6. XIS Data Analysis

6.1 Introduction

The XIS consists of four CCD detectors, three of which are ``front-illuminated'' (FI) and one ``back-illuminated'' (BI). The BI chip has an increased effective area at low ($< 1$keV) energies with a small decrease at higher energies. Although the detectors have seen significant improvements since the ASCA SIS, the data reduction is expected to be quite similar to that of ASCA SIS and Chandra ACIS.

Users should familiarize themselves with the current issues with the XIS and XIS analysis (the loss of XIS2, SCI, energy scale of non-SCI data, energy scale of SCI data, contamination, and timing mode) in Chapter5.

6.2 Content of the Cleaned Event Files

XIS data begin as part of the RPT telemetry downloaded from Suzaku, and is converted into a collection of FITS files by the mk1stfits routine at ISAS. mk1stfits does not reject any events or apply any calibration to the data but merely converts RPT into FITS files. Once the files have been processed through the pipeline (second FITS file, SFF), they are included in the standard data download in the directory xis/event_uf. The calibration steps are summarized in this table.

Table 6.1: XIS calibration steps

Calibration Item	Tool	Comments
Calibrate Sky Coordinates	xiscoord	Attitude wobble is now modeled
Assigning Pixel Quality	xisputpixelquality
Compute PI	xispi	Works for data with and without SCI

Unless there is an update specific to the data in question, users should assume that these steps need not be repeated.

The XIS mk2ndfits pipeline task is then run on the mk1stfits output to create filtered, calibrated output event files, which are placed in the event_cl subdirectory. There are two broad classes of screening, event by event and by good-time intervals (GTI). The former includes event grade, which encodes the pattern of charge distribution among neighboring pixels and can be used to distinguish between X-ray and charged particle events. The GTI screening is used to select time intervals where the instrument is pointed atably at the source without being blocked by the Earth, and to exclude high background intervals.

The Version 2 screening criteria are summarized in this table:

Table 6.2: XIS Screening Criteria

Type	Criterion	Comments
Event by event	GRADE=0:0 2:4 6:6	ASCA grades indicating X-ray events
	STATUS=0:524287	Bad columns, charge injection rows removed
	cleansis	Flickering pixels are removed
GTI	AOCU_HK_CNT3_NML_P==1	Attitude control in pointing mode
	ANG_DIST$<$1.5	Instantaneous pointing within 1.5 arcmin of mean.
	Sn_DRATE$<$3	Telemetry rate SuperHigh, High, or Medium
	SAA_HXD==0	Satellite is outside SAA
	T_SAA_HXD$>$436	Time since SAA passage $>$436 sec
	ELV$>$5	Pointing direction $>$5 deg above Earth
	DYE_ELV$>$20	and $>$20 deg above sunlit limb of Earth

6.3 Updating CTI calibration

The XIS team has updated the CALDB files ae_xiN_makepi_20071031.fits, which are used by xispi which calculates the PI values. The files include time-dependent CTI paramters for the SCI-on data, and thus eneble us to correct the decrease in the gain after 2006 September.

The processed pipeline version 2.1.6.16 is the first version to use these revised makepie files. Users should check the pipeline version used for processing their data by reading the PROCVER keyword in their data files.

Version 2 processing pipeline used older versions of the makepi files up to V2.1.5.15. For SCI-on XIS data taken 2006 September, this resulted in the gain of Mn K alpha calibration line decreasing at a rate of about 30 eV/year in the FI chips -- see http://suzaku.gsfc.nasa.gov/docs/suzaku/analysis/xis_v2.html.

Users can reprocess their own SCI-on data (processing version 2.x) as follows.

First, run xispi to recalculate the PI values. Note that the XIS HK files are in the xis/hk subdirectory.

example% xispi infile=ae101005070xi0_0_3x3n066z_uf.evt.gz \
               outfile=ae101005070xi0_0_3x3n066z_uf_new.evt \
               hkfile=../hk/ae101005070xi0_0.hk.gz

Hidden paramter, makepifile should be set to CALDB if accessing the latest CALDB, or explicitly specify ae_xi0_makepi_20071031.fits.

Since the grade determination is based on the CTI-corrected pulse height values in the PHAS column, users should reprocess starting with the unfiltered event files. Once all unfiltered event files are reprocessed with xispi, they must be screened. For convenience, we provide an xselect script
http://suzaku.gsfc.nasa.gov/docs/suzaku/analysis/xisrepro.xco, which references event selection criterion file
http://suzaku.gsfc.nasa.gov/docs/suzaku/analysis/xis_event.sel and the standard good-time interval selection file
http://suzaku.gsfc.nasa.gov/docs/suzaku/analysis/xis_mkf.sel. Users should download these three files into the current working directory, make sure the filter file (.mkf in ../../auxil directory) is uncompressed, read in the updated unscreened event file(s) into xselect, then type

xsel > @xisrepro

This will cause xselect to apply the event selection, remove flickering pixels (using cleansis), and apply the standard GTI selection. If desired, users can edit xis_mkf.sel to adjust the screening criteria. Xselect will pause and ask the users to give the output (screened) event file name.

6.4 Extracting Products

The primary tool for extracting data products (spectra, lightcurves, exposure maps) from XIS data is xselect, which is part of the general HEAsoft distribution. xselect can apply filters which select user-defined times, sky regions, or particular event flags. It then uses the filtered events to create a (binned) spectrum (as well as generating the necessary calibration files), a lightcurve, or an exposure map. Basic parameters commonly used for common data screening are in the filter, or mkf, file.

6.4.1 Additional screening

Additional filtering can be applied to the screened data at this stage using the ``select mkf'' command at this stage. Xselect assumes that the filter file is located in ../../auxil relative to the current working directory, with the file name *.mkf. Users who prefer to work under a different directory can use the set mkfdir command to change the location of the filter file. With the default set-up, it is necessary to uncompress the filter file and ensure it has a file name ending with .mkf.

Additional filtering could include applying a more strict version of the screening already applied in pipeline processing. For example, some observations may be more sensitive to the effects of solar X-rays scattered from the sunlit Earth. In this case, users may want to experiment applying DYE_ELV$>$25 to the data and see if it makes a difference.

Another item that affects the particle background rate is geomagnetic cut-off rigidity (COR, which is in the mkf file; a slightly updated version, COR2, is currently available only in the ehk file). For example, applying the criterion ``COR$>$6'' can reduce the effective exposure time somewhat but may improve the signal-to-noise ratio.

One final screening concerns telemetry saturation. It is not expected that this is a major issue in the majority of observations, as long as low telemetry rate data are excluded, hence the pipeline does not apply GTIs based on non-saturation of telemetry. However, GTI files for intervals of unsaturated telemetry are available in the xis/hk subdirectory with filename ending in _tel_uf.gti, and these can be applied by using the ``select time file'' command in xselect.

In general, users are encouraged to explore the effects of different values for all the cuts and selections described above on their own dataset by making lightcurves of mkf parameters.

6.4.2 Region Selection

For a point source, circular extraction regions centered on the source should be used to extract source spectra and light curves. We recommend a a relatively large radius, e.g., 250 pixels (260 arcsec), which encircles 99% of the point source flux, whenever possible. (As of 2007 December, there is a calibration problem for small extraction region that is severe for radii of order 1 arcmin or less.) As the vignetting is relatively small, a large fraction of the remainder of the XIS chip is in principle available for background subtraction.

6.4.2.1 Sky regions

It often happens that users want to extract light curves or energy spectra from some specific regions on the sky. Such region selection can be done on the ``SKY'' image displayed by ds9/saoimage; select a region and create a region file to use for the xselect ``filter region'' command. Region files should be created in ds9 using the ds9/funtools format and equatorial J2000 coordinate system. Sky coordinates are the default image coordinates in xselect. After using other coordinates, enter set image sky to go back to sky coordinates.

6.4.2.2 Detector regions

Particular regions within a single detector may be selected using Detector coordinates. Use set image det command before extracting images. While Detector coordinates are defined so that all the XIS images have the same direction (§3.3), the four XIS sensors on the baseplate are rotated by $90^{\circ}$ or $180^{\circ}$ relative to each other. The ACT coordinates are the actual location on the CCD chip, which may be useful when investigating instrumental characteristics on particular chip positions (such as extracting the calibration source spectra). set image raw followed by extract image will extract XIS ACT images. XIS performance will be dependent on Segments, and particular Segments may be selected with the select event command. Events on Segment A, B, C and D have ``SEGMENT'' column value 0, 1, 2, 3 and 4 respectively.

6.4.2.3 BACKSCAL

The area of the extraction region, as a fraction of total area of the coordinate space (sky or detector), is recorded in the extracted spectra in the BACKSCAL keyword. Xspec automatically scales the background using the ratio of the BACKSCAL keywords before subtracting it from the source spectrum. For timing analysis, users must manually check the BACKSCAL keywords and subtract the scaled version of the background light curve from the source light curve.

6.5 Generating RMF and ARF files

6.5.1 Generating RMF and ARF with xisresp

We offer a script, xisresp, that runs xisrmfgen and xissimarfgen, on a $\beta$-test basis. The usage is:

xisresp  <filename> <slow|medium|fast> <region-file> extend? echo?

Xisresp is available at:
http://suzaku.gsfc.nasa.gov/docs/suzaku/analysis/xisresp

6.5.2 Combining Spectral files and Responses using addascaspec

Addascaspec is available as an ASCA FTOOL which can be used to combine the spectra and responses of Suzaku XIS (FI chip) data. It requires a 4-line Ascii file, listing the source spectral files, background spectral files, ARF files, and RMF files. It should have two or three columns depending on the number of active FI XIS units. For example, create the following file

x0.pha x2.pha x3.pha
x0b.pha x2b.pha x3b.pha
x0.arf x2.arf x3.arf
x0.rmf x2.rmf x3.rmf

and call it fi.add (this assumes a specific but obvious file naming convention). Then,

example% addascaspec fi.add fi.pha fi.rsp fi_b.pha

will run several FTOOLS to create a combined source spectral file (fi.pha), a combined background spectral file (fi_b.pha), and a combined (RMF x ARF) response file (fi.rsp). Note that the operation to multiply and add the individual response files may be extremely memory-intensive, depending on the quality and the size of the original response files.

6.5.3 Generating RMF files using xisrmfgen

XIS response generator, xisrmfgen, takes into account the time variation of the energy response, appropriate for XIS data obtained with or without spaced-row charge injection (SCI). It is relatively straightforward to use and we have included below an example.

> xisrmfgen
xisrmfgen version 2006-11-26
Name of input PI or IMAGE file or NONE[xis0-5b5w.pi]
Name of output RMF[xis0-5b5w.rmf]

The information concerning the instrument, clock mode and the date of observation is directly from the header of the spectral file given^6.1.

Note that xisrmfgen requires the spectral file to have a WMAP (weighted map) in detector coordinates. This is the default in the current and recent (HEAsoft 6.1.2 or later) releases of xselect, although older versions defaulted to sky coordinates.

The following warning message:

xisrmfgen: WARNING: Weighted map or image is not in DET coordinate.
xisrmfgen: WARNING: Use constant weight on whole CCD.

is the indication that the WMAP is in SKY coordinates. In this case, xisrmfgen generates a response file assuming a constant WMAP over the whole CCD. The current xisrmfgen does not consider spatial variation of spectral response on the CCD chip, which is negligible for the current data. Therefore, the practical effect of this is negligible. Nevertheless, it is advisable to generate spectral files with the DET coordinate WMAP. To do so using older versions of xselect, issue the command:

xsel:SUZAKU-XIS1-STANDARD  set wmapname detx dety

6.5.4 Generating ARF files using xissimarfgen

Xissimarfgen is a ray-tracing based generator of ancillary response files (ARFs) for the Suzaku XIS. It is a powerful tool, which however has far more parameters and modes of usage than a typical guest observer would need (or want to know about). Since xissimarfgen calculates ARFs through Monte-Carlo simulations (it ray-traces X-ray photons through Suzaku XRT and XIS and counting the number of events detected in the user-defined extraction regions), users need to simulate a sufficient number of photons to limit the statistical errors to an acceptable level.

For further details, users should refer to the paper by Ishisaki et al. in the Publication of the Astronomical Society of Japan (Ishisaki et al. 2007, PASJ, 59, 113;
http://arxiv.org/abs/astro-ph/0610118).

6.5.4.1 Example: Point Source ARF

Here, we give an example of generating an ARF file for a point source observed on-axis, using the data set ID 100012010. The following is an XIS1 image of the observation, in which one can see a bright point source at the center. We assume that a spectrum from the white encircled region in the image has been extracted, and show how to generate a corresponding ARF file.

Figure: An example of point source extraction region.

Region files with the ds9 format in the physical coordinates can be fed into xissimarfgen; when using this combination, the binning used to extract the image does not matter. To save a source region, one specifies the coordinate system ``Physical'' in the ``File Coordinate System'' row in the ``Region'' menu on ds9. Here is etacar_phys.reg:

# Region file format: DS9 version 3.0
# Filename: ae100012010xi1_1_5x5n001_cl.evt.gz[EVENTS]
global color=green font="helvetica 10 normal" select=1 edit=1 \
move=1 delete=1 include=1 fixed=0 source
physical;circle(784.5,786.5,172.71158)

corresponding to the white encircled region above in the physical coordinates. Then, run the following

xissimarfgen clobber=yes \
instrume=XIS1 \
pointing=AUTO \
source_mode=J2000 \
source_ra=161.264962 \
source_dec=-59.684517 \
num_region=1 \
region_mode=SKYREG \
regfile1=etacar_phys.reg \
arffile1=xis1_etacar.arf \
limit_mode=NUM_PHOTON \
num_photon=400000 \
phafile=etacar.pi \
detmask=none \
gtifile=100012010/xis/event_cl/ae100012010xi1_1_3x3n001_cl.evt \
attitude=100012010/auxil/ae100012010.att \
rmffile=ae_xi1_20060213.rmf \
estepfile=default

Some options specify calibration files or Monte-Carlo simulation parameters that can be adjusted each time xissimarfgen is run. These are:

• The pointing option AUTO takes care of the referencing coordinate system
• In this example, we use the ``limit_mode'' option NUM_PHOTON and set the number of simulated photons (``num_photon'') to 400,000, to minimize the Poisson noise in the ARF.
• Through spectrum passed using the ``phafile'' parameter, xissimarfgen knows the XIS observing mode such as the window option and spaced-row charge injection option.
• In this example, we do not use the ``detmask'' option since the calibration source events do not fall on the source region.
• The default selection for the ``estepfile'' option has a sufficient energy resolution for most purposes.

Other options fixed by the observation or by the upstream analysis. These are:

• The ``instrume'' option is XIS1, set by the spectrum being analyzed.
• In this example, we specify the source position in the J2000 coordinate system. Thus, the ``source_mode'' is J2000. Therefore we also input the source coordinates [(R.A., Dec.)(J2000) = (161.264962, -59.684517)] using the ``source_ra'' and ``source_dec'' parameters. See the example below for using the physical (X, Y) coordinate.
• The ``num_region'' option should be 1 since, in this case, we generate only one ARF file. The ``region_mode'' parameter is set tp SKYREG since the region file is described in the sky coordinate system. The region file name, etacar_phys.reg, is specified via the ``regfile1'' parameter.
• The output ARF file name xis1_etacar.arf is specified using the ``arffile1'' parameter.
• To take the attitude wobble into account, the attitude file in the auxil directory, is loaded using the ``attitude'' parameter. To specify the time span of the observation, a FITS file with the GTI table of the observation (ae100012010xi1_1_3x3n001_cl.evt in this case) is loaded using the gtifile parameter.
• We also specify the RMF to be used in spectral fitting (ae_xi1_20060213c.rmf in this case).

The ``pixq_[min,max,and,eql]'' parameters are not specified in the command line since we use the default setting (Bad columns, pixels, and charge injection rows are excluded; the calibration source region is not subtracted).

Here is an example, in which the source position is specified in the SKYXY coordinate.

xissimarfgen clobber=yes \
instrume=XIS1 \
pointing=AUTO \
source_mode=SKYXY \
source_x=784.5 \
source_y=786.5 \
num_region=1 \
region_mode=SKYREG \
regfile1=etacar_phys.reg \
arffile1=xis1_etacar.arf \
limit_mode=NUM_PHOTON \
num_photon=400000 \
phafile=none \
detmask=none \
gtifile=100012010/xis/event_cl/ae100012010xi1_1_3x3n001_cl.evt \
attitude=100012010/auxil/ae100012010.att \
rmffile=ae_xi1_20060213.rmf \
estepfile=default

6.5.4.2 Example: ARF of a Uniformly Extended Source

Here, we show an example of generating an ARF file for a uniformly extended source, using observtion 102002010. The following is an XIS0 image of the observation, in which the strong emission from SNR E0102.2$-$7219 is evident. Here, we try to search for possible extended emission from the surrounding areas. In this analysis, we screened out the calibration source so as not to degrade the data quality significantly. To do so, type

XSEL> select events "(STATUS<524287)&&(STATUS%(2**17)<2**16)"

in xselect.

Figure: An example showing extended source extraction regions.

As can be seen in this image, events at the two corners, where the calibration sources are located, have been removed. Here, we extract two spectra from the top-left half and bottom-right half of this image, whose region files are described by files e0102_tophalf_phys.reg

# Region file format: DS9 version 3.0
# Filename: xsel_image.xsl
global color=green font="helvetica 10 normal" select=1 edit=1 \
move=1 delete=1 include=1 fixed=0 source
physical;box(543.14102,923.78203,1027.6537,502.82032,60)
physical;-circle(756.5,788.5,200)

and e0102_bottomhalf_phys.reg

# Region file format: DS9 version 3.0
# Filename: /local/data/subaru2/kenji/AstroE2/E0102/070119/102002010/xis/event_cl/xsel_image.xsl
global color=green font="helvetica 10 normal" select=1 edit=1 move=1 delete=1 include=1 fixed=0 source
physical;box(985.31535,667.85314,1026.428,507.58708,60)
physical;-circle(756.5,788.5,200)

Then, the appropriate ARFs can be generated using the following command.

xissimarfgen clobber=yes \
instrume=XIS0 \
pointing=AUTO \
source_mode=UNIFORM \
source_rmin=0 \
source_rmax=20 \
num_region=2 \
region_mode=SKYREG \
regfile1=e0102_tophalf_phys.reg \
regfile2=e0102_bottomhalf_phys.reg \
arffile1=e0102_tophalf.arf \
arffile2=e0102_bottomhalf.arf \
limit_mode=MIXED \
num_photon=2000000 \
accuracy=0.005 \
phafile=e0102_tophalf.pi \
detmask=none \
gtifile=../xis/ae102020010xi0_cl.evt \
attitude=../auxil/ae102020010.att \
rmffile=e0102_tophalf.rmf \
estepfile=medium

As in the point source example, certain parameters specify calibration files or Monte-Carlo simulation parameters that can be adjusted for each run of xissimarfgen

• The pointing option AUTO takes care of the referencing coordinate system.
• This set-up (the parameter ``source_rmax''=20, see below) also simulates emission from outside of the detector field of view. This is useful for considering contribution from the stray light, but, since many of the simulated photons do not reach the detector and hence discarded, more photons than in a point source case need to be simulated to obtain enough statistics (The ``num_photon'' parameter is 2,000,000, in this example). This requires a long computation time. To reduce the computation time in the hard energy band ($> \sim$10 keV) where such high photon statistics is generally unnecessary, we specify the MIXED option of ``limit_mode'' and also ``accuracy''=0.005 and the calculating energy step is reduced to medium.
• The calibration source region is masked in arf calculation with the default set-up. If you wish to include it, type ``pixq_and=0.''
• The charge injection rows are automatically masked by inputting a spectrum file of this observation (e0102_tophalf.pi) using the ``phafile'' parameter (or by using a special setting of ``pixq_'' parameter).

Other parameters depend on the data or on the upstream analysis.

• The ``instrume'' parameter is set to XIS0, appropriate for the spectral file in question.
• The source emission is assumed to be UNIFORM, which is specified using the ``source_mode'' parameter. We assume source emission from an r=20arcmin encircled region centered at on-axis (source_rmin=0, source_rmax=20) so that the source emission significantly larger than the detector field of view.
• The ``num_region'' parameter is set to 2 since, in this example, we generate two ARFs (one for the top region and the other for the bottom) (``regfile1''=nep_tophalf_phys.reg, ``regfile2''=nep_bottomhalf_phys.reg), in one go. The ``region_mode'' parameter is set to SKYREG to reflect the coordinate system used in the region file.
• The two output ARF file names are specified using parameters ``arffile1'' and ``arffile2.''
• To take the attitude wobble into account, the attitude file in the auxil directory (ae102020010.att) is loaded using the ``attitude'' parameter. To specify the time span of the observation, a FITS file with the GTI table of the observation (ae102020010xi0_cl.evt in this case) is loaded using the gtifile parameter.
• We also specify the RMF to be used in spectral fitting (e0102_tophalf.rmf in this case).

To double-check that the intended source region was used by xissimarfgen, it can be displayed using ds9. For example, type

> ds9 e0102_tophalf.arf

while the selected STATUS bits can be confirmed in the standard output from xissimarfgen.

Note that the ARF files generated using the above command are normalized to the sizes of defined emitting regions. In the above example, the xspec output (e.g., the normalization parameter, the flux) assumes emission from an encircled region with 20 arcmin radius.

6.5.4.3 Caveats when generating ARFs in sky coordinates

Users may need to specify the sky reference position when generating ARFs in the SKY coordinates. Please refer to Appendix 2.3 of Ishisaki et al. (2006) for more details.

When users choose

• source_mode = SKYFITS
  • No need for the users to specify this: ``skyref'' is automatically read from the FITS header keywords.
• source_mode = SKYXY or region_mode = SKYFITS, SKYREG, SKYCIRC
  • If pointing = USER
    • Users must specify the ``ref_alpha,'' ``ref_delta,'' and ``ref_roll'' parameters, which are used for ``skyref.''
  • If pointing = AUTO (default)
    • If an attitude file is supplied
      • No need for user action: ``skyref'' is read from the header of the attitude file: Recommended
    • If attitude= NONE
      • Users must specify the Euler angles, from which ``skyref'' is calculated.

6.5.4.4 Tips for Reducing Run Time of xissimargfgen

1. Reducing the number of energy bins in ARFs

   Computation time of an arf table is proportional to the number of calculating energy steps, which are set up with the ``estepfile'' parameter:

   estepfile [filename]
      Energy step file or built-in steps. The built-in energy steps are:
      "full" : calculate effective area for each RMF energy bin. Very slow.
      "dense" or "default" : dense sampling (2303 steps). Slow.
      "medium" : medium sampling (157 steps). Moderate.
      "sparse" : sparse sampling (55 steps). Fast.
   

   Fits of a decent spectrum do not improve significantly with an ARF generated with estepfile=default compared with an arf with estepfile=medium, but arfs with the default energy step need 14.67 (= 2303/157) times longer computation time to be made than those with the medium energy step.

2. Optimizing the ``num_photon'' and ``accuracy'' parameters

   When limit_mode=NUM_PHOTON, computation time is also proportional to the number of faked photons set up at the ``num_photon'' parameter.

   For a point source ARF, limit_mode=NUM_PHOTON, num_photon=400000 is recommended, but limit_mode=MIXED, num_photon=200000 accuracy=0.005 is acceptable for faint sources.

   For a uniform sky ARF, limit_mode=MIXED, num_photon=2000000, and accuracy=0.005 is recommended.

   For ARFs of extended sources (including uniform sky ARFs), visual inspection of the accuracy of ARFs, by plotting the effective area in xspec, is highly refcommended.

3. Running xissimarfgen with a fast CPU using a fast code

   The Monte-Carlo ray-tracing simulation runs numerous floating point calculations, and so Athlon64 usually runs xissimarfgen faster than Pentium4. If available, 64-bit codes compiled on the 64-bit Linux runs about 1.5 times faster than 32-bit codes on the same PC.

4. Running ARF caluculations for different sensors (XIS0/1/2/3) on different machines

5. Generating ARFs of multiple accumulation regions in the same observation at once.

6. Defining the smallest emission region possible when generating diffuse source ARFs

   If an emission region defined at the ``source_image'' parameter is too large compared with the event extraction region, computation time gets slower without improving quality of the simulation. For generating a uniform sky ARF, we recommend source_mode=UNIFORM, source_rmin=0, and source_rmax=20.

   Similarly, if the spacecraft attitude is not stable after a maneuver and the emission region goes out from the event accumulation region, the ARF calculation becomes slow.

6.5.5 Tips for Faster Spectral Fits of XIS Data

1. Rebinning a RMF

   Because the standard RMF of Suzaku XIS has 7900 energy bins (2 eV step, 0.2 - 16 keV) times 4096 PI bins, xspec needs much memory to read the RMF and time to calculate a spectral fit model. This fine-step matrix is usually over-sampled for moderate flux sources with featureless X-ray spectra (e.g., AGNs).

   Users can rebin the RMF in both channel- and energy-spaces with rbnrmf. Note that the spectral file also needs to be rebinned, when the RMF is rebinned in the channel-space. Users can also specify the channel-space rebin factor using the ``rebin'' parameter of the tt xisrmfgen.

   The RMF energy bins are determined with the default set of parameters
   ebin_lowermost=0.20, ebin_uppermost=16.0, and ebin_width=2.0. Users who are only interested in the soft band spectrum can reduce the RMF size by 25% with ebin_uppermost=12.0. When the spectral model to fit is featureless (no strong emission lines), ebin_width=4.0 or ebin_width=8.0 will give almost the same fit result. Older version of RMF, e.g., ae_xi0_20050916.rmf, in the CALDB has non-equal energy bin with 4096 steps in 0.2-12.0 keV. Users can copy these energy steps, by specifying

   ebin_mode=1 ebinfile=ae_xi0_20050916.rmf
   

   ARFs must be re-created when the RMF energy bins are changed.

2. Combining XIS0, (XIS2,) and XIS3

   The XIS team recommends adding the spectra and response for the units with the frontside illuminated (FI) chips. XIS1 spectrum, however, must be fitted separate since its (backside illuminated, or BI chip) response is distinctly different from those of FI chips.

6.6 Subtracting the non X-ray Background

Screened XIS event data still include particle and X-ray background events. These contributions can best be estimated from off-source area of the same XIS CCD chip, but this is not always possible for extended sources. Alternatively, we can estimate particle background during the observations of the target from the night Earth data, which have been collected by the XIS team and stored in CALDB. Related files are:

ae_xi?_nxbsciof_YYYYMMDD.fits: SCI-OFF event file
ae_xi?_nxbscion_YYYYMMDD.fits: SCI-ON event file
ae_xi?_nxbvdchk_YYYYMMDD.fits: HK file with the detector temperature
ae_xis_nxbcorhk_YYYYMMDD.fits: HK file of the cut-off rigidity
ae_xis_nxborbit_YYYYMMDD.fits: orbit file

Although users may analyze these data however they see fit, the XIS team has developed a tool that collects the appropriate NXB data from CALDB and automatically generates NXB images and spectra. The tool xisnxbgen is available in the HEAsoft version 6.4 or later.

6.6.1 Xisnxbgen

Tawa et al. (2008; PASJ in press) have shown that XIS NXB varies with the cut-off-ridigity (COR) value at the satellite location. Based on this result, xisnxbgen sorts NXB data by COR values, generates an NXB spectrum and image for each COR range (defined by the ``sortstep'' option), and combine them weighted by exposure time ratio of each COR range during GTIs in the user's spectral file. The default NXB indicator is COR2 (revised cut-off rigidity). The other indicators such as obsolete cut-off rigidity COR and PINUD rate, which can be calculated with aemkpinudhk, are also available by setting up at the hidden option, sortkey.

Here, we show an example of generating NXB spectrum and image. First, we need to make a source spectral FITS file, which we call etacar_nebula_x0.pi in this example, and name the product NXB spectral file etacar_nebula_nxb.pi. We also need to input the source region file (etacar_nebula_x0.reg), from which we created etacar_nebula_x0.pi, and the coordinate system (SKYREG), on which the region file is described. The attitude and orbital files for the data are ae402039010.orb and ae402039010.att, respectively, which are found in the auxil directory in the data distribution.

Then type

> xisnxbgen etacar_nebula_nxb.pi etacar_nebula_x0.pi SKYREG etacar_nebula_x0.reg \
ae402039010.orb ae402039010.att

Xisnxbgen first displays all the option you choose after the text ANL: *** xisnxbgen show parameter ***. We recommend you confirm that the options are specified as intended, and wait until the product etacar_nebula_nxb.pi is obtained. The product file has an NXB spectrum in the 1st extension, an NXB image in the detector coordinate in the 2nd extension, and an NXB image in the sky coordinate in the 3rd extension. The sky coordinate map in the 3rd extension ignores the region file selection, i.e. you will get a sky NXB background image of an entire CCD chip in any set-ups (You can see the detector/sky background images with ds9. Type on a command line, ds9 etacar_nebula_nxb.pi[2] or ds9 etacar_nebula_nxb.pi[3], as appropriate.) You can feed the product to xspec as background, or use it for NXB subtraction on the sky image.

To produce an NXB image within a certain energy range, specify the lower and upper boundary PI values (3.65 eV/channel) using the pi_min and pi_max parameters. For example,

> xisnxbgen etacar_nebula_nxb.pi etacar_nebula_x0.pi SKYREG etacar_nebula_x0.reg \
pi_min=274 pi_max=548 ae402039010.orb ae402039010.att

The product NXB spectral file is not affected by these options, that is, it also has values below pi_min and above pi_max.

Here are things to be considers in using xisnxbgen.

• Xisnxbgen automatically chooses appropriate CALDB files based on header information of the input spectral file (specified using the phafile parameter), including whether data were taken with Spaced-row Charge Injection options on (SCI-on) or off (SCI-off).

• Xisnxbgen automatically runs xispi, xisputpixelquality, and cleansis on the NXB data to use the latest calibration unless you specify apply_xisftools=no (this option requires that the user have run xispi etc. on the NXB files and specify the result explicitly, e.g., xisnxbgen apply_xisftools=no nxbevent=nxb.evt).

  Except when apply_xisftools=no is specified, xisnxbgen then screens out events that do not satisfy event selection criteria specified using the hidden parameters grades, enable_pixq, pixq_min, pixq_max, pixq_and and pixq_eql. If you apply the standard filtering criteria^6.2to the source data or start from cleaned event data without further data screening, you do not need to change the default parameters. See definition of these parameters in subsection6.5.4.

• Region files need to be described in sky coordinates (SKYFITS/SKYREG/SKYEXPR) or detector coordinates (DETFITS/DETREG/DETEXPR).

• Xisnxbgen projects an NXB map in the detector coordinate onto the sky coordinate plane, only considering the satellite wobbling. That is, NXB variation during observations is averaged over the entire CCD chip before the projection, and any NXB variations that are correlated with the attitude wobble will not be properly reflected. We thus recommend to remove data taken during large pointing offsets, for example, just after the satellite maneuver.

• Considering possible long-term NXB variation and steady decay of the $^{55}$Fe calibration isotope (2.73 year half-life), by default, xisnxbgen extracts events from the NXB database between (TSTART - 150 days) and (TSTOP + 150 days), in which TSTART and TSTOP are referred to the header of the input spectral file. However, some observations may have limited NXB data between the default extracting interval and need to redefine wider accumulation interval of NXB data to obtain enough photon statistics.

  You can check effective accumulation time of NXB data from the standard output of xisnxbgen runs. See the sample outputs below. The first table shows exposure time within each COR2 grid of the input spectrum and the second does effective accumulation times of NXB data. If the accumulation time is not significantly longer than the exposure time of your spectrum, you should better widen the range of the data accumulation interval.

===========================================
COR2          :  EXPOSURE (s)  FRACTION (%)
-------------------------------------------
  0.0 -   4.0 :       1184.0         2.161
  4.0 -   5.0 :       3560.0         6.498
  5.0 -   6.0 :       3224.0         5.885
  6.0 -   7.0 :       3672.0         6.703
  7.0 -   8.0 :       3408.0         6.221
  8.0 -   9.0 :       3808.0         6.951
  9.0 -  10.0 :       4288.0         7.827
 10.0 -  11.0 :       5096.0         9.302
 11.0 -  12.0 :       7368.0        13.449
 12.0 -  13.0 :       6440.0        11.755
 13.0 -  99.0 :      12736.0        23.248
-------------------------------------------
          SUM :      54784.0       100.000
        TOTAL :      54784.0       100.000
-------------------------------------------
........
........
===================================================================
COR2          :  EXPOSURE (s)  FRACTION (%)  SPEC (cts) IMAGE (cts)
-------------------------------------------------------------------
  0.0 -   4.0 :       4584.0         1.254        37.2       878.0
  4.0 -   5.0 :      19136.0         5.235       129.3      3077.0
  5.0 -   6.0 :      18816.0         5.148       122.7      2547.0
  6.0 -   7.0 :      18640.0         5.099       104.1      2275.0
  7.0 -   8.0 :      20520.0         5.614       104.4      2308.0
  8.0 -   9.0 :      23792.0         6.509       112.0      2491.0
  9.0 -  10.0 :      43136.0        11.801       162.7      4004.0
 10.0 -  11.0 :      45496.0        12.446       179.9      4098.0
 11.0 -  12.0 :      42992.0        11.761       174.1      3710.0
 12.0 -  13.0 :      44456.0        12.162       171.2      3698.0
 13.0 -  99.0 :      83968.0        22.971       310.0      7219.0
-------------------------------------------------------------------
          SUM :     365536.0       100.000      1607.6     36305.0
        TOTAL :     365536.0       100.000     36305.0     36305.0
-------------------------------------------------------------------
    EFFECTIVE :     370262.3       101.293      1679.1     37775.9
-------------------------------------------------------------------

6.7 Creating an exposure map

For the study of extended sources with the XIS, it is necessary to know the exposure times as well as vignetting at various sky locations within the XIS image.

6.7.1 Types of Exposure Maps

One type of exposure map can be created by simply considering the detector field of view and the spacecraft attitude, the result being the actual exposure time per sky pixel. Such exposure maps can be created by using xisexpmapgen, which allows users to exclude unused pixels such as bad columns, hot/flickering pixels, SCI rows, and the 55Fe calibration source area. See section below as well as the help file of xisexpmapgen for further details.

In the other type, the effective exposure times per sky pixel are calculated, taking into account the vignetting of the XRT. Below, we describe how to use xissim to simulate a ``flat field'' image for this purpose.

6.7.2 Running xissim

As an example, we show how to simulate an XIS0 flat field image at 2.45 keV of the observation sequence 102002010. The attitude wobbles during this observation are included in the simulation by supplying the attitude file and a GTI table.

> xissim instrume=XIS0 enable_photongen=yes photon_flux=1 flux_emin=1.0 \\
flux_emax=10.0 spec_mode=1 image_mode=2 time_mode=0 limit_mode=1 energy=2.45 \\
ra=16.0083 dec=-72.0313 sky_r_min=0 sky_r_max=20 exposure=15825.09 \\
pointing=AUTO gtifile=cleaned.evt\[GTI\] attitude=ae102002010.att \\
ea1=16.007012398071 ea2=162.031577674707 ea3=29.330729822566 \\
xis_rmffile=/FTP/caldb/data/suzaku/xis/cpf/ae_xi0_20060213.rmf \\
outfile=sim_x0.fits phafile=allarea.pi

Notes:

• In this example, we supply the name of the event file after screening (cleaned.evt) as the ``gtifile'' parameter value, and use a spectral file made from cleaned.evt (allarea.pi) as the ``phafile'' value (this is used by xissim to determine the observation mode, such as the window and the spaced charge injection options; cleaned.evt would also work).
• The Euler angles (ea1, ea2 and ea3 parameters) are used if, any time during the specified good time intervals, the attitude file does not have data. These can be obtained from the header keywords MEAN_EA1, MEAN_EA2, and MEAN_EA3 in the event file.
• The value of the ``exposure'' parameter should be equal to (or an integer multiple of) the actual exposure time of the observation, to consider the effect of the attitude wobbles correctly. Increase the value of the ``photon_flux'' if more photons are needed.
• In the above example, simulation is carried out for a single energy (spec_mode=1) of 2.45 keV (energy=2.45). To consider a range of photon energies, change spec_mode to 0, and supply a QDP file of the spectral model (``qdp_spec_file''), which can be created in XSPEC with ``iplot model'' command.

Note that the output file has only $\sim$10% of the seed photons. This is because most of the photons are absorbed or blocked by mirrors or instruments.

6.7.3 Extracting a flat field image using xselect

The simulated events created by xissim have the STATUS information, which describes the quality of each simulated photon. Thus the simulated event files should be screened using the same STATUS criteria as was used for the observed events (see Table6.2).

Then the flat field image can be extracted in xselect, making sure that the same XY binning as the observed image is used.

6.7.4 Smoothing the flat field image (optional)

It is difficult to avoid statistical fluctuation in a simulated flat field map, so it is often desirable to smooth the map using, e.g., ximage or ds9. We assume that the flat field map has been smoothed, with the file name flatfield_smo.img.

6.7.4.1 Trimming the flat field map (optional)

A smoothed map generally has rough edges, so it is useful to trim such a map with a masking image, which can be done using xisexpmapgen.

> xisexpmapgen expmap.img cleaned.evt ae102002010.att

Here ae102002010.att is the attitude file, and cleaned.evt is used as the value of the ``phafile'' parameter to supply XIS mode (such as the window option).

The output file (expmap.img) contains two maps; a mask image in detector coordinates in the 1st extension and an exposure map in sky coordinates in the 2nd extension. Here, we generate a mask image in sky coordinates, and so use the image in the 2nd extension.

By displaying the 2nd extension, one can empirically determine a good threshold for masking. For a threshold of 5000 s, for example, use:

> fimgtrim infile=expmap.img\[2\] threshlo=5000 threshup=5000 \\
const_lo=0 const_up=1 outfile=skymaskmap.img

This produces a masking image, called skymaskmap.img. This may have to be rebinned to match the binning of the exposure map (by default, xselect bins Suzaku images by a factor of 8), before multiplying with the smoothed flatfield image.

> fimgbin skymaskmap.img skymaskmap_8bin.img 8
> farith flatfield_smo.img skymaskmap_8bin.img flatfield_smo_trim_8bin.img "*"

6.7.5 Applying the flat field image

> farith input.img\[0\] flatfield_smo_trim_8bin.img input_vigcor.img "/"

The above produces a vignetting corrected image. The flat field image can be scaled to make it a true effective exposure time map, although the normalization depends on the purpose of such an operation.

Depending on the scientific objectives, it may well be desirable to subtract particle, cosmic X-ray, or Galactic X-ray background from the observed image before dividing by the flat field.

6.8 Initial Processing: the details

The remainder of this chapter describes the details of the initial processing for the XIS. These steps, already performed in the processing pipeline, can be repeated by users if necessary.

6.8.1 Calculating Sky Coordinates

xiscoord combines the position of the observed counts on the XIS detector with the orbit and attitude information to calculate the ACT, DEC, FOC and sky X/Y values for XIS event files. xiscoord uses either the attitude file assigned on the basis of the event input file name (the default), or fixed Euler angles if the parameter attitude is set to EULER. The RA and DEC used by the program can be either read from the header of the input event file or set manually.

In this case the command is:

xiscoord infile=filename_uf.evt.gz outfile=xiscoord_outfile.fits \
attitude=DEFAULT pointing=KEY

where
infile is the XIS event fits file name.
outfile is the name of the output file created - see caveat below
attitude indicates where to get the attitude information
pointing indicates where to read the RA and Dec - a pointing set to KEY reads them from the header of the input event file
Users should be aware of the following points: 1) When the attitude parameter is set to ``Default", the code searches for a file named ***.att in the SAME directory as the input file. This can be bypassed by specifying the full path to the file on the command line.
2) We have found that xiscoord does not produce output files on several unsupported plateforms (Mandrake 10,..). Users are advised to check the supported plateforms (see http://heasarc.gsfc.nasa.gov/docs/software/lheasoft) and run only on a supported platform.

6.8.2 Put Pixel Quality

xisputpixelquality runs on the output of xiscoord

The command is:

xisputpixelquality xiscoord_outfile.fits xisputpixelquality_outfile.fits

where
infile is the XIS event fits file name (output from xiscoord)
outfile is the name of the output file created

Hidden parameters, badcolumfile and calmaskfile, should point to CALDB. Users may want to examine the differences (if any) between the input and the output files of xisputpixelquality.

6.8.3 Computing the PI for XIS events

As its name indicates, the xispi routine calculates the XIS PI and grades values from the PHAs. In addition to the input event file, the routine needs the CALDB files ae_xi[0-3]_makepi_[date].fits and the housekeeping file associated with the input event file. If the CALDB option is not set properly and the file has to be input manually, users should check which is the latest ``makepi" file to be used. The command to run xispi is:

xispi infile=xisputpixelquality_outfile.fits outfile=xispi_outfile.fits =
hkfile=HKFILE.fits makepifille=CALDB

where
infile is the XIS event fits file name.
outfile is the output file name.
hkfile is the House Keeping file located in the xis/hk directory. This is not the hk file from the auxil directory
makepifile is a hidden parameter, set by default to CALDB.

6.9 Standard Screening

Both bad pixel filtering and grade selections are done by the processing pipeline and implemented in the cleaned files distributed to the users. Users can find a complete example of filtering at: http://lheawww.gsfc.nasa.gov/users/kaa/xselect/suzaku.html. In addition, we provide an xselect command file and files containing event and mkf selection expressions via:
http://suzaku.gsfc.nasa.gov/docs/suzaku/analysis/sci_gain_update.html. We explain the steps below.

6.9.1 Bad pixel filtering

The cleaning of hot and flickering pixels is done in cleansis and available as a standalone script at the GOF website http://suzaku.gsfc.nasa.gov. cleansis was originally written for analysis of the ASCA SIS data and removes hot and flickering pixels based on a Poissonian analysis. It has since been adapted for work on SWIFT and Suzaku . This generalized version is available in all releases after 6.0.6 of HEAsoft. Users should make sure that their version of HEAsoft is current.

To run cleansis on Suzaku XIS event files type from the command line cleansis chipcol=SEGMENT, give the input and output filenames and use the default values of the remaining parameters.

6.9.2 Grade Filters

The GRADE column shows the event grade, which is determined from the distribution of pulse heights among the 5x5 (or 3x3 or 2x2) pixels. The standard spectral responses provided by the XIS team will assume GRADE 0,2,3,4, and 6. You may select only events with these grades (within the xselect task):
select event "GRADE==0||GRADE==2||GRADE==3||GRADE==4||GRADE==6" or equivalently filter grade "0,2-4,6"

The Suzaku instrument teams recommend the following cuts be applied within xselect.

select mkf  "SAA_HXD==0 && T_SAA_HXD>436 && ELV> 5 && DYE_ELV>20" \ 
mkf_name=MKF_filename  mkf_dir=/path-to-the-MKF-file/

Notes:
1) mkf_name and mkf_dir should be set automatically by xselect on read events.
2) select mkf command creates a time filter of good times. To actually filter the events, users must then issue the command ``extract events"

Satellites, such as Suzaku launched into low-Earth orbit pass through the South Atlantic Anomaly (SAA). During a passage, the high particle flux makes the instruments unusable. The mkf column SAA_HXD has a value of 0 when the satellite is not in the SAA and so the selection condition is SAA_HXD==0 (this is based on the current extent of the SAA as determined empirically using the HXD data). Even when the satellite emerges from the SAA, the background is still high, the mkf column T_SAA_HXD indicates the amount of time since an SAA passage. For the XIS, T_SAA_HXD can be as low as 60 seconds. However, the HXD background stays high for much longer. The instrument teams have recommended adopting the same condition for both instruments, hence the cut of T_SAA_HXD $>$436 imposed on the XIS data.

The two last cuts are recommended by the instrument teams to reduce the contamination from the Earth's atmosphere. The first is applied to the elevation angle, mkf column ELV, the angle between the target and the Earth's limb. Only data with an elevation angle larger than 5 should be considered. The second concerns the elevation angle from the day Earth rim and helps reduce contamination in the Nitrogen and Oxygen lines from X-rays scattered on the Earth's atmosphere. Users who can ignore the low energy part of their spectrum (below 0.6 keV) may want to explore the possibility of relaxing the cut on DYE_ELV.

Footnotes

... given^6.1

It is also possible to run xisrmfgen without specifying a spectral file; see the help file for details

... criteria^6.2

see http://heasarc.gsfc.nasa.gov/docs/suzaku/processing/criteria_xis.html