Notes on analyzing Suzaku data using XSELECT

These notes have been superseded by the Suzaku Data Reduction Guide.
These notes are still somewhat preliminary and experimental. They cover cleaning XIS hot and flickering pixels, how to filter by grade, how to select events based on housekeeping information, making XIS and HXD products (especially spectra), how to use xselect to catalog all the event files for a source, and how to make summed images of all 4 XIS.

It is assumed that the data is from v1 processing although this really only changes the directory structure. If you are using v0.7 processed data then you will need to explicitly set the directory and name for the mkf file, for which you will be prompted at the appropriate point.

The latest version of HEAsoft (6.1.1) should be installed.

Cleaning XIS hot/flickering pixels

The cleansis ftool originally written for ASCA SIS by Eric Gotthelf has been generalized first for Swift XRT and now for Suzaku XIS. This can either be run standalone or within xselect. We will take as an example cleaning an xis0 dataset : 
                         **  XSELECT V2.4   **
 
> Enter session name >[xsel] 
xsel:SUZAKU > set datadir xis/event_uf
 
Setting data directory to
/Volumes/Documents/DATA/Suzaku/PSR1509/100009010/xis/event_uf/
Setting mkf directory to
/Volumes/Documents/DATA/Suzaku/PSR1509/100009010/auxil/
 
xsel:SUZAKU > read e ae100009010xi0_1_3x3n000_uf.evt
...
...
...
        OBJECT      DATE-OBS    TIME-OBS    DATE-END    TIME-END	EDITMODE
      1 PSR1509-58  2005-08-23  08:38:23    2005-08-24  15:39:03      3x3
Note that the mkf directory has been set automatically. Now we run the cleansis tool using the xselect command sisclean : 
xsel:SUZAKU-XIS0-STANDARD > sisclean
> Which method (1=constant cutoff, 2=Poisson test)? >[2] 2
> Clean cell size for local background estimation (odd integer >
1)>[5] 
> Enter the log poission prob for clean threshold (must be < 0)
>[-5.24] 
> Zero background threshold >[3] 
> Lower cutoff for hot pixel search >[0] 
> Upper cutoff for hot pixel search >[4095] 
...
...
...
         By chip   :             0            1            2            3
 
 Pixels rejected   :          1229          237          242         1395
 
 Image counts      :        668652       985903       788148       600290
 Image cts rejected:         41560         7453        14560        18910
 Image cts rej (%) :          6.22         0.76         1.85         3.15
 
    filtering data...
 
 Total counts      :        668656       985903       788148       600290
 Total cts rejected:         41560         7453        14560        18910
 Total cts rej (%) :          6.22         0.76         1.85         3.15
 
 Number of clean counts accepted  :      2960514
 
    writing history cards...
    copying extensions...
    writing out hot pixs...
 
 Number of rejected pixels        :         3103
 
    updating NEVENTS keywords...
    closing data file...
    closing clean file...
If we were running cleansis standalone we would need to specify the command line argument chipcol=SEGMENT as well as the input and output filenames.

Filter by grade

Filtering by grade can be performed by two possible commands eg 
xsel> filter grade "0,2-4,6"
xsel> filter column "GRADE=0:0 2:4 6:6"
The latter was required for earlier Suzaku processing versions which did not have the TLMIN/MAX keywords for the GRADE column.

Selecting on housekeeping information

After the set-up above we can get a list of available housekeeping parameters by show param mkf. To select events based on housekeeping information use select mkf and then give either a C-style or Fortran-style selection string. This will create a GTI file which will be used for any subsequent products (using extract or bin). This GTI file can be saved by save mkf_sel. The standard XIS selection used in processing is : 
xsel:SUZAKU-XIS0-STANDARD > select mkf "SAA==0 && T_SAA> 436 && COR > 6 && ELV>10 && DYE_ELV>20"
PREFR keyword found in header, using prefr =   0.0
POSTFR keyword found in header, using postfr = 1.0
xsel:SUZAKU-XIS0-STANDARD > show filters
 
 *** SELECTIONS ***
 
 A filter file selection has been made from file:
   ae100009010.mkf
 The selection expression was:
   SAA==0 && T_SAA> 436 && COR > 6 && ELV>10 && DYE_ELV>20
 
 *** FILTERS ***
 
     NONE
To plot lightcurves of any of the housekeeping parameters use mkfbin followed by plot mkf.

Selecting data for the HXD works exactly the same way : 


                         **  XSELECT V2.4   **
 
> Enter session name >[xsel] 
xsel:SUZAKU > set datadir hxd/event_uf
 
Setting data directory to /Volumes/Documents/DATA/Suzaku/PSR1509/100009010/hxd/event_uf/
Setting mkf directory to /Volumes/Documents/DATA/Suzaku/PSR1509/100009010/auxil/
 
xsel:SUZAKU > read e ae100009010hxd_1_wel_uf.evt
...
...
...
        OBJECT      DETNAM      DATE-OBS    TIME-OBS    DATE-END    TIME-END
      1 PSR1509-58  WELL        2005-08-23  08:38:27    2005-08-24  15:39:13

xsel:SUZAKU-HXD-WELL_PIN > select mkf "SAA_HXD==0 && T_SAA_HXD>436 && ELV>5 && ANG_DIST<1.5 && HXD_DTRATE<3 && AOCU_HK_CNT3_NML_P==1 && COR>8 && HXD_HV_W0_CAL>700 && HXD_HV_W1_CAL>700 && HXD_HV_W2_CAL>700 && HXD_HV_W3_CAL>700 && HXD_HV_T0_CAL>700 && HXD_HV_T1_CAL>700 && HXD_HV_T2_CAL>700 && HXD_HV_T3_CAL>700"
PREFR keyword found in header, using prefr =   0.0
POSTFR keyword found in header, using postfr = 1.0
xsel:SUZAKU-HXD-WELL_PIN > show filters
 
 *** SELECTIONS ***
 
 A filter file selection has been made from file:
   ae100009010.mkf
 The selection expression was:
   SAA_HXD==0 && T_SAA_HXD>436 && ELV>5 && ANG_DIST<1.5 && HXD_DTRATE<3 && AOCU_HK_CNT3_NML_P==1 && COR>8 && HXD_HV_W0_CAL>700 && HXD_HV_W1_CAL>700 && HXD_HV_W2_CAL>700 && HXD_HV_W3_CAL>700 && HXD_HV_T0_CAL>700 && HXD_HV_T1_CAL>700 && HXD_HV_T2_CAL>700 &&
 
 *** FILTERS ***
 
     NONE

Generating XIS products in xselect

Xselect sets reasonable default options for XIS products. The image and wmap are binned up 8 times and when being written out the spectrum is truncated at 4096 channels to match the available response matrix files. Here is an example extracting a spectrum and lightcurve from the central source in the field from the XIS0 cleaned data. 
                         **  XSELECT V2.4   **
 
> Enter session name >[xsel] 
xsel:SUZAKU > read e
> Enter the Event file dir >[] xis/event_cl
> Enter Event file list >[] ae100009010xi0_0_3x3n000_cl.evt ae100009010xi0_0_5x5n000_cl.evt
...
...
...
        OBJECT      DATE-OBS    TIME-OBS    DATE-END    TIME-END    EDITMODE
      1 PSR1509-58  2005-08-23  08:38:23    2005-08-24  20:36:39    3x3
      2 PSR1509-58  2005-08-23  09:04:07    2005-08-24  07:40:07    5x5

 
xsel:SUZAKU-XIS0-STANDARD > extract image
extractor v4.67     11 Jul 2006
 Getting FITS WCS Keywords
 Doing file: /Volumes/Documents/DATA/Suzaku/PSR1509/100009010/xis/event_cl/ae100009010xi0_0_3x3n000_cl.evt
100% completed
          Total      Good    Bad: Region      Time     Phase     Grade     Cut
         414896    414896              0         0         0         0         0
 Doing file: /Volumes/Documents/DATA/Suzaku/PSR1509/100009010/xis/event_cl/ae100009010xi0_0_5x5n000_cl.evt
100% completed
          Total      Good    Bad: Region      Time     Phase     Grade     Cut
          20470     20470              0         0         0         0         0
===============================================================================
   Grand Total      Good   Bad:  Region      Time     Phase     Grade    Cut
        435366    435366              0         0         0         0         0
   in  61551.     seconds
 Image            has   435366 counts for  7.073     counts/sec
xsel:SUZAKU-XIS0-STANDARD > plot image
This final command launches ds9. We use that to define a region around the bright point source then save the region to a file. This file should be in the ds9/funtools format (selected using the Region->File Format menu) and in Equatorial J2000 coordinates (Region->File Coordinate System). Unfortunately, xselect doesn't automatically know about this region selection so you now need to tell it then extract the spectra and lightcurves : 
xsel:SUZAKU-XIS0-STANDARD > filter region source.reg
xsel:SUZAKU-XIS0-STANDARD > extract all           
extractor v4.67     11 Jul 2006
 Getting FITS WCS Keywords
 Doing file: /Volumes/Documents/DATA/Suzaku/PSR1509/100009010/xis/event_cl/ae100009010xi0_0_3x3n000_cl.evt
100% completed
          Total      Good    Bad: Region      Time     Phase     Grade     Cut
         414896    111165         303731         0         0         0         0
 Doing file: /Volumes/Documents/DATA/Suzaku/PSR1509/100009010/xis/event_cl/ae100009010xi0_0_5x5n000_cl.evt
100% completed
          Total      Good    Bad: Region      Time     Phase     Grade     Cut
          20470      5455          15015         0         0         0         0
===============================================================================
   Grand Total      Good   Bad:  Region      Time     Phase     Grade    Cut
        435366    116620         318746         0         0         0         0
   in  61551.     seconds
 Fits light curve has   116620 counts for  1.895     counts/sec
 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   116620 counts for  1.895     counts/sec
 ... written the PHA data Extension
 Image            has   116620 counts for  1.895     counts/sec
It is a good idea to check for any problems with the lightcurve. 
xsel:SUZAKU-XIS0-STANDARD > plot curve
If this show excursions due to increased background that has not been excluded by selecting on housekeeping parameters than additional times can be excised using 
xsel:SUZAKU-XIS0-STANDARD > filter time cursor
and following the instructions. The extract command write the output files to temporary filenames which can be converted to your own names by 
xsel:SUZAKU-XIS0-STANDARD > save spectrum source.pi
The data will be grouped using the following command:
 
bad 1-81,3290-4095&exit
 
> Group ( or rebin ) the spectra before outputting? >[yes]
The save command also gives you the option of setting some channels as bad. These can then be swiftly ignored in xspec using the command ignore bad. For some missions the save spectrum command will also generate the appropriate rmf and arf, this is not yet available for Suzaku. The lightcurve can be saved similarly : 
xsel:SUZAKU-XIS0-STANDARD > save curve source.lc
It is also sometimes useful to extract a new events file using only the events from good times and/or the region selected. To do that you just 
xsel:SUZAKU-XIS0-STANDARD > extract events
...
xsel:SUZAKU-XIS0-STANDARD > save events source.evt
which will combine the events from the two files read in and filter them on region and the good time intervals created by selection on housekeeping parameters.

Generating HXD products in xselect

Extraction of HXD products is similar to that for the XIS with the simplication that there is no region filtering necessary but with the complication that the PIN and GSO events must be separated. At the moment the background subtraction and response matrix for the GSO are still under development so we will illustrate the use of PIN data only. The cleaned data from the standard processing is already split into separate files for the PIN and GSO however if you do need to do this yourself the easiest method is to use the command filter column "DET_TYPE=1:1". 
                         **  XSELECT V2.4   **
 
> Enter session name >[xsel] 
readxsel:SUZAKU > read e
> Enter the Event file dir >[] hxd/event_cl
> Enter Event file list >[] ae100009010hxd_0_pinno_cl.evt
...
...
...
        OBJECT      DETNAM      DATE-OBS    TIME-OBS    DATE-END    TIME-END
      1 PSR1509-58  WELL_PIN    2005-08-23  08:38:27    2005-08-24  20:38:01

xsel:SUZAKU-HXD-WELL_PIN > extr all
...
xsel:SUZAKU-HXD-WELL_PIN > save spectrum pin.pi
As for the XIS, we do not yet automatically calculate arfs and rmfs. We expect to add this later along with automatic calculation of a background spectrum.

Making summed images from all 4 XIS

The easiest way to do this is not within xselect but within ximage. Suppose the four event files are called xis0.evt, xis1.evt, xis2.evt, and xis3.evt. Then the following ximage commands produce a summed image. 
read/rebin=4 xis0.evt
save
read/rebin=4 xis1.evt
sum
save
read/rebin=4 xis2.evt
sum
save
read/rebin=4 xis3.evt
sum
save
smooth
The rebinning and final smooth produce an image well-matched to the psf. To produce an image from a restricted range of PI bins replace the read commands by eg 
read/rebin=4/ecol=PI/emin=200/emax=1500 xis0.evt

A service of the Laboratory for High Energy Astrophysics (LHEA) at NASA's GSFC
Responsible NASA Official: Phil Newman
Curator: Keith Arnaud

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This file was last modified on Wednesday, 14-Mar-2012 17:31:10 EDT