Notes on analysing Suzaku data with XSELECT

Luigi Gallo

6 December 2005

This is intended as a guide for analysing Suzaku X-ray data using XSELECT. The available public data have been processed and cleaned following current procedures. Prior to downloading the data please read carefully the calibration notes and disclaimers on the public data page. If XSELECT, XSPEC or FTOOLS are currently not installed on your system the software can be downloaded from the HEAsoft site. Specific information about XSELECT can be found in the User's Guide.

Preliminaries

  1. Make a working directory, for example:

    unix% mkdir n2110
  2. Select the data from the Suzaku public data site:
    http://www.astro.isas.jaxa.jp/suzaku/pub/
    by clicking on the desired object. Here you will find information about the observation as well as the data products. The event files can be downloaded separately for each instrument. The tar file should contain all the data, but that may not yet be the case for all of the observations.

    Also download the housekeeping files (click on EHK) and save them to your working directory.

  3. Un-tar the files:

    unix% tar xvf 100012010.tar

  4. Unzip the files:

    unix% gunzip */*

  5. If not already so, arrange your working directory such that it contains three directories: /xis, /hxd and /auxil, which contain the XIS event, HXD event and housekeeping files, respectively. XSELECT will assume that the housekeeping files are located in ../auxil with respect to the data directory.

  6. Before starting XSELECT for the first time you may wish to set some parameters so that they will be defined for all subsequent invocations of XSELECT. For example, you can set the program used to plot images to ds9 by: 
    unix> pset xselect imagedisp="ds9 -unix_only"
    Also, if you would like to define the default mission to Suzaku: 
    unix> pset xselect default_mission="SUZAKU"

  7. You are now ready to start XSELECT. Upon starting XSELECT you will be prompted for a session name. In these first steps you should also define the mission (if not done so by default as shown above), instrument and data directory. 
    unix% xselect

                         **  XSELECT V2.3   **

> Enter session name >[xsel] n2110
n2110:ASCA > set mission suzaku
n2110:SUZAKU > set instr xis0
n2110:SUZAKU-XIS0 > set datadir xis

Setting data directory to /home/lgallo/SUZAKU/ngc2110/xis/
Setting mkf directory to /home/lgallo/SUZAKU/ngc2110/auxil/

  8. Read in the desired event file. 
    n2110:SUZAKU-XIS0 > read events ae20050916_0850_1956_xis0_3x3_cl2.evt

 Notes: XSELECT set up for      SUZAKU
 Time keyword is TIME       in units of s
 Default timing binsize =   16.000

Setting...
 Image  keywords   = X          Y           with binning =    8
 WMAP   keywords   = X          Y           with binning =    8
 Energy keyword   = PI                     with binning =    1

Getting Min and Max for Energy Column...
Got min and max for PI:     0   4095

Got the minimum time resolution of the read data:   8.0000
MJDREF =  5.1544000742870E+04 with TIMESYS = TT
 Number of files read in:  1

******************** Observation Catalogue ********************

Data Directory is: /home/lgallo/SUZAKU/ngc2110/xis/
HK Directory is: /home/lgallo/SUZAKU/ngc2110/xis/


        OBJECT      DATE-OBS    TIME-OBS    DATE-END    TIME-END    EDITMODE
      1 NGC_2110    2005-09-16  08:49:42    2005-09-18  19:55:50    3x3
    In this example I am only considering one event file for simplicity. In principle, since mode-specific responses are not yet available, the 5x5, 3x3 and 2x2 data for each telescope can be combined, in which case one would group the event files with quotations, i.e. : 
     read events "file1.evt file2.evt".
    Notice that the event file *_cl2.evt is the file which has been cleaned with "cleansis". Also, keep in mind that XSELECT assumes the housekeeping files are in the directory ../auxil, relative to the working directory (usually xis/).

  9. To get a feel for the data you have, the 'extract all' command will dump an image, light curve, and spectrum. 
    n2110:SUZAKU-XIS0-STANDARD > extract all

extractor v4.56      7 Sep 2005
 Getting FITS WCS Keywords
 Doing file: /home/lgallo/SUZAKU/ngc2110/xis/ae20050916_0850_1956_xis0_3x3_cl2.evt
100% completed
          Total      Good    Bad: Region      Time     Phase     Grade     Cut
         235840    234116              0         0         0         0      1724
   Grand Total      Good   Bad:  Region      Time     Phase     Grade    Cut
        235840    234116              0         0         0         0      1724
   in  61064.     seconds
 Fits light curve has   234116 counts for  3.834     counts/sec
 Thresholding removed significant counts
 Try exposure=0.0 on the extract command in xselect
 or lcthresh=0.0 if running extractor stand-alone
 Thresholding removed more than half the bins
 Try exposure=0.0 on the extract command in xselect
 or lcthresh=0.0 if running extractor stand-alone
 Spectrum         has   234116 counts for  3.834     counts/sec
 ... written the PHA data Extension
 Image            has   234116 counts for  3.834     counts/sec

    To view the light curve, spectrum, image: 

    xsel:SUZAKU-XIS-1-STANDARD >  plot curve
xsel:SUZAKU-XIS-1-STANDARD >  plot spectrum
n2110:SUZAKU-XIS0-STANDARD > plot image
    The "standard" (still evolving) filter criteria have already been applied to this data; they correspond to: 
    xsel:SUZAKU-XIS-1-STANDARD > select mkf "SAA==0 && ELV > 5 && DYE_ELV > 20 && T_SAA > 256"
    You can also set any other time, space, or energy filters as will be demonstrated below.

Creating a point-source XIS spectrum

The goal here is to produce a pha file which can be analysed in XSPEC.

  1. To extract a spectrum from a certain region of the event file we first start DS9.
    n2110:SUZAKU-XIS0-STANDARD > plot image
  2. Select the region of interest, for example a circle around a point source. Then save this extraction region as an "SAOimage" (e.g. src.reg). Before pushing "save" make certain to set the file format to "SAOimage". On your DS9 display push: 
    Region --> file format --> SAOimage
  3. Select a background region in a similar manner and also save this region (e.g. bkg.reg).

  4. Enter the source (+background) region (src.reg) as a filter for the "extract" command: 
    n2110:SUZAKU-XIS0-STANDARD > filter region src.reg
    To confirm that you have done this, you can type "show stat" at anytime: 
    n2110:SUZAKU-XIS0-STANDARD > show stat

              *** Status of XSELECT ***

Plot device is /XW

 *** MISSION ***

SUZAKU NONE XIS0 STANDARD
Time keyword is TIME       in units of s
Default timing binsize =   16.000
Minimum timing resolution:   8.0000
Energy keyword is PI         with binning     1
Max and min for PI        :     0    4095
 Image keywords   = X          Y           with binning =    8
 WMAP  keywords   = X          Y           with binning =    8

 *** DATA ***

The data directory is /home/lgallo/SUZAKU/ngc2110/xis/
The mkf directory is /home/lgallo/SUZAKU/ngc2110/auxil/

The obscat n2110_read_cat.xsl has been made.

One data file has been read in.
GTI files are in use.

 *** PRODUCTS ***

 A spectrum has been accumulated.
 A curve has been accumulated.
 An image has been accumulated.

 *** SELECTIONS ***

     NONE

 *** FILTERS ***

 Spatial selections have been read in from:
    src.reg
  5. You can now extract a source (+background) spectrum based on the extraction region you have selected: 
    n2110:SUZAKU-XIS0-STANDARD > extract spectrum
extractor v4.56      7 Sep 2005
 Getting FITS WCS Keywords
 Doing file: /home/lgallo/SUZAKU/ngc2110/xis/ae20050916_0850_1956_xis0_3x3_cl2.evt
100% completed
          Total      Good    Bad: Region      Time     Phase     Grade     Cut
         235840    179064          56637         0         0         0       139
   Grand Total      Good   Bad:  Region      Time     Phase     Grade    Cut
        235840    179064          56637         0         0         0       139
   in  61064.     seconds
 Spectrum         has   179064 counts for  2.932     counts/sec
 ... written the PHA data Extension
  6. Save the spectrum as a pha file which can be used in XSPEC. 
    n2110:SUZAKU-XIS0-STANDARD > save spectrum n2110_xis0_3x3_src
    The .pha extension is added.

  7. Following the same process also extract the background spectrum. First we must change the filter region which is currently set to src.reg. 
    n2110:SUZAKU-XIS0-STANDARD > filter region -src.reg
    Now apply the background extraction region 
    n2110:SUZAKU-XIS0-STANDARD > filter region bkg.reg
    In principle, multiple files can be handled at one time thus we could remove one region and add another in one step. However, care must be taken in placing the files in the correct order. Alternatively, one can simply type: 
    n2110:SUZAKU-XIS0-STANDARD > clear region
    to remove all existing regions, before adding a new region. 
    n2110:SUZAKU-XIS0-STANDARD > show stat

              *** Status of XSELECT ***

Plot device is /XW

 *** MISSION ***

SUZAKU NONE XIS0 STANDARD
Time keyword is TIME       in units of s
Default timing binsize =   16.000
Minimum timing resolution:   8.0000
Energy keyword is PI         with binning     1
Max and min for PI        :     0    4095
 Image keywords   = X          Y           with binning =    8
 WMAP  keywords   = X          Y           with binning =    8

 *** DATA ***

The data directory is /home/lgallo/SUZAKU/ngc2110/xis/
The mkf directory is /home/lgallo/SUZAKU/ngc2110/auxil/

The obscat n2110_read_cat.xsl has been made.

One data file has been read in.
GTI files are in use.

 *** PRODUCTS ***

 A spectrum has been accumulated.
 A curve has been accumulated.
 An image has been accumulated.

 *** SELECTIONS ***

     NONE

 *** FILTERS ***

 Spatial selections have been read in from:
    bkg.reg
  8. Now extract the background spectrum. 
     
n2110:SUZAKU-XIS0-STANDARD > extract spectrum
extractor v4.56      7 Sep 2005
 Getting FITS WCS Keywords
 Doing file: /home/lgallo/SUZAKU/ngc2110/xis/ae20050916_0850_1956_xis0_3x3_cl2.evt
100% completed
          Total      Good    Bad: Region      Time     Phase     Grade     Cut
         235840      1240         234522         0         0         0        78
   Grand Total      Good   Bad:  Region      Time     Phase     Grade    Cut
        235840      1240         234522         0         0         0        78
   in  61064.     seconds
 Spectrum         has     1240 counts for 2.0307E-02 counts/sec
 ... written the PHA data Extension
  9. Save the background spectrum as a pha file: 
    n2110:SUZAKU-XIS0-STANDARD > save spec n2110_xis0_3x3_bkg
  10. You now have background and source pha files which can be handled by XSPEC and FTOOLS in a standard way. The files can be group according to counts or channels using "grppha". The relative normalisation between the source and background spectra are taken care of by the "BACKSCAL" keyword in the headers. Current XIS response matrices are available at: http://www.astro.isas.jaxa.jp/suzaku/pub/xis/.

Creating a XIS broadband light curve

The process is basically identical to producing a spectrum. A source (+background) curve and a background curve are created and then manipulated outside XSELECT with
XRONOS. In fact, steps 1-4 of the spectral analysis above are identical. For the time being we will only concentrate on broadband light curves of extragalactic sources (i.e. no barycentric correction is done).

  1. To extract a light curve from a certain region of the event file. We first start DS9 to select a specific region.
    n2110:SUZAKU-XIS0-STANDARD > plot image
  2. Select the region of interest, for example a circle around a point source. Then save this extraction region as an "SAOimage" (e.g. src.reg). Before pushing "save" make certain to set the file format to "SAOimage". On your DS9 display push: 
    Region --> file format --> SAOimage
  3. Select a background region in a similar manner and also save this region (e.g. bkg.reg).

  4. Enter the source (+background) region (src.reg) as a filter for the "extract" command: 
    n2110:SUZAKU-XIS0-STANDARD > filter region src.reg
    To confirm that you have done this, you can type "show stat" at anytime: 
    n2110:SUZAKU-XIS0-STANDARD > show stat

              *** Status of XSELECT ***

Plot device is /XW

 *** MISSION ***

SUZAKU NONE XIS0 STANDARD
Time keyword is TIME       in units of s
Default timing binsize =   16.000
Minimum timing resolution:   8.0000
Energy keyword is PI         with binning     1
Max and min for PI        :     0    4095
 Image keywords   = X          Y           with binning =    8
 WMAP  keywords   = X          Y           with binning =    8

 *** DATA ***

The data directory is /home/lgallo/SUZAKU/ngc2110/xis/
The mkf directory is /home/lgallo/SUZAKU/ngc2110/auxil/

The obscat n2110_read_cat.xsl has been made.

One data file has been read in.
GTI files are in use.

 *** PRODUCTS ***

 A spectrum has been accumulated.
 A curve has been accumulated.
 An image has been accumulated.

 *** SELECTIONS ***

     NONE

 *** FILTERS ***

 Spatial selections have been read in from:
    src.reg
    Notice that the default bin size is 16 s.

  5. You can now extract a source (+background) light curve based of the extraction region you have selected: 
    n2110:SUZAKU-XIS0-STANDARD > extract curve
extractor v4.56      7 Sep 2005
 Getting FITS WCS Keywords
 Doing file: /home/lgallo/SUZAKU/ngc2110/xis/ae20050916_0850_1956_xis0_3x3_cl2.evt
100% completed
          Total      Good    Bad: Region      Time     Phase     Grade     Cut
         235840    179064          56637         0         0         0       139

   Grand Total      Good   Bad:  Region      Time     Phase     Grade    Cut
        235840    179064          56637         0         0         0       139
   in  61064.     seconds
 Fits light curve has   179064 counts for  2.932     counts/sec
 Thresholding removed significant counts
 Try exposure=0.0 on the extract command in xselect
 or lcthresh=0.0 if running extractor stand-alone
 Thresholding removed more than half the bins
 Try exposure=0.0 on the extract command in xselect
 or lcthresh=0.0 if running extractor stand-alone
  6. Save the source (+background) light curve which can be used in XRONOS. 
    n2110:SUZAKU-XIS0-STANDARD > save curve n2110_xis0_3x3_srcb_16s
    The extension .lc is added automatically.

  7. Following the same process also extract the background light curve. First we must change the filter region which is currently set to src.reg. Here, we will demonstrate this in one step. 
    n2110:SUZAKU-XIS0-STANDARD > filter region "-src.reg bkg.reg"
    or, 
    n2110:SUZAKU-XIS0-STANDARD > clear region 
n2110:SUZAKU-XIS0-STANDARD > filter region bkg.reg
    And check to see that this was done correctly: 
    n2110:SUZAKU-XIS0-STANDARD > show stat

              *** Status of XSELECT ***

Plot device is /XW

 *** MISSION ***

SUZAKU NONE XIS0 STANDARD
Time keyword is TIME       in units of s
Default timing binsize =   16.000
Minimum timing resolution:   8.0000
Energy keyword is PI         with binning     1
Max and min for PI        :     0    4095
 Image keywords   = X          Y           with binning =    8
 WMAP  keywords   = X          Y           with binning =    8

 *** DATA ***

The data directory is /home/lgallo/SUZAKU/ngc2110/xis/
The mkf directory is /home/lgallo/SUZAKU/ngc2110/auxil/

The obscat n2110_read_cat.xsl has been made.

One data file has been read in.
GTI files are in use.

 *** PRODUCTS ***

 A spectrum has been accumulated.
 A curve has been accumulated.
 An image has been accumulated.

 *** SELECTIONS ***

     NONE

 *** FILTERS ***

 Spatial selections have been read in from:
    bkg.reg
  8. Save the background light curve: 
    n2110:SUZAKU-XIS0-STANDARD > save curve n2110_xis0_3x3_bkg_16s
    The background light curve can now be subtracted from the source (+background) light curve in the standard way using the XRONOS package.

    Creating an HXD spectrum

    The process is essential the same as extracting an XIS spectrum. If available, cleaned event files for the PIN (*_hxd_wel_pin_cl.evt.gz) and/or GSO (*_hxd_wel_gso_cl.evt.gz) are found in the source directory.

    After unzipping the files, each event file can be read into xselect as usual: 

    n2110:SUZAKU-HXD-STANDARD > read events *_hxd_wel_pin_cl.evt

    Without need to define an extraction region, a source plus background spectrum can be extracted and saved: 

    n2110:SUZAKU-HXD-STANDARD > extract spectrum
n2110:SUZAKU-HXD-STANDARD > save spectrum *_hxd_wel_pin_cl
    The created pha file can now be read by XSPEC. The background and response matrices are available at http://www.astro.isas.jaxa.jp/suzaku/pub/hxd/

    List of things to do

    This document is work in progress a will be improved over the following days.