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Last modified: December 2013

URL: http://cxc.harvard.edu/ciao/ahelp/mkgarf.html
AHELP for CIAO 4.9

mkgarf

Context: tools

Synopsis

Generate a Chandra Grating ARF for one detector element.

Syntax

mkgarf  asphistfile outfile order sourcepixelx sourcepixely engrid
obsfile osipfile maskfile detsubsys grating_arm pbkfile [mirror]
[dafile] [ardlibparfile] [geompar] [verbose] [clobber]

Description

The grating ARF (auxiliary response function) is a table of effective area vs. energy for a specific observation. It depends upon the observational details through the aim-point, which determines where the mean chip-gap locations are in the spectrum, and through the aspect, which moves the image around on the detector.

This program computes the ARF for a single detector element. Multiple ARFs can be combined with dmarfadd. There is also the fullgarf script, which makes the grating ARF for an observation (including asphist and mkgarf for each chip, followed by dmarfadd).

The mkgarf program generates an ARF file in standard format accepted for use in spectral analysis packages such as xspec or sherpa. It requires a parameter file and an aspect histogram as its minimum set of input files. Additionally, the energy grid may be specified via a grid parameter, an ASCII file, or by reference to a grating RMF. A scale factor due to order-sorting clipping of the PHA can be applied through the OSIP (Order Sorting, Integrated Probability) file parameter.

The detailed definition of a grating ARF is beyond the scope of this document. The reader is referred to Davis (2001) for its definition and its use in spectral analysis.

Calibration information (QEs, effective areas, bad pixels) is computed by the ARDLIB software library that is linked to mkgarf. ARDLIB has its has its own parameter file, ardlib.par, which contains more than 50 parameters. Consult the ARDLIB documentation for information about specific ardlib.par parameters.

Although this program may be used to compute a type of zeroth order grating ARF, its use is not recommended for this purpose. Instead, the user should use the `mkarf' program.

While the output product is back-compatible with existing software and formats, we have extended the format to add some grating-specific content. The table's columns are:

Col Num Name Unit Type
1 ENERG_LO keV Real4
2 ENERG_HI keV Real4
3 SPECRESP cm**2 Real4
4 BIN_LO angstrom Real4
5 BIN_HI angstrom Real4
6 FRACEXPO 1 Real4

The BIN_LO and BIN_HI columns are CXC additions; they are by default filled with the bin wavelengths in Angstroms (which is usually a linear coordinate). FRACEXPO is also a CXC addition. It is the fraction of the exposure on good detector area (without dither, it would be 1.0 on good pixels, 0.0 for bad pixels or coordinates off the detector). FRACEXPO is required by pileup modeling programs.

The file header contains keywords identifying the grating, order, and zero-order source; for example:

GRATING HETG String Grating
TG_SRCID 0 Int4 source index
TG_M 1 Int4 Grating Order
TG_PART 2 Int4 MEG(2), HEG(1), or LEG(3)

Note that mkgarf operates on one chip at a time. These individual responses are then weighted and added by dmarfadd. A shell script is available (fullgarf) which run the chip-dependent programs (asphist, mkgarf), and combines the responses into one ARF (superseded scripts are mkgarf_hetgs and mkgarf_letgs).

Example 1

mkgarf detsubsys="ACIS-S1" outfile="acis_s1_garf.fits"
engrid="grid(acis_grmf.fits[2][cols ENERG_LO,ENERG_HI])"
obsfile=evt2.fits dafile=NONE order=-1
asphistfile="acisf01318_ah5.fits[ASPHIST]"

Compute a grating ARF for order -1 on ACIS-S1 on an energy grid defined in acis_rmf.fits (in particular columns ENERG_LO and ENERG_HI of the second block in the file) and write it to acis_s1_arf.fits.

Example 2

mkgarf detsubsys="ACIS-S2" outfile="acis_s2_garf.fits"
engrid="grid(acis_s2_grmf.fits[2][cols ENERG_LO,ENERG_HI])" order=-3
asphistfile="acisf00459_ah6.fits[ASPHIST]" obsfile=evt2.fits
dafile=CALDB

Compute a grating ARF for order -3 on ACIS-S2. The dafile parameter is set to apply the dead area correction.

Example 3

mkgarf detsubsys="ACIS-S4;QUADRANT=1" outfile="acis_s4q1_arf.fits"
dafile=NONE engrid="0.1:10.0:0.01" obsfile=evt2.fits

Compute a grating ARF for use with events that fall into the first quadrant. The last example illustrates the use of ARDLIB qualifiers or options. In particular, this causes the QE computed by ARDLIB to be 0 for pixels not in the first quadrant of ACIS-S4. The energy grid runs from 0.1 keV to 10.0 keV in steps of 0.01 keV.

Example 4

mkgarf detsubsys="ACIS-S2;contam=no"
outfile="acis_s2_nocontam_arf.fits" dafile=NONE engrid="0.1:10.0:0.01"
obsfile=evt2.fits

Compute a grating ARF without including the ACIS contamination. This is another example illustrating the use of ARDLIB qualifiers or options.

Parameters

name type ftype def reqd
asphistfile string     yes
outfile string     yes
order integer     yes
sourcepixelx real     yes
sourcepixely real     yes
engrid string     yes
obsfile string     yes
osipfile string     yes
maskfile string     yes
detsubsys string     yes
grating_arm string     yes
pbkfile string input   yes
mirror string      
dafile string input CALDB  
ardlibparfile string      
geompar string   geom  
verbose integer      
clobber boolean      

Detailed Parameter Descriptions

Parameter=asphistfile (string required)

The name of file containing the binned aspect history in the form of an aspect histogram created by asphist.

Note that each ACIS CCD has its own GTI file. This means that each chip will have its own aspect histogram file.

Variations in the the mirror effective area are assumed to be small on the scale of the dither pattern. Hence, the mean aspect offsets will be used to deduce the mirror effective area. This means that the aspect offsets should be small, typically less than 100 ACIS sky pixels (50 arcsec) in magnitude.

Parameter=outfile (string required)

The name of the grating ARF file that this program will generate.

Parameter=order (integer required)

The diffraction order. The magnitude is limited by the orders' efficiencies tabulated in the calibration database grating files. (-11 to +11 for HEG and MEG, and -25 to 25 for LETG).

Parameter=sourcepixelx (real required)

Parameter=sourcepixely (real required)

These parameters specify the (x,y) sky position of the point source, in the appropriate tangent plane pixel system for the detector. This should be the same as the zero-order centroid in the region used by tg_resolve_events for the source, and which are tabulated in the binned spectrum file (`pha2.fits').

Parameter=engrid (string required)

Energy grid specification string. This string may specify either a file or an explicit energy grid. For example, to read a grid from the block MATRIX of an RMF file called rmf.fits, use:

"engrid=grid(rmf.fits[MATRIX][cols ENERG_LO,ENERG_HI])"

To specify an explicit grid running from 0.3 keV to 10.0 keV in 0.01 keV increment steps, use:

"engrid=0.3:10.0:0.01"

To use an ASCII file which contains two columns, the energ_lo and energ_hi, use:

"engrid=grid(myfile.tbl)"

Note that the preferred grid is linear in wavelength, since this reflects the natural dispersion of photons onto the detector. For back-compatibility, we write the grid in energy units in ascending order. To get a linear-wavelength grid, the first or third engrid forms must be used. Energy grids are required to be in ascending order.

Parameter=obsfile (string required)

The name of a FITS file, such as a level 2 event file, containing keywords which specify the mission, detector, SIM offsets, start time, etc.

Parameter=osipfile (string required)

This parameter is used only when computing an ARF for an ACIS chip. Its value specifies the name of the order sorting table used extract nth order counts based upon the spatially dependent PHA fractions associated with the extraction region. "OSIP" stands for "Order Sorting and Integrated Probability". A value of "NONE" may be used to indicate that no such file is to be applied. If "NONE" is used, the it is assumed that the integrated probability is 1.0. The value, CALDB, indicates that the highest version for the most recent date before the observation date will be retrieved from the calibration data base.

Parameter=maskfile (string required)

The mask file (msk1.fits) for the observation. The mask file is needed in particular when a window or subarray was used. A value of "NONE" indicates that no mask file will be applied.

More information on the mask file is available in the CIAO Dictionary.

Parameter=detsubsys (string required)

The value of this parameter is passed to ARDLIB to select a particular detector subsystem so that the appropriate QE can be computed. It specifies the specific chip or MCP of the detector for which the exposure map is to be computed. For Chandra, it must specify one of the following detector subsystems:

HRC-I
HRC-S1, HRC-S2, HRC-S3
ACIS-I0, ACIS-I1, ACIS-I2, ACIS-I3
ACIS-S0, ACIS-S1, ACIS-S2, ACIS-S3, ACIS-S4, ACIS-S5

The following qualifiers or options are supported for these detectors:

QE=value
IDEAL (equivalent to QE=1)
WINDOW=xmin,ymin,xmax,ymax
REGION=BOX(xcenter,ycenter,xsize,ysize)
REGION=RECTANGLE(xmin,xmax,ymin,ymax)

Note that only simple rectangular regions are supported.

For ACIS, one may select filter bad pixels based upon the status column in the bad pixel files by using the BPMASK qualifier:

BPMASK=hex value    (Specified as, e.g., 0x1f9ff)
BPMASK=dec value    (Specified as, e.g., 129535)
BPMASK=FAINT        (=0x1f9ff, 129535)
BPMASK=VFAINT       (=0x1ffff, 131071)

If this option is not present, the default is FAINT.

Parameter=grating_arm (string required)

The grating arm to be used. The value of this parameter must be one of "HEG", "MEG", or "LEG".

Parameter=pbkfile (string required filetype=input)

Deprecated. See below.

Parameter=mirror (string)

For Chandra (a.k.a. AXAF), the mirror parameter must be set to "HRMA". However, the following ardlib qualifiers are also supported:

AREA=value
SHELL=value (possible values: 1,3,4,6)
BITMAP=value

For example, to compute an instrument map for using shells 1 and 3, which corresponds to the bitmap "1100", use "HRMA;bitmap=1100" for the value of this parameter. To compute using a mirror area of 1, use "HRMA;AREA=1".

Parameter=dafile (string filetype=input default=CALDB)

ACIS "dead area" coefficients file, which may have the values "NONE" (no dead area computation), CALDB (for automatic lookup), or an explicit file reference to an ACIS "dead area" coefficients FITS table.

The ACIS dead area refers to a slight decrease in detector efficiency due to the background cosmic ray flux which temporarily renders some pixels useless. The calibration product is a coefficient (per CCD) which gives the fractional area lost (or "deadened") per second. Since the area lost increases with time, the magnitude of the effect depends upon the ACIS clocking parameters (number of rows, window location, frame-time) which determine how long a pixel was exposed to the background cosmic ray flux during the primary exposure and during electronic readout from the frame-store area. For full-frame timed-exposure, the dead area is about 4% at maximum CHIPY and about 2% at the readout. It is smaller for subarrays.

The dafile parameter is ignored for HRC data.

Parameter=ardlibparfile (string)

The name of the parameter file to be used by ARDLIB. Typically, "ardlib.par" will be used.

The parameter file contains only one explicit CALDB parameter (osip). Other such parameters are contained in ardlib.par. This parameter file is selectable using the `ardlibparfile' parameter. Calibration files are specified implicitely via the `DetSubsys' and `Mirror' parameter described below. Most default to CALDB, but can be made explicit for customized use.

Parameter=geompar (string default=geom)

The name of the Pixlib Geometry parameter file.

Parameter=verbose (integer)

The verbosity level for messages.

Parameter=clobber (boolean)

If set to yes, existing output files will be removed.

Deprecation of 'pbkfile' parameter

In CIAO 4.6, the ACIS parameter block file is no longer a required input to this tool. Therefore the 'pbkfile' parameter has been deprecated. The parameter has been retained for now but it is non functional.

This change is made possible by a series of header keyword updates that were made in Chandra standard data processing and are replicated in the chandra_repro script. Four new keywords: SUM_2X2, FEP_CCD, ORC_MODE, and OCLKPAIR have been added to the standard ACIS event file, that, in addition to existing keywords, provide the tool the information needed for the ACIS Dead Area calibration.

These keywords are required to use this tool in CIAO 4.6. Data from the archive with ASCDSVER newer than DS8.4.2 will already have these keywords. This will be the default for all but a few early observations. Users with data that was created prior to ASCDSVER=8.4.2 will need to follow one of these paths to use CIAO 4.6.

  • Retrieve most recent data from Chandra archive. All but a few datasets in the Chandra archive have been reprocessed to include these keywords (the earliest observations). The last bulk reprocessing included several updates including corrections for aspect "drift" within an observation as well as updated timing information. A summary of the updates can be found here: http://cxc.harvard.edu/cda/repro4.html
  • Reprocess the data through chandra_repro. This will update the headers with the new keywords and ensure that the other calibrations are consistent with the latest CALDB.
  • Just update the headers using the r4_header_update script. This will just add new keywords to the event file without any other calibration updates.

Tool Version

The command "mkgarf --version" prints the version of mkgarf and the associated libraries. This is useful when reporting problems with the tool.

Bugs

Caveats

Warnings related to missing SUM_2X2, OCLKPAIR, FEP_CCD, or ORC_MODE keywords

Users trying to run this tool with old versions of data products, those created with ASCDSVER less than version 8.4.2, may see warnings like


FITSIO status = 202: keyword not found in header
*** ERROR: *** Unable to get the value of `SUM_2X2' in /data/acisf04425_000N003_evt1.fits

Users should consult the Watch Out page for more information on this topic an information on how to upgrade their data products.

*** WARNING: The ARF was computed to be zero at all the specified energies.
             This is probably due to an incorrect source position

There are some cases where this is expected to happen, e.g, a mask truncates the order or the chip was turned off.

However, if you get this error for all orders and chips, then something is wrong. There are a few possible situations:

  1. An incorrect source position was input to the sourcepixelx and sourcepixely parameters. Confirm that the source position is correct, and re-run the tool if it's not.

  2. You are attempting to create a gARF for an order that does not fall on that plate, e.g. a positive order on HRC-S3. Refer to the Analysis Guide for Chandra High Resolution Spectroscopy for more information.

*** Warning: CYCLE not found or invalid in /tmp/imap_3.fits --- assuming 'P'

The CIAO response tools will issue this warning if the CYCLE keyword is missing from the file header. The CYCLE keyword is needed in alternating mode observations (also referred to as interleaved mode) to indicate which frame time was used in the file. If you are not working with interleaved data, you can ignore the warning.

The What is the CYCLE keyword? FAQ explains further about this keyword.

See Also

calibration
ardlib
psf
psf
tools
acis_bkgrnd_lookup, acis_fef_lookup, acis_set_ardlib, addresp, aprates, asphist, combine_grating_spectra, combine_spectra, dither_region, dmarfadd, dmextract, eff2evt, fullgarf, hrc_bkgrnd_lookup, make_instmap_weights, mean_energy_map, mkacisrmf, mkarf, mkexpmap, mkgrmf, mkinstmap, mkpsfmap, mkrmf, mkwarf, psextract, psf_project_ray, readout_bkg, rmfimg, sky2tdet, specextract

Last modified: December 2013
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