public void TomoExportParticles(string path, ProcessingOptionsTomoSubReconstruction options, float3[] coordinates, float3[] angles)
{
if (!SendCommand(new NamedSerializableObject("TomoExportParticles",
path,
options,
coordinates,
angles)))
{
throw new Exception("Couldn't export the particles!");
}
}
static void Main(string[] args)
{
CultureInfo.DefaultThreadCurrentCulture = CultureInfo.InvariantCulture;
CultureInfo.DefaultThreadCurrentUICulture = CultureInfo.InvariantCulture;
//if (!Debugger.IsAttached)
// Debugger.Launch();
if (args.Length < 3)
{
return;
}
DeviceID = int.Parse(args[0]) % GPU.GetDeviceCount();
PipeName = args[1];
bool DebugMode = bool.Parse(args[2]);
GPU.SetDevice(DeviceID);
Console.WriteLine($"Running on GPU #{DeviceID} ({GPU.GetFreeMemory(DeviceID)} MB free) through {PipeName}\n");
Formatter = new BinaryFormatter();
Heartbeat = new Thread(new ThreadStart(() =>
{
if (!DebugMode)
{
while (true)
{
try
{
NamedPipeClientStream PipeHeartbeat = new NamedPipeClientStream(".", PipeName + "_heartbeat", PipeDirection.In);
PipeHeartbeat.Connect(5000);
PipeHeartbeat.Dispose();
}
catch
{
if (!Terminating)
{
Process.GetCurrentProcess().Kill();
}
}
}
}
}));
Heartbeat.Start();
while (true)
{
PipeReceive = new NamedPipeClientStream(".", PipeName + "_out", PipeDirection.In);
PipeReceive.Connect();
NamedSerializableObject Command = (NamedSerializableObject)Formatter.Deserialize(PipeReceive);
PipeReceive.Dispose();
Console.WriteLine($"Received \"{Command.Name}\", with {Command.Content.Length} arguments, for GPU #{GPU.GetDevice()}, {GPU.GetFreeMemory(DeviceID)} MB free");
try
{
Stopwatch Watch = new Stopwatch();
Watch.Start();
if (Command.Name == "Exit")
{
Movie.WriteAverageAsync?.Wait();
SendSuccessStatus(true);
Process.GetCurrentProcess().Kill();
return;
}
else if (Command.Name == "Ping")
{
Console.WriteLine("Ping!");
}
else if (Command.Name == "SetHeaderlessParams")
{
HeaderlessDims = (int2)Command.Content[0];
HeaderlessOffset = (long)Command.Content[1];
HeaderlessType = (string)Command.Content[2];
Console.WriteLine($"Set headerless parameters to {HeaderlessDims}, {HeaderlessOffset}, {HeaderlessType}");
}
else if (Command.Name == "LoadGainRef")
{
GainRef?.Dispose();
DefectMap?.Dispose();
string GainPath = (string)Command.Content[0];
bool FlipX = (bool)Command.Content[1];
bool FlipY = (bool)Command.Content[2];
bool Transpose = (bool)Command.Content[3];
string DefectsPath = (string)Command.Content[4];
if (!string.IsNullOrEmpty(GainPath))
{
GainRef = LoadAndPrepareGainReference(GainPath, FlipX, FlipY, Transpose);
}
if (!string.IsNullOrEmpty(DefectsPath))
{
DefectMap = LoadAndPrepareDefectMap(DefectsPath, FlipX, FlipY, Transpose);
}
Console.WriteLine($"Loaded gain reference and defect map: {GainRef}, {FlipX}, {FlipY}, {Transpose}, {DefectsPath}");
}
else if (Command.Name == "LoadStack")
{
OriginalStack?.Dispose();
string Path = (string)Command.Content[0];
decimal ScaleFactor = (decimal)Command.Content[1];
int EERGroupFrames = (int)Command.Content[2];
HeaderEER.GroupNFrames = EERGroupFrames;
OriginalStack = LoadAndPrepareStack(Path, ScaleFactor);
OriginalStackOwner = Helper.PathToNameWithExtension(Path);
Console.WriteLine($"Loaded stack: {OriginalStack}, {ScaleFactor}");
}
else if (Command.Name == "MovieProcessCTF")
{
string Path = (string)Command.Content[0];
ProcessingOptionsMovieCTF Options = (ProcessingOptionsMovieCTF)Command.Content[1];
if (Helper.PathToNameWithExtension(Path) != OriginalStackOwner)
{
throw new Exception("Currently loaded stack doesn't match the movie requested for processing!");
}
Movie M = new Movie(Path);
M.ProcessCTF(OriginalStack, Options);
M.SaveMeta();
Console.WriteLine($"Processed CTF for {Path}");
}
else if (Command.Name == "MovieProcessMovement")
{
string Path = (string)Command.Content[0];
ProcessingOptionsMovieMovement Options = (ProcessingOptionsMovieMovement)Command.Content[1];
if (Helper.PathToNameWithExtension(Path) != OriginalStackOwner)
{
throw new Exception("Currently loaded stack doesn't match the movie requested for processing!");
}
Movie M = new Movie(Path);
M.ProcessShift(OriginalStack, Options);
M.SaveMeta();
Console.WriteLine($"Processed movement for {Path}");
}
else if (Command.Name == "MovieExportMovie")
{
string Path = (string)Command.Content[0];
ProcessingOptionsMovieExport Options = (ProcessingOptionsMovieExport)Command.Content[1];
if (Helper.PathToNameWithExtension(Path) != OriginalStackOwner)
{
throw new Exception("Currently loaded stack doesn't match the movie requested for processing!");
}
Movie M = new Movie(Path);
M.ExportMovie(OriginalStack, Options);
M.SaveMeta();
Console.WriteLine($"Exported movie for {Path}");
}
else if (Command.Name == "MovieExportParticles")
{
string Path = (string)Command.Content[0];
ProcessingOptionsParticlesExport Options = (ProcessingOptionsParticlesExport)Command.Content[1];
float2[] Coordinates = (float2[])Command.Content[2];
if (Helper.PathToNameWithExtension(Path) != OriginalStackOwner)
{
throw new Exception("Currently loaded stack doesn't match the movie requested for processing!");
}
Movie M = new Movie(Path);
M.ExportParticles(OriginalStack, Coordinates, Options);
M.SaveMeta();
Console.WriteLine($"Exported {Coordinates.Length} particles for {Path}");
}
else if (Command.Name == "TomoProcessCTF")
{
string Path = (string)Command.Content[0];
ProcessingOptionsMovieCTF Options = (ProcessingOptionsMovieCTF)Command.Content[1];
TiltSeries T = new TiltSeries(Path);
T.ProcessCTFSimultaneous(Options);
T.SaveMeta();
Console.WriteLine($"Processed CTF for {Path}");
}
else if (Command.Name == "TomoExportParticles")
{
string Path = (string)Command.Content[0];
ProcessingOptionsTomoSubReconstruction Options = (ProcessingOptionsTomoSubReconstruction)Command.Content[1];
float3[] Coordinates = (float3[])Command.Content[2];
float3[] Angles = Command.Content[3] != null ? (float3[])Command.Content[3] : null;
TiltSeries T = new TiltSeries(Path);
T.ReconstructSubtomos(Options, Coordinates, Angles);
T.SaveMeta();
Console.WriteLine($"Exported {Coordinates.Length} particles for {Path}");
}
else if (Command.Name == "MPAPreparePopulation")
{
string Path = (string)Command.Content[0];
MPAPopulation = new Population(Path);
foreach (var species in MPAPopulation.Species)
{
Console.Write($"Preparing {species.Name} for refinement... ");
species.PrepareRefinementRequisites(true, DeviceID);
Console.WriteLine("Done.");
}
}
else if (Command.Name == "MPARefine")
{
string Path = (string)Command.Content[0];
string WorkingDirectory = (string)Command.Content[1];
string LogPath = (string)Command.Content[2];
ProcessingOptionsMPARefine Options = (ProcessingOptionsMPARefine)Command.Content[3];
DataSource Source = (DataSource)Command.Content[4];
Movie Item = null;
if (Helper.PathToExtension(Path).ToLower() == ".tomostar")
{
Item = new TiltSeries(Path);
}
else
{
Item = new Movie(Path);
}
GPU.SetDevice(DeviceID);
Item.PerformMultiParticleRefinement(WorkingDirectory, Options, MPAPopulation.Species.ToArray(), Source, GainRef, DefectMap, (message) =>
{
Console.WriteLine(message);
bool Success = false;
int Tries = 0;
while (!Success && Tries < 10)
{
try
{
using (TextWriter Writer = File.AppendText(LogPath))
Writer.WriteLine(message);
Success = true;
}
catch
{
Thread.Sleep(100);
Tries++;
}
}
});
Item.SaveMeta();
GPU.CheckGPUExceptions();
Console.WriteLine($"Finished refining {Item.Name}");
}
else if (Command.Name == "MPASaveProgress")
{
string Path = (string)Command.Content[0];
MPAPopulation.SaveRefinementProgress(Path);
}
else if (Command.Name == "TryAllocatePinnedMemory")
{
long[] ChunkSizes = (long[])Command.Content[0];
IntPtr[] Chunks = new IntPtr[ChunkSizes.Length];
for (int i = 0; i < ChunkSizes.Length; i++)
{
Chunks[i] = GPU.MallocHostPinned(ChunkSizes[i] / sizeof(float));
//Dummies.Add(Helper.ArrayOfSequence(0, (int)(ChunkSizes[i] / sizeof(float) / 2), 1));
}
GPU.CheckGPUExceptions();
//for (int i = 0; i < ChunkSizes.Length; i++)
// GPU.FreeHostPinned(Chunks[i]);
Console.WriteLine($"Successfully allocated {ChunkSizes.Sum()} bytes of pinned memory");
}
Watch.Stop();
Console.WriteLine((Watch.ElapsedMilliseconds / 1000f).ToString("F3"));
Console.WriteLine("");
SendSuccessStatus(true);
}
catch (Exception e)
{
Console.WriteLine(e.ToString());
File.WriteAllText($"worker_{DeviceID}_crash.txt", e.ToString());
//Console.Read();
SendSuccessStatus(false);
}
}
}
private async void ButtonWrite_OnClick(object sender, RoutedEventArgs e)
{
System.Windows.Forms.SaveFileDialog SaveDialog = new System.Windows.Forms.SaveFileDialog
{
Filter = "STAR Files|*.star"
};
System.Windows.Forms.DialogResult ResultSave = SaveDialog.ShowDialog();
if (ResultSave.ToString() == "OK")
{
ExportPath = SaveDialog.FileName;
}
else
{
return;
}
decimal _OutputAngPix = OutputAngPix;
int _BoxSize = BoxSize;
int _Diameter = Diameter;
bool _ReconstructVolume = ReconstructVolume;
bool _ReconstructSeries = ReconstructSeries;
bool _ApplyShift = ApplyShift;
decimal _ShiftX = ShiftX;
decimal _ShiftY = ShiftY;
decimal _ShiftZ = ShiftZ;
bool _ReconstructPrerotated = ReconstructPrerotated;
bool _ReconstructDoLimitDose = ReconstructDoLimitDose;
int _ReconstructNTilts = ReconstructNTilts;
bool _InputInvert = InputInvert;
bool _InputNormalize = InputNormalize;
bool _OutputNormalize = OutputNormalize;
bool _ReconstructMakeSparse = ReconstructMakeSparse;
if (!_ReconstructVolume)
{
_ReconstructPrerotated = true;
}
float3 AdditionalShiftAngstrom = new float3((float)_ShiftX,
(float)_ShiftY,
(float)_ShiftZ);
ProgressWrite.Visibility = Visibility.Visible;
ProgressWrite.IsIndeterminate = true;
PanelButtons.Visibility = Visibility.Collapsed;
PanelRemaining.Visibility = Visibility.Visible;
foreach (var element in DisableWhileProcessing)
{
element.IsEnabled = false;
}
MainWindow MainWindow = (MainWindow)Application.Current.MainWindow;
await Task.Run(() =>
{
List <Star> AllSourceTables = new List <Star>();
string[] AllSourceHashes = Helper.GetUniqueElements(Species.Particles.Select(p => p.SourceHash)).ToArray();
AllSourceHashes = AllSourceHashes.Where(h => Sources.Any(s => s.Files.ContainsKey(h))).ToArray();
foreach (var source in Sources)
{
if (!source.IsTiltSeries)
{
continue;
}
#region Get all movies that can potentially be used
List <string> ValidSourceHashes = AllSourceHashes.Where(h => source.Files.ContainsKey(h)).ToList();
List <string> ValidSourcePaths = ValidSourceHashes.Select(k => System.IO.Path.Combine(source.FolderPath, source.Files[k])).ToList();
List <string> ValidMovieNames = ValidSourcePaths.Select(p => Helper.PathToName(p)).ToList();
List <TiltSeries> ValidSeries = ValidSourcePaths.Select(p => new TiltSeries(p)).ToList();
List <Particle> Particles = Species.Particles.Where(p => ValidSourceHashes.Contains(p.SourceHash)).ToList();
Particles.Sort((a, b) => a.SourceHash.CompareTo(b.SourceHash));
#endregion
if (IsCanceled)
{
return;
}
#region Create worker processes
int NDevices = GPU.GetDeviceCount();
List <int> UsedDevices = MainWindow.GetDeviceList();
List <int> UsedDeviceProcesses = Helper.Combine(Helper.ArrayOfFunction(i => UsedDevices.Select(d => d + i *NDevices).ToArray(), 1)).ToList();
WorkerWrapper[] Workers = new WorkerWrapper[GPU.GetDeviceCount() * 1];
foreach (var gpuID in UsedDeviceProcesses)
{
Workers[gpuID] = new WorkerWrapper(gpuID);
Workers[gpuID].SetHeaderlessParams(new int2(1, 1),
0,
"float32");
Workers[gpuID].LoadGainRef(source.GainPath,
source.GainFlipX,
source.GainFlipY,
source.GainTranspose,
source.DefectsPath);
}
#endregion
List <Star> SourceTables = new List <Star>();
{
Dispatcher.Invoke(() => ProgressWrite.MaxValue = AllSourceHashes.Length);
Helper.ForEachGPU(ValidSeries, (series, gpuID) =>
{
if (IsCanceled)
{
return;
}
Stopwatch ItemTime = new Stopwatch();
ItemTime.Start();
string SeriesHash = series.GetDataHash();
Star TableOut = new Star(new string[] { "rlnMagnification",
"rlnDetectorPixelSize",
"rlnCoordinateX",
"rlnCoordinateY",
"rlnCoordinateZ",
"rlnAngleRot",
"rlnAngleTilt",
"rlnAnglePsi",
"rlnImageName",
"rlnCtfImage",
"rlnRandomSubset" });
ProcessingOptionsTomoSubReconstruction ExportOptions = new ProcessingOptionsTomoSubReconstruction()
{
PixelSizeX = source.PixelSizeX,
PixelSizeY = source.PixelSizeY,
PixelSizeAngle = source.PixelSizeAngle,
BinTimes = (decimal)Math.Log((double)(_OutputAngPix / source.PixelSizeMean), 2.0),
GainPath = source.GainPath,
DefectsPath = source.DefectsPath,
GainFlipX = source.GainFlipX,
GainFlipY = source.GainFlipY,
GainTranspose = source.GainTranspose,
Dimensions = new float3((float)source.DimensionsX,
(float)source.DimensionsY,
(float)source.DimensionsZ),
Suffix = "_" + Species.NameSafe,
BoxSize = _BoxSize,
ParticleDiameter = _Diameter,
Invert = _InputInvert,
NormalizeInput = _InputNormalize,
NormalizeOutput = _OutputNormalize,
PrerotateParticles = _ReconstructPrerotated,
DoLimitDose = _ReconstructDoLimitDose,
NTilts = Math.Min(series.NTilts, Math.Min(source.FrameLimit, _ReconstructNTilts)),
MakeSparse = _ReconstructMakeSparse
};
Particle[] SeriesParticles = Particles.Where(p => p.SourceHash == SeriesHash).ToArray();
int NParticles = SeriesParticles.Length;
#region Process particle positions and angles
float3[] Positions = new float3[NParticles *series.NTilts];
float3[] Angles = new float3[NParticles *series.NTilts];
int[] Subsets = SeriesParticles.Select(p => p.RandomSubset + 1).ToArray();
float MinDose = MathHelper.Min(series.Dose);
float MaxDose = MathHelper.Max(series.Dose);
float[] InterpolationSteps = Helper.ArrayOfFunction(i => (series.Dose[i] - MinDose) / (MaxDose - MinDose), series.NTilts);
for (int p = 0; p < NParticles; p++)
{
float3[] ParticlePositions = SeriesParticles[p].GetCoordinateSeries(InterpolationSteps);
float3[] ParticleAngles = SeriesParticles[p].GetAngleSeries(InterpolationSteps);
if (_ApplyShift)
{
Matrix3 R0 = Matrix3.Euler(ParticleAngles[0] * Helper.ToRad);
float3 RotatedShift = R0 *AdditionalShiftAngstrom;
for (int t = 0; t < ParticlePositions.Length; t++)
{
ParticlePositions[t] += RotatedShift;
}
}
if (!_ReconstructPrerotated)
{
Matrix3 R0I = Matrix3.Euler(ParticleAngles[0] * Helper.ToRad).Transposed();
for (int t = 0; t < ParticleAngles.Length; t++)
{
ParticleAngles[t] = Matrix3.EulerFromMatrix(R0I *Matrix3.Euler(ParticleAngles[t] * Helper.ToRad)) * Helper.ToDeg;
}
}
for (int t = 0; t < series.NTilts; t++)
{
Positions[p *series.NTilts + t] = ParticlePositions[t];
Angles[p *series.NTilts + t] = ParticleAngles[t];
}
string PathSubtomo = series.SubtomoDir + $"{series.RootName}{ExportOptions.Suffix}_{p:D7}_{ExportOptions.BinnedPixelSizeMean:F2}A.mrc";
string PathCTF = (series.SubtomoDir + $"{series.RootName}{ExportOptions.Suffix}_{p:D7}_ctf_{ExportOptions.BinnedPixelSizeMean:F2}A.mrc");
Uri UriStar = new Uri(ExportPath);
PathSubtomo = UriStar.MakeRelativeUri(new Uri(PathSubtomo)).ToString();
PathCTF = UriStar.MakeRelativeUri(new Uri(PathCTF)).ToString();
TableOut.AddRow(new List <string>()
{
"10000.0",
ExportOptions.BinnedPixelSizeMean.ToString("F5", CultureInfo.InvariantCulture),
(ParticlePositions[0].X / (float)ExportOptions.BinnedPixelSizeMean).ToString("F5", CultureInfo.InvariantCulture),
(ParticlePositions[0].Y / (float)ExportOptions.BinnedPixelSizeMean).ToString("F5", CultureInfo.InvariantCulture),
(ParticlePositions[0].Z / (float)ExportOptions.BinnedPixelSizeMean).ToString("F5", CultureInfo.InvariantCulture),
(_ReconstructPrerotated ? 0 : SeriesParticles[p].Angles[0].X).ToString("F5", CultureInfo.InvariantCulture),
(_ReconstructPrerotated ? 0 : SeriesParticles[p].Angles[0].Y).ToString("F5", CultureInfo.InvariantCulture),
(_ReconstructPrerotated ? 0 : SeriesParticles[p].Angles[0].Z).ToString("F5", CultureInfo.InvariantCulture),
PathSubtomo,
PathCTF,
Subsets[p].ToString()
});
}
#endregion
#region Finally, reconstruct the actual sub-tomos
if (_ReconstructVolume)
{
Workers[gpuID].TomoExportParticles(series.Path, ExportOptions, Positions, Angles);
}
else
{
series.ReconstructParticleSeries(ExportOptions, Positions, Angles, Subsets, ExportPath, out TableOut);
}
lock (AllSourceTables)
AllSourceTables.Add(TableOut);
#endregion
#region Add this micrograph's table to global collection, update remaining time estimate
lock (AllSourceTables)
{
Timings.Add(ItemTime.ElapsedMilliseconds / (float)UsedDeviceProcesses.Count);
int MsRemaining = (int)(MathHelper.Mean(Timings) * (AllSourceHashes.Length - AllSourceTables.Count));
TimeSpan SpanRemaining = new TimeSpan(0, 0, 0, 0, MsRemaining);
Dispatcher.Invoke(() => TextRemaining.Text = SpanRemaining.ToString((int)SpanRemaining.TotalHours > 0 ? @"hh\:mm\:ss" : @"mm\:ss"));
Dispatcher.Invoke(() =>
{
ProgressWrite.IsIndeterminate = false;
ProgressWrite.Value = AllSourceTables.Count;
});
}
#endregion
}, 1, UsedDeviceProcesses);
}
Thread.Sleep(10000); // Writing out particles is async, so if workers are killed immediately they may not write out everything
foreach (var worker in Workers)
{
worker?.Dispose();
}
if (IsCanceled)
{
return;
}
}
if (AllSourceTables.Count > 0)
{
(new Star(AllSourceTables.ToArray())).Save(ExportPath);
}
});
Close?.Invoke();
}
private async void ButtonWrite_OnClick(object sender, RoutedEventArgs e)
{
System.Windows.Forms.SaveFileDialog SaveDialog = new System.Windows.Forms.SaveFileDialog
{
Filter = "STAR Files|*.star"
};
System.Windows.Forms.DialogResult ResultSave = SaveDialog.ShowDialog();
if (ResultSave.ToString() == "OK")
{
ExportPath = SaveDialog.FileName;
}
else
{
return;
}
bool Invert = (bool)CheckInvert.IsChecked;
bool Normalize = (bool)CheckNormalize.IsChecked;
bool Preflip = (bool)CheckPreflip.IsChecked;
bool Relative = (bool)CheckRelative.IsChecked;
bool Filter = (bool)CheckFilter.IsChecked;
bool Manual = (bool)CheckManual.IsChecked;
int BoxSize = (int)Options.Tasks.Export2DBoxSize;
int NormDiameter = (int)Options.Tasks.Export2DParticleDiameter;
bool DoVolumes = (bool)RadioVolume.IsChecked;
if (!DoVolumes)
{
Options.Tasks.TomoSubReconstructPrerotated = true;
}
bool MakeSparse = (bool)CheckSparse.IsChecked;
float3 AdditionalShiftAngstrom = (bool)CheckShiftParticles.IsChecked ?
new float3((float)SliderShiftParticlesX.Value,
(float)SliderShiftParticlesY.Value,
(float)SliderShiftParticlesZ.Value) :
new float3(0);
ProgressWrite.Visibility = Visibility.Visible;
ProgressWrite.IsIndeterminate = true;
PanelButtons.Visibility = Visibility.Collapsed;
PanelRemaining.Visibility = Visibility.Visible;
foreach (var element in DisableWhileProcessing)
{
element.IsEnabled = false;
}
await Task.Run(() =>
{
#region Get all movies that can potentially be used
List <TiltSeries> ValidSeries = Series.Where(v =>
{
if (!Filter && v.UnselectFilter && v.UnselectManual == null)
{
return(false);
}
if (!Manual && v.UnselectManual != null && (bool)v.UnselectManual)
{
return(false);
}
if (v.OptionsCTF == null)
{
return(false);
}
return(true);
}).ToList();
List <string> ValidMovieNames = ValidSeries.Select(m => m.RootName).ToList();
#endregion
#region Read table and intersect its micrograph set with valid movies
Star TableIn;
if (Options.Tasks.InputOnePerItem)
{
List <Star> Tables = new List <Star>();
foreach (var item in Series)
{
string StarPath = InputFolder + item.RootName + InputSuffix;
if (File.Exists(StarPath))
{
Star TableItem = new Star(StarPath);
if (!TableItem.HasColumn("rlnMicrographName"))
{
TableItem.AddColumn("rlnMicrographName", item.Name);
}
else
{
TableItem.SetColumn("rlnMicrographName", Helper.ArrayOfConstant(item.Name, TableItem.RowCount));
}
Tables.Add(TableItem);
}
}
TableIn = new Star(Tables.ToArray());
}
else
{
TableIn = new Star(ImportPath);
}
if (!TableIn.HasColumn("rlnMicrographName"))
{
throw new Exception("Couldn't find rlnMicrographName column.");
}
if (!TableIn.HasColumn("rlnCoordinateX"))
{
throw new Exception("Couldn't find rlnCoordinateX column.");
}
if (!TableIn.HasColumn("rlnCoordinateY"))
{
throw new Exception("Couldn't find rlnCoordinateY column.");
}
if (!TableIn.HasColumn("rlnCoordinateZ"))
{
throw new Exception("Couldn't find rlnCoordinateZ column.");
}
Dictionary <string, List <int> > Groups = new Dictionary <string, List <int> >();
{
string[] ColumnMicNames = TableIn.GetColumn("rlnMicrographName");
for (int r = 0; r < ColumnMicNames.Length; r++)
{
if (!Groups.ContainsKey(ColumnMicNames[r]))
{
Groups.Add(ColumnMicNames[r], new List <int>());
}
Groups[ColumnMicNames[r]].Add(r);
}
Groups = Groups.ToDictionary(group => Helper.PathToName(group.Key), group => group.Value);
Groups = Groups.Where(group => ValidMovieNames.Any(n => group.Key.Contains(n))).ToDictionary(group => group.Key, group => group.Value);
}
bool[] RowsIncluded = new bool[TableIn.RowCount];
foreach (var group in Groups)
{
foreach (var r in group.Value)
{
RowsIncluded[r] = true;
}
}
List <int> RowsNotIncluded = new List <int>();
for (int r = 0; r < RowsIncluded.Length; r++)
{
if (!RowsIncluded[r])
{
RowsNotIncluded.Add(r);
}
}
ValidSeries = ValidSeries.Where(v => Groups.Any(n => n.Key.Contains(v.RootName))).ToList();
if (ValidSeries.Count == 0) // Exit if there is nothing to export, otherwise errors will be thrown below
{
return;
}
#endregion
#region Make sure all columns are there
if (!TableIn.HasColumn("rlnMagnification"))
{
TableIn.AddColumn("rlnMagnification", "10000.0");
}
else
{
TableIn.SetColumn("rlnMagnification", Helper.ArrayOfConstant("10000.0", TableIn.RowCount));
}
if (!TableIn.HasColumn("rlnDetectorPixelSize"))
{
TableIn.AddColumn("rlnDetectorPixelSize", Options.Tasks.TomoSubReconstructPixel.ToString("F5", CultureInfo.InvariantCulture));
}
else
{
TableIn.SetColumn("rlnDetectorPixelSize", Helper.ArrayOfConstant(Options.Tasks.TomoSubReconstructPixel.ToString("F5", CultureInfo.InvariantCulture), TableIn.RowCount));
}
if (!TableIn.HasColumn("rlnCtfMaxResolution"))
{
TableIn.AddColumn("rlnCtfMaxResolution", "999.0");
}
if (!TableIn.HasColumn("rlnImageName"))
{
TableIn.AddColumn("rlnImageName", "None");
}
if (!TableIn.HasColumn("rlnCtfImage"))
{
TableIn.AddColumn("rlnCtfImage", "None");
}
List <Star> SeriesTablesOut = new List <Star>();
#endregion
if (IsCanceled)
{
return;
}
#region Create worker processes
int NDevices = GPU.GetDeviceCount();
List <int> UsedDevices = Options.MainWindow.GetDeviceList();
List <int> UsedDeviceProcesses = Helper.Combine(Helper.ArrayOfFunction(i => UsedDevices.Select(d => d + i *NDevices).ToArray(), MainWindow.GlobalOptions.ProcessesPerDevice)).ToList();
WorkerWrapper[] Workers = new WorkerWrapper[GPU.GetDeviceCount() * MainWindow.GlobalOptions.ProcessesPerDevice];
foreach (var gpuID in UsedDeviceProcesses)
{
Workers[gpuID] = new WorkerWrapper(gpuID);
Workers[gpuID].SetHeaderlessParams(new int2(Options.Import.HeaderlessWidth, Options.Import.HeaderlessHeight),
Options.Import.HeaderlessOffset,
Options.Import.HeaderlessType);
Workers[gpuID].LoadGainRef(Options.Import.CorrectGain ? Options.Import.GainPath : "",
Options.Import.GainFlipX,
Options.Import.GainFlipY,
Options.Import.GainTranspose,
Options.Import.CorrectDefects ? Options.Import.DefectsPath : "");
}
#endregion
Star TableOut = null;
{
Dictionary <string, Star> MicrographTables = new Dictionary <string, Star>();
#region Get coordinates and angles
float[] PosX = TableIn.GetColumn("rlnCoordinateX").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray();
float[] PosY = TableIn.GetColumn("rlnCoordinateY").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray();
float[] PosZ = TableIn.GetColumn("rlnCoordinateZ").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray();
float[] ShiftX = TableIn.HasColumn("rlnOriginX") ? TableIn.GetColumn("rlnOriginX").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
float[] ShiftY = TableIn.HasColumn("rlnOriginY") ? TableIn.GetColumn("rlnOriginY").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
float[] ShiftZ = TableIn.HasColumn("rlnOriginZ") ? TableIn.GetColumn("rlnOriginZ").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
if (Options.Tasks.TomoSubReconstructNormalizedCoords)
{
for (int r = 0; r < TableIn.RowCount; r++)
{
PosX[r] *= (float)Options.Tomo.DimensionsX * (float)Options.PixelSizeMean;
PosY[r] *= (float)Options.Tomo.DimensionsY * (float)Options.PixelSizeMean;
PosZ[r] *= (float)Options.Tomo.DimensionsZ * (float)Options.PixelSizeMean;
}
}
else
{
for (int r = 0; r < TableIn.RowCount; r++)
{
PosX[r] = (PosX[r] - ShiftX[r]) * (float)Options.Tasks.InputPixelSize;
PosY[r] = (PosY[r] - ShiftY[r]) * (float)Options.Tasks.InputPixelSize;
PosZ[r] = (PosZ[r] - ShiftZ[r]) * (float)Options.Tasks.InputPixelSize;
}
}
float[] AngleRot = TableIn.HasColumn("rlnAngleRot") && Options.Tasks.TomoSubReconstructPrerotated ? TableIn.GetColumn("rlnAngleRot").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
float[] AngleTilt = TableIn.HasColumn("rlnAngleTilt") && Options.Tasks.TomoSubReconstructPrerotated ? TableIn.GetColumn("rlnAngleTilt").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
float[] AnglePsi = TableIn.HasColumn("rlnAnglePsi") && Options.Tasks.TomoSubReconstructPrerotated ? TableIn.GetColumn("rlnAnglePsi").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
if (TableIn.HasColumn("rlnOriginX"))
{
TableIn.RemoveColumn("rlnOriginX");
}
if (TableIn.HasColumn("rlnOriginY"))
{
TableIn.RemoveColumn("rlnOriginY");
}
if (TableIn.HasColumn("rlnOriginZ"))
{
TableIn.RemoveColumn("rlnOriginZ");
}
if (AdditionalShiftAngstrom.Length() > 0)
{
for (int r = 0; r < TableIn.RowCount; r++)
{
Matrix3 R = Matrix3.Euler(AngleRot[r] * Helper.ToRad,
AngleTilt[r] * Helper.ToRad,
AnglePsi[r] * Helper.ToRad);
float3 RotatedShift = R *AdditionalShiftAngstrom;
PosX[r] += RotatedShift.X;
PosY[r] += RotatedShift.Y;
PosZ[r] += RotatedShift.Z;
}
}
if (Options.Tasks.TomoSubReconstructPrerotated)
{
if (TableIn.HasColumn("rlnAngleRot"))
{
TableIn.RemoveColumn("rlnAngleRot");
TableIn.AddColumn("rlnAngleRot", "0");
}
if (TableIn.HasColumn("rlnAngleTilt"))
{
TableIn.RemoveColumn("rlnAngleTilt");
TableIn.AddColumn("rlnAngleTilt", "0");
}
if (TableIn.HasColumn("rlnAnglePsi"))
{
TableIn.RemoveColumn("rlnAnglePsi");
TableIn.AddColumn("rlnAnglePsi", "0");
}
}
#endregion
Dispatcher.Invoke(() => ProgressWrite.MaxValue = ValidSeries.Count);
//Dispatcher.Invoke(() =>
//{
// ProgressWrite.IsIndeterminate = true;
// TextRemaining.Text = "?:??";
//});
Helper.ForEachGPU(ValidSeries, (series, gpuID) =>
{
if (IsCanceled)
{
return;
}
Stopwatch ItemTime = new Stopwatch();
ItemTime.Start();
ProcessingOptionsTomoSubReconstruction ExportOptions = Options.GetProcessingTomoSubReconstruction();
#region Update row values
List <int> GroupRows = Groups.First(n => n.Key.Contains(series.RootName)).Value;
int pi = 0;
foreach (var r in GroupRows)
{
TableIn.SetRowValue(r, "rlnCtfMaxResolution", series.CTFResolutionEstimate.ToString("F1", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnCoordinateX", (PosX[r] / (float)ExportOptions.BinnedPixelSizeMean).ToString("F3", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnCoordinateY", (PosY[r] / (float)ExportOptions.BinnedPixelSizeMean).ToString("F3", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnCoordinateZ", (PosZ[r] / (float)ExportOptions.BinnedPixelSizeMean).ToString("F3", CultureInfo.InvariantCulture));
#region Figure out relative or absolute path to sub-tomo and its CTF
string PathSubtomo = series.SubtomoDir + $"{series.RootName}{ExportOptions.Suffix}_{pi:D7}_{ExportOptions.BinnedPixelSizeMean:F2}A.mrc";
string PathCTF = //MakeSparse ?
//(series.SubtomoDir + $"{series.RootName}_{pi:D7}_ctf_{ExportOptions.BinnedPixelSizeMean:F2}A.tif") :
(series.SubtomoDir + $"{series.RootName}{ExportOptions.Suffix}_{pi:D7}_ctf_{ExportOptions.BinnedPixelSizeMean:F2}A.mrc");
if (Relative)
{
Uri UriStar = new Uri(ExportPath);
PathSubtomo = UriStar.MakeRelativeUri(new Uri(PathSubtomo)).ToString();
PathCTF = UriStar.MakeRelativeUri(new Uri(PathCTF)).ToString();
}
#endregion
TableIn.SetRowValue(r, "rlnImageName", PathSubtomo);
TableIn.SetRowValue(r, "rlnCtfImage", PathCTF);
pi++;
}
#endregion
#region Populate micrograph table with rows for all exported particles
Star MicrographTable = new Star(TableIn.GetColumnNames());
foreach (var r in GroupRows)
{
MicrographTable.AddRow(TableIn.GetRow(r).ToList());
}
#endregion
#region Finally, reconstruct the actual sub-tomos
float3[] TomoPositions = Helper.Combine(GroupRows.Select(r => Helper.ArrayOfConstant(new float3(PosX[r], PosY[r], PosZ[r]), series.NTilts)).ToArray());
float3[] TomoAngles = Helper.Combine(GroupRows.Select(r => Helper.ArrayOfConstant(new float3(AngleRot[r], AngleTilt[r], AnglePsi[r]), series.NTilts)).ToArray());
if (DoVolumes)
{
Workers[gpuID].TomoExportParticles(series.Path, ExportOptions, TomoPositions, TomoAngles);
//series.ReconstructSubtomos(ExportOptions, TomoPositions, TomoAngles);
lock (MicrographTables)
MicrographTables.Add(series.RootName, MicrographTable);
}
else
{
Star SeriesTable;
Random Rand = new Random(123);
int[] Subsets = Helper.ArrayOfFunction(i => Rand.Next(1, 3), GroupRows.Count);
series.ReconstructParticleSeries(ExportOptions, TomoPositions, TomoAngles, Subsets, ExportPath, out SeriesTable);
lock (MicrographTables)
MicrographTables.Add(series.RootName, SeriesTable);
}
#endregion
#region Add this micrograph's table to global collection, update remaining time estimate
lock (MicrographTables)
{
Timings.Add(ItemTime.ElapsedMilliseconds / (float)UsedDeviceProcesses.Count);
int MsRemaining = (int)(MathHelper.Mean(Timings) * (ValidSeries.Count - MicrographTables.Count));
TimeSpan SpanRemaining = new TimeSpan(0, 0, 0, 0, MsRemaining);
Dispatcher.Invoke(() => TextRemaining.Text = SpanRemaining.ToString((int)SpanRemaining.TotalHours > 0 ? @"hh\:mm\:ss" : @"mm\:ss"));
Dispatcher.Invoke(() =>
{
ProgressWrite.IsIndeterminate = false;
ProgressWrite.Value = MicrographTables.Count;
});
}
#endregion
}, 1, UsedDeviceProcesses);
if (MicrographTables.Count > 0)
{
TableOut = new Star(MicrographTables.Values.ToArray());
}
}
Thread.Sleep(10000); // Writing out particles is async, so if workers are killed immediately they may not write out everything
foreach (var worker in Workers)
{
worker?.Dispose();
}
if (IsCanceled)
{
return;
}
TableOut.Save(ExportPath);
});
Close?.Invoke();
}
private async void ButtonWrite_OnClick(object sender, RoutedEventArgs e)
{
bool Invert = (bool)CheckInvert.IsChecked;
bool Normalize = (bool)CheckNormalize.IsChecked;
bool Preflip = (bool)CheckPreflip.IsChecked;
bool Relative = (bool)CheckRelative.IsChecked;
bool Filter = (bool)CheckFilter.IsChecked;
bool Manual = (bool)CheckManual.IsChecked;
int BoxSize = (int)Options.Tasks.Export2DBoxSize;
int NormDiameter = (int)Options.Tasks.Export2DParticleDiameter;
ProgressWrite.Visibility = Visibility.Visible;
ProgressWrite.IsIndeterminate = true;
PanelButtons.Visibility = Visibility.Collapsed;
PanelRemaining.Visibility = Visibility.Visible;
foreach (var element in DisableWhileProcessing)
{
element.IsEnabled = false;
}
await Task.Run(() =>
{
#region Get all movies that can potentially be used
List <TiltSeries> ValidSeries = Series.Where(v =>
{
if (!Filter && v.UnselectFilter && v.UnselectManual == null)
{
return(false);
}
if (!Manual && v.UnselectManual != null && (bool)v.UnselectManual)
{
return(false);
}
if (v.OptionsCTF == null)
{
return(false);
}
return(true);
}).ToList();
List <string> ValidMovieNames = ValidSeries.Select(m => m.RootName).ToList();
#endregion
#region Read table and intersect its micrograph set with valid movies
Star TableIn;
if (Options.Tasks.InputOnePerItem)
{
List <Star> Tables = new List <Star>();
foreach (var item in Series)
{
string StarPath = InputFolder + item.RootName + InputSuffix;
if (File.Exists(StarPath))
{
Star TableItem = new Star(StarPath);
if (!TableItem.HasColumn("rlnMicrographName"))
{
TableItem.AddColumn("rlnMicrographName", item.Name);
}
else
{
TableItem.SetColumn("rlnMicrographName", Helper.ArrayOfConstant(item.Name, TableItem.RowCount));
}
Tables.Add(TableItem);
}
}
TableIn = new Star(Tables.ToArray());
}
else
{
TableIn = new Star(ImportPath);
}
if (!TableIn.HasColumn("rlnMicrographName"))
{
throw new Exception("Couldn't find rlnMicrographName column.");
}
if (!TableIn.HasColumn("rlnCoordinateX"))
{
throw new Exception("Couldn't find rlnCoordinateX column.");
}
if (!TableIn.HasColumn("rlnCoordinateY"))
{
throw new Exception("Couldn't find rlnCoordinateY column.");
}
if (!TableIn.HasColumn("rlnCoordinateZ"))
{
throw new Exception("Couldn't find rlnCoordinateZ column.");
}
Dictionary <string, List <int> > Groups = new Dictionary <string, List <int> >();
{
string[] ColumnMicNames = TableIn.GetColumn("rlnMicrographName");
for (int r = 0; r < ColumnMicNames.Length; r++)
{
if (!Groups.ContainsKey(ColumnMicNames[r]))
{
Groups.Add(ColumnMicNames[r], new List <int>());
}
Groups[ColumnMicNames[r]].Add(r);
}
Groups = Groups.ToDictionary(group => Helper.PathToName(group.Key), group => group.Value);
Groups = Groups.Where(group => ValidMovieNames.Any(n => group.Key.Contains(n))).ToDictionary(group => group.Key, group => group.Value);
}
bool[] RowsIncluded = new bool[TableIn.RowCount];
foreach (var group in Groups)
{
foreach (var r in group.Value)
{
RowsIncluded[r] = true;
}
}
List <int> RowsNotIncluded = new List <int>();
for (int r = 0; r < RowsIncluded.Length; r++)
{
if (!RowsIncluded[r])
{
RowsNotIncluded.Add(r);
}
}
ValidSeries = ValidSeries.Where(v => Groups.Any(n => n.Key.Contains(v.RootName))).ToList();
if (ValidSeries.Count == 0) // Exit if there is nothing to export, otherwise errors will be thrown below
{
return;
}
#endregion
#region Make sure all columns are there
if (!TableIn.HasColumn("rlnMagnification"))
{
TableIn.AddColumn("rlnMagnification", "10000.0");
}
else
{
TableIn.SetColumn("rlnMagnification", Helper.ArrayOfConstant("10000.0", TableIn.RowCount));
}
if (!TableIn.HasColumn("rlnDetectorPixelSize"))
{
TableIn.AddColumn("rlnDetectorPixelSize", Options.Tasks.TomoSubReconstructPixel.ToString("F5", CultureInfo.InvariantCulture));
}
else
{
TableIn.SetColumn("rlnDetectorPixelSize", Helper.ArrayOfConstant(Options.Tasks.TomoSubReconstructPixel.ToString("F5", CultureInfo.InvariantCulture), TableIn.RowCount));
}
if (!TableIn.HasColumn("rlnCtfMaxResolution"))
{
TableIn.AddColumn("rlnCtfMaxResolution", "999.0");
}
if (!TableIn.HasColumn("rlnImageName"))
{
TableIn.AddColumn("rlnImageName", "None");
}
if (!TableIn.HasColumn("rlnCtfImage"))
{
TableIn.AddColumn("rlnCtfImage", "None");
}
#endregion
int MaxDevices = 999;
int UsedDevices = Math.Min(MaxDevices, GPU.GetDeviceCount());
if (IsCanceled)
{
return;
}
Star TableOut = null;
{
Dictionary <string, Star> MicrographTables = new Dictionary <string, Star>();
#region Get coordinates and angles
float[] PosX = TableIn.GetColumn("rlnCoordinateX").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray();
float[] PosY = TableIn.GetColumn("rlnCoordinateY").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray();
float[] PosZ = TableIn.GetColumn("rlnCoordinateZ").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray();
float[] ShiftX = TableIn.HasColumn("rlnOriginX") ? TableIn.GetColumn("rlnOriginX").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
float[] ShiftY = TableIn.HasColumn("rlnOriginY") ? TableIn.GetColumn("rlnOriginY").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
float[] ShiftZ = TableIn.HasColumn("rlnOriginZ") ? TableIn.GetColumn("rlnOriginZ").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
if (Options.Tasks.TomoSubReconstructNormalizedCoords)
{
for (int r = 0; r < TableIn.RowCount; r++)
{
PosX[r] *= (float)Options.Tomo.DimensionsX * (float)Options.PixelSizeMean;
PosY[r] *= (float)Options.Tomo.DimensionsY * (float)Options.PixelSizeMean;
PosZ[r] *= (float)Options.Tomo.DimensionsZ * (float)Options.PixelSizeMean;
}
}
else
{
for (int r = 0; r < TableIn.RowCount; r++)
{
PosX[r] = (PosX[r] - ShiftX[r]) * (float)Options.Tasks.InputPixelSize;
PosY[r] = (PosY[r] - ShiftY[r]) * (float)Options.Tasks.InputPixelSize;
PosZ[r] = (PosZ[r] - ShiftZ[r]) * (float)Options.Tasks.InputPixelSize;
}
}
float[] AngleRot = TableIn.HasColumn("rlnAngleRot") && Options.Tasks.TomoSubReconstructPrerotated ? TableIn.GetColumn("rlnAngleRot").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
float[] AngleTilt = TableIn.HasColumn("rlnAngleTilt") && Options.Tasks.TomoSubReconstructPrerotated ? TableIn.GetColumn("rlnAngleTilt").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
float[] AnglePsi = TableIn.HasColumn("rlnAnglePsi") && Options.Tasks.TomoSubReconstructPrerotated ? TableIn.GetColumn("rlnAnglePsi").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray() : new float[TableIn.RowCount];
if (TableIn.HasColumn("rlnOriginX"))
{
TableIn.RemoveColumn("rlnOriginX");
}
if (TableIn.HasColumn("rlnOriginY"))
{
TableIn.RemoveColumn("rlnOriginY");
}
if (TableIn.HasColumn("rlnOriginZ"))
{
TableIn.RemoveColumn("rlnOriginZ");
}
if (Options.Tasks.TomoSubReconstructPrerotated)
{
if (TableIn.HasColumn("rlnAngleRot"))
{
TableIn.RemoveColumn("rlnAngleRot");
TableIn.AddColumn("rlnAngleRot", "0");
}
if (TableIn.HasColumn("rlnAngleTilt"))
{
TableIn.RemoveColumn("rlnAngleTilt");
TableIn.AddColumn("rlnAngleTilt", "0");
}
if (TableIn.HasColumn("rlnAnglePsi"))
{
TableIn.RemoveColumn("rlnAnglePsi");
TableIn.AddColumn("rlnAnglePsi", "0");
}
}
#endregion
Dispatcher.Invoke(() => ProgressWrite.MaxValue = ValidSeries.Count);
Helper.ForEachGPU(ValidSeries, (series, gpuID) =>
{
if (IsCanceled)
{
return;
}
Stopwatch ItemTime = new Stopwatch();
ItemTime.Start();
ProcessingOptionsTomoSubReconstruction ExportOptions = Options.GetProcessingTomoSubReconstruction();
#region Update row values
List <int> GroupRows = Groups.First(n => n.Key.Contains(series.RootName)).Value;
int pi = 0;
foreach (var r in GroupRows)
{
TableIn.SetRowValue(r, "rlnCtfMaxResolution", series.CTFResolutionEstimate.ToString("F1", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnCoordinateX", (PosX[r] / (float)ExportOptions.BinnedPixelSizeMean).ToString("F3", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnCoordinateY", (PosY[r] / (float)ExportOptions.BinnedPixelSizeMean).ToString("F3", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnCoordinateZ", (PosZ[r] / (float)ExportOptions.BinnedPixelSizeMean).ToString("F3", CultureInfo.InvariantCulture));
#region Figure out relative or absolute path to sub-tomo and its CTF
string PathSubtomo = series.SubtomoDir + $"{series.RootName}_{pi:D7}_{ExportOptions.BinnedPixelSizeMean:F2}A.mrc";
string PathCTF = series.SubtomoDir + $"{series.RootName}_{pi:D7}_ctf_{ExportOptions.BinnedPixelSizeMean:F2}A.mrc";
if (Relative)
{
Uri UriStar = new Uri(ExportPath);
PathSubtomo = UriStar.MakeRelativeUri(new Uri(PathSubtomo)).ToString();
PathCTF = UriStar.MakeRelativeUri(new Uri(PathCTF)).ToString();
}
#endregion
TableIn.SetRowValue(r, "rlnImageName", PathSubtomo);
TableIn.SetRowValue(r, "rlnCtfImage", PathCTF);
pi++;
}
#endregion
#region Populate micrograph table with rows for all exported particles
Star MicrographTable = new Star(TableIn.GetColumnNames());
foreach (var r in GroupRows)
{
MicrographTable.AddRow(TableIn.GetRow(r).ToList());
}
#endregion
#region Finally, reconstruct the actual sub-tomos
float3[] TomoPositions = Helper.Combine(GroupRows.Select(r => Helper.ArrayOfConstant(new float3(PosX[r], PosY[r], PosZ[r]), series.NTilts)).ToArray());
float3[] TomoAngles = Helper.Combine(GroupRows.Select(r => Helper.ArrayOfConstant(new float3(AngleRot[r], AngleTilt[r], AnglePsi[r]), series.NTilts)).ToArray());
series.ReconstructSubtomos(ExportOptions, TomoPositions, TomoAngles);
#endregion
#region Add this micrograph's table to global collection, update remaining time estimate
lock (MicrographTables)
{
MicrographTables.Add(series.RootName, MicrographTable);
Timings.Add(ItemTime.ElapsedMilliseconds / (float)UsedDevices);
int MsRemaining = (int)(MathHelper.Mean(Timings) * (ValidSeries.Count - MicrographTables.Count));
TimeSpan SpanRemaining = new TimeSpan(0, 0, 0, 0, MsRemaining);
Dispatcher.Invoke(() => TextRemaining.Text = SpanRemaining.ToString((int)SpanRemaining.TotalHours > 0 ? @"hh\:mm\:ss" : @"mm\:ss"));
Dispatcher.Invoke(() =>
{
ProgressWrite.IsIndeterminate = false;
ProgressWrite.Value = MicrographTables.Count;
});
}
#endregion
}, 1);
if (MicrographTables.Count > 0)
{
TableOut = new Star(MicrographTables.Values.ToArray());
}
}
if (IsCanceled)
{
return;
}
TableOut.Save(ExportPath);
});
Close?.Invoke();
}
