This page explains how to process GAOES-RV data with IRAF reduction package as general high-dispersion spectra whose R is ∼ 65,000.

For QL in the Seimei telescope observation environment, start from this procedure (Make Flat).

The slit length direction of the GAOES-RV spectrum is not parallel to the line of CCD pixels.
Therefore, it is necessary to add up after performing wavelength calibration by tracing one pixel at a time in the dispersion direction.

This process can be done by using the following IRAF cl-scripts.

    https://github.com/chimari/hds_iraf

The scripts are involved in the reduction package for Subaru/HDS.
The gaoes package has been confirmed to work with IRAF v2.16.2, V2.17, and PyRAF environment.

Install the entire of hds_iraf package.

1. Just download all files of hds_iraf packages, then add

   set    hdshome = 'home$IRAF/hds_iraf/'
   task   $hds.pkg = 'hdshome$hds.cl'
   set    gaoeshome = 'home$IRAF/hds_iraf/'
   task   $gaoes.pkg = 'gaoeshome$gaoes.cl'

   in your login.cl .
   * Please change ''home$IRAF/hds_iraf/'' to the directory in which you put your hds_iraf package.
2. Load gaoes packages after started the IRAF shell.

   ecl> gaoes
     ***************************************************************
     ***************************************************************
     **         Seimei GAOES-RV IRAF Reduction Package            **
     ************************** CAUTION !!! ************************
     ** This package is always under development.                 **
     ** Check the latest package via                              **
     **       git clone https://github.com/chimari/hds_iraf       **
     **                                                           **
     **     This package is developed by Akito Tajitsu (NAOJ)     **
     **                               last update : 2023/03/27    **
     ***************************************************************
     ***************************************************************
   
         gaoes_comp        gaoes_linear      gaoes_overscan    mkblaze           wacosm11
         gaoes_ecfw        gaoes_linstab     grql              sed               wacosm3
         gaoes_flat        gaoes_linstat     hdsmk1d           wacosm1
   gaoes>

3. Please see here for more details about HDS IRAF package.

    http://www.o.kwasan.kyoto-u.ac.jp/inst/gaoes-rv/GAOES-RV_ql-20240926.tar.gz

The archive file includes reference frames and databace files (aperture, flat, comparison, mask, and blaze function) and python scripts for QL application (grlog).
Extract the archive and put the "GAOES-RV_ql/" directory into an appropriate place (HOME$/IRAF/GAOES-RV_ql/ is the default for grlog).

Start

1. You need to create a new your working directory.
2. Copy reference and database files in ''GAOES-RV_ql-XXXXXXXX.tar.gz'' into your working directory.
3. The current file tree of your working directory should be

   work
   ├── Ap.GAOES-RV.f8(fc).fits
   ├── ThAr.GAOES-RV.f8(fc).center.fits
   ├── Mask.GAOES-RV.ocs_ecfw.fits
   ├── cBlaze.GAOES-RV.f8(fc).fits
   └── database
       ├── apAp.GAOES-RV.f8(fc)
       └── ecThAr.GAOES-RV.f8(fc).center

   "f8" is for the octagon fiber and "fc" is for the circular fiber.

making Flat

1. Make a list of flat frames, in which involves 8 digits of raw GRA fits files.

   00000299
   00000300
   00000301
   00000302
   00000303
   00000304
   00000305
   00000306
   00000307
   00000308
   00000309
   00000310
   00000311
   00000312
   00000313

   You can easily create the file using this command

   seq -f "%08g" 299 313 > flat.in

2. Use the task ''gaose_flat''.

   PACKAGE = hds
      TASK = gaoes_flat
   
   inlist  =              flat.in  input flat image list
   indirec = /home/taji/work4/20221015  directory of RAW data
   outimg  =         Flat20221015  output flat image
   
   (ref_ap =       Ap.GAOES-RV.f8) Aperture reference image
   (apflag =                  yes) Create new aperture reference? (yes/no)
   (new_ap =           Ap20221015) New aperture image
   
   (st_x   =                  -54) Start pixel to extract
   (ed_x   =                   53) End pixel to extract
   
   (scatter=                  yes) apscatter? (yes/no)
   (normali=                  yes) apnormalize? (yes/no)
   
   (mode   =                    q)

   • inlist : created list file
   • indirec : directory name of raw data
   • outimage : flat file name to be created (add ''.ac'' for apscattered, and ''.nm'' for apnormalized to this file name)

   • ref_ap : aperture reference (should be ''Ap.GAOES-RV''
   • apflag : create a new aperture reference from the created flat image (''yes'' in usual)
   • new_ap : new aperture reference image to be created

   • st_x : minimum aperture for flat (∼ -54 in usual)
   • ed_x : maximum aperture for flat (∼ 53 in usual)

   • scatter : apscatter ? (''yes'' in usual)
   • normalize : apnormalize ? (''yes'' in usual)
3. The task ''gaoes_flat'' with the above parameter creates these files.
   • Flat20221015.fits (imcombined flat)
   • Flat20221015.sc.fits (scattered light subtracted flat by apscatter)
   • Flat20221015.sc.nm.fits (normalized by apnormalize) ⇒ Input 2 for ''grql''
   • Ap20221015.fits (aperture reference) ⇒ Input 1 for ''grql''
   • database/apAp20221015 (aperture table)

making Comparison

1. Use the task ''gaose_comp''.

PACKAGE = hds
   TASK = gaoes_comp

inid    =             00000315  input ID of ThAr frame
indirec = /home/taji/work4/20221015  directory of RAW data
outimg  =         ThAr20221015  output comparison image

(ref_ap =           Ap20221015) Aperture reference image
(ref_com= ThAr.GAOES-RV.f8.center) Wavelength reference (1D comparison) image

(mode   =                    q)

• inid : 8 digit of ThAr GRA frame
• indirec : the directory where raw data are stored
• outimg : comparison frame name to be created

• ref_ap : aperture reference frame (created by ''gaoes_flat'')
• ref_com : wavelength calibrated reference (downloaded ''ThAr.GAOES-RV.center'' in usual)
2. gaoes_comp with the above parameters creates these files.
   • ThAr20221015.fits (overscanned 2D comparison image) ⇒ Input 4 for ''grql''
   • ThAr20221015.center.fits (1D comparison spectrum traced the center 1 px of the 2D comparison image) ⇒ Input 3 for ''grql''
   • database/ecThAr20221015.center (the wavelength table of the 1D spectrum)

Object frame reduction

1. Using flat and comparison frames made by the above procedures, reduce each object frame with the task ''grql''.

   PACKAGE = gaoes
      TASK = grql
   
   inid    =             00000944  Input frame ID
   (indirec=                   ..) directory of RAW data
   
   (batch  =                   no) Batch Mode?
   (inlist =                     ) Input file list for batch-mode
   
   (interac=                  yes) Run task interactively? (yes/no)
   
   (ref_ap =       Ap.GAOES-RV.fc) Aperture reference image
   (flatimg= Flat.GAOES-RV.fc.sc.nm) ApNormalized flat image
   (thar1d = ThAr.GAOES-RV.fc.center) 1D wavelength-calibrated ThAr image
   (thar2d =     ThAr.GAOES-RV.fc) 2D ThAr image
   
   (st_x   =                  -54) Start pixel to extract
   (ed_x   =                   53) End pixel to extract
   
   (cosmicr=                  yes) Cosmic Ray Rejection?
   (scatter=                  yes) Scattered Light Subtraction?
   (ecfw   =                  yes) Extract / Flat-fielding / Wavelength calib.?
   (getcnt =                  yes) Measure spectrum count?
   (mk1d   =                   no) Make order combined 1d spectrum?
   (splot  =                  yes) Splot Spectrum?
   
                                   ### Cosmic-Ray Rejection. ###
   (cr_proc=               wacosm) CR rejection procedure (wacosm|lacos)?
                                   ### Parameters for wacosm11 ###
   (cr_wbas=                2000.) Baseline for wacosm11
                                   ### Parameters for lacos_spec ###
   (cr_ldis=                   no) Confirm w/Display? (need DS9)
   (cr_lgai=                 1.67) gain (electron/ADU)
   (cr_lrea=                  4.4) read noise (electrons)
   (cr_lxor=                    9) order of object fit (0=no fit)
   (cr_lyor=                    3) order of sky line fit (0=no fit)
   (cr_lcli=                  10.) detection limit for cosmic rays(sigma)
   (cr_lfra=                   3.) fractional detection limit fro neighbouring pix
   (cr_lobj=                   5.) contrast limit between CR and underlying object
   (cr_lnit=                    4) maximum number of iterations
   
                                   ### Scattered-light Subtraction ###
   (sc_inte=                  yes) Run apscatter interactively?
   
                                   ### Get Spectrum Count. ###
   (ge_line=                    2) Order line to get count
   (ge_stx =                 2150) Start pixel to get count
   (ge_edx =                 2400) End pixel to get count
   (ge_low =                   1.) Low rejection in sigma of fit
   (ge_high=                   0.) High rejection in sigma of fit
   
                                   ### Make 1D spectrum ###
   (m1_blaz=                     ) Blaze Function
   (m1_mask=                     ) Mask Image
   (m1_stx =                   60) Start X for trimming
   (m1_edx =                 4120) Endt X for trimming
   
                                   ### Splot ###
   (sp_line=                    1) Splot image line/aperture to plot
   
   (clean  =                  yes) Clean up intermediate images? (yes/no)
   (mode   =                    q)

   • inid : 8 digit of Object GRA frame
   • indirec : the directory where raw data are stored

   • batch : yes / no for batch mode (see below)
   • inlist : input file list for batch mode

   • ref_ap: Aperture reference image ⇐ Input 1 produced by ''gaoes_flat''
   • flatimg: Normalized flat image ⇐ Input 2 produced by ''gaoes_flat''
   • thar1d: 1D comparison spectrum ⇐ Input 3 produced by ''gaoes_comp''
   • thar2d: 2D comparison image ⇐ Input 4 produced by ''gaoes_comp''

   • st_x: minimum aperture for object frame. (should be the same value used in ''gaoes_flat'' ,∼ -54 in usual)
   • ed_x: maximum aperture for object frame. (should be the same value used in ''gaoes_flat'' ,∼ 53 in usual)

   • cosmicr: Do or skip Cosmic ray removal.
   • scatter: Do or skip Scattered light subtraction.
   • ecfw: Do or skip Extract / Flat-fielding / Wavelength calibration.
   • getcnt: Automatic Count measurement.
   • mk1d: Make complete 1D spectrum using blaze function.
   • splot: Do or skip plotting the resultant spectrum.

   • cr_proc: Cosmic Ray removal procedure (wacosm / lacos)
   • cr_wbas: Baseline of wacosm11.
   • cr_l*: parameters for lacos (You need to install STSDASS to use lacos_spec).

   • sc_inte: Run apscatter interactively? (yes/no)

   • ge_line: Echelle order line for automatic count measurement
   • ge_stx: Start pixel in Echelle order for automatic count measurement
   • ge_edx: End pixel in Echelle order for automatic count measurement

   • m1_blaz: Blaze function for make 1D spectrum
   • m1_mask: Mask image for make 1D spectrum
   • m1_stx: Start pixel for scombine
   • m1_edx: End pixel for scombine

   • sp_line: Order number for splot
2. With the above parameters, grql produces these files.
   • G00000266o.fits (overscanned image)
   • G00000266oc.fits (after cosmic ray removed)
   • G00000266ocs.fits (after scatterd light subtracted)
   • G00000266ocs_ecfw.fits (extracted + flat-fielded + wavelength calibrated spectrum) = filnal resultant
   • G00000266ocs_ecfw_1d.fits (full 1D spectrum) = filnal resultant
3. If you want to run grql for 2 or more object frames, you can use batch mode. Create a list file, in which 8 digit numbers of GRA are stored.

   00000321
   00000322
   00000323
   00000324
   00000325
   ...

   Then, run grql with ''batch=yes'' and inlist=(object list file).
4. If you want to run grql in command line of ecl, the 8 digit number of object GRA must be enclosed in double quotations.

   ecl> grql "00000321"

We have now obtained a multi-order echelle spectrum.
From now on, as an option, we will explain how to create a complete one-dimensional spectrum by connecting orders.

Make Mask

1. Analyze one flat frame with grql in the same way as an object frame, and create G?????????ocs_ecfw.fits. (Until this point, set mk1d=no in grql)
2. Use the task "gaoes_mkmask"

   PACKAGE = gaoes
   TASK = gaoes_mkmask
   
   inimage =    G00000997ocs_ecfw  Input Flat image 
   mask    =        Mask.00000977  New Mask image 
   
   (mode   =                    q)

   On each order when run, you will be asked as

   >>> Do you want to correct this order? (y/n) : 

   . Enter "y" if there is a bad pixel or an order edge and you want to correct it.
   If you enter y, each order will be plotted, so move the cursor to one end of the range (X direction) you want to erase and press the "a" key. The values in that range will be zero. If you need to modify this order any more

   >>> Do you want to correct this order MORE? (y/n) :

   answer "n" to proceed to the next order.
   Repeating this for 15 orders creates a mask that eliminates unwanted areas.
   Basically what you need to remove is only
   • Order of both ends (Order 1, 15)
   • Order 3, Bad pixel around 5790A
   . (So Mask.GAOES-RV.ocs_ecfw.fits included in the reference package can be suitable most of cases.) 　　　

PACKAGE = gaoes
   TASK = rvgaoes

inimage =     SN2023ixf_Fcalib  Input image
outimage=  SN2023ixf_Fcalib.rv  Output image

(observa=               seimei) Observatory
(mode   =                    q)

1. Requirements
   
   • Linux environment where Gtk+3 can be used. (It has not been confirmed on Mac OS)
   • Environment where PyRAF can be used.
2. Preparation for PyRAF environment
   PyRAF can be installed via astroconda/miniconda, and in Ubuntu it can be installed easily via

   sudo apt-get install astro-iraf python3-pyraf

   Make sure that pyraf can be started from the command line. (If you are using conda environment, do "conda activate iraf37" etc.)
   Please confirm that pyraf can be started from the command line in this environment and that the gaoes package can be loaded in it.
    
3. Download grlog
   You can download the source code of grlog via github.

   git clone https://github.com/chimari/grlog
   cd grlog/
   ./configure --with-gtk3
   (If the above does not work correctly)  ./autogen.sh --with-gtk3
   make
   sudo make install

   You need to install GtK+3, openssl development environment to make grlog.
    
4. Download / Preparation of hds_iraf and reference (GAOES-RV_ql) packages
   Download hds_iraf CL script package via github.

   git clone https://github.com/chimari/hds_iraf

   And place hds_iraf directory to an appropriate directory.
   Download GAOES-RV_ql-XXXXXXXX.tar.gz (Find at the top of this page.), in wihch python scripts and reference frames for IRAF are included. And place GAOES-RV_ql/ directory in an appropriate directory.
   Add these lines

   set    hdshome = 'home$IRAF/hds_iraf/'
   task   $hds.pkg = 'hdshome$hds.cl'
   set    obsdb    = "hdshome$obsdb.dat"
   set    gaoeshome = 'home$IRAF/hds_iraf/'
   task   $gaoes.pkg = 'gaoeshome$gaoes.cl'

   to your login.cl for IRAF.
    
5. Start up grlog
   Start by specifying the directory where the raw data (GRA*fits) is placed at the end of the command line argument.

   grlog [-s shared_dir] [-w work_dir] [-l login.cl_dir] [-h] [-u] data_dir

   You can use the following command line options.

   Option	Directory	Description	Default
   -s	Shared Directory	The directory where the reference and QL python scipts are located.	HOME$/IRAF/GAOES-RV_ql/
   -w	Work Directory	The working directory for QL.	<Data Directory>/ql/
   -l	login.cl Directory	The direcotry in which login.cl for IRAF is located.	HOME$/
   the last argument	Data Directory	The directory in which raw data frames (GRA*.fits) are located.	(You must specify it in the command line.)

   If your raw data frames are stored in /home/taji/work/GAOES-RV/20230401/, the reference frames are located in、/home/taji/IRAF/GAOES-RV_ql, and you use /home/taji/login.cl,

   grlog /home/taji/work/GAOES-RV/20230401

   stars its process creating its working directory "/home/taji/work/GAOES-RV/20230401/ql/".
    
6. Setting for PyRAF
   Please setup the commands for PyRAF via Config → PyRAF setups in the GUI menu. "Terminal command for PyRAF" is the terminal command for starting the python script for PyRAF. Normally, you can leave it as xterm (the command to start PyRAF is passed under -e).
   "Python command" is a python command required to start a python script for PyRAF such as "splot.py". If you need

   python3 splot.py

   when starting "splot.py" under the Shared directory, enter "python3". If you can start it only

   splot.py

   in your command line, please leave it as a blank.
    
7. Make Flat and Apeture
   Flat and Aperture reference are created simultaneously from flat data.
   When creating them for the first time, "Ap.GAOES-RV.f8.fits" under GAOES-RV_ql/ (automatically copied to your work directory) is used as a reference to recreate Aperture.
   Select multiple flat frames as shown below and press the "Flat" button. Hit enter twice to accept (yes) in the xterm. If a new flat (apscattered and apnormalized) and a new aperture reference are created correctly, "F" marks will appear in the "CAL" column of the table.  
8. Make Comparison
   When creating for the first time, wavelength calibration data will be created using the reference to "ThAr.GAOES-RV.f8.center.fits" under GAOES-RV_ql/ (automatically copied to your work directory).
   Select the ThAr frame you want to use as a wavelength calibration comparison in the table and press the "ThAr" button.
   The ecindentify fit screen will pop up with the ecreidentify already done. Please add lines in the reference table with "l" key. And fit by "f" key. It should be OK, if the fitting rms is about 0.002 .
   If the wavelength calibration data is created normally, a "C" mark will appear in the CAL column of the table.  
9. Make Blaze function
   Create a blaze function by performing a continuous light fit on the analyzed flat as well as object frames. This prcoess is required to make full 1D spectrum of objects (connecting each order of the echelle).
   First, select one frame of flat and press the "Obj" button to analyze it. After the analyze has been finished ("ˆ" will apeare in QL column of the table), select the same frame and push "Blaze" button. The continuum task is launched. So, performe the continuum fit excluding order edges and bad pixels.
   Please refer to here for details and operation.
    
10. Make Mask (not necessary in usual
    As with "Blaze", you can also create a mask for the analyzed flat using the "Mask" button.
    Basically, you can leave "Mask.GAOES-RV.ocs_ecfw.fits" which is automatically copied under GAOES-RV_ql/, we won′t explain it here.
     
11. Check CAL setting
    You can check the current set CAL frame by pressing the gear mark button next to "Blaze" in the lower "Calibration" section. "Aperture", "Flat", "Wavelength reference", etc. are automatically set when each is successfully created. If you want to change it, you can change it with the button on the right of each frame.
    In particular, if you want to recreate "Flat" or "ThAr" from the same frames, set the default file "Flat(ThAr).GAOES-RV..." once in this window and then create it again. (The database is deleted once to avoid overwriting, if you try to recreate a new one.)  
12. Object analysis
    After preparing CAL as above (if not prepared, reference below GAOES-RV_ql/ will be used), select a object frame, and press the "Obj" button to analyze it.
    You can select the order of echelle or the full 1D spectrum (1D spec) to display in the "splot" task.
    Also, in the "Get Spectrum Count" section, you can specify which pixels of which order for automatic measurement of the spectrum count.
    You can also select multiple object frames for batch processing. Spectral plotting is skipped during batch processing. Press the "q" key in the graphics window to quit plotting. It is a specification that cannot run multiple analysis processes at once.
    When the analysis is completed, the QL column of the table is marked with a circle, and the approximate count (number of photons) is entered in the e^- column.  
13. Save Observation Log
    The log can be output to a CSV file with File → Save Log in the menu.  

contact to: Akito Tajitsu (Okayama Branch, Subaru Telescope, NAOJ, NINS)      Last modified: Mon Dec 9 10:41:47 JST 2024