5. ``README FIRST" for the Suzaku Data Analysis

5.1 Introduction

This chapter contains the details of the current status of the data analysis. Users should check this chapter to answer the following questions:

• Which significant changes occured to the instruments through the history of the Suzaku mission, and hence what should I expect in the data given the date of observation?
• What significant software changes have been provided by the Suzaku team, and are there useful tools that have become available since the last time I analyzed Suzaku data?
• Which significant calibration changes have been provided by the instrument teams? What are the major remaining calibration issues?

Users should also consult the following web pages:
http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/watchout.html
http://www.astro.isas.jaxa.jp/suzaku/analysis/xis/
which serve a similar purpose to this chapter but may be updated more frequently; and
http://heasarc.gsfc.nasa.gov/docs/suzaku/aehp_proc.html
http://www.astro.isas.jaxa.jp/suzaku/process
for information regarding the processing pipeline; and
http://www.astro.isas.jaxa.jp/suzaku/process/caveats/
which contains the calibration uncertainties.
Furthermore, users are encouraged to contact us via the comment webpage at
http://heasarc.gsfc.nasa.gov/cgi-bin/Feedback.

5.2 On-board Changes

5.2.1 XIS2 Loss

One of the XIS units with an FI chip, XIS2, suffered catastrophic damage on 2006 November 9. Since then, no astronomically useful data have been obtained with XIS2, although some diagnostic mode data are taken. Users should therefore not expect any cleaned event files for XIS2 observations taken after 2006 November 9.

Since December 20, the default telemetry allocation to XIS units have been updated to 3:3:1:3 for XIS0:1:2:3. Observations of bright objects before and after this dates may be affected differently by telemetry saturation.

5.2.2 XIS0 Anomaly

An anomaly occurred in XIS0 on 2009 June 23. In this case the leak charge is confined within a portion of the CCD resulting in a dead area in segment A (ACTX$\sim$80 to $\sim$140). Therefore, an area discriminator (ACTX=70$-$150) is applied, in order to discard pseudo-events due to leak charge. How the leak charge affects the calibration of not only segment A but also the other segments is currently under investigation. Preliminary analysis indicates a very small but a detectable change in the gain of XIS0. Detailed information can be found in the Suzaku memo available at http://www.astro.isas.ac.jp/suzaku/doc/suzakumemo/suzakumemo-2010-01.pdf.

5.2.3 XIS1 Anomaly

The XIS1 showed an anomaly, starting 2009 December 18, some time between 12:50 UT and 14:10 UT. A bright and persistent spot ($\sim$90 pixels in FWHM) suddenly appeared at the end of the segment C in all images taken during day-earth observations, while none was found during night-earth observations. The XIS team believes that the anomaly stems from optical light leaked from a hole in the optical blocking filter created by a micrometeorite hit. The XIS team continues to operate the XIS1 in the same way as before the anomaly. Science observations of soft diffuse emission with low surface brightness might be impacted by data degradation. Possible effects under investigation are: increased inaccuracy of the calibration (flux calibration), increased noise due to optical and UV light, and a decreased rate of effective data recording (due to an increase in spurious events). Detailed information can be found in the Suzaku memo available at http://www.astro.isas.ac.jp/suzaku/doc/suzakumemo/suzakumemo-2010-03v2.pdf.

5.2.4 XIS Spaced-Row Charge Injection (SCI)

The cumulative effect of in-orbit radiation damage creates charge traps in CCDs, leading to an ever increasing charge transfer inefficiency (CTI). This changes the PHA-Energy conversion factor as a function of the number of transfers before the charge can be read out, hence on the position on the CCD. This also degrades the spectral resolution.

The ability to inject charge into the CCD chips has been designed into Suzaku XIS. This can be used to fill the charge traps and therefore ameliorate the effects of the CTI. This operation is called spaced-row charge injection, or SCI:
http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/sci.html. In 2006 September, SCI has been used for selected observations to test its effectiveness. Once this has been confirmed, it was offered as an option to all users in 2006 November. Since 2007 April (Cycle 2 observations), the use of SCI is the default.

With Version 2 processing, this is purely a data quality issue. Users need not take action, since information about the SCI operation is encoded in the CI keyword, which is read by Suzaku FTOOLS as necessary and the appropriate calibration is used. However, users may wish to check the value of this keyword. The value of the CI keyword should be 0 for observations without SCI, and 2 for observations with SCI.

5.2.5 Better SCI for XIS1 starting 2011 May

From the start of the SCI operation, a charge equal to the one produced by a 6keV X-ray photon (``6keV equivalent'') was injected for the FI devices while a smaller amount (``2keV equivalent'') was used for the BI device, XIS1. It has now been shown that with an increased SCI amount of 6keV equivalent for XIS1 the high-energy response improves significantly with no measurable degradation of the low-energy response. Therefore, this change has been implemented for the Normal mode since 2011 June 1st. Other mode options (Window, Burst) will be supported within a few months. Telemetry saturation due to the increased SCI is avoided by the introduction of a new clock pattern masking the charge leakage. A revision of the XIS1 detector response is required, with the release of the new version being foreseen for later in 2011. Further developments will be posted on the Suzaku web pages. More information can also be found in the Suzaku memo available at http://www.astro.isas.ac.jp/suzaku/doc/suzakumemo/suzakumemo-2011-01.pdf.

5.2.6 PIN Epochs: Low Energy Threshold & Responses

The bias voltage on-board and low energy threshold in the ground processing of various subsets of PIN units have been adjusted since launch to reduce noise events. This changes the characteristics of these PIN units in several discrete steps.

With Version 2 processing, data from all PIN units should be analyzed together. However, due to the changes in the bias voltage and the software threshold, response matrices appropriate for the epoch of the observation (see Tab. 7.3 in chapter 7) should be used in spectral fitting.

5.2.7 Additional Attitude Wobble

Since launch, the 3-axis attitude control using the Inertial Reference Unit (IRU) had been done with the combination of IRU-X/Z/S1. On December 18th, 2009, a switch from IRU-S1 to S2 was performed. The IRU-S2 or S1 controls the attitude in the DET-X direction while the IRU-X controls the attitude in the DET-Y direction. Since the switch, the accuracy of the attitude control along the DET-X axis declined by roughly a factor of two, though the behavior is different from observation to observation. The effects listed in the following are among the consequences.

Possible pointing determination errors between December 18th, 2009 and June 15th, 2010: XIS images may be elongated along the direction of the DET-X axis by 1arcmin. The recommended treatment is to:

• Apply the attitude correction tool ``aeattcorr.sl'', see section 5.3.3. It works to reduce the pointing determination error if the target is bright and point-like, producing a sharper image. Caveat: If there is a clear double image of the source this tool cannot be used.
• Choose the extraction region to be as large as possible.

On June 15th, 2010, another gyro, IRU-Y, was activated. The IRU-Y is more sensitive to the attitude of the DET-X direction than is the IRU-S2. Now the IRU-S2 is used for attitude control, and the IRU-Y for attitude determination. The pointing determination error will generally be back to what it had been before December 18th, 2009.

Possible flux variations of the XIS data taken after Dec 18th, 2009: The pointing direction is corrected on the ground to within the calibration uncertainties. The calibration error of the pointing direction correction is larger for the data taken between December 18th, 2009 and June 15th, 2010 (see above). The image is reconstructed before the data are distributed to the users. But even in the attitude corrected data the count rate of the XIS detectors might vary by up to a few tens of percent. The variability is larger for off-axis sources because the variability results from a change of the effective area, where the XRT vignetting function is smooth on-axis while sharp off-axis (suzakumemo 2008-05). The count rate varies with the 96min satellite orbit. The recommended treatment is to:

• Spectral analysis: run the arf generator xissimarfgen with the attitude(=???.att) option. The xissimarfgen tool calculates the variation of the effective area and produces an arf file that takes the effective area variation into account.
• Temporal analysis: use the xissim tool with attitude and gtifile options to simulate the effective area variation. A recipe for correcting the light curves will be announced in the future.

Photometry using XIS1 with a window option: The arteficial flux variation described above is most pronounced for the XIS1, especially when operated with a narrow window option such as 1/4 or 1/8 and/or at the HXD aimpoint. The inaccuracy in the attitude control along the DET-X axis is larger than along the DET-Y direction since December 18th, 2009. Unfortunately, the narrower boundary of the window option is set on the DET-X axis for XIS1 (and the inoperable XIS2) while it is on the DET-Y axis for the others (XIS0 and 3).

Detailed information and example images can be found in the Suzaku memos available at http://www.astro.isas.ac.jp/suzaku/doc/suzakumemo/ (2010-04, -05, -06).

5.3 XIS Software Tools, Recipes

5.3.1 Reprocessing and Screening: Aepipeline

Since 2010 the FTOOL aepipeline is available. It can be used to apply the newest energy calibration, as well as to perform data screeening for both XIS and HXD data. See section 6.4 for more information on using aepipeline for XIS data.

5.3.2 Cleansis Runaway Problem

The FTOOL ``cleansis'' is applied in Suzaku data processing, when going from the unscreened (in the event_uf subdirectory) to the cleaned (event_cl) event files. When users reprocess data (e.g., to apply a new gain calibration), it is generally recommended to start with unscreened data, and the use of cleansis is one of the recommended screening steps. This tool was originally written for the ASCA SIS. Its algorithm is inherently statistical: it examines the distribution of the number of counts per raw detector pixels, and rejects those that have far more counts than likely. This step is usually repeated to eliminate lower level flickering pixels.

The versions of cleansis in HEAsoft v6.7 and earlier occasionally suffer from a runaway problem, creating a hole in the XIS data near the peak of the image. Users who encounter such a hole should first check if one is present in the unscreened event data. If this is the case, this is most likely due to a severe case of photon pile-up and is unrelated to cleansis. If, on the other hand, the hole is seen only in the cleaned data, cleansis is the likely cause.

The version of cleansis available since HEAsoft 6.8 incorporates an improvement in the algorithm which greatly reduces, if not completely eliminates, instances of such runaways. Alternatively, there are two run-time parameters that can be adjusted to reduce or eliminate this problem:

• The runaway problem only occurs when iteration is applied. The user can set iterate=no to avoid it (default: yes).
• The default probability is set to a level such that the number of non-flickering pixels that are incorrectly eliminated (due to statistical fluctuations) is approximately one per XIS segment. The probability (default: $logprob=-5.2$) can be lowered (to, say, $logprob=-7.2$).

Both these methods can prevent the runaway, at the possible cost of retaining some low-level flickering pixels in the screened data.

5.3.3 Improved Attitude Correction and Pile-Up Estimation

Section 6.7 provides a general description of the pile-up effect and gives typical count rate ranges that can be observed with minimal pile-up (Fig. 6.3). Here, two externally contributed routines, aeattcor.sl and pile_estimate.sl, are introduced, which were especially designed to aid in the analysis of Suzaku data that might be afflicted by photon pile-up. Both are scripts written in S-lang and are designed to be run on the command line using ISIS, the Interactive Spectral Analysis System, as a driver. Both utilize a number of S-Lang Modules Packages. For all intents and purposes, the scripts behave similar to typical Unix command line tools. They are available from http://space.mit.edu/ASC/software/suzaku/.

The tool aeattcor.sl further improves the attitude correction for the slow wobbling of the optical axis for bright sources by using their detected image to create a new attitude file. Note that this tool cannot be used if a clear double image of the source is visible in the image. pile_estimate.sl is designed to be run after aeattcor.sl. It will create an image that will show an estimated, minimum pile-up fraction for user specified levels. This allows the user to create a region file that excludes the most piled areas, and then estimate the effective pile-up fraction of the remaining events.

5.3.4 Exposure Maps, Vignetting Correction

For the study of extended sources with the Suzaku XIS, it is necessary to know the exposure times as well as vignetting at various sky locations within the XIS image. One type of exposure maps 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 $^{55}$Fe calibration source area. For the other type, the effective exposure times per sky pixel are calculated, taking into account the vignetting of the XRT. A detailed description can be found in section 6.9 of the XIS chapter and at http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/expomap.html. It consists of the following steps:

• Simulating an event file using xissim.
• Extracting a flat field image using xselect.
• Smoothing and trimming the flat field image (optional, e.g., using ximage or ds9, and xisexpmapgen, fimgbin, fimgtrim, farith).
• Applying the flat field image using farith.

5.3.5 XIS Non X-Ray Background Estimation

Before Suzaku FTOOLS Version 7, the tool mk_corweighted_bgd_v1.1.pl and the data set of night Earth observations released from the XIS team were used to estimate the non X-ray background (NXB).

With Suzaku FTOOLS Version 7, which was a part of HEAsoft v6.4 released in December, 2007, the tool was upgraded to xisnxbgen and was released as one of the official FTOOLS. The NXB database was released as a part of the official Suzaku CALDB.

Now users should use xisnxbgen with the Suzaku CALDB instead of mk_corweighted_bgd_v1.1.pl to estimate the NXB. The tool mk_corweighted_bgd_v1.1.pl is now obsolete. The FTOOLS help document and section 6.8.1 give detailed information about xisnxbgen.

5.3.6 XIS Burst Option Exposure Times

The XIS team has released a version of xistime allowing to apply the option ``bstgti=yes'' as part of the Suzaku FTOOLS V14 in HEAsoft v6.8. This produces detailed good time intervals (GTIs). Previously, the GTIs of the XIS event files did not contain the detailed GTI information for burst mode data (e.g., one line for each 2 second exposure separated by 8 seconds). This led to inaccuracies in the exposure times after data filtering.

Note that the GTI extension may then contain a large number of rows, potentially causing problems in down-stream software. Also note that this option works even when the data were taken without burst mode, but in this case its application is not recommended.

5.3.7 Timing Mode

From AO-5 on, the Timing mode is used for a restricted numbers of observations, with a total exposure of less than 5% of the total observing time. However, the calibration accuracy of the Timing mode remains worse compared to the normal mode, and there are some operational restrictions. A recipe for reducing Timing mode data can be found at http://www.astro.isas.jaxa.jp/suzaku/analysis/xis/

Due to comparably large numbers of hot/flickering pixels in the BI CCD, which would lead to telemetry saturation, and due to increased charge leakage in XIS0 in the Timing mode since the 2009 anomaly, the Timing mode is available only for XIS3. Since only one dimensional information is available in the Timing mode, the distinction between X-ray and non-X-ray events becomes inaccurate. This means that the Timing mode has a significantly higher non-X-ray background than the Normal mode. Preliminary analysis showed that the non-X-ray background in the Timing mode is one or two orders of magnitude larger than in the Normal mode. Because the available data are limited, its detailed behavior, e.g., dependence on the cut-off rigidity, is not known.

The in-flight calibration of the Timing mode is on-going and is expected to improve in the near future. However, it will not reach that of the normal mode, because (1) the Spaced-row Charge Injection (SCI) is not available on board and (2) the CTI correction is difficult in the ground processing. The updated calibration information of the Timing mode will be released as part of the CALDB. Unavailability of the SCI or the CTI correction means that the energy scale and resolution are significantly different from those of the normal mode. Preliminary analysis showed that the gain was lower than the nominal value by $\sim$10% and the energy resolution had degraded to $\sim$5% at 5.9 keV in early 2009. The former may be corrected if appropriate calibration information becomes available, but the latter not.

In addition, the effective area of the CCDs may change in the Timing mode: even a small number of hot pixels produces a relatively large dead area in the CCD, which reduces the effective area. This reduction could be time dependent, because some of the hot pixels often disappear and reappear. It should be noted that the accuracy of the ARF file may also be degraded, because we need to use a rectangular extraction region for the Timing mode.

The nominal time resolution in the Timing mode is 7.8ms, but this depends on the image size of the X-ray source. If the X-ray image is much larger than 128 pixels ($\sim$2arcmin) along the Y-address, the time resolution may become worse than 7.8ms. Because the Y-address represents the photon arrival time in the Timing mode, the image extension (in the Y-direction) works as a low-pass filter. This means that, even for a point source, some signal is leaked to the adjacent time bins due to the tail of the XRT PSF. Therefore, the frequency response is somewhat reduced near the Nyquist frequency of the nominal time resolution of 7.8ms.

5.4 HXD Software Tools, Recipes

5.4.1 Reprocessing and Screening: Aepipeline

Since 2010 the FTOOL aepipeline is available. It can be used to apply the newest energy calibration, as well as to perform data screeening for both HXD and XIS data. See section 7.4 and 7.6.3 for more information on using aepipeline for HXD data.

5.4.2 HXD Spectra and Lightcurves: Extraction Tools

Since 2010 a set of FTOOLS is available that can be used to extract PIN (hxdpinxbpi, section 7.5.6) and GSO (hxdgsoxbpi, section 7.7.2) spectra, as well as PIN (hxdpinxblc, section 7.8.1) and GSO (hxdgsoxblc, section 7.9.1) lightcurves. These tools also perform additional tasks like background extraction or deadtime correction where necessary. See fhelp texts for these tools or sections indicated in the previous sentence for more detailed information.

5.5 XIS Calibration Updates

5.5.1 Contamination Model $\leq$ Suzaku FTOOLS Version 17

Figure 5.1: An empirical model for the on-axis contamination evolution, assuming DEHP (C$_{24}$H$_{38}$O$_4$, or C/O=6 by number) as contaminant. Crosses indicate the C column density of the contaminant derived from the E0102$-$72 observations. Solid lines indicate the best fit C/O=6 empirical model to the time evolution of the contamination for each sensor. Note that an updated contaminant composition is in use since Suzaku FTOOLS version 18 (section 5.5.2), an update of this figure is in preparation.

In late November 2005, contamination in the optical path of each sensor became apparent. Spectra of celestial sources show that the contaminant is predominantly carbon. Monitoring of 1E 0102.2-7219 and RX J1856.5-3754 shows that the contamination is increasing at a different rate for each sensor leading to an equivalent additional column density of C of $\sim 4.5-7 \times 10^{18}$cm$^{-2}$ (as of Jul 2009; see Fig. 5.1).

Observations of the bright earth show that the contaminant is twice as thick at the center of the field of view than at the edge, a pattern that tracks the temperature distribution on the optical blocking filter (OBF). This suggests that the contaminant is on the spacecraft side of the OBF, rather than on the CCD detector surfaces.

Intitial studies suggested that the contaminant is mainly DEHP (C$_{\rm 24}$H$_{\rm 38}$O$_{\rm 4}$, or C/O=6 by number). While the C/O = 6 description has been used for calibration up to Suzaku FTOOLS version 17, continued study of the material's exact composition by the XIS team allowed for the implementation of a further fine-tuned model with Suzaku FTOOLS version 18, see section 5.5.2 below.

The ARF generator xissimarfgen takes the contamination effect into account. That is, the ARF calculated with xissimarfgen by default includes transmission through the contaminant. For Suzaku FTOOLS Version 17 this corresponds to CALDB file tags 20081023 [XIS1, 2, 3] and 20090128 [XIS0] taking data up to March 15, 2008, and December 14, 2008, into account, respectively. Transmission values beyond those dates are extrapolated. Note that Suzaku FTOOLS Version 17 is not compatible with any newer CALDB contamination files than the ones quoted here, i.e., not with those used for the new contamination model described below.

The FTOOL xiscontamicalc is handy for determining contaminant transmission values at specified detector coordinates and dates, and for manually changing transmission information in an ARF file.

5.5.2 Contamination Model $\geq$ Suzaku FTOOLS Version 18

Figure 5.2: Comparison between spectral fits using the old (left panel; C/O=6; Suzaku FTOOLS Version 17 and earlier) and new (right panel; C, O, H variable; Suzaku FTOOLS Version 18 and later) contamination composition model. Residuals at soft energies, especially in the 0.4-0.5keV band, improve with the new model.

For a general introduction to XIS contamination modeling see section 5.5.1 above. With Suzaku FTOOLS Version 18 an improved contamination model has been released. While the spatial dependence is same as the previous version, the elemental composition (C, O, H) of the contamination is now variable allowing for more accurate spectral modeling, especially in the 0.4-0.5keV energy range.

As for the old C/O=6 model, the ARF generator xissimarfgen takes the contamination effect into account for the new model. That is, the ARF calculated with xissimarfgen by default includes transmission through the contaminant. For Suzaku FTOOLS Version 18 this corresponds to CALDB file tag 20091201 [XIS0-3] taking data up to June 26, 2009, into account. Transmission values beyond those dates are extrapolated. Note that Suzaku FTOOLS Version 17 is not compatible with these new CALDB contamination files, only with earlier ones, while Suzaku FTOOLS Version 18 can handle both.

The FTOOL xiscontamicalc is handy for determining contaminant transmission values at specified detector coordinates and dates, and for manually changing transmission information in an ARF file.

5.5.3 XIS Reprocessing History

Table 5.1 gives a list of revisions of the makepi CALDB files that are used in the processing pipeline since V2.1.6.13:

Table 5.1: Revisions of the makepi file.

CALDB Update	File Name	Comments
2007-06-27	ae_xiN_makepi_20070611.fits
2007-07-31	ae_xiN_makepi_20070730.fits
2007-11-01	ae_xiN_makepi_20071031.fits	Important for SCI-on$^a$
2008-02-01	ae_xiN_makepi_20080131.fits
2008-09-05	ae_xiN_makepi_20080825.fits	Important for SCI-off $2\times2^b$
2009-08-13	ae_xiN_makepi_20090615.fits
2010-02-18	ae_xiN_makepi_20091202.fits
2010-11-08	ae_xiN_makepi_20100929.fits

$^a$ http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/sci_gain_update.html

$^b$ http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/watchout.html

The energy scale calibration for both SCI and non-SCI data is included in Version 2 processing, and in general achieves an accuracy of 0.2% at 6keV.

Significant makepi updates will continue to be annouced on the Suzaku GOF web pages.

For window mode data only the Suzaku FTOOLS Version 12 xispi or later should be used to perform the reprocessing, see
http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/xis_window.html for details.

5.5.4 Energy Scale for SCI Data

The XIS team constantly updates CTI and gain calibration of XIS data taken with SCI (Table 5.1). Note that cleaned data from processing Version 2.1.6.15 or earlier suffer from time and energy dependent effects in energy scale calibration, and should therefore be reprocessed. This can be done by running xispi on unscreened files (running it on screened files will lead to inaccurate results, since new calibration changes the event grades, which are used for screening). The updated files must then be screened to produce new cleaned files. See: http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/sci_gain_update.html for more detailed instructions. Also see section 5.3.1 above for the introduction of a high-level script for both, reprocessing and screening.

5.5.5 Energy Scale for SCI-Off Data of 2006

For some non-SCI data taken in 2006, the energy scale calibration is noticeably worse than stated above. Discrepancies of up to 40eV have been noticed among different XIS units.

5.5.6 Energy Scale for Window Option Data

A discrepancy in the energy scale of window option data compared to the full window data has been resolved with an xispi update in Version 12 of the Suzaku FTOOLS by incorporating a CTI correction formula that takes the two types of charge transfer into account. With this, the energy scale of the FI and BI data in 1/4 window mode with SCI-off are in agreement to within $\pm20$eV at 6keV with that of the full window mode (before 40eV for the FI CCD and 60eV for the BI CCD). For the SCI-on data good agreement between the full window and the 1/4 window modes has subsequently been shown as well.

5.5.7 Energy Scale for $2\times 2$ Editing Mode Data

For SCI-off data there was an offset in the $2\times 2$ mode energy scale relative to the $3\times3$/$5\times5$ modes. This is believed to have been fixed with the release of the ae_xiN_makepi_20080825.fits files in 2008 September. Users should apply the new calibration using the same procedure as for SCI-on data processed with V2.1.6.15 or earlier.

The energy scale for $2\times 2$ mode with charge injection is expected to be similar to those of the $3\times3$/$5\times5$ modes. However, this expectation has not yet been verified with actual calibration. Users of $2\times 2$ mode data with SCI should carefully check for gain discrepancies before combining $2\times 2$ events with $3\times3$/$5\times5$ events. Note that $3\times3$ and $5\times5$ events can generally be combined.

5.5.8 Calibration Uncertaincies near 2keV

Figure 5.3: Example for typical residuals around 2keV due to instrumental effects (blue: BI - XIS1, red, combined FI - XIS0+3), with respect to a smooth continuum fit (top) and modeled with two Gaussian lines (bottom), see text for line energies (Suchy et al., 2011, ApJ, 733, 15.

Spectral modeling residuals that are often seen in the 1.7keV to 2.3keV region, especially for bright sources, are probably due to imperfect calibration of the instrumental Si K edge at $\sim$1.8keV (and maybe some influence of imperfect calibration of the instrumental Si K-alpha fluorescence line at $\sim$1.7keV as well) and the Au M edge at $\sim$2.2keV. This issue is currently being investigated by the XIS team. An example is shown in Fig. 5.3, where residuals of a spectral fit to data from a 500mCrab bright outburst of the accreting pulsar 1A1118$-$61 are displayed (Suchy et al., 2011, ApJ, in press [arXiv:1103.1370]), for a smooth continuum model (top) and a model with two additional Gaussian lines (bottom) at 1.82$\pm$0.01keV (BI, ``emission'') or 1.89$\pm$0.01keV (FI, ``absorption'') as well as 2.21$\pm$0.01keV (BI and FI).

5.5.9 XRT/XIS Effective Area

The 2008-07-09 release of the Suzaku CALDB contains an updated calibration of the XRTs and the corresponding updates to the XIS quantum efficiency files, while the Suzaku FTOOLS release Version 8 contains updates of the raytracing library used by the xissim and xissimarfgen response generator tools (older versions of these tools do not work with the new calibration files, while the new version of the raytracing library is backward compatible with the older calibration files). The new calibration can be applied without reprocessing the event data. The only requirement is to re-generate the response files using xisrmfgen and xissimarfgen.

As part of this release the vignetting and imaging calibrations have been updated. The geometry parameters for each quadrant of each XRT have now been individually adjusted. As a result, the calibration of the point-spread function (PSF)/encircled energy function (EEF) has improved, particularly beyond 2arcmin from the image center. The simulated EEF now coincides with the observed values within 4% from 1 to 6arcmin radius.

The combination of the XRT and XIS calibration changes regarding the effective area is such that, for observations at the XIS nominal position, analyzed using a large (e.g., 250 pixel radius) extraction region, changes are relatively small. Note, however, that the relative normalization for the PIN data is now 1.16 and 1.18 for the Crab nebula observed at the XIS and HXD nominal positions, respectively (with estimated errors of 0.015). Note also that the changes in the EEF and in the vignetting calibration affect the effective area calibration as a function of source location and extraction region radius. Be advised that effective area calibration may have changed significantly for some extraction regions.

5.6 HXD Calibration Updates

5.6.1 PIN Energy Range

With the current PIN response matrices of all epochs, systematic uncertainties of 5% and 3% remain in the $12-15$keV and the $>15$keV range, respectively. The HXD instrument team recommends to ignore data below 15keV. The energy scale of individual PIN diodes is under study in order to fine-tune the response matrix.

5.6.2 GSO Gain Calibration

Figure 5.4: HXD-PIN (black) and HXD-GSO (red) spectra and fit residuals for the Crab as observed on 2005 Sep. 15 using the nominal HXD pointing position. The adopted model is wabs$\times$bknpowerlaw, with $N_{\rm{H}}$=3.8$\times$10$^{21}$cm$^{-2}$, photon indices of 2.09 and 2.27, a break energy of 103keV, and a nomalization of 10.9photos keV$^{-1}$ cm$^{-2}$ s$^{-1}$ (at 1keV). To illustrate the effect of the correction arf file, fit residuals without applying the file are displayed as well (blue). The 20% difference of the 70-400keV flux between the data and the model without the arf and the bump-like residual around 50-70keV due to calibration uncertainties around the Gd-K edge are reduced by introducing the correction arf file, resulting in better agreement with the HXD-PIN spectrum.

On 2010, March 29, the HXD team has released updated software (as part of the Suzaku FTOOLS version 16 within HEAsoft v6.9) as well as calibration files (as part of the HXD CALDB release 20100323), implementing a revised gain calibration of the HXD-GSO data. This extends the low energy limit of the usable GSO data from 70keV down to 50keV. Note that a new type of CALDB gain history calibration file, new non X-ray background files, and new response $+$ correction arf files have to be applied (Fig. 5.4). One of the most important differences in the analysis is that instead of the old type of GSO gain calibration file, ae_hxd_gsoght_YYYYMMDD.fits, the new type, ae_hxd_gsogpt_YYYYMMDD.fits, has to be used with hxdpi. Details are described by Yamada et al., 2011, PASJ 63, No. 5, and at
http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/gso_newgain.html and
http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/gso_newarf.html.
Support for the old software/calibration/backgrounds for new observations has stopped for observations from 2010 spring onwards. However, older observations can be reduced with both, the new and the old set up, the latter by using hxdpi_old in Suzaku FTOOLS version 16+, instead of hxdpi, for reprocessing.

Figure 5.5: Relative flux normalization between different XIS sensors. The ratio of the best-fit normalization values are compared between two sensors at the XIS and the HXD nominal positions. Observations of a power-law source in the Normal clocking mode were used. The best-fit constant values are indicated by solid lines.

5.7 Cross Calibration

5.7.1 Flux Cross Calibration: XIS0,1,3

Table 5.2: Relative flux normalization between different sensors.

Position	Ratio	Mean	Standard deviation
XIS-norm	XIS1/XIS0	1.026	0.016
	XIS3/XIS0	1.014	0.017
HXD-norm	XIS1/XIS0	1.004	0.019
	XIS3/XIS0	0.980	0.022

The stability of the relative flux normalization between the three XIS sensors is shown in Fig. 5.5. No significant time dependence is found. The relative normalization remains constant. The mean and standard deviation are summarized in Table 5.2, separately for the XIS and HXD nominal positions.

5.7.2 Flux Cross Calibration: XIS and HXD

Observations of the Crab have been used to study the cross-normalization of XIS and HXD. With Version 2 processed data, the normalization of PIN data relative to XIS0 data is currently 1.16 for observations at the XIS nominal position, and 1.18 for those at the HXD nominal position (with estimated errors of 0.015).

The normalization of the GSO relative to the PIN was found to be $\sim0.8$. This discrepancy can be considerably reduced with the temporary workaround of applying the GSO ``correction arf'' in addition to the standard arf, see
http://heasarc.gsfc.nasa.gov/docs/suzaku/analysis/gso_newarf.html.

Cross normalization factors should be taken into account in joint spectral fits of XIS and HXD data.

5.7.3 Flux and Spectral Shape Cross Calibration: Multi-Mission

See, e.g., Tsujimoto et al., A&A, 525, 25 (2011).