public TiltSeries(string path)
: base(path)
{
if (Angles.Length < Dimensions.Z) // In case angles and dose haven't been read and stored in .xml yet.
{
if (File.Exists(DirectoryName + RootName + ".star"))
{
Star Table = new Star(DirectoryName + RootName + ".star");
if (!Table.HasColumn("wrpDose") || !Table.HasColumn("wrpAngleTilt"))
throw new Exception("STAR file has no wrpDose or wrpTilt column.");
List<float> TempAngles = new List<float>();
List<float> TempDose = new List<float>();
for (int i = 0; i < Table.RowCount; i++)
{
TempAngles.Add(float.Parse(Table.GetRowValue(i, "wrpAngleTilt")));
TempDose.Add(float.Parse(Table.GetRowValue(i, "wrpDose")));
}
if (TempAngles.Count == 0)
throw new Exception("Metadata must contain 2 values per tilt: angle, dose.");
if (TempAngles.Count != Dimensions.Z)
throw new Exception("Metadata must contain one line for each image in tilt series.");
Angles = TempAngles.ToArray();
Dose = TempDose.ToArray();
}
else
{
HeaderMRC Header = new HeaderMRC(new BinaryReader(File.OpenRead(Path)));
if (Header.ImodTilt != null)
{
Angles = Header.ImodTilt;
Dose = new float[Angles.Length];
}
else
throw new Exception("A .meta file with angles and accumulated dose, or at least tilt angle data in the .ali's header are needed to work with tilt series.");
}
}
}
public Star(Star[] tables)
{
List<string> Common = new List<string>(tables[0].GetColumnNames());
foreach (var table in tables)
Common.RemoveAll(c => !table.HasColumn(c));
foreach (string name in Common)
NameMapping.Add(name, NameMapping.Count);
foreach (var table in tables)
{
int[] ColumnIndices = Common.Select(c => table.GetColumnID(c)).ToArray();
for (int r = 0; r < table.RowCount; r++)
{
List<string> Row = new List<string>(Common.Count);
for (int c = 0; c < ColumnIndices.Length; c++)
Row.Add(table.GetRowValue(r, ColumnIndices[c]));
AddRow(Row);
}
}
}
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;
}
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 void PerformOptimizationStep(Star tableIn, Image tiltStack, int size, int3 volumeDimensions, Dictionary<int, Projector> references, float resolution, Dictionary<int, Projector> outReconstructions, Dictionary<int, Projector> outCTFReconstructions)
{
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[] ParticleOrigins2 = new float3[NParticles];
float3[] ParticleAngles = new float3[NParticles];
float3[] ParticleAngles2 = 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");
string[] ColumnPosX2 = tableIn.GetColumn("rlnOriginXPrior");
string[] ColumnPosY2 = tableIn.GetColumn("rlnOriginYPrior");
string[] ColumnPosZ2 = tableIn.GetColumn("rlnOriginZPrior");
string[] ColumnAngleRot2 = tableIn.GetColumn("rlnAngleRotPrior");
string[] ColumnAngleTilt2 = tableIn.GetColumn("rlnAngleTiltPrior");
string[] ColumnAnglePsi2 = tableIn.GetColumn("rlnAnglePsiPrior");
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 Pos2 = Pos;
//if (ColumnPosX2 != null && ColumnPosY2 != null && ColumnPosZ2 != null)
// Pos2 = new float3(float.Parse(ColumnPosX2[RowIndices[i]], CultureInfo.InvariantCulture),
// float.Parse(ColumnPosY2[RowIndices[i]], CultureInfo.InvariantCulture),
// float.Parse(ColumnPosZ2[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;
ParticleOrigins2[i] = Pos2 - Shift;
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));
float3 Angle2 = Angle;
//if (ColumnAngleRot2 != null && ColumnAngleTilt2 != null && ColumnAnglePsi2 != null)
// Angle2 = new float3(float.Parse(ColumnAngleRot2[RowIndices[i]], CultureInfo.InvariantCulture),
// float.Parse(ColumnAngleTilt2[RowIndices[i]], CultureInfo.InvariantCulture),
// float.Parse(ColumnAnglePsi2[RowIndices[i]], CultureInfo.InvariantCulture));
ParticleAngles[i] = Angle;
ParticleAngles2[i] = Angle2;
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();
ParticleOrigins2 = SubsetContinuousIDs.Select(i => ParticleOrigins2[i]).ToArray();
ParticleAngles = SubsetContinuousIDs.Select(i => ParticleAngles[i]).ToArray();
ParticleAngles2 = SubsetContinuousIDs.Select(i => ParticleAngles2[i]).ToArray();
ParticleSubset = SubsetContinuousIDs.Select(i => ParticleSubset[i]).ToArray();
#endregion
if (GridMovementX.Dimensions.Elements() == 1)
{
int MaxSlice = SubsetRanges.Last().Value.Item2 > 100 ? 1 : 1;
GridMovementX = new CubicGrid(new int3(MaxSlice, MaxSlice, NTilts));
GridMovementY = new CubicGrid(new int3(MaxSlice, MaxSlice, NTilts));
//GridLocalX = new CubicGrid(new int3(4, 4, 4));
//GridLocalY = new CubicGrid(new int3(4, 4, 4));
//GridLocalZ = new CubicGrid(new int3(4, 4, 4));
GridAngleX = new CubicGrid(new int3(1, 1, NTilts));
GridAngleY = new CubicGrid(new int3(1, 1, NTilts));
GridAngleZ = new CubicGrid(new int3(1, 1, NTilts));
}
if (GridLocalX.Dimensions.Elements() == 1)
{
GridLocalX = new CubicGrid(new int3(4, 4, 4));
GridLocalY = new CubicGrid(new int3(4, 4, 4));
GridLocalZ = new CubicGrid(new int3(4, 4, 4));
}
//else
//{
// GridMovementX = GridMovementX.Resize(new int3(4, 4, NTilts));
// GridMovementY = GridMovementY.Resize(new int3(4, 4, NTilts));
//}
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
float2[] ExtractedAt = new float2[NParticles * NTilts];
// Extract images, mask and resize them, create CTFs
Image ParticleImages = new Image(new int3(CoarseSize, CoarseSize, NParticles * NTilts), true, true);
Image ParticleCTFs = new Image(new int3(CoarseSize, CoarseSize, NParticles * NTilts), true);
Image ParticleWeights = null;
Image ShiftFactors = null;
#region Preflight
float KeepBFac = GlobalBfactor;
GlobalBfactor = 0;
{
Image CTFCoords = GetCTFCoords(CoarseSize, size);
#region Precalculate vectors for shifts in Fourier space
{
float2[] ShiftFactorsData = new float2[(CoarseSize / 2 + 1) * CoarseSize];
for (int y = 0; y < CoarseSize; y++)
for (int x = 0; x < CoarseSize / 2 + 1; x++)
{
int xx = x;
int yy = y < CoarseSize / 2 + 1 ? y : y - CoarseSize;
ShiftFactorsData[y * (CoarseSize / 2 + 1) + x] = new float2((float)-xx / size * 2f * (float)Math.PI,
(float)-yy / size * 2f * (float)Math.PI);
}
ShiftFactors = new Image(ShiftFactorsData, new int3(CoarseSize, CoarseSize, 1), true);
}
#endregion
#region Create mask with soft edge
Image Mask;
Image MaskSubt;
{
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();
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 <= 30)
MaskBigData[y * size + x] = 1;
else
MaskBigData[y * size + x] = 0;
}
}
MaskSubt = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize));
MaskSubt.RemapToFT();
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 extract & preprocess images for entire tilt series
for (int p = 0; p < NParticles; p++)
{
float3 ParticleCoords = ParticleOrigins[p];
float3[] Positions = GetPositionInImages(ParticleCoords);
float3[] ProjAngles = GetParticleAngleInImages(ParticleCoords, ParticleAngles[p]);
Image Extracted = new Image(new int3(size, size, NTilts));
float[][] ExtractedData = Extracted.GetHost(Intent.Write);
float3[] Residuals = new float3[NTilts];
Image SubtrahendsCTF = new Image(new int3(CoarseSize, CoarseSize, NTilts), true);
// Create CTFs
{
CTFStruct[] CTFParams = new CTFStruct[NTilts];
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.GetDeviceSlice(NTilts * p, Intent.Write),
CTFCoords.GetDevice(Intent.Read),
(uint)CoarseDims.ElementsFFT(),
Params,
false,
(uint)NTilts);
}
//{
// CTFStruct[] CTFParams = new CTFStruct[NTilts];
// 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 = 1;
// CurrCTF.Bfactor = 0;
// Params[t] = CurrCTF.ToStruct();
// }
// GPU.CreateCTF(SubtrahendsCTF.GetDevice(Intent.Write),
// CTFCoords.GetDevice(Intent.Read),
// (uint)CoarseDims.ElementsFFT(),
// Params,
// false,
// (uint)NTilts);
//}
// Extract images
{
for (int t = 0; t < NTilts; t++)
{
ExtractedAt[p * NTilts + t] = new float2(Positions[t].X, Positions[t].Y);
Positions[t] -= size / 2;
int2 IntPosition = new int2((int)Positions[t].X, (int)Positions[t].Y);
float2 Residual = new float2(-(Positions[t].X - IntPosition.X), -(Positions[t].Y - IntPosition.Y));
Residuals[t] = new float3(Residual / size * CoarseSize);
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];
}
}
}
GPU.NormParticles(Extracted.GetDevice(Intent.Read),
Extracted.GetDevice(Intent.Write),
new int3(size, size, 1),
(uint)(MainWindow.Options.ExportParticleRadius / CTF.PixelSize),
true,
(uint)NTilts);
Image Scaled = Extracted.AsScaled(new int2(CoarseSize, CoarseSize));
//Scaled.WriteMRC("d_scaled.mrc");
Extracted.Dispose();
Scaled.ShiftSlices(Residuals);
Scaled.RemapToFT();
//GPU.NormalizeMasked(Scaled.GetDevice(Intent.Read),
// Scaled.GetDevice(Intent.Write),
// MaskSubt.GetDevice(Intent.Read),
// (uint)Scaled.ElementsSliceReal,
// (uint)NTilts);
//{
// //Image SubtrahendsFT = subtrahendReference.Project(new int2(CoarseSize, CoarseSize), ProjAngles, CoarseSize / 2);
// //SubtrahendsFT.Multiply(SubtrahendsCTF);
// //Image Subtrahends = SubtrahendsFT.AsIFFT();
// //SubtrahendsFT.Dispose();
// ////GPU.NormalizeMasked(Subtrahends.GetDevice(Intent.Read),
// //// Subtrahends.GetDevice(Intent.Write),
// //// MaskSubt.GetDevice(Intent.Read),
// //// (uint)Subtrahends.ElementsSliceReal,
// //// (uint)NTilts);
// //Scaled.Subtract(Subtrahends);
// //Subtrahends.Dispose();
// Image FocusMaskFT = maskReference.Project(new int2(CoarseSize, CoarseSize), ProjAngles, CoarseSize / 2);
// Image FocusMask = FocusMaskFT.AsIFFT();
// FocusMaskFT.Dispose();
// Scaled.Multiply(FocusMask);
// FocusMask.Dispose();
//}
Scaled.MultiplySlices(Mask);
GPU.FFT(Scaled.GetDevice(Intent.Read),
ParticleImages.GetDeviceSlice(p * NTilts, Intent.Write),
CoarseDims,
(uint)NTilts);
Scaled.Dispose();
SubtrahendsCTF.Dispose();
}
}
#endregion
ParticleCTFs.MultiplySlices(FourierMask);
Mask.Dispose();
FourierMask.Dispose();
MaskSubt.Dispose();
Image ParticleCTFsAbs = new Image(ParticleCTFs.GetDevice(Intent.Read), ParticleCTFs.Dims, true);
ParticleCTFsAbs.Abs();
ParticleWeights = ParticleCTFsAbs.AsSum2D();
ParticleCTFsAbs.Dispose();
{
float[] ParticleWeightsData = ParticleWeights.GetHost(Intent.ReadWrite)[0];
float Max = MathHelper.Max(ParticleWeightsData);
for (int i = 0; i < ParticleWeightsData.Length; i++)
ParticleWeightsData[i] /= Max;
}
CTFCoords.Dispose();
//Image CheckImages = ParticleImages.AsIFFT();
//CheckImages.WriteMRC("d_particleimages.mrc");
//CheckImages.Dispose();
//ParticleCTFs.WriteMRC("d_particlectfs.mrc");
}
GlobalBfactor = KeepBFac;
#endregion
bool DoPerParticleMotion = true;
bool DoImageAlignment = true;
#region BFGS evaluation and gradient
double[] StartParams;
Func<double[], Tuple<float2[], float3[]>> GetImageShiftsAndAngles;
Func<double[], float2[]> GetImageShifts;
Func<float3[], Image> GetProjections;
Func<double[], double[]> EvalIndividual;
Func<double[], double> Eval;
Func<double[], double[]> Gradient;
{
List<double> StartParamsList = new List<double>();
StartParamsList.AddRange(CreateVectorFromGrids(Dimensions.X));
StartParamsList.AddRange(CreateVectorFromParameters(ParticleOrigins, ParticleOrigins2, ParticleAngles, ParticleAngles2, size));
StartParams = StartParamsList.ToArray();
// Remember where the values for each grid are stored in the optimized vector
List<Tuple<int, int>> VectorGridRanges = new List<Tuple<int, int>>();
List<int> GridElements = new List<int>();
List<int> GridSliceElements = new List<int>();
{
int Start = 0;
VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridMovementX.Dimensions.Elements()));
Start += (int)GridMovementX.Dimensions.Elements();
VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridMovementY.Dimensions.Elements()));
Start += (int)GridMovementY.Dimensions.Elements();
VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridAngleX.Dimensions.Elements()));
Start += (int)GridAngleX.Dimensions.Elements();
VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridAngleY.Dimensions.Elements()));
Start += (int)GridAngleY.Dimensions.Elements();
VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridAngleZ.Dimensions.Elements()));
Start += (int)GridAngleZ.Dimensions.Elements();
VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridLocalX.Dimensions.Elements()));
Start += (int)GridLocalX.Dimensions.Elements();
VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridLocalY.Dimensions.Elements()));
Start += (int)GridLocalY.Dimensions.Elements();
VectorGridRanges.Add(new Tuple<int, int>(Start, Start + (int)GridLocalZ.Dimensions.Elements()));
GridElements.Add((int)GridMovementX.Dimensions.Elements());
GridElements.Add((int)GridMovementY.Dimensions.Elements());
GridElements.Add((int)GridAngleX.Dimensions.Elements());
GridElements.Add((int)GridAngleY.Dimensions.Elements());
GridElements.Add((int)GridAngleZ.Dimensions.Elements());
GridElements.Add((int)GridLocalX.Dimensions.Elements());
GridElements.Add((int)GridLocalY.Dimensions.Elements());
GridElements.Add((int)GridLocalZ.Dimensions.Elements());
GridSliceElements.Add((int)GridMovementX.Dimensions.ElementsSlice());
GridSliceElements.Add((int)GridMovementY.Dimensions.ElementsSlice());
GridSliceElements.Add((int)GridAngleX.Dimensions.ElementsSlice());
GridSliceElements.Add((int)GridAngleY.Dimensions.ElementsSlice());
GridSliceElements.Add((int)GridAngleZ.Dimensions.ElementsSlice());
GridSliceElements.Add((int)GridLocalX.Dimensions.ElementsSlice());
GridSliceElements.Add((int)GridLocalY.Dimensions.ElementsSlice());
GridSliceElements.Add((int)GridLocalZ.Dimensions.ElementsSlice());
}
int NVectorGridParams = VectorGridRanges.Last().Item2;
int NVectorParticleParams = NParticles * 12;
GetImageShiftsAndAngles = input =>
{
// Retrieve particle positions & angles, and grids from input vector
float3[] NewPositions, NewPositions2, NewAngles, NewAngles2;
GetParametersFromVector(input, NParticles, size, out NewPositions, out NewPositions2, out NewAngles, out NewAngles2);
SetGridsFromVector(input, Dimensions.X);
// Using current positions, angles and grids, get parameters for image shifts and reference projection angles
float2[] ImageShifts = new float2[NParticles * NTilts];
float3[] ImageAngles = new float3[NParticles * NTilts];
float3[] PerTiltPositions = new float3[NParticles * NTilts];
float3[] PerTiltAngles = new float3[NParticles * NTilts];
int[] SortedDosePrecalc = IndicesSortedDose;
for (int p = 0; p < NParticles; p++)
{
if (DoPerParticleMotion)
{
float3 CoordsDiff = NewPositions2[p] - NewPositions[p];
float3 AnglesDiff = NewAngles2[p] - NewAngles[p];
for (int t = 0; t < NTilts; t++)
{
float DoseID = SortedDosePrecalc[t] / (float)(NTilts - 1);
PerTiltPositions[p * NTilts + t] = NewPositions[p] + CoordsDiff * DoseID;
PerTiltAngles[p * NTilts + t] = NewAngles[p] + AnglesDiff * DoseID;
}
}
else
{
for (int t = 0; t < NTilts; t++)
{
PerTiltPositions[p * NTilts + t] = NewPositions[p];
PerTiltAngles[p * NTilts + t] = NewAngles[p];
}
}
}
float3[] CurrPositions = GetPositionInImages(PerTiltPositions);
float3[] CurrAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles);
for (int i = 0; i < ImageShifts.Length; i++)
{
ImageShifts[i] = new float2(ExtractedAt[i].X - CurrPositions[i].X,
ExtractedAt[i].Y - CurrPositions[i].Y); // -diff because those are extraction positions, i. e. opposite direction of shifts
ImageAngles[i] = CurrAngles[i];
}
return new Tuple<float2[], float3[]>(ImageShifts, ImageAngles);
};
GetImageShifts = input =>
{
// Retrieve particle positions & angles, and grids from input vector
float3[] NewPositions, NewPositions2, NewAngles, NewAngles2;
GetParametersFromVector(input, NParticles, size, out NewPositions, out NewPositions2, out NewAngles, out NewAngles2);
SetGridsFromVector(input, Dimensions.X);
// Using current positions, angles and grids, get parameters for image shifts and reference projection angles
float2[] ImageShifts = new float2[NParticles * NTilts];
float3[] PerTiltPositions = new float3[NParticles * NTilts];
int[] SortedDosePrecalc = IndicesSortedDose;
for (int p = 0; p < NParticles; p++)
{
if (DoPerParticleMotion)
{
float3 CoordsDiff = NewPositions2[p] - NewPositions[p];
float3 AnglesDiff = NewAngles2[p] - NewAngles[p];
for (int t = 0; t < NTilts; t++)
{
float DoseID = SortedDosePrecalc[t] / (float)(NTilts - 1);
PerTiltPositions[p * NTilts + t] = NewPositions[p] + CoordsDiff * DoseID;
}
}
else
{
for (int t = 0; t < NTilts; t++)
PerTiltPositions[p * NTilts + t] = NewPositions[p];
}
}
float3[] CurrPositions = GetPositionInImages(PerTiltPositions);
for (int i = 0; i < ImageShifts.Length; i++)
ImageShifts[i] = new float2(ExtractedAt[i].X - CurrPositions[i].X,
ExtractedAt[i].Y - CurrPositions[i].Y); // -diff because those are extraction positions, i. e. opposite direction of shifts
return ImageShifts;
};
GetProjections = imageAngles =>
{
Image Projections = new Image(IntPtr.Zero, new int3(CoarseSize, CoarseSize, NParticles * NTilts), true, true);
foreach (var subset in SubsetRanges)
{
Projector Reference = references[subset.Key];
int SubsetStart = subset.Value.Item1 * NTilts;
int SubsetEnd = subset.Value.Item2 * NTilts;
float3[] SubsetAngles = imageAngles.Skip(SubsetStart).Take(SubsetEnd - SubsetStart).ToArray();
GPU.ProjectForward(Reference.Data.GetDevice(Intent.Read),
Projections.GetDeviceSlice(SubsetStart, Intent.Write),
Reference.Data.Dims,
new int2(CoarseSize, CoarseSize),
Helper.ToInterleaved(SubsetAngles),
Reference.Oversampling,
(uint)(SubsetEnd - SubsetStart));
}
/*Image CheckProjections = Projections.AsIFFT();
//CheckProjections.RemapFromFT();
CheckProjections.WriteMRC("d_projections.mrc");
CheckProjections.Dispose();*/
return Projections;
};
EvalIndividual = input =>
{
Tuple<float2[], float3[]> ShiftsAndAngles = GetImageShiftsAndAngles(input);
Image Projections = GetProjections(ShiftsAndAngles.Item2);
float[] Results = new float[NParticles * NTilts];
GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read),
Projections.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
ParticleCTFs.GetDevice(Intent.Read),
ParticleWeights.GetDevice(Intent.Read),
new int2(CoarseSize, CoarseSize),
Helper.ToInterleaved(ShiftsAndAngles.Item1),
Results,
(uint)(NParticles * NTilts));
Projections.Dispose();
return Results.Select(i => (double)i).ToArray();
};
int OptimizationIterations = 0;
bool GetOut = false;
double Delta = 0.1;
float Delta2 = 2 * (float)Delta;
int[] WarpGridIDs = { 5, 6, 7 };
Dictionary<int, float2[][]> WiggleWeightsWarp = new Dictionary<int, float2[][]>();
foreach (var gridID in WarpGridIDs)
{
int NElements = GridElements[gridID];
WiggleWeightsWarp.Add(gridID, new float2[NElements][]);
for (int ge = 0; ge < NElements; ge++)
{
double[] InputMinus = new double[StartParams.Length], InputPlus = new double[StartParams.Length];
for (int i = 0; i < StartParams.Length; i++)
{
InputMinus[i] = StartParams[i];
InputPlus[i] = StartParams[i];
}
InputMinus[VectorGridRanges[gridID].Item1 + ge] -= Delta;
InputPlus[VectorGridRanges[gridID].Item1 + ge] += Delta;
float2[] ImageShiftsPlus = GetImageShifts(InputPlus);
float2[] ImageShiftsMinus = GetImageShifts(InputMinus);
float2[] Weights = new float2[ImageShiftsPlus.Length];
for (int i = 0; i < ImageShiftsPlus.Length; i++)
Weights[i] = (ImageShiftsPlus[i] - ImageShiftsMinus[i]) / Delta2;
WiggleWeightsWarp[gridID][ge] = Weights;
}
}
Eval = input =>
{
double Result = EvalIndividual(input).Sum();
lock (tableIn)
Debug.WriteLine(GPU.GetDevice() + ", " + RootName + ": " + Result);
OptimizationIterations++;
return Result;
};
Func<double[], double[], double, double[]> GradientParticles = (inputMinus, inputPlus, delta) =>
{
double[] EvalMinus = EvalIndividual(inputMinus);
double[] EvalPlus = EvalIndividual(inputPlus);
double[] Diff = new double[EvalMinus.Length];
for (int i = 0; i < Diff.Length; i++)
Diff[i] = (EvalPlus[i] - EvalMinus[i]) / (2 * delta);
return Diff;
};
Gradient = input =>
{
double[] Result = new double[input.Length];
if (OptimizationIterations > 60)
return Result;
float2[] ImageShiftGradients = new float2[NParticles * NTilts];
#region Compute gradient for individual image shifts
{
Tuple<float2[], float3[]> ShiftsAndAngles = GetImageShiftsAndAngles(input);
Image Projections = GetProjections(ShiftsAndAngles.Item2);
float2[] ShiftsXPlus = new float2[NParticles * NTilts];
float2[] ShiftsXMinus = new float2[NParticles * NTilts];
float2[] ShiftsYPlus = new float2[NParticles * NTilts];
float2[] ShiftsYMinus = new float2[NParticles * NTilts];
float2 DeltaX = new float2((float)Delta, 0);
float2 DeltaY = new float2(0, (float)Delta);
for (int i = 0; i < ShiftsXPlus.Length; i++)
{
ShiftsXPlus[i] = ShiftsAndAngles.Item1[i] + DeltaX;
ShiftsXMinus[i] = ShiftsAndAngles.Item1[i] - DeltaX;
ShiftsYPlus[i] = ShiftsAndAngles.Item1[i] + DeltaY;
ShiftsYMinus[i] = ShiftsAndAngles.Item1[i] - DeltaY;
}
float[] ScoresXPlus = new float[NParticles * NTilts];
float[] ScoresXMinus = new float[NParticles * NTilts];
float[] ScoresYPlus = new float[NParticles * NTilts];
float[] ScoresYMinus = new float[NParticles * NTilts];
GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read),
Projections.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
ParticleCTFs.GetDevice(Intent.Read),
ParticleWeights.GetDevice(Intent.Read),
new int2(CoarseSize, CoarseSize),
Helper.ToInterleaved(ShiftsXPlus),
ScoresXPlus,
(uint)(NParticles * NTilts));
GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read),
Projections.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
ParticleCTFs.GetDevice(Intent.Read),
ParticleWeights.GetDevice(Intent.Read),
new int2(CoarseSize, CoarseSize),
Helper.ToInterleaved(ShiftsXMinus),
ScoresXMinus,
(uint)(NParticles * NTilts));
GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read),
Projections.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
ParticleCTFs.GetDevice(Intent.Read),
ParticleWeights.GetDevice(Intent.Read),
new int2(CoarseSize, CoarseSize),
Helper.ToInterleaved(ShiftsYPlus),
ScoresYPlus,
(uint)(NParticles * NTilts));
GPU.TomoRefineGetDiff(ParticleImages.GetDevice(Intent.Read),
Projections.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
ParticleCTFs.GetDevice(Intent.Read),
ParticleWeights.GetDevice(Intent.Read),
new int2(CoarseSize, CoarseSize),
Helper.ToInterleaved(ShiftsYMinus),
ScoresYMinus,
(uint)(NParticles * NTilts));
Projections.Dispose();
for (int i = 0; i < ImageShiftGradients.Length; i++)
{
ImageShiftGradients[i] = new float2((ScoresXPlus[i] - ScoresXMinus[i]) / Delta2,
(ScoresYPlus[i] - ScoresYMinus[i]) / Delta2);
}
}
#endregion
// First, do particle parameters, i. e. 3D position within tomogram, rotation, across 2 points in time
// Altering each particle's parameters results in a change in its NTilts images, but nothing else
{
int[] TranslationIDs = DoPerParticleMotion ? new[] { 0, 1, 2, 3, 4, 5 } : new[] { 0, 1, 2 };
int[] RotationIDs = DoPerParticleMotion ? new [] {6, 7, 8, 9, 10, 11} : new [] { 6, 7, 8};
foreach (var paramID in RotationIDs)
{
double[] InputMinus = new double[input.Length], InputPlus = new double[input.Length];
for (int i = 0; i < input.Length; i++)
{
InputMinus[i] = input[i];
InputPlus[i] = input[i];
}
for (int p = 0; p < NParticles; p++)
{
InputMinus[NVectorGridParams + p * 12 + paramID] -= Delta;
InputPlus[NVectorGridParams + p * 12 + paramID] += Delta;
}
double[] ResultParticles = GradientParticles(InputMinus, InputPlus, Delta);
for (int p = 0; p < NParticles; p++)
{
double ParticleSum = 0;
for (int t = 0; t < NTilts; t++)
ParticleSum += ResultParticles[p * NTilts + t];
Result[NVectorGridParams + p * 12 + paramID] = ParticleSum;
}
}
// Translation-related gradients can all be computed efficiently from previously retrieved per-image gradients
foreach (var paramID in TranslationIDs)
{
double[] InputMinus = new double[input.Length], InputPlus = new double[input.Length];
for (int i = 0; i < input.Length; i++)
{
InputMinus[i] = input[i];
InputPlus[i] = input[i];
}
for (int p = 0; p < NParticles; p++)
{
InputMinus[NVectorGridParams + p * 12 + paramID] -= Delta;
InputPlus[NVectorGridParams + p * 12 + paramID] += Delta;
}
float2[] ImageShiftsPlus = GetImageShifts(InputPlus);
float2[] ImageShiftsMinus = GetImageShifts(InputMinus);
for (int p = 0; p < NParticles; p++)
{
double ParticleSum = 0;
for (int t = 0; t < NTilts; t++)
{
int i = p * NTilts + t;
float2 ShiftDelta = (ImageShiftsPlus[i] - ImageShiftsMinus[i]) / Delta2;
float ShiftGradient = ShiftDelta.X * ImageShiftGradients[i].X + ShiftDelta.Y * ImageShiftGradients[i].Y;
ParticleSum += ShiftGradient;
}
Result[NVectorGridParams + p * 12 + paramID] = ParticleSum;
}
}
// If there is no per-particle motion, just copy the gradients for these parameters from parameterIDs 0-5
if (!DoPerParticleMotion)
{
int[] RedundantIDs = { 3, 4, 5, 9, 10, 11 };
foreach (var paramID in RedundantIDs)
for (int p = 0; p < NParticles; p++)
Result[NVectorGridParams + p * 12 + paramID] = Result[NVectorGridParams + p * 12 + paramID - 3];
}
}
// Now deal with grids. Each grid slice (i. e. temporal point) will correspond to one tilt only, thus the gradient
// for each slice is the (weighted, in case of spatial resolution) sum of NParticles images in the corresponding tilt.
if (DoImageAlignment)
{
int[] RotationGridIDs = { 2, 3, 4 };
foreach (var gridID in RotationGridIDs)
{
int SliceElements = GridSliceElements[gridID];
for (int se = 0; se < SliceElements; se++)
{
double[] InputMinus = new double[input.Length], InputPlus = new double[input.Length];
for (int i = 0; i < input.Length; i++)
{
InputMinus[i] = input[i];
InputPlus[i] = input[i];
}
for (int gp = VectorGridRanges[gridID].Item1 + se; gp < VectorGridRanges[gridID].Item2; gp += SliceElements)
{
InputMinus[gp] -= Delta;
InputPlus[gp] += Delta;
}
double[] ResultParticles = GradientParticles(InputMinus, InputPlus, Delta);
for (int i = 0; i < ResultParticles.Length; i++)
{
int GridTime = i % NTilts;
Result[VectorGridRanges[gridID].Item1 + GridTime * SliceElements + se] += ResultParticles[i];
}
}
}
// Translation-related gradients can all be computed efficiently from previously retrieved per-image gradients
int[] TranslationGridIDs = { 0, 1 };
foreach (var gridID in TranslationGridIDs)
{
int SliceElements = GridSliceElements[gridID];
for (int se = 0; se < SliceElements; se++)
{
double[] InputMinus = new double[input.Length], InputPlus = new double[input.Length];
for (int i = 0; i < input.Length; i++)
{
InputMinus[i] = input[i];
InputPlus[i] = input[i];
}
for (int gp = VectorGridRanges[gridID].Item1 + se; gp < VectorGridRanges[gridID].Item2; gp += SliceElements)
{
InputMinus[gp] -= Delta;
InputPlus[gp] += Delta;
}
float2[] ImageShiftsPlus = GetImageShifts(InputPlus);
float2[] ImageShiftsMinus = GetImageShifts(InputMinus);
for (int i = 0; i < ImageShiftsPlus.Length; i++)
{
float2 ShiftDelta = (ImageShiftsPlus[i] - ImageShiftsMinus[i]) / Delta2;
float ShiftGradient = ShiftDelta.X * ImageShiftGradients[i].X + ShiftDelta.Y * ImageShiftGradients[i].Y;
int GridSlice = i % NTilts;
Result[VectorGridRanges[gridID].Item1 + GridSlice * SliceElements + se] += ShiftGradient;
}
}
}
// Warp grids don't have any shortcuts for getting multiple gradients at once, so they use pre-calculated wiggle weights
foreach (var gridID in WarpGridIDs)
{
int NElements = GridElements[gridID];
for (int ge = 0; ge < NElements; ge++)
{
float2[] Weights = WiggleWeightsWarp[gridID][ge];
for (int i = 0; i < Weights.Length; i++)
{
float2 ShiftDelta = Weights[i];
float ShiftGradient = ShiftDelta.X * ImageShiftGradients[i].X + ShiftDelta.Y * ImageShiftGradients[i].Y;
Result[VectorGridRanges[gridID].Item1 + ge] += ShiftGradient;
}
}
}
}
return Result;
};
}
#endregion
BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Gradient);
Optimizer.Epsilon = 3e-7;
Optimizer.Maximize(StartParams);
float3[] OptimizedOrigins, OptimizedOrigins2, OptimizedAngles, OptimizedAngles2;
GetParametersFromVector(StartParams, NParticles, size, out OptimizedOrigins, out OptimizedOrigins2, out OptimizedAngles, out OptimizedAngles2);
SetGridsFromVector(StartParams, Dimensions.X);
#region Calculate correlation scores, update table with new positions and angles
{
double[] ImageScores = EvalIndividual(StartParams);
float[] ParticleScores = new float[NParticles];
for (int i = 0; i < ImageScores.Length; i++)
ParticleScores[i / NTilts] += (float)ImageScores[i];
//if (!tableIn.HasColumn("rlnOriginXPrior"))
// tableIn.AddColumn("rlnOriginXPrior");
//if (!tableIn.HasColumn("rlnOriginYPrior"))
// tableIn.AddColumn("rlnOriginYPrior");
//if (!tableIn.HasColumn("rlnOriginZPrior"))
// tableIn.AddColumn("rlnOriginZPrior");
//if (!tableIn.HasColumn("rlnAngleRotPrior"))
// tableIn.AddColumn("rlnAngleRotPrior");
//if (!tableIn.HasColumn("rlnAngleTiltPrior"))
// tableIn.AddColumn("rlnAngleTiltPrior");
//if (!tableIn.HasColumn("rlnAnglePsiPrior"))
// tableIn.AddColumn("rlnAnglePsiPrior");
lock (tableIn)
for (int p = 0; p < NParticles; p++)
{
int Row = RowIndices[SubsetContinuousIDs[p]];
tableIn.SetRowValue(Row, "rlnCoordinateX", OptimizedOrigins[p].X.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(Row, "rlnCoordinateY", OptimizedOrigins[p].Y.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(Row, "rlnCoordinateZ", OptimizedOrigins[p].Z.ToString(CultureInfo.InvariantCulture));
//tableIn.SetRowValue(Row, "rlnOriginXPrior", OptimizedOrigins2[p].X.ToString(CultureInfo.InvariantCulture));
//tableIn.SetRowValue(Row, "rlnOriginYPrior", OptimizedOrigins2[p].Y.ToString(CultureInfo.InvariantCulture));
//tableIn.SetRowValue(Row, "rlnOriginZPrior", OptimizedOrigins2[p].Z.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(Row, "rlnAngleRot", OptimizedAngles[p].X.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(Row, "rlnAngleTilt", OptimizedAngles[p].Y.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(Row, "rlnAnglePsi", OptimizedAngles[p].Z.ToString(CultureInfo.InvariantCulture));
//tableIn.SetRowValue(Row, "rlnAngleRotPrior", OptimizedAngles2[p].X.ToString(CultureInfo.InvariantCulture));
//tableIn.SetRowValue(Row, "rlnAngleTiltPrior", OptimizedAngles2[p].Y.ToString(CultureInfo.InvariantCulture));
//tableIn.SetRowValue(Row, "rlnAnglePsiPrior", OptimizedAngles2[p].Z.ToString(CultureInfo.InvariantCulture));
tableIn.SetRowValue(Row, "rlnParticleSelectZScore", ParticleScores[p].ToString(CultureInfo.InvariantCulture));
}
}
#endregion
ParticleImages?.Dispose();
ParticleCTFs?.Dispose();
ParticleWeights?.Dispose();
ShiftFactors?.Dispose();
#region Extract particles at full resolution and back-project them into the reconstruction volumes
{
GPU.SetDevice(0);
Image CTFCoords = GetCTFCoords(size, size);
int[] SortedDosePrecalc = IndicesSortedDose;
foreach (var subsetRange in SubsetRanges)
{
lock (outReconstructions[subsetRange.Key])
{
for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++)
{
float3[] PerTiltPositions = new float3[NTilts];
float3[] PerTiltAngles = new float3[NTilts];
float3 CoordsDiff = OptimizedOrigins2[p] - OptimizedOrigins[p];
float3 AnglesDiff = OptimizedAngles2[p] - OptimizedAngles[p];
for (int t = 0; t < NTilts; t++)
{
float DoseID = SortedDosePrecalc[t] / (float)(NTilts - 1);
PerTiltPositions[t] = OptimizedOrigins[p] + CoordsDiff * DoseID;
PerTiltAngles[t] = OptimizedAngles[p] + AnglesDiff * DoseID;
}
Image FullParticleImages = GetSubtomoImages(tiltStack, size, PerTiltPositions, true);
Image FullParticleCTFs = GetSubtomoCTFs(PerTiltPositions, CTFCoords);
FullParticleImages.Multiply(FullParticleCTFs);
FullParticleCTFs.Abs();
float3[] FullParticleAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles);
outReconstructions[subsetRange.Key].BackProject(FullParticleImages, FullParticleCTFs, FullParticleAngles);
FullParticleImages.Dispose();
FullParticleCTFs.Dispose();
}
for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++)
{
float3[] PerTiltPositions = new float3[NTilts];
float3[] PerTiltAngles = new float3[NTilts];
float3 CoordsDiff = OptimizedOrigins2[p] - OptimizedOrigins[p];
float3 AnglesDiff = OptimizedAngles2[p] - OptimizedAngles[p];
for (int t = 0; t < NTilts; t++)
{
float DoseID = SortedDosePrecalc[t] / (float)(NTilts - 1);
PerTiltPositions[t] = OptimizedOrigins[p] + CoordsDiff * DoseID;
PerTiltAngles[t] = OptimizedAngles[p] + AnglesDiff * DoseID;
}
float3[] FullParticleAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles);
Image FullParticleCTFs = GetSubtomoCTFs(PerTiltPositions, CTFCoords, false);
Image FullParticleCTFWeights = GetSubtomoCTFs(PerTiltPositions, CTFCoords, true);
// CTF has to be converted to complex numbers with imag = 0
float2[] CTFsComplexData = new float2[FullParticleCTFs.ElementsComplex];
float[] CTFWeightsData = new float[FullParticleCTFs.ElementsComplex];
float[] CTFsContinuousData = FullParticleCTFs.GetHostContinuousCopy();
float[] CTFWeightsContinuousData = FullParticleCTFWeights.GetHostContinuousCopy();
for (int i = 0; i < CTFsComplexData.Length; i++)
{
CTFsComplexData[i] = new float2(Math.Abs(CTFsContinuousData[i] * CTFWeightsContinuousData[i]), 0);
CTFWeightsData[i] = Math.Abs(CTFWeightsContinuousData[i]);
}
Image CTFsComplex = new Image(CTFsComplexData, FullParticleCTFs.Dims, true);
Image CTFWeights = new Image(CTFWeightsData, FullParticleCTFs.Dims, true);
outCTFReconstructions[subsetRange.Key].BackProject(CTFsComplex, CTFWeights, FullParticleAngles);
FullParticleCTFs.Dispose();
FullParticleCTFWeights.Dispose();
CTFsComplex.Dispose();
CTFWeights.Dispose();
}
outReconstructions[subsetRange.Key].FreeDevice();
outCTFReconstructions[subsetRange.Key].FreeDevice();
}
}
CTFCoords.Dispose();
}
#endregion
SaveMeta();
}
public void AddToPerAngleReconstructions(Star tableIn, Image tiltStack, int size, int3 volumeDimensions, Dictionary<int, Projector[]> perAngleReconstructions, Dictionary<int, Projector[]> perAngleWeights)
{
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 (!Directory.Exists(WeightOptimizationDir))
Directory.CreateDirectory(WeightOptimizationDir);
#endregion
#region Get subtomo positions from table
float3[] ParticleOrigins = new float3[NParticles];
float3[] ParticleOrigins2 = new float3[NParticles];
float3[] ParticleAngles = new float3[NParticles];
float3[] ParticleAngles2 = 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");
string[] ColumnPosX2 = tableIn.GetColumn("rlnOriginXPrior");
string[] ColumnPosY2 = tableIn.GetColumn("rlnOriginYPrior");
string[] ColumnPosZ2 = tableIn.GetColumn("rlnOriginZPrior");
string[] ColumnAngleRot2 = tableIn.GetColumn("rlnAngleRotPrior");
string[] ColumnAngleTilt2 = tableIn.GetColumn("rlnAngleTiltPrior");
string[] ColumnAnglePsi2 = tableIn.GetColumn("rlnAnglePsiPrior");
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 Pos2 = Pos;
if (ColumnPosX2 != null && ColumnPosY2 != null && ColumnPosZ2 != null)
Pos2 = new float3(float.Parse(ColumnPosX2[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY2[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosZ2[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;
ParticleOrigins2[i] = Pos2 - Shift;
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));
float3 Angle2 = Angle;
if (ColumnAngleRot2 != null && ColumnAngleTilt2 != null && ColumnAnglePsi2 != null)
Angle2 = new float3(float.Parse(ColumnAngleRot2[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAngleTilt2[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAnglePsi2[RowIndices[i]], CultureInfo.InvariantCulture));
ParticleAngles[i] = Angle;
ParticleAngles2[i] = Angle2;
ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]);
}
}
#endregion
List<int> SubsetIDs = new List<int>();
foreach (var i in ParticleSubset)
if (!SubsetIDs.Contains(i))
SubsetIDs.Add(i);
SubsetIDs.Sort();
SubsetIDs.Remove(1);
SubsetIDs.Remove(2);
foreach (int subsetID in SubsetIDs)
{
for (int t = 0; t < NTilts; t++)
{
int AngleID = t;
lock (perAngleReconstructions[subsetID][t])
{
AddToReconstructionOneAngle(tiltStack,
subsetID,
size,
ParticleOrigins,
ParticleOrigins2,
ParticleAngles,
ParticleAngles2,
ParticleSubset,
AngleID,
perAngleReconstructions[subsetID][t],
perAngleWeights[subsetID][t]);
perAngleReconstructions[subsetID][t].FreeDevice();
perAngleWeights[subsetID][t].FreeDevice();
}
}
}
}
public void ProcessParticleShift(MapHeader originalHeader, Image originalStack, Star stardata, Image refft, Image maskft, int dimbox, decimal scaleFactor)
{
// Deal with dimensions and grids.
int NFrames = originalHeader.Dimensions.Z;
int2 DimsImage = new int2(originalHeader.Dimensions);
int2 DimsRegion = new int2(dimbox, dimbox);
decimal SubdivisionRatio = 4M;
List<int3> PyramidSizes = new List<int3>();
PyramidSizes.Add(new int3(MainWindow.Options.GridMoveX, MainWindow.Options.GridMoveX, Math.Min(NFrames, MainWindow.Options.GridMoveZ)));
while (true)
{
int3 Previous = PyramidSizes.Last();
int NewZ = Math.Min((int)Math.Round(Previous.Z / SubdivisionRatio), Previous.Z - 1);
if (NewZ < 2)
break;
PyramidSizes.Add(new int3(Previous.X * 2, Previous.Y * 2, NewZ));
}
PyramidShiftX.Clear();
PyramidShiftY.Clear();
float3[] PositionsGrid, PositionsGridPerFrame;
float2[] PositionsExtraction, PositionsShift;
float3[] ParticleAngles;
List<int> RowIndices = new List<int>();
{
string[] ColumnNames = stardata.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnNames.Length; i++)
if (ColumnNames[i].Contains(RootName))
RowIndices.Add(i);
string[] ColumnOriginX = stardata.GetColumn("rlnCoordinateX");
string[] ColumnOriginY = stardata.GetColumn("rlnCoordinateY");
string[] ColumnShiftX = stardata.GetColumn("rlnOriginX");
string[] ColumnShiftY = stardata.GetColumn("rlnOriginY");
string[] ColumnAngleRot = stardata.GetColumn("rlnAngleRot");
string[] ColumnAngleTilt = stardata.GetColumn("rlnAngleTilt");
string[] ColumnAnglePsi = stardata.GetColumn("rlnAnglePsi");
PositionsGrid = new float3[RowIndices.Count];
PositionsGridPerFrame = new float3[RowIndices.Count * NFrames];
PositionsExtraction = new float2[RowIndices.Count];
PositionsShift = new float2[RowIndices.Count * NFrames];
ParticleAngles = new float3[RowIndices.Count];
{
int i = 0;
foreach (var nameIndex in RowIndices)
{
float OriginX = float.Parse(ColumnOriginX[nameIndex]);
float OriginY = float.Parse(ColumnOriginY[nameIndex]);
float ShiftX = float.Parse(ColumnShiftX[nameIndex]);
float ShiftY = float.Parse(ColumnShiftY[nameIndex]);
PositionsExtraction[i] = new float2(OriginX - ShiftX, OriginY - ShiftY);
PositionsGrid[i] = new float3((OriginX - ShiftX) / DimsImage.X, (OriginY - ShiftY) / DimsImage.Y, 0.5f);
for (int z = 0; z < NFrames; z++)
{
PositionsGridPerFrame[z * RowIndices.Count + i] = new float3(PositionsGrid[i].X,
PositionsGrid[i].Y,
(float)z / (NFrames - 1));
PositionsShift[z * RowIndices.Count + i] = GetShiftFromPyramid(PositionsGridPerFrame[z * RowIndices.Count + i]);
}
ParticleAngles[i] = new float3(float.Parse(ColumnAngleRot[nameIndex]) * Helper.ToRad,
float.Parse(ColumnAngleTilt[nameIndex]) * Helper.ToRad,
float.Parse(ColumnAnglePsi[nameIndex]) * Helper.ToRad);
i++;
}
}
}
int NPositions = PositionsGrid.Length;
if (NPositions == 0)
return;
int MinFreqInclusive = (int)(MainWindow.Options.MovementRangeMin * DimsRegion.X / 2);
int MaxFreqExclusive = (int)(MainWindow.Options.MovementRangeMax * DimsRegion.X / 2);
int NFreq = MaxFreqExclusive - MinFreqInclusive;
int CentralFrame = NFrames / 2;
int MaskExpansions = 4; // Math.Max(1, PyramidSizes[0].Z / 3);
int[] MaskSizes = new int[MaskExpansions];
// Allocate memory and create all prerequisites:
int MaskLength;
Image ShiftFactors;
Image Phases;
Image Projections;
Image Shifts;
Image InvSigma;
{
List<long> Positions = new List<long>();
List<float2> Factors = new List<float2>();
List<float2> Freq = new List<float2>();
int Min2 = MinFreqInclusive * MinFreqInclusive;
int Max2 = MaxFreqExclusive * MaxFreqExclusive;
for (int y = 0; y < DimsRegion.Y; y++)
{
int yy = y - DimsRegion.X / 2;
for (int x = 0; x < DimsRegion.X / 2 + 1; x++)
{
int xx = x - DimsRegion.X / 2;
int r2 = xx * xx + yy * yy;
if (r2 >= Min2 && r2 < Max2)
{
Positions.Add(y * (DimsRegion.X / 2 + 1) + x);
Factors.Add(new float2((float)xx / DimsRegion.X * 2f * (float)Math.PI,
(float)yy / DimsRegion.X * 2f * (float)Math.PI));
float Angle = (float)Math.Atan2(yy, xx);
float r = (float)Math.Sqrt(r2);
Freq.Add(new float2(r, Angle));
}
}
}
// Addresses for CTF simulation
Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true);
{
float2[] CoordsData = new float2[CTFCoordsCart.ElementsSliceComplex];
Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) => CoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, a));
CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData });
CTFCoordsCart.RemapToFT();
}
float[] ValuesDefocus = GridCTF.GetInterpolatedNative(PositionsGrid);
CTFStruct[] PositionsCTF = ValuesDefocus.Select(v =>
{
CTF Altered = CTF.GetCopy();
Altered.PixelSizeDelta = 0;
Altered.Defocus = (decimal)v;
//Altered.Bfactor = -MainWindow.Options.MovementBfactor;
return Altered.ToStruct();
}).ToArray();
// Sort everyone with ascending distance from center.
List<KeyValuePair<float, int>> FreqIndices = Freq.Select((v, i) => new KeyValuePair<float, int>(v.X, i)).ToList();
FreqIndices.Sort((a, b) => a.Key.CompareTo(b.Key));
int[] SortedIndices = FreqIndices.Select(v => v.Value).ToArray();
Helper.Reorder(Positions, SortedIndices);
Helper.Reorder(Factors, SortedIndices);
Helper.Reorder(Freq, SortedIndices);
long[] RelevantMask = Positions.ToArray();
ShiftFactors = new Image(Helper.ToInterleaved(Factors.ToArray()));
MaskLength = RelevantMask.Length;
// Get mask sizes for different expansion steps.
for (int i = 0; i < MaskExpansions; i++)
{
float CurrentMaxFreq = MinFreqInclusive + (MaxFreqExclusive - MinFreqInclusive) / (float)MaskExpansions * (i + 1);
MaskSizes[i] = Freq.Count(v => v.X * v.X < CurrentMaxFreq * CurrentMaxFreq);
}
Phases = new Image(IntPtr.Zero, new int3(MaskLength, NPositions, NFrames), false, true, false);
Projections = new Image(IntPtr.Zero, new int3(MaskLength, NPositions, NFrames), false, true, false);
InvSigma = new Image(IntPtr.Zero, new int3(MaskLength, 1, 1));
Image ParticleMasksFT = maskft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample);
Image ParticleMasks = ParticleMasksFT.AsIFFT();
ParticleMasksFT.Dispose();
ParticleMasks.RemapFromFT();
Parallel.ForEach(ParticleMasks.GetHost(Intent.ReadWrite), slice =>
{
for (int i = 0; i < slice.Length; i++)
slice[i] = (Math.Max(2f, Math.Min(25f, slice[i])) - 2) / 23f;
});
Image ProjectionsSparse = refft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample);
Image InvSigmaSparse = new Image(new int3(DimsRegion), true);
{
int GroupNumber = int.Parse(stardata.GetRowValue(RowIndices[0], "rlnGroupNumber"));
//Star SigmaTable = new Star("D:\\rado27\\RefineWarppolish\\run1_model.star", "data_model_group_" + GroupNumber);
Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber);
float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray();
float[] Sigma2NoiseData = InvSigmaSparse.GetHost(Intent.Write)[0];
Helper.ForEachElementFT(new int2(DimsRegion.X, DimsRegion.Y), (x, y, xx, yy, r, angle) =>
{
int ir = (int)r;
float val = 0;
if (ir < SigmaValues.Length)
{
if (SigmaValues[ir] != 0f)
val = 1f / SigmaValues[ir];
}
Sigma2NoiseData[y * (DimsRegion.X / 2 + 1) + x] = val;
});
float MaxSigma = MathHelper.Max(Sigma2NoiseData);
for (int i = 0; i < Sigma2NoiseData.Length; i++)
Sigma2NoiseData[i] /= MaxSigma;
InvSigmaSparse.RemapToFT();
}
//InvSigmaSparse.WriteMRC("d_sigma2noise.mrc");
float PixelSize = (float)CTF.PixelSize;
float PixelDelta = (float)CTF.PixelSizeDelta;
float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad;
GPU.CreateParticleShift(originalStack.GetDevice(Intent.Read),
DimsImage,
NFrames,
Helper.ToInterleaved(PositionsExtraction),
Helper.ToInterleaved(PositionsShift),
NPositions,
DimsRegion,
RelevantMask,
(uint)RelevantMask.Length,
ParticleMasks.GetDevice(Intent.Read),
ProjectionsSparse.GetDevice(Intent.Read),
PositionsCTF,
CTFCoordsCart.GetDevice(Intent.Read),
InvSigmaSparse.GetDevice(Intent.Read),
PixelSize + PixelDelta / 2,
PixelSize - PixelDelta / 2,
PixelAngle,
Phases.GetDevice(Intent.Write),
Projections.GetDevice(Intent.Write),
InvSigma.GetDevice(Intent.Write));
InvSigmaSparse.Dispose();
ParticleMasks.Dispose();
ProjectionsSparse.Dispose();
CTFCoordsCart.Dispose();
originalStack.FreeDevice();
Shifts = new Image(new float[NPositions * NFrames * 2]);
}
#region Fit movement
{
int NPyramidPoints = 0;
float[][][] WiggleWeights = new float[PyramidSizes.Count][][];
for (int p = 0; p < PyramidSizes.Count; p++)
{
CubicGrid WiggleGrid = new CubicGrid(PyramidSizes[p]);
NPyramidPoints += (int)PyramidSizes[p].Elements();
WiggleWeights[p] = WiggleGrid.GetWiggleWeights(PositionsGridPerFrame);
}
double[] StartParams = new double[NPyramidPoints * 2];
for (int m = 3; m < MaskExpansions; m++)
{
for (int currentGrid = 0; currentGrid < PyramidSizes.Count; currentGrid++)
{
Action<double[]> SetPositions = input =>
{
// Construct CubicGrids and get interpolated shift values.
float[] AlteredX = new float[PositionsGridPerFrame.Length];
float[] AlteredY = new float[PositionsGridPerFrame.Length];
int Offset = 0;
foreach (var size in PyramidSizes)
{
int Elements = (int)size.Elements();
CubicGrid GridX = new CubicGrid(size, input.Skip(Offset).Take(Elements).Select(v => (float)v).ToArray());
AlteredX = MathHelper.Plus(AlteredX, GridX.GetInterpolatedNative(PositionsGridPerFrame));
CubicGrid GridY = new CubicGrid(size, input.Skip(NPyramidPoints + Offset).Take(Elements).Select(v => (float)v).ToArray());
AlteredY = MathHelper.Plus(AlteredY, GridY.GetInterpolatedNative(PositionsGridPerFrame));
Offset += Elements;
}
// Finally, set the shift values in the device array.
float[] ShiftData = Shifts.GetHost(Intent.Write)[0];
for (int i = 0; i < PositionsGridPerFrame.Length; i++)
{
ShiftData[i * 2] = AlteredX[i];
ShiftData[i * 2 + 1] = AlteredY[i];
}
};
Func<double[], double> Eval = input =>
{
SetPositions(input);
float[] Diff = new float[NPositions * NFrames];
GPU.ParticleShiftGetDiff(Phases.GetDevice(Intent.Read),
Projections.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
InvSigma.GetDevice(Intent.Read),
(uint)MaskLength,
(uint)MaskSizes[m],
Shifts.GetDevice(Intent.Read),
Diff,
(uint)NPositions,
(uint)NFrames);
//for (int i = 0; i < Diff.Length; i++)
//Diff[i] = Diff[i] * 100f;
double Score = Diff.Sum();
//Debug.WriteLine(Score);
return Score;
};
Func<double[], double[]> Grad = input =>
{
SetPositions(input);
float[] Diff = new float[NPositions * NFrames * 2];
GPU.ParticleShiftGetGrad(Phases.GetDevice(Intent.Read),
Projections.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
InvSigma.GetDevice(Intent.Read),
(uint)MaskLength,
(uint)MaskSizes[m],
Shifts.GetDevice(Intent.Read),
Diff,
(uint)NPositions,
(uint)NFrames);
//for (int i = 0; i < Diff.Length; i++)
//Diff[i] = Diff[i] * 100f;
float[] DiffX = new float[NPositions * NFrames], DiffY = new float[NPositions * NFrames];
for (int i = 0; i < DiffX.Length; i++)
{
DiffX[i] = Diff[i * 2];
DiffY[i] = Diff[i * 2 + 1];
}
double[] Result = new double[input.Length];
int Offset = 0;
for (int p = 0; p < PyramidSizes.Count; p++)
{
//if (p == currentGrid)
Parallel.For(0, (int)PyramidSizes[p].Elements(), i =>
{
Result[Offset + i] = MathHelper.ReduceWeighted(DiffX, WiggleWeights[p][i]);
Result[NPyramidPoints + Offset + i] = MathHelper.ReduceWeighted(DiffY, WiggleWeights[p][i]);
});
Offset += (int)PyramidSizes[p].Elements();
}
return Result;
};
BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Grad);
//Optimizer.Corrections = 20;
Optimizer.Minimize(StartParams);
}
{
PyramidShiftX.Clear();
PyramidShiftY.Clear();
int Offset = 0;
foreach (var size in PyramidSizes)
{
int Elements = (int)size.Elements();
CubicGrid GridX = new CubicGrid(size, StartParams.Skip(Offset).Take(Elements).Select(v => (float)v).ToArray());
PyramidShiftX.Add(GridX);
CubicGrid GridY = new CubicGrid(size, StartParams.Skip(NPyramidPoints + Offset).Take(Elements).Select(v => (float)v).ToArray());
PyramidShiftY.Add(GridY);
Offset += Elements;
}
}
}
}
#endregion
ShiftFactors.Dispose();
Phases.Dispose();
Projections.Dispose();
Shifts.Dispose();
InvSigma.Dispose();
SaveMeta();
}
private void ButtonPolishParticles_OnClick(object sender, RoutedEventArgs e)
{
System.Windows.Forms.OpenFileDialog Dialog = new System.Windows.Forms.OpenFileDialog
{
Filter = "STAR Files|*.star",
Multiselect = false
};
System.Windows.Forms.DialogResult Result = Dialog.ShowDialog();
if (Result == System.Windows.Forms.DialogResult.OK)
{
System.Windows.Forms.SaveFileDialog SaveDialog = new System.Windows.Forms.SaveFileDialog
{
Filter = "STAR Files|*.star"
};
System.Windows.Forms.DialogResult SaveResult = SaveDialog.ShowDialog();
if (SaveResult == System.Windows.Forms.DialogResult.OK)
{
Thread ProcessThread = new Thread(() =>
{
Star TableIn = new Star(Dialog.FileName);
if (TableIn.GetColumn("rlnCtfImage") == null)
TableIn.AddColumn("rlnCtfImage");
string[] ColumnNames = TableIn.GetColumn("rlnMicrographName");
string[] ColumnCoordsX = TableIn.GetColumn("rlnCoordinateX");
string[] ColumnCoordsY = TableIn.GetColumn("rlnCoordinateY");
Star TableOut = new Star(TableIn.GetColumnNames());
Image ImageGain = null;
if (!string.IsNullOrEmpty(Options.GainPath) && Options.CorrectGain)
try
{
ImageGain = StageDataLoad.LoadMap(Options.GainPath,
new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight),
MainWindow.Options.InputDatOffset,
ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));
}
catch
{
return;
}
foreach (var movie in Options.Movies)
if (movie.DoProcess)
{
MapHeader OriginalHeader = null;
Image OriginalStack = null;
decimal ScaleFactor = 1M / (decimal)Math.Pow(2, (double)Options.PostBinTimes);
PrepareHeaderAndMap(movie.Path, ImageGain, ScaleFactor, out OriginalHeader, out OriginalStack);
//OriginalStack.WriteMRC("d_stack.mrc");
movie.UpdateStarDefocus(TableIn, ColumnNames, ColumnCoordsX, ColumnCoordsY);
movie.ExportParticlesMovie(TableIn, TableOut, OriginalHeader, OriginalStack, Options.ExportParticleSize, Options.ExportParticleRadius, ScaleFactor);
OriginalStack?.Dispose();
//Debug.WriteLine(movie.Path);
TableOut.Save(SaveDialog.FileName);
}
TableOut.Save(SaveDialog.FileName);
ImageGain?.Dispose();
});
ProcessThread.Start();
}
}
}
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 static float[] LoadFloat(string path, string name1 = null)
{
Star TableIn = new Star(path);
return (name1 == null ? TableIn.GetColumn(0) : TableIn.GetColumn(name1)).Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray();
}
public void PerformComparison(MapHeader originalHeader, Star stardata, Image refft, Image maskft, decimal scaleFactor)
{
int NFrames = originalHeader.Dimensions.Z;
int2 DimsImage = new int2(originalHeader.Dimensions);
float3[] PositionsGrid;
float3[] PositionsShift;
float3[] ParticleAngles;
List<int> RowIndices = new List<int>();
{
string[] ColumnNames = stardata.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnNames.Length; i++)
if (ColumnNames[i].Contains(RootName))
RowIndices.Add(i);
string[] ColumnOriginX = stardata.GetColumn("rlnCoordinateX");
string[] ColumnOriginY = stardata.GetColumn("rlnCoordinateY");
string[] ColumnShiftX = stardata.GetColumn("rlnOriginX");
string[] ColumnShiftY = stardata.GetColumn("rlnOriginY");
string[] ColumnAngleRot = stardata.GetColumn("rlnAngleRot");
string[] ColumnAngleTilt = stardata.GetColumn("rlnAngleTilt");
string[] ColumnAnglePsi = stardata.GetColumn("rlnAnglePsi");
PositionsGrid = new float3[RowIndices.Count];
PositionsShift = new float3[RowIndices.Count];
ParticleAngles = new float3[RowIndices.Count];
{
int i = 0;
foreach (var nameIndex in RowIndices)
{
float OriginX = float.Parse(ColumnOriginX[nameIndex]);
float OriginY = float.Parse(ColumnOriginY[nameIndex]);
float ShiftX = float.Parse(ColumnShiftX[nameIndex]);
float ShiftY = float.Parse(ColumnShiftY[nameIndex]);
PositionsGrid[i] = new float3((OriginX - ShiftX) / DimsImage.X, (OriginY - ShiftY) / DimsImage.Y, 0);
PositionsShift[i] = new float3(ShiftX, ShiftY, 0f);
ParticleAngles[i] = new float3(-float.Parse(ColumnAngleRot[nameIndex]) * Helper.ToRad,
-float.Parse(ColumnAngleTilt[nameIndex]) * Helper.ToRad,
-float.Parse(ColumnAnglePsi[nameIndex]) * Helper.ToRad);
i++;
}
}
}
int NPositions = PositionsGrid.Length;
if (NPositions == 0)
return;
Image Particles = StageDataLoad.LoadMap(ParticlesPath, new int2(1, 1), 0, typeof (float));
int2 DimsRegion = new int2(Particles.Dims.X, Particles.Dims.X);
Particles.ShiftSlices(PositionsShift);
int MinFreqInclusive = (int)(MainWindow.Options.MovementRangeMin * DimsRegion.X / 2);
int MaxFreqExclusive = (int)(MainWindow.Options.MovementRangeMax * DimsRegion.X / 2);
int NFreq = MaxFreqExclusive - MinFreqInclusive;
Image ParticleMasksFT = maskft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample);
Image ParticleMasks = ParticleMasksFT.AsIFFT();
ParticleMasksFT.Dispose();
ParticleMasks.RemapFromFT();
Parallel.ForEach(ParticleMasks.GetHost(Intent.ReadWrite), slice =>
{
for (int i = 0; i < slice.Length; i++)
slice[i] = (Math.Max(2f, Math.Min(25f, slice[i])) - 2) / 23f;
});
Image ProjectionsFT = refft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample);
Image Projections = ProjectionsFT.AsIFFT();
ProjectionsFT.Dispose();
// Addresses for CTF simulation
Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true);
{
float2[] CoordsData = new float2[CTFCoordsCart.ElementsSliceComplex];
Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) => CoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, a));
CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData });
CTFCoordsCart.RemapToFT();
}
float[] ValuesDefocus = GridCTF.GetInterpolatedNative(PositionsGrid);
CTFStruct[] PositionsCTF = ValuesDefocus.Select(v =>
{
CTF Altered = CTF.GetCopy();
Altered.Defocus = (decimal)v;
//Altered.Bfactor = -MainWindow.Options.MovementBfactor;
return Altered.ToStruct();
}).ToArray();
Image Scores = new Image(IntPtr.Zero, new int3(NPositions, 1, 1));
GPU.CompareParticles(Particles.GetDevice(Intent.Read),
ParticleMasks.GetDevice(Intent.Read),
Projections.GetDevice(Intent.Read),
DimsRegion,
CTFCoordsCart.GetDevice(Intent.Read),
PositionsCTF,
MinFreqInclusive,
MaxFreqExclusive,
Scores.GetDevice(Intent.Write),
(uint)NPositions);
float[] ScoresData = Scores.GetHost(Intent.Read)[0];
for (int p = 0; p < NPositions; p++)
{
stardata.SetRowValue(RowIndices[p], "rlnCtfFigureOfMerit", ScoresData[p].ToString(CultureInfo.InvariantCulture));
}
Scores.Dispose();
Projections.Dispose();
ParticleMasks.Dispose();
CTFCoordsCart.Dispose();
Particles.Dispose();
}
public void ExportParticlesMovieOld(Star table, int size)
{
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = table.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName))
RowIndices.Add(i);
if (RowIndices.Count == 0)
return;
if (!Directory.Exists(ParticlesDir))
Directory.CreateDirectory(ParticlesDir);
if (!Directory.Exists(ParticleCTFDir))
Directory.CreateDirectory(ParticleCTFDir);
MapHeader OriginalHeader = MapHeader.ReadFromFile(Path,
new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight),
MainWindow.Options.InputDatOffset,
ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));
/*Image OriginalStack = StageDataLoad.LoadMap(Path,
new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight),
MainWindow.Options.InputDatOffset,
ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));*/
//OriginalStack.Xray(20f);
int3 Dims = OriginalHeader.Dimensions;
int3 DimsRegion = new int3(size, size, 1);
int NParticles = RowIndices.Count / Dimensions.Z;
float PixelSize = (float)(MainWindow.Options.CTFPixelMin + MainWindow.Options.CTFPixelMax) * 0.5f;
float PixelDelta = (float)(MainWindow.Options.CTFPixelMax - MainWindow.Options.CTFPixelMin) * 0.5f;
float PixelAngle = (float)MainWindow.Options.CTFPixelAngle / (float)(180.0 / Math.PI);
Image CTFCoords;
{
float2[] CTFCoordsData = new float2[DimsRegion.ElementsSlice()];
//Helper.ForEachElementFT(new int2(DimsRegion), (x, y, xx, yy) =>
for (int y = 0; y < DimsRegion.Y; y++)
for (int x = 0; x < DimsRegion.X / 2 + 1; x++)
{
int xx = x;
int yy = y < DimsRegion.Y / 2 + 1 ? y : y - DimsRegion.Y;
float xs = xx / (float)DimsRegion.X;
float ys = yy / (float)DimsRegion.Y;
float r = (float)Math.Sqrt(xs * xs + ys * ys);
float angle = (float)(Math.Atan2(yy, xx));
float CurrentPixelSize = PixelSize + PixelDelta * (float)Math.Cos(2f * (angle - PixelAngle));
CTFCoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / CurrentPixelSize, angle);
} //);
CTFCoords = new Image(CTFCoordsData, DimsRegion.Slice(), true);
//CTFCoords.RemapToFT();
}
Image CTFFreq = CTFCoords.AsReal();
Image CTFStack = new Image(new int3(size, size, NParticles * Dimensions.Z), true);
int CTFStackIndex = 0;
string[] ColumnPosX = table.GetColumn("rlnCoordinateX");
string[] ColumnPosY = table.GetColumn("rlnCoordinateY");
int3[] Origins = new int3[NParticles];
for (int i = 0; i < NParticles; i++)
Origins[i] = new int3((int)double.Parse(ColumnPosX[RowIndices[i]]) - DimsRegion.X * 2 / 2,
(int)double.Parse(ColumnPosY[RowIndices[i]]) - DimsRegion.Y * 2 / 2,
0);
int IndexOffset = RowIndices[0];
string[] ColumnOriginX = table.GetColumn("rlnOriginX");
string[] ColumnOriginY = table.GetColumn("rlnOriginY");
string[] ColumnPriorX = table.GetColumn("rlnOriginXPrior");
string[] ColumnPriorY = table.GetColumn("rlnOriginYPrior");
float2[] ShiftPriors = new float2[NParticles];
for (int i = 0; i < NParticles; i++)
ShiftPriors[i] = new float2(float.Parse(ColumnPriorX[IndexOffset + i]),
float.Parse(ColumnPriorY[IndexOffset + i]));
float2[][] ParticleTracks = new float2[NParticles][];
for (int i = 0; i < NParticles; i++)
{
ParticleTracks[i] = new float2[Dimensions.Z];
for (int z = 0; z < Dimensions.Z; z++)
ParticleTracks[i][z] = new float2(float.Parse(ColumnOriginX[IndexOffset + z * NParticles + i]) - ShiftPriors[i].X,
float.Parse(ColumnOriginY[IndexOffset + z * NParticles + i]) - ShiftPriors[i].Y);
}
Image AverageFT = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true, true);
Image AveragePS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Image Weights = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Weights.Fill(1e-6f);
Image FrameParticles = new Image(IntPtr.Zero, new int3(DimsRegion.X * 2, DimsRegion.Y * 2, NParticles));
float StepZ = 1f / Math.Max(Dims.Z - 1, 1);
for (int z = 0; z < Dims.Z; z++)
{
float CoordZ = z * StepZ;
/*GPU.Extract(OriginalStack.GetDeviceSlice(z, Intent.Read),
FrameParticles.GetDevice(Intent.Write),
Dims.Slice(),
new int3(DimsRegion.X * 2, DimsRegion.Y * 2, 1),
Helper.ToInterleaved(Origins),
(uint)NParticles);*/
// Shift particles
{
float3[] Shifts = new float3[NParticles];
for (int i = 0; i < NParticles; i++)
{
float NormX = Math.Max(0.15f, Math.Min((float)Origins[i].X / Dims.X, 0.85f));
float NormY = Math.Max(0.15f, Math.Min((float)Origins[i].Y / Dims.Y, 0.85f));
float3 Coords = new float3(NormX, NormY, CoordZ);
Shifts[i] = new float3(GridMovementX.GetInterpolated(Coords) + ParticleTracks[i][z].X,
GridMovementY.GetInterpolated(Coords) + ParticleTracks[i][z].Y,
0f);
}
FrameParticles.ShiftSlices(Shifts);
}
Image FrameParticlesCropped = FrameParticles.AsPadded(new int2(DimsRegion));
Image FrameParticlesFT = FrameParticlesCropped.AsFFT();
FrameParticlesCropped.Dispose();
Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
PS.Fill(1f);
// Apply motion blur filter.
{
const int Samples = 11;
float StartZ = (z - 0.75f) * StepZ;
float StopZ = (z + 0.75f) * StepZ;
float2[] Shifts = new float2[Samples * NParticles];
for (int p = 0; p < NParticles; p++)
{
float NormX = Math.Max(0.15f, Math.Min((float)Origins[p].X / Dims.X, 0.85f));
float NormY = Math.Max(0.15f, Math.Min((float)Origins[p].Y / Dims.Y, 0.85f));
for (int zz = 0; zz < Samples; zz++)
{
float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz;
float3 Coords = new float3(NormX, NormY, zp);
Shifts[p * Samples + zz] = new float2(GridMovementX.GetInterpolated(Coords),
GridMovementY.GetInterpolated(Coords));
}
}
Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write),
DimsRegion,
Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()),
Samples,
(uint)NParticles);
PS.Multiply(MotionFilter);
//MotionFilter.WriteMRC("motion.mrc");
MotionFilter.Dispose();
}
// Apply CTF.
if (CTF != null)
{
CTFStruct[] Structs = new CTFStruct[NParticles];
for (int p = 0; p < NParticles; p++)
{
CTF Altered = CTF.GetCopy();
Altered.Defocus = (decimal)GridCTF.GetInterpolated(new float3(float.Parse(ColumnPosX[RowIndices[p]]) / Dims.X,
float.Parse(ColumnPosY[RowIndices[p]]) / Dims.Y,
z * StepZ));
Structs[p] = Altered.ToStruct();
}
Image CTFImage = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateCTF(CTFImage.GetDevice(Intent.Write),
CTFCoords.GetDevice(Intent.Read),
(uint)CTFCoords.ElementsSliceComplex,
Structs,
false,
(uint)NParticles);
//CTFImage.Abs();
PS.Multiply(CTFImage);
//CTFImage.WriteMRC("ctf.mrc");
CTFImage.Dispose();
}
// Apply dose weighting.
/*{
float3 NikoConst = new float3(0.245f, -1.665f, 2.81f);
// Niko's formula expects e-/A2/frame, we've got e-/px/frame -- convert!
float FrameDose = (float)MainWindow.Options.CorrectDosePerFrame * (z + 0.5f) / (PixelSize * PixelSize);
Image DoseImage = new Image(IntPtr.Zero, DimsRegion, true);
GPU.DoseWeighting(CTFFreq.GetDevice(Intent.Read),
DoseImage.GetDevice(Intent.Write),
(uint)DoseImage.ElementsSliceComplex,
new[] { FrameDose },
NikoConst,
1);
PS.MultiplySlices(DoseImage);
//DoseImage.WriteMRC("dose.mrc");
DoseImage.Dispose();
}*/
// Copy custom CTF into the CTF stack
GPU.CopyDeviceToDevice(PS.GetDevice(Intent.Read),
new IntPtr((long)CTFStack.GetDevice(Intent.Write) + CTFStack.ElementsSliceReal * NParticles * z * sizeof (float)),
CTFStack.ElementsSliceReal * NParticles);
Image PSAbs = new Image(PS.GetDevice(Intent.Read), new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
PSAbs.Abs();
FrameParticlesFT.Multiply(PSAbs);
AverageFT.Add(FrameParticlesFT);
Weights.Add(PSAbs);
PS.Multiply(PSAbs);
AveragePS.Add(PS);
PS.Dispose();
FrameParticlesFT.Dispose();
PSAbs.Dispose();
// Write paths to custom CTFs into the .star
for (int i = 0; i < NParticles; i++)
{
string ParticleCTFPath = (CTFStackIndex + 1).ToString("D6") + "@particlectf/" + RootName + ".mrcs";
table.SetRowValue(RowIndices[NParticles * z + i], "rlnCtfImage", ParticleCTFPath);
CTFStackIndex++;
}
}
FrameParticles.Dispose();
CTFCoords.Dispose();
CTFFreq.Dispose();
AverageFT.Divide(Weights);
AveragePS.Divide(Weights);
Weights.Dispose();
Image AverageParticles = AverageFT.AsIFFT();
AverageFT.Dispose();
GPU.NormParticles(AverageParticles.GetDevice(Intent.Read), AverageParticles.GetDevice(Intent.Write), DimsRegion, (uint)(90f / PixelSize), true, (uint)NParticles);
HeaderMRC ParticlesHeader = new HeaderMRC
{
Pixelsize = new float3(PixelSize, PixelSize, PixelSize)
};
AverageParticles.WriteMRC(ParticlesPath, ParticlesHeader);
AverageParticles.Dispose();
//OriginalStack.Dispose();
CTFStack.WriteMRC(DirectoryName + "particlectf/" + RootName + ".mrcs");
CTFStack.Dispose();
/*for (int i = 0; i < NParticles; i++)
{
string ParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs";
table.SetRowValue(RowIndices[i], "rlnImageName", ParticlePath);
}*/
AveragePS.Dispose();
//table.RemoveRows(RowIndices.Skip(NParticles).ToArray());
}
public void ExportParticlesMovie(Star tableIn, Star tableOut, MapHeader originalHeader, Image originalStack, int size, float particleradius, decimal scaleFactor)
{
int CurrentDevice = GPU.GetDevice();
#region Make sure directories exist.
lock (tableIn)
{
if (!Directory.Exists(ParticleMoviesDir))
Directory.CreateDirectory(ParticleMoviesDir);
if (!Directory.Exists(ParticleCTFMoviesDir))
Directory.CreateDirectory(ParticleCTFMoviesDir);
}
#endregion
#region Get row indices for all, and individual halves
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName))
RowIndices.Add(i);
//RowIndices = RowIndices.Take(13).ToList();
List<int> RowIndices1 = new List<int>();
List<int> RowIndices2 = new List<int>();
for (int i = 0; i < RowIndices.Count; i++)
if (tableIn.GetRowValue(RowIndices[i], "rlnRandomSubset") == "1")
RowIndices1.Add(RowIndices[i]);
else
RowIndices2.Add(RowIndices[i]);
#endregion
if (RowIndices.Count == 0)
return;
#region Auxiliary variables
List<int> TableOutIndices = new List<int>();
int3 Dims = originalHeader.Dimensions;
Dims.Z = 36;
int3 DimsRegion = new int3(size, size, 1);
int3 DimsPadded = new int3(size * 2, size * 2, 1);
int NParticles = RowIndices.Count;
int NParticles1 = RowIndices1.Count;
int NParticles2 = RowIndices2.Count;
float PixelSize = (float)CTF.PixelSize / 1.00f;
float PixelDelta = (float)CTF.PixelSizeDelta / 1.00f;
float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad;
#endregion
#region Prepare initial coordinates and shifts
string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX");
string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY");
string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX");
string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY");
int3[] Origins1 = new int3[NParticles1];
int3[] Origins2 = new int3[NParticles2];
float3[] ResidualShifts1 = new float3[NParticles1];
float3[] ResidualShifts2 = new float3[NParticles2];
lock (tableIn) // Writing to the table, better be on the safe side
{
// Half1: Add translational shifts to coordinates, sans the fractional part
for (int i = 0; i < NParticles1; i++)
{
float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices1[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY[RowIndices1[i]], CultureInfo.InvariantCulture)) * 1.00f;
float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices1[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginY[RowIndices1[i]], CultureInfo.InvariantCulture)) * 1.00f;
Origins1[i] = new int3((int)(Pos.X - Shift.X),
(int)(Pos.Y - Shift.Y),
0);
ResidualShifts1[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X),
-MathHelper.ResidualFraction(Pos.Y - Shift.Y),
0f);
tableIn.SetRowValue(RowIndices1[i], "rlnCoordinateX", Origins1[i].X.ToString());
tableIn.SetRowValue(RowIndices1[i], "rlnCoordinateY", Origins1[i].Y.ToString());
tableIn.SetRowValue(RowIndices1[i], "rlnOriginX", "0.0");
tableIn.SetRowValue(RowIndices1[i], "rlnOriginY", "0.0");
}
// Half2: Add translational shifts to coordinates, sans the fractional part
for (int i = 0; i < NParticles2; i++)
{
float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices2[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY[RowIndices2[i]], CultureInfo.InvariantCulture)) * 1.00f;
float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices2[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginY[RowIndices2[i]], CultureInfo.InvariantCulture)) * 1.00f;
Origins2[i] = new int3((int)(Pos.X - Shift.X),
(int)(Pos.Y - Shift.Y),
0);
ResidualShifts2[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X),
-MathHelper.ResidualFraction(Pos.Y - Shift.Y),
0f);
tableIn.SetRowValue(RowIndices2[i], "rlnCoordinateX", Origins2[i].X.ToString());
tableIn.SetRowValue(RowIndices2[i], "rlnCoordinateY", Origins2[i].Y.ToString());
tableIn.SetRowValue(RowIndices2[i], "rlnOriginX", "0.0");
tableIn.SetRowValue(RowIndices2[i], "rlnOriginY", "0.0");
}
}
#endregion
#region Allocate memory for particle and PS stacks
Image ParticleStackAll = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles * Dims.Z));
Image ParticleStack1 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1 * Dims.Z));
Image ParticleStack2 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2 * Dims.Z));
Image PSStackAll = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles * Dims.Z), true);
Image PSStack1 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1 * Dims.Z), true);
Image PSStack2 = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2 * Dims.Z), true);
Image FrameParticles1 = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles1));
Image FrameParticles2 = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles2));
float[][] ParticleStackData = ParticleStackAll.GetHost(Intent.Write);
float[][] ParticleStackData1 = ParticleStack1.GetHost(Intent.Write);
float[][] ParticleStackData2 = ParticleStack2.GetHost(Intent.Write);
float[][] PSStackData = PSStackAll.GetHost(Intent.Write);
float[][] PSStackData1 = PSStack1.GetHost(Intent.Write);
float[][] PSStackData2 = PSStack2.GetHost(Intent.Write);
#endregion
#region Create rows in outTable
lock (tableOut) // Creating rows in outTable, this absolutely needs to be staged sequentially
{
for (int z = 0; z < Dims.Z; z++)
{
for (int i = 0; i < NParticles; i++)
{
int Index = i < NParticles1 ? RowIndices1[i] : RowIndices2[i - NParticles1];
string OriParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs";
string ParticleName = (z * NParticles + i + 1).ToString("D6") + "@particlemovies/" + RootName + "_particles.mrcs";
string ParticleCTFName = (z * NParticles + i + 1).ToString("D6") + "@particlectfmovies/" + RootName + "_particlectf.mrcs";
List<string> NewRow = tableIn.GetRow(Index).Select(v => v).ToList(); // Get copy of original row.
NewRow[tableOut.GetColumnIndex("rlnOriginalParticleName")] = OriParticlePath;
NewRow[tableOut.GetColumnIndex("rlnAngleRotPrior")] = tableIn.GetRowValue(Index, "rlnAngleRot");
NewRow[tableOut.GetColumnIndex("rlnAngleTiltPrior")] = tableIn.GetRowValue(Index, "rlnAngleTilt");
NewRow[tableOut.GetColumnIndex("rlnAnglePsiPrior")] = tableIn.GetRowValue(Index, "rlnAnglePsi");
NewRow[tableOut.GetColumnIndex("rlnOriginXPrior")] = "0.0";
NewRow[tableOut.GetColumnIndex("rlnOriginYPrior")] = "0.0";
NewRow[tableOut.GetColumnIndex("rlnImageName")] = ParticleName;
NewRow[tableOut.GetColumnIndex("rlnCtfImage")] = ParticleCTFName;
NewRow[tableOut.GetColumnIndex("rlnMicrographName")] = (z + 1).ToString("D6") + "@stack/" + RootName + "_movie.mrcs";
TableOutIndices.Add(tableOut.RowCount);
tableOut.AddRow(NewRow);
}
}
}
#endregion
#region For every frame, extract particles from each half; shift, correct, and norm them
float StepZ = 1f / Math.Max(Dims.Z - 1, 1);
for (int z = 0; z < Dims.Z; z++)
{
float CoordZ = z * StepZ;
#region Extract, correct, and norm particles
#region Half 1
{
if (originalStack != null)
GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read),
FrameParticles1.GetDevice(Intent.Write),
Dims.Slice(),
DimsPadded,
Helper.ToInterleaved(Origins1.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()),
(uint)NParticles1);
// Shift particles
{
float3[] Shifts = new float3[NParticles1];
for (int i = 0; i < NParticles1; i++)
{
float3 Coords = new float3((float)Origins1[i].X / Dims.X, (float)Origins1[i].Y / Dims.Y, CoordZ);
Shifts[i] = ResidualShifts1[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f;
}
FrameParticles1.ShiftSlices(Shifts);
}
Image FrameParticlesCropped = FrameParticles1.AsPadded(new int2(DimsRegion));
Image FrameParticlesCorrected = FrameParticlesCropped.AsAnisotropyCorrected(new int2(DimsRegion),
PixelSize + PixelDelta / 2f,
PixelSize - PixelDelta / 2f,
PixelAngle,
6);
FrameParticlesCropped.Dispose();
GPU.NormParticles(FrameParticlesCorrected.GetDevice(Intent.Read),
FrameParticlesCorrected.GetDevice(Intent.Write),
DimsRegion,
(uint)(particleradius / PixelSize),
true,
(uint)NParticles1);
float[][] FrameParticlesCorrectedData = FrameParticlesCorrected.GetHost(Intent.Read);
for (int n = 0; n < NParticles1; n++)
{
ParticleStackData[z * NParticles + n] = FrameParticlesCorrectedData[n];
ParticleStackData1[z * NParticles1 + n] = FrameParticlesCorrectedData[n];
}
//FrameParticlesCorrected.WriteMRC("intermediate_particles1.mrc");
FrameParticlesCorrected.Dispose();
}
#endregion
#region Half 2
{
if (originalStack != null)
GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read),
FrameParticles2.GetDevice(Intent.Write),
Dims.Slice(),
DimsPadded,
Helper.ToInterleaved(Origins2.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()),
(uint)NParticles2);
// Shift particles
{
float3[] Shifts = new float3[NParticles2];
for (int i = 0; i < NParticles2; i++)
{
float3 Coords = new float3((float)Origins2[i].X / Dims.X, (float)Origins2[i].Y / Dims.Y, CoordZ);
Shifts[i] = ResidualShifts2[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f;
}
FrameParticles2.ShiftSlices(Shifts);
}
Image FrameParticlesCropped = FrameParticles2.AsPadded(new int2(DimsRegion));
Image FrameParticlesCorrected = FrameParticlesCropped.AsAnisotropyCorrected(new int2(DimsRegion),
PixelSize + PixelDelta / 2f,
PixelSize - PixelDelta / 2f,
PixelAngle,
6);
FrameParticlesCropped.Dispose();
GPU.NormParticles(FrameParticlesCorrected.GetDevice(Intent.Read),
FrameParticlesCorrected.GetDevice(Intent.Write),
DimsRegion,
(uint)(particleradius / PixelSize),
true,
(uint)NParticles2);
float[][] FrameParticlesCorrectedData = FrameParticlesCorrected.GetHost(Intent.Read);
for (int n = 0; n < NParticles2; n++)
{
ParticleStackData[z * NParticles + NParticles1 + n] = FrameParticlesCorrectedData[n];
ParticleStackData2[z * NParticles2 + n] = FrameParticlesCorrectedData[n];
}
//FrameParticlesCorrected.WriteMRC("intermediate_particles2.mrc");
FrameParticlesCorrected.Dispose();
}
#endregion
#endregion
#region PS Half 1
{
Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles1), true);
PS.Fill(1f);
// Apply motion blur filter.
#region Motion blur weighting
{
const int Samples = 11;
float StartZ = (z - 0.5f) * StepZ;
float StopZ = (z + 0.5f) * StepZ;
float2[] Shifts = new float2[Samples * NParticles1];
for (int p = 0; p < NParticles1; p++)
{
float NormX = (float)Origins1[p].X / Dims.X;
float NormY = (float)Origins1[p].Y / Dims.Y;
for (int zz = 0; zz < Samples; zz++)
{
float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz;
float3 Coords = new float3(NormX, NormY, zp);
Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords) * 1.00f;
}
}
Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles1), true);
GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write),
DimsRegion,
Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()),
Samples,
(uint)NParticles1);
PS.Multiply(MotionFilter);
//MotionFilter.WriteMRC("motion.mrc");
MotionFilter.Dispose();
}
#endregion
float[][] PSData = PS.GetHost(Intent.Read);
for (int n = 0; n < NParticles1; n++)
PSStackData[z * NParticles + n] = PSData[n];
//PS.WriteMRC("intermediate_ps1.mrc");
PS.Dispose();
}
#endregion
#region PS Half 2
{
Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles2), true);
PS.Fill(1f);
// Apply motion blur filter.
#region Motion blur weighting
{
const int Samples = 11;
float StartZ = (z - 0.5f) * StepZ;
float StopZ = (z + 0.5f) * StepZ;
float2[] Shifts = new float2[Samples * NParticles2];
for (int p = 0; p < NParticles2; p++)
{
float NormX = (float)Origins2[p].X / Dims.X;
float NormY = (float)Origins2[p].Y / Dims.Y;
for (int zz = 0; zz < Samples; zz++)
{
float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz;
float3 Coords = new float3(NormX, NormY, zp);
Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords) * 1.00f;
}
}
Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles2), true);
GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write),
DimsRegion,
Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()),
Samples,
(uint)NParticles2);
PS.Multiply(MotionFilter);
//MotionFilter.WriteMRC("motion.mrc");
MotionFilter.Dispose();
}
#endregion
float[][] PSData = PS.GetHost(Intent.Read);
for (int n = 0; n < NParticles2; n++)
PSStackData[z * NParticles + NParticles1 + n] = PSData[n];
//PS.WriteMRC("intermediate_ps2.mrc");
PS.Dispose();
}
#endregion
}
FrameParticles1.Dispose();
FrameParticles2.Dispose();
originalStack.FreeDevice();
#endregion
HeaderMRC ParticlesHeader = new HeaderMRC
{
Pixelsize = new float3(PixelSize, PixelSize, PixelSize)
};
// Do translation and rotation BFGS per particle
{
float MaxHigh = 2.6f;
CubicGrid GridX = new CubicGrid(new int3(NParticles1, 1, 2));
CubicGrid GridY = new CubicGrid(new int3(NParticles1, 1, 2));
CubicGrid GridRot = new CubicGrid(new int3(NParticles1, 1, 2));
CubicGrid GridTilt = new CubicGrid(new int3(NParticles1, 1, 2));
CubicGrid GridPsi = new CubicGrid(new int3(NParticles1, 1, 2));
int2 DimsCropped = new int2(DimsRegion / (MaxHigh / PixelSize / 2f)) / 2 * 2;
#region Get coordinates for CTF and Fourier-space shifts
Image CTFCoords;
Image ShiftFactors;
{
float2[] CTFCoordsData = new float2[(DimsCropped.X / 2 + 1) * DimsCropped.Y];
float2[] ShiftFactorsData = new float2[(DimsCropped.X / 2 + 1) * DimsCropped.Y];
for (int y = 0; y < DimsCropped.Y; y++)
for (int x = 0; x < DimsCropped.X / 2 + 1; x++)
{
int xx = x;
int yy = y < DimsCropped.Y / 2 + 1 ? y : y - DimsCropped.Y;
float xs = xx / (float)DimsRegion.X;
float ys = yy / (float)DimsRegion.Y;
float r = (float)Math.Sqrt(xs * xs + ys * ys);
float angle = (float)(Math.Atan2(yy, xx));
CTFCoordsData[y * (DimsCropped.X / 2 + 1) + x] = new float2(r / PixelSize, angle);
ShiftFactorsData[y * (DimsCropped.X / 2 + 1) + x] = new float2((float)-xx / DimsRegion.X * 2f * (float)Math.PI,
(float)-yy / DimsRegion.X * 2f * (float)Math.PI);
}
CTFCoords = new Image(CTFCoordsData, new int3(DimsCropped), true);
ShiftFactors = new Image(ShiftFactorsData, new int3(DimsCropped), true);
}
#endregion
#region Get inverse sigma2 spectrum for this micrograph from Relion's model.star
Image Sigma2Noise = new Image(new int3(DimsCropped), true);
{
int GroupNumber = int.Parse(tableIn.GetRowValue(RowIndices[0], "rlnGroupNumber"));
//Star SigmaTable = new Star("D:\\rado27\\Refine3D\\run1_ct5_it009_half1_model.star", "data_model_group_" + GroupNumber);
Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber);
float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray();
float[] Sigma2NoiseData = Sigma2Noise.GetHost(Intent.Write)[0];
Helper.ForEachElementFT(DimsCropped, (x, y, xx, yy, r, angle) =>
{
int ir = (int)r;
float val = 0;
if (ir < SigmaValues.Length && ir >= size / (50f / PixelSize) && ir < DimsCropped.X / 2)
{
if (SigmaValues[ir] != 0f)
val = 1f / SigmaValues[ir];
}
Sigma2NoiseData[y * (DimsCropped.X / 2 + 1) + x] = val;
});
float MaxSigma = MathHelper.Max(Sigma2NoiseData);
for (int i = 0; i < Sigma2NoiseData.Length; i++)
Sigma2NoiseData[i] /= MaxSigma;
Sigma2Noise.RemapToFT();
}
//Sigma2Noise.WriteMRC("d_sigma2noise.mrc");
#endregion
#region Initialize particle angles for both halves
float3[] ParticleAngles1 = new float3[NParticles1];
float3[] ParticleAngles2 = new float3[NParticles2];
for (int p = 0; p < NParticles1; p++)
ParticleAngles1[p] = new float3(float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAngleRot")),
float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAngleTilt")),
float.Parse(tableIn.GetRowValue(RowIndices1[p], "rlnAnglePsi")));
for (int p = 0; p < NParticles2; p++)
ParticleAngles2[p] = new float3(float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAngleRot")),
float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAngleTilt")),
float.Parse(tableIn.GetRowValue(RowIndices2[p], "rlnAnglePsi")));
#endregion
#region Prepare masks
Image Masks1, Masks2;
{
// Half 1
{
Image Volume = StageDataLoad.LoadMap(MainWindow.Options.MaskPath, new int2(1, 1), 0, typeof (float));
Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
Image VolMaskFT = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
Image MasksFT = VolMaskFT.AsProjections(ParticleAngles1.Select(v => new float3(v.X * Helper.ToRad, v.Y * Helper.ToRad, v.Z * Helper.ToRad)).ToArray(),
new int2(DimsRegion),
MainWindow.Options.ProjectionOversample);
VolMaskFT.Dispose();
Masks1 = MasksFT.AsIFFT();
MasksFT.Dispose();
Masks1.RemapFromFT();
Parallel.ForEach(Masks1.GetHost(Intent.ReadWrite), slice =>
{
for (int i = 0; i < slice.Length; i++)
slice[i] = (Math.Max(2f, Math.Min(50f, slice[i])) - 2) / 48f;
});
}
// Half 2
{
Image Volume = StageDataLoad.LoadMap(MainWindow.Options.MaskPath, new int2(1, 1), 0, typeof(float));
Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
Image VolMaskFT = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
Image MasksFT = VolMaskFT.AsProjections(ParticleAngles2.Select(v => new float3(v.X * Helper.ToRad, v.Y * Helper.ToRad, v.Z * Helper.ToRad)).ToArray(),
new int2(DimsRegion),
MainWindow.Options.ProjectionOversample);
VolMaskFT.Dispose();
Masks2 = MasksFT.AsIFFT();
MasksFT.Dispose();
Masks2.RemapFromFT();
Parallel.ForEach(Masks2.GetHost(Intent.ReadWrite), slice =>
{
for (int i = 0; i < slice.Length; i++)
slice[i] = (Math.Max(2f, Math.Min(50f, slice[i])) - 2) / 48f;
});
}
}
//Masks1.WriteMRC("d_masks1.mrc");
//Masks2.WriteMRC("d_masks2.mrc");
#endregion
#region Load and prepare references for both halves
Image VolRefFT1;
{
Image Volume = StageDataLoad.LoadMap(MainWindow.Options.ReferencePath, new int2(1, 1), 0, typeof(float));
//GPU.Normalize(Volume.GetDevice(Intent.Read), Volume.GetDevice(Intent.Write), (uint)Volume.ElementsReal, 1);
Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
VolRefFT1 = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
}
VolRefFT1.FreeDevice();
Image VolRefFT2;
{
// Can't assume there is a second half, but certainly hope so
string Half2Path = MainWindow.Options.ReferencePath;
if (Half2Path.Contains("half1"))
Half2Path = Half2Path.Replace("half1", "half2");
Image Volume = StageDataLoad.LoadMap(Half2Path, new int2(1, 1), 0, typeof(float));
//GPU.Normalize(Volume.GetDevice(Intent.Read), Volume.GetDevice(Intent.Write), (uint)Volume.ElementsReal, 1);
Image VolumePadded = Volume.AsPadded(Volume.Dims * MainWindow.Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
VolRefFT2 = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
}
VolRefFT2.FreeDevice();
#endregion
#region Prepare particles: group and resize to DimsCropped
Image ParticleStackFT1 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles1 * Dims.Z / 3), true, true);
{
GPU.CreatePolishing(ParticleStack1.GetDevice(Intent.Read),
ParticleStackFT1.GetDevice(Intent.Write),
Masks1.GetDevice(Intent.Read),
new int2(DimsRegion),
DimsCropped,
NParticles1,
Dims.Z);
ParticleStack1.FreeDevice();
Masks1.Dispose();
/*Image Amps = ParticleStackFT1.AsIFFT();
Amps.RemapFromFT();
Amps.WriteMRC("d_particlestackft1.mrc");
Amps.Dispose();*/
}
Image ParticleStackFT2 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles2 * Dims.Z / 3), true, true);
{
GPU.CreatePolishing(ParticleStack2.GetDevice(Intent.Read),
ParticleStackFT2.GetDevice(Intent.Write),
Masks2.GetDevice(Intent.Read),
new int2(DimsRegion),
DimsCropped,
NParticles2,
Dims.Z);
ParticleStack1.FreeDevice();
Masks2.Dispose();
/*Image Amps = ParticleStackFT2.AsIFFT();
Amps.RemapFromFT();
Amps.WriteMRC("d_particlestackft2.mrc");
Amps.Dispose();*/
}
#endregion
Image Projections1 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles1 * Dims.Z / 3), true, true);
Image Projections2 = new Image(IntPtr.Zero, new int3(DimsCropped.X, DimsCropped.Y, NParticles2 * Dims.Z / 3), true, true);
Image Shifts1 = new Image(new int3(NParticles1, Dims.Z / 3, 1), false, true);
float3[] Angles1 = new float3[NParticles1 * Dims.Z / 3];
CTFStruct[] CTFParams1 = new CTFStruct[NParticles1 * Dims.Z / 3];
Image Shifts2 = new Image(new int3(NParticles2, Dims.Z / 3, 1), false, true);
float3[] Angles2 = new float3[NParticles2 * Dims.Z / 3];
CTFStruct[] CTFParams2 = new CTFStruct[NParticles2 * Dims.Z / 3];
float[] BFacs =
{
-3.86f,
0.00f,
-17.60f,
-35.24f,
-57.48f,
-93.51f,
-139.57f,
-139.16f
};
#region Initialize defocus and phase shift values
float[] InitialDefoci1 = new float[NParticles1 * (Dims.Z / 3)];
float[] InitialPhaseShifts1 = new float[NParticles1 * (Dims.Z / 3)];
float[] InitialDefoci2 = new float[NParticles2 * (Dims.Z / 3)];
float[] InitialPhaseShifts2 = new float[NParticles2 * (Dims.Z / 3)];
for (int z = 0, i = 0; z < Dims.Z / 3; z++)
{
for (int p = 0; p < NParticles1; p++, i++)
{
InitialDefoci1[i] = GridCTF.GetInterpolated(new float3((float)Origins1[p].X / Dims.X,
(float)Origins1[p].Y / Dims.Y,
(float)(z * 3 + 1) / (Dims.Z - 1)));
InitialPhaseShifts1[i] = GridCTFPhase.GetInterpolated(new float3((float)Origins1[p].X / Dims.X,
(float)Origins1[p].Y / Dims.Y,
(float)(z * 3 + 1) / (Dims.Z - 1)));
CTF Alt = CTF.GetCopy();
Alt.PixelSize = (decimal)PixelSize;
Alt.PixelSizeDelta = 0;
Alt.Defocus = (decimal)InitialDefoci1[i];
Alt.PhaseShift = (decimal)InitialPhaseShifts1[i];
//Alt.Bfactor = (decimal)BFacs[z];
CTFParams1[i] = Alt.ToStruct();
}
}
for (int z = 0, i = 0; z < Dims.Z / 3; z++)
{
for (int p = 0; p < NParticles2; p++, i++)
{
InitialDefoci2[i] = GridCTF.GetInterpolated(new float3((float)Origins2[p].X / Dims.X,
(float)Origins2[p].Y / Dims.Y,
(float)(z * 3 + 1) / (Dims.Z - 1)));
InitialPhaseShifts2[i] = GridCTFPhase.GetInterpolated(new float3((float)Origins2[p].X / Dims.X,
(float)Origins2[p].Y / Dims.Y,
(float)(z * 3 + 1) / (Dims.Z - 1)));
CTF Alt = CTF.GetCopy();
Alt.PixelSize = (decimal)PixelSize;
Alt.PixelSizeDelta = 0;
Alt.Defocus = (decimal)InitialDefoci2[i];
Alt.PhaseShift = (decimal)InitialPhaseShifts2[i];
//Alt.Bfactor = (decimal)BFacs[z];
CTFParams2[i] = Alt.ToStruct();
}
}
#endregion
#region SetPositions lambda
Action<double[]> SetPositions = input =>
{
float BorderZ = 0.5f / (Dims.Z / 3);
GridX = new CubicGrid(new int3(NParticles, 1, 2), input.Take(NParticles * 2).Select(v => (float)v).ToArray());
GridY = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 1).Take(NParticles * 2).Select(v => (float)v).ToArray());
float[] AlteredX = GridX.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
float[] AlteredY = GridY.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
GridRot = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 2).Take(NParticles * 2).Select(v => (float)v).ToArray());
GridTilt = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 3).Take(NParticles * 2).Select(v => (float)v).ToArray());
GridPsi = new CubicGrid(new int3(NParticles, 1, 2), input.Skip(NParticles * 2 * 4).Take(NParticles * 2).Select(v => (float)v).ToArray());
float[] AlteredRot = GridRot.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
float[] AlteredTilt = GridTilt.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
float[] AlteredPsi = GridPsi.GetInterpolatedNative(new int3(NParticles, 1, Dims.Z / 3), new float3(0, 0, BorderZ));
float[] ShiftData1 = Shifts1.GetHost(Intent.Write)[0];
float[] ShiftData2 = Shifts2.GetHost(Intent.Write)[0];
for (int z = 0; z < Dims.Z / 3; z++)
{
// Half 1
for (int p = 0; p < NParticles1; p++)
{
int i1 = z * NParticles1 + p;
int i = z * NParticles + p;
ShiftData1[i1 * 2] = AlteredX[i];
ShiftData1[i1 * 2 + 1] = AlteredY[i];
Angles1[i1] = new float3(AlteredRot[i] * 1f * Helper.ToRad, AlteredTilt[i] * 1f * Helper.ToRad, AlteredPsi[i] * 1f * Helper.ToRad);
}
// Half 2
for (int p = 0; p < NParticles2; p++)
{
int i2 = z * NParticles2 + p;
int i = z * NParticles + NParticles1 + p;
ShiftData2[i2 * 2] = AlteredX[i];
ShiftData2[i2 * 2 + 1] = AlteredY[i];
Angles2[i2] = new float3(AlteredRot[i] * 1f * Helper.ToRad, AlteredTilt[i] * 1f * Helper.ToRad, AlteredPsi[i] * 1f * Helper.ToRad);
}
}
};
#endregion
#region EvalIndividuals lambda
Func<double[], bool, double[]> EvalIndividuals = (input, redoProj) =>
{
SetPositions(input);
if (redoProj)
{
GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Write),
VolRefFT1.Dims,
DimsCropped,
Helper.ToInterleaved(Angles1),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles1 * Dims.Z / 3));
GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Write),
VolRefFT2.Dims,
DimsCropped,
Helper.ToInterleaved(Angles2),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles2 * Dims.Z / 3));
}
/*{
Image ProjectionsAmps = Projections1.AsIFFT();
ProjectionsAmps.RemapFromFT();
ProjectionsAmps.WriteMRC("d_projectionsamps1.mrc");
ProjectionsAmps.Dispose();
}
{
Image ProjectionsAmps = Projections2.AsIFFT();
ProjectionsAmps.RemapFromFT();
ProjectionsAmps.WriteMRC("d_projectionsamps2.mrc");
ProjectionsAmps.Dispose();
}*/
float[] Diff1 = new float[NParticles1];
float[] DiffAll1 = new float[NParticles1 * (Dims.Z / 3)];
GPU.PolishingGetDiff(ParticleStackFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
CTFCoords.GetDevice(Intent.Read),
CTFParams1,
Sigma2Noise.GetDevice(Intent.Read),
DimsCropped,
Shifts1.GetDevice(Intent.Read),
Diff1,
DiffAll1,
(uint)NParticles1,
(uint)Dims.Z / 3);
float[] Diff2 = new float[NParticles2];
float[] DiffAll2 = new float[NParticles2 * (Dims.Z / 3)];
GPU.PolishingGetDiff(ParticleStackFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
CTFCoords.GetDevice(Intent.Read),
CTFParams2,
Sigma2Noise.GetDevice(Intent.Read),
DimsCropped,
Shifts2.GetDevice(Intent.Read),
Diff2,
DiffAll2,
(uint)NParticles2,
(uint)Dims.Z / 3);
double[] DiffBoth = new double[NParticles];
for (int p = 0; p < NParticles1; p++)
DiffBoth[p] = Diff1[p];
for (int p = 0; p < NParticles2; p++)
DiffBoth[NParticles1 + p] = Diff2[p];
return DiffBoth;
};
#endregion
Func<double[], double> Eval = input =>
{
float Result = MathHelper.Mean(EvalIndividuals(input, true).Select(v => (float)v)) * NParticles;
Debug.WriteLine(Result);
return Result;
};
Func<double[], double[]> Grad = input =>
{
SetPositions(input);
GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Write),
VolRefFT1.Dims,
DimsCropped,
Helper.ToInterleaved(Angles1),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles1 * Dims.Z / 3));
GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Write),
VolRefFT2.Dims,
DimsCropped,
Helper.ToInterleaved(Angles2),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles2 * Dims.Z / 3));
double[] Result = new double[input.Length];
double Step = 0.1;
int NVariables = 10; // (Shift + Euler) * 2
for (int v = 0; v < NVariables; v++)
{
double[] InputPlus = new double[input.Length];
for (int i = 0; i < input.Length; i++)
{
int iv = i / NParticles;
if (iv == v)
InputPlus[i] = input[i] + Step;
else
InputPlus[i] = input[i];
}
double[] ScorePlus = EvalIndividuals(InputPlus, v >= 4);
double[] InputMinus = new double[input.Length];
for (int i = 0; i < input.Length; i++)
{
int iv = i / NParticles;
if (iv == v)
InputMinus[i] = input[i] - Step;
else
InputMinus[i] = input[i];
}
double[] ScoreMinus = EvalIndividuals(InputMinus, v >= 4);
for (int i = 0; i < NParticles; i++)
Result[v * NParticles + i] = (ScorePlus[i] - ScoreMinus[i]) / (Step * 2.0);
}
return Result;
};
double[] StartParams = new double[NParticles * 2 * 5];
for (int i = 0; i < NParticles * 2; i++)
{
int p = i % NParticles;
StartParams[NParticles * 2 * 0 + i] = 0;
StartParams[NParticles * 2 * 1 + i] = 0;
if (p < NParticles1)
{
StartParams[NParticles * 2 * 2 + i] = ParticleAngles1[p].X / 1.0;
StartParams[NParticles * 2 * 3 + i] = ParticleAngles1[p].Y / 1.0;
StartParams[NParticles * 2 * 4 + i] = ParticleAngles1[p].Z / 1.0;
}
else
{
p -= NParticles1;
StartParams[NParticles * 2 * 2 + i] = ParticleAngles2[p].X / 1.0;
StartParams[NParticles * 2 * 3 + i] = ParticleAngles2[p].Y / 1.0;
StartParams[NParticles * 2 * 4 + i] = ParticleAngles2[p].Z / 1.0;
}
}
BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Grad);
Optimizer.Epsilon = 3e-7;
Optimizer.Maximize(StartParams);
#region Calculate particle quality for high frequencies
float[] ParticleQuality = new float[NParticles * (Dims.Z / 3)];
{
Sigma2Noise.Dispose();
Sigma2Noise = new Image(new int3(DimsCropped), true);
{
int GroupNumber = int.Parse(tableIn.GetRowValue(RowIndices[0], "rlnGroupNumber"));
//Star SigmaTable = new Star("D:\\rado27\\Refine3D\\run1_ct5_it009_half1_model.star", "data_model_group_" + GroupNumber);
Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber);
float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray();
float[] Sigma2NoiseData = Sigma2Noise.GetHost(Intent.Write)[0];
Helper.ForEachElementFT(DimsCropped, (x, y, xx, yy, r, angle) =>
{
int ir = (int)r;
float val = 0;
if (ir < SigmaValues.Length && ir >= size / (4.0f / PixelSize) && ir < DimsCropped.X / 2)
{
if (SigmaValues[ir] != 0f)
val = 1f / SigmaValues[ir] / (ir * 3.14f);
}
Sigma2NoiseData[y * (DimsCropped.X / 2 + 1) + x] = val;
});
float MaxSigma = MathHelper.Max(Sigma2NoiseData);
for (int i = 0; i < Sigma2NoiseData.Length; i++)
Sigma2NoiseData[i] /= MaxSigma;
Sigma2Noise.RemapToFT();
}
//Sigma2Noise.WriteMRC("d_sigma2noiseScore.mrc");
SetPositions(StartParams);
GPU.ProjectForward(VolRefFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Write),
VolRefFT1.Dims,
DimsCropped,
Helper.ToInterleaved(Angles1),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles1 * Dims.Z / 3));
GPU.ProjectForward(VolRefFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Write),
VolRefFT2.Dims,
DimsCropped,
Helper.ToInterleaved(Angles2),
MainWindow.Options.ProjectionOversample,
(uint)(NParticles2 * Dims.Z / 3));
float[] Diff1 = new float[NParticles1];
float[] ParticleQuality1 = new float[NParticles1 * (Dims.Z / 3)];
GPU.PolishingGetDiff(ParticleStackFT1.GetDevice(Intent.Read),
Projections1.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
CTFCoords.GetDevice(Intent.Read),
CTFParams1,
Sigma2Noise.GetDevice(Intent.Read),
DimsCropped,
Shifts1.GetDevice(Intent.Read),
Diff1,
ParticleQuality1,
(uint)NParticles1,
(uint)Dims.Z / 3);
float[] Diff2 = new float[NParticles2];
float[] ParticleQuality2 = new float[NParticles2 * (Dims.Z / 3)];
GPU.PolishingGetDiff(ParticleStackFT2.GetDevice(Intent.Read),
Projections2.GetDevice(Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
CTFCoords.GetDevice(Intent.Read),
CTFParams2,
Sigma2Noise.GetDevice(Intent.Read),
DimsCropped,
Shifts2.GetDevice(Intent.Read),
Diff2,
ParticleQuality2,
(uint)NParticles2,
(uint)Dims.Z / 3);
for (int z = 0; z < Dims.Z / 3; z++)
{
for (int p = 0; p < NParticles1; p++)
ParticleQuality[z * NParticles + p] = ParticleQuality1[z * NParticles1 + p];
for (int p = 0; p < NParticles2; p++)
ParticleQuality[z * NParticles + NParticles1 + p] = ParticleQuality2[z * NParticles2 + p];
}
}
#endregion
lock (tableOut) // Only changing cell values, but better be safe in case table implementation changes later
{
GridX = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Take(NParticles * 2).Select(v => (float)v).ToArray());
GridY = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 1).Take(NParticles * 2).Select(v => (float)v).ToArray());
float[] AlteredX = GridX.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
float[] AlteredY = GridY.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
GridRot = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 2).Take(NParticles * 2).Select(v => (float)v).ToArray());
GridTilt = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 3).Take(NParticles * 2).Select(v => (float)v).ToArray());
GridPsi = new CubicGrid(new int3(NParticles, 1, 2), Optimizer.Solution.Skip(NParticles * 2 * 4).Take(NParticles * 2).Select(v => (float)v).ToArray());
float[] AlteredRot = GridRot.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
float[] AlteredTilt = GridTilt.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
float[] AlteredPsi = GridPsi.GetInterpolated(new int3(NParticles, 1, Dims.Z), new float3(0, 0, 0));
for (int i = 0; i < TableOutIndices.Count; i++)
{
int p = i % NParticles;
int z = i / NParticles;
float Defocus = 0, PhaseShift = 0;
if (p < NParticles1)
{
Defocus = GridCTF.GetInterpolated(new float3((float)Origins1[p].X / Dims.X,
(float)Origins1[p].Y / Dims.Y,
(float)z / (Dims.Z - 1)));
PhaseShift = GridCTFPhase.GetInterpolated(new float3((float)Origins1[p].X / Dims.X,
(float)Origins1[p].Y / Dims.Y,
(float)z / (Dims.Z - 1)));
}
else
{
p -= NParticles1;
Defocus = GridCTF.GetInterpolated(new float3((float)Origins2[p].X / Dims.X,
(float)Origins2[p].Y / Dims.Y,
(float)z / (Dims.Z - 1)));
PhaseShift = GridCTFPhase.GetInterpolated(new float3((float)Origins2[p].X / Dims.X,
(float)Origins2[p].Y / Dims.Y,
(float)z / (Dims.Z - 1)));
}
tableOut.SetRowValue(TableOutIndices[i], "rlnOriginX", AlteredX[i].ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnOriginY", AlteredY[i].ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnAngleRot", (-AlteredRot[i]).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnAngleTilt", (-AlteredTilt[i]).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnAnglePsi", (-AlteredPsi[i]).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnDefocusU", ((Defocus + (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnDefocusV", ((Defocus - (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnPhaseShift", (PhaseShift * 180f).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnCtfFigureOfMerit", (ParticleQuality[(z / 3) * NParticles + (i % NParticles)]).ToString(CultureInfo.InvariantCulture));
tableOut.SetRowValue(TableOutIndices[i], "rlnMagnification", ((float)MainWindow.Options.CTFDetectorPixel * 10000f / PixelSize).ToString());
}
}
VolRefFT1.Dispose();
VolRefFT2.Dispose();
Projections1.Dispose();
Projections2.Dispose();
Sigma2Noise.Dispose();
ParticleStackFT1.Dispose();
ParticleStackFT2.Dispose();
Shifts1.Dispose();
Shifts2.Dispose();
CTFCoords.Dispose();
ShiftFactors.Dispose();
ParticleStack1.Dispose();
ParticleStack2.Dispose();
PSStack1.Dispose();
PSStack2.Dispose();
}
// Write movies to disk asynchronously, so the next micrograph can load.
Thread SaveThread = new Thread(() =>
{
GPU.SetDevice(CurrentDevice); // It's a separate thread, make sure it's using the same device
ParticleStackAll.WriteMRC(ParticleMoviesPath, ParticlesHeader);
//ParticleStackAll.WriteMRC("D:\\gala\\particlemovies\\" + RootName + "_particles.mrcs", ParticlesHeader);
ParticleStackAll.Dispose();
PSStackAll.WriteMRC(ParticleCTFMoviesPath);
//PSStackAll.WriteMRC("D:\\rado27\\particlectfmovies\\" + RootName + "_particlectf.mrcs");
PSStackAll.Dispose();
});
SaveThread.Start();
}
public void ExportParticles(Star tableIn, Star tableOut, MapHeader originalHeader, Image originalStack, int size, float particleradius, decimal scaleFactor)
{
if (!tableIn.HasColumn("rlnAutopickFigureOfMerit"))
tableIn.AddColumn("rlnAutopickFigureOfMerit");
List<int> RowIndices = new List<int>();
string[] ColumnMicrographName = tableIn.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnMicrographName.Length; i++)
if (ColumnMicrographName[i].Contains(RootName))
RowIndices.Add(i);
if (RowIndices.Count == 0)
return;
if (!Directory.Exists(ParticlesDir))
Directory.CreateDirectory(ParticlesDir);
if (!Directory.Exists(ParticleCTFDir))
Directory.CreateDirectory(ParticleCTFDir);
int3 Dims = originalHeader.Dimensions;
int3 DimsRegion = new int3(size, size, 1);
int3 DimsPadded = new int3(size * 2, size * 2, 1);
int NParticles = RowIndices.Count;
float PixelSize = (float)CTF.PixelSize;
float PixelDelta = (float)CTF.PixelSizeDelta;
float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad;
/*Image CTFCoords;
Image CTFFreq;
{
float2[] CTFCoordsData = new float2[(DimsRegion.X / 2 + 1) * DimsRegion.Y];
float[] CTFFreqData = new float[(DimsRegion.X / 2 + 1) * DimsRegion.Y];
for (int y = 0; y < DimsRegion.Y; y++)
for (int x = 0; x < DimsRegion.X / 2 + 1; x++)
{
int xx = x;
int yy = y < DimsRegion.Y / 2 + 1 ? y : y - DimsRegion.Y;
float xs = xx / (float)DimsRegion.X;
float ys = yy / (float)DimsRegion.Y;
float r = (float)Math.Sqrt(xs * xs + ys * ys);
float angle = (float)(Math.Atan2(yy, xx));
float CurrentPixelSize = PixelSize + PixelDelta * (float)Math.Cos(2f * (angle - PixelAngle));
CTFCoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, angle);
CTFFreqData[y * (DimsRegion.X / 2 + 1) + x] = r / CurrentPixelSize;
}
CTFCoords = new Image(CTFCoordsData, DimsRegion.Slice(), true);
CTFFreq = new Image(CTFFreqData, DimsRegion.Slice(), true);
}*/
string[] ColumnPosX = tableIn.GetColumn("rlnCoordinateX");
string[] ColumnPosY = tableIn.GetColumn("rlnCoordinateY");
string[] ColumnOriginX = tableIn.GetColumn("rlnOriginX");
string[] ColumnOriginY = tableIn.GetColumn("rlnOriginY");
int3[] Origins = new int3[NParticles];
float3[] ResidualShifts = new float3[NParticles];
for (int i = 0; i < NParticles; i++)
{
float2 Pos = new float2(float.Parse(ColumnPosX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY[RowIndices[i]], CultureInfo.InvariantCulture)) * 1.00f;
float2 Shift = new float2(float.Parse(ColumnOriginX[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnOriginY[RowIndices[i]], CultureInfo.InvariantCulture)) * 1.00f;
Origins[i] = new int3((int)(Pos.X - Shift.X),
(int)(Pos.Y - Shift.Y),
0);
ResidualShifts[i] = new float3(-MathHelper.ResidualFraction(Pos.X - Shift.X),
-MathHelper.ResidualFraction(Pos.Y - Shift.Y),
0f);
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateX", Origins[i].X.ToString());
tableIn.SetRowValue(RowIndices[i], "rlnCoordinateY", Origins[i].Y.ToString());
tableIn.SetRowValue(RowIndices[i], "rlnOriginX", "0.0");
tableIn.SetRowValue(RowIndices[i], "rlnOriginY", "0.0");
}
Image AverageFT = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true, true);
Image AveragePS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Image Weights = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
Weights.Fill(1e-6f);
Image FrameParticles = new Image(IntPtr.Zero, new int3(DimsPadded.X, DimsPadded.Y, NParticles));
float StepZ = 1f / Math.Max(Dims.Z - 1, 1);
for (int z = 0; z < Dims.Z; z++)
{
float CoordZ = z * StepZ;
if (originalStack != null)
GPU.Extract(originalStack.GetDeviceSlice(z, Intent.Read),
FrameParticles.GetDevice(Intent.Write),
Dims.Slice(),
DimsPadded,
Helper.ToInterleaved(Origins.Select(v => new int3(v.X - DimsPadded.X / 2, v.Y - DimsPadded.Y / 2, 0)).ToArray()),
(uint)NParticles);
// Shift particles
{
float3[] Shifts = new float3[NParticles];
for (int i = 0; i < NParticles; i++)
{
float3 Coords = new float3((float)Origins[i].X / Dims.X, (float)Origins[i].Y / Dims.Y, CoordZ);
Shifts[i] = ResidualShifts[i] + new float3(GetShiftFromPyramid(Coords)) * 1.00f;
}
FrameParticles.ShiftSlices(Shifts);
}
Image FrameParticlesCropped = FrameParticles.AsPadded(new int2(DimsRegion));
Image FrameParticlesFT = FrameParticlesCropped.AsFFT();
FrameParticlesCropped.Dispose();
//Image PS = new Image(new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
//PS.Fill(1f);
// Apply motion blur filter.
#region Motion blur weighting
/*{
const int Samples = 11;
float StartZ = (z - 0.5f) * StepZ;
float StopZ = (z + 0.5f) * StepZ;
float2[] Shifts = new float2[Samples * NParticles];
for (int p = 0; p < NParticles; p++)
{
float NormX = (float)Origins[p].X / Dims.X;
float NormY = (float)Origins[p].Y / Dims.Y;
for (int zz = 0; zz < Samples; zz++)
{
float zp = StartZ + (StopZ - StartZ) / (Samples - 1) * zz;
float3 Coords = new float3(NormX, NormY, zp);
Shifts[p * Samples + zz] = GetShiftFromPyramid(Coords);
}
}
Image MotionFilter = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateMotionBlur(MotionFilter.GetDevice(Intent.Write),
DimsRegion,
Helper.ToInterleaved(Shifts.Select(v => new float3(v.X, v.Y, 0)).ToArray()),
Samples,
(uint)NParticles);
PS.Multiply(MotionFilter);
//MotionFilter.WriteMRC("motion.mrc");
MotionFilter.Dispose();
}*/
#endregion
// Apply CTF.
#region CTF weighting
/*if (CTF != null)
{
CTFStruct[] Structs = new CTFStruct[NParticles];
for (int p = 0; p < NParticles; p++)
{
CTF Altered = CTF.GetCopy();
Altered.Defocus = (decimal)GridCTF.GetInterpolated(new float3(Origins[p].X / Dims.X,
Origins[p].Y / Dims.Y,
z * StepZ));
Structs[p] = Altered.ToStruct();
}
Image CTFImage = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
GPU.CreateCTF(CTFImage.GetDevice(Intent.Write),
CTFCoords.GetDevice(Intent.Read),
(uint)CTFCoords.ElementsSliceComplex,
Structs,
false,
(uint)NParticles);
//CTFImage.Abs();
PS.Multiply(CTFImage);
//CTFImage.WriteMRC("ctf.mrc");
CTFImage.Dispose();
}*/
#endregion
// Apply dose.
#region Dose weighting
/*{
float3 NikoConst = new float3(0.245f, -1.665f, 2.81f);
// Niko's formula expects e-/A2/frame, we've got e-/px/frame -- convert!
float FrameDose = (float)MainWindow.Options.CorrectDosePerFrame * (z + 0.5f) / (PixelSize * PixelSize);
Image DoseImage = new Image(IntPtr.Zero, DimsRegion, true);
GPU.DoseWeighting(CTFFreq.GetDevice(Intent.Read),
DoseImage.GetDevice(Intent.Write),
(uint)DoseImage.ElementsSliceComplex,
new[] { FrameDose },
NikoConst,
1);
PS.MultiplySlices(DoseImage);
//DoseImage.WriteMRC("dose.mrc");
DoseImage.Dispose();
}*/
#endregion
//Image PSAbs = new Image(PS.GetDevice(Intent.Read), new int3(DimsRegion.X, DimsRegion.Y, NParticles), true);
//PSAbs.Abs();
//FrameParticlesFT.Multiply(PS);
AverageFT.Add(FrameParticlesFT);
//Weights.Add(PSAbs);
//PS.Multiply(PS);
//AveragePS.Add(PS);
//PS.Dispose();
FrameParticlesFT.Dispose();
//PSAbs.Dispose();
}
FrameParticles.Dispose();
//CTFCoords.Dispose();
//AverageFT.Divide(Weights);
//AveragePS.Divide(Weights);
//AverageFT.Multiply(AveragePS);
Weights.Dispose();
Image AverageParticlesUncorrected = AverageFT.AsIFFT();
AverageFT.Dispose();
Image AverageParticles = AverageParticlesUncorrected.AsAnisotropyCorrected(new int2(DimsRegion),
(float)(CTF.PixelSize + CTF.PixelSizeDelta / 2M),
(float)(CTF.PixelSize - CTF.PixelSizeDelta / 2M),
(float)CTF.PixelSizeAngle * Helper.ToRad,
8);
AverageParticlesUncorrected.Dispose();
GPU.NormParticles(AverageParticles.GetDevice(Intent.Read),
AverageParticles.GetDevice(Intent.Write),
DimsRegion,
(uint)(particleradius / (PixelSize / 1.00f)),
true,
(uint)NParticles);
HeaderMRC ParticlesHeader = new HeaderMRC
{
Pixelsize = new float3(PixelSize, PixelSize, PixelSize)
};
AverageParticles.WriteMRC(ParticlesPath, ParticlesHeader);
AverageParticles.Dispose();
//AveragePS.WriteMRC(ParticleCTFPath, ParticlesHeader);
AveragePS.Dispose();
float[] DistanceWeights = new float[NParticles];
for (int p1 = 0; p1 < NParticles - 1; p1++)
{
float2 Pos1 = new float2(Origins[p1].X, Origins[p1].Y);
for (int p2 = p1 + 1; p2 < NParticles; p2++)
{
float2 Pos2 = new float2(Origins[p2].X, Origins[p2].Y);
float2 Diff = Pos2 - Pos1;
float Dist = Diff.X * Diff.X + Diff.Y * Diff.Y;
Dist = 1f / Dist;
DistanceWeights[p1] += Dist;
DistanceWeights[p2] += Dist;
}
}
for (int i = 0; i < NParticles; i++)
{
string ParticlePath = (i + 1).ToString("D6") + "@particles/" + RootName + "_particles.mrcs";
tableIn.SetRowValue(RowIndices[i], "rlnImageName", ParticlePath);
//string ParticleCTFsPath = (i + 1).ToString("D6") + "@particlectf/" + RootName + "_particlectf.mrcs";
//tableIn.SetRowValue(RowIndices[i], "rlnCtfImage", ParticleCTFsPath);
tableIn.SetRowValue(RowIndices[i], "rlnAutopickFigureOfMerit", DistanceWeights[i].ToString(CultureInfo.InvariantCulture));
}
}
public void UpdateStarDefocus(Star table, string[] columnNames, string[] columnCoordsX, string[] columnCoordsY)
{
List<int> NameIndices = new List<int>();
string InvariantRoot = RootName;
for (int i = 0; i < columnNames.Length; i++)
if (columnNames[i].Contains(InvariantRoot))
NameIndices.Add(i);
//if (NameIndices.Count == 0)
//Debug.WriteLine(RootName + ": " + NameIndices.Count);
foreach (var nameIndex in NameIndices)
{
float CoordX = float.Parse(columnCoordsX[nameIndex], CultureInfo.InvariantCulture);
float CoordY = float.Parse(columnCoordsY[nameIndex], CultureInfo.InvariantCulture);
float LocalDefocus = GridCTF.GetInterpolated(new float3(CoordX / (Dimensions.X * 0.5f), CoordY / (Dimensions.Y * 0.5f), 4f / 37f));
table.SetRowValue(nameIndex, "rlnDefocusU", ((LocalDefocus + (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture));
table.SetRowValue(nameIndex, "rlnDefocusV", ((LocalDefocus - (float)CTF.DefocusDelta / 2f) * 1e4f).ToString(CultureInfo.InvariantCulture));
table.SetRowValue(nameIndex, "rlnDefocusAngle", ((float)CTF.DefocusAngle).ToString(CultureInfo.InvariantCulture));
// Go from pixel size to magnification
float Mag = (float)(MainWindow.Options.CTFDetectorPixel * 10000M / (CTF.PixelSize / 1.00M));
table.SetRowValue(nameIndex, "rlnMagnification", Mag.ToString(CultureInfo.InvariantCulture));
//table.SetRowValue(nameIndex, "rlnSphericalAberration", ((float)CTF.Cs).ToString(CultureInfo.InvariantCulture));
//float LocalPhaseShift = GridCTFPhase.GetInterpolated(new float3(0.5f, 0.5f, 4f / 37f));
//table.SetRowValue(nameIndex, "rlnPhaseShift", (LocalPhaseShift * 180f).ToString(CultureInfo.InvariantCulture));
}
}
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 MakePerTomogramReconstructions(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 (!Directory.Exists(WeightOptimizationDir))
Directory.CreateDirectory(WeightOptimizationDir);
#endregion
#region Get subtomo positions from table
float3[] ParticleOrigins = new float3[NParticles];
float3[] ParticleOrigins2 = new float3[NParticles];
float3[] ParticleAngles = new float3[NParticles];
float3[] ParticleAngles2 = 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");
string[] ColumnPosX2 = tableIn.GetColumn("rlnOriginXPrior");
string[] ColumnPosY2 = tableIn.GetColumn("rlnOriginYPrior");
string[] ColumnPosZ2 = tableIn.GetColumn("rlnOriginZPrior");
string[] ColumnAngleRot2 = tableIn.GetColumn("rlnAngleRotPrior");
string[] ColumnAngleTilt2 = tableIn.GetColumn("rlnAngleTiltPrior");
string[] ColumnAnglePsi2 = tableIn.GetColumn("rlnAnglePsiPrior");
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 Pos2 = Pos;
if (ColumnPosX2 != null && ColumnPosY2 != null && ColumnPosZ2 != null)
Pos2 = new float3(float.Parse(ColumnPosX2[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosY2[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnPosZ2[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;
ParticleOrigins2[i] = Pos2 - 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));
float3 Angle2 = Angle;
if (ColumnAngleRot2 != null && ColumnAngleTilt2 != null && ColumnAnglePsi2 != null)
Angle2 = new float3(float.Parse(ColumnAngleRot2[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAngleTilt2[RowIndices[i]], CultureInfo.InvariantCulture),
float.Parse(ColumnAnglePsi2[RowIndices[i]], CultureInfo.InvariantCulture));
ParticleAngles[i] = Angle;
ParticleAngles2[i] = Angle2;
ParticleSubset[i] = int.Parse(ColumnSubset[RowIndices[i]]);
}
}
#endregion
List<int> SubsetIDs = new List<int>();
foreach (var i in ParticleSubset)
if (!SubsetIDs.Contains(i))
SubsetIDs.Add(i);
SubsetIDs.Sort();
for (int subset = 0; subset < SubsetIDs.Count; subset++)
{
if (File.Exists(WeightOptimizationDir + $"{RootName}_subset{SubsetIDs[subset]}.mrc"))
continue;
Tuple<Image, Image> Reconstruction = MakeReconstructionOneTomogram(tiltStack,
SubsetIDs[subset],
size,
ParticleOrigins,
ParticleOrigins2,
ParticleAngles,
ParticleAngles2,
ParticleSubset);
Reconstruction.Item1.WriteMRC(WeightOptimizationDir + $"{RootName}_subset{SubsetIDs[subset]}.mrc");
Reconstruction.Item1.Dispose();
Reconstruction.Item2.WriteMRC(WeightOptimizationDir + $"{RootName}_subset{SubsetIDs[subset]}.weight.mrc");
Reconstruction.Item2.Dispose();
}
}
private void ButtonExportParticles_OnClick(object sender, RoutedEventArgs e)
{
System.Windows.Forms.OpenFileDialog Dialog = new System.Windows.Forms.OpenFileDialog
{
Filter = "STAR Files|*.star",
Multiselect = false
};
System.Windows.Forms.DialogResult Result = Dialog.ShowDialog();
if (Result == System.Windows.Forms.DialogResult.OK)
{
System.Windows.Forms.SaveFileDialog SaveDialog = new System.Windows.Forms.SaveFileDialog
{
Filter = "STAR Files|*.star"
};
System.Windows.Forms.DialogResult SaveResult = SaveDialog.ShowDialog();
if (SaveResult == System.Windows.Forms.DialogResult.OK)
{
Thread ProcessThread = new Thread(() =>
{
Star TableIn = new Star(Dialog.FileName);
//if (TableIn.GetColumn("rlnCtfImage") == null)
// TableIn.AddColumn("rlnCtfImage");
string[] ColumnNames = TableIn.GetColumn("rlnMicrographName");
string[] Excluded = Options.Movies.Where(m => m.Status == ProcessingStatus.Skip).Select(m => m.RootName).ToArray();
List<int> ForDelete = new List<int>();
for (int r = 0; r < TableIn.RowCount; r++)
for (int ex = 0; ex < Excluded.Length; ex++)
if (ColumnNames[r].Contains(Excluded[ex]))
ForDelete.Add(r);
TableIn.RemoveRows(ForDelete.ToArray());
ColumnNames = TableIn.GetColumn("rlnMicrographName");
string[] ColumnCoordsX = TableIn.GetColumn("rlnCoordinateX");
string[] ColumnCoordsY = TableIn.GetColumn("rlnCoordinateY");
Star TableOut = new Star(TableIn.GetColumnNames());
int MaxDevices = 999;
int UsedDevices = Math.Min(MaxDevices, GPU.GetDeviceCount());
Queue<DeviceToken> Devices = new Queue<DeviceToken>();
for (int d = 0; d < UsedDevices; d++)
Devices.Enqueue(new DeviceToken(d));
//for (int d = 0; d < UsedDevices; d++)
// Devices.Enqueue(new DeviceToken(d));
int NTokens = Devices.Count;
DeviceToken[] IOSync = new DeviceToken[UsedDevices];
for (int d = 0; d < UsedDevices; d++)
IOSync[d] = new DeviceToken(d);
Image[] ImageGain = new Image[UsedDevices];
if (!string.IsNullOrEmpty(Options.GainPath) && Options.CorrectGain && File.Exists(Options.GainPath))
for (int d = 0; d < UsedDevices; d++)
try
{
GPU.SetDevice(d);
ImageGain[d] = StageDataLoad.LoadMap(Options.GainPath,
new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight),
MainWindow.Options.InputDatOffset,
ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));
}
catch
{
return;
}
//Dictionary<int, Projector>[] DeviceReferences = new Dictionary<int, Projector>[GPU.GetDeviceCount()];
//Dictionary<int, Projector>[] DeviceReconstructions = new Dictionary<int, Projector>[GPU.GetDeviceCount()];
//Dictionary<int, Projector>[] DeviceCTFReconstructions = new Dictionary<int, Projector>[GPU.GetDeviceCount()];
//for (int d = 0; d < GPU.GetDeviceCount(); d++)
//{
// GPU.SetDevice(d);
// Dictionary<int, Projector> References = new Dictionary<int, Projector>();
// {
// Image Ref1 = StageDataLoad.LoadMap("F:\\badaben\\vlion123\\warp_ref1.mrc", new int2(1, 1), 0, typeof(float));
// Image Ref2 = StageDataLoad.LoadMap("F:\\badaben\\vlion123\\warp_ref2.mrc", new int2(1, 1), 0, typeof(float));
// Image Ref3 = StageDataLoad.LoadMap("F:\\badaben\\vlion123\\warp_ref3.mrc", new int2(1, 1), 0, typeof(float));
// Image Ref4 = StageDataLoad.LoadMap("F:\\badaben\\vlion123\\warp_ref4.mrc", new int2(1, 1), 0, typeof(float));
// //Image Ref5 = StageDataLoad.LoadMap("F:\\badaben\\vlion12\\warp_ref5.mrc", new int2(1, 1), 0, typeof(float));
// //Image Ref6 = StageDataLoad.LoadMap("F:\\badaben\\vlion12\\warp_ref6.mrc", new int2(1, 1), 0, typeof(float));
// //Image Ref1 = StageDataLoad.LoadMap("F:\\badaben\\chloro\\warp_ref1.mrc", new int2(1, 1), 0, typeof(float));
// //Image Ref2 = StageDataLoad.LoadMap("F:\\badaben\\chloro\\warp_ref2.mrc", new int2(1, 1), 0, typeof(float));
// //Image Ref3 = StageDataLoad.LoadMap("F:\\stefanribo\\vlion\\mini_warp_ref3.mrc", new int2(1, 1), 0, typeof(float));
// //Image Ref4 = StageDataLoad.LoadMap("F:\\stefanribo\\vlion\\mini_warp_ref4.mrc", new int2(1, 1), 0, typeof(float));
// References.Add(1, new Projector(Ref1, 2));
// References.Add(2, new Projector(Ref2, 2));
// References.Add(3, new Projector(Ref3, 2));
// References.Add(4, new Projector(Ref4, 2));
// //References.Add(5, new Projector(Ref5, 2));
// //References.Add(6, new Projector(Ref6, 2));
// //References.Add(3, new Projector(Ref3, 2));
// Ref1.Dispose();
// Ref2.Dispose();
// Ref3.Dispose();
// Ref4.Dispose();
// //Ref5.Dispose();
// //Ref6.Dispose();
// }
// DeviceReferences[d] = References;
// Dictionary<int, Projector> Reconstructions = new Dictionary<int, Projector>();
// foreach (var reference in References)
// {
// Reconstructions.Add(reference.Key, new Projector(reference.Value.Dims, reference.Value.Oversampling));
// Reconstructions[reference.Key].FreeDevice();
// }
// DeviceReconstructions[d] = Reconstructions;
// Dictionary<int, Projector> CTFReconstructions = new Dictionary<int, Projector>();
// foreach (var reference in References)
// {
// CTFReconstructions.Add(reference.Key, new Projector(reference.Value.Dims, reference.Value.Oversampling));
// CTFReconstructions[reference.Key].FreeDevice();
// }
// DeviceCTFReconstructions[d] = CTFReconstructions;
//}
int NTilts = (int)MathHelper.Max(Options.Movies.Select(m => (float)((TiltSeries)m).NTilts));
Dictionary<int, Projector[]> PerAngleReconstructions = new Dictionary<int, Projector[]>();
Dictionary<int, Projector[]> PerAngleWeightReconstructions = new Dictionary<int, Projector[]>();
//{
// int[] ColumnSubset = TableIn.GetColumn("rlnRandomSubset").Select(s => int.Parse(s)).ToArray();
// List<int> SubsetIDs = new List<int>();
// foreach (var subset in ColumnSubset)
// if (!SubsetIDs.Contains(subset))
// SubsetIDs.Add(subset);
// SubsetIDs.Sort();
// SubsetIDs.Remove(1);
// SubsetIDs.Remove(2);
// int Size = Options.ExportParticleSize;
// //foreach (var subsetID in SubsetIDs)
// //{
// // PerAngleReconstructions.Add(subsetID, new Projector[NTilts]);
// // PerAngleWeightReconstructions.Add(subsetID, new Projector[NTilts]);
// // for (int t = 0; t < NTilts; t++)
// // {
// // PerAngleReconstructions[subsetID][t] = new Projector(new int3(Size, Size, Size), 2);
// // PerAngleReconstructions[subsetID][t].FreeDevice();
// // PerAngleWeightReconstructions[subsetID][t] = new Projector(new int3(Size, Size, Size), 2);
// // PerAngleWeightReconstructions[subsetID][t].FreeDevice();
// // }
// //}
//}
foreach (var movie in Options.Movies)
if (movie.DoProcess)
{
//if (((TiltSeries)movie).GlobalBfactor < -200)
// continue;
while (Devices.Count <= 0)
Thread.Sleep(20);
DeviceToken CurrentDevice;
lock (Devices)
CurrentDevice = Devices.Dequeue();
Thread DeviceThread = new Thread(() =>
{
GPU.SetDevice(CurrentDevice.ID);
MapHeader OriginalHeader = null;
Image OriginalStack = null;
decimal ScaleFactor = 1M / (decimal)Math.Pow(2, (double)Options.PostBinTimes);
lock (IOSync[CurrentDevice.ID])
PrepareHeaderAndMap(movie.Path, ImageGain[CurrentDevice.ID], ScaleFactor, out OriginalHeader, out OriginalStack);
if (movie.GetType() == typeof (Movie))
{
movie.UpdateStarDefocus(TableIn, ColumnNames, ColumnCoordsX, ColumnCoordsY);
//movie.ExportParticles(TableIn, TableOut, OriginalHeader, OriginalStack, Options.ExportParticleSize, Options.ExportParticleRadius, ScaleFactor);
}
else if (movie.GetType() == typeof (TiltSeries))
{
//((TiltSeries)movie).ExportSubtomos(TableIn, OriginalStack, Options.ExportParticleSize, new int3(928, 928, 300));
//((TiltSeries)movie).ExportSubtomos(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3712, 3712, 1400));
//((TiltSeries)movie).Reconstruct(OriginalStack, 128, 3.42f * 4 * 2, new int3(3712, 3712, 1400));
/*for (int refinement = 0; refinement < 20; refinement++)
{*/
//OriginalStack.FreeDevice();
//((TiltSeries)movie).PerformOptimizationStep(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3712, 3712, 1400), DeviceReferences[CurrentDevice.ID], 22f, DeviceReconstructions[0], DeviceCTFReconstructions[0]);
//((TiltSeries)movie).RealspaceRefineGlobal(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3838, 3710, 1200), References, 30, 2, "D4", Reconstructions);
//Image Simulated = ((TiltSeries)movie).SimulateTiltSeries(TableIn, OriginalStack.Dims, Options.ExportParticleSize, new int3(3712, 3712, 1200), References, 15);
//Simulated.WriteMRC("d_simulatedseries.mrc");
//((TiltSeries)movie).AlignTiltMovies(TableIn, OriginalStack.Dims, Options.ExportParticleSize, new int3(3712, 3712, 1200), References, 100);
/*TableIn.Save(SaveDialog.FileName + $".it{refinement:D2}.star");
}*/
//((TiltSeries)movie).ExportSubtomos(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3712, 3712, 1400));
//Image Reference = StageDataLoad.LoadMap("F:\\chloroplastribo\\vlion\\warp_ref3.mrc", new int2(1, 1), 0, typeof (float));
//((TiltSeries)movie).Correlate(OriginalStack, Reference, 128, 40, 400, new int3(3712, 3712, 1400), 2, "C1");
//Reference.Dispose();
//GPU.SetDevice(0);
//((TiltSeries)movie).MakePerTomogramReconstructions(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3712, 3712, 1400));
//((TiltSeries)movie).AddToPerAngleReconstructions(TableIn, OriginalStack, Options.ExportParticleSize, new int3(3710, 3710, 1400), PerAngleReconstructions, PerAngleWeightReconstructions);
}
OriginalStack?.Dispose();
//Debug.WriteLine(movie.Path);
//TableIn.Save(SaveDialog.FileName);
lock (Devices)
Devices.Enqueue(CurrentDevice);
Debug.WriteLine("Done: " + movie.RootName);
});
DeviceThread.Start();
}
while (Devices.Count != NTokens)
Thread.Sleep(20);
for (int d = 0; d < UsedDevices; d++)
{
ImageGain[d]?.Dispose();
}
//for (int d = 0; d < DeviceReferences.Length; d++)
//{
// GPU.SetDevice(d);
// foreach (var reconstruction in DeviceReconstructions[d])
// {
// if (d == 0)
// {
// Image ReconstructedMap = reconstruction.Value.Reconstruct(false);
// //ReconstructedMap.WriteMRC($"F:\\chloroplastribo\\vlion\\warped_{reconstruction.Key}_nodeconv.mrc");
// Image ReconstructedCTF = DeviceCTFReconstructions[d][reconstruction.Key].Reconstruct(true);
// Image ReconstructedMapFT = ReconstructedMap.AsFFT(true);
// ReconstructedMap.Dispose();
// int Dim = ReconstructedMap.Dims.Y;
// int DimFT = Dim / 2 + 1;
// int R2 = Dim / 2 - 2;
// R2 *= R2;
// foreach (var slice in ReconstructedCTF.GetHost(Intent.ReadWrite))
// {
// for (int y = 0; y < Dim; y++)
// {
// int yy = y < Dim / 2 + 1 ? y : y - Dim;
// yy *= yy;
// for (int x = 0; x < DimFT; x++)
// {
// int xx = x * x;
// slice[y * DimFT + x] = xx + yy < R2 ? Math.Max(1e-2f, slice[y * DimFT + x]) : 1f;
// }
// }
// }
// ReconstructedMapFT.Divide(ReconstructedCTF);
// ReconstructedMap = ReconstructedMapFT.AsIFFT(true);
// ReconstructedMapFT.Dispose();
// //GPU.SphereMask(ReconstructedMap.GetDevice(Intent.Read),
// // ReconstructedMap.GetDevice(Intent.Write),
// // ReconstructedMap.Dims,
// // (float)(ReconstructedMap.Dims.X / 2 - 8),
// // 8,
// // 1);
// ReconstructedMap.WriteMRC($"F:\\badaben\\vlion123\\warped_{reconstruction.Key}.mrc");
// ReconstructedMap.Dispose();
// }
// reconstruction.Value.Dispose();
// DeviceReferences[d][reconstruction.Key].Dispose();
// DeviceCTFReconstructions[d][reconstruction.Key].Dispose();
// }
//}
//string WeightOptimizationDir = ((TiltSeries)Options.Movies[0]).WeightOptimizationDir;
//foreach (var subset in PerAngleReconstructions)
//{
// for (int t = 0; t < NTilts; t++)
// {
// Image Reconstruction = PerAngleReconstructions[subset.Key][t].Reconstruct(false);
// PerAngleReconstructions[subset.Key][t].Dispose();
// Reconstruction.WriteMRC(WeightOptimizationDir + $"subset{subset.Key}_tilt{t.ToString("D3")}.mrc");
// Reconstruction.Dispose();
// foreach (var slice in PerAngleWeightReconstructions[subset.Key][t].Weights.GetHost(Intent.ReadWrite))
// for (int i = 0; i < slice.Length; i++)
// slice[i] = Math.Min(1, slice[i]);
// Image WeightReconstruction = PerAngleWeightReconstructions[subset.Key][t].Reconstruct(true);
// PerAngleWeightReconstructions[subset.Key][t].Dispose();
// WeightReconstruction.WriteMRC(WeightOptimizationDir + $"subset{subset.Key}_tilt{t.ToString("D3")}.weight.mrc");
// WeightReconstruction.Dispose();
// }
//}
TableIn.Save(SaveDialog.FileName);
});
ProcessThread.Start();
}
}
}
public void PerformGlobalParticleAlignment(Star tableIn,
Image tiltStack,
int size,
int3 volumeDimensions,
Dictionary<int, Projector> references,
float resolution,
int healpixOrder,
string symmetry,
float offsetRange,
float offsetStep,
Dictionary<int, Projector> outReconstructions,
Dictionary<int, Projector> outCTFReconstructions)
{
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[] ParticleOrigins2 = new float3[NParticles];
float3[] ParticleAngles = new float3[NParticles];
float3[] ParticleAngles2 = 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 Pos2 = Pos;
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;
ParticleOrigins2[i] = Pos2 - Shift;
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));
float3 Angle2 = Angle;
ParticleAngles[i] = Angle;
ParticleAngles2[i] = Angle2;
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();
ParticleOrigins2 = SubsetContinuousIDs.Select(i => ParticleOrigins2[i]).ToArray();
ParticleAngles = SubsetContinuousIDs.Select(i => ParticleAngles[i]).ToArray();
ParticleAngles2 = SubsetContinuousIDs.Select(i => ParticleAngles2[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
float2[] ExtractedAt = new float2[NParticles * NTilts];
// Extract images, mask and resize them, create CTFs
Image ParticleImages = new Image(new int3(CoarseSize, CoarseSize, NParticles * NTilts), true, true);
Image ParticleCTFs = new Image(new int3(CoarseSize, CoarseSize, NParticles * NTilts), true);
Image ParticleWeights = null;
Image ShiftFactors = null;
#region Preflight
float KeepBFac = GlobalBfactor;
GlobalBfactor = 0;
{
Image CTFCoords = GetCTFCoords(CoarseSize, size);
#region Precalculate vectors for shifts in Fourier space
{
float2[] ShiftFactorsData = new float2[(CoarseSize / 2 + 1) * CoarseSize];
for (int y = 0; y < CoarseSize; y++)
for (int x = 0; x < CoarseSize / 2 + 1; x++)
{
int xx = x;
int yy = y < CoarseSize / 2 + 1 ? y : y - CoarseSize;
ShiftFactorsData[y * (CoarseSize / 2 + 1) + x] = new float2((float)-xx / size * 2f * (float)Math.PI,
(float)-yy / size * 2f * (float)Math.PI);
}
ShiftFactors = new Image(ShiftFactorsData, new int3(CoarseSize, CoarseSize, 1), true);
}
#endregion
#region Create mask with soft edge
Image Mask;
Image MaskSubt;
{
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();
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 <= 30)
MaskBigData[y * size + x] = 1;
else
MaskBigData[y * size + x] = 0;
}
}
MaskSubt = MaskBig.AsScaled(new int2(CoarseSize, CoarseSize));
MaskSubt.RemapToFT();
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 extract & preprocess images for entire tilt series
for (int p = 0; p < NParticles; p++)
{
float3 ParticleCoords = ParticleOrigins[p];
float3[] Positions = GetPositionInImages(ParticleCoords);
float3[] ProjAngles = GetParticleAngleInImages(ParticleCoords, ParticleAngles[p]);
Image Extracted = new Image(new int3(size, size, NTilts));
float[][] ExtractedData = Extracted.GetHost(Intent.Write);
float3[] Residuals = new float3[NTilts];
Image SubtrahendsCTF = new Image(new int3(CoarseSize, CoarseSize, NTilts), true);
// Create CTFs
{
CTFStruct[] CTFParams = new CTFStruct[NTilts];
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.GetDeviceSlice(NTilts * p, Intent.Write),
CTFCoords.GetDevice(Intent.Read),
(uint)CoarseDims.ElementsFFT(),
Params,
false,
(uint)NTilts);
}
// Extract images
{
for (int t = 0; t < NTilts; t++)
{
ExtractedAt[p * NTilts + t] = new float2(Positions[t].X, Positions[t].Y);
Positions[t] -= size / 2;
int2 IntPosition = new int2((int)Positions[t].X, (int)Positions[t].Y);
float2 Residual = new float2(-(Positions[t].X - IntPosition.X), -(Positions[t].Y - IntPosition.Y));
Residuals[t] = new float3(Residual / size * CoarseSize);
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];
}
}
}
GPU.NormParticles(Extracted.GetDevice(Intent.Read),
Extracted.GetDevice(Intent.Write),
new int3(size, size, 1),
(uint)(MainWindow.Options.ExportParticleRadius / CTF.PixelSize),
true,
(uint)NTilts);
Image Scaled = Extracted.AsScaled(new int2(CoarseSize, CoarseSize));
//Scaled.WriteMRC("d_scaled.mrc");
Extracted.Dispose();
Scaled.ShiftSlices(Residuals);
Scaled.RemapToFT();
//GPU.NormalizeMasked(Scaled.GetDevice(Intent.Read),
// Scaled.GetDevice(Intent.Write),
// MaskSubt.GetDevice(Intent.Read),
// (uint)Scaled.ElementsSliceReal,
// (uint)NTilts);
//{
// //Image SubtrahendsFT = subtrahendReference.Project(new int2(CoarseSize, CoarseSize), ProjAngles, CoarseSize / 2);
// //SubtrahendsFT.Multiply(SubtrahendsCTF);
// //Image Subtrahends = SubtrahendsFT.AsIFFT();
// //SubtrahendsFT.Dispose();
// ////GPU.NormalizeMasked(Subtrahends.GetDevice(Intent.Read),
// //// Subtrahends.GetDevice(Intent.Write),
// //// MaskSubt.GetDevice(Intent.Read),
// //// (uint)Subtrahends.ElementsSliceReal,
// //// (uint)NTilts);
// //Scaled.Subtract(Subtrahends);
// //Subtrahends.Dispose();
// Image FocusMaskFT = maskReference.Project(new int2(CoarseSize, CoarseSize), ProjAngles, CoarseSize / 2);
// Image FocusMask = FocusMaskFT.AsIFFT();
// FocusMaskFT.Dispose();
// Scaled.Multiply(FocusMask);
// FocusMask.Dispose();
//}
Scaled.MultiplySlices(Mask);
GPU.FFT(Scaled.GetDevice(Intent.Read),
ParticleImages.GetDeviceSlice(p * NTilts, Intent.Write),
CoarseDims,
(uint)NTilts);
Scaled.Dispose();
SubtrahendsCTF.Dispose();
}
}
#endregion
ParticleCTFs.MultiplySlices(FourierMask);
Mask.Dispose();
FourierMask.Dispose();
MaskSubt.Dispose();
Image ParticleCTFsAbs = new Image(ParticleCTFs.GetDevice(Intent.Read), ParticleCTFs.Dims, true);
ParticleCTFsAbs.Abs();
ParticleWeights = ParticleCTFsAbs.AsSum2D();
ParticleCTFsAbs.Dispose();
{
float[] ParticleWeightsData = ParticleWeights.GetHost(Intent.ReadWrite)[0];
float Max = MathHelper.Max(ParticleWeightsData);
for (int i = 0; i < ParticleWeightsData.Length; i++)
ParticleWeightsData[i] /= Max;
}
CTFCoords.Dispose();
//Image CheckImages = ParticleImages.AsIFFT();
//CheckImages.WriteMRC("d_particleimages.mrc");
//CheckImages.Dispose();
//ParticleCTFs.WriteMRC("d_particlectfs.mrc");
}
GlobalBfactor = KeepBFac;
#endregion
#region Global alignment
Func<float3[], float2[]> GetImageShifts = input =>
{
// Using current positions, angles and grids, get parameters for image shifts
float2[] ImageShifts = new float2[NParticles * NTilts];
float3[] PerTiltPositions = new float3[NParticles * NTilts];
for (int p = 0; p < NParticles; p++)
for (int t = 0; t < NTilts; t++)
PerTiltPositions[p * NTilts + t] = input[p];
float3[] CurrPositions = GetPositionInImages(PerTiltPositions);
for (int i = 0; i < ImageShifts.Length; i++)
ImageShifts[i] = new float2(ExtractedAt[i].X - CurrPositions[i].X,
ExtractedAt[i].Y - CurrPositions[i].Y); // -diff because those are extraction positions, i. e. opposite direction of shifts
return ImageShifts;
};
Func<float3[], float3[]> GetImageAngles = input =>
{
int NAngles = input.Length;
float3 VolumeCenter = new float3(VolumeDimensions.X / 2, VolumeDimensions.Y / 2, VolumeDimensions.Z / 2);
float3[] PerTiltPositions = new float3[NAngles * NTilts];
float3[] PerTiltAngles = new float3[NAngles * NTilts];
for (int a = 0; a < NAngles; a++)
for (int t = 0; t < NTilts; t++)
{
PerTiltPositions[a * NTilts + t] = VolumeCenter;
PerTiltAngles[a * NTilts + t] = input[a];
}
float3[] ImageAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles);
return ImageAngles;
};
float3[] RelativeOffsets;
{
List<float3> RelativeOffsetList = new List<float3>();
int NSteps = (int)Math.Ceiling(offsetRange / offsetStep);
for (int z = -NSteps; z <= NSteps; z++)
for (int y = -NSteps; y <= NSteps; y++)
for (int x = -NSteps; x <= NSteps; x++)
{
float R = (float)Math.Sqrt(x * x + y * y + z * z) * offsetStep;
if (R > offsetRange + 1e-6f)
continue;
RelativeOffsetList.Add(new float3(x * offsetStep, y * offsetStep, z * offsetStep));
}
RelativeOffsets = RelativeOffsetList.ToArray();
}
float3[] HealpixAngles = Helper.GetHealpixAngles(healpixOrder, symmetry).Select(a => a * Helper.ToRad).ToArray();
float3[] ProjectionAngles = GetImageAngles(HealpixAngles);
float3[] OptimizedOrigins = new float3[NParticles];
float3[] OptimizedAngles = new float3[NParticles];
float[] BestScores = new float[NParticles].Select(v => -float.MaxValue).ToArray();
int BatchAngles = 128;
Image Projections = new Image(new int3(CoarseSize, CoarseSize, BatchAngles * NTilts), true, true);
foreach (var subset in SubsetRanges)
{
int NSubset = subset.Value.Item2 - subset.Value.Item1;
float[] ImageOffsets = new float[NSubset * NTilts * RelativeOffsets.Length * 2];
for (int o = 0; o < RelativeOffsets.Length; o++)
{
float3[] OffsetOrigins = new float3[NSubset];
for (int p = 0; p < NSubset; p++)
OffsetOrigins[p] = ParticleOrigins[subset.Value.Item1 + p] + RelativeOffsets[o];
float[] TheseOffsets = Helper.ToInterleaved(GetImageShifts(OffsetOrigins));
Array.Copy(TheseOffsets, 0, ImageOffsets, TheseOffsets.Length * o, TheseOffsets.Length);
}
int[] ShiftIDs = new int[NSubset];
int[] AngleIDs = new int[NSubset];
float[] SubsetScores = new float[NSubset];
GPU.TomoGlobalAlign(ParticleImages.GetDeviceSlice(subset.Value.Item1 * NTilts, Intent.Read),
ShiftFactors.GetDevice(Intent.Read),
ParticleCTFs.GetDeviceSlice(subset.Value.Item1 * NTilts, Intent.Read),
ParticleWeights.GetDeviceSlice(subset.Value.Item1 * NTilts, Intent.Read),
new int2(CoarseDims),
references[subset.Key].Data.GetDevice(Intent.Read),
references[subset.Key].Data.Dims,
references[subset.Key].Oversampling,
Helper.ToInterleaved(ProjectionAngles),
(uint)HealpixAngles.Length,
ImageOffsets,
(uint)RelativeOffsets.Length,
(uint)NSubset,
(uint)NTilts,
AngleIDs,
ShiftIDs,
SubsetScores);
for (int i = 0; i < NSubset; i++)
{
OptimizedOrigins[subset.Value.Item1 + i] = ParticleOrigins[subset.Value.Item1 + i] + RelativeOffsets[ShiftIDs[i]];
OptimizedAngles[subset.Value.Item1 + i] = HealpixAngles[AngleIDs[i]];
BestScores[subset.Value.Item1 + i] = SubsetScores[i];
}
}
Projections.Dispose();
#endregion
ParticleImages?.Dispose();
ParticleCTFs?.Dispose();
ParticleWeights?.Dispose();
ShiftFactors?.Dispose();
#region Extract particles at full resolution and back-project them into the reconstruction volumes
{
GPU.SetDevice(0);
Image CTFCoords = GetCTFCoords(size, size);
int[] SortedDosePrecalc = IndicesSortedDose;
foreach (var subsetRange in SubsetRanges)
{
lock (outReconstructions[subsetRange.Key])
{
for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++)
{
float3[] PerTiltPositions = new float3[NTilts];
float3[] PerTiltAngles = new float3[NTilts];
for (int t = 0; t < NTilts; t++)
{
PerTiltPositions[t] = OptimizedOrigins[p];
PerTiltAngles[t] = OptimizedAngles[p];
}
Image FullParticleImages = GetSubtomoImages(tiltStack, size, PerTiltPositions, true);
Image FullParticleCTFs = GetSubtomoCTFs(PerTiltPositions, CTFCoords);
FullParticleImages.Multiply(FullParticleCTFs);
FullParticleCTFs.Abs();
float3[] FullParticleAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles);
outReconstructions[subsetRange.Key].BackProject(FullParticleImages, FullParticleCTFs, FullParticleAngles);
FullParticleImages.Dispose();
FullParticleCTFs.Dispose();
}
for (int p = subsetRange.Value.Item1; p < subsetRange.Value.Item2; p++)
{
float3[] PerTiltPositions = new float3[NTilts];
float3[] PerTiltAngles = new float3[NTilts];
for (int t = 0; t < NTilts; t++)
{
PerTiltPositions[t] = OptimizedOrigins[p];
PerTiltAngles[t] = OptimizedAngles[p];
}
float3[] FullParticleAngles = GetParticleAngleInImages(PerTiltPositions, PerTiltAngles);
Image FullParticleCTFs = GetSubtomoCTFs(PerTiltPositions, CTFCoords, false);
Image FullParticleCTFWeights = GetSubtomoCTFs(PerTiltPositions, CTFCoords, true);
// CTF has to be converted to complex numbers with imag = 0
float2[] CTFsComplexData = new float2[FullParticleCTFs.ElementsComplex];
float[] CTFWeightsData = new float[FullParticleCTFs.ElementsComplex];
float[] CTFsContinuousData = FullParticleCTFs.GetHostContinuousCopy();
float[] CTFWeightsContinuousData = FullParticleCTFWeights.GetHostContinuousCopy();
for (int i = 0; i < CTFsComplexData.Length; i++)
{
CTFsComplexData[i] = new float2(Math.Abs(CTFsContinuousData[i] * CTFWeightsContinuousData[i]), 0);
CTFWeightsData[i] = Math.Abs(CTFWeightsContinuousData[i]);
}
Image CTFsComplex = new Image(CTFsComplexData, FullParticleCTFs.Dims, true);
Image CTFWeights = new Image(CTFWeightsData, FullParticleCTFs.Dims, true);
outCTFReconstructions[subsetRange.Key].BackProject(CTFsComplex, CTFWeights, FullParticleAngles);
FullParticleCTFs.Dispose();
FullParticleCTFWeights.Dispose();
CTFsComplex.Dispose();
CTFWeights.Dispose();
}
outReconstructions[subsetRange.Key].FreeDevice();
outCTFReconstructions[subsetRange.Key].FreeDevice();
}
}
CTFCoords.Dispose();
}
#endregion
SaveMeta();
}
private void ButtonStartProcessing_OnClick(object sender, RoutedEventArgs e)
{
if (!IsProcessing)
{
foreach (var item in DisableWhenRunning)
item.IsEnabled = false;
ButtonStartProcessing.Content = "STOP PROCESSING";
IsProcessing = true;
Thread ProcessThread = new Thread(() =>
{
int MaxDevices = 999;
int UsedDevices = Math.Min(MaxDevices, GPU.GetDeviceCount());
Image[] ImageGain = new Image[UsedDevices];
if (!string.IsNullOrEmpty(Options.GainPath) && Options.CorrectGain && File.Exists(Options.GainPath))
for (int d = 0; d < UsedDevices; d++)
try
{
GPU.SetDevice(d);
ImageGain[d] = StageDataLoad.LoadMap(Options.GainPath,
new int2(MainWindow.Options.InputDatWidth, MainWindow.Options.InputDatHeight),
MainWindow.Options.InputDatOffset,
ImageFormatsHelper.StringToType(MainWindow.Options.InputDatType));
}
catch
{
return;
}
Image[] VolRefFT = new Image[UsedDevices], VolMaskFT = new Image[UsedDevices];
if ((Options.ProcessCTF && Options.ProcessParticleCTF) || (Options.ProcessMovement && Options.ProcessParticleShift))
if (File.Exists(Options.ReferencePath) && File.Exists(Options.MaskPath))
{
for (int d = 0; d < UsedDevices; d++)
{
GPU.SetDevice(d);
{
Image Volume = StageDataLoad.LoadMap(Options.ReferencePath, new int2(1, 1), 0, typeof (float));
Image VolumePadded = Volume.AsPadded(Volume.Dims * Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
VolRefFT[d] = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
}
{
Image Volume = StageDataLoad.LoadMap(Options.MaskPath, new int2(1, 1), 0, typeof (float));
Image VolumePadded = Volume.AsPadded(Volume.Dims * Options.ProjectionOversample);
Volume.Dispose();
VolumePadded.RemapToFT(true);
VolMaskFT[d] = VolumePadded.AsFFT(true);
VolumePadded.Dispose();
}
}
}
Star ParticlesStar = null;
if (File.Exists(Options.DataStarPath))
ParticlesStar = new Star(Options.DataStarPath);
Queue<DeviceToken> Devices = new Queue<DeviceToken>();
for (int d = 0; d < UsedDevices; d++)
Devices.Enqueue(new DeviceToken(d));
//for (int d = 0; d < UsedDevices; d++)
// Devices.Enqueue(new DeviceToken(d));
int NTokens = Devices.Count;
DeviceToken[] IOSync = new DeviceToken[UsedDevices];
for (int d = 0; d < UsedDevices; d++)
IOSync[d] = new DeviceToken(d);
foreach (var Movie in Options.Movies)
{
if (!IsProcessing)
break;
if (Movie.Status != ProcessingStatus.Skip && Movie.Status != ProcessingStatus.Processed)
{
while (Devices.Count <= 0)
Thread.Sleep(20);
if (!IsProcessing)
break;
DeviceToken CurrentDevice;
lock (Devices)
CurrentDevice = Devices.Dequeue();
Thread DeviceThread = new Thread(() =>
{
GPU.SetDevice(CurrentDevice.ID);
MapHeader OriginalHeader = null;
Image OriginalStack = null;
decimal ScaleFactor = 1M / (decimal)Math.Pow(2, (double)Options.PostBinTimes);
lock (IOSync[CurrentDevice.ID])
PrepareHeaderAndMap(Movie.Path, ImageGain[CurrentDevice.ID], ScaleFactor, out OriginalHeader, out OriginalStack);
/*OriginalHeader = MapHeader.ReadFromFile(Movie.Path,
new int2(Options.InputDatWidth, Options.InputDatHeight),
Options.InputDatOffset,
ImageFormatsHelper.StringToType(Options.InputDatType));*/
//try
{
if (Options.ProcessMovement)
{
if (!Options.ProcessParticleShift)
Movie.ProcessShift(OriginalHeader, OriginalStack, ScaleFactor);
else
Movie.ProcessParticleShift(OriginalHeader,
OriginalStack,
ParticlesStar,
VolRefFT[CurrentDevice.ID],
VolMaskFT[CurrentDevice.ID],
VolRefFT[CurrentDevice.ID].Dims.X / Options.ProjectionOversample,
ScaleFactor);
}
if (Options.ProcessCTF)
{
if (!Options.ProcessParticleCTF)
Movie.ProcessCTF(OriginalHeader, OriginalStack, true, ScaleFactor);
else
Movie.ProcessParticleCTF(OriginalHeader,
OriginalStack,
ParticlesStar,
VolRefFT[CurrentDevice.ID],
VolMaskFT[CurrentDevice.ID],
VolRefFT[CurrentDevice.ID].Dims.X / Options.ProjectionOversample,
ScaleFactor);
}
if (Options.PostAverage || Options.PostStack)
Movie.CreateCorrected(OriginalHeader, OriginalStack);
//Movie.PerformComparison(OriginalHeader, ParticlesStar, VolRefFT, VolMaskFT, ScaleFactor);
//((TiltSeries)Movie).Reconstruct(OriginalStack, 128, 3.42f * 4 * 2, new int3(3712, 3712, 1400));
//Image Reference = StageDataLoad.LoadMap("F:\\badaben\\ref.mrc", new int2(1, 1), 0, typeof(float));
//((TiltSeries)Movie).Correlate(OriginalStack, Reference, 128, 80, 400, new int3(3712, 3712, 1400), 2, "C1");
//Reference.Dispose();
Movie.Status = ProcessingStatus.Processed;
}
/*catch
{
Movie.Status = ProcessingStatus.Unprocessed;
}*/
OriginalStack?.Dispose();
lock (Devices)
Devices.Enqueue(CurrentDevice);
});
DeviceThread.Start();
}
}
while (Devices.Count != NTokens)
Thread.Sleep(20);
//ParticlesStar.Save("F:\\rado27\\20S_defocused_dataset_part1\\warpmaps2\\run1_it017_data_everything.star");
//MoviesStar.Save("D:\\rado27\\Refine3D\\run1_ct5_data_movies.star");
for (int d = 0; d < UsedDevices; d++)
{
ImageGain[d]?.Dispose();
VolRefFT[d]?.Dispose();
VolMaskFT[d]?.Dispose();
}
});
ProcessThread.Start();
}
else
{
foreach (var item in DisableWhenRunning)
item.IsEnabled = true;
ButtonStartProcessing.Content = "START PROCESSING";
IsProcessing = false;
}
}
public void ProcessParticleCTF(MapHeader originalHeader, Image originalStack, Star stardata, Image refft, Image maskft, int dimbox, decimal scaleFactor)
{
//CTF.Cs = MainWindow.Options.CTFCs;
#region Dimensions and grids
int NFrames = originalHeader.Dimensions.Z;
int2 DimsImage = new int2(originalHeader.Dimensions);
int2 DimsRegion = new int2(dimbox, dimbox);
float3[] PositionsGrid;
float3[] PositionsExtraction;
float3[] ParticleAngles;
List<int> RowIndices = new List<int>();
{
string[] ColumnNames = stardata.GetColumn("rlnMicrographName");
for (int i = 0; i < ColumnNames.Length; i++)
if (ColumnNames[i].Contains(RootName))
RowIndices.Add(i);
string[] ColumnOriginX = stardata.GetColumn("rlnCoordinateX");
string[] ColumnOriginY = stardata.GetColumn("rlnCoordinateY");
string[] ColumnShiftX = stardata.GetColumn("rlnOriginX");
string[] ColumnShiftY = stardata.GetColumn("rlnOriginY");
string[] ColumnAngleRot = stardata.GetColumn("rlnAngleRot");
string[] ColumnAngleTilt = stardata.GetColumn("rlnAngleTilt");
string[] ColumnAnglePsi = stardata.GetColumn("rlnAnglePsi");
PositionsGrid = new float3[RowIndices.Count];
PositionsExtraction = new float3[RowIndices.Count];
ParticleAngles = new float3[RowIndices.Count];
{
int i = 0;
foreach (var nameIndex in RowIndices)
{
float OriginX = float.Parse(ColumnOriginX[nameIndex]);
float OriginY = float.Parse(ColumnOriginY[nameIndex]);
float ShiftX = float.Parse(ColumnShiftX[nameIndex]);
float ShiftY = float.Parse(ColumnShiftY[nameIndex]);
PositionsExtraction[i] = new float3(OriginX - ShiftX - dimbox / 2, OriginY - ShiftY - dimbox / 2, 0f);
PositionsGrid[i] = new float3((OriginX - ShiftX) / DimsImage.X, (OriginY - ShiftY) / DimsImage.Y, 0);
ParticleAngles[i] = new float3(float.Parse(ColumnAngleRot[nameIndex]) * Helper.ToRad,
float.Parse(ColumnAngleTilt[nameIndex]) * Helper.ToRad,
float.Parse(ColumnAnglePsi[nameIndex]) * Helper.ToRad);
i++;
}
}
}
int NPositions = PositionsGrid.Length;
if (NPositions == 0)
return;
int CTFGridX = MainWindow.Options.GridCTFX;
int CTFGridY = MainWindow.Options.GridCTFY;
int CTFGridZ = Math.Min(NFrames, MainWindow.Options.GridCTFZ);
int FrameGroupSize = CTFGridZ > 1 ? 12 : 1;
int NFrameGroups = CTFGridZ > 1 ? NFrames / FrameGroupSize : 1;
GridCTF = GridCTF.Resize(new int3(CTFGridX, CTFGridY, CTFGridZ));
GridCTFPhase = GridCTFPhase.Resize(new int3(1, 1, CTFGridZ));
int NSpectra = NFrameGroups * NPositions;
int MinFreqInclusive = (int)(MainWindow.Options.CTFRangeMin * DimsRegion.X / 2);
int MaxFreqExclusive = (int)(MainWindow.Options.CTFRangeMax * DimsRegion.X / 2);
int NFreq = MaxFreqExclusive - MinFreqInclusive;
float PixelSize = (float)CTF.PixelSize;
float PixelDelta = (float)CTF.PixelSizeDelta;
float PixelAngle = (float)CTF.PixelSizeAngle * Helper.ToRad;
#endregion
#region Allocate GPU memory
Image CTFSpectra = new Image(IntPtr.Zero, new int3(DimsRegion.X, DimsRegion.X, NSpectra), true, true);
Image CTFCoordsCart = new Image(new int3(DimsRegion), true, true);
Image ParticleRefs = refft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample);
/*Image ParticleRefsIFT = ParticleRefs.AsIFFT();
ParticleRefsIFT.WriteMRC("d_particlerefs.mrc");
ParticleRefsIFT.Dispose();*/
#endregion
// Extract movie regions, create individual spectra in Cartesian coordinates.
#region Create spectra
Image ParticleMasksFT = maskft.AsProjections(ParticleAngles, DimsRegion, MainWindow.Options.ProjectionOversample);
Image ParticleMasks = ParticleMasksFT.AsIFFT();
ParticleMasksFT.Dispose();
Parallel.ForEach(ParticleMasks.GetHost(Intent.ReadWrite), slice =>
{
for (int i = 0; i < slice.Length; i++)
slice[i] = (Math.Max(2f, Math.Min(25f, slice[i])) - 2) / 23f;
});
int3[] PositionsExtractionPerFrame = new int3[PositionsExtraction.Length * NFrames];
for (int z = 0; z < NFrames; z++)
{
for (int p = 0; p < NPositions; p++)
{
float3 Coords = new float3(PositionsGrid[p].X, PositionsGrid[p].Y, z / (float)(NFrames - 1));
float2 Offset = GetShiftFromPyramid(Coords);
PositionsExtractionPerFrame[z * NPositions + p] = new int3((int)Math.Round(PositionsExtraction[p].X - Offset.X),
(int)Math.Round(PositionsExtraction[p].Y - Offset.Y),
0);
}
}
float3[] PositionsGridPerFrame = new float3[NSpectra];
for (int z = 0; z < NFrameGroups; z++)
{
for (int p = 0; p < NPositions; p++)
{
float3 Coords = new float3(PositionsGrid[p].X, PositionsGrid[p].Y, (z * FrameGroupSize + FrameGroupSize / 2) / (float)(NFrames - 1));
PositionsGridPerFrame[z * NPositions + p] = Coords;
}
}
GPU.CreateParticleSpectra(originalStack.GetDevice(Intent.Read),
DimsImage,
NFrames,
PositionsExtractionPerFrame,
NPositions,
ParticleMasks.GetDevice(Intent.Read),
DimsRegion,
CTFGridZ > 1,
FrameGroupSize,
PixelSize + PixelDelta / 2f,
PixelSize - PixelDelta / 2f,
PixelAngle,
CTFSpectra.GetDevice(Intent.Write));
originalStack.FreeDevice(); // Won't need it in this method anymore.
ParticleMasks.Dispose();
/*Image CTFSpectraIFT = CTFSpectra.AsIFFT();
CTFSpectraIFT.RemapFromFT();
CTFSpectraIFT.WriteMRC("d_ctfspectra.mrc");
CTFSpectraIFT.Dispose();*/
#endregion
// Populate address arrays for later.
#region Init addresses
{
float2[] CoordsData = new float2[CTFCoordsCart.ElementsSliceComplex];
Helper.ForEachElementFT(DimsRegion, (x, y, xx, yy, r, a) => CoordsData[y * (DimsRegion.X / 2 + 1) + x] = new float2(r / DimsRegion.X, a));
CTFCoordsCart.UpdateHostWithComplex(new[] { CoordsData });
CTFCoordsCart.RemapToFT();
}
#endregion
// Band-pass filter reference projections
{
Image BandMask = new Image(new int3(DimsRegion.X, DimsRegion.Y, 1), true);
float[] BandMaskData = BandMask.GetHost(Intent.Write)[0];
float[] CTFCoordsData = CTFCoordsCart.GetHost(Intent.Read)[0];
for (int i = 0; i < BandMaskData.Length; i++)
BandMaskData[i] = (CTFCoordsData[i * 2] >= MinFreqInclusive / (float)DimsRegion.X && CTFCoordsData[i * 2] < MaxFreqExclusive / (float)DimsRegion.X) ? 1 : 0;
ParticleRefs.MultiplySlices(BandMask);
BandMask.Dispose();
}
Image Sigma2Noise = new Image(new int3(DimsRegion), true);
{
int GroupNumber = int.Parse(stardata.GetRowValue(RowIndices[0], "rlnGroupNumber"));
Star SigmaTable = new Star(MainWindow.Options.ModelStarPath, "data_model_group_" + GroupNumber);
float[] SigmaValues = SigmaTable.GetColumn("rlnSigma2Noise").Select(v => float.Parse(v)).ToArray();
float[] Sigma2NoiseData = Sigma2Noise.GetHost(Intent.Write)[0];
Helper.ForEachElementFT(new int2(DimsRegion.X, DimsRegion.Y), (x, y, xx, yy, r, angle) =>
{
int ir = (int)r;
float val = 0;
if (ir < SigmaValues.Length)
{
if (SigmaValues[ir] != 0f)
val = 1f / SigmaValues[ir];
}
Sigma2NoiseData[y * (DimsRegion.X / 2 + 1) + x] = val;
});
float MaxSigma = MathHelper.Max(Sigma2NoiseData);
for (int i = 0; i < Sigma2NoiseData.Length; i++)
Sigma2NoiseData[i] /= MaxSigma;
Sigma2Noise.RemapToFT();
}
Sigma2Noise.WriteMRC("d_sigma2noise.mrc");
// Do BFGS optimization of defocus, astigmatism and phase shift,
// using 2D simulation for comparison
#region BFGS
{
// Wiggle weights show how the defocus on the spectra grid is altered
// by changes in individual anchor points of the spline grid.
// They are used later to compute the dScore/dDefocus values for each spectrum
// only once, and derive the values for each anchor point from them.
float[][] WiggleWeights = GridCTF.GetWiggleWeights(PositionsGridPerFrame);
float[][] WiggleWeightsPhase = GridCTFPhase.GetWiggleWeights(PositionsGridPerFrame);
// Helper method for getting CTFStructs for the entire spectra grid.
Func<double[], CTF, float[], float[], CTFStruct[]> EvalGetCTF = (input, ctf, defocusValues, phaseValues) =>
{
decimal AlteredDelta = (decimal)input[input.Length - 2];
decimal AlteredAngle = (decimal)(input[input.Length - 1] * 20 / (Math.PI / 180));
CTF Local = ctf.GetCopy();
Local.DefocusDelta = AlteredDelta;
Local.DefocusAngle = AlteredAngle;
Local.PixelSizeDelta = 0;
CTFStruct LocalStruct = Local.ToStruct();
CTFStruct[] LocalParams = new CTFStruct[defocusValues.Length];
for (int i = 0; i < LocalParams.Length; i++)
{
LocalParams[i] = LocalStruct;
LocalParams[i].Defocus = defocusValues[i] * -1e-6f;
LocalParams[i].PhaseShift = phaseValues[i] * (float)Math.PI;
}
return LocalParams;
};
// Simulate with adjusted CTF, compare to originals
#region Eval and Gradient methods
Func<double[], double> Eval = input =>
{
CubicGrid Altered = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v).ToArray());
float[] DefocusValues = Altered.GetInterpolatedNative(PositionsGridPerFrame);
CubicGrid AlteredPhase = new CubicGrid(GridCTFPhase.Dimensions, input.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v).ToArray());
float[] PhaseValues = AlteredPhase.GetInterpolatedNative(PositionsGridPerFrame);
CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);
float[] Result = new float[LocalParams.Length];
GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read),
CTFCoordsCart.GetDevice(Intent.Read),
ParticleRefs.GetDevice(Intent.Read),
Sigma2Noise.GetDevice(Intent.Read),
(uint)CTFSpectra.ElementsSliceComplex,
LocalParams,
Result,
(uint)NFrameGroups,
(uint)NPositions);
float Score = 0;
for (int i = 0; i < Result.Length; i++)
Score += Result[i];
Score /= NSpectra;
if (float.IsNaN(Score) || float.IsInfinity(Score))
throw new Exception("Bad score.");
return Score * 1.0;
};
Func<double[], double[]> Gradient = input =>
{
const float Step = 0.001f;
double[] Result = new double[input.Length];
// In 0D grid case, just get gradient for all 4 parameters.
// In 1+D grid case, do simple gradient for astigmatism and phase...
int StartComponent = input.Length - 2;
//int StartComponent = 0;
/*for (int i = StartComponent; i < input.Length; i++)
{
double[] UpperInput = new double[input.Length];
input.CopyTo(UpperInput, 0);
UpperInput[i] += Step;
double UpperValue = Eval(UpperInput);
double[] LowerInput = new double[input.Length];
input.CopyTo(LowerInput, 0);
LowerInput[i] -= Step;
double LowerValue = Eval(LowerInput);
Result[i] = (UpperValue - LowerValue) / (2f * Step);
}*/
float[] ResultPlus = new float[NSpectra];
float[] ResultMinus = new float[NSpectra];
// ..., take shortcut for defoci...
{
CubicGrid AlteredPhase = new CubicGrid(GridCTFPhase.Dimensions, input.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v).ToArray());
float[] PhaseValues = AlteredPhase.GetInterpolatedNative(PositionsGridPerFrame);
{
CubicGrid AlteredPlus = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v + Step).ToArray());
float[] DefocusValues = AlteredPlus.GetInterpolatedNative(PositionsGridPerFrame);
CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);
GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read),
CTFCoordsCart.GetDevice(Intent.Read),
ParticleRefs.GetDevice(Intent.Read),
Sigma2Noise.GetDevice(Intent.Read),
(uint)CTFSpectra.ElementsSliceComplex,
LocalParams,
ResultPlus,
(uint)NFrameGroups,
(uint)NPositions);
}
{
CubicGrid AlteredMinus = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v - Step).ToArray());
float[] DefocusValues = AlteredMinus.GetInterpolatedNative(PositionsGridPerFrame);
CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);
GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read),
CTFCoordsCart.GetDevice(Intent.Read),
ParticleRefs.GetDevice(Intent.Read),
Sigma2Noise.GetDevice(Intent.Read),
(uint)CTFSpectra.ElementsSliceComplex,
LocalParams,
ResultMinus,
(uint)NFrameGroups,
(uint)NPositions);
}
float[] LocalGradients = new float[ResultPlus.Length];
for (int i = 0; i < LocalGradients.Length; i++)
LocalGradients[i] = ResultPlus[i] - ResultMinus[i];
// Now compute gradients per grid anchor point using the precomputed individual gradients and wiggle factors.
Parallel.For(0, GridCTF.Dimensions.Elements(), i => Result[i] = MathHelper.ReduceWeighted(LocalGradients, WiggleWeights[i]) / LocalGradients.Length / (2f * Step) * 1f);
}
// ..., and take shortcut for phases.
if (MainWindow.Options.CTFDoPhase)
{
CubicGrid AlteredPlus = new CubicGrid(GridCTF.Dimensions, input.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v).ToArray());
float[] DefocusValues = AlteredPlus.GetInterpolatedNative(PositionsGridPerFrame);
{
CubicGrid AlteredPhasePlus = new CubicGrid(GridCTFPhase.Dimensions, input.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v + Step).ToArray());
float[] PhaseValues = AlteredPhasePlus.GetInterpolatedNative(PositionsGridPerFrame);
CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);
GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read),
CTFCoordsCart.GetDevice(Intent.Read),
ParticleRefs.GetDevice(Intent.Read),
Sigma2Noise.GetDevice(Intent.Read),
(uint)CTFSpectra.ElementsSliceComplex,
LocalParams,
ResultPlus,
(uint)NFrameGroups,
(uint)NPositions);
}
{
CubicGrid AlteredPhaseMinus = new CubicGrid(GridCTFPhase.Dimensions, input.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v - Step).ToArray());
float[] PhaseValues = AlteredPhaseMinus.GetInterpolatedNative(PositionsGridPerFrame);
CTFStruct[] LocalParams = EvalGetCTF(input, CTF, DefocusValues, PhaseValues);
GPU.ParticleCTFCompareToSim(CTFSpectra.GetDevice(Intent.Read),
CTFCoordsCart.GetDevice(Intent.Read),
ParticleRefs.GetDevice(Intent.Read),
Sigma2Noise.GetDevice(Intent.Read),
(uint)CTFSpectra.ElementsSliceComplex,
LocalParams,
ResultMinus,
(uint)NFrameGroups,
(uint)NPositions);
}
float[] LocalGradients = new float[ResultPlus.Length];
for (int i = 0; i < LocalGradients.Length; i++)
LocalGradients[i] = ResultPlus[i] - ResultMinus[i];
// Now compute gradients per grid anchor point using the precomputed individual gradients and wiggle factors.
Parallel.For(0, GridCTFPhase.Dimensions.Elements(), i => Result[i + GridCTF.Dimensions.Elements()] = MathHelper.ReduceWeighted(LocalGradients, WiggleWeightsPhase[i]) / LocalGradients.Length / (2f * Step) * 1f);
}
foreach (var i in Result)
if (double.IsNaN(i) || double.IsInfinity(i))
throw new Exception("Bad score.");
return Result;
};
#endregion
#region Maximize normalized cross-correlation
double[] StartParams = new double[GridCTF.Dimensions.Elements() + GridCTFPhase.Dimensions.Elements() + 2];
for (int i = 0; i < GridCTF.Dimensions.Elements(); i++)
StartParams[i] = GridCTF.FlatValues[i];
for (int i = 0; i < GridCTFPhase.Dimensions.Elements(); i++)
StartParams[i + GridCTF.Dimensions.Elements()] = GridCTFPhase.FlatValues[i];
StartParams[StartParams.Length - 2] = (double)CTF.DefocusDelta;
StartParams[StartParams.Length - 1] = (double)CTF.DefocusAngle / 20 * (Math.PI / 180);
BroydenFletcherGoldfarbShanno Optimizer = new BroydenFletcherGoldfarbShanno(StartParams.Length, Eval, Gradient);
/*{
Past = 1,
Delta = 1e-6,
MaxLineSearch = 15,
Corrections = 20
};*/
double[] BestStart = new double[StartParams.Length];
for (int i = 0; i < BestStart.Length; i++)
BestStart[i] = StartParams[i];
double BestValue = Eval(StartParams);
for (int o = 0; o < 1; o++)
{
/*for (int step = 0; step < 150; step++)
{
float Adjustment = (step - 75) / 75f * 0.075f;
double[] Adjusted = new double[StartParams.Length];
for (int j = 0; j < Adjusted.Length; j++)
if (j < GridCTF.Dimensions.Elements())
Adjusted[j] = StartParams[j] + Adjustment;
else
Adjusted[j] = StartParams[j];
double NewValue = Eval(Adjusted);
if (NewValue > BestValue)
{
BestValue = NewValue;
for (int j = 0; j < GridCTF.Dimensions.Elements(); j++)
BestStart[j] = StartParams[j] + Adjustment;
}
}
for (int i = 0; i < GridCTF.Dimensions.Elements(); i++)
StartParams[i] = BestStart[i];*/
Optimizer.Maximize(StartParams);
}
#endregion
#region Retrieve parameters
decimal NewDefocus = (decimal)MathHelper.Mean(StartParams.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v));
Debug.WriteLine(CTF.Defocus - NewDefocus);
CTF.Defocus = (decimal)MathHelper.Mean(StartParams.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v));
CTF.DefocusDelta = (decimal)StartParams[StartParams.Length - 2];
CTF.DefocusAngle = (decimal)(StartParams[StartParams.Length - 1] * 20 / (Math.PI / 180));
CTF.PhaseShift = (decimal)MathHelper.Mean(StartParams.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v));
GridCTF = new CubicGrid(GridCTF.Dimensions, StartParams.Take((int)GridCTF.Dimensions.Elements()).Select(v => (float)v).ToArray());
GridCTFPhase = new CubicGrid(GridCTFPhase.Dimensions, StartParams.Skip((int)GridCTF.Dimensions.Elements()).Take((int)GridCTFPhase.Dimensions.Elements()).Select(v => (float)v).ToArray());
#endregion
Sigma2Noise.Dispose();
}
#endregion
ParticleRefs.Dispose();
//ParticleAmps.Dispose();
CTFSpectra.Dispose();
CTFCoordsCart.Dispose();
Simulated1D = GetSimulated1D();
CTFQuality = GetCTFQuality();
SaveMeta();
}
