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 ButtonExport_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 DoAverage = (bool)RadioAverage.IsChecked;
bool DoStack = (bool)RadioStack.IsChecked;
bool DoDenoisingPairs = (bool)RadioDenoising.IsChecked;
bool DoOnlyStar = (bool)RadioStar.IsChecked;
bool Invert = (bool)CheckInvert.IsChecked;
bool Normalize = (bool)CheckNormalize.IsChecked;
bool Preflip = (bool)CheckPreflip.IsChecked;
float AngPix = (float)Options.Tasks.InputPixelSize;
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(async() =>
{
#region Get all movies that can potentially be used
List <Movie> ValidMovies = Movies.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 = ValidMovies.Select(m => m.RootName).ToList();
if (ValidMovies.Count == 0)
{
await Dispatcher.Invoke(async() =>
{
await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Oopsie",
"No items were found to extract particles from.\n" +
"Please make sure the names match, estimate the CTF for all items, and review your filtering thresholds.");
});
}
#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 Movies)
{
string StarPath = InputFolder + item.RootName + InputSuffix + ".star";
if (File.Exists(StarPath))
{
Star TableItem = new Star(StarPath);
if (!TableItem.HasColumn("rlnMicrographName"))
{
TableItem.AddColumn("rlnMicrographName", item.Name);
}
if (item.PickingThresholds.ContainsKey(InputSuffix) && TableItem.HasColumn("rlnAutopickFigureOfMerit"))
{
float Threshold = (float)item.PickingThresholds[InputSuffix];
float[] Scores = TableItem.GetColumn("rlnAutopickFigureOfMerit").Select(v => float.Parse(v, CultureInfo.InvariantCulture)).ToArray();
int[] InvalidRows = Helper.ArrayOfSequence(0, TableItem.RowCount, 1).Where(i => Scores[i] < Threshold).ToArray();
TableItem.RemoveRows(InvalidRows);
}
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.");
}
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.Contains(group.Key)).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);
}
}
ValidMovies = ValidMovies.Where(v => Groups.ContainsKey(v.RootName)).ToList();
if (ValidMovies.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.GetProcessingParticleExport().BinnedPixelSizeMean.ToString("F5", CultureInfo.InvariantCulture));
}
else
{
TableIn.SetColumn("rlnDetectorPixelSize", Helper.ArrayOfConstant(Options.GetProcessingParticleExport().BinnedPixelSizeMean.ToString("F5", CultureInfo.InvariantCulture), TableIn.RowCount));
}
if (!TableIn.HasColumn("rlnVoltage"))
{
TableIn.AddColumn("rlnVoltage", "300.0");
}
if (!TableIn.HasColumn("rlnSphericalAberration"))
{
TableIn.AddColumn("rlnSphericalAberration", "2.7");
}
if (!TableIn.HasColumn("rlnAmplitudeContrast"))
{
TableIn.AddColumn("rlnAmplitudeContrast", "0.07");
}
if (!TableIn.HasColumn("rlnPhaseShift"))
{
TableIn.AddColumn("rlnPhaseShift", "0.0");
}
if (!TableIn.HasColumn("rlnDefocusU"))
{
TableIn.AddColumn("rlnDefocusU", "0.0");
}
if (!TableIn.HasColumn("rlnDefocusV"))
{
TableIn.AddColumn("rlnDefocusV", "0.0");
}
if (!TableIn.HasColumn("rlnDefocusAngle"))
{
TableIn.AddColumn("rlnDefocusAngle", "0.0");
}
if (!TableIn.HasColumn("rlnCtfMaxResolution"))
{
TableIn.AddColumn("rlnCtfMaxResolution", "999.0");
}
if (!TableIn.HasColumn("rlnImageName"))
{
TableIn.AddColumn("rlnImageName", "None");
}
if (!TableIn.HasColumn("rlnMicrographName"))
{
TableIn.AddColumn("rlnMicrographName", "None");
}
#endregion
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();
if (IsCanceled)
{
return;
}
#region Create worker processes
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);
if (!string.IsNullOrEmpty(Options.Import.GainPath) && Options.Import.CorrectGain)
{
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
#region Load gain reference if needed
//Image[] ImageGain = new Image[NDevices];
//if (!string.IsNullOrEmpty(Options.Import.GainPath) && Options.Import.CorrectGain && File.Exists(Options.Import.GainPath))
// for (int d = 0; d < NDevices; d++)
// {
// GPU.SetDevice(d);
// ImageGain[d] = MainWindow.LoadAndPrepareGainReference();
// }
#endregion
bool Overwrite = true;
if (DoAverage || DoStack)
{
foreach (var movie in ValidMovies)
{
bool FileExists = File.Exists((DoAverage ? movie.ParticlesDir : movie.ParticleMoviesDir) + movie.RootName + Options.Tasks.OutputSuffix + ".mrcs");
if (FileExists)
{
await Dispatcher.Invoke(async() =>
{
var DialogResult = await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Some particle files already exist. Overwrite them?",
"",
MessageDialogStyle.AffirmativeAndNegative,
new MetroDialogSettings()
{
AffirmativeButtonText = "Yes",
NegativeButtonText = "No"
});
if (DialogResult == MessageDialogResult.Negative)
{
Overwrite = false;
}
});
break;
}
}
}
Star TableOut = null;
{
Dictionary <string, Star> MicrographTables = new Dictionary <string, Star>();
#region Get coordinates
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[] 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];
for (int r = 0; r < TableIn.RowCount; r++)
{
PosX[r] -= ShiftX[r];
PosY[r] -= ShiftY[r];
}
if (TableIn.HasColumn("rlnOriginX"))
{
TableIn.RemoveColumn("rlnOriginX");
}
if (TableIn.HasColumn("rlnOriginY"))
{
TableIn.RemoveColumn("rlnOriginY");
}
#endregion
Dispatcher.Invoke(() => ProgressWrite.MaxValue = ValidMovies.Count);
Helper.ForEachGPU(ValidMovies, (movie, gpuID) =>
{
if (IsCanceled)
{
return;
}
Stopwatch ItemTime = new Stopwatch();
ItemTime.Start();
MapHeader OriginalHeader = MapHeader.ReadFromFile(movie.Path);
#region Set up export options
ProcessingOptionsParticlesExport ExportOptions = Options.GetProcessingParticleExport();
ExportOptions.DoAverage = DoAverage;
ExportOptions.DoDenoisingPairs = DoDenoisingPairs;
ExportOptions.DoStack = DoStack;
ExportOptions.Invert = Invert;
ExportOptions.Normalize = Normalize;
ExportOptions.PreflipPhases = Preflip;
ExportOptions.Dimensions = OriginalHeader.Dimensions.MultXY((float)Options.PixelSizeMean);
ExportOptions.BoxSize = BoxSize;
ExportOptions.Diameter = NormDiameter;
#endregion
bool FileExists = File.Exists((DoAverage ? movie.ParticlesDir : movie.ParticleMoviesDir) + movie.RootName + ExportOptions.Suffix + ".mrcs");
#region Load and prepare original movie
//Image OriginalStack = null;
decimal ScaleFactor = 1M / (decimal)Math.Pow(2, (double)ExportOptions.BinTimes);
if (!DoOnlyStar && (!FileExists || Overwrite))
{
Workers[gpuID].LoadStack(movie.Path, ScaleFactor, ExportOptions.EERGroupFrames);
}
//MainWindow.LoadAndPrepareHeaderAndMap(movie.Path, ImageGain[gpuID], ScaleFactor, out OriginalHeader, out OriginalStack);
if (IsCanceled)
{
//foreach (Image gain in ImageGain)
// gain?.Dispose();
//OriginalStack?.Dispose();
return;
}
#endregion
#region Figure out relative or absolute path to particle stack
string PathStack = (ExportOptions.DoStack ? movie.ParticleMoviesDir : movie.ParticlesDir) + movie.RootName + ExportOptions.Suffix + ".mrcs";
string PathMicrograph = movie.Path;
if (Relative)
{
Uri UriStar = new Uri(ExportPath);
PathStack = UriStar.MakeRelativeUri(new Uri(PathStack)).ToString();
PathMicrograph = UriStar.MakeRelativeUri(new Uri(PathMicrograph)).ToString();
}
#endregion
#region Update row values
List <int> GroupRows = Groups[movie.RootName];
List <float2> Positions = new List <float2>();
float Astigmatism = (float)movie.CTF.DefocusDelta / 2;
float PhaseShift = movie.OptionsCTF.DoPhase ? movie.GridCTFPhase.GetInterpolated(new float3(0.5f)) * 180 : 0;
int ImageNameIndex = TableIn.GetColumnID("rlnImageName");
foreach (var r in GroupRows)
{
float3 Position = new float3(PosX[r] * AngPix / ExportOptions.Dimensions.X,
PosY[r] * AngPix / ExportOptions.Dimensions.Y,
0.5f);
float LocalDefocus = movie.GridCTFDefocus.GetInterpolated(Position);
TableIn.SetRowValue(r, "rlnDefocusU", ((LocalDefocus + Astigmatism) * 1e4f).ToString("F1", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnDefocusV", ((LocalDefocus - Astigmatism) * 1e4f).ToString("F1", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnDefocusAngle", movie.CTF.DefocusAngle.ToString("F1", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnVoltage", movie.CTF.Voltage.ToString("F1", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnSphericalAberration", movie.CTF.Cs.ToString("F4", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnAmplitudeContrast", movie.CTF.Amplitude.ToString("F3", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnPhaseShift", PhaseShift.ToString("F1", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnCtfMaxResolution", movie.CTFResolutionEstimate.ToString("F1", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnCoordinateX", (PosX[r] * AngPix / (float)ExportOptions.BinnedPixelSizeMean).ToString("F2", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnCoordinateY", (PosY[r] * AngPix / (float)ExportOptions.BinnedPixelSizeMean).ToString("F2", CultureInfo.InvariantCulture));
TableIn.SetRowValue(r, "rlnImageName", PathStack);
TableIn.SetRowValue(r, "rlnMicrographName", PathMicrograph);
Positions.Add(new float2(PosX[r] * AngPix,
PosY[r] * AngPix));
}
#endregion
#region Populate micrograph table with rows for all exported particles
Star MicrographTable = new Star(TableIn.GetColumnNames());
int StackDepth = (ExportOptions.DoAverage || ExportOptions.DoDenoisingPairs || DoOnlyStar)
? 1
: (OriginalHeader.Dimensions.Z - ExportOptions.SkipFirstN - ExportOptions.SkipLastN) /
ExportOptions.StackGroupSize;
int pi = 0;
for (int i = 0; i < StackDepth; i++)
{
foreach (var r in GroupRows)
{
List <string> Row = TableIn.GetRow(r).ToList();
Row[ImageNameIndex] = (++pi).ToString("D7") + "@" + Row[ImageNameIndex];
MicrographTable.AddRow(Row);
}
}
#endregion
#region Finally, process and export the actual particles
if (!DoOnlyStar && (!FileExists || Overwrite))
{
Workers[gpuID].MovieExportParticles(movie.Path, ExportOptions, Positions.ToArray());
//movie.ExportParticles(OriginalStack, Positions.ToArray(), ExportOptions);
//OriginalStack.Dispose();
}
#endregion
#region Add this micrograph's table to global collection, update remaining time estimate
lock (MicrographTables)
{
MicrographTables.Add(movie.RootName, MicrographTable);
Timings.Add(ItemTime.ElapsedMilliseconds / (float)NDevices);
int MsRemaining = (int)(MathHelper.Mean(Timings) * (ValidMovies.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 particle stacks is async, so if workers are killed immediately they may not write out everything
foreach (var worker in Workers)
{
worker?.Dispose();
}
//foreach (Image gain in ImageGain)
// gain?.Dispose();
if (IsCanceled)
{
return;
}
TableOut.Save(ExportPath);
});
DataContext = null;
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();
}