HETG/ACIS-S Grating ARFs
CIAO 4.0 Science Threads
OverviewLast Update: 30 May 2008 - fullgarf v4.1.3 (Unix head and tail commands replaced by pget and dmkeypar); thread images are inline Synopsis: 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. Purpose: To create grating ARFs for an HETG/ACIS-S observation. Read this thread if: you are working with an HETG/ACIS-S observation and intend to model and fit the spectra. Related Links:
|
Contents
- Get Started
- The ACIS Dead Area Correction
- Determine the Orders of the Observation
- Run fullgarf
- The "ARF was computed to be zero at all energies" Warning
- Summary
- Parameter files:
- History
- Images
Get Started
Sample ObsID used: 459 (HETG/ACIS-S, 3C 273)
File types needed: evt2; pha2; asol1; bpix1; msk1; pbk0
If you created a new bad pixel file by running the New ACIS Bad Pixel File: Identify ACIS Hot Pixels and Cosmic Ray Afterglows thread, use that file in this analysis. Otherwise, use the bpix1.fits file from the Archive. Make sure that you have set up ardlib to use the same bad pixel file.
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.
Download the script
This thread uses the fullgarf script; for information about the script, consult the help file ("ahelp fullgarf"):
unix% grep version_ `which fullgarf` version_str="4.1.3" version_date="23 May 2008"
Please check that you are using the most recent version before continuing. If you do not have the script installed or need to update to a newer version, please refer to the Scripts page.
Using the mask file
To make sure that the gARF file is correct, set the maskfile parameter to the observation-specific msk1.fits file. If you are working with continuous-clocking (CC) mode data, be sure to read the ACIS Pipeline-Processed Mask Files caveat as well.
The ACIS Dead Area Correction
As of CIAO 4.0, the application of the dead area correction is turned on by default. The pbkfile and dafile parameters were added to fullgarf in order to apply the calibration.
The "dead area" is a fractional area loss per unit time due to cosmic ray flux incident on the ACIS detector. Calibration to account for this ACIS "dead area" was included in CALDB 3.3.0 on 15 December 2006. The correction is non-zero for the 8 front-illuminated (FI) ACIS chips; the effect is not detectable for the back-illuminated (BI) chips, so there is no correction applied to them.
Refer to the ACIS Dead Area Correction why topic for more information, including how to "turn off" the correction, e.g. if you would like to compare results with and without it applied.
Determine the Orders of the Observation
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 acisf00459N002_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). In Figure 1, there are twelve rows (all +/- orders for HEG and MEG) for the HETG observation.
![[The pha2 file displayed in prism, the CIAO file viewer]](prism.gif)
[Version: full-size]
Figure 1: Viewing the pha2 file in prism
For ACIS/HETG observations, as the one shown here, there are twelve rows in the PHA2 file: +/- 1, 2, and 3 orders for both HEG and MEG.
Run fullgarf
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=acisf00459N002_pha2.fits unix% pset fullgarf pharow=1 unix% pset fullgarf evtfile=acisf00459N002_evt2.fits unix% pset fullgarf asol=@pcad_asol1.lis unix% pset fullgarf engrid="grid(rmf.fits[cols ENERG_LO,ENERG_HI])" unix% pset fullgarf dtffile=")evtfile" unix% pset fullgarf badpix=acis_459_new_bpix1.fits unix% pset fullgarf maskfile=acisf00459_000N002_msk1.fits unix% pset fullgarf pbkfile=acisf063875928N002_pbk0.fits unix% pset fullgarf dafile=CALDB unix% pset fullgarf rootname=acisf00459
In many cases there will be more than one asol1.fits file for an observation. All the files must be input to the asol parameter, either as a list or as a stack (see ahelp stack for more information). For example, here we used:
unix% more pcad_asol1.lis pcadf063874624N002_asol1.fits pcadf063875522N002_asol1.fits pcadf063902942N002_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) (acisf00459N002_pha2.fits):
Row in Type II PHA file (ignored if Type I) (0:99) (1):
Event file (acisf00459N002_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)evtfile -> acisf00459N002_evt2.fits):
Bad pixel file; (filename|NONE|CALDB) (acis_459_new_bpix1.fits):
Output rootname (acisf00459):
NONE, or the name of the parameter block file (acisf063875928N002_pbk0.fits):
NONE, or name of ACIS window mask file (acisf00459_000N002_msk1.fits):
Getting the pha file type . . .
Grating arm is HEG, order=-3
Source location is X=4124.919921875, Y=4068.340087890625
Detector is ACIS
Will run asphist for ccd_id= 4 5 6 7
asphist infile=@pcad_asol1.lis outfile=acisf00459_ah4.fits evtfile=acisf00459N002_evt2.fits[ccd_id=4]
dtffile=acisf00459N002_evt2.fits
asphist infile=@pcad_asol1.lis outfile=acisf00459_ah5.fits evtfile=acisf00459N002_evt2.fits[ccd_id=5]
dtffile=acisf00459N002_evt2.fits
asphist infile=@pcad_asol1.lis outfile=acisf00459_ah6.fits evtfile=acisf00459N002_evt2.fits[ccd_id=6]
dtffile=acisf00459N002_evt2.fits
asphist infile=@pcad_asol1.lis outfile=acisf00459_ah7.fits evtfile=acisf00459N002_evt2.fits[ccd_id=7]
dtffile=acisf00459N002_evt2.fits
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] engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB
pbkfile=acisf063875928N002_pbk0.fits maskfile=acisf00459_000N002_msk1.fits 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_S1_HEG_-3.fits asphistfile=acisf00459_ah5.fits
[ASPHIST] engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB
pbkfile=acisf063875928N002_pbk0.fits maskfile=acisf00459_000N002_msk1.fits mode=hl verb=0
***ARDLIB warning: Filename acisf00459N002_evt2.fits does not specify an extension. Assuming the first "interesting" extension.
mkgarf detsubsys=ACIS-S2 order=-3 grating_arm=HEG outfile=acisf00459_S2_HEG_-3.fits asphistfile=acisf00459_ah6.fits
[ASPHIST] engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB
pbkfile=acisf063875928N002_pbk0.fits maskfile=acisf00459_000N002_msk1.fits mode=hl verb=0
***ARDLIB warning: Filename acisf00459N002_evt2.fits does not specify an extension. Assuming the first "interesting" extension.
mkgarf detsubsys=ACIS-S3 order=-3 grating_arm=HEG outfile=acisf00459_S3_HEG_-3.fits asphistfile=acisf00459_ah7.fits
[ASPHIST] engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB
pbkfile=acisf063875928N002_pbk0.fits maskfile=acisf00459_000N002_msk1.fits mode=hl verb=0
***ARDLIB warning: Filename acisf00459N002_evt2.fits does not specify an extension. Assuming the first "interesting" extension.
*** 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 ARDLIB warning may be ignored; it is explained in this FAQ. The aspect-related error from mkgarf may be ignored; it is explained in this FAQ. 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.
The "ARF was computed to be zero at all energies" Warning
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:
-
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.
-
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 Helpdesk for assistance.
Summary
The thread is now complete. The grating ARFs for this dataset are:
acisf00459HEG_-1_garf.fits acisf00459MEG_-1_garf.fits acisf00459HEG_-2_garf.fits acisf00459MEG_-2_garf.fits acisf00459HEG_-3_garf.fits acisf00459MEG_-3_garf.fits acisf00459HEG_1_garf.fits acisf00459MEG_1_garf.fits acisf00459HEG_2_garf.fits acisf00459MEG_2_garf.fits acisf00459HEG_3_garf.fits acisf00459MEG_3_garf.fits
Parameters for /home/username/cxcds_param/fullgarf.par
phafile = acisf00459N002_pha2.fits Input PHA file (Type I or II)
pharow = 1 Row in Type II PHA file (ignored if Type I)
evtfile = acisf00459N002_evt2.fits Event file
asol = @pcad_asol1.lis Aspect offsets file
engrid = grid(rmf.fits[cols ENERG_LO,ENERG_HI]) Energy grid spec
dtffile = )evtfile -> acisf00459N002_evt2.fits 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_000N002_msk1.fits NONE, or name of ACIS window mask file
pbkfile = acisf063875928N002_pbk0.fits NONE, or the name of the parameter block 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.
|
History
| 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 degradation 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 |
