public static ProcessingStatus GetMovieProcessingStatus(Movie movie, ProcessingOptionsMovieCTF optionsCTF, ProcessingOptionsMovieMovement optionsMovement, ProcessingOptionsBoxNet optionsBoxNet, ProcessingOptionsMovieExport optionsExport, Warp.Options options, bool considerFilter = true)
{
bool DoCTF = options.ProcessCTF;
bool DoMovement = options.ProcessMovement;
bool DoBoxNet = options.ProcessPicking;
bool DoExport = optionsExport.DoAverage || optionsExport.DoStack || optionsExport.DoDeconv;
ProcessingStatus Status = ProcessingStatus.Processed;
if (movie.UnselectManual != null && (bool)movie.UnselectManual)
{
Status = ProcessingStatus.LeaveOut;
}
else if (movie.OptionsCTF == null && movie.OptionsMovement == null && movie.OptionsMovieExport == null)
{
Status = ProcessingStatus.Unprocessed;
}
else
{
if (DoCTF && (movie.OptionsCTF == null || movie.OptionsCTF != optionsCTF))
{
Status = ProcessingStatus.Outdated;
}
else if (DoMovement && (movie.OptionsMovement == null || movie.OptionsMovement != optionsMovement))
{
Status = ProcessingStatus.Outdated;
}
else if (DoBoxNet && (movie.OptionsBoxNet == null || movie.OptionsBoxNet != optionsBoxNet))
{
Status = ProcessingStatus.Outdated;
}
else if (DoExport && (movie.OptionsMovieExport == null || movie.OptionsMovieExport != optionsExport))
{
Status = ProcessingStatus.Outdated;
}
}
if (Status == ProcessingStatus.Processed && movie.UnselectFilter && movie.UnselectManual == null && considerFilter)
{
Status = ProcessingStatus.FilteredOut;
}
return(Status);
}
private async void ButtonAddLocal_OnClick(object sender, RoutedEventArgs e)
{
System.Windows.Forms.OpenFileDialog OpenDialog = new System.Windows.Forms.OpenFileDialog();
OpenDialog.Filter = "Warp Folder Settings|*.settings|Warp Data Source|*.source";
System.Windows.Forms.DialogResult OpenResult = OpenDialog.ShowDialog();
if (OpenResult.ToString() == "OK")
{
FileInfo Info = new FileInfo(OpenDialog.FileName);
#region Check if user wants to use an existing source file instead
//if (Info.Extension.ToLower() == ".settings" &&
// File.Exists(OpenDialog.FileName.Substring(0, OpenDialog.FileName.LastIndexOf(".")) + ".source"))
//{
// var Result = await ((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Similar source file found",
// $"Would you like to use {Helper.PathToName(Info.Name) + ".source"} instead?",
// MessageDialogStyle.AffirmativeAndNegativeAndSingleAuxiliary,
// new MetroDialogSettings
// {
// AffirmativeButtonText = "Use existing source",
// NegativeButtonText = "Replace with new source from settings",
// FirstAuxiliaryButtonText = "Cancel"
// });
// if (Result == MessageDialogResult.FirstAuxiliary) // Cancel
// {
// return;
// }
// else if (Result == MessageDialogResult.Affirmative) // Use existing .source
// {
// OpenDialog.FileName = OpenDialog.FileName.Substring(0, OpenDialog.FileName.LastIndexOf(".")) + ".source";
// Info = new FileInfo(OpenDialog.FileName);
// }
//}
#endregion
if (Info.Extension.ToLower() == ".settings")
{
#region Load preprocessing options
Warp.Options Options = new Warp.Options();
try
{
Options.Load(OpenDialog.FileName);
}
catch
{
await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Oopsie",
$"An error was encountered when reading {Info.Name}.",
MessageDialogStyle.Affirmative);
return;
}
#endregion
#region Load items with metadata
string FileExtension = Options.Import.Extension;
var AvailableFiles = Directory.EnumerateFiles(Info.DirectoryName, FileExtension).ToArray();
Movie[] Items = new Movie[AvailableFiles.Length];
string[] MatchingStarNames = null;
if (FileExtension != "*.tomostar" && AvailableFiles.Length > 0)
{
Movie First = new Movie(AvailableFiles[0]);
MatchingStarNames = Directory.EnumerateFiles(First.MatchingDir, "*.star").ToArray();
}
{
var ProgressDialog = await((MainWindow)Application.Current.MainWindow).ShowProgressAsync("Loading metadata...", "");
ProgressDialog.Maximum = AvailableFiles.Count();
await Task.Run(() =>
{
int Done = 0;
Parallel.For(0, AvailableFiles.Length, i =>
{
string file = AvailableFiles[i];
string XmlPath = file.Substring(0, file.LastIndexOf(".")) + ".xml";
if (File.Exists(XmlPath))
{
Items[i] = (FileExtension == "*.tomostar" ? new TiltSeries(file) : new Movie(file, MatchingStarNames));
}
lock (Items)
ProgressDialog.SetProgress(++Done);
});
});
await ProgressDialog.CloseAsync();
}
if (Items.Length == 0)
{
await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Oopsie",
$"No micrographs or tilt series found to match these settings.",
MessageDialogStyle.Affirmative);
return;
}
#endregion
#region Figure out filtering status
#region Astigmatism statistics
Movie[] ItemsWithCTF = Items.Where(v => v.OptionsCTF != null && v.CTF != null).ToArray();
List <float2> AstigmatismPoints = new List <float2>(ItemsWithCTF.Length);
foreach (var item in ItemsWithCTF)
{
AstigmatismPoints.Add(new float2((float)Math.Cos((float)item.CTF.DefocusAngle * 2 * Helper.ToRad) * (float)item.CTF.DefocusDelta,
(float)Math.Sin((float)item.CTF.DefocusAngle * 2 * Helper.ToRad) * (float)item.CTF.DefocusDelta));
}
float2 AstigmatismMean = new float2();
float AstigmatismStd = 0.1f;
if (AstigmatismPoints.Count > 0)
{
AstigmatismMean = new float2();
foreach (var point in AstigmatismPoints)
{
AstigmatismMean += point;
}
AstigmatismMean /= AstigmatismPoints.Count;
AstigmatismStd = 0;
foreach (var point in AstigmatismPoints)
{
AstigmatismStd += (point - AstigmatismMean).LengthSq();
}
AstigmatismStd = (float)Math.Max(1e-4, Math.Sqrt(AstigmatismStd / AstigmatismPoints.Count));
}
#endregion
int[] ParticleCounts = Items.Select(item => item.GetParticleCount(Options.Filter.ParticlesSuffix)).ToArray();
bool HaveParticles = ParticleCounts.Any(v => v > 0);
foreach (var item in Items)
{
bool FilterStatus = true;
if (item.OptionsCTF != null)
{
FilterStatus &= item.CTF.Defocus >= Options.Filter.DefocusMin && item.CTF.Defocus <= Options.Filter.DefocusMax;
float AstigmatismDeviation = (new float2((float)Math.Cos((float)item.CTF.DefocusAngle * 2 * Helper.ToRad) * (float)item.CTF.DefocusDelta,
(float)Math.Sin((float)item.CTF.DefocusAngle * 2 * Helper.ToRad) * (float)item.CTF.DefocusDelta) - AstigmatismMean).Length() / AstigmatismStd;
FilterStatus &= AstigmatismDeviation <= (float)Options.Filter.AstigmatismMax;
FilterStatus &= item.CTFResolutionEstimate <= Options.Filter.ResolutionMax;
FilterStatus &= item.CTF.PhaseShift >= Options.Filter.PhaseMin && item.CTF.PhaseShift <= Options.Filter.PhaseMax;
FilterStatus &= item.GetParticleCount(Options.Filter.ParticlesSuffix) >= Options.Filter.ParticlesMin;
}
if (item.OptionsMovement != null)
{
FilterStatus &= item.MeanFrameMovement <= Options.Filter.MotionMax;
}
item.UnselectFilter = !FilterStatus;
}
ProcessingOptionsMovieCTF OptionsCTF = Options.GetProcessingMovieCTF();
ProcessingOptionsMovieMovement OptionsMovement = Options.GetProcessingMovieMovement();
ProcessingOptionsBoxNet OptionsBoxNet = Options.GetProcessingBoxNet();
ProcessingOptionsMovieExport OptionsExport = Options.GetProcessingMovieExport();
List <Movie> ItemsProcessed = new List <Movie>();
List <Movie> ItemsFilteredOut = new List <Movie>();
List <Movie> ItemsUnselected = new List <Movie>();
foreach (Movie item in Items)
{
ProcessingStatus Status = GetMovieProcessingStatus(item, OptionsCTF, OptionsMovement, OptionsBoxNet, OptionsExport, Options);
if (Status == ProcessingStatus.Processed || (Status == ProcessingStatus.Outdated && !item.UnselectFilter))
{
ItemsProcessed.Add(item);
}
else if (Status == ProcessingStatus.FilteredOut || (Status == ProcessingStatus.Outdated && item.UnselectFilter))
{
ItemsFilteredOut.Add(item);
}
else if (Status == ProcessingStatus.LeaveOut)
{
ItemsUnselected.Add(item);
}
}
#endregion
#region Figure out how many frames/tilts there are to use
int UsableFrames = 1;
if (Items[0].GetType() == typeof(Movie))
{
UsableFrames = MapHeader.ReadFromFile(Items[0].Path).Dimensions.Z;
}
else
{
UsableFrames = ((TiltSeries)Items[0]).NTilts;
}
#endregion
#region Show dialog
CustomDialog Dialog = new CustomDialog();
Dialog.HorizontalContentAlignment = HorizontalAlignment.Center;
DialogCreateSourceFromSettings DialogContent = new DialogCreateSourceFromSettings();
DialogContent.TextTitle.Text = $"Create data source from\n{Info.Name}";
DialogContent.StatsSeriesStatusProcessed.Values = new ChartValues <ObservableValue> {
new ObservableValue(ItemsProcessed.Count)
};
DialogContent.StatsSeriesStatusUnfiltered.Values = new ChartValues <ObservableValue> {
new ObservableValue(ItemsFilteredOut.Count)
};
DialogContent.StatsSeriesStatusUnselected.Values = new ChartValues <ObservableValue> {
new ObservableValue(ItemsUnselected.Count)
};
DialogContent.SliderFrames.Value = UsableFrames;
DialogContent.SliderFrames.MaxValue = UsableFrames;
DialogContent.Close += () =>
{
((MainWindow)Application.Current.MainWindow).HideMetroDialogAsync(Dialog);
};
DialogContent.Create += async() =>
{
#region Create source metadata and check if one with the same path already exists
DataSource NewSource = new DataSource
{
PixelSizeX = Options.PixelSizeX,
PixelSizeY = Options.PixelSizeY,
PixelSizeAngle = Options.PixelSizeAngle,
DimensionsX = Options.Tomo.DimensionsX,
DimensionsY = Options.Tomo.DimensionsY,
DimensionsZ = Options.Tomo.DimensionsZ,
FrameLimit = (int)DialogContent.SliderFrames.Value,
GainPath = Options.Import.CorrectGain ? Options.Import.GainPath : "",
GainFlipX = Options.Import.GainFlipX,
GainFlipY = Options.Import.GainFlipY,
GainTranspose = Options.Import.GainTranspose,
DosePerAngstromFrame = Options.Import.DosePerAngstromFrame,
Name = DialogContent.TextSourceName.Text,
Path = Info.DirectoryName + "\\" + Helper.RemoveInvalidChars(DialogContent.TextSourceName.Text) + ".source"
};
if (Population.Sources.Any(s => s.Path == NewSource.Path))
{
await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Oopsie",
$"{Helper.PathToNameWithExtension(NewSource.Path)} already exists in this population. Please choose a different name.",
MessageDialogStyle.Affirmative);
return;
}
await((MainWindow)Application.Current.MainWindow).HideMetroDialogAsync(Dialog);
#endregion
#region Add all items and their data hashes
List <Movie> AllItems = new List <Movie>(ItemsProcessed);
if ((bool)DialogContent.CheckFilter.IsChecked)
{
AllItems.AddRange(ItemsFilteredOut);
}
if ((bool)DialogContent.CheckManual.IsChecked)
{
AllItems.AddRange(ItemsUnselected);
}
if (AllItems.Count == 0)
{
await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Oopsie",
$"No micrographs or tilt series found to match these settings.",
MessageDialogStyle.Affirmative);
return;
}
{
var ProgressDialog = await((MainWindow)Application.Current.MainWindow).ShowProgressAsync("Calculating data hashes...", "");
ProgressDialog.Maximum = AllItems.Count;
await Task.Run(() =>
{
int Done = 0;
foreach (var item in AllItems)
{
NewSource.Files.Add(item.GetDataHash(), item.Name);
ProgressDialog.SetProgress(++Done);
}
});
await ProgressDialog.CloseAsync();
}
#endregion
#region Check for overlapping hashes
string[] Overlapping = Helper.Combine(Population.Sources.Select(s => s.Files.Where(f => NewSource.Files.ContainsKey(f.Key)).Select(f => f.Value).ToArray()));
if (Overlapping.Length > 0)
{
string Offenders = "";
for (int o = 0; o < Math.Min(5, Overlapping.Length); o++)
{
Offenders += "\n" + Overlapping[o];
}
if (Overlapping.Length > 5)
{
Offenders += $"\n... and {Overlapping.Length - 5} more.";
}
await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Oopsie",
"The new source contains files that are already used in this population:" + Offenders,
MessageDialogStyle.Affirmative);
return;
}
#endregion
{
var ProgressDialog = await((MainWindow)Application.Current.MainWindow).ShowProgressAsync("Committing initial version...", "");
ProgressDialog.Maximum = AllItems.Count;
await Task.Run(() =>
{
NewSource.Commit();
});
await ProgressDialog.CloseAsync();
}
Population.Sources.Add(NewSource);
UpdateGridItems();
};
Dialog.Content = DialogContent;
await((MainWindow)Application.Current.MainWindow).ShowMetroDialogAsync(Dialog, new MetroDialogSettings()
{
});
#endregion
}
else
{
try
{
if (Population.Sources.Any(s => s.Path == OpenDialog.FileName))
{
await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Oopsie",
"This data source is already part of this population.",
MessageDialogStyle.Affirmative);
return;
}
DataSource NewSource = DataSource.FromFile(OpenDialog.FileName);
Population.Sources.Add(NewSource);
UpdateGridItems();
}
catch
{
await((MainWindow)Application.Current.MainWindow).ShowMessageAsync("Oopsie",
$"An error was encountered when reading {Info.Name}.",
MessageDialogStyle.Affirmative);
return;
}
}
}
}