static void Main(string[] args)
{
Console.Beep();
Console.ForegroundColor = ConsoleColor.Yellow;
Console.WriteLine("*******************************************************");
Console.WriteLine("* MERCATOR/HERMES *");
Console.WriteLine("* SPECTRA REDUCTION PIPELINE *");
Console.WriteLine("*******************************************************");
Console.ForegroundColor = ConsoleColor.White;
//Image.Save("file.fit");
//goto STOP;
//InitFile.ReadInitFile("INIT.dat");
Init.Initialize("INIT.dat");
if (Init.ErrorString != "")
{
Console.WriteLine("Error in INIT file!");
Console.WriteLine(Init.ErrorString);
goto STOP;
}
string dir_main = (string)Init.Value("DIR_MAIN");
if (!Directory.Exists(dir_main))
{
try
{
Directory.CreateDirectory(dir_main);
}
catch
{
Console.WriteLine("Cannot create main directory.\r\n");
goto STOP;
}
}
string[] bias_files = null, flat_files = null, thar_files = null, obj_files = null;
Console.WriteLine("Searching for Bias, Flat, ThAr and Object files...");
try
{
bias_files = ImageSelector.GetFilesByHDU(
(string)Init.Value("DIR_BIAS"), (string)Init.Value("FMASK_BIAS"), "IMAGETYP", "*");
flat_files = ImageSelector.GetFilesByHDU(
(string)Init.Value("DIR_FLAT"), (string)Init.Value("FMASK_FLAT"), "IMAGETYP", "*");
thar_files = ImageSelector.GetFilesByHDU(
(string)Init.Value("DIR_CLBR"), (string)Init.Value("FMASK_CLBR"), "IMAGETYP", "*");
obj_files = ImageSelector.GetFilesByHDU(
(string)Init.Value("DIR_OBJ"), (string)Init.Value("FMASK_OBJ"), "IMAGETYP", "*");
}
catch
{
Console.WriteLine("Error in files searching...");
goto STOP;
}
Console.WriteLine("Bias files number: {0}", bias_files.Length);
Console.WriteLine("Flat files number: {0}", flat_files.Length);
Console.WriteLine("ThAr files number: {0}", thar_files.Length);
Console.WriteLine("Object files number: {0}", obj_files.Length);
if (bias_files.Length == 0 || flat_files.Length == 0 ||
thar_files.Length == 0 || obj_files.Length == 0)
{
Console.WriteLine("Some necessary files were not found...");
goto STOP;
}
Image[] biases = new Image[bias_files.Length];
Image[] flats = new Image[flat_files.Length];
Image[] thars = new Image[thar_files.Length];
Image[] objects = new Image[obj_files.Length];
// Loading and averaging of bias images;
Console.WriteLine("Loading Bias images...");
for (int i = 0; i < bias_files.Length; i++)
{
Console.WriteLine("->" + bias_files[i]);
biases[i] = new Image();
biases[i].LoadImage(bias_files[i]);
if ((bool)Init.Value("TRIM_ON"))
{
biases[i] = biases[i].Trim(
(int)Init.Value("TRIM_STR1"), (int)Init.Value("TRIM_COL1"),
(int)Init.Value("TRIM_STR2"), (int)Init.Value("TRIM_COL2"));
}
//Console.WriteLine("MEAN = {0:0.00}; STDDEV = {1:0.00}",
// Statistics.Mean(biases[i]), Statistics.StdDev(biases[i]));
}
Console.WriteLine("Bias images averaging...");
Image bias_aver = ImageCombinator.Median(biases);
for (int i = 0; i < bias_files.Length; i++)
{
biases[i] = null;
}
// Loading and averaging of flat images;
Console.WriteLine("Loading Flat images...");
for (int i = 0; i < flat_files.Length; i++)
{
Console.WriteLine("->" + flat_files[i]);
flats[i] = new Image();
flats[i].LoadImage(flat_files[i]);
if ((bool)Init.Value("TRIM_ON"))
{
flats[i] = flats[i].Trim(
(int)Init.Value("TRIM_STR1"), (int)Init.Value("TRIM_COL1"),
(int)Init.Value("TRIM_STR2"), (int)Init.Value("TRIM_COL2"));
}
}
Console.WriteLine("Flat images averaging...");
Image flat_aver = ImageCombinator.Median(flats);
for (int i = 0; i < flat_files.Length; i++)
{
flats[i] = null;
}
// Loading and averaging of Th-Ar images;
Console.WriteLine("Loading Th-Ar images...");
for (int i = 0; i < thar_files.Length; i++)
{
Console.WriteLine("->" + thar_files[i]);
thars[i] = new Image();
thars[i].LoadImage(thar_files[i]);
if ((bool)Init.Value("TRIM_ON"))
{
thars[i] = thars[i].Trim(
(int)Init.Value("TRIM_STR1"), (int)Init.Value("TRIM_COL1"),
(int)Init.Value("TRIM_STR2"), (int)Init.Value("TRIM_COL2"));
}
}
Console.WriteLine("ThAr images averaging...");
Image Thar_aver = ImageCombinator.Median(thars);
for (int i = 0; i < thar_files.Length; i++)
{
thars[i] = null;
}
Console.WriteLine("Bias subtraction from averanged Flat image...");
Image flat_aver_db = new Image();
flat_aver_db = flat_aver - bias_aver;
Console.WriteLine("Bias subtraction from averanged ThAr image...");
Image Thar_aver_db = Thar_aver - bias_aver;
//Console.WriteLine("Replasing pixels values:\r\n negative -> 1 for flat;\r\n negative -> 0 for Th-Ar;");
for (int i = 0; i < flat_aver_db.NAXIS1; i++)
{
for (int j = 0; j < flat_aver_db.NAXIS2; j++)
{
if (flat_aver_db[i, j] <= 0)
{
flat_aver_db[i, j] = 1;
}
if (Thar_aver_db[i, j] < 0)
{
Thar_aver_db[i, j] = 0;
}
}
}
Console.WriteLine("Search for order locations...");
flat_aver_db.Tr();
int polinim_degree_order = 3;
Locator.Locate(ref flat_aver_db, polinim_degree_order);
double[][] pos_ord = Locator.Ord_Pos;
double[][] pos_min = Locator.Min_Pos;
double[][] fluxes;
// Flat spectra extraction;
Console.WriteLine("Extraction of the flat spectra...");
int bkg_mode = (int)Init.Value("BKG_MODE");
int aperture_wing = (int)Init.Value("APER_WING");
int bkg_oo = 0, bkg_ox = 0, bkg_sw = 0, bkg_step = 0;
if (bkg_mode == 0)
{
bkg_sw = (int)Init.Value("BKG_SW");
Extractor.ExtractMode1(flat_aver_db, pos_ord, pos_min, aperture_wing, bkg_sw);
}
if (bkg_mode == 1)
{
bkg_sw = (int)Init.Value("BKG_SW");
bkg_oo = (int)Init.Value("BKG_OO");
bkg_ox = (int)Init.Value("BKG_OX");
bkg_step = (int)Init.Value("BKG_STEP");
Image bkg_im = Background.Fit(flat_aver_db, pos_min, bkg_ox, bkg_oo, bkg_sw, bkg_step);
Extractor.ExtractMode2(flat_aver_db, bkg_im, pos_ord, pos_min, aperture_wing);
}
fluxes = Extractor.FluxDebiased;
Saver.SaveOrderedDistribution(fluxes, dir_main + "\\Flat_Orders.dat");
Saver.SaveOrderedDistribution(Extractor.fluxes_min_init, dir_main + "\\BKG_FLAT.DAT");
Saver.SaveOrderedDistribution(Extractor.fluxes_min_smoothed, dir_main + "\\BKG_SMOOTH_FLAT.DAT");
// Flat spectra normalization;
Console.ForegroundColor = ConsoleColor.Yellow;
Console.WriteLine("Flat spectra normalization...");
Console.ForegroundColor = ConsoleColor.White;
Normator.Norm(fluxes, 12, 0, 13);
Saver.SaveOrderedDistribution(Normator.OrdersNorm, dir_main + "\\Flat_Orders_Norm.dat");
Saver.SaveOrderedDistribution(Normator.FitCurves, dir_main + "\\Flat_Orders_Fit.dat");
// Th-Ar spectra extraction;
Console.ForegroundColor = ConsoleColor.Yellow;
Console.WriteLine("Extraction of the Th-Ar spectrum...");
Console.ForegroundColor = ConsoleColor.White;
Thar_aver_db.Tr();
if (bkg_mode == 0)
{
Extractor.ExtractMode1(Thar_aver_db, pos_ord, pos_min, aperture_wing, bkg_sw);
}
if (bkg_mode == 1)
{
Image bkg_im = Background.Fit(flat_aver_db, pos_min, bkg_ox, bkg_oo, bkg_sw, bkg_step);
Extractor.ExtractMode2(Thar_aver_db, bkg_im, pos_ord, pos_min, aperture_wing);
}
fluxes = Extractor.FluxDebiased;
Saver.SaveOrderedDistribution(fluxes, dir_main + "\\thar_extacted.txt");
// Wavelength calibration;
double[][] lambdas;
Console.ForegroundColor = ConsoleColor.Yellow;
Console.WriteLine("Wavelength calibration...");
Console.ForegroundColor = ConsoleColor.White;
EcheData.LoadDispCurves("CalibrationCurves.dat");
int oo = (int)Init.Value("WAVE_OO");
int ox = (int)Init.Value("WAVE_OX");
int iterNum = (int)Init.Value("WAVE_NINER");
double cutLimit = (double)Init.Value("WAVE_REJ");
double fluxLimit = (double)Init.Value("WAVE_THRESH");
Console.WriteLine("OO = {0}; OX = {1}; Reject = {2}; IterNum = {3}; FluxLimit = {4}",
oo, ox, cutLimit, iterNum, fluxLimit);
int x_trim_left = 0;
if ((bool)Init.Value("TRIM_ON"))
{
x_trim_left = (int)Init.Value("TRIM_STR1");
}
WLCalibration.Calibrate(fluxes, oo, ox, cutLimit, iterNum, fluxLimit, x_trim_left);
lambdas = WLCalibration.Lambdas;
Saver.SaveOrderedDistribution(lambdas, dir_main + "\\lambdas.dat");
// processing object images;
Console.ForegroundColor = ConsoleColor.Yellow;
Console.WriteLine("Processing object spectra...");
Console.ForegroundColor = ConsoleColor.White;
Image object_image = null;
for (int i = 0; i < obj_files.Length; i++)
{
// Lading object image;
Console.WriteLine("Loading Object image {0}", obj_files[i]);
object_image = new Image();
object_image.LoadImage(obj_files[i]);
if ((bool)Init.Value("TRIM_ON"))
{
object_image = object_image.Trim(
(int)Init.Value("TRIM_STR1"), (int)Init.Value("TRIM_COL1"),
(int)Init.Value("TRIM_STR2"), (int)Init.Value("TRIM_COL2"));
}
// Bias subtraction;
Console.WriteLine("Bias subtraction...");
object_image = object_image - bias_aver;
for (int j = 0; j < object_image.NAXIS1; j++)
{
for (int k = 0; k < object_image.NAXIS2; k++)
{
if (object_image[j, k] < 0)
{
object_image[j, k] = 0;
}
}
}
object_image.Tr();
// Cosmic rays removal;
Smooth.DoSmooth(ref object_image);
// Create directory for extracted spectra;
string dirName = obj_files[i].Substring(0, obj_files[i].IndexOf(".fit"));
int first = obj_files[i].LastIndexOf("\\");
int last = obj_files[i].IndexOf(".fit");
string fileName = dirName + "\\" + obj_files[i].Substring(first, last - first);
Directory.CreateDirectory(dirName);
Console.WriteLine("Extraction spectra from {0} ", obj_files[i].Substring(first));
if (bkg_mode == 0)
{
bkg_sw = (int)Init.Value("BKG_SW");
Extractor.ExtractMode1(object_image, pos_ord, pos_min, aperture_wing, bkg_sw);
}
if (bkg_mode == 1)
{
Image bkg_im = Background.Fit(flat_aver_db, pos_min, bkg_ox, bkg_oo, bkg_sw, bkg_step);
Extractor.ExtractMode2(object_image, bkg_im, pos_ord, pos_min, aperture_wing);
}
fluxes = Extractor.FluxDebiased;
//double[][] backgr = Extractor.Background;
//Saver.SaveOrderedDistribution(backgr, fileName + "_bkg.dat");
//Saver.SaveOrderedDistribution(fluxes, fileName + "_x.dat");
for (int k = 0; k < fluxes.Length; k++)
{
for (int j = 0; j < fluxes[0].Length; j++)
{
fluxes[k][j] = fluxes[k][j] / Normator.OrdersNorm[k][j];
}
}
Saver.SaveLambdaIntensTable(lambdas, fluxes, dirName + "\\" + "spectra_all.dat");
for (int k = 0; k < fluxes.Length; k++)
{
StreamWriter sw = new StreamWriter(fileName +
string.Format("_{0:000}", k) + ".dat");
for (int j = 0; j < fluxes[k].Length; j++)
{
sw.WriteLine(
string.Format("{0:0000.0000}\t{1:0.00000E000}",
lambdas[k][j], fluxes[k][j]).Replace(",", "."));
}
sw.Close();
}
}
//output.Close();
STOP:
Console.ForegroundColor = ConsoleColor.Yellow;
Console.WriteLine("End of the pipeline. Press any key to exit...");
Console.Beep();
Console.ReadKey();
}
public static void Locate(ref Image im, int polynom_degree)
{
double[] order_centers = new double[2];
int wing = 2;
int middle = im.NAXIS2 / 2;
Image slice = new Image(im.NAXIS1, 1 + 2 * wing);
for (int i = 0; i < slice.NAXIS1; i++)
{
for (int j = 0; j < slice.NAXIS2; j++)
{
slice[i, j] = im[i, middle - wing + j];
}
}
double[] aver_column = new double[im.NAXIS1];
for (int i = 0; i < aver_column.Length; i++)
{
aver_column[i] = Statistics.Median(slice.GetRow(i));
}
StreamWriter sw = new StreamWriter((string)Init.Value("DIR_MAIN") + "\\Slice.txt");
for (int i = 0; i < aver_column.Length - 1; i++)
{
sw.WriteLine("{0}\t{1}", i, aver_column[i].ToString());
}
sw.Close();
// Search for orders locations in cetral slit;
double[] xmax_0 = new double[5000];
int orders_count = 0;
int dist = 5; // for ZTSh
EcheData.LoadOrdMidPos("OrdPos.dat", (int)Init.Value("TRIM_COL1"));
double[] xmax = new double[EcheData.ord_mid_pos.Length];
for (int i = 0; i < xmax.Length; i++)
{
xmax[i] = (double)EcheData.ord_mid_pos[i];
}
for (int i = 0; i < xmax.Length; i++)
{
int x1 = (int)xmax[i] - dist;
int x2 = (int)xmax[i] + dist;
if (x1 < 0)
{
x1 = 0;
}
if (x2 > aver_column.Length - 1)
{
x2 = aver_column.Length - 1;
}
int xm = x1;
double max = aver_column[x1];
for (int j = x1 + 1; j <= x2; j++)
{
if (aver_column[j] > max)
{
max = aver_column[j];
xm = j;
}
}
xmax[i] = xm;
}
orders_count = xmax.Length;
// Orders Tracing;
pos_ord = new double[orders_count][];
for (int i = 0; i < pos_ord.Length; i++)
{
pos_ord[i] = new double[im.NAXIS2];
}
for (int i = 0; i < pos_ord.Length; i++)
{
pos_ord[i][middle] = xmax[i];
}
int nwin = 8;
int o1 = 0, o2 = 0;
for (int i = middle - 1; i >= 0; i--)
{
for (int n = o1; n < orders_count + o2; n++)
{
int n1 = (int)pos_ord[n][i + 1] - nwin;
int n2 = (int)pos_ord[n][i + 1] + nwin;
double max = 0;
for (int k = n1; k <= n2; k++)
{
if (im[k, i] > max)
{
pos_ord[n][i] = k;
max = im[k, i];
}
}
}
}
for (int i = middle + 1; i < im.NAXIS2; i++)
{
for (int n = o1; n < orders_count + o2; n++)
{
int n1 = (int)pos_ord[n][i - 1] - nwin;
int n2 = (int)pos_ord[n][i - 1] + nwin;
double max = 0;
for (int k = n1; k <= n2; k++)
{
if (im[k, i] > max)
{
pos_ord[n][i] = k;
max = im[k, i];
}
}
}
}
pos_min = new double[pos_ord.Length + 1][];
for (int i = 0; i < pos_min.Length; i++)
{
pos_min[i] = new double[im.NAXIS2];
}
for (int i = 0; i < im.NAXIS2; i++)
{
for (int n = 1; n < pos_min.Length - 1; n++)
{
int n1 = (int)pos_ord[n - 1][i];
int n2 = (int)pos_ord[n][i];
double min = double.MaxValue;
for (int k = n1; k <= n2; k++)
{
if (im[k, i] < min)
{
pos_min[n][i] = k;
min = im[k, i];
}
}
}
}
for (int i = 0; i < im.NAXIS2; i++)
{
pos_min[0][i] = pos_min[1][i] - (pos_min[2][i] - pos_min[1][i]);
if (pos_min[0][i] < 0)
{
pos_min[0][i] = 0;
}
}
for (int i = 0; i < im.NAXIS2; i++)
{
pos_min[pos_min.Length - 1][i] = pos_min[pos_min.Length - 2][i] +
(pos_min[pos_min.Length - 2][i] - pos_min[pos_min.Length - 3][i]);
if (pos_min[pos_min.Length - 1][i] > aver_column.Length - 1)
{
pos_min[pos_min.Length - 1][i] = aver_column.Length - 1;
}
}
Saver.SaveOrderedDistribution(pos_min, (string)Init.Value("DIR_MAIN") + "\\trace_min.txt");
Saver.SaveColumn(xmax, (string)Init.Value("DIR_MAIN") + "\\orders_ident.dat");
double[] pixels_x = new double[im.NAXIS2];
for (int i = 0; i < pixels_x.Length; i++)
{
pixels_x[i] = i;
}
GravImprove(im, ref pos_min, ref pos_ord);
Saver.SaveOrderedDistribution(pos_ord, (string)Init.Value("DIR_MAIN") + "\\trace.txt");
for (int i = 0; i < pos_ord.Length; i++)
{
ImproveTraces(pixels_x, ref pos_ord[i], polynom_degree);
}
for (int i = 0; i < pos_min.Length; i++)
{
ImproveTraces(pixels_x, ref pos_min[i], polynom_degree);
}
Saver.SaveOrderedDistribution(pos_ord, (string)Init.Value("DIR_MAIN") + "\\orders_impoved.dat");
Saver.SaveOrderedDistribution(pos_min, (string)Init.Value("DIR_MAIN") + "\\mins_improved.dat");
for (int i = 0; i < xmax.Length; i++)
{
xmax[i] = pos_ord[i][middle];
}
Saver.SaveColumn(xmax, (string)Init.Value("DIR_MAIN") + "\\Orders.txt");
}
public static void IdentOrders(ref double[][] pos_ord, ref double[][] pos_min, int column)
{
double[][] pos_ord_1 = new double[ord_mid_pos.Length][];
for (int i = 0; i < pos_ord_1.Length; i++)
{
pos_ord_1[i] = new double[pos_ord[0].Length];
}
double[][] pos_min_1 = new double[ord_mid_pos.Length + 1][];
for (int i = 0; i < pos_min_1.Length; i++)
{
pos_min_1[i] = new double[pos_min[0].Length];
}
int shift = 0;
int ident_orders_count = 0;
for (int i = 0; i < pos_ord_1.Length; i++)
{
int k_min = 0;
double diff_min = double.MaxValue;
double diff;
for (int j = 0; j < pos_ord.Length; j++)
{
diff = Math.Abs(pos_ord[j][column] - ord_mid_pos[i]);
if (diff < diff_min)
{
k_min = j;
diff_min = diff;
if (i == 0)
{
shift = j;
}
}
}
if (i > 0)
{
if (pos_ord[k_min][column] == pos_ord_1[i - 1][column])
{
break;
}
}
ident_orders_count++;
for (int j = 0; j < pos_ord_1[i].Length; j++)
{
pos_ord_1[i][j] = pos_ord[k_min][j];
}
}
Array.Resize(ref pos_ord_1, ident_orders_count);
Array.Resize(ref pos_min_1, ident_orders_count + 1);
for (int i = 0; i < pos_min_1.Length; i++)
{
for (int j = 0; j < pos_min_1[i].Length; j++)
{
pos_min_1[i][j] = pos_min[i + shift - 1][j];
}
}
pos_min = pos_min_1;
pos_ord = pos_ord_1;
double[] pos_ord_slice = new double[pos_ord.Length];
for (int i = 0; i < pos_ord_slice.Length; i++)
{
pos_ord_slice[i] = pos_ord[i][column];
}
double[] pos_min_slice = new double[pos_min.Length];
for (int i = 0; i < pos_min_slice.Length; i++)
{
pos_min_slice[i] = pos_min[i][column];
}
Saver.SaveColumn(pos_ord_slice, InitFile.DirectoryMain + "\\orders_ident.dat");
Saver.SaveColumn(pos_min_slice, InitFile.DirectoryMain + "\\minima_ident.dat");
}
