LETG/ACIS-S Grating ARFs

CIAO 4.0 Science Threads

Overview

Last 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 LETG/ACIS-S observation.

Read this thread if:

you are working with an LETG/ACIS-S observation and intend to model and fit the spectra.

Related Links:

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 Degradation 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.

Proceed to the HTML or hardcopy (PDF: A4 | letter) version of the thread.

Get Started
- Download the script
- Using the mask file
The ACIS Dead Area Correction
Determine the Orders of the Observation
Run fullgarf
Summary
Parameter files:
- fullgarf
History
Images
- Figure 1: Viewing the pha2 file in prism

Get Started

Sample ObsID used: 1198 (LETG/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 acisf01198N002_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 six rows (all +/- orders for LEG) for the LETG observation.

[Thumbnail image: The pha2 file displayed in prism, the CIAO file viewer]

[Version: full-size]

[Print media version: The pha2 file displayed in prism, the CIAO file viewer]

Figure 1: Viewing the pha2 file in prism

For ACIS/LETG observations, as the one shown here, there are six rows in the PHA2 file: +/- 1, 2, and 3 orders for LEG.

Run fullgarf

It is necessary to run fullgarf for each order that will be modeled, up to six times (once for each row in the PHA file).

For row 2, LEG, order = -2:

unix% punlearn fullgarf
unix% pset fullgarf phafile=acisf01198N002_pha2.fits
unix% pset fullgarf pharow=2
unix% pset fullgarf evtfile=acisf01198N002_evt2.fits
unix% pset fullgarf asol=pcadf063832996N002_asol1.fits
unix% pset fullgarf engrid="grid(rmf.fits[cols ENERG_LO,ENERG_HI])"
unix% pset fullgarf dtffile=")evtfile"
unix% pset fullgarf badpix=acis_1198_new_bpix1.fits
unix% pset fullgarf maskfile=acisf01198_000N002_msk1.fits
unix% pset fullgarf pbkfile=acisf063833861N002_pbk0.fits
unix% pset fullgarf dafile=CALDB
unix% pset fullgarf rootname=acisf01198

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).

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) (acisf01198N002_pha2.fits): 
Row in Type II PHA file (ignored if Type I) (0:99) (2): 
Event file  (acisf01198N002_evt2.fits): 
Aspect offsets file (pcadf063832996N002_asol1.fits): 
Energy grid spec (grid(rmf.fits[cols ENERG_LO,ENERG_HI])): 
Dead time correction factor; ACIS->evt file; HRC -> dtf file (')evtfile'): 
Bad pixel file; (filename|NONE|CALDB) (acis_1198_new_bpix1.fits): 
Output rootname (acisf01198): 
NONE, or the name of the parameter block file (acisf063833861N002_pbk0.fits): 
NONE, or name of ACIS window mask file (acisf01198_000N002_msk1.fits):    
Getting the pha file type . . .

Grating arm is LEG, order=-2  
Source location is X=4162.240234375, Y=4084.679931640625
  
Detector is ACIS 
Will run asphist for ccd_id= 4 5 6 7 
  
   
asphist infile=pcadf063832996N002_asol1.fits outfile=acisf01198_ah4.fits 
evtfile=acisf01198N002_evt2.fits[ccd_id=4] dtffile=acisf01198N002_evt2.fits
   
asphist infile=pcadf063832996N002_asol1.fits outfile=acisf01198_ah5.fits 
evtfile=acisf01198N002_evt2.fits[ccd_id=5] dtffile=acisf01198N002_evt2.fits
   
asphist infile=pcadf063832996N002_asol1.fits outfile=acisf01198_ah6.fits 
evtfile=acisf01198N002_evt2.fits[ccd_id=6] dtffile=acisf01198N002_evt2.fits
   
asphist infile=pcadf063832996N002_asol1.fits outfile=acisf01198_ah7.fits 
evtfile=acisf01198N002_evt2.fits[ccd_id=7] dtffile=acisf01198N002_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=-2 grating_arm=LEG outfile=acisf01198_S0_LEG_-2.fits asphistfile=acisf01198_ah
4.fits[ASPHIST] engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB pbkfile=acisf063833861N002_pbk0.fits 
pbkfile=acisf063833861N002_pbk0.fits maskfile=acisf01198_000N002_msk1.fits mode=hl verb=0
***ARDLIB warning: Filename acisf01198N002_evt2.fits does not specify an extension. Assuming the first "interesting" extension.
  
mkgarf detsubsys=ACIS-S1 order=-2 grating_arm=LEG outfile=acisf01198_S1_LEG_-2.fits asphistfile=acisf01198_ah
5.fits[ASPHIST] engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB pbkfile=acisf063833861N002_pbk0.fits 
pbkfile=acisf063833861N002_pbk0.fits maskfile=acisf01198_000N002_msk1.fits mode=hl verb=0
***ARDLIB warning: Filename acisf01198N002_evt2.fits does not specify an extension. Assuming the first "interesting" extension.
   
mkgarf detsubsys=ACIS-S2 order=-2 grating_arm=LEG outfile=acisf01198_S2_LEG_-2.fits asphistfile=acisf01198_ah
6.fits[ASPHIST] engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB pbkfile=acisf063833861N002_pbk0.fits 
pbkfile=acisf063833861N002_pbk0.fits maskfile=acisf01198_000N002_msk1.fits mode=hl verb=0 
***ARDLIB warning: Filename acisf01198N002_evt2.fits does not specify an extension. Assuming the first "interesting" extension.
   
mkgarf detsubsys=ACIS-S3 order=-2 grating_arm=LEG outfile=acisf01198_S3_LEG_-2.fits asphistfile=acisf01198_ah
7.fits[ASPHIST] engrid=grid(rmf.fits[cols ENERG_LO,ENERG_HI]) osipfile=CALDB dafile=CALDB pbkfile=acisf063833861N002_pbk0.fits 
pbkfile=acisf063833861N002_pbk0.fits maskfile=acisf01198_000N002_msk1.fits mode=hl verb=0 
***ARDLIB warning: Filename acisf01198N002_evt2.fits does not specify an extension. Assuming the first "interesting" extension.
   
   
Finished creating grating arfs for ccd_id= 4 5 6 7 
   
dmarfadd @thisfile.istemporary acisf01198LEG_-2_garf.fits
  
fullgarf finished.

The ARDLIB warning may be ignored; it is explained in this FAQ. You may also see an aspect-related error from mkgarf; it is explained in this FAQ and may be ignored. The content of the parameter file may be checked using plist fullgarf.

The script is run in a similar way for the remaining rows.

Summary

The thread is now complete. The grating ARFs for this dataset are:

  acisf01198LEG_-1_garf.fits    acisf01198LEG_1_garf.fits
  acisf01198LEG_-2_garf.fits    acisf01198LEG_2_garf.fits
  acisf01198LEG_-3_garf.fits    acisf01198LEG_3_garf.fits


Parameters for /home/username/cxcds_param/fullgarf.par


       phafile = acisf01198N002_pha2.fits Input PHA file (Type I or II)
        pharow = 2                Row in Type II PHA file (ignored if Type I)
       evtfile = acisf01198N002_evt2.fits Event file 
          asol = pcadf063832996N002_asol1.fits Aspect offsets file
        engrid = grid(rmf.fits[cols ENERG_LO,ENERG_HI]) Energy grid spec
       dtffile = )evtfile -> acisf01198N002_evt2.fits Dead time correction factor; ACIS->evt file; HRC -> dtf file
        badpix = acis_1198_new_bpix1.fits Bad pixel file; (filename|NONE|CALDB)
      rootname = acisf01198       Output rootname
      maskfile = acisf01198_000N002_msk1.fits NONE, or name of ACIS window mask file
      pbkfile  = acisf063833861N002_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
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
23 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 updates
30 May 2008	fullgarf v4.1.3 (Unix head and tail commands replaced by `pget` and `dmkeypar`); thread images are inline