public void CopyKey(string key, MiniFits from)
{
}
static void Main(string[] args)
{
string dataFile = "";
try
{
//Make it crash nicely when run without a filename
dataFile = args[0];
}
catch (Exception e)
{
Console.WriteLine("No filename passed, now exiting" + e);
return;
}
var frame = new MiniFits(dataFile, false);
var rowStride = frame.ReadDecimalKey("ROWSTRID");
var colStride = frame.ReadDecimalKey("COLSTRID");
var primaryDark = 0.0;
var secondaryDark = 0.0;
try
{
// Older frames don't specify dark counts, so let these gracefully fail
primaryDark = (double)frame.ReadDecimalKey("DARKCNTA");
secondaryDark = (double)frame.ReadDecimalKey("DARKCNTB");
}
catch (Exception)
{
frame.ClearErrorStatus();
}
var region = frame.ReadStringKey("SCANAREA")
.Split(' ')
.Select(x => decimal.Parse(x))
.ToArray();
var overscanColumns = 0;
try
{
// Older frames don't specify the overscan
overscanColumns = frame.ReadIntegerKey("OVERSCAN");
}
catch (Exception)
{
frame.ClearErrorStatus();
}
Console.WriteLine("Overscan columns: {0}", overscanColumns);
var inWidth = frame.Dimensions[0];
var inHeight = frame.Dimensions[1];
var binning = (int)Math.Round(rowStride / colStride);
if (binning <= 0)
throw new InvalidOperationException("Invalid row or column stride");
var outWidth = (inWidth - 2 * overscanColumns) / binning;
var outHeight = inHeight;
var binnedFile = Path.GetDirectoryName(dataFile) + Path.DirectorySeparatorChar + Path.GetFileNameWithoutExtension(dataFile) + ".binned.fits";
using (var binned = new MiniFits(binnedFile, new[] { outWidth, outHeight, 3 }, MiniFitsType.F64, true))
{
// Define the image coordinates for the display program
// Physical coordinates
binned.WriteKey("LTM1_1", 1 / (colStride * binning), 6);
binned.WriteKey("LTM1_2", 0);
binned.WriteKey("LTM2_1", 0);
binned.WriteKey("LTM2_2", 1 / rowStride, 6);
binned.WriteKey("LTV1", -region[0] / (colStride * binning) - 0.5m, 6);
binned.WriteKey("LTV2", -region[1] / rowStride - 0.5m, 6);
// WCS coordinates
binned.WriteKey("CTYPE1", "LINEAR");
binned.WriteKey("CUNIT1", "mm");
binned.WriteKey("CRPIX1", 0);
binned.WriteKey("CRVAL1", region[0] + colStride * binning / 2, 6);
binned.WriteKey("CDELT1", colStride * binning, 6);
binned.WriteKey("CTYPE2", "LINEAR");
binned.WriteKey("CUNIT2", "mm");
binned.WriteKey("CRPIX2", 0);
binned.WriteKey("CRVAL2", region[1] + rowStride / 2, 6);
binned.WriteKey("CDELT2", rowStride, 6);
binned.WriteKey("WCSNAME", "Scan Pos.");
var data = frame.ReadU16ImageData();
var frameStride = outWidth * outHeight;
var binnedData = new double[frameStride * 3];
for (var i = 0; i < outHeight; i++)
{
for (var j = 0; j < outWidth; j++)
{
var primaryOffset = inWidth * i + binning * j + overscanColumns;
var secondaryOffset = primaryOffset + inWidth * inHeight;
var primaryBinned = 0.0;
var secondaryBinned = 0.0;
for (var k = 0; k < binning; k++)
{
primaryBinned += data[primaryOffset + k] - primaryDark;
secondaryBinned += data[secondaryOffset + k] - secondaryDark;
}
var outIndex = i * outWidth + j;
binnedData[outIndex] = primaryBinned / secondaryBinned;
binnedData[outIndex + frameStride] = primaryBinned;
binnedData[outIndex + 2 * frameStride] = secondaryBinned;
}
}
binned.WriteImageData(binnedData);
}
}
public void StartScan(Configuration config)
{
if (asyncControl.IsAlive)
{
OnLogMessage("Invalid thread state. Aborting scan.");
return;
}
if (Status == HardwareStatus.Error)
{
OnLogMessage("Hardware status is error. Aborting scan.");
return;
}
cancelScan = false;
asyncControl = new Thread(() =>
{
try
{
var startColumn = (int)((config.Origin.X - config.RowOverscan) * config.XStepsPerMM);
var endColumn = (int)((config.Origin.X + config.Size.Width + config.RowOverscan) * config.XStepsPerMM);
var overscanCols = (int)(config.Origin.X * config.XStepsPerMM) - startColumn;
if (startColumn < 0)
{
OnLogMessage("Overscan region extends outside the scannable region. Inset the scan area or reduce the overscan.");
return;
}
OnLogMessage(string.Format("Counter columns {0} to {1}, overscan {2}", startColumn, endColumn, overscanCols));
var rows = (int)Math.Ceiling(config.Size.Height / config.RowStride);
var columns = endColumn - startColumn + 1;
var dimensions = new[] { columns, rows, 2 };
using (var fits = new MiniFits(config.DataFile, dimensions, MiniFitsType.U16, true))
{
fits.WriteKey("OPERATOR", config.Operator, null);
fits.WriteKey("DATETIME", DateTime.Now.ToString("G"), "Time at the start of the scan");
fits.WriteKey("DESCRIPT", config.Description, null);
fits.WriteKey("SCANAREA", string.Format("{0:F3} {1:F3} {2:F3} {3:F3}", config.Origin.X, config.Origin.Y, config.Size.Width, config.Size.Height), "The requested scan area (X Y W H in mm)");
fits.WriteKey("ROWSTART", startColumn, "The step count of the first data column");
fits.WriteKey("ROWSTRID", config.RowStride, 6, "The step size between rows (in mm)");
fits.WriteKey("ROWSPEED", config.ScanSpeed, 4, "The row scan speed (in mm/minute)");
fits.WriteKey("OVERSCAN", overscanCols, 6, "The row overscan before/after the horizontal scan area (in columns).");
fits.WriteKey("COLSTRID", config.ColumnStride, 6, "The step size between columns (in mm)");
fits.WriteKey("DARKCNTA", config.PrimaryDarkCounts, 4, "Mean dark counts per unbinned pixel for detector A");
fits.WriteKey("DARKCNTB", config.SecondaryDarkCounts, 4, "Mean dark counts per unbinned pixel for detector B");
var data = new ushort[rows * columns * 2];
OnLogMessage("Moving to start position.");
UpdateStatus(HardwareStatus.Homing);
printer.MoveToHome();
counter.ZeroPositionCounter();
printer.MoveToPosition(0, config.Origin.Y, config.FocusHeight, config.SlewSpeed);
printer.MoveToPosition(config.Origin.X - config.RowOverscan, config.Origin.Y, config.FocusHeight, config.SlewSpeed);
UpdateStatus(HardwareStatus.Scanning);
OnLogMessage("Starting scan.");
double TotalTime=1;
// Scan rows
for (var i = 0; i < rows; i+=1)
{
var StartTime = DateTime.Now;
if (cancelScan)
break;
OnLogMessage("Starting read at: " + counter.ReadPositionCounter().ToString());
OnLogMessage(string.Format("Scanning row {0} of {1} ({2:F0}%)", i + 1, rows, i * 100 / rows));
counter.Start();
// Collect photons while scanning left -> right
// Scanning in one direction only ensures that the same optical configuration is used for each row
printer.MoveDeltaX(config.Size.Width + 2 * config.RowOverscan, config.ScanSpeed);
counter.Stop();
// Read and save data to file
var primary = counter.ReadHistogram(CounterChannel.Primary, startColumn, endColumn);
var secondary = counter.ReadHistogram(CounterChannel.Secondary, startColumn, endColumn);
Array.Copy(primary, 0, data, i * columns, columns);
Array.Copy(secondary, 0, data, (rows + i) * columns, columns);
//OnLogMessage(string.Join(" ", primary));
fits.WriteImageData(data);
counter.ResetHistogram();
UpdateStatus(HardwareStatus.Scanning, i * 100m / rows);
// Return to the start of the next row
printer.MoveDeltaX(-(config.Size.Width + 2 * config.RowOverscan), config.SlewSpeed);
printer.MoveDeltaY(config.RowStride, config.ScanSpeed);
/**
//Scan on the way back too
OnLogMessage("Starting at " + counter.ReadPositionCounter().ToString());
printer.MoveDeltaY(config.RowStride, config.ScanSpeed);
counter.Start();
printer.MoveDeltaX(-1 * (config.Size.Width + (2 * config.RowOverscan)), config.ScanSpeed);
counter.Stop();
primary = counter.ReadHistogram(CounterChannel.Primary, startColumn, endColumn);
secondary = counter.ReadHistogram(CounterChannel.Secondary, startColumn, endColumn);
counter.ResetHistogram();
Array.Copy(primary, 0, data, (i + 1) * columns, columns);
Array.Copy(secondary, 0, data, (rows + i + 1) * columns, columns);
fits.WriteImageData(data);
*/
//Calculate total, average and finish times
TimeSpan RowTime = DateTime.Now - StartTime;
TotalTime += RowTime.TotalSeconds;
var AverageRowTime = TotalTime / (i+1);
DateTime ECT=DateTime.Now;
ECT=ECT.AddSeconds(AverageRowTime*(rows-i));
OnLogMessage(string.Format("Time elapsed: {0}s, Average Time per row: {1}s", TotalTime.ToString("f0"), AverageRowTime.ToString("f0")));
OnLogMessage("Estimated Completion: " + ECT.ToLongTimeString());
}
OnLogMessage("Scan complete.");
UpdateStatus(HardwareStatus.Homing);
printer.MoveToHome();
UpdateStatus(HardwareStatus.Idle);
}
}
catch (PrinterException e)
{
OnLogMessage("Printer error: " + e.Message);
UpdateStatus(HardwareStatus.Error);
CloseSerialConnections();
}
catch (CounterException e)
{
OnLogMessage("Counter error: " + e.Message);
UpdateStatus(HardwareStatus.Error);
// TODO: Send emergency stop (M112)
CloseSerialConnections();
}
catch (MiniFitsException e)
{
OnLogMessage("File error: " + e.Message);
UpdateStatus(HardwareStatus.Error);
// TODO: Turn off laser and home printer
// TODO: Send emergency stop (M112)
CloseSerialConnections();
}
});
asyncControl.Start();
}
