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();
}
}
}
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();
}
}
}