HETG/ACIS-S Grating ARFs
CIAO 4.8 Science Threads
fullgarf is a script that creates a grating ARF for a particular order and grating of an observation. While the mkgarf tool will create a grating ARF for an individual chip given an aspect histogram, this script creates ARFS for each chip, creating aspect histograms as necessary. The script then combines the individual ARFS into one for the full array.
To create grating ARFs for an HETG/ACIS-S observation.
- About the Instrument: ACIS & HETG
- Analysis Guide for Chandra High Resolution Spectroscopy: an in-depth discussion of grating analysis.
Continuous Clocking Mode why topic: additional information for users working with CC-mode data.
ACIS QE Contamination why topic: correcting for the change in low-energy ACIS QE associated with the deposition of one or more materials on the ACIS detectors or optical blocking filters.
Last Update: 22 Dec 2014 - Reviewed CIAO 4.7; minor edits only.
- About the Chandra Grating Data Archive and Catalog
- Script It
- Get Started
- Determine the Orders of the Observation
- Run fullgarf
- The "ARF was computed to be zero at all energies" Warning
- Parameter files:
The Chandra Grating Data Archive and Catalog (TGCat) is a browsable interface to analysis-quality spectral products (binned spectra and corresponding response files). TGCat makes it easy to find observations of a particular object, type of object, or type of observation, to quickly assess the quality and potential usefulness of the spectra with pre-computed graphics or custom-generated plots of binned and combined counts or fluxe spectra. Spectra, responses, event files, and summary products may be downloaded as a package.
TGCat runs standard CIAO tools, but also includes customized extractions for non-standard cases to refine the zeroth order position or to use regions appropriate for extended sources. Non-standard extractions details are provided in "verification and validation" comments for users.
Most public grating observations are available and new ones are added soon after they are released. See the list of of observations not included for exceptions. Many of the observations currently in this list will be included when we add enhanced processing for more difficult cases (multiple sources, very extended sources).
Please consider using the spectrum and responses (PHA, ARF, and RMF files) from TGCat in your analysis.
The creation of the grating ARF and RMF is now automated.
chandra_repro will now automatically create the RMF and ARF for grating spectra. The results are stored in a tg/ subdirectory of the output directory.
Also, the mktgresp tool will create all the ARFs and RMFs for the grating spectra in a type II PHA file using the default grids and standard calibrations files. Just simply run
unix% mktgresp pha2 evt2 root_filename
If you have run chandra_repro or mktgresp then you are done with this thread and may move onto fitting and modeling your spectra. If you need to customize your responses or want to learn more details of the step by step processing steps you can continue with this thread.
Download the sample data: 459 (HETG/ACIS-S, 3C 273)
unix% download_chandra_obsid 459
It is assumed that you have created a gRMF for your observation by running the Create Grating RMFs for ACIS-S Observations thread, which is called rmf.fits.
An ARF needs to be calculated for each order in the observation. We can use Prism to examine the pha2 file and determine how many orders there are:
unix% prism acisf00459_repro_pha2.fits &
The tg_m column indicates the order of the observation (+/- 1, +/- 2, +/- 3) and the tg_part column indicates the grating (1 = HEG, 2 = MEG, 3 = LEG). The twelve rows (all +/- orders for HEG and MEG) for the HETG observation are shown in Figure 1.
It is necessary to run fullgarf for each order that will be modeled, up to twelve times (once for each row in the PHA file).
For row 1, HEG, order = -3:
unix% punlearn fullgarf unix% pset fullgarf phafile=acisf00459_repro_pha2.fits unix% pset fullgarf pharow=1 unix% pset fullgarf evtfile=acisf00459_repro_evt2.fits unix% pset fullgarf asol=@pcad_asol1.lis unix% pset fullgarf engrid="grid(rmf.fits[cols ENERG_LO,ENERG_HI])" unix% pset fullgarf badpix=acisf00459_repro_bpix1.fits unix% pset fullgarf maskfile=acisf00459_000N003_msk1.fits unix% pset fullgarf dafile=CALDB unix% pset fullgarf rootname=acisf00459
unix% cat pcad_asol1.lis pcadf063874624N003_asol1.fits
Now run the tool:
unix% fullgarf Will use /home/username/cxcds_param4/fullgarf.par for the parameter file. /home/username/cxcds_param4/fullgarf.par contains 15 parameters . . . Input PHA file (Type I or II) (acisf00459_repor_pha2.fits): Row in Type II PHA file (ignored if Type I) (0:99) (1): Event file (acisf00459_repro_evt2.fits): Aspect offsets file (@pcad_asol1.lis): Energy grid spec (grid(rmf.fits[cols ENERG_LO,ENERG_HI])): Dead time correction factor; ACIS->evt file; HRC -> dtf file (): Bad pixel file; (filename|NONE|CALDB) (acis_459_new_bpix1.fits): Output rootname (acisf00459): NONE, or name of ACIS window mask file (acisf00459_000N003_msk1.fits): Getting the pha file type . . . Grating arm is HEG, order=-3 Source location is X=4122.22509765625, Y=4071.310546875 Detector is ACIS Will run asphist for ccd_id= 4 5 6 7 asphist infile=@pcad_asol1.lis outfile=acisf00459_ah4.fits evtfile=acisf00459_repro_evt2.fits[ccd_id=4] dtffile= # asphist (CIAO 4.3): WARNING: 'pcadf063874624N003_asol1.fits' has no records fall in event gti's. asphist infile=@pcad_asol1.lis outfile=acisf00459_ah5.fits evtfile=acisf00459_repro_evt2.fits[ccd_id=5] dtffile= asphist infile=@pcad_asol1.lis outfile=acisf00459_ah6.fits evtfile=acisf00459_repro_evt2.fits[ccd_id=6] dtffile= asphist infile=@pcad_asol1.lis outfile=acisf00459_ah7.fits evtfile=acisf00459_repro_evt2.fits[ccd_id=7] dtffile= Finished creating aspect histograms for ccd_id= 4 5 6 7 Will run mkgarf for the same ccd_id list mkgarf detsubsys=ACIS-S0 order=-3 grating_arm=HEG outfile=acisf00459_S0_HEG_-3.fits asphistfile=acisf00459_ah4.fits[ASPHIST] obsfile=acisf00459_repro_evt2.fits engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB pbkfile= maskfile=acisf00459_000N003_msk1.fits mirror=HRMA sourcepixelx=4122.22509765625 sourcepixely=4071.310546875 mode=hl verb=0 *** ERROR: aspect histogram acisf00459_ah4.fits[ASPHIST] contains no rows mkgarf detsubsys=ACIS-S1 order=-3 grating_arm=HEG outfile=acisf00459_S0_HEG_-3.fits asphistfile=acisf00459_ah4.fits[ASPHIST] obsfile=acisf00459_repro_evt2.fits engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB pbkfile= maskfile=acisf00459_000N003_msk1.fits mirror=HRMA sourcepixelx=4122.22509765625 sourcepixely=4071.310546875 mode=hl verb=0 mkgarf detsubsys=ACIS-S2 order=-3 grating_arm=HEG outfile=acisf00459_S0_HEG_-3.fits asphistfile=acisf00459_ah4.fits[ASPHIST] obsfile=acisf00459_repro_evt2.fits engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB pbkfile= maskfile=acisf00459_000N003_msk1.fits mirror=HRMA sourcepixelx=4122.22509765625 sourcepixely=4071.310546875 mode=hl verb=0 mkgarf detsubsys=ACIS-S3 order=-3 grating_arm=HEG outfile=acisf00459_S0_HEG_-3.fits asphistfile=acisf00459_ah4.fits[ASPHIST] obsfile=acisf00459_repro_evt2.fits engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB pbkfile= maskfile=acisf00459_000N003_msk1.fits mirror=HRMA sourcepixelx=4122.22509765625 sourcepixely=4071.310546875 mode=hl verb=0 *** WARNING: The ARF was computed to be zero at all the specified energies. This is probably due to an incorrect source position Finished creating grating arfs for ccd_id= 4 5 6 7 dmarfadd @thisfile.istemporary acisf00459HEG_-3_garf.fits fullgarf finished.
The aspect-related error from mkgarf may be ignored; it is explained in the fullgarf bug page. Read the "ARF was computed to be zero at all energies" section for an explanation of the final warning.
The content of the parameter file may be checked using plist fullgarf.
The script is run in a similar way for the remaining rows.
At this point, you should have the spectra, gARFs, and gRMFs necessary for fitting the data. The Fitting Grating Data thread shows how to load the data and responses, define a model, and fit the spectra.
In order to use Gaussian statistics to fit a model to a dataset, it is often necessary to "group" the data - i.e. combine channels until you have enough counts. Before fitting the data in Sherpa, read the Grouping a Grating Spectrum thread for more information.
When running mkgarf, a warning of this form may be printed:
*** WARNING: The ARF was computed to be zero at all the specified energies. This is probably due to an incorrect source position
There are a few possible situations that are causing this:
You are attempting to create a gARF for an order that does not fall on that plate, e.g. there is only a bit of negative orders on ACIS-S3.
There are some cases where this happens because the mask truncates the order on a chip.
If none of these items resolves the problem, contact the CXC Helpdesk for assistance.
Parameters for /home/username/cxcds_param/fullgarf.par phafile = acisf00459N004_pha2.fits Input PHA file (Type I or II) pharow = 1 Row in Type II PHA file (ignored if Type I) evtfile = acisf00459N004_evt2.fits Event file asol = @pcad_asol1.lis Aspect offsets file engrid = grid(rmf.fits[cols ENERG_LO,ENERG_HI]) Energy grid spec dtffile = Dead time correction factor; ACIS->evt file; HRC -> dtf file badpix = acis_459_new_bpix1.fits Bad pixel file; (filename|NONE|CALDB) rootname = acisf00459 Output rootname maskfile = acisf00459_000N003_msk1.fits NONE, or name of ACIS window mask file (dafile = CALDB) NONE, CALDB, or name of ACIS dead-area calibration file (osipfile = CALDB) NONE or Name of fits file with order sorting info (clobber = no) Clobber existing output files? This is passed to ALL child processes. (verbose = 0) Control the level of diagnostic output. 0=>least. (mode = hl) Mode flags. Set to 'ql' to enable querying, 'hl' to suppress.
|23 Dec 2004||updated for CIAO 3.2: canned gRMFs are no longer available in the CALDB, removed "Choosing an RMF" section|
|06 Dec 2005||updated for CIAO 3.3: the fullgarf script has been updated to version 3.3.1 for the new asphist tool syntax; corresponding changes to screen output|
|01 Dec 2006||reviewed for CIAO 3.4: no changes|
|26 Feb 2007||fullgarf v4.0.1: Four new parameters have been added, all of which are used by the mkgarf tool: pbkfile, dafile, osipfile, and maskfile; see "ahelp fullgarf" for details on each new parameter. Added ACIS dead area correction section|
|11 Jan 2008||updated for CIAO 4.0: fullgarf v4.1.1 (parameter updates for applying ACIS dead area correction, which is turned on by default); ACIS QE contamination link moved to "Related Links" section; removed outdated calibration information ; added "ARF was computed to be zero at all energies" section|
|30 May 2008||fullgarf v4.1.3 (Unix head and tail commands replaced by pget and dmkeypar); thread images are inline|
|12 Feb 2009||updated for CIAO 4.1: "ARDLIB warning ... Assuming the first "interesting" extension." no longer printed; input data must have a CTI_APP keyword|
|19 Feb 2009||added Fitting section|
|06 May 2009||check the version of the CIAO scripts package instead of the individual script|
|01 Jun 2009||fullgarf updated in 01 Jun 2009 scripts package: If bad pixel file is not supplied, use the one from the CALDB. Previously, the script would set the bad pixel file to "NONE" in this case.|
|16 Jun 2009||added About the Chandra Grating Data Archive and Catalog section|
|12 Jan 2010||updated for CIAO 4.2: ObsID 459 file versions and corresponding minor changes to screen output; calibration update - the ACIS QE contamination model has been upgraded to vN0005.|
|15 Dec 2010||updated for CIAO 4.3: new ACIS contamination calibration file|
|01 Mar 2011||CALDB 4.4.2 release: fix to the header of the ACIS QE contamination file. Prior to this release, CIAO would fail when trying to look up the contamination model correction for chips ACIS-8 (S4) and ACIS-9 (S5).|
|20 Jul 2011||required software updates are listed in Synopsis|
|10 Jan 2012||reviewed for CIAO 4.4: no changes|
|12 Mar 2012||it isn't necessary to set the fullgarf dtffile parameter for ACIS data, since the DTCOR value is retrieved from the evtfile in this case.|
|03 Dec 2012||Review for CIAO 4.5; no changes|
|24 Apr 2013||Add pointer to new mktgresp tool.|
|03 Dec 2013||Review for CIAO 4.6. pbkfile has been removed from fullgarf. The data used in this threads is from very early in the mission and must be reprocessed to be used in CIAO 4.6.|
|22 Dec 2014||Reviewed CIAO 4.7; minor edits only.|