public CubicGrid(int3 dimensions, float valueMin, float valueMax, Dimension gradientDirection)
{
Dimensions = dimensions;
Values = new float[dimensions.Z, dimensions.Y, dimensions.X];
float Step = valueMax - valueMin;
if (gradientDirection == Dimension.X)
Step /= Math.Max(1, dimensions.X - 1);
else if (gradientDirection == Dimension.Y)
Step /= Math.Max(1, dimensions.Y - 1);
else if (gradientDirection == Dimension.Z)
Step /= Math.Max(1, dimensions.Z - 1);
for (int z = 0; z < dimensions.Z; z++)
for (int y = 0; y < dimensions.Y; y++)
for (int x = 0; x < dimensions.X; x++)
{
float Value = valueMin;
if (gradientDirection == Dimension.X)
Value += x * Step;
if (gradientDirection == Dimension.Y)
Value += y * Step;
if (gradientDirection == Dimension.Z)
Value += z * Step;
Values[z, y, x] = Value;
}
Spacing = new float3(1f / Math.Max(1, dimensions.X - 1), 1f / Math.Max(1, dimensions.Y - 1), 1f / Math.Max(1, dimensions.Z - 1));
}
public static void GetPlans(int3 dims, int oversampling, out int planForw, out int planBack, out int planForwCTF)
{
int Oversampled = dims.X * oversampling;
int3 DimsOversampled = new int3(Oversampled, Oversampled, Oversampled);
planForw = GPU.CreateFFTPlan(DimsOversampled, 1);
planBack = GPU.CreateIFFTPlan(DimsOversampled, 1);
planForwCTF = GPU.CreateFFTPlan(dims, 1);
}
public Image(float[][] data, int3 dims, bool isft = false, bool iscomplex = false, bool ishalf = false)
{
Dims = dims;
IsFT = isft;
IsComplex = iscomplex;
IsHalf = ishalf;
_HostData = data;
IsHostDirty = true;
}
public Image(float2[][] data, int3 dims, bool isft = false, bool ishalf = false)
{
Dims = dims;
IsFT = isft;
IsComplex = true;
IsHalf = ishalf;
UpdateHostWithComplex(data);
IsHostDirty = true;
}
public Projector(int3 dims, int oversampling)
{
Dims = dims;
Oversampling = oversampling;
int Oversampled = 2 * (oversampling * (Dims.X / 2) + 1) + 1;
DimsOversampled = new int3(Oversampled, Oversampled, Oversampled);
Data = new Image(IntPtr.Zero, DimsOversampled, true, true);
Weights = new Image(IntPtr.Zero, DimsOversampled, true, false);
}
public CubicGrid(int3 dimensions, float[] values)
{
Values = new float[dimensions.Z, dimensions.Y, dimensions.X];
Dimensions = dimensions;
Spacing = new float3(1f / Math.Max(1, Dimensions.X - 1), 1f / Math.Max(1, Dimensions.Y - 1), 1f / Math.Max(1, Dimensions.Z - 1));
for (int z = 0; z < Dimensions.Z; z++)
for (int y = 0; y < Dimensions.Y; y++)
for (int x = 0; x < Dimensions.X; x++)
Values[z, y, x] = values[(z * Dimensions.Y + y) * Dimensions.X + x];
}
public Image(float[] data, int3 dims, bool isft = false, bool iscomplex = false, bool ishalf = false)
{
Dims = dims;
IsFT = isft;
IsComplex = iscomplex;
IsHalf = ishalf;
float[][] Slices = new float[dims.Z][];
int i = 0;
for (int z = 0; z < dims.Z; z++)
{
Slices[z] = new float[ElementsSliceReal];
for (int j = 0; j < Slices[z].Length; j++)
Slices[z][j] = data[i++];
}
_HostData = Slices;
IsHostDirty = true;
}
public Projector(Image data, int oversampling)
{
Dims = data.Dims;
Oversampling = oversampling;
int Oversampled = 2 * (oversampling * (Dims.X / 2) + 1) + 1;
DimsOversampled = new int3(Oversampled, Oversampled, Oversampled);
float[] Continuous = data.GetHostContinuousCopy();
float[] Initialized = new float[(DimsOversampled.X / 2 + 1) * DimsOversampled.Y * DimsOversampled.Z * 2];
CPU.InitProjector(Dims, Oversampling, Continuous, Initialized);
float2[] Initialized2 = Helper.FromInterleaved2(Initialized);
Data = new Image(Initialized2, DimsOversampled, true);
//Data = Data.AsAmplitudes();
//Data.WriteMRC("d_proj.mrc");
Weights = new Image(DimsOversampled, true, false);
}
public static int3 GetMapDimensions(string path)
{
int3 Dims = new int3(1, 1, 1);
FileInfo Info = new FileInfo(path);
using (BinaryReader Reader = new BinaryReader(OpenWithBigBuffer(path)))
{
if (Info.Extension.ToLower() == ".mrc" || Info.Extension.ToLower() == ".mrcs")
{
HeaderMRC Header = new HeaderMRC(Reader);
Dims = Header.Dimensions;
}
else if (Info.Extension.ToLower() == ".em")
{
HeaderEM Header = new HeaderEM(Reader);
Dims = Header.Dimensions;
}
else
throw new Exception("Format not supported.");
}
return Dims;
}
public void Correlate(Image tiltStack, Image reference, int size, float lowpassAngstrom, float highpassAngstrom, int3 volumeDimensions, int healpixOrder, string symmetry = "C1")
{
if (!Directory.Exists(CorrelationDir))
Directory.CreateDirectory(CorrelationDir);
float DownscaleFactor = lowpassAngstrom / (float)(CTF.PixelSize * 2);
Image DownscaledStack = tiltStack.AsScaledMassive(new int2(tiltStack.Dims) / DownscaleFactor / 2 * 2);
tiltStack.FreeDevice();
float HighpassNyquist = (float)(CTF.PixelSize * 2) * DownscaleFactor / highpassAngstrom;
DownscaledStack.Bandpass(HighpassNyquist, 1, false);
Image ScaledReference = reference.AsScaled(reference.Dims / DownscaleFactor / 2 * 2);
reference.FreeDevice();
Image PaddedReference = ScaledReference.AsPadded(new int3(size, size, size));
ScaledReference.Dispose();
PaddedReference.Bandpass(HighpassNyquist, 1, true);
Projector ProjectorReference = new Projector(PaddedReference, 2);
PaddedReference.Dispose();
VolumeDimensions = volumeDimensions / DownscaleFactor / 2 * 2;
int SizeCropped = size / 2;
int3 Grid = (VolumeDimensions + SizeCropped - 1) / SizeCropped;
List<float3> GridCoords = new List<float3>();
for (int z = 0; z < Grid.Z; z++)
for (int y = 0; y < Grid.Y; y++)
for (int x = 0; x < Grid.X; x++)
GridCoords.Add(new float3(x * SizeCropped + SizeCropped / 2,
y * SizeCropped + SizeCropped / 2,
z * SizeCropped + SizeCropped / 2));
float3[] HealpixAngles = Helper.GetHealpixAngles(healpixOrder, symmetry).Select(a => a * Helper.ToRad).ToArray();
Image CTFCoords = GetCTFCoords(size, (int)(size * DownscaleFactor));
float[] OutputCorr = new float[VolumeDimensions.Elements()];
int PlanForw, PlanBack, PlanForwCTF;
Projector.GetPlans(new int3(size, size, size), 2, out PlanForw, out PlanBack, out PlanForwCTF);
int BatchSize = 16;
for (int b = 0; b < GridCoords.Count; b += BatchSize)
{
int CurBatch = Math.Min(BatchSize, GridCoords.Count - b);
Image Subtomos = new Image(IntPtr.Zero, new int3(size, size, size * CurBatch), true, true);
Image SubtomoCTFs = new Image(IntPtr.Zero, new int3(size, size, size * CurBatch), true);
for (int st = 0; st < CurBatch; st++)
{
Image ImagesFT = GetSubtomoImages(DownscaledStack, size, GridCoords[b + st], true);
Image CTFs = GetSubtomoCTFs(GridCoords[b + st], CTFCoords);
//Image CTFWeights = GetSubtomoCTFs(GridCoords[b + st], CTFCoords, true, true);
ImagesFT.Multiply(CTFs); // Weight and phase-flip image FTs by CTF, which still has its sign here
//ImagesFT.Multiply(CTFWeights);
CTFs.Abs(); // CTF has to be positive from here on since image FT phases are now flipped
// CTF has to be converted to complex numbers with imag = 0, and weighted by itself
float2[] CTFsComplexData = new float2[CTFs.ElementsComplex];
float[] CTFsContinuousData = CTFs.GetHostContinuousCopy();
for (int i = 0; i < CTFsComplexData.Length; i++)
CTFsComplexData[i] = new float2(CTFsContinuousData[i] * CTFsContinuousData[i], 0);
Image CTFsComplex = new Image(CTFsComplexData, CTFs.Dims, true);
Projector ProjSubtomo = new Projector(new int3(size, size, size), 2);
lock (GPU.Sync)
ProjSubtomo.BackProject(ImagesFT, CTFs, GetAngleInImages(GridCoords[b + st]));
Image Subtomo = ProjSubtomo.Reconstruct(false, PlanForw, PlanBack, PlanForwCTF);
ProjSubtomo.Dispose();
/*Image CroppedSubtomo = Subtomo.AsPadded(new int3(SizeCropped, SizeCropped, SizeCropped));
CroppedSubtomo.WriteMRC(ParticlesDir + RootName + "_" + (b + st).ToString("D5") + ".mrc");
CroppedSubtomo.Dispose();*/
Projector ProjCTF = new Projector(new int3(size, size, size), 2);
lock (GPU.Sync)
ProjCTF.BackProject(CTFsComplex, CTFs, GetAngleInImages(GridCoords[b + st]));
Image SubtomoCTF = ProjCTF.Reconstruct(true, PlanForw, PlanBack, PlanForwCTF);
ProjCTF.Dispose();
GPU.FFT(Subtomo.GetDevice(Intent.Read), Subtomos.GetDeviceSlice(size * st, Intent.Write), Subtomo.Dims, 1);
GPU.CopyDeviceToDevice(SubtomoCTF.GetDevice(Intent.Read), SubtomoCTFs.GetDeviceSlice(size * st, Intent.Write), SubtomoCTF.ElementsReal);
ImagesFT.Dispose();
CTFs.Dispose();
//CTFWeights.Dispose();
CTFsComplex.Dispose();
Subtomo.Dispose();
SubtomoCTF.Dispose();
}
Image BestCorrelation = new Image(IntPtr.Zero, new int3(size, size, size * CurBatch));
Image BestRot = new Image(IntPtr.Zero, new int3(size, size, size * CurBatch));
Image BestTilt = new Image(IntPtr.Zero, new int3(size, size, size * CurBatch));
Image BestPsi = new Image(IntPtr.Zero, new int3(size, size, size * CurBatch));
GPU.CorrelateSubTomos(ProjectorReference.Data.GetDevice(Intent.Read),
ProjectorReference.Oversampling,
ProjectorReference.Data.Dims,
Subtomos.GetDevice(Intent.Read),
SubtomoCTFs.GetDevice(Intent.Read),
new int3(size, size, size),
(uint)CurBatch,
Helper.ToInterleaved(HealpixAngles),
(uint)HealpixAngles.Length,
MainWindow.Options.ExportParticleRadius / ((float)CTF.PixelSize * DownscaleFactor),
BestCorrelation.GetDevice(Intent.Write),
BestRot.GetDevice(Intent.Write),
BestTilt.GetDevice(Intent.Write),
BestPsi.GetDevice(Intent.Write));
for (int st = 0; st < CurBatch; st++)
{
Image ThisCorrelation = new Image(BestCorrelation.GetDeviceSlice(size * st, Intent.Read), new int3(size, size, size));
Image CroppedCorrelation = ThisCorrelation.AsPadded(new int3(SizeCropped, SizeCropped, SizeCropped));
//CroppedCorrelation.WriteMRC(CorrelationDir + RootName + "_" + (b + st).ToString("D5") + ".mrc");
float[] SubCorr = CroppedCorrelation.GetHostContinuousCopy();
int3 Origin = new int3(GridCoords[b + st]) - SizeCropped / 2;
for (int z = 0; z < SizeCropped; z++)
{
int zVol = Origin.Z + z;
if (zVol >= VolumeDimensions.Z)
continue;
for (int y = 0; y < SizeCropped; y++)
{
int yVol = Origin.Y + y;
if (yVol >= VolumeDimensions.Y)
continue;
for (int x = 0; x < SizeCropped; x++)
{
int xVol = Origin.X + x;
if (xVol >= VolumeDimensions.X)
continue;
OutputCorr[(zVol * VolumeDimensions.Y + yVol) * VolumeDimensions.X + xVol] = SubCorr[(z * SizeCropped + y) * SizeCropped + x];
}
}
}
CroppedCorrelation.Dispose();
ThisCorrelation.Dispose();
}
Subtomos.Dispose();
SubtomoCTFs.Dispose();
BestCorrelation.Dispose();
BestRot.Dispose();
BestTilt.Dispose();
BestPsi.Dispose();
}
GPU.DestroyFFTPlan(PlanForw);
GPU.DestroyFFTPlan(PlanBack);
GPU.DestroyFFTPlan(PlanForwCTF);
CTFCoords.Dispose();
ProjectorReference.Dispose();
DownscaledStack.Dispose();
Image OutputCorrImage = new Image(OutputCorr, VolumeDimensions);
OutputCorrImage.WriteMRC(CorrelationDir + RootName + ".mrc");
OutputCorrImage.Dispose();
}
public void ExportSubtomos(Star tableIn, Image tiltStack, int size, int3 volumeDimensions)
{
VolumeDimensions = volumeDimensions;
#region Get rows from table
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName + "."))
RowIndices.Add(i);
//if (RowIndices.Count == 0)
// return;
int NParticles = RowIndices.Count;
#endregion
#region Make sure all columns and directories are there
if (!tableIn.HasColumn("rlnImageName"))
tableIn.AddColumn("rlnImageName");
if (!tableIn.HasColumn("rlnCtfImage"))
tableIn.AddColumn("rlnCtfImage");
if (!Directory.Exists(ParticlesDir))
Directory.CreateDirectory(ParticlesDir);
if (!Directory.Exists(ParticleCTFDir))
Directory.CreateDirectory(ParticleCTFDir);
#endregion
#region Get subtomo positions from table
float3[] Origins = new float3[NParticles];
float3[] ParticleAngles = new float3[NParticles];
{
string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX");
string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY");
string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ");
string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX");
string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY");
string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ");
string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot");
string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt");
string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi");
for (int i = 0; i < NParticles; i++)
{
float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture));
float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture));
//Origins[i] *= new float3(3838f / 959f, 3710f / 927f, 4f);
Origins[i] = Pos - Shift;
float3 Angle = new float3(0, 0, 0);
if (ColumnAngleRot != null && ColumnAngleTilt != null && ColumnAnglePsi != null)
Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture));
ParticleAngles[i] = Angle;
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", Origins[i].X.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", Origins[i].Y.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateZ", Origins[i].Z.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0");
tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0");
tableIn.SetRowValue(RowIndices[i], "rlnOriginZ", "0.0");
//tableIn.SetRowValue(RowIndices[i], "rlnAngleRot", "0.0");
//tableIn.SetRowValue(RowIndices[i], "rlnAngleTilt", "0.0");
//tableIn.SetRowValue(RowIndices[i], "rlnAnglePsi", "0.0");
}
}
#endregion
tiltStack.FreeDevice();
/*int SizeCropped = 50;//size / 2;
int3 Grid = (VolumeDimensions + SizeCropped - 1) / SizeCropped;
List<float3> GridCoords = new List<float3>();
for (int z = 0; z < Grid.Z; z++)
for (int y = 0; y < Grid.Y; y++)
for (int x = 0; x < Grid.X; x++)
GridCoords.Add(new float3(x * SizeCropped + SizeCropped / 2,
y * SizeCropped + SizeCropped / 2,
z * SizeCropped + SizeCropped / 2));
Origins = GridCoords.ToArray();
NParticles = Origins.Length;*/
if (NParticles == 0)
return;
Image CTFCoords = GetCTFCoords(size, size);
int PlanForw, PlanBack, PlanForwCTF;
Projector.GetPlans(new int3(size, size, size), 2, out PlanForw, out PlanBack, out PlanForwCTF);
//Parallel.For(0, NParticles, new ParallelOptions() { MaxDegreeOfParallelism = 1 }, p =>
for (int p = 0; p < NParticles; p++)
{
lock (tableIn)
{
tableIn.SetRowValue(RowIndices[p], "rlnImageName", "particles/" + RootName + "_" + p.ToString("D5") + ".mrc");
tableIn.SetRowValue(RowIndices[p], "rlnCtfImage", "particlectf/" + RootName + "_" + p.ToString("D5") + ".mrc");
//tableIn.Save("D:\\rubisco\\luisexported.star");
}
if (File.Exists(ParticlesDir + RootName + "_" + p.ToString("D5") + ".mrc"))
return;
Image Subtomo, SubtomoCTF;
GetSubtomo(tiltStack, Origins[p], ParticleAngles[p], CTFCoords, out Subtomo, out SubtomoCTF, PlanForw, PlanBack, PlanForwCTF);
//Image SubtomoCropped = Subtomo.AsPadded(new int3(SizeCropped, SizeCropped, SizeCropped));
Subtomo.WriteMRC(ParticlesDir + RootName + "_" + p.ToString("D5") + ".mrc");
SubtomoCTF.WriteMRC(ParticleCTFDir + RootName + "_" + p.ToString("D5") + ".mrc");
//SubtomoCropped.Dispose();
Subtomo?.Dispose();
SubtomoCTF?.Dispose();
}//);
GPU.DestroyFFTPlan(PlanForw);
GPU.DestroyFFTPlan(PlanBack);
GPU.DestroyFFTPlan(PlanForwCTF);
CTFCoords.Dispose();
}
public CubicGrid Resize(int3 newSize)
{
float[] Result = new float[newSize.Elements()];
float StepX = 1f / Math.Max(1, newSize.X - 1);
float StepY = 1f / Math.Max(1, newSize.Y - 1);
float StepZ = 1f / Math.Max(1, newSize.Z - 1);
for (int z = 0, i = 0; z < newSize.Z; z++)
for (int y = 0; y < newSize.Y; y++)
for (int x = 0; x < newSize.X; x++, i++)
Result[i] = GetInterpolated(new float3(x * StepX, y * StepY, z * StepZ));
return new CubicGrid(newSize, Result);
}
public static int3 Min(int3 o1, int3 o2)
{
return(new int3(Math.Min(o1.X, o2.X), Math.Min(o1.Y, o2.Y), Math.Min(o1.Z, o2.Z)));
}
public static CubicGrid Load(XPathNavigator nav)
{
int3 Dimensions = new int3(int.Parse(nav.GetAttribute("Width", ""), CultureInfo.InvariantCulture),
int.Parse(nav.GetAttribute("Height", ""), CultureInfo.InvariantCulture),
int.Parse(nav.GetAttribute("Depth", ""), CultureInfo.InvariantCulture));
float[,,] Values = new float[Dimensions.Z, Dimensions.Y, Dimensions.X];
foreach (XPathNavigator nodeNav in nav.SelectChildren("Node", ""))
{
//try
{
int X = int.Parse(nodeNav.GetAttribute("X", ""), CultureInfo.InvariantCulture);
int Y = int.Parse(nodeNav.GetAttribute("Y", ""), CultureInfo.InvariantCulture);
int Z = int.Parse(nodeNav.GetAttribute("Z", ""), CultureInfo.InvariantCulture);
float Value = float.Parse(nodeNav.GetAttribute("Value", ""), CultureInfo.InvariantCulture);
Values[Z, Y, X] = Value;
}
//catch { }
}
return new CubicGrid(Values);
}
public float[] GetInterpolatedNative(int3 valueGrid, float3 border)
{
float[] Result = new float[valueGrid.Elements()];
float StepX = (1f - border.X * 2) / Math.Max(1, valueGrid.X - 1);
float OffsetX = border.X;
float StepY = (1f - border.Y * 2) / Math.Max(1, valueGrid.Y - 1);
float OffsetY = border.Y;
float StepZ = (1f - border.Z * 2) / Math.Max(valueGrid.Z - 1, 1);
float OffsetZ = valueGrid.Z == 1 ? 0.5f : border.Z;
CPU.CubicInterpOnGrid(Dimensions, FlatValues, Spacing, valueGrid, new float3(StepX, StepY, StepZ), new float3(OffsetX, OffsetY, OffsetZ), Result);
return Result;
}
public static float[] MatchVolumeIntensities(float3[] atoms, Image volume, Image mask, float radius, out float sigma, out float correlation, float blobRadius = 1.0f, float blobAlpha = 6f)
{
int3 Dims = volume.Dims;
float[] MaskData = mask.GetHostContinuousCopy();
List <int> MaskIndices = new List <int>();
for (int i = 0; i < MaskData.Length; i++)
{
if (MaskData[i] == 1)
{
MaskIndices.Add(i);
}
}
int3 DimsUpscaled = Dims * 2;
DimsUpscaled.Z = DimsUpscaled.Z > 2 ? DimsUpscaled.Z : 1;
Image VolumeUpscaled;
if (DimsUpscaled.Z == 1)
{
VolumeUpscaled = volume.AsScaled(new int2(DimsUpscaled));
}
else
{
VolumeUpscaled = volume.AsScaled(DimsUpscaled);
}
volume.FreeDevice();
VolumeUpscaled.FreeDevice();
float[] VolumeData = volume.GetHostContinuousCopy();
float[] VolumeDataUpscaled = VolumeUpscaled.GetHostContinuousCopy();
float[] VolumeSparse = new float[MaskIndices.Count];
for (int i = 0; i < MaskIndices.Count; i++)
{
VolumeSparse[i] = VolumeData[MaskIndices[i]];
}
MathHelper.NormalizeInPlace(VolumeSparse);
Func <float, float[]> GetIntensities = s =>
{
float[] Result = new float[atoms.Length];
float3[] Normalized = atoms.Select(a => a * 2 * new float3(1f / (DimsUpscaled.X - 1), 1f / (DimsUpscaled.Y - 1), 1f / (DimsUpscaled.Z - 1))).ToArray();
CubicGrid Grid = new CubicGrid(DimsUpscaled, VolumeDataUpscaled);
Result = Grid.GetInterpolatedNative(Normalized);
return(Result);
};
Func <double[], double> Eval = input =>
{
float[] CurIntensities = GetIntensities((float)Math.Log(input[0]));
Image Simulated = GetVolumeFromAtoms(atoms, volume.Dims, (float)Math.Log(input[0]), CurIntensities, blobRadius, blobAlpha);
float[] SimulatedData = Simulated.GetHostContinuousCopy();
float[] SimulatedSparse = new float[MaskIndices.Count];
for (int i = 0; i < MaskIndices.Count; i++)
{
SimulatedSparse[i] = SimulatedData[MaskIndices[i]];
}
MathHelper.NormalizeInPlace(SimulatedSparse);
float[] Corr = MathHelper.Mult(SimulatedSparse, VolumeSparse);
return(Corr.Sum() / Corr.Length);
};
sigma = radius * 1f;
float[] FinalIntensities = GetIntensities(sigma);
correlation = (float)Eval(new[] { Math.Exp(sigma) });
return(FinalIntensities);
}
public static Vector3 Reciprocal(int3 v)
{
return new Vector3(1f / v.X, 1f / v.Y, 1f / v.Z);
}
public static float3[] FillWithEquidistantPoints(Image mask, int n, out float R)
{
float3 MaskCenter = mask.AsCenterOfMass();
float[] MaskData = mask.GetHostContinuousCopy();
int3 Dims = mask.Dims;
float3[] BestSolution = null;
float a = 0, b = Dims.X / 2;
R = (a + b) / 2;
float3 Offset = new float3(0, 0, 0);
for (int o = 0; o < 2; o++)
{
for (int i = 0; i < 10; i++)
{
R = (a + b) / 2;
float Root3 = (float)Math.Sqrt(3);
float ZTerm = (float)(2 * Math.Sqrt(6) / 3);
float SpacingX = R * 2;
float SpacingY = Root3 * R;
float SpacingZ = ZTerm * R;
int3 DimsSphere = new int3(Math.Min(512, (int)Math.Ceiling(Dims.X / SpacingX)),
Math.Min(512, (int)Math.Ceiling(Dims.Y / SpacingX)),
Math.Min(512, (int)Math.Ceiling(Dims.Z / SpacingX)));
BestSolution = new float3[DimsSphere.Elements()];
for (int z = 0; z < DimsSphere.Z; z++)
{
for (int y = 0; y < DimsSphere.Y; y++)
{
for (int x = 0; x < DimsSphere.X; x++)
{
BestSolution[DimsSphere.ElementFromPosition(x, y, z)] = new float3(2 * x + (y + z) % 2,
Root3 * (y + 1 / 3f * (z % 2)),
ZTerm * z) * R + Offset;
}
}
}
List <float3> InsideMask = BestSolution.Where(p =>
{
int3 ip = new int3(p);
if (ip.X >= 0 && ip.X < Dims.X && ip.Y >= 0 && ip.Y < Dims.Y && ip.Z >= 0 && ip.Z < Dims.Z)
{
return(MaskData[Dims.ElementFromPosition(new int3(p))] == 1);
}
return(false);
}).ToList();
BestSolution = InsideMask.ToArray();
if (BestSolution.Length == n)
{
break;
}
else if (BestSolution.Length < n)
{
b = R;
}
else
{
a = R;
}
}
float3 CenterOfPoints = MathHelper.Mean(BestSolution);
Offset = MaskCenter - CenterOfPoints;
a = 0.8f * R;
b = 1.2f * R;
}
BestSolution = BestSolution.Select(v => v + Offset).ToArray();
return(BestSolution);
}
public static Image GetVolumeFromAtoms(float3[] atoms, int3 dims, float sigma, float[] weights = null, float blobRadius = 1.0f, float blobAlpha = 6f)
{
if (weights == null)
{
weights = atoms.Select(v => 1f).ToArray();
}
float BlobRadius = blobRadius * (sigma / 0.5f);
float BlobAlpha = blobAlpha;
int BlobOrder = 0;
KaiserTable KaiserT = new KaiserTable(1000, BlobRadius, BlobAlpha, BlobOrder);
int SigmaExtent = (int)Math.Ceiling(BlobRadius);
float[] VolumeData = new float[dims.Elements()];
sigma = 2 * sigma * sigma;
float[][] ParallelVolumes = new float[10][];
for (int i = 0; i < ParallelVolumes.Length; i++)
{
ParallelVolumes[i] = new float[VolumeData.Length];
}
Parallel.For(0, 10, p =>
{
for (int a = p; a < atoms.Length; a += 10)
{
float3 atom = atoms[a];
float weight = weights[a];
int3 IAtom = new int3(atom);
int StartZ = Math.Max(0, IAtom.Z - SigmaExtent);
int EndZ = Math.Min(dims.Z - 1, IAtom.Z + SigmaExtent);
for (int z = StartZ; z <= EndZ; z++)
{
int StartY = Math.Max(0, IAtom.Y - SigmaExtent);
int EndY = Math.Min(dims.Y - 1, IAtom.Y + SigmaExtent);
for (int y = StartY; y <= EndY; y++)
{
int StartX = Math.Max(0, IAtom.X - SigmaExtent);
int EndX = Math.Min(dims.X - 1, IAtom.X + SigmaExtent);
for (int x = StartX; x <= EndX; x++)
{
float3 Pos = new float3(x, y, z);
//ParallelVolumes[p][(z * dims.Y + y) * dims.X + x] += (float)Math.Exp(-(Pos - atom).LengthSq() / sigma) * weight;
ParallelVolumes[p][(z * dims.Y + y) * dims.X + x] += KaiserT.GetValue((Pos - atom).Length()) * weight;
}
}
}
}
});
for (int p = 0; p < ParallelVolumes.Length; p++)
{
for (int i = 0; i < VolumeData.Length; i++)
{
VolumeData[i] += ParallelVolumes[p][i];
}
}
return(new Image(VolumeData, dims));
}
public static float[] Extract(float[] volume, int3 dimsvolume, int3 centerextract, int3 dimsextract)
{
int3 Origin = new int3(centerextract.X - dimsextract.X / 2,
centerextract.Y - dimsextract.Y / 2,
centerextract.Z - dimsextract.Z / 2);
float[] Extracted = new float[dimsextract.Elements()];
unsafe
{
fixed(float *volumePtr = volume)
fixed(float *ExtractedPtr = Extracted)
for (int z = 0; z < dimsextract.Z; z++)
{
for (int y = 0; y < dimsextract.Y; y++)
{
for (int x = 0; x < dimsextract.X; x++)
{
int3 Pos = new int3((Origin.X + x + dimsvolume.X) % dimsvolume.X,
(Origin.Y + y + dimsvolume.Y) % dimsvolume.Y,
(Origin.Z + z + dimsvolume.Z) % dimsvolume.Z);
float Val = volumePtr[(Pos.Z * dimsvolume.Y + Pos.Y) * dimsvolume.X + Pos.X];
ExtractedPtr[(z * dimsextract.Y + y) * dimsextract.X + x] = Val;
}
}
}
}
return(Extracted);
}
public float3(int3 v)
{
X = v.X;
Y = v.Y;
Z = v.Z;
}
public int2(int3 v)
{
X = v.X;
Y = v.Y;
}
public HeaderRaw(int3 dims, long offsetBytes, Type valueType)
{
Dimensions = dims;
OffsetBytes = offsetBytes;
ValueType = valueType;
}
public CubicGrid(float[,,] values)
{
Values = values;
Dimensions = new int3(values.GetLength(2), values.GetLength(1), values.GetLength(0));
Spacing = new float3(1f / Math.Max(1, Dimensions.X - 1), 1f / Math.Max(1, Dimensions.Y - 1), 1f / Math.Max(1, Dimensions.Z - 1));
}
public HeaderMRC(BinaryReader reader)
{
Dimensions = new int3(reader.ReadBytes(3 * sizeof(int)));
Mode = (MRCDataType)reader.ReadInt32();
StartSubImage = new int3(reader.ReadBytes(3 * sizeof(int)));
Griddimensions = new int3(reader.ReadBytes(3 * sizeof(int)));
Pixelsize = new float3(reader.ReadBytes(3 * sizeof(float))) / new float3(Dimensions.X, Dimensions.Y, Dimensions.Z);
Angles = new float3(reader.ReadBytes(3 * sizeof(float)));
MapOrder = new int3(reader.ReadBytes(3 * sizeof(int)));
MinValue = reader.ReadSingle();
MaxValue = reader.ReadSingle();
MeanValue = reader.ReadSingle();
SpaceGroup = reader.ReadInt32();
ExtendedBytes = reader.ReadInt32();
CreatorID = reader.ReadInt16();
ExtraData1 = reader.ReadBytes(30);
NInt = reader.ReadInt16();
NReal = reader.ReadInt16();
ExtraData2 = reader.ReadBytes(28);
IDType = reader.ReadInt16();
Lens = reader.ReadInt16();
ND1 = reader.ReadInt16();
ND2 = reader.ReadInt16();
VD1 = reader.ReadInt16();
VD2 = reader.ReadInt16();
TiltOriginal = new float3(reader.ReadBytes(3 * sizeof(float)));
TiltCurrent = new float3(reader.ReadBytes(3 * sizeof(float)));
Origin = new float3(reader.ReadBytes(3 * sizeof(float)));
CMap = reader.ReadBytes(4);
Stamp = reader.ReadBytes(4);
StdDevValue = reader.ReadSingle();
NumLabels = reader.ReadInt32();
for (int i = 0; i < 10; i++)
Labels[i] = reader.ReadBytes(80);
// In case this is from SerialEM, check how big ExtendedBytes should be at least to read per-frame data
ImodHasTilt = (NReal & (1 << 0)) > 0;
ImodHasMontage = (NReal & (1 << 1)) > 0;
ImodHasStagePos = (NReal & (1 << 2)) > 0;
ImodHasMagnification = (NReal & (1 << 3)) > 0;
ImodHasIntensity = (NReal & (1 << 4)) > 0;
ImodHasExposure = (NReal & (1 << 5)) > 0;
int BytesPerSection = (ImodHasTilt ? 2 : 0) +
(ImodHasMontage ? 6 : 0) +
(ImodHasStagePos ? 4 : 0) +
(ImodHasMagnification ? 2 : 0) +
(ImodHasIntensity ? 2 : 0) +
(ImodHasExposure ? 4 : 0);
if (BytesPerSection * Dimensions.Z > ExtendedBytes) // Not from SerialEM, ignore extended header
{
Extended = reader.ReadBytes(ExtendedBytes);
}
else // SerialEM extended header, read one section per frame
{
if (ImodHasTilt)
ImodTilt = new float[Dimensions.Z];
if (ImodHasMagnification)
ImodMagnification = new float[Dimensions.Z];
if (ImodHasIntensity)
ImodIntensity = new float[Dimensions.Z];
if (ImodHasExposure)
ImodExposure = new float[Dimensions.Z];
for (int i = 0; i < Dimensions.Z; i++)
{
if (ImodHasTilt)
ImodTilt[i] = reader.ReadInt16() / 100f;
if (ImodHasMontage)
reader.ReadBytes(6);
if (ImodHasStagePos)
reader.ReadBytes(4);
if (ImodHasMagnification)
ImodMagnification[i] = reader.ReadInt16() / 100f;
if (ImodHasIntensity)
ImodIntensity[i] = reader.ReadInt16() / 2500f;
if (ImodHasExposure)
{
float val = reader.ReadSingle();
/*int s1 = reader.ReadInt16();
int s2 = reader.ReadInt16();
float val = Math.Sign(s1) * (Math.Abs(s1) * 256 + (Math.Abs(s2) % 256)) * (float)Math.Pow(2, Math.Sign(s2) * (Math.Abs(s2) / 256f));*/
ImodExposure[i] = val;
}
}
}
}
public long ElementFromPositionLong(int3 position)
{
return(((long)position.Z * (long)Y + (long)position.Y) * (long)X + (long)position.X);
}
/// <summary>
/// Implementation of Marching Cubes based on http://paulbourke.net/geometry/polygonise/
/// </summary>
/// <param name="volume">Volume intensity values</param>
/// <param name="dims">Volume dimensions</param>
/// <param name="angpix">Angstrom per pixel</param>
/// <param name="threshold">Isosurface threshold</param>
/// <returns></returns>
public static Mesh FromVolume(float[] volume, int3 dims, float angpix, float threshold)
{
Triangle[][] CellTriangles = new Triangle[volume.Length][];
unsafe
{
fixed (float* volumePtr = volume)
for (int z = 0; z < dims.Z - 1; z++)
{
float zz = (z - dims.Z / 2) * angpix;
for (int y = 0; y < dims.Y - 1; y++)
{
float yy = (y - dims.Y / 2) * angpix;
for (int x = 0; x < dims.X - 1; x++)
{
float xx = (x - dims.X / 2) * angpix;
Vector3[] p = new Vector3[8];
float[] val = new float[8];
p[0] = new Vector3(xx, yy, zz);
p[1] = new Vector3(xx + angpix, yy, zz);
p[2] = new Vector3(xx + angpix, yy + angpix, zz);
p[3] = new Vector3(xx, yy + angpix, zz);
p[4] = new Vector3(xx, yy, zz + angpix);
p[5] = new Vector3(xx + angpix, yy, zz + angpix);
p[6] = new Vector3(xx + angpix, yy + angpix, zz + angpix);
p[7] = new Vector3(xx, yy + angpix, zz + angpix);
val[0] = volumePtr[((z + 0) * dims.Y + (y + 0)) * dims.X + (x + 0)];
val[1] = volumePtr[((z + 0) * dims.Y + (y + 0)) * dims.X + (x + 1)];
val[2] = volumePtr[((z + 0) * dims.Y + (y + 1)) * dims.X + (x + 1)];
val[3] = volumePtr[((z + 0) * dims.Y + (y + 1)) * dims.X + (x + 0)];
val[4] = volumePtr[((z + 1) * dims.Y + (y + 0)) * dims.X + (x + 0)];
val[5] = volumePtr[((z + 1) * dims.Y + (y + 0)) * dims.X + (x + 1)];
val[6] = volumePtr[((z + 1) * dims.Y + (y + 1)) * dims.X + (x + 1)];
val[7] = volumePtr[((z + 1) * dims.Y + (y + 1)) * dims.X + (x + 0)];
CellTriangles[(z * dims.Y + y) * dims.X + x] = Polygonize(p, val, threshold);
}
}
}
}
Mesh NewMesh = new Mesh();
for (int i = 0; i < CellTriangles.Length; i++)
{
if (CellTriangles[i] == null)
continue;
foreach (var tri in CellTriangles[i])
{
NewMesh.Vertices.Add(tri.V0);
NewMesh.Vertices.Add(tri.V1);
NewMesh.Vertices.Add(tri.V2);
tri.ID = NewMesh.Triangles.Count;
NewMesh.Triangles.Add(tri);
}
}
NewMesh.UpdateGraph();
NewMesh.UpdateVertexIDs();
return NewMesh;
}
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 float[] GetInterpolated(int3 valueGrid, float3 border)
{
float[] Result = new float[valueGrid.Elements()];
float StepX = (1f - border.X * 2) / Math.Max(1, valueGrid.X - 1);
float OffsetX = border.X;
float StepY = (1f - border.Y * 2) / Math.Max(1, valueGrid.Y - 1);
float OffsetY = border.Y;
float StepZ = (1f - border.Z * 2) / Math.Max(valueGrid.Z - 1, 1);
float OffsetZ = valueGrid.Z == 1 ? 0.5f : border.Z;
for (int z = 0, i = 0; z < valueGrid.Z; z++)
for (int y = 0; y < valueGrid.Y; y++)
for (int x = 0; x < valueGrid.X; x++, i++)
Result[i] = GetInterpolated(new float3(x * StepX + OffsetX, y * StepY + OffsetY, z * StepZ + OffsetZ));
return Result;
}
public uint ElementFromPosition(int3 position)
{
return(((uint)position.Z * (uint)Y + (uint)position.Y) * (uint)X + (uint)position.X);
}
public float[][] GetWiggleWeights(int3 valueGrid, float3 border)
{
float[][] Result = new float[Dimensions.Elements()][];
for (int i = 0; i < Result.Length; i++)
{
float[] PlusValues = new float[Dimensions.Elements()];
PlusValues[i] = 1f;
CubicGrid PlusGrid = new CubicGrid(Dimensions, PlusValues);
Result[i] = PlusGrid.GetInterpolatedNative(valueGrid, border);
}
return Result;
}
public void AlignTiltMovies(Star tableIn, int3 stackDimensions, int size, int3 volumeDimensions, Dictionary<int, Projector> references, float resolution)
{
Star TableSeries = new Star(DirectoryName + RootName + ".star");
Image SimulatedSeries = StageDataLoad.LoadMap("d_simulatedseries.mrc", new int2(1, 1), 0, typeof (float));
//Image SimulatedSeries = StageDataLoad.LoadMap(DirectoryName + RootName + ".ali", new int2(1, 1), 0, typeof(float));
Image AlignedSeries = new Image(SimulatedSeries.Dims);
for (int t = 26; t < NTilts; t++)
{
Image TiltMovie = StageDataLoad.LoadMap(DirectoryName + TableSeries.GetRowValue(t, "wrpMovieName"), new int2(1, 1), 0, typeof (float));
Image Template = new Image(SimulatedSeries.GetHost(Intent.Read)[t], SimulatedSeries.Dims.Slice());
float MovieAngle = float.Parse(TableSeries.GetRowValue(t, "wrpAnglePsi"), CultureInfo.InvariantCulture);
//float2 MovieShift = new float2(-float.Parse(TableSeries.GetRowValue(t, "wrpShiftX"), CultureInfo.InvariantCulture),
// -float.Parse(TableSeries.GetRowValue(t, "wrpShiftY"), CultureInfo.InvariantCulture));
float2 MovieShift = new float2(5.64f, -21f);
Image Aligned = AlignOneTiltMovie(TiltMovie, Template, MovieAngle, MovieShift, resolution);
AlignedSeries.GetHost(Intent.Write)[t] = Aligned.GetHost(Intent.Read)[0];
Aligned.Dispose();
TiltMovie.Dispose();
Template.Dispose();
}
SimulatedSeries.Dispose();
AlignedSeries.WriteMRC(DirectoryName + RootName + ".aligned");
AlignedSeries.Dispose();
}
public void ProcessCTFOneAngle(Image angleImage,
float angle,
bool fromScratch,
bool fixAstigmatism,
float2 astigmatism,
CTF previousCTF,
CubicGrid previousGrid,
Cubic1D previousBackground,
Cubic1D previousScale,
out CTF thisCTF,
out CubicGrid thisGrid,
out float2[] thisPS1D,
out Cubic1D thisBackground,
out Cubic1D thisScale,
out Image thisPS2D)
{
CTF TempCTF = previousCTF != null ? previousCTF.GetCopy() : new CTF();
float2[] TempPS1D = null;
Cubic1D TempBackground = null, TempScale = null;
CubicGrid TempGrid = null;
#region Dimensions and grids
int NFrames = angleImage.Dims.Z;
int2 DimsImage = angleImage.DimsSlice;
int2 DimsRegion = new int2(MainWindow.Options.CTFWindow, MainWindow.Options.CTFWindow);
float OverlapFraction = 0.5f;
int2 DimsPositionGrid;
int3[] PositionGrid = Helper.GetEqualGridSpacing(DimsImage, new int2(DimsRegion.X, DimsRegion.Y), OverlapFraction, out DimsPositionGrid);
int NPositions = (int)DimsPositionGrid.Elements();
if (previousGrid == null)
TempGrid = new CubicGrid(new int3(2, 2, 1));
else
TempGrid = new CubicGrid(new int3(2, 2, 1), previousGrid.FlatValues);
bool CTFSpace = true;
bool CTFTime = false;
int3 CTFSpectraGrid = new int3(DimsPositionGrid.X, DimsPositionGrid.Y, 1);
int MinFreqInclusive = (int)(MainWindow.Options.CTFRangeMin * DimsRegion.X / 2);
int MaxFreqExclusive = (int)(MainWindow.Options.CTFRangeMax * DimsRegion.X / 2);
int NFreq = MaxFreqExclusive - MinFreqInclusive;
#endregion
#region Allocate GPU memory
Image CTFSpectra = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.X, (int)CTFSpectraGrid.Elements()), true);
Image CTFMean = new Image(IntPtr.Zero, new int3(DimsRegion), true);
Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true);
Image CTFCoordsPolarTrimmed = new Image(new int3(NFreq, DimsRegion.X, 1), false, true);
#endregion
// Extract movie regions, create individual spectra in Cartesian coordinates and their mean.
#region Create spectra
GPU.CreateSpectra(angleImage.GetDevice(Intent.Read),
DimsImage,
NFrames,
PositionGrid,
NPositions,
DimsRegion,
CTFSpectraGrid,
CTFSpectra.GetDevice(Intent.Write),
CTFMean.GetDevice(Intent.Write));
angleImage.FreeDevice(); // Won't need it in this method anymore.
#endregion
// Populate address arrays for later.
#region Init addresses
{
float2[] CoordsData = new float2[CTFCoordsCart.ElementsSliceComplex];
Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) => CoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r, a));
CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData });
CoordsData = new float2[NFreq * DimsRegion.X];
Helper.ForEachElement(CTFCoordsPolarTrimmed.DimsSlice, (x, y) =>
{
float Angle = ((float)y / DimsRegion.X + 0.5f) * (float)Math.PI;
float Ny = 1f / DimsRegion.X;
CoordsData[y * NFreq + x] = new float2((x + MinFreqInclusive) * Ny, Angle);
});
CTFCoordsPolarTrimmed.UpdateHostWithComplex(new[] { CoordsData });
}
#endregion
// Retrieve average 1D spectrum from CTFMean (not corrected for astigmatism yet).
#region Initial 1D spectrum
{
Image CTFAverage1D = new Image(IntPtr.Zero, new int3(DimsRegion.X / 2, 1, 1));
GPU.CTFMakeAverage(CTFMean.GetDevice(Intent.Read),
CTFCoordsCart.GetDevice(Intent.Read),
(uint)CTFMean.ElementsSliceReal,
(uint)DimsRegion.X,
new[] { new CTF().ToStruct() },
new CTF().ToStruct(),
0,
(uint)DimsRegion.X / 2,
null,
1,
CTFAverage1D.GetDevice(Intent.Write));
//CTFAverage1D.WriteMRC("CTFAverage1D.mrc");
float[] CTFAverage1DData = CTFAverage1D.GetHost(Intent.Read)[0];
float2[] ForPS1D = new float2[DimsRegion.X / 2];
for (int i = 0; i < ForPS1D.Length; i++)
ForPS1D[i] = new float2((float)i / DimsRegion.X, (float)Math.Round(CTFAverage1DData[i], 4));
TempPS1D = ForPS1D;
CTFAverage1D.Dispose();
}
#endregion
#region Background fitting methods
Action UpdateBackgroundFit = () =>
{
float2[] ForPS1D = TempPS1D.Skip(Math.Max(5, MinFreqInclusive / 2)).ToArray();
Cubic1D.FitCTF(ForPS1D,
v => v.Select(x => TempCTF.Get1D(x / (float)TempCTF.PixelSize, true)).ToArray(),
TempCTF.GetZeros(),
TempCTF.GetPeaks(),
out TempBackground,
out TempScale);
};
Action<bool> UpdateRotationalAverage = keepbackground =>
{
float[] MeanData = CTFMean.GetHost(Intent.Read)[0];
Image CTFMeanCorrected = new Image(new int3(DimsRegion), true);
float[] MeanCorrectedData = CTFMeanCorrected.GetHost(Intent.Write)[0];
// Subtract current background estimate from spectra, populate coords.
Helper.ForEachElementFT(DimsRegion,
(x, y, xx, yy, r, a) =>
{
int i = y * (DimsRegion.X / 2 + 1) + x;
MeanCorrectedData[i] = MeanData[i] - TempBackground.Interp(r / DimsRegion.X);
});
Image CTFAverage1D = new Image(IntPtr.Zero, new int3(DimsRegion.X / 2, 1, 1));
GPU.CTFMakeAverage(CTFMeanCorrected.GetDevice(Intent.Read),
CTFCoordsCart.GetDevice(Intent.Read),
(uint)CTFMeanCorrected.DimsEffective.ElementsSlice(),
(uint)DimsRegion.X,
new[] { TempCTF.ToStruct() },
TempCTF.ToStruct(),
0,
(uint)DimsRegion.X / 2,
null,
1,
CTFAverage1D.GetDevice(Intent.Write));
//CTFAverage1D.WriteMRC("CTFAverage1D.mrc");
float[] RotationalAverageData = CTFAverage1D.GetHost(Intent.Read)[0];
float2[] ForPS1D = new float2[TempPS1D.Length];
if (keepbackground)
for (int i = 0; i < ForPS1D.Length; i++)
ForPS1D[i] = new float2((float)i / DimsRegion.X, RotationalAverageData[i] + TempBackground.Interp((float)i / DimsRegion.X));
else
for (int i = 0; i < ForPS1D.Length; i++)
ForPS1D[i] = new float2((float)i / DimsRegion.X, RotationalAverageData[i]);
MathHelper.UnNaN(ForPS1D);
TempPS1D = ForPS1D;
CTFMeanCorrected.Dispose();
CTFAverage1D.Dispose();
};
#endregion
// Fit background to currently best average (not corrected for astigmatism yet).
{
float2[] ForPS1D = TempPS1D.Skip(MinFreqInclusive).Take(Math.Max(2, NFreq / 2)).ToArray();
float[] CurrentBackground;
//if (previousBackground == null)
{
int NumNodes = Math.Max(3, (int)((MainWindow.Options.CTFRangeMax - MainWindow.Options.CTFRangeMin) * 5M));
TempBackground = Cubic1D.Fit(ForPS1D, NumNodes); // This won't fit falloff and scale, because approx function is 0
CurrentBackground = TempBackground.Interp(TempPS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq / 2).ToArray();
}
/*else
{
CurrentBackground = previousBackground.Interp(TempPS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq / 2).ToArray();
TempBackground = new Cubic1D(previousBackground.Data);
}*/
float[] Subtracted1D = new float[ForPS1D.Length];
for (int i = 0; i < ForPS1D.Length; i++)
Subtracted1D[i] = ForPS1D[i].Y - CurrentBackground[i];
MathHelper.NormalizeInPlace(Subtracted1D);
float ZMin = (float)MainWindow.Options.CTFZMin;
float ZMax = (float)MainWindow.Options.CTFZMax;
float PhaseMin = 0f;
float PhaseMax = MainWindow.Options.CTFDoPhase ? 1f : 0f;
if (previousCTF != null)
{
ZMin = (float)previousCTF.Defocus - 0.5f;
ZMax = (float)previousCTF.Defocus + 0.5f;
if (PhaseMax > 0)
{
PhaseMin = (float)previousCTF.PhaseShift - 0.3f;
PhaseMax = (float)previousCTF.PhaseShift + 0.3f;
}
}
float ZStep = (ZMax - ZMin) / 100f;
float BestZ = 0, BestPhase = 0, BestScore = -999;
for (float z = ZMin; z <= ZMax + 1e-5f; z += ZStep)
{
for (float p = PhaseMin; p <= PhaseMax; p += 0.01f)
{
CTF CurrentParams = new CTF
{
PixelSize = (MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5M,
Defocus = (decimal)z,
PhaseShift = (decimal)p,
Cs = MainWindow.Options.CTFCs,
Voltage = MainWindow.Options.CTFVoltage,
Amplitude = MainWindow.Options.CTFAmplitude
};
float[] SimulatedCTF = CurrentParams.Get1D(TempPS1D.Length, true).Skip(MinFreqInclusive).Take(Math.Max(2, NFreq / 2)).ToArray();
MathHelper.NormalizeInPlace(SimulatedCTF);
float Score = MathHelper.CrossCorrelate(Subtracted1D, SimulatedCTF);
if (Score > BestScore)
{
BestScore = Score;
BestZ = z;
BestPhase = p;
}
}
}
TempCTF = new CTF
{
PixelSize = (MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5M,
Defocus = (decimal)BestZ,
PhaseShift = (decimal)BestPhase,
Cs = MainWindow.Options.CTFCs,
Voltage = MainWindow.Options.CTFVoltage,
Amplitude = MainWindow.Options.CTFAmplitude
};
UpdateRotationalAverage(true); // This doesn't have a nice background yet.
UpdateBackgroundFit(); // Now get a reasonably nice background.
}
// Fit defocus, (phase shift), (astigmatism) to average background-subtracted spectrum,
// which is in polar coords at this point (for equal weighting of all frequencies).
#region Grid search
if (fromScratch)
{
Image CTFMeanPolarTrimmed = CTFMean.AsPolar((uint)MinFreqInclusive, (uint)(MinFreqInclusive + NFreq / 1));
// Subtract current background.
Image CurrentBackground = new Image(TempBackground.Interp(TempPS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq / 1).ToArray());
CTFMeanPolarTrimmed.SubtractFromLines(CurrentBackground);
CurrentBackground.Dispose();
// Normalize for CC (not strictly needed, but it's converted for fp16 later, so let's be on the safe side of the fp16 range.
GPU.Normalize(CTFMeanPolarTrimmed.GetDevice(Intent.Read), CTFMeanPolarTrimmed.GetDevice(Intent.Write), (uint)CTFMeanPolarTrimmed.ElementsReal, 1);
//CTFMeanPolarTrimmed.WriteMRC("ctfmeanpolartrimmed.mrc");
CTF StartParams = new CTF
{
PixelSize = (MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5M,
PixelSizeDelta = Math.Abs(MainWindow.Options.CTFPixelMax - MainWindow.Options.CTFPixelMin),
PixelSizeAngle = MainWindow.Options.CTFPixelAngle,
Defocus = TempCTF.Defocus, // (MainWindow.Options.CTFZMin + MainWindow.Options.CTFZMax) * 0.5M,
DefocusDelta = 0,
DefocusAngle = 0,
PhaseShift = TempCTF.PhaseShift,
Cs = MainWindow.Options.CTFCs,
Voltage = MainWindow.Options.CTFVoltage,
Amplitude = MainWindow.Options.CTFAmplitude
};
CTFFitStruct FitParams = new CTFFitStruct
{
Defocus = new float3(-0.4e-6f,
0.4e-6f,
0.025e-6f),
Defocusdelta = new float3(0, 0.8e-6f, 0.02e-6f),
Astigmatismangle = new float3(0, 2 * (float)Math.PI, 1 * (float)Math.PI / 18),
Phaseshift = MainWindow.Options.CTFDoPhase ? new float3(-0.2f * (float)Math.PI, 0.2f * (float)Math.PI, 0.025f * (float)Math.PI) : new float3(0, 0, 0)
};
CTFStruct ResultStruct = GPU.CTFFitMean(CTFMeanPolarTrimmed.GetDevice(Intent.Read),
CTFCoordsPolarTrimmed.GetDevice(Intent.Read),
CTFMeanPolarTrimmed.DimsSlice,
StartParams.ToStruct(),
FitParams,
true);
TempCTF.FromStruct(ResultStruct);
TempCTF.Defocus = Math.Max(TempCTF.Defocus, MainWindow.Options.CTFZMin);
CTFMeanPolarTrimmed.Dispose();
UpdateRotationalAverage(true); // This doesn't have a nice background yet.
UpdateBackgroundFit(); // Now get a reasonably nice background.
UpdateRotationalAverage(true); // This time, with the nice background.
UpdateBackgroundFit(); // Make the background even nicer!
}
else if (previousCTF != null)
{
TempCTF.DefocusDelta = previousCTF.DefocusDelta;
TempCTF.DefocusAngle = previousCTF.DefocusAngle;
}
if (fixAstigmatism)
{
TempCTF.DefocusDelta = (decimal)astigmatism.X;
TempCTF.DefocusAngle = (decimal)astigmatism.Y;
}
#endregion
if (previousGrid == null)
TempGrid = new CubicGrid(TempGrid.Dimensions, (float)TempCTF.Defocus, (float)TempCTF.Defocus, Dimension.X);
// Do BFGS optimization of defocus, astigmatism and phase shift,
// using 2D simulation for comparison
#region BFGS
bool[] CTFSpectraConsider = new bool[CTFSpectraGrid.Elements()];
for (int i = 0; i < CTFSpectraConsider.Length; i++)
CTFSpectraConsider[i] = true;
int NCTFSpectraConsider = CTFSpectraConsider.Length;
{
Image CTFSpectraPolarTrimmed = CTFSpectra.AsPolar((uint)MinFreqInclusive, (uint)(MinFreqInclusive + NFreq));
CTFSpectra.FreeDevice(); // This will only be needed again for the final PS1D.
#region Create background and scale
float[] CurrentScale = TempScale.Interp(TempPS1D.Select(p => p.X).ToArray());
Image CTFSpectraScale = new Image(new int3(NFreq, DimsRegion.X, 1));
float[] CTFSpectraScaleData = CTFSpectraScale.GetHost(Intent.Write)[0];
// Trim polar to relevant frequencies, and populate coordinates.
Parallel.For(0, DimsRegion.X, y =>
{
for (int x = 0; x < NFreq; x++)
CTFSpectraScaleData[y * NFreq + x] = CurrentScale[x + MinFreqInclusive];
});
//CTFSpectraScale.WriteMRC("ctfspectrascale.mrc");
// Background is just 1 line since we're in polar.
Image CurrentBackground = new Image(TempBackground.Interp(TempPS1D.Select(p => p.X).ToArray()).Skip(MinFreqInclusive).Take(NFreq).ToArray());
#endregion
CTFSpectraPolarTrimmed.SubtractFromLines(CurrentBackground);
CurrentBackground.Dispose();
// Normalize background-subtracted spectra.
GPU.Normalize(CTFSpectraPolarTrimmed.GetDevice(Intent.Read),
CTFSpectraPolarTrimmed.GetDevice(Intent.Write),
(uint)CTFSpectraPolarTrimmed.ElementsSliceReal,
(uint)CTFSpectraGrid.Elements());
//CTFSpectraPolarTrimmed.WriteMRC("ctfspectrapolartrimmed.mrc");
#region Convert to fp16
Image CTFSpectraPolarTrimmedHalf = CTFSpectraPolarTrimmed.AsHalf();
CTFSpectraPolarTrimmed.Dispose();
Image CTFSpectraScaleHalf = CTFSpectraScale.AsHalf();
CTFSpectraScale.Dispose();
Image CTFCoordsPolarTrimmedHalf = CTFCoordsPolarTrimmed.AsHalf();
#endregion
// Wiggle weights show how the defocus on the spectra grid is altered
// by changes in individual anchor points of the spline grid.
// They are used later to compute the dScore/dDefocus values for each spectrum
// only once, and derive the values for each anchor point from them.
float[][] WiggleWeights = TempGrid.GetWiggleWeights(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));
// Helper method for getting CTFStructs for the entire spectra grid.
Func<double[], CTF, float[], CTFStruct[]> EvalGetCTF = (input, ctf, defocusValues) =>
{
decimal AlteredPhase = MainWindow.Options.CTFDoPhase ? (decimal)input[input.Length - 3] : 0;
decimal AlteredDelta = (decimal)input[input.Length - 2];
decimal AlteredAngle = (decimal)(input[input.Length - 1] * 20 / (Math.PI / 180));
CTF Local = ctf.GetCopy();
Local.PhaseShift = AlteredPhase;
Local.DefocusDelta = AlteredDelta;
Local.DefocusAngle = AlteredAngle;
CTFStruct LocalStruct = Local.ToStruct();
CTFStruct[] LocalParams = new CTFStruct[defocusValues.Length];
for (int i = 0; i < LocalParams.Length; i++)
{
LocalParams[i] = LocalStruct;
LocalParams[i].Defocus = defocusValues[i] * -1e-6f;
}
return LocalParams;
};
// Simulate with adjusted CTF, compare to originals
#region Eval and Gradient methods
Func<double[], double> Eval = input =>
{
CubicGrid Altered = new CubicGrid(TempGrid.Dimensions, input.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v).ToArray());
float[] DefocusValues = Altered.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));
CTFStruct[] LocalParams = EvalGetCTF(input, TempCTF, DefocusValues);
float[] Result = new float[LocalParams.Length];
GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
CTFSpectraScaleHalf.GetDevice(Intent.Read),
(uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
LocalParams,
Result,
(uint)LocalParams.Length);
float Score = 0;
for (int i = 0; i < Result.Length; i++)
if (CTFSpectraConsider[i])
Score += Result[i];
Score /= NCTFSpectraConsider;
if (float.IsNaN(Score) || float.IsInfinity(Score))
throw new Exception("Bad score.");
return (1.0 - Score) * 1000.0;
};
Func<double[], double[]> Gradient = input =>
{
const float Step = 0.005f;
double[] Result = new double[input.Length];
// In 0D grid case, just get gradient for all 4 parameters.
// In 1+D grid case, do simple gradient for astigmatism and phase...
int StartComponent = input.Length - 3;
//int StartComponent = 0;
for (int i = StartComponent; i < input.Length; i++)
{
if (fixAstigmatism && i > StartComponent)
continue;
double[] UpperInput = new double[input.Length];
input.CopyTo(UpperInput, 0);
UpperInput[i] += Step;
double UpperValue = Eval(UpperInput);
double[] LowerInput = new double[input.Length];
input.CopyTo(LowerInput, 0);
LowerInput[i] -= Step;
double LowerValue = Eval(LowerInput);
Result[i] = (UpperValue - LowerValue) / (2f * Step);
}
float[] ResultPlus = new float[CTFSpectraGrid.Elements()];
float[] ResultMinus = new float[CTFSpectraGrid.Elements()];
// ..., take shortcut for defoci...
{
{
CubicGrid AlteredPlus = new CubicGrid(TempGrid.Dimensions, input.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v + Step).ToArray());
float[] DefocusValues = AlteredPlus.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));
CTFStruct[] LocalParams = EvalGetCTF(input, TempCTF, DefocusValues);
GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
CTFSpectraScaleHalf.GetDevice(Intent.Read),
(uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
LocalParams,
ResultPlus,
(uint)LocalParams.Length);
}
{
CubicGrid AlteredMinus = new CubicGrid(TempGrid.Dimensions, input.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v - Step).ToArray());
float[] DefocusValues = AlteredMinus.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));
CTFStruct[] LocalParams = EvalGetCTF(input, TempCTF, DefocusValues);
GPU.CTFCompareToSim(CTFSpectraPolarTrimmedHalf.GetDevice(Intent.Read),
CTFCoordsPolarTrimmedHalf.GetDevice(Intent.Read),
CTFSpectraScaleHalf.GetDevice(Intent.Read),
(uint)CTFSpectraPolarTrimmedHalf.ElementsSliceReal,
LocalParams,
ResultMinus,
(uint)LocalParams.Length);
}
float[] LocalGradients = new float[ResultPlus.Length];
for (int i = 0; i < LocalGradients.Length; i++)
LocalGradients[i] = ResultMinus[i] - ResultPlus[i];
// Now compute gradients per grid anchor point using the precomputed individual gradients and wiggle factors.
Parallel.For(0, TempGrid.Dimensions.Elements(), i => Result[i] = MathHelper.ReduceWeighted(LocalGradients, WiggleWeights[i]) / LocalGradients.Length / (2f * Step) * 1000f);
}
foreach (var i in Result)
if (double.IsNaN(i) || double.IsInfinity(i))
throw new Exception("Bad score.");
return Result;
};
#endregion
#region Minimize first time with potential outpiers
double[] StartParams = new double[TempGrid.Dimensions.Elements() + 3];
for (int i = 0; i < TempGrid.Dimensions.Elements(); i++)
StartParams[i] = TempGrid.FlatValues[i];
StartParams[StartParams.Length - 3] = (double)TempCTF.PhaseShift;
StartParams[StartParams.Length - 2] = (double)TempCTF.DefocusDelta;
StartParams[StartParams.Length - 1] = (double)TempCTF.DefocusAngle / 20 * (Math.PI / 180);
// Compute correlation for individual spectra, and throw away those that are >.75 sigma worse than mean.
BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Gradient)
{
Past = 1,
Delta = 1e-6,
MaxLineSearch = 15,
Corrections = 20
};
Optimizer.Minimize(StartParams);
#endregion
#region Retrieve parameters
TempCTF.Defocus = (decimal)MathHelper.Mean(Optimizer.Solution.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v));
TempCTF.PhaseShift = (decimal)Optimizer.Solution[StartParams.Length - 3];
TempCTF.DefocusDelta = (decimal)Optimizer.Solution[StartParams.Length - 2];
TempCTF.DefocusAngle = (decimal)(Optimizer.Solution[StartParams.Length - 1] * 20 / (Math.PI / 180));
if (TempCTF.DefocusDelta < 0)
{
TempCTF.DefocusAngle += 90;
TempCTF.DefocusDelta *= -1;
}
TempCTF.DefocusAngle = ((int)TempCTF.DefocusAngle + 180 * 99) % 180;
TempGrid = new CubicGrid(TempGrid.Dimensions, Optimizer.Solution.Take((int)TempGrid.Dimensions.Elements()).Select(v => (float)v).ToArray());
#endregion
// Dispose GPU resources manually because GC can't be bothered to do it in time.
CTFSpectraPolarTrimmedHalf.Dispose();
CTFCoordsPolarTrimmedHalf.Dispose();
CTFSpectraScaleHalf.Dispose();
#region Get nicer envelope fit
{
{
Image CTFSpectraBackground = new Image(new int3(DimsRegion), true);
float[] CTFSpectraBackgroundData = CTFSpectraBackground.GetHost(Intent.Write)[0];
// Construct background in Cartesian coordinates.
Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) =>
{
CTFSpectraBackgroundData[y * CTFSpectraBackground.DimsEffective.X + x] = TempBackground.Interp(r / DimsRegion.X);
});
CTFSpectra.SubtractFromSlices(CTFSpectraBackground);
float[] DefocusValues = TempGrid.GetInterpolatedNative(CTFSpectraGrid, new float3(DimsRegion.X / 2f / DimsImage.X, DimsRegion.Y / 2f / DimsImage.Y, 0));
CTFStruct[] LocalParams = DefocusValues.Select(v =>
{
CTF Local = TempCTF.GetCopy();
Local.Defocus = (decimal)v + 0.0M;
return Local.ToStruct();
}).ToArray();
Image CTFAverage1D = new Image(IntPtr.Zero, new int3(DimsRegion.X / 2, 1, 1));
CTF CTFAug = TempCTF.GetCopy();
CTFAug.Defocus += 0.0M;
GPU.CTFMakeAverage(CTFSpectra.GetDevice(Intent.Read),
CTFCoordsCart.GetDevice(Intent.Read),
(uint)CTFSpectra.ElementsSliceReal,
(uint)DimsRegion.X,
LocalParams,
CTFAug.ToStruct(),
0,
(uint)DimsRegion.X / 2,
CTFSpectraConsider.Select(v => v ? 1 : 0).ToArray(),
(uint)CTFSpectraGrid.Elements(),
CTFAverage1D.GetDevice(Intent.Write));
CTFSpectra.AddToSlices(CTFSpectraBackground);
float[] RotationalAverageData = CTFAverage1D.GetHost(Intent.Read)[0];
float2[] ForPS1D = new float2[TempPS1D.Length];
for (int i = 0; i < ForPS1D.Length; i++)
ForPS1D[i] = new float2((float)i / DimsRegion.X, (float)Math.Round(RotationalAverageData[i], 4) + TempBackground.Interp((float)i / DimsRegion.X));
MathHelper.UnNaN(ForPS1D);
TempPS1D = ForPS1D;
CTFSpectraBackground.Dispose();
CTFAverage1D.Dispose();
CTFSpectra.FreeDevice();
}
TempCTF.Defocus = Math.Max(TempCTF.Defocus, MainWindow.Options.CTFZMin);
UpdateBackgroundFit();
}
#endregion
}
#endregion
// Subtract background from 2D average and write it to disk.
// This image is used for quick visualization purposes only.
#region PS2D update
{
int3 DimsAverage = new int3(DimsRegion.X, DimsRegion.X / 2, 1);
float[] Average2DData = new float[DimsAverage.Elements()];
float[] OriginalAverageData = CTFMean.GetHost(Intent.Read)[0];
for (int y = 0; y < DimsAverage.Y; y++)
{
int yy = y * y;
for (int x = 0; x < DimsAverage.Y; x++)
{
int xx = DimsRegion.X / 2 - x - 1;
xx *= xx;
float r = (float)Math.Sqrt(xx + yy) / DimsRegion.X;
Average2DData[y * DimsAverage.X + x] = OriginalAverageData[(y + DimsRegion.X / 2) * (DimsRegion.X / 2 + 1) + x] - TempBackground.Interp(r);
}
for (int x = 0; x < DimsRegion.X / 2; x++)
{
int xx = x * x;
float r = (float)Math.Sqrt(xx + yy) / DimsRegion.X;
Average2DData[y * DimsAverage.X + x + DimsRegion.X / 2] = OriginalAverageData[(DimsRegion.X / 2 - y) * (DimsRegion.X / 2 + 1) + (DimsRegion.X / 2 - 1 - x)] - TempBackground.Interp(r);
}
}
thisPS2D = new Image(Average2DData, DimsAverage);
}
#endregion
for (int i = 0; i < TempPS1D.Length; i++)
TempPS1D[i].Y -= TempBackground.Interp(TempPS1D[i].X);
CTFSpectra.Dispose();
CTFMean.Dispose();
CTFCoordsCart.Dispose();
CTFCoordsPolarTrimmed.Dispose();
thisPS1D = TempPS1D;
thisBackground = TempBackground;
thisScale = TempScale;
thisCTF = TempCTF;
thisGrid = TempGrid;
}
public static int3 Max(int3 o1, int o2)
{
return(new int3(Math.Max(o1.X, o2), Math.Max(o1.Y, o2), Math.Max(o1.Z, o2)));
}
public CubicGrid(int3 dimensions)
{
Values = new float[dimensions.Z, dimensions.Y, dimensions.X];
Dimensions = dimensions;
Spacing = new float3(1f / Math.Max(1, Dimensions.X - 1), 1f / Math.Max(1, Dimensions.Y - 1), 1f / Math.Max(1, Dimensions.Z - 1));
}
public void RealspaceRefineGlobal(Star tableIn, Image tiltStack, int size, int3 volumeDimensions, Dictionary<int, Projector> references, float resolution, int healpixorder, string symmetry, Dictionary<int, Projector> outReconstructions)
{
VolumeDimensions = volumeDimensions;
#region Get rows from table
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName))
RowIndices.Add(i);
if (RowIndices.Count == 0)
return;
int NParticles = RowIndices.Count;
#endregion
#region Make sure all columns and directories are there
if (!tableIn.HasColumn("rlnImageName"))
tableIn.AddColumn("rlnImageName");
if (!tableIn.HasColumn("rlnCtfImage"))
tableIn.AddColumn("rlnCtfImage");
if (!tableIn.HasColumn("rlnParticleSelectZScore"))
tableIn.AddColumn("rlnParticleSelectZScore");
if (!Directory.Exists(ParticlesDir))
Directory.CreateDirectory(ParticlesDir);
if (!Directory.Exists(ParticleCTFDir))
Directory.CreateDirectory(ParticleCTFDir);
#endregion
#region Get subtomo positions from table
float3[] ParticleOrigins = new float3[NParticles];
float3[] ParticleAngles = new float3[NParticles];
int[] ParticleSubset = new int[NParticles];
{
string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX");
string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY");
string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ");
string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX");
string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY");
string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ");
string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot");
string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt");
string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi");
string[] ColumnSubset = tableIn.GetColumn("rlnRandomSubset");
for (int i = 0; i < NParticles; i++)
{
float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture));
float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture));
ParticleOrigins[i] = Pos - Shift;
//ParticleOrigins[i] /= new float3(3838f / 959f, 3710f / 927f, 4f);
float3 Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture));
ParticleAngles[i] = Angle;
if (ColumnSubset != null)
ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]);
else
ParticleSubset[i] = (i % 2) + 1;
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", ParticleOrigins[i].X.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", ParticleOrigins[i].Y.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateZ", ParticleOrigins[i].Z.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0");
tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0");
tableIn.SetRowValue(RowIndices[i], "rlnOriginZ", "0.0");
}
}
#endregion
#region Deal with subsets
List<int> SubsetIDs = new List<int>();
foreach (var i in ParticleSubset)
if (!SubsetIDs.Contains(i))
SubsetIDs.Add(i);
SubsetIDs.Sort();
// For each subset, create a list of its particle IDs
Dictionary<int, List<int>> SubsetParticleIDs = SubsetIDs.ToDictionary(subsetID => subsetID, subsetID => new List<int>());
for (int i = 0; i < ParticleSubset.Length; i++)
SubsetParticleIDs[ParticleSubset[i]].Add(i);
foreach (var list in SubsetParticleIDs.Values)
list.Sort();
// Note where each subset starts and ends in a unified, sorted (by subset) particle ID list
Dictionary<int, Tuple<int, int>> SubsetRanges = new Dictionary<int, Tuple<int, int>>();
{
int Start = 0;
foreach (var pair in SubsetParticleIDs)
{
SubsetRanges.Add(pair.Key, new Tuple<int, int>(Start, Start + pair.Value.Count));
Start += pair.Value.Count;
}
}
List<int> SubsetContinuousIDs = new List<int>();
foreach (var pair in SubsetParticleIDs)
SubsetContinuousIDs.AddRange(pair.Value);
// Reorder particle information to match the order of SubsetContinuousIDs
ParticleOrigins = SubsetContinuousIDs.Select(i => ParticleOrigins[i]).ToArray();
ParticleAngles = SubsetContinuousIDs.Select(i => ParticleAngles[i]).ToArray();
ParticleSubset = SubsetContinuousIDs.Select(i => ParticleSubset[i]).ToArray();
#endregion
int CoarseSize = (int)Math.Round(size * ((float)CTF.PixelSize * 2 / resolution)) / 2 * 2;
int3 CoarseDims = new int3(CoarseSize, CoarseSize, 1);
// Create mask, CTF coords, reference projections, shifts
Image Mask;
Image CTFCoords = GetCTFCoords(CoarseSize, size);
Dictionary<int, Image> SubsetProjections = new Dictionary<int, Image>();
float3[] AnglesOri = Helper.GetHealpixAngles(healpixorder, symmetry);
List<float3> Shifts = new List<float3>();
for (int z = -1; z <= 1; z++)
for (int y = -1; y <= 1; y++)
for (int x = -1; x <= 1; x++)
if (x * x + y * y + z * z <= 1)
Shifts.Add(new float3((float)x / CoarseSize * size * 0.5f, (float)y / CoarseSize * size * 0.5f, (float)z / CoarseSize * size * 0.5f));
#region Preflight
{
#region Create mask with soft edge
{
Image MaskBig = new Image(new int3(size, size, 1));
float MaskRadius = MainWindow.Options.ExportParticleRadius / (float)CTF.PixelSize;
float SoftEdge = 16f;
float[] MaskBigData = MaskBig.GetHost(Intent.Write)[0];
for (int y = 0; y < size; y++)
{
int yy = y - size / 2;
yy *= yy;
for (int x = 0; x < size; x++)
{
int xx = x - size / 2;
xx *= xx;
float R = (float)Math.Sqrt(xx + yy);
if (R <= MaskRadius)
MaskBigData[y * size + x] = 1;
else
MaskBigData[y * size + x] = (float)(Math.Cos(Math.Min(1, (R - MaskRadius) / SoftEdge) * Math.PI) * 0.5 + 0.5);
}
}
MaskBig.WriteMRC("d_maskbig.mrc");
Mask = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize));
Mask.RemapToFT();
MaskBig.Dispose();
}
Mask.WriteMRC("d_masksmall.mrc");
#endregion
#region Create projections for each angular sample, adjusted for each tilt
foreach (var subset in SubsetRanges)
{
float3[] AnglesAlt = new float3[AnglesOri.Length * NTilts];
for (int t = 0; t < NTilts; t++)
{
for (int a = 0; a < AnglesOri.Length; a++)
{
float GridStep = 1f / (NTilts - 1);
float3 GridCoords = new float3(0.5f, 0.5f, t * GridStep);
Matrix3 ParticleMatrix = Matrix3.Euler(AnglesOri[a].X * Helper.ToRad,
AnglesOri[a].Y * Helper.ToRad,
AnglesOri[a].Z * Helper.ToRad);
Matrix3 TiltMatrix = Matrix3.Euler(0, -AnglesCorrect[t] * Helper.ToRad, 0);
Matrix3 CorrectionMatrix = Matrix3.RotateZ(GridAngleZ.GetInterpolated(GridCoords) * Helper.ToRad) *
Matrix3.RotateY(GridAngleY.GetInterpolated(GridCoords) * Helper.ToRad) *
Matrix3.RotateX(GridAngleX.GetInterpolated(GridCoords) * Helper.ToRad);
Matrix3 Rotation = CorrectionMatrix * TiltMatrix * ParticleMatrix;
AnglesAlt[a * NTilts + t] = Matrix3.EulerFromMatrix(Rotation);
}
}
Image ProjFT = references[subset.Key].Project(new int2(CoarseSize, CoarseSize), AnglesAlt, CoarseSize / 2);
Image CheckProj = ProjFT.AsIFFT();
CheckProj.RemapFromFT();
CheckProj.WriteMRC("d_proj.mrc");
CheckProj.Dispose();
ProjFT.FreeDevice();
SubsetProjections[subset.Key] = ProjFT;
}
#endregion
}
#endregion
float3[] OptimizedShifts = new float3[NParticles];
float3[] OptimizedAngles = new float3[NParticles];
#region Correlate each particle with all projections
foreach (var subset in SubsetRanges)
{
Image Projections = SubsetProjections[subset.Key];
for (int p = subset.Value.Item1; p < subset.Value.Item2; p++)
//Parallel.For(subset.Value.Item1, subset.Value.Item2, new ParallelOptions { MaxDegreeOfParallelism = 4 }, p =>
{
Image ParticleImages;
Image ParticleCTFs = new Image(new int3(CoarseSize, CoarseSize, NTilts), true);
Image ParticleWeights;
// Positions the particles were extracted at/shifted to, to calculate effectively needed shifts later
float3[] ExtractedAt = new float3[NTilts];
float3 ParticleCoords = ParticleOrigins[p];
float3[] Positions = GetPositionInImages(ParticleCoords);
#region Create CTFs
{
float GridStep = 1f / (NTilts - 1);
CTFStruct[] Params = new CTFStruct[NTilts];
for (int t = 0; t < NTilts; t++)
{
decimal Defocus = (decimal)Positions[t].Z;
decimal DefocusDelta = (decimal)GridCTFDefocusDelta.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep));
decimal DefocusAngle = (decimal)GridCTFDefocusAngle.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep));
CTF CurrCTF = CTF.GetCopy();
CurrCTF.Defocus = Defocus;
CurrCTF.DefocusDelta = DefocusDelta;
CurrCTF.DefocusAngle = DefocusAngle;
CurrCTF.Scale = (decimal)Math.Cos(Angles[t] * Helper.ToRad);
CurrCTF.Bfactor = (decimal)-Dose[t] * 8;
Params[t] = CurrCTF.ToStruct();
}
GPU.CreateCTF(ParticleCTFs.GetDevice(Intent.Write),
CTFCoords.GetDevice(Intent.Read),
(uint)CoarseDims.ElementsFFT(),
Params,
false,
(uint)NTilts);
}
#endregion
#region Weights are sums of the 2D CTFs
{
Image CTFAbs = new Image(ParticleCTFs.GetDevice(Intent.Read), ParticleCTFs.Dims, true);
CTFAbs.Abs();
ParticleWeights = CTFAbs.AsSum2D();
CTFAbs.Dispose();
{
float[] Weights = ParticleWeights.GetHost(Intent.ReadWrite)[0];
float Sum = Weights.Sum();
for (int i = 0; i < Weights.Length; i++)
Weights[i] /= Sum;
}
}
#endregion
#region Extract images
{
Image Extracted = new Image(new int3(size, size, NTilts));
float[][] ExtractedData = Extracted.GetHost(Intent.Write);
Parallel.For(0, NTilts, t =>
{
ExtractedAt[t] = new float3((int)Positions[t].X, (int)Positions[t].Y, 0);
Positions[t] -= size / 2;
int2 IntPosition = new int2((int)Positions[t].X, (int)Positions[t].Y);
float[] OriginalData;
lock (tiltStack)
OriginalData = tiltStack.GetHost(Intent.Read)[t];
float[] ImageData = ExtractedData[t];
for (int y = 0; y < size; y++)
{
int PosY = (y + IntPosition.Y + tiltStack.Dims.Y) % tiltStack.Dims.Y;
for (int x = 0; x < size; x++)
{
int PosX = (x + IntPosition.X + tiltStack.Dims.X) % tiltStack.Dims.X;
ImageData[y * size + x] = -OriginalData[PosY * tiltStack.Dims.X + PosX];
}
}
});
ParticleImages = Extracted.AsScaled(new int2(CoarseSize, CoarseSize));
ParticleImages.RemapToFT();
//Scaled.WriteMRC("d_particleimages.mrc");
Extracted.Dispose();
}
#endregion
Image ProjectionsConv = new Image(IntPtr.Zero, Projections.Dims, true, true);
GPU.MultiplyComplexSlicesByScalar(Projections.GetDevice(Intent.Read),
ParticleCTFs.GetDevice(Intent.Read),
ProjectionsConv.GetDevice(Intent.Write),
ParticleCTFs.ElementsComplex,
(uint)AnglesOri.Length);
Image ProjectionsReal = ProjectionsConv.AsIFFT();
GPU.NormalizeMasked(ProjectionsReal.GetDevice(Intent.Read),
ProjectionsReal.GetDevice(Intent.Write),
Mask.GetDevice(Intent.Read),
(uint)ProjectionsReal.ElementsSliceReal,
(uint)ProjectionsReal.Dims.Z);
//ProjectionsReal.WriteMRC("d_projconv.mrc");
ProjectionsConv.Dispose();
#region For each particle offset, correlate each tilt image with all reference projection
float[][] AllResults = new float[Shifts.Count][];
//for (int s = 0; s < Shifts.Count; s++)
Parallel.For(0, Shifts.Count, new ParallelOptions { MaxDegreeOfParallelism = 2 }, s =>
{
AllResults[s] = new float[AnglesOri.Length];
float3 ParticleCoordsAlt = ParticleOrigins[p] - Shifts[s];
float3[] PositionsAlt = GetPositionInImages(ParticleCoordsAlt);
float3[] PositionDiff = new float3[NTilts];
for (int t = 0; t < NTilts; t++)
PositionDiff[t] = (ExtractedAt[t] - PositionsAlt[t]) / size * CoarseSize;
float[] ShiftResults = new float[AnglesOri.Length];
GPU.TomoRealspaceCorrelate(ProjectionsReal.GetDevice(Intent.Read),
new int2(CoarseSize, CoarseSize),
(uint)AnglesOri.Length,
(uint)NTilts,
ParticleImages.GetDevice(Intent.Read),
ParticleCTFs.GetDevice(Intent.Read),
Mask.GetDevice(Intent.Read),
ParticleWeights.GetDevice(Intent.Read),
Helper.ToInterleaved(PositionDiff),
ShiftResults);
AllResults[s] = ShiftResults;
});
#endregion
ProjectionsReal.Dispose();
ParticleImages.Dispose();
ParticleCTFs.Dispose();
ParticleWeights.Dispose();
#region Find best offset/angle combination and store it in table
float3 BestShift = new float3(0, 0, 0);
float3 BestAngle = new float3(0, 0, 0);
float BestScore = -1e30f;
for (int s = 0; s < Shifts.Count; s++)
for (int a = 0; a < AnglesOri.Length; a++)
if (AllResults[s][a] > BestScore)
{
BestScore = AllResults[s][a];
BestAngle = AnglesOri[a];
BestShift = Shifts[s];
}
tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnOriginX", BestShift.X.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnOriginY", BestShift.Y.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnOriginZ", BestShift.Z.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnAngleRot", BestAngle.X.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnAngleTilt", BestAngle.Y.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnAnglePsi", BestAngle.Z.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[SubsetContinuousIDs[p]], "rlnParticleSelectZScore", BestScore.ToString(CultureInfo.InvariantCulture));
OptimizedShifts[p] = BestShift;
OptimizedAngles[p] = BestAngle;
#endregion
}
// Dispose all projections for this subset, they won't be needed later
SubsetProjections[subset.Key].Dispose();
}
#endregion
CTFCoords.Dispose();
#region Back-project with hopefully better parameters
{
CTFCoords = GetCTFCoords(size, size);
foreach (var subsetRange in SubsetRanges)
{
for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++)
{
float3 ParticleCoords = ParticleOrigins[p] - OptimizedShifts[p];
Image FullParticleImages = GetSubtomoImages(tiltStack, size, ParticleCoords, true);
Image FullParticleCTFs = GetSubtomoCTFs(ParticleCoords, CTFCoords);
//Image FullParticleCTFWeights = GetSubtomoCTFs(ParticleCoords, CTFCoords, true, true);
FullParticleImages.Multiply(FullParticleCTFs);
//FullParticleImages.Multiply(FullParticleCTFWeights);
FullParticleCTFs.Multiply(FullParticleCTFs);
float3[] FullParticleAngles = GetParticleAngleInImages(ParticleCoords, OptimizedAngles[p]);
outReconstructions[subsetRange.Key].BackProject(FullParticleImages, FullParticleCTFs, FullParticleAngles);
FullParticleImages.Dispose();
FullParticleCTFs.Dispose();
//FullParticleCTFWeights.Dispose();
}
}
CTFCoords.Dispose();
}
#endregion
}
public HeaderEM(BinaryReader reader)
{
MachineCoding = reader.ReadByte();
OS9 = reader.ReadByte();
Invalid = reader.ReadByte();
Mode = (EMDataType)reader.ReadByte();
Dimensions = new int3(reader.ReadBytes(3 * sizeof(int)));
Comment = reader.ReadBytes(80);
Voltage = reader.ReadInt32();
Cs = (float)reader.ReadInt32() / 1000f;
Aperture = reader.ReadInt32();
Magnification = reader.ReadInt32();
CCDMagnification = (float)reader.ReadInt32() / 1000f;
ExposureTime = (float)reader.ReadInt32() / 1000f;
PixelSize = (float)reader.ReadInt32() / 1000f;
EMCode = reader.ReadInt32();
CCDPixelsize = (float)reader.ReadInt32() / 1000f;
CCDArea = (float)reader.ReadInt32() / 1000f;
Defocus = reader.ReadInt32();
Astigmatism = reader.ReadInt32();
AstigmatismAngle = (float)reader.ReadInt32() / 1000f;
FocusIncrement = (float)reader.ReadInt32() / 1000f;
DQE = (float)reader.ReadInt32() / 1000f;
C2Intensity = (float)reader.ReadInt32() / 1000f;
SlitWidth = reader.ReadInt32();
EnergyOffset = reader.ReadInt32();
TiltAngle = (float)reader.ReadInt32() / 1000f;
TiltAxis = (float)reader.ReadInt32() / 1000f;
NoName1 = reader.ReadInt32();
NoName2 = reader.ReadInt32();
NoName3 = reader.ReadInt32();
MarkerPosition = new int2(reader.ReadBytes(2 * sizeof(int)));
Resolution = reader.ReadInt32();
Density = reader.ReadInt32();
Contrast = reader.ReadInt32();
NoName4 = reader.ReadInt32();
CenterOfMass = new int3(reader.ReadBytes(3 * sizeof(int)));
Height = reader.ReadInt32();
NoName5 = reader.ReadInt32();
DreiStrahlBereich = reader.ReadInt32();
AchromaticRing = reader.ReadInt32();
Lambda = reader.ReadInt32();
DeltaTheta = reader.ReadInt32();
NoName6 = reader.ReadInt32();
NoName7 = reader.ReadInt32();
UserData = reader.ReadBytes(256);
}
public void Reconstruct(Image tiltStack, int size, float lowpassAngstrom, int3 volumeDimensions)
{
if (!Directory.Exists(ReconstructionDir))
Directory.CreateDirectory(ReconstructionDir);
if (File.Exists(ReconstructionDir + RootName + ".mrc"))
return;
VolumeDimensions = volumeDimensions;
float DownscaleFactor = lowpassAngstrom / (float)(CTF.PixelSize * 2);
Image DownscaledStack = tiltStack.AsScaledMassive(new int2(tiltStack.Dims) / DownscaleFactor / 2 * 2);
tiltStack.FreeDevice();
GPU.Normalize(DownscaledStack.GetDevice(Intent.Read),
DownscaledStack.GetDevice(Intent.Write),
(uint)DownscaledStack.ElementsSliceReal,
(uint)DownscaledStack.Dims.Z);
int3 VolumeDimensionsCropped = volumeDimensions / DownscaleFactor / 2 * 2;
int SizeCropped = size / 4;
int3 Grid = (VolumeDimensionsCropped + SizeCropped - 1) / SizeCropped;
List<float3> GridCoords = new List<float3>();
for (int z = 0; z < Grid.Z; z++)
for (int y = 0; y < Grid.Y; y++)
for (int x = 0; x < Grid.X; x++)
GridCoords.Add(new float3(x * SizeCropped + SizeCropped / 2,
y * SizeCropped + SizeCropped / 2,
z * SizeCropped + SizeCropped / 2));
Image CTFCoords = GetCTFCoords(size, (int)(size * DownscaleFactor));
float[] OutputRec = new float[VolumeDimensionsCropped.Elements()];
int PlanForw, PlanBack, PlanForwCTF;
Projector.GetPlans(new int3(size, size, size), 2, out PlanForw, out PlanBack, out PlanForwCTF);
for (int p = 0; p < GridCoords.Count; p++)
{
Image ImagesFT = GetSubtomoImages(DownscaledStack, size, GridCoords[p] * DownscaleFactor, false, 1f / DownscaleFactor);
Image CTFs = GetSubtomoCTFs(GridCoords[p] * DownscaleFactor, CTFCoords);
//Image CTFWeights = GetSubtomoCTFs(GridCoords[p], CTFCoords, true, true);
ImagesFT.Multiply(CTFs); // Weight and phase-flip image FTs by CTF, which still has its sign here
//ImagesFT.Multiply(CTFWeights);
CTFs.Abs(); // Since everything is already phase-flipped, weights are positive
Projector ProjSubtomo = new Projector(new int3(size, size, size), 2);
lock (GPU.Sync)
ProjSubtomo.BackProject(ImagesFT, CTFs, GetAngleInImages(GridCoords[p] * DownscaleFactor));
Image Subtomo = ProjSubtomo.Reconstruct(false, PlanForw, PlanBack, PlanForwCTF);
Image SubtomoCropped = Subtomo.AsPadded(new int3(SizeCropped, SizeCropped, SizeCropped));
Subtomo.Dispose();
ProjSubtomo.Dispose();
/*Image CroppedSubtomo = Subtomo.AsPadded(new int3(SizeCropped, SizeCropped, SizeCropped));
CroppedSubtomo.WriteMRC(ParticlesDir + RootName + "_" + (b + st).ToString("D5") + ".mrc");
CroppedSubtomo.Dispose();*/
ImagesFT.Dispose();
CTFs.Dispose();
//CTFWeights.Dispose();
float[] SubtomoData = SubtomoCropped.GetHostContinuousCopy();
int3 Origin = new int3(GridCoords[p]) - SizeCropped / 2;
for (int z = 0; z < SizeCropped; z++)
{
int zVol = Origin.Z + z;
if (zVol >= VolumeDimensionsCropped.Z)
continue;
for (int y = 0; y < SizeCropped; y++)
{
int yVol = Origin.Y + y;
if (yVol >= VolumeDimensionsCropped.Y)
continue;
for (int x = 0; x < SizeCropped; x++)
{
int xVol = Origin.X + x;
if (xVol >= VolumeDimensionsCropped.X)
continue;
OutputRec[(zVol * VolumeDimensionsCropped.Y + yVol) * VolumeDimensionsCropped.X + xVol] = -SubtomoData[(z * SizeCropped + y) * SizeCropped + x];
}
}
}
SubtomoCropped.Dispose();
}
GPU.DestroyFFTPlan(PlanForw);
GPU.DestroyFFTPlan(PlanBack);
GPU.DestroyFFTPlan(PlanForwCTF);
CTFCoords.Dispose();
DownscaledStack.Dispose();
Image OutputRecImage = new Image(OutputRec, VolumeDimensionsCropped);
OutputRecImage.WriteMRC(ReconstructionDir + RootName + ".mrc");
OutputRecImage.Dispose();
}
public MainWindow()
{
try
{
Options.DeviceCount = GPU.GetDeviceCount();
if (Options.DeviceCount <= 0)
throw new Exception();
}
catch (Exception)
{
MessageBox.Show("No CUDA devices found, shutting down.");
Close();
}
GPU.MemoryChanged += () => Options.UpdateGPUStats();
DataContext = Options;
Options.PropertyChanged += Options_PropertyChanged;
Closing += MainWindow_Closing;
InitializeComponent();
DisableWhenRunning = new List<UIElement>
{
GridOptionsIO,
GridOptionsPreprocessing,
GridOptionsParticles,
GridOptionsCTF,
GridOptionsMovement,
GridOptionsGrids,
GridOptionsPostprocessing
};
if (File.Exists("Previous.settings"))
Options.Load("Previous.settings");
for (int i = 0; i < GPU.GetDeviceCount(); i++)
{
GPU.SetDevice(i);
Console.WriteLine($"Device {i}:");
Console.WriteLine($"Free memory: {GPU.GetFreeMemory(i)} MB");
Console.WriteLine($"Total memory: {GPU.GetTotalMemory(i)} MB");
}
GPU.SetDevice(0);
Options.UpdateGPUStats();
// Create mockup
{
float2[] SplinePoints = { new float2(0f, 0f), new float2(1f / 3f, 1f)};//, new float2(2f / 3f, 0f)};//, new float2(1f, 1f) };
Cubic1D ReferenceSpline = new Cubic1D(SplinePoints);
Cubic1DShort ShortSpline = Cubic1DShort.GetInterpolator(SplinePoints);
for (float i = -1f; i < 2f; i += 0.01f)
{
float Reference = ReferenceSpline.Interp(i);
float Test = ShortSpline.Interp(i);
if (Math.Abs(Reference - Test) > 1e-6f)
throw new Exception();
}
Random Rnd = new Random(123);
int3 GridDim = new int3(1, 1, 1);
float[] GridValues = new float[GridDim.Elements()];
for (int i = 0; i < GridValues.Length; i++)
GridValues[i] = (float)Rnd.NextDouble();
CubicGrid CGrid = new CubicGrid(GridDim, GridValues);
float[] Managed = CGrid.GetInterpolated(new int3(16, 16, 16), new float3(0, 0, 0));
float[] Native = CGrid.GetInterpolatedNative(new int3(16, 16, 16), new float3(0, 0, 0));
for (int i = 0; i < Managed.Length; i++)
if (Math.Abs(Managed[i] - Native[i]) > 1e-6f)
throw new Exception();
Matrix3 A = new Matrix3(1, 2, 3, 4, 5, 6, 7, 8, 9);
Matrix3 B = new Matrix3(11, 12, 13, 14, 15, 16, 17, 18, 19);
Matrix3 C = A * B;
// Euler matrix
{
Matrix3 E = Matrix3.Euler(0 * Helper.ToRad, 20 * Helper.ToRad, 0 * Helper.ToRad);
float3 EE = Matrix3.EulerFromMatrix(E.Transposed()) * Helper.ToDeg;
float3 Transformed = E * new float3(1, 0, 0);
Transformed.Y = 0;
}
//float3[] HealpixAngles = Helper.GetHealpixAngles(3, "D4");
// Deconvolve reconstructions using a separate CTF
//{
// for (int i = 1; i <= 24; i++)
// {
// Image Map = StageDataLoad.LoadMap($"F:\\stefanribo\\vlion\\warped_{i}.mrc", new int2(1, 1), 0, typeof(float));
// Image MapFT = Map.AsFFT(true);
// Map.Dispose();
// Image CTF = StageDataLoad.LoadMap($"F:\\stefanribo\\vlion\\warped_ctf_{i}.mrc", new int2(1, 1), 0, typeof(float));
// foreach (var slice in CTF.GetHost(Intent.ReadWrite))
// for (int s = 0; s < slice.Length; s++)
// slice[s] = Math.Max(1e-3f, slice[s]);
// MapFT.Divide(CTF);
// Map = MapFT.AsIFFT(true);
// MapFT.Dispose();
// Map.WriteMRC($"F:\\stefanribo\\vlion\\warped_deconv_{i}.mrc");
// Map.Dispose();
// }
//}
//{
// Image SumFT = new Image(new int3(220, 220, 220), true, true);
// Image SumWeights = new Image(new int3(220, 220, 220), true);
// int read = 0;
// foreach (var tomoPath in Directory.EnumerateFiles("F:\\stefanribo\\oridata\\particles", "tomo*.mrc"))
// {
// FileInfo Info = new FileInfo(tomoPath);
// Image Tomo = StageDataLoad.LoadMap(tomoPath, new int2(1, 1), 0, typeof(float));
// Image TomoFT = Tomo.AsFFT(true);
// Tomo.Dispose();
// Image TomoWeights = StageDataLoad.LoadMap("F:\\stefanribo\\oridata\\particlectf\\" + Info.Name, new int2(1, 1), 0, typeof(float));
// TomoFT.Multiply(TomoWeights);
// TomoWeights.Multiply(TomoWeights);
// SumFT.Add(TomoFT);
// SumWeights.Add(TomoWeights);
// TomoFT.Dispose();
// TomoWeights.Dispose();
// Debug.WriteLine(read++);
// }
// foreach (var slice in SumWeights.GetHost(Intent.ReadWrite))
// {
// for (int i = 0; i < slice.Length; i++)
// {
// slice[i] = Math.Max(1e-3f, slice[i]);
// }
// }
// SumFT.Divide(SumWeights);
// Image Sum = SumFT.AsIFFT(true);
// Sum.WriteMRC("F:\\stefanribo\\oridata\\particles\\weightedaverage.mrc");
// SumFT.Dispose();
// SumWeights.Dispose();
// Sum.Dispose();
//}
//{
// Image Subtrahend = StageDataLoad.LoadMap("E:\\martinsried\\stefan\\membranebound\\vlion\\relion_subtrahend.mrc", new int2(1, 1), 0, typeof(float));
// Image SubtrahendFT = Subtrahend.AsFFT(true);
// int read = 0;
// foreach (var tomoPath in Directory.EnumerateFiles("E:\\martinsried\\stefan\\membranebound\\oridata\\particles", "tomo*.mrc"))
// {
// FileInfo Info = new FileInfo(tomoPath);
// Image Tomo = StageDataLoad.LoadMap(tomoPath, new int2(1, 1), 0, typeof(float));
// Image TomoFT = Tomo.AsFFT(true);
// Tomo.Dispose();
// Image TomoWeights = StageDataLoad.LoadMap("E:\\martinsried\\stefan\\membranebound\\oridata\\particlectf\\" + Info.Name, new int2(1, 1), 0, typeof(float));
// Image SubtrahendFTMult = new Image(SubtrahendFT.GetDevice(Intent.Read), SubtrahendFT.Dims, true, true);
// SubtrahendFTMult.Multiply(TomoWeights);
// TomoFT.Subtract(SubtrahendFTMult);
// Tomo = TomoFT.AsIFFT(true);
// Tomo.WriteMRC("D:\\stefanribo\\particles\\" + Info.Name);
// Tomo.Dispose();
// TomoFT.Dispose();
// SubtrahendFTMult.Dispose();
// TomoWeights.Dispose();
// Debug.WriteLine(read++);
// }
//}
//{
// Image SubtRef1 = StageDataLoad.LoadMap("E:\\martinsried\\stefan\\membranebound\\vlion\\warp_subtrahend.mrc", new int2(1, 1), 0, typeof(float));
// Projector Subt = new Projector(SubtRef1, 2);
// SubtRef1.Dispose();
// Image ProjFT = Subt.Project(new int2(220, 220), new[] { new float3(0, 0, 0) }, 110);
// Image Proj = ProjFT.AsIFFT();
// Proj.RemapFromFT();
// Proj.WriteMRC("d_testproj.mrc");
//}
// Projector
/*{
Image MapForProjector = StageDataLoad.LoadMap("E:\\youwei\\run36_half1_class001_unfil.mrc", new int2(1, 1), 0, typeof (float));
Projector Proj = new Projector(MapForProjector, 2);
Image Projected = Proj.Project(new int2(240, 240), new[] { new float3(0, 0, 0) }, 120);
Projected = Projected.AsIFFT();
Projected.RemapFromFT();
Projected.WriteMRC("d_projected.mrc");
}*/
// Backprojector
/*{
Image Dot = new Image(new int3(32, 32, 360));
for (int a = 0; a < 360; a++)
Dot.GetHost(Intent.Write)[a][0] = 1;
Dot = Dot.AsFFT();
Dot.AsAmplitudes().WriteMRC("d_dot.mrc");
Image DotWeights = new Image(new int3(32, 32, 360), true);
for (int a = 0; a < 360; a++)
for (int i = 0; i < DotWeights.ElementsSliceReal; i++)
DotWeights.GetHost(Intent.Write)[a][i] = 1;
float3[] Angles = new float3[360];
for (int a = 0; a < 360; a++)
Angles[a] = new float3(0, a * Helper.ToRad * 0.05f, 0);
Projector Proj = new Projector(new int3(32, 32, 32), 2);
Proj.BackProject(Dot, DotWeights, Angles);
Proj.Weights.WriteMRC("d_weights.mrc");
//Image Re = Proj.Data.AsImaginary();
//Re.WriteMRC("d_projdata.mrc");
Image Rec = Proj.Reconstruct(true);
Rec.WriteMRC("d_rec.mrc");
}*/
//Star Models = new Star("D:\\rado27\\Refine3D\\run1_ct5_it005_half1_model.star", "data_model_group_2");
//Debug.WriteLine(Models.GetRow(0)[0]);
/*Image Volume = StageDataLoad.LoadMap("F:\\carragher20s\\ref256.mrc", new int2(1, 1), 0, typeof (float));
Image VolumePadded = Volume.AsPadded(new int3(512, 512, 512));
VolumePadded.WriteMRC("d_padded.mrc");
Volume.Dispose();
VolumePadded.RemapToFT(true);
Image VolumeFT = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
Image VolumeProjFT = VolumeFT.AsProjections(new[] { new float3(Helper.ToRad * 0, Helper.ToRad * 0, Helper.ToRad * 0) }, new int2(256, 256), 2f);
Image VolumeProj = VolumeProjFT.AsIFFT();
VolumeProjFT.Dispose();
VolumeProj.RemapFromFT();
VolumeProj.WriteMRC("d_proj.mrc");
VolumeProj.Dispose();*/
/*Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.44.54.mrc"));
Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.49.06.mrc"));
Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.50.48.mrc"));
Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.52.16.mrc"));
Options.Movies.Add(new Movie(@"D:\Dev\warp\May19_21.53.43.mrc"));
CTFDisplay.PS2D = new BitmapImage();*/
/*float2[] SimCoords = new float2[512 * 512];
for (int y = 0; y < 512; y++)
for (int x = 0; x < 512; x++)
{
int xcoord = x - 512, ycoord = y - 512;
SimCoords[y * 512 + x] = new float2((float) Math.Sqrt(xcoord * xcoord + ycoord * ycoord),
(float) Math.Atan2(ycoord, xcoord));
}
float[] Sim2D = new CTF {Defocus = -2M}.Get2D(SimCoords, 512, true);
byte[] Sim2DBytes = new byte[Sim2D.Length];
for (int i = 0; i < 512 * 512; i++)
Sim2DBytes[i] = (byte) (Sim2D[i] * 255f);
BitmapSource Sim2DSource = BitmapSource.Create(512, 512, 96, 96, PixelFormats.Indexed8, BitmapPalettes.Gray256, Sim2DBytes, 512);
CTFDisplay.Simulated2D = Sim2DSource;*/
/*float2[] PointsPS1D = new float2[512];
for (int i = 0; i < PointsPS1D.Length; i++)
PointsPS1D[i] = new float2(i, (float) Math.Exp(-i / 300f));
CTFDisplay.PS1D = PointsPS1D;
float[] SimCTF = new CTF { Defocus = -2M }.Get1D(512, true);
float2[] PointsSim1D = new float2[SimCTF.Length];
for (int i = 0; i < SimCTF.Length; i++)
PointsSim1D[i] = new float2(i, SimCTF[i] * (float)Math.Exp(-i / 100f) + (float)Math.Exp(-i / 300f));
CTFDisplay.Simulated1D = PointsSim1D;*/
/*CubicGrid Grid = new CubicGrid(new int3(5, 5, 5), 0, 0, Dimension.X);
Grid.Values[2, 2, 2] = 1f;
float[] Data = new float[11 * 11 * 11];
int i = 0;
for (float z = 0f; z < 1.05f; z += 0.1f)
for (float y = 0f; y < 1.05f; y += 0.1f)
for (float x = 0f; x < 1.05f; x += 0.1f)
Data[i++] = Grid.GetInterpolated(new float3(x, y, z));
Image DataImage = new Image(Data, new int3(11, 11, 11));
DataImage.WriteMRC("bla.mrc");
Image GPUImage = new Image(DataImage.GetDevice(Intent.Read), new int3(11, 11, 11));
GPUImage.WriteMRC("gpu.mrc");*/
/*CubicGrid WiggleGrid = new CubicGrid(new int3(2, 2, 1));
float[][] WiggleWeights = WiggleGrid.GetWiggleWeights(new int3(3, 3, 1));*/
}
}
public Image SimulateTiltSeries(Star tableIn, int3 stackDimensions, int size, int3 volumeDimensions, Dictionary<int, Projector> references, float resolution)
{
VolumeDimensions = volumeDimensions;
Image SimulatedStack = new Image(stackDimensions);
#region Get rows from table
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName))
RowIndices.Add(i);
if (RowIndices.Count == 0)
return SimulatedStack;
int NParticles = RowIndices.Count;
#endregion
#region Make sure all columns and directories are there
if (!tableIn.HasColumn("rlnImageName"))
tableIn.AddColumn("rlnImageName");
if (!tableIn.HasColumn("rlnCtfImage"))
tableIn.AddColumn("rlnCtfImage");
if (!tableIn.HasColumn("rlnParticleSelectZScore"))
tableIn.AddColumn("rlnParticleSelectZScore");
if (!Directory.Exists(ParticlesDir))
Directory.CreateDirectory(ParticlesDir);
if (!Directory.Exists(ParticleCTFDir))
Directory.CreateDirectory(ParticleCTFDir);
#endregion
#region Get subtomo positions from table
float3[] ParticleOrigins = new float3[NParticles];
float3[] ParticleAngles = new float3[NParticles];
int[] ParticleSubset = new int[NParticles];
{
string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX");
string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY");
string[] ColumnPosZ = tableIn.GetColumn("rlnCoordinateZ");
string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX");
string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY");
string[] ColumnOriginZ = tableIn.GetColumn("rlnOriginZ");
string[] ColumnAngleRot = tableIn.GetColumn("rlnAngleRot");
string[] ColumnAngleTilt = tableIn.GetColumn("rlnAngleTilt");
string[] ColumnAnglePsi = tableIn.GetColumn("rlnAnglePsi");
string[] ColumnSubset = tableIn.GetColumn("rlnRandomSubset");
for (int i = 0; i < NParticles; i++)
{
float3 Pos = new float3(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosZ[RowIndices[i]], CultureInfo.InvariantCulture));
float3 Shift = new float3(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginZ[RowIndices[i]], CultureInfo.InvariantCulture));
ParticleOrigins[i] = Pos - Shift;
//ParticleOrigins[i] /= new float3(3838f / 959f, 3710f / 927f, 4f);
float3 Angle = new float3(float.Parse(ColumnAngleRot[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAngleTilt[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAnglePsi[RowIndices[i]], CultureInfo.InvariantCulture));
ParticleAngles[i] = Angle;
ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]);
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", ParticleOrigins[i].X.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", ParticleOrigins[i].Y.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateZ", ParticleOrigins[i].Z.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0");
tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0");
tableIn.SetRowValue(RowIndices[i], "rlnOriginZ", "0.0");
}
}
#endregion
#region Deal with subsets
List<int> SubsetIDs = new List<int>();
foreach (var i in ParticleSubset)
if (!SubsetIDs.Contains(i))
SubsetIDs.Add(i);
SubsetIDs.Sort();
// For each subset, create a list of its particle IDs
Dictionary<int, List<int>> SubsetParticleIDs = SubsetIDs.ToDictionary(subsetID => subsetID, subsetID => new List<int>());
for (int i = 0; i < ParticleSubset.Length; i++)
SubsetParticleIDs[ParticleSubset[i]].Add(i);
foreach (var list in SubsetParticleIDs.Values)
list.Sort();
// Note where each subset starts and ends in a unified, sorted (by subset) particle ID list
Dictionary<int, Tuple<int, int>> SubsetRanges = new Dictionary<int, Tuple<int, int>>();
{
int Start = 0;
foreach (var pair in SubsetParticleIDs)
{
SubsetRanges.Add(pair.Key, new Tuple<int, int>(Start, Start + pair.Value.Count));
Start += pair.Value.Count;
}
}
List<int> SubsetContinuousIDs = new List<int>();
foreach (var pair in SubsetParticleIDs)
SubsetContinuousIDs.AddRange(pair.Value);
// Reorder particle information to match the order of SubsetContinuousIDs
ParticleOrigins = SubsetContinuousIDs.Select(i => ParticleOrigins[i]).ToArray();
ParticleAngles = SubsetContinuousIDs.Select(i => ParticleAngles[i]).ToArray();
ParticleSubset = SubsetContinuousIDs.Select(i => ParticleSubset[i]).ToArray();
#endregion
int CoarseSize = (int)Math.Round(size * ((float)CTF.PixelSize * 2 / resolution)) / 2 * 2;
int3 CoarseDims = new int3(CoarseSize, CoarseSize, 1);
// Positions the particles were extracted at/shifted to, to calculate effectively needed shifts later
float3[] ExtractedAt = new float3[NParticles * NTilts];
// Extract images, mask and resize them, create CTFs
#region Preflight
{
Image CTFCoords = GetCTFCoords(CoarseSize, size);
#region Create mask with soft edge
Image Mask;
{
Image MaskBig = new Image(new int3(size, size, 1));
float MaskRadius = MainWindow.Options.ExportParticleRadius / (float)CTF.PixelSize;
float SoftEdge = 16f;
float[] MaskBigData = MaskBig.GetHost(Intent.Write)[0];
for (int y = 0; y < size; y++)
{
int yy = y - size / 2;
yy *= yy;
for (int x = 0; x < size; x++)
{
int xx = x - size / 2;
xx *= xx;
float R = (float)Math.Sqrt(xx + yy);
if (R <= MaskRadius)
MaskBigData[y * size + x] = 1;
else
MaskBigData[y * size + x] = (float)(Math.Cos(Math.Min(1, (R - MaskRadius) / SoftEdge) * Math.PI) * 0.5 + 0.5);
}
}
MaskBig.WriteMRC("d_maskbig.mrc");
Mask = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize));
MaskBig.Dispose();
}
Mask.WriteMRC("d_masksmall.mrc");
#endregion
#region Create Fourier space mask
Image FourierMask = new Image(CoarseDims, true);
{
float[] FourierMaskData = FourierMask.GetHost(Intent.Write)[0];
int MaxR2 = CoarseSize * CoarseSize / 4;
for (int y = 0; y < CoarseSize; y++)
{
int yy = y < CoarseSize / 2 + 1 ? y : y - CoarseSize;
yy *= yy;
for (int x = 0; x < CoarseSize / 2 + 1; x++)
{
int xx = x * x;
int R2 = yy + xx;
FourierMaskData[y * (CoarseSize / 2 + 1) + x] = R2 < MaxR2 ? 1 : 0;
}
}
}
#endregion
#region For each particle, create CTFs and projections, and insert them into the simulated tilt series
for (int p = 0; p < NParticles; p++)
{
Image ParticleImages;
Image ParticleCTFs = new Image(new int3(CoarseSize, CoarseSize, NTilts), true);
float3 ParticleCoords = ParticleOrigins[p];
float3[] Positions = GetPositionInImages(ParticleCoords);
// Create CTFs
{
float GridStep = 1f / (NTilts - 1);
CTFStruct[] Params = new CTFStruct[NTilts];
for (int t = 0; t < NTilts; t++)
{
decimal Defocus = (decimal)Positions[t].Z;
decimal DefocusDelta = (decimal)GridCTFDefocusDelta.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep));
decimal DefocusAngle = (decimal)GridCTFDefocusAngle.GetInterpolated(new float3(0.5f, 0.5f, t * GridStep));
CTF CurrCTF = CTF.GetCopy();
CurrCTF.Defocus = Defocus;
CurrCTF.DefocusDelta = DefocusDelta;
CurrCTF.DefocusAngle = DefocusAngle;
CurrCTF.Scale = (decimal)Math.Cos(Angles[t] * Helper.ToRad);
CurrCTF.Bfactor = (decimal)-Dose[t] * 8;
Params[t] = CurrCTF.ToStruct();
}
GPU.CreateCTF(ParticleCTFs.GetDevice(Intent.Write),
CTFCoords.GetDevice(Intent.Read),
(uint)CoarseDims.ElementsFFT(),
Params,
false,
(uint)NTilts);
ParticleCTFs.MultiplySlices(FourierMask);
}
// Make projections
{
float3[] ImageShifts = new float3[NTilts];
float3[] ImageAngles = new float3[NTilts];
float3[] CurrPositions = GetPositionInImages(ParticleOrigins[p]);
float3[] CurrAngles = GetParticleAngleInImages(ParticleOrigins[p], ParticleAngles[p]);
for (int t = 0; t < NTilts; t++)
{
ImageShifts[t] = new float3(CurrPositions[t].X - (int)CurrPositions[t].X, // +diff because we are shifting the projections into experimental data frame
CurrPositions[t].Y - (int)CurrPositions[t].Y,
CurrPositions[t].Z - (int)CurrPositions[t].Z);
ImageAngles[t] = CurrAngles[t];
}
Image ProjectionsFT = new Image(IntPtr.Zero, new int3(CoarseSize, CoarseSize, NTilts), true, true);
Projector Reference = references[ParticleSubset[p]];
GPU.ProjectForward(Reference.Data.GetDevice(Intent.Read),
ProjectionsFT.GetDevice(Intent.Write),
Reference.Data.Dims,
new int2(CoarseSize, CoarseSize),
Helper.ToInterleaved(ImageAngles),
Reference.Oversampling,
(uint)NTilts);
ProjectionsFT.Multiply(ParticleCTFs);
Image Projections = ProjectionsFT.AsIFFT();
ProjectionsFT.Dispose();
Projections.RemapFromFT();
GPU.NormParticles(Projections.GetDevice(Intent.Read),
Projections.GetDevice(Intent.Write),
new int3(CoarseSize, CoarseSize, 1),
(uint)(MainWindow.Options.ExportParticleRadius / CTF.PixelSize * (CTF.PixelSize * 2 / (decimal)resolution)),
true,
(uint)NTilts);
Projections.MultiplySlices(Mask);
ParticleImages = Projections.AsScaled(new int2(size, size));
Projections.Dispose();
ParticleImages.ShiftSlices(ImageShifts);
}
// Extract images
{
for (int t = 0; t < NTilts; t++)
{
Positions[t] -= size / 2;
int2 IntPosition = new int2((int)Positions[t].X, (int)Positions[t].Y);
float[] SimulatedData;
lock (SimulatedStack)
SimulatedData = SimulatedStack.GetHost(Intent.Write)[t];
float[] ImageData = ParticleImages.GetHost(Intent.Read)[t];
for (int y = 0; y < size; y++)
{
int PosY = (y + IntPosition.Y + SimulatedStack.Dims.Y) % SimulatedStack.Dims.Y;
for (int x = 0; x < size; x++)
{
int PosX = (x + IntPosition.X + SimulatedStack.Dims.X) % SimulatedStack.Dims.X;
SimulatedData[PosY * SimulatedStack.Dims.X + PosX] += ImageData[y * size + x];
}
}
}
}
ParticleImages.Dispose();
ParticleCTFs.Dispose();
}
#endregion
Mask.Dispose();
FourierMask.Dispose();
CTFCoords.Dispose();
}
#endregion
return SimulatedStack;
}
