevice(Intent.Write),
new int3(Dim),
Helper.ToInterleaved(Angle),
Helper.ToInterleaved(Position),
(uint)MapSamples);
//ExtractedSource[MapID].WriteMRC("d_extractedsource.mrc", true);
GPU.DestroyTexture(Texture[0], TextureArray[0]);
}
{
ulong[] Texture = new ulong[1], TextureArray = new ulong[1];
GPU.CreateTexture3D(Map2.GetDevice(Intent.Read), Map2.Dims, Texture, TextureArray, true);
//Map2.FreeDevice();
GPU.Rotate3DExtractAt(Texture[0],
Map2.Dims,
ExtractedTarget[m].GetDevice(Intent.Write),
new int3(Dim),
Helper.ToInterleaved(Angle),
Helper.ToInterleaved(Position),
(uint)MapSamples);
//ExtractedTarget.WriteMRC("d_extractedtarget.mrc", true);
GPU.DestroyTexture(Texture[0], TextureArray[0]);
}
//Map1.FreeDevice();
//Map2.FreeDevice();
}
float[] PredictedData = null, Loss = null;
{
float CurrentLearningRate = 0.0001f * (float)Math.Pow(10, -iter / (float)niterations * 2);
for (int m = 0; m < ShuffledMapIDs.Length; m++)
{
int MapID = m;
bool Twist = Rand.Next(2) == 0;
if (Twist)
{
network.Train(ExtractedSource[MapID].GetDevice(Intent.Read),
ExtractedTarget[MapID].GetDevice(Intent.Read),
CurrentLearningRate,
0,
out PredictedData,
out Loss);
}
else
{
network.Train(ExtractedTarget[MapID].GetDevice(Intent.Read),
ExtractedSource[MapID].GetDevice(Intent.Read),
CurrentLearningRate,
0,
out PredictedData,
out Loss);
}
}
}
Debug.WriteLine($"{iter + 1}/{niterations}");
progressCallback?.Invoke($"{iter + 1}/{niterations}");
}
Debug.WriteLine("\nDone training!\n");
#endregion
}
return(HalvesForDenoising1.ToArray(), HalvesForDenoising2.ToArray(), StatsForDenoising.ToArray());
}
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 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);
}