private static bool LoadFitsFileInternal <TData>(
string fileName, IFITSTimeStampReader timeStampReader,
out TData[,] pixels, out TData medianValue, out Type pixelDataType, out float frameExposure, out bool hasNegativePixels, out short minRawValue, out uint maxVal,
CheckOpenedFitsFileCallback callback, LoadFitsDataCallback <TData> loadDataCallback)
{
Fits fitsFile = new Fits();
using (BufferedFile bf = new BufferedFile(fileName, FileAccess.Read, FileShare.ReadWrite))
{
fitsFile.Read(bf);
BasicHDU imageHDU = fitsFile.GetHDU(0);
Array pixelsArray = (Array)imageHDU.Data.DataArray;
return(LoadFitsDataInternal <TData>(
imageHDU, pixelsArray, fileName, timeStampReader,
out pixels, out medianValue, out pixelDataType, out frameExposure, out hasNegativePixels, out minRawValue, out maxVal,
callback, loadDataCallback));
}
}
public static ThreeAxisFITSCubeFrameStream OpenFile(string fileName, VideoController videoController)
{
var fitsFile = new Fits();
var bufferedFile = new BufferedFile(fileName, FileAccess.Read, FileShare.ReadWrite);
fitsFile.Read(bufferedFile);
var imageHDU = fitsFile.GetHDU(0);
ThreeAxisFITSCubeFrameStream fitsStream = null;
videoController.SetCursor(Cursors.WaitCursor);
try
{
var hasher = new SHA1CryptoServiceProvider();
hasher.Initialize();
byte[] combinedFileNamesBytes = Encoding.UTF8.GetBytes(fileName);
var hash = hasher.ComputeHash(combinedFileNamesBytes, 0, combinedFileNamesBytes.Length);
var fitsFileHash = Convert.ToBase64String(hash);
var frm = new frmDefineFitsCube3D(imageHDU, fitsFileHash, videoController);
if (videoController.ShowDialog(frm) == DialogResult.OK)
{
videoController.SetFlipSettings(frm.FlipVertically, frm.FlipHorizontally);
fitsStream = new ThreeAxisFITSCubeFrameStream(
fileName, fitsFile, bufferedFile, imageHDU, frm.TimeStampReader,
frm.WidthIndex, frm.HeightIndex, frm.FrameIndex,
frm.MinPixelValue, frm.MaxPixelValue, frm.BitPix, frm.NegPixCorrection);
}
}
finally
{
if (fitsStream == null)
{
bufferedFile.Dispose();
}
}
return(fitsStream);
}
private BasicHDU ReadFIT(string fileName)
{
Fits f = new Fits(fileName);
try
{
BasicHDU hdus = f.ReadHDU();
if (hdus != null)
{
hdus.Info();
// TEST: NUM SHARP TEST
ImageHDU imgHdu = (ImageHDU)f.GetHDU(0);
numSharp.InitImage(imgHdu, fileName);
}
return(hdus);
}
catch (Exception e)
{
throw e;
}
}
public static FitsCubeType GetFitsCubeType(string fileName)
{
Fits fitsFile = new Fits();
using (BufferedFile bf = new BufferedFile(fileName, FileAccess.Read, FileShare.ReadWrite))
{
fitsFile.Read(bf);
BasicHDU imageHDU = fitsFile.GetHDU(0);
if (fitsFile.NumberOfHDUs == 1 && imageHDU.Axes.Length == 3)
{
return(FitsCubeType.ThreeAxisCube);
}
if (fitsFile.NumberOfHDUs > 1 && imageHDU.Axes.Length == 2)
{
return(FitsCubeType.MultipleHDUsCube);
}
}
return(FitsCubeType.NotACube);
}
public static FitsType GetFitsType(string fileName)
{
Fits fitsFile = new Fits();
using (BufferedFile bf = new BufferedFile(fileName, FileAccess.Read, FileShare.ReadWrite))
{
fitsFile.Read(bf);
BasicHDU imageHDU = fitsFile.GetHDU(0);
if (fitsFile.NumberOfHDUs == 1 && imageHDU.Axes.Length == 3 && imageHDU.Axes[0] == 3)
{
return(FitsType.RGBFrames);
}
if (fitsFile.NumberOfHDUs == 1 && imageHDU.Axes.Length == 2)
{
return(FitsType.SingleFrame);
}
}
return(FitsType.Invalid);
}
private void BuildCalSpecDb()
{
var db = new CalSpecDatabase();
int totalBad = 0;
string[] lines2 = File.ReadAllLines(@"F:\WORK\tangra3\Tangra 3\VideoOperations\Spectroscopy\AbsFluxCalibration\Standards\AbsFlux-TangraStars.csv");
for (int i = 1; i < lines2.Length; i++)
{
string[] tokens = lines2[i].Split(',');
string calSpecId = tokens[0].Trim();
string RA_FK5_Hours = tokens[1].Trim();
string DEG_FK5_Deg = tokens[2].Trim();
string pmRA = tokens[3].Trim();
string pmDec = tokens[4].Trim();
string specType = tokens[5].Trim();
string magV = tokens[6].Trim();
string magBV = tokens[7].Trim();
string absFluxId = tokens[8].Trim();
string stisFlag = tokens[9].Trim();
string fitsFilePath = tokens[10].Trim();
int stisFrom = int.Parse(tokens[11].Trim());
int stisTo = int.Parse(tokens[12].Trim());
string tyc2 = tokens[13].Trim();
string ucac4 = tokens[14].Trim();
if (!string.IsNullOrEmpty(pmRA) && !string.IsNullOrEmpty(pmDec))
{
var star = new CalSpecStar()
{
CalSpecStarId = calSpecId,
AbsFluxStarId = absFluxId,
STIS_Flag = stisFlag,
FITS_File = fitsFilePath,
TYC2 = tyc2,
U4 = ucac4,
pmRA = double.Parse(pmRA),
pmDE = double.Parse(pmDec),
MagV = double.Parse(magV),
MagBV = double.Parse(magBV),
SpecType = specType,
RA_J2000_Hours = AstroConvert.ToRightAcsension(RA_FK5_Hours),
DE_J2000_Deg = AstroConvert.ToDeclination(DEG_FK5_Deg)
};
string filePath = Path.GetFullPath(@"Z:\CALSPEC\current_calspec\" + fitsFilePath);
using (var bf = new BufferedFile(filePath, FileAccess.Read, FileShare.ReadWrite))
{
var fitsFile = new Fits();
fitsFile.Read(bf);
BasicHDU imageHDU = fitsFile.GetHDU(1);
var table = (ColumnTable)imageHDU.Data.DataArray;
double[] wavelengths = (double[])table.Columns[0];
float[] fluxes = (float[])table.Columns[1];
short[] goodnessFlags = (short[])table.Columns[5];
for (int j = 0; j < fluxes.Length; j++)
{
if (wavelengths[j] < stisFrom)
{
continue;
}
if (wavelengths[j] > stisTo)
{
break;
}
if (goodnessFlags[j] != 0)
{
star.DataPoints.Add(wavelengths[j], fluxes[j]);
}
else
{
totalBad++;
}
}
fitsFile.Close();
}
db.Stars.Add(star);
}
}
using (var compressedStream = new FileStream(@"F:\WORK\tangra3\Tangra 3\VideoOperations\Spectroscopy\AbsFluxCalibration\Standards\CalSpec.db", FileMode.CreateNew, FileAccess.Write))
using (var deflateStream = new DeflateStream(compressedStream, CompressionMode.Compress, true))
{
using (var writer = new BinaryWriter(deflateStream))
{
db.Serialize(writer);
}
}
using (var compressedStream = new FileStream(@"F:\WORK\tangra3\Tangra 3\VideoOperations\Spectroscopy\AbsFluxCalibration\Standards\CalSpec.db", FileMode.Open, FileAccess.Read))
using (var deflateStream = new DeflateStream(compressedStream, CompressionMode.Decompress, true))
{
using (var reader = new BinaryReader(deflateStream))
{
var db2 = new CalSpecDatabase(reader);
Trace.WriteLine(db2.Stars.Count);
}
}
MessageBox.Show(totalBad.ToString() + " bad entries excluded.");
string[] fitsFiles = Directory.GetFiles(@"Z:\CALSPEC\current_calspec", "*.fit");
var dist = new Dictionary <int, int>();
foreach (string filePath in fitsFiles)
{
using (var bf = new BufferedFile(filePath, FileAccess.Read, FileShare.ReadWrite))
{
var fitsFile = new Fits();
fitsFile.Read(bf);
var bld = new StringBuilder();
BasicHDU headerHDU = fitsFile.GetHDU(0);
BasicHDU imageHDU = fitsFile.GetHDU(1);
for (int i = 0; i < headerHDU.Header.NumberOfCards; i++)
{
string cardString = headerHDU.Header.GetCard(i);
bld.AppendFormat("# {0}\r\n", cardString);
}
for (int i = 0; i < imageHDU.Header.NumberOfCards; i++)
{
string cardString = imageHDU.Header.GetCard(i);
bld.AppendFormat("# {0}\r\n", cardString);
}
var table = (ColumnTable)imageHDU.Data.DataArray;
if (table.Columns.Length == 7 &&
table.Columns[0] is double[] && table.Columns[1] is float[] && table.Columns[2] is float[] && table.Columns[3] is float[] &&
table.Columns[4] is float[] && table.Columns[5] is short[] && table.Columns[6] is float[])
{
double[] wavelengths = (double[])table.Columns[0];
float[] fluxes = (float[])table.Columns[1];
float[] col2 = (float[])table.Columns[2];
float[] col3 = (float[])table.Columns[3];
float[] col4 = (float[])table.Columns[4];
short[] goodnessFlags = (short[])table.Columns[5];
float[] exposures = (float[])table.Columns[6];
for (int i = 0; i < fluxes.Length; i++)
{
if (wavelengths[i] < 2000)
{
continue;
}
if (wavelengths[i] > 15000)
{
break;
}
bld.Append(wavelengths[i].ToString().PadLeft(20));
bld.Append(fluxes[i].ToString().PadLeft(20));
bld.Append(col2[i].ToString().PadLeft(20));
bld.Append(col3[i].ToString().PadLeft(20));
bld.Append(col4[i].ToString().PadLeft(20));
bld.Append(goodnessFlags[i].ToString().PadLeft(15));
bld.Append(exposures[i].ToString().PadLeft(15));
bld.AppendLine();
int expMS = (int)Math.Round(exposures[i] * 1000);
if (!dist.ContainsKey(expMS))
{
dist.Add(expMS, 0);
}
dist[expMS]++;
}
}
string outFileName = Path.ChangeExtension(filePath, ".txt");
File.WriteAllText(outFileName, bld.ToString());
fitsFile.Close();
}
}
var output = new StringBuilder();
foreach (int key in dist.Keys)
{
output.AppendFormat("{0}s = {1}\r\n", (key / 1000.0).ToString("0.0"), dist[key]);
}
MessageBox.Show(output.ToString());
}
private void BuildAbsFlux()
{
var indexFile = new StringBuilder();
indexFile.AppendLine("BD and HD CALSPEC stars with STIS fluxes between 3000 and 10000 Angstroms");
indexFile.AppendLine("Name FK5_Coordinates_J2000 Type Mag B-V File_Name");
foreach (CalSpecStar star in CalSpecDatabase.Instance.Stars)
{
if (star.AbsFluxStarId.StartsWith("TYC"))
{
continue;
}
string modifiedId = star.AbsFluxStarId.Replace(" ", "_");
if (modifiedId.Length < 10)
{
modifiedId += "_";
}
while (modifiedId.Length < 10)
{
int firstUnderScorePos = modifiedId.IndexOf("_");
modifiedId = modifiedId.Substring(0, firstUnderScorePos) + "_" + modifiedId.Substring(firstUnderScorePos);
}
string raStr = AstroConvert.ToStringValue(star.RA_J2000_Hours, "HH MM SS.TTT");
string deStr = AstroConvert.ToStringValue(star.DE_J2000_Deg, "+DD MM SS.TT");
string dataFileName = Path.GetFileNameWithoutExtension(star.FITS_File) + "_t1.txt";
string line = string.Format("{0}{1} {2} {3}{4} {5} {6}\r\n",
modifiedId.PadRight(14), raStr, deStr,
star.SpecType.PadRight(7),
star.MagV.ToString("0.00").PadLeft(5),
star.MagBV.ToString("0.00").PadLeft(5),
dataFileName);
indexFile.Append(line);
string filePath = Path.GetFullPath(@"Z:\CALSPEC\current_calspec\" + star.FITS_File);
double wavelengthFrom = star.DataPoints.Keys.Min();
double wavelengthTo = star.DataPoints.Keys.Max();
using (var bf = new BufferedFile(filePath, FileAccess.Read, FileShare.ReadWrite))
{
var fitsFile = new Fits();
fitsFile.Read(bf);
BasicHDU imageHDU = fitsFile.GetHDU(1);
var table = (ColumnTable)imageHDU.Data.DataArray;
double[] wavelengths = (double[])table.Columns[0];
float[] fluxes = (float[])table.Columns[1];
float[] col2 = (float[])table.Columns[2];
float[] col3 = (float[])table.Columns[3];
float[] col4 = (float[])table.Columns[4];
short[] goodnessFlags = (short[])table.Columns[5];
float[] exposures = (float[])table.Columns[6];
var dataFile = new StringBuilder();
dataFile.AppendLine(" WAVELENGTH FLUX STATERROR SYSERROR FWHM DATAQUAL TOTEXP");
dataFile.AppendLine(" 1D 1E 1E 1E 1E 1I 1E");
dataFile.AppendLine(" ANGSTROMS FLAM FLAM FLAM ANGSTROMS NONE SEC");
for (int j = 0; j < fluxes.Length; j++)
{
if (wavelengths[j] < wavelengthFrom)
{
continue;
}
if (wavelengths[j] > wavelengthTo)
{
break;
}
string dataLine = string.Format("{0}{1}{2}{3}{4} {5}{6}",
((int)Math.Round(wavelengths[j])).ToString().PadLeft(16),
fluxes[j].ToString("E4").PadLeft(14),
col2[j].ToString("E4").PadLeft(14),
col3[j].ToString("E4").PadLeft(14),
col4[j].ToString("#.0").PadLeft(13),
goodnessFlags[j].ToString(),
exposures[j].ToString("E1").PadLeft(12));
dataFile.AppendLine(dataLine);
}
fitsFile.Close();
File.WriteAllText(@"Z:\AbsFlux\v3\" + dataFileName, dataFile.ToString());
}
}
File.WriteAllText(@"Z:\AbsFlux\v3\AbsFluxCALSPECstars.txt", indexFile.ToString());
}
//public static FITSData LoadFitsFile(string fileName, BasicHDU hdu, Array pixels, IFITSTimeStampReader timeStampReader, int negativePixelCorrection)
//{
//}
public static FITSData LoadFitsFile(string fileName, IFITSTimeStampReader timeStampReader, int negativePixelCorrection)
{
var rv = new FITSData();
Fits fitsFile = new Fits();
using (BufferedFile bf = new BufferedFile(fileName, FileAccess.Read, FileShare.ReadWrite))
{
fitsFile.Read(bf);
rv.HDU = fitsFile.GetHDU(0);
rv.Width = rv.HDU.Axes[1];
rv.Height = rv.HDU.Axes[0];
Array pixelsArray = (Array)rv.HDU.Data.DataArray;
rv.PixelStats = new PixelStats();
rv.PixelStats.BZero = GetBZero(rv.HDU);
rv.PixelStats.RawBitPix = rv.HDU.BitPix;
uint mask = (uint)(((uint)1 << rv.PixelStats.RawBitPix) - 1);
rv.PixelStats.BitPix = rv.PixelStats.RawBitPix;
if (rv.PixelStats.BitPix < 0)
{
/* float and double are -32 and -64 respectively */
// Pretending float data is 16 bit. This is the maximum currently supported by Tangra
// Not using a mask here, and the pixel values will be converted further down
mask = 0;
}
rv.PixelsFlat = Load16BitImageData(pixelsArray, rv.Height, rv.Width, rv.PixelStats.BZero - negativePixelCorrection, mask,
out rv.PixelStats.MedianPixelValue, out rv.PixelStats.PixelType,
out rv.PixelStats.HasNegativePixels, out rv.PixelStats.MinPixelValue,
out rv.PixelStats.MaxPixelValue);
rv.PixelStats.BitPix = GetBppForMaxPixelValue(rv.PixelStats.MaxPixelValue);
if (rv.PixelStats.BitPix == 32)
{
// Tangra only supports up to 16 bit so convert down to 16 bit
int shift = Math.Max(0, (int)Math.Ceiling(Math.Abs(rv.HDU.BitPix) / 16.0) - 1);
for (int y = 0; y < rv.Height; y++)
{
for (int x = 0; x < rv.Width; x++)
{
rv.PixelsFlat[x + y * rv.Width] = rv.PixelsFlat[x + y * rv.Width] >> shift;
}
}
rv.PixelStats.BitPix = 16;
}
}
// Read Timestamp & Exposure
if (timeStampReader != null)
{
bool isMidPoint;
rv.Timestamp = timeStampReader.ParseExposure(fileName, rv.HDU.Header, out isMidPoint, out rv.Exposure);
}
// Read card from header
rv.Cards = new Dictionary <string, string>();
var cursor = rv.HDU.Header.GetCursor();
while (cursor.MoveNext())
{
HeaderCard card = rv.HDU.Header.FindCard((string)cursor.Key);
if (card != null && !string.IsNullOrWhiteSpace(card.Key) && card.Key != "END")
{
if (rv.Cards.ContainsKey(card.Key))
{
rv.Cards[card.Key] += "\r\n" + card.Value;
}
else
{
rv.Cards.Add(card.Key, card.Value);
}
}
}
return(rv);
}
public void MakeDataFile()
{
string pathToCorr = "";
if (GlobalVariables.LocalPlateSolve)
{
pathToCorr = @"c:\cygwin\home\astro\solve.corr";
}
else
{
pathToCorr = GlobalVariables.Path2 + "\\corr.fits";
}
// Fits f = new Fits(GlobalVariables.Path2 + "\\corr.fits"); // original
Fits f = new Fits(pathToCorr);
BinaryTableHDU h = (BinaryTableHDU)f.GetHDU(1);
// Object[] row23 = h.GetRow(23);
Object col_x = h.GetColumn(0);
Object col_y = h.GetColumn(1);
Object col_ra = h.GetColumn(2);
Object col_dec = h.GetColumn(3);
float[] x = new float[h.NRows];
float[] y = new float[h.NRows];
float[] ra = new float[h.NRows];
float[] dec = new float[h.NRows];
GlobalVariables.CorrFileLines = h.NRows;
int i = 0;
foreach (float item in (dynamic)col_x)
{
x[i] = (dynamic)(item);
i++;
}
i = 0;
foreach (float item2 in (dynamic)col_y)
{
y[i] = (dynamic)(item2);
i++;
}
i = 0;
foreach (float item in (dynamic)col_ra)
{
ra[i] = (dynamic)(item) / 15;
i++;
}
i = 0;
foreach (float item2 in (dynamic)col_dec)
{
dec[i] = (dynamic)(item2);
i++;
}
using (StreamWriter sr = new StreamWriter(GlobalVariables.Path2 + "\\corr2text.txt"))
{
// sr.WriteLine(" x " + " y ");
for (i = 0; i < x.Length; i++)
{
sr.WriteLine(x[i] + " \t" + y[i] + " \t" + ra[i] + " \t" + dec[i]);
}
sr.Dispose();
}
Log("Corr2text file complete in " + GlobalVariables.Path2);
}
