private void SimulateTEM(ref ProgressReporter progressReporter, ref Stopwatch timer, ref CancellationToken ct)
{
mCL.initialiseCTEMSimulation(CurrentResolution, SimRegion.xStart, SimRegion.yStart, SimRegion.xFinish, SimRegion.yFinish, isFull3D, isFD, dz, integrals);
// Reset atoms incase TDS has been used
mCL.sortStructure(false);
// Use Background worker to progress through each step
var NumberOfSlices = 0;
mCL.getNumberSlices(ref NumberOfSlices, isFD);
// Seperate into setup, loop over slices and final steps to allow for progress reporting.
for (var i = 1; i <= NumberOfSlices; i++)
{
if (ct.IsCancellationRequested == true)
{
break;
}
timer.Start();
mCL.doMultisliceStep(i, NumberOfSlices);
timer.Stop();
var mem = mCL.getCLMemoryUsed();
// Report progress of the work.
float ms = timer.ElapsedMilliseconds;
progressReporter.ReportProgress((val) =>
{
CancelButton.IsEnabled = true;
UI_UpdateSimulationProgress(ms, NumberOfSlices, 1, 1, i, mem);
}, i);
}
}
private void SimulateCBED(int TDSruns, ref ProgressReporter progressReporter, ref Stopwatch timer, ref CancellationToken ct)
{
mCL.initialiseSTEMSimulation(CurrentResolution, SimRegion.xStart, SimRegion.yStart, SimRegion.xFinish, SimRegion.yFinish, isFull3D, isFD, dz, integrals, 1);
//int posX = CurrentResolution / 2;
//int posY = CurrentResolution / 2;
var posx = (CBED_xpos - SimRegion.xStart) / pixelScale;
var posy = (CBED_ypos - SimRegion.yStart) / pixelScale;
// Use Background worker to progress through each step
var NumberOfSlices = 0;
mCL.getNumberSlices(ref NumberOfSlices, isFD);
// Seperate into setup, loop over slices and final steps to allow for progress reporting.
var runs = 1;
if (doTDS_CBED)
{
runs = TDSruns;
}
TDSImage = new float[CurrentResolution * CurrentResolution];
for (var j = 0; j < runs; j++)
{
mCL.sortStructure(doTDS_CBED);
mCL.initialiseSTEMWaveFunction(posx, posy, 1);
for (var i = 1; i <= NumberOfSlices; i++)
{
if (ct.IsCancellationRequested == true)
{
break;
}
timer.Start();
mCL.doMultisliceStep(i, NumberOfSlices);
timer.Stop();
var mem = mCL.getCLMemoryUsed();
float ms = timer.ElapsedMilliseconds;
// Report progress of the work.
progressReporter.ReportProgress((val) =>
{
CancelButton.IsEnabled = true;
// Note: code passed to "ReportProgress" can access UI elements freely.
UI_UpdateSimulationProgress(ms, NumberOfSlices, runs, j, i, mem);
}, i);
}
// After a complete run if TDS need to sum up the DIFF...
//mCL.AddTDSDiffImage(TDSImage, CurrentResolution);
mCL.getDiffImage(TDSImage, CurrentResolution);
// Sum it in C++ also for the stem pixel measurement...
//mCL.AddTDS();
if (ct.IsCancellationRequested == true)
{
break;
}
progressReporter.ReportProgress((val) =>
{
CancelButton.IsEnabled = false;
UpdateTDSImage();
}, j);
}
}
private void SimulateSTEM(int TDSruns, ref ProgressReporter progressReporter, ref Stopwatch timer, ref CancellationToken ct, int multistem)
{
LockedDetectors = Detectors;
LockedArea = STEMRegion;
foreach (DetectorItem dt in LockedDetectors)
{
dt.PixelScaleX = LockedArea.getxInterval;
dt.PixelScaleY = LockedArea.getyInterval;
dt.SetPositionReadoutElements(ref LeftXCoord, ref LeftYCoord);
}
if (LockedDetectors.Count == 0)
{
var result = MessageBox.Show("No Detectors Have Been Set", "", MessageBoxButton.OK, MessageBoxImage.Error);
return;
}
int numPix = LockedArea.xPixels * LockedArea.yPixels;
int pix = 0;
foreach (DetectorItem i in LockedDetectors)
{
i.ImageData = new float[numPix];
i.Min = float.MaxValue;
i.Max = float.MinValue;
}
int runs = 1;
if (doTDS_STEM)
{
runs = TDSruns;
}
int totalPix = numPix * runs;
mCL.initialiseSTEMSimulation(CurrentResolution, SimRegion.xStart, SimRegion.yStart, SimRegion.xFinish, SimRegion.yFinish, isFull3D, isFD, dz, integrals, multistem);
float xInterval = LockedArea.getxInterval;
float yInterval = LockedArea.getyInterval;
//List<float[]> TDSImages = new List<float[]>();
List <float> fCoordxs = new List <float>();
List <Tuple <Int32, Int32> > Pixels = new List <Tuple <Int32, Int32> >();
for (int posY = 0; posY < LockedArea.yPixels; posY++)
{
for (int posX = 0; posX < LockedArea.xPixels; posX++)
{
Pixels.Add(new Tuple <Int32, Int32>(posX, posY));
}
}
for (int j = 0; j < runs; j++)
{
Shuffler.Shuffle <Tuple <Int32, Int32> >(Pixels);
// Reset image contrast limits for every run....
foreach (DetectorItem i in LockedDetectors)
{
i.Min = float.MaxValue;
i.Max = float.MinValue;
}
//for (int posY = 0; posY < LockedArea.yPixels * LockedArea.xPixels; posY+=multistem) // won't loop over end?
//{
int posY = 0;
int conPix = multistem;
// numPix
// multistem
while (posY < numPix)
{
mCL.sortStructure(doTDS_STEM);
int thisPosY = posY;
if (posY + multistem > numPix && posY + multistem - numPix + 1 < multistem)
{
conPix = numPix - posY;
posY = numPix;
}
else
{
posY += multistem;
}
for (int i = 1; i <= conPix; i++)
{
mCL.initialiseSTEMWaveFunction(((LockedArea.xStart + Pixels[(thisPosY + i - 1)].Item1 * xInterval - SimRegion.xStart) / pixelScale),
((LockedArea.yStart + Pixels[(thisPosY + i - 1)].Item2 * yInterval - SimRegion.yStart) / pixelScale), i);
}
// Use Background worker to progress through each step
int NumberOfSlices = 0;
mCL.getNumberSlices(ref NumberOfSlices, isFD);
// Seperate into setup, loop over slices and final steps to allow for progress reporting.
for (int i = 1; i <= NumberOfSlices; i++)
{
if (ct.IsCancellationRequested == true)
{
break;
}
timer.Start();
mCL.doMultisliceStep(i, NumberOfSlices, conPix);
timer.Stop();
int mem = mCL.getCLMemoryUsed();
float ms = timer.ElapsedMilliseconds;
progressReporter.ReportProgress((val) =>
{
CancelButton.IsEnabled = true;
// Note: code passed to "ReportProgress" can access UI elements freely.
UI_UpdateSimulationProgressSTEM(ms, totalPix, pix, NumberOfSlices, i, mem);
}, i);
}
pix += conPix;
if (ct.IsCancellationRequested == true)
{
break;
}
for (int i = 1; i <= conPix; i++)
{
// After a complete run if TDS need to sum up the DIFF...
//mCL.AddTDSDiffImage(TDSImages[i-1], CurrentResolution,i);
// Sum it in C++ also for the stem pixel measurement...
//mCL.AddTDS(i);
mCL.getSTEMDiff(i);
}
progressReporter.ReportProgress((val) =>
{
CancelButton.IsEnabled = false;
//UpdateTDSImage();
}, j);
for (int p = 1; p <= conPix; p++)
{
// loop through and get each STEM pixel for each detector at the same time
foreach (DetectorItem i in LockedDetectors)
{
float pixelVal = mCL.getSTEMPixel(i.Inner, i.Outer, i.xCentre, i.yCentre, p);
float newVal = i.ImageData[LockedArea.xPixels * Pixels[thisPosY + p - 1].Item2 + Pixels[thisPosY + p - 1].Item1] + pixelVal;
i.ImageData[LockedArea.xPixels * Pixels[thisPosY + p - 1].Item2 + Pixels[thisPosY + p - 1].Item1] = newVal;
//if (j == runs-1) // Only use final values to set contrast limits
//{
if (newVal < i.Min)
{
i.Min = newVal;
}
if (newVal > i.Max)
{
i.Max = newVal;
}
//}
}
}
// This will update display after each tds run...
progressReporter.ReportProgress((val) =>
{
foreach (DetectorItem i in LockedDetectors)
{
UpdateDetectorImage(i);
}
}, thisPosY);
if (ct.IsCancellationRequested == true)
{
break;
}
}
// Reset TDS arrays after pixel values retrieved
//mCL.ClearTDS(multistem);
//fCoordxs.Clear();
if (ct.IsCancellationRequested == true)
{
break;
}
}
}
private void SimulationMethod(bool select_TEM, bool select_STEM, bool select_CBED, int TDSruns, ref ProgressReporter progressReporter, ref Stopwatch timer, ref CancellationToken ct)
{
// Add Pixelscale to image tabs and diffraction then run simulation
if (select_TEM)
{
EWDisplay.PixelScaleX = pixelScale;
DiffDisplay.PixelScaleX = pixelScale;
EWDisplay.PixelScaleY = pixelScale;
DiffDisplay.PixelScaleY = pixelScale;
EWDisplay.xStartPosition = SimRegion.xStart;
EWDisplay.yStartPosition = SimRegion.yStart;
SimulateTEM(ref progressReporter, ref timer, ref ct);
}
else if (select_STEM)
{
UInt64 mem = mCL.getCLdevGlobalMemory();
UInt64 multi64 = mem / ((UInt64)CurrentResolution * (UInt64)CurrentResolution * 8 * 4);
int multistem = (int)multi64;
DiffDisplay.PixelScaleX = pixelScale;
DiffDisplay.PixelScaleY = pixelScale;
SimulateSTEM(TDSruns, ref progressReporter, ref timer, ref ct, multistem);
}
else if (select_CBED)
{
DiffDisplay.PixelScaleX = pixelScale;
DiffDisplay.PixelScaleY = pixelScale;
SimulateCBED(TDSruns, ref progressReporter, ref timer, ref ct);
}
}
// Simulation Button
private void SimulationButton(object sender, RoutedEventArgs e)
{
select_TEM = TEMRadioButton.IsChecked == true;
select_STEM = STEMRadioButton.IsChecked == true;
select_CBED = CBEDRadioButton.IsChecked == true;
if (!TestSimulationPrerequisites())
{
return;
}
Application.Current.Resources["Accent"] = Application.Current.Resources["ErrorColOrig"];
CurrentResolution = Resolution;
CurrentPixelScale = pixelScale;
CurrentWavelength = wavelength;
CurrentVoltage = ImagingParameters.kilovoltage;
// DiffDisplay.tCanvas.Width = CurrentResolution;
// DiffDisplay.tCanvas.Height = CurrentResolution;
SimulateEWButton.IsEnabled = false;
SimulateImageButton.IsEnabled = false;
var TDSruns = 1;
if (select_STEM)
{
TDSruns = Convert.ToInt32(STEM_TDSCounts.Text);
}
else if (select_CBED)
{
TDSruns = Convert.ToInt32(CBED_TDSCounts.Text);
}
this.cancellationTokenSource = new CancellationTokenSource();
var cancellationToken = this.cancellationTokenSource.Token;
var progressReporter = new ProgressReporter();
// Pull options from dialog
Single.TryParse(SliceDz.Text, out dz);
Int32.TryParse(Full3DIntegrals.Text, out integrals);
CancelButton.IsEnabled = false;
var task = Task.Factory.StartNew(() =>
{
Thread.CurrentThread.Priority = ThreadPriority.Normal;
var timer = new Stopwatch();
// Upload Simulation Parameters to c++ class
mCL.setCTEMParams(ImagingParameters.df, ImagingParameters.astigmag, ImagingParameters.astigang, ImagingParameters.kilovoltage, ImagingParameters.spherical, ImagingParameters.beta, ImagingParameters.delta, ImagingParameters.aperturemrad, ImagingParameters.astig2mag, ImagingParameters.astig2ang, ImagingParameters.b2mag, ImagingParameters.b2ang);
mCL.setSTEMParams(ProbeParameters.df, ProbeParameters.astigmag, ProbeParameters.astigang, ProbeParameters.kilovoltage, ProbeParameters.spherical, ProbeParameters.beta, ProbeParameters.delta, ProbeParameters.aperturemrad);
SimulationMethod(select_TEM, select_STEM, select_CBED, TDSruns, ref progressReporter, ref timer, ref cancellationToken);
}, cancellationToken);
// This runs on UI Thread so can access UI, probably better way of doing image though.
//SimWorker.RunWorkerCompleted += delegate(object s, RunWorkerCompletedEventArgs args)
progressReporter.RegisterContinuation(task, () =>
{
CancelButton.IsEnabled = false;
ProgressBar1.Value = 100;
ProgressBar2.Value = 100;
if (select_STEM)
{
if (LockedDetectors.Count == 0)
{
SimulateEWButton.IsEnabled = true;
return;
}
foreach (var i in LockedDetectors)
{
UpdateDetectorImage(i);
}
// just select the first tab for convenience
LockedDetectors[0].Tab.IsSelected = true;
SaveImageButton.IsEnabled = true;
}
else if (select_CBED)
{
UpdateTDSImage();
SaveImageButton2.IsEnabled = true;
}
else
{
UpdateEWImage();
EWDisplay.Tab.IsSelected = true;
UpdateDiffractionImage();
SaveImageButton.IsEnabled = true;
SaveImageButton2.IsEnabled = true;
SimulateImageButton.IsEnabled = true;
}
Application.Current.Resources["Accent"] = Application.Current.Resources["AccentOrig"];
SimulateEWButton.IsEnabled = true;
});
}
private void ImportStructureButton(object sender, RoutedEventArgs e)
{
var openDialog = new Microsoft.Win32.OpenFileDialog
{
FileName = "file name",
DefaultExt = ".xyz",
Filter = "XYZ Coordinates (.xyz)|*.xyz"
};
// Set defaults for file dialog.
var result = openDialog.ShowDialog();
if (result == true)
{
var fName = openDialog.FileName;
fileNameLabel.Text = System.IO.Path.GetFileName(fName);
fileNameLabel.ToolTip = fName;
// Now pass filename through to unmanaged where atoms can be imported inside structure class...
mCL.importStructure(openDialog.FileName);
mCL.uploadParameterisation();
// Update some dialogs if everything went OK.
var Len = 0;
float MinX = 0;
float MinY = 0;
float MinZ = 0;
float MaxX = 0;
float MaxY = 0;
float MaxZ = 0;
mCL.getStructureDetails(ref Len, ref MinX, ref MinY, ref MinZ, ref MaxX, ref MaxY, ref MaxZ);
HaveStructure = true;
WidthLabel.Content = (MaxX - MinX).ToString("f2") + " Å";
HeightLabel.Content = (MaxY - MinY).ToString("f2") + " Å";
DepthLabel.Content = (MaxZ - MinZ).ToString("f2") + " Å";
AtomNoLabel.Content = Len.ToString();
if (!userSTEMarea)
{
STEMRegion.xFinish = Convert.ToSingle((MaxX - MinX).ToString("f2"));
STEMRegion.yFinish = Convert.ToSingle((MaxY - MinY).ToString("f2"));
}
if (!userSIMarea)
{
SimRegion.xFinish = Convert.ToSingle((MaxX - MinX).ToString("f2"));
SimRegion.yFinish = Convert.ToSingle((MaxY - MinY).ToString("f2"));
}
UpdatePx();
// Now we want to sorting the atoms ready for the simulation process do this in a background worker...
this.cancellationTokenSource = new CancellationTokenSource();
var cancellationToken = this.cancellationTokenSource.Token;
var progressReporter = new ProgressReporter();
var task = Task.Factory.StartNew(() =>
{
// This is where we start sorting the atoms in the background ready to be processed later...
mCL.sortStructure(false);
return(0);
}, cancellationToken);
// This runs on UI Thread so can access UI, probably better way of doing image though.
progressReporter.RegisterContinuation(task, () =>
{
IsSorted = true;
});
}
}
