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added options to export ctf parameters as csv and subtomogram without ctf correction #401

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6 changes: 3 additions & 3 deletions WarpLib/Movie/Movie.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -1674,14 +1674,14 @@ public virtual Image GetImagesForOneParticle(ProcessingOptionsBase options, Imag

#region GetCTFs methods

public virtual Image GetCTFsForOneParticle(ProcessingOptionsBase options, float3 coords, Image ctfCoords, Image gammaCorrection, bool weighted = true, bool weightsonly = false, bool useglobalweights = false, Image result = null)
public virtual Image GetCTFsForOneParticle(ProcessingOptionsBase options, float3 coords, Image ctfCoords, Image gammaCorrection, bool weighted = true, bool weightsonly = false, bool useglobalweights = false, Image result = null, string outputpath = "")
{
float3[] PerFrameCoords = Helper.ArrayOfConstant(coords, NFrames);

return GetCTFsForOneParticle(options, PerFrameCoords, ctfCoords, gammaCorrection, weighted, weightsonly, useglobalweights, result);
return GetCTFsForOneParticle(options, PerFrameCoords, ctfCoords, gammaCorrection, weighted, weightsonly, useglobalweights, result, outputpath);
}

public virtual Image GetCTFsForOneParticle(ProcessingOptionsBase options, float3[] coordsMoving, Image ctfCoords, Image gammaCorrection, bool weighted = true, bool weightsonly = false, bool useglobalweights = false, Image result = null)
public virtual Image GetCTFsForOneParticle(ProcessingOptionsBase options, float3[] coordsMoving, Image ctfCoords, Image gammaCorrection, bool weighted = true, bool weightsonly = false, bool useglobalweights = false, Image result = null, string outputpath = "")
{
float3[] ImagePositions = GetPositionInAllFrames(coordsMoving);

Expand Down
21 changes: 20 additions & 1 deletion WarpLib/OptionsWarp.cs
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Expand Up @@ -680,6 +680,9 @@ public ProcessingOptionsTomoSubReconstruction GetProcessingTomoSubReconstruction

MakeSparse = Tasks.TomoSubReconstructMakeSparse,

OutputCTFCSV = Tasks.TomoSubReconstructCTFCSV,
CorrectCTF = Tasks.TomoSubReconstructCorrectCTF,

UseCPU = Tasks.UseCPU
});

Expand Down Expand Up @@ -2080,6 +2083,22 @@ public bool TomoSubReconstructMakeSparse
get { return _TomoSubReconstructMakeSparse; }
set { if (value != _TomoSubReconstructMakeSparse) { _TomoSubReconstructMakeSparse = value; OnPropertyChanged(); } }
}

private bool _TomoSubReconstructCTFCSV = true;
[WarpSerializable]
public bool TomoSubReconstructCTFCSV
{
get { return _TomoSubReconstructCTFCSV; }
set { if (value != _TomoSubReconstructCTFCSV) { _TomoSubReconstructCTFCSV = value; OnPropertyChanged(); } }
}

private bool _TomoSubReconstructCorrectCTF = true;
[WarpSerializable]
public bool TomoSubReconstructCorrectCTF
{
get { return _TomoSubReconstructCorrectCTF; }
set { if (value != _TomoSubReconstructCorrectCTF) { _TomoSubReconstructCorrectCTF = value; OnPropertyChanged(); } }
}

#endregion

Expand Down Expand Up @@ -2320,4 +2339,4 @@ public enum ProcessingStatus
FilteredOut = 4,
LeaveOut = 5
}
}
}
39 changes: 29 additions & 10 deletions WarpLib/TiltSeries/TiltSeries.ReconstructSubtomos.cs
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Expand Up @@ -135,6 +135,7 @@ public void ReconstructSubtomos(ProcessingOptionsTomoSubReconstruction options,
ProjectorsMultiplicity[threadID].Weights.Fill(0);
CTFsComplex[threadID].Fill(new float2(1, 0));
CTFs[threadID].Fill(1);
CTFsAbs[threadID].Fill(1); //if dont correct ctf, voxel weight is 1

ProjectorsMultiplicity[threadID].BackProject(CTFsComplex[threadID], CTFs[threadID], !options.PrerotateParticles ? GetAngleInAllTilts(ParticlePositions) : GetParticleAngleInAllTilts(ParticlePositions, ParticleAngles), MagnificationCorrection);
ProjectorsMultiplicity[threadID].Weights.Min(1);
Expand All @@ -146,7 +147,10 @@ public void ReconstructSubtomos(ProcessingOptionsTomoSubReconstruction options,
Timing.Finish("ExtractImageData");

Timing.Start("CreateRawCTF");
GetCTFsForOneParticle(options, ParticlePositions, CTFCoords, null, true, false, false, CTFs[threadID]);
if (options.OutputCTFCSV)
GetCTFsForOneParticle(options, ParticlePositions, CTFCoords, null, true, false, false, CTFs[threadID], System.IO.Path.Combine(SubtomoDir, $"{RootName}{options.Suffix}_{p:D7}_ctf_{options.BinnedPixelSizeMean:F2}A.csv"));
else
GetCTFsForOneParticle(options, ParticlePositions, CTFCoords, null, true, false, false, CTFs[threadID]);
GetCTFsForOneParticle(options, ParticlePositions, CTFCoords, null, false, false, false, CTFsUnweighted[threadID]);
Timing.Finish("CreateRawCTF");

Expand All @@ -156,24 +160,34 @@ public void ReconstructSubtomos(ProcessingOptionsTomoSubReconstruction options,
// Subtomo is (Image * CTFweighted) / abs(CTFunweighted)
// 3D CTF is (CTFweighted * CTFweighted) / abs(CTFweighted)

ImagesFT[threadID].Multiply(CTFs[threadID]);
//GPU.Abs(CTFs[threadID].GetDevice(Intent.Read),
// CTFsAbs[threadID].GetDevice(Intent.Write),
// CTFs[threadID].ElementsReal);
CTFsAbs[threadID].Abs();
//MOD: if correct subtomo
if (options.CorrectCTF)
{
ImagesFT[threadID].Multiply(CTFs[threadID]);
//GPU.Abs(CTFs[threadID].GetDevice(Intent.Read),
// CTFsAbs[threadID].GetDevice(Intent.Write),
// CTFs[threadID].ElementsReal);
}

CTFsComplex[threadID].Fill(new float2(1, 0));
CTFsComplex[threadID].Multiply(CTFsUnweighted[threadID]); // What the raw image is like: unweighted, unflipped
if (options.CorrectCTF)
CTFsComplex[threadID].Multiply(CTFsUnweighted[threadID]); // What the raw image is like: unweighted, unflipped
CTFsComplex[threadID].Multiply(CTFs[threadID]); // Weight by the same CTF as raw image: weighted, unflipped

CTFsUnweighted[threadID].Abs();
if (options.CorrectCTF)
CTFsUnweighted[threadID].Abs();

#region Sub-tomo

Projectors[threadID].Data.Fill(0);
Projectors[threadID].Weights.Fill(0);

Timing.Start("ProjectImageData");
Projectors[threadID].BackProject(ImagesFT[threadID], CTFsUnweighted[threadID], !options.PrerotateParticles ? GetAngleInAllTilts(ParticlePositions) : GetParticleAngleInAllTilts(ParticlePositions, ParticleAngles), MagnificationCorrection);
if (options.CorrectCTF)
Projectors[threadID].BackProject(ImagesFT[threadID], CTFsUnweighted[threadID], !options.PrerotateParticles ? GetAngleInAllTilts(ParticlePositions) : GetParticleAngleInAllTilts(ParticlePositions, ParticleAngles), MagnificationCorrection);
else
Projectors[threadID].BackProject(ImagesFT[threadID], CTFsAbs[threadID], !options.PrerotateParticles ? GetAngleInAllTilts(ParticlePositions) : GetParticleAngleInAllTilts(ParticlePositions, ParticleAngles), MagnificationCorrection);
Timing.Finish("ProjectImageData");

//Projectors[threadID].Weights.Fill(1);
Expand Down Expand Up @@ -212,7 +226,10 @@ public void ReconstructSubtomos(ProcessingOptionsTomoSubReconstruction options,
Projectors[threadID].Data.Fill(0);
Projectors[threadID].Weights.Fill(0);

Projectors[threadID].BackProject(CTFsComplex[threadID], CTFsUnweighted[threadID], !options.PrerotateParticles ? GetAngleInAllTilts(ParticlePositions) : GetParticleAngleInAllTilts(ParticlePositions, ParticleAngles), MagnificationCorrection);
if (options.CorrectCTF)
Projectors[threadID].BackProject(CTFsComplex[threadID], CTFsUnweighted[threadID], !options.PrerotateParticles ? GetAngleInAllTilts(ParticlePositions) : GetParticleAngleInAllTilts(ParticlePositions, ParticleAngles), MagnificationCorrection);
else
Projectors[threadID].BackProject(CTFsComplex[threadID], CTFsAbs[threadID], !options.PrerotateParticles ? GetAngleInAllTilts(ParticlePositions) : GetParticleAngleInAllTilts(ParticlePositions, ParticleAngles), MagnificationCorrection);

//Projectors[threadID].Weights.Fill(1);
Projectors[threadID].Data.Multiply(ProjectorsMultiplicity[threadID].Weights);
Expand Down Expand Up @@ -343,4 +360,6 @@ public class ProcessingOptionsTomoSubReconstruction : TomoProcessingOptionsBase
[WarpSerializable] public int NTilts { get; set; }
[WarpSerializable] public bool MakeSparse { get; set; }
[WarpSerializable] public bool UseCPU { get; set; }
}
[WarpSerializable] public bool CorrectCTF { get; set; }
[WarpSerializable] public bool OutputCTFCSV { get; set; }
}
25 changes: 22 additions & 3 deletions WarpLib/TiltSeries/TiltSeries.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -945,16 +945,16 @@ public override Image GetImagesForOneParticle(ProcessingOptionsBase options, Ima

#region GetCTFs methods

public override Image GetCTFsForOneParticle(ProcessingOptionsBase options, float3 coords, Image ctfCoords, Image gammaCorrection, bool weighted = true, bool weightsonly = false, bool useglobalweights = false, Image result = null)
public override Image GetCTFsForOneParticle(ProcessingOptionsBase options, float3 coords, Image ctfCoords, Image gammaCorrection, bool weighted = true, bool weightsonly = false, bool useglobalweights = false, Image result = null, string outputpath = "")
{
float3[] PerTiltCoords = new float3[NTilts];
for (int i = 0; i < NTilts; i++)
PerTiltCoords[i] = coords;

return GetCTFsForOneParticle(options, PerTiltCoords, ctfCoords, gammaCorrection, weighted, weightsonly, useglobalweights, result);
return GetCTFsForOneParticle(options, PerTiltCoords, ctfCoords, gammaCorrection, weighted, weightsonly, useglobalweights, result, outputpath);
}

public override Image GetCTFsForOneParticle(ProcessingOptionsBase options, float3[] coordsMoving, Image ctfCoords, Image gammaCorrection, bool weighted = true, bool weightsonly = false, bool useglobalweights = false, Image result = null)
public override Image GetCTFsForOneParticle(ProcessingOptionsBase options, float3[] coordsMoving, Image ctfCoords, Image gammaCorrection, bool weighted = true, bool weightsonly = false, bool useglobalweights = false, Image result = null, string outputpath = "")
{
float3[] ImagePositions = GetPositionInAllTilts(coordsMoving);

Expand Down Expand Up @@ -1017,6 +1017,25 @@ public override Image GetCTFsForOneParticle(ProcessingOptionsBase options, float
Params[t] = CurrCTF.ToStruct();
}

if (outputpath != "")
{
using (StreamWriter writer = new StreamWriter(outputpath))
{
string output = string.Join(", ", typeof(CTFStruct)
.GetFields()
.Select(field => $"{field.Name}"));
writer.WriteLine($"TiltAngle, X, Y, Z, {output}");

for (int t = 0; t < NTilts; t++)
{
string output_t = string.Join(", ", typeof(CTFStruct)
.GetFields()
.Select(field => $"{field.GetValue(Params[t])}"));
writer.WriteLine($"{Angles[t]}, {coordsMoving[t].X}, {coordsMoving[t].Y}, {coordsMoving[t].Z}, {output_t}");
}
}
}

Image Result = result == null ? new Image(IntPtr.Zero, new int3(ctfCoords.Dims.X, ctfCoords.Dims.Y, NTilts), true) : result;
GPU.CreateCTF(Result.GetDevice(Intent.Write),
ctfCoords.GetDevice(Intent.Read),
Expand Down
12 changes: 10 additions & 2 deletions WarpTools/Commands/Tiltseries/ExportParticlesTiltseries.cs
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Expand Up @@ -75,7 +75,7 @@ class ExportParticlesTiltseriesOptions : DistributedOptions

[Option("3d", HelpText = "Output particles as 3d images (subtomograms)")]
public bool Output3DParticles { get; set; }

[OptionGroup("Expert options")]
[Option("dont_normalize_input",
HelpText =
Expand All @@ -87,6 +87,12 @@ class ExportParticlesTiltseriesOptions : DistributedOptions
"Don't normalize output particle volumes (only works with --3d)")]
public bool DontNormalizeSubtomos { get; set; }

[Option("output_ctf_csv", HelpText = "Export CTF parameters as CSV files")]
public bool OutputCTFCSV { get; set; }

[Option("dont_correct_ctf_3d", HelpText = "Dont apply ctf correction to 3d subtomogram")]
public bool DontCorrectCTFSubtomos { get; set; }

[Option("n_tilts",
HelpText =
"Number of tilt images to include in the output, images with the lowest overall exposure will be included first",
Expand Down Expand Up @@ -457,6 +463,8 @@ private ProcessingOptionsTomoSubReconstruction PrepareWarpWorkerExportOptions(
options.Tasks.Export2DBoxSize = cli.OutputBoxSize;
options.Tasks.Export2DParticleDiameter = cli.OutputBoxSize;
options.Tasks.InputNormalize = !cli.DontNormalizeInputImages;
options.Tasks.TomoSubReconstructCTFCSV = cli.OutputCTFCSV;
options.Tasks.TomoSubReconstructCorrectCTF = !cli.DontCorrectCTFSubtomos;

options.Tasks.OutputNormalize =
cli.Output3DParticles && !cli.DontNormalizeSubtomos;
Expand Down Expand Up @@ -1168,4 +1176,4 @@ int maxMissingTilts


}
}
}