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##
## HOWTO
## Analyze Chandra ACIS data
##
## Weitian LI <liweitianux@gmail.com>
## Updated: 2017-02-07
##
Step-by-step guide to analyze ACIS data:
(1) Create new level=2 events with newest calibrations, and build
"manifest.yaml" for later use:
$ chandra_repro indir=. outdir=repro verbose=2
$ touch manifest.yaml
$ update_manifest.py -r repro
(??) <TODO> build 'results.yaml' (ra_ned, dec_ned, nh, z, etc.)
(2) $ mkdir -p evt bkg img spc/profile mass
(3) $ cd evt
$ ln -s ../*_repro_evt2.fits .
(4) $ clean_evt2.py
(5) $ cd ../bkg
$ ln -s ../evt/evt2*_clean.fits .
(6) $ make_blanksky.py
(7) $ ds9 evt2*_clean.fits
Select some region on the CCD edges that are as far from the
extended source as possible as the *local background*, then
save to a region file: 'lbkg.reg'.
(8) Estimate the total photon counts within the local background region:
$ dmlist "evt2*_clean.fits[sky=region(lbkg.reg)][energy=400:8000]" counts
Enlarge the regions if the total photon counts are too small
(e.g., say 3,000).
(9) Query the redshift from NED and nH from the HEASARC nH tool
(10) $ ciao_bkg_spectra.sh reg=lbkg.reg
(11) $ xspec
xspec> @xspec_lbkg_model.xcm
xspec> fit
xspec> cpd /xs
xspec> pl l del
xspec> @<path>/xspec_bkgcorr.tcl
(??) <TODO> If the background correction does not look good, e.g., the source
is very distant and compact and the emission is very faint, then it is
recommended to just use the *local background*.
Therefore, shrink the above 'lbkg.reg' accordingly and save as
'localbkg.reg', then extract the local background spectrum:
$ punlearn dmextract
$ dmextract infile="evt2_*_clean.fits[sky=region(localbkg.reg)][bin pi" \
outfile=localbkg.pi
(??) <TODO> Add background spectrum to manifest:
$ manifest.py setpath bkg_spec <bkgcorr_blanksky_lbkg.pi | localbkg.pi>
(12) $ cd ../img
$ ln -s ../evt/evt2*_clean.fits .
$ ln -s ../bkg/bkgcorr_blanksky_lbkg.pi . # maybe 'lbkg.pi'
(??) <TODO> create an image (0.7-2 keV) to determine the centroid
$ event2image.py -H 2000
(13) $ ds9 evt2*_clean.fits
Roughly select the source center and save the region as 'cstart.reg'
(??) <TODO> Calculate the X-ray centroid:
$ calc_centroid.py -s cstart.reg -i img_c*_e700-2000.fits -V
Check whether the calculated centroid is OK; if not, manually
adjust the centroid position, and overwrite 'centroid.reg'
(??) <TODO> Generate regions for SBP extraction (sbprofile.reg):
$ make_sbprofile_reg.py -b <bkgd> -V
(??) <TODO> Generate regions for deprojected spectral analysis (rspec.reg):
$ chandra_genspcreg.sh evt2_c*_clean.fits <bkgd> centroid.reg rspec.reg
$ manifest.py setpath rspec_reg rspec.reg
(15) $ cd ../spc/profile
$ ln -s ../../evt/evt2*_clean.fits .
$ ln -s ../../bkg/bkgcorr_blanksky_lbkg.pi . # maybe 'lbkg.pi'
$ ln -s ../../img/rspec.reg img_rspec.reg
(16) ds9 open 'evt2*_clean.fits' with regs 'img_rspec.reg';
adjust the regions and save as 'rspec.reg'
(18) $ ciao_deproj_spectra.sh reg=rspec.reg
(19) Fit the radial spectra to derive the radial temperature profile,
as well as the average temperature and abundance:
$ xspec
xspec> @xspec_deproj.xcm
xspec> fit
(tweaks parameters when necessary)
xspec> @<path>/xspec_tprofile.tcl
(calculate average temperature and abundance)
xspec> @<path>/xspec_avg_tz.tcl
xspec> exit
(20) Fix 'NULL' values in 'tprofile.qdp', 'tprofile.txt' & 'tz_average.txt'
(21) $ cd ../../img;
(22) create config '<NAME>_expcorr.conf' (for batch process):
basedir ..
reg sbprofile.reg
nh <nh>
z <redshift>
temp <avg_temp>
abund <avg_abund>
(23) $ ciao_expcorr_sbp.sh basedir=.. nh=<nh> z=<redshift> temp=<avg_temp> abund=<avg_abund>
## --------------------------------------------------------
(24) $ cd ../mass
$ ln -s ../img/sbprofile.txt .
$ ln -s ../spc/profile/tprofile.txt .
(25) Copy the sample config files located at 'files' directory:
* mass.conf
* wang2012_param.txt
* sbp_sbeta.conf
* sbp_dbeta.conf
(26) Fill 'nH', 'abund' in 'mass.conf';
and 'z' in 'sbp_sbeta.conf' and 'sbp_dbeta.conf'
(27) $ fittp tprofile.txt wang2012_param.txt
(28) $ qdp fit_result.qdp
(check fitted temperature profile, and adjust parameter accordingly)
(29) $ fitsbp sbp_sbeta.conf mass.conf # single-beta sbp
$ fitsbp sbp_dbeta.conf mass.conf # double-beta sbp
(30) $ qdp sbp_fit.qdp # check fitted sbp
(31) $ ln -s sbp_sbeta.conf sbp.cfg # use single-beta
$ ln -s sbp_dbeta.conf sbp.cfg # use double-beta
(32) $ fitnfw <z> [rmin_kpc]
(33) $ qdp nfw_fit_result.qdp # check fitted nfw profile, and ajust 'rmin_kpc'
(34) Update 'nfw_rmin_kpc' in 'mass.conf
(35) $ fitmass mass.conf c # calculate the central values
(36) $ fitmass mass.conf 2>&1 | tee mass_<date>.log # calculate mass data
(37) Update the INFO.json with calculated values from 'final_result.txt':
$ collect_infodata.sh
(38) $ cd ../img
$ chandra_update_xcentroid.sh
(39) $ cd ../spc/profile
(40) $ ciao_r500avgt.sh inner=0.1 outer=0.5 # check 0.5R500 range
$ ciao_r500avgt.sh inner=0.2 outer=0.5
(41) $ xspec
xspec> @xspec_r500avgt_0.1-0.5.xcm
xspec> fit; cpd /xs; pl l del;
xspec> error 1.0 2 3
(calculate the 1 sigma errors for temperature and abundance)
(42) update the following values in the INFO.json file:
* 'T(0.1-0.5 R500)'
* 'Z(0.1-0.5 R500)'
(43) repeat the above two steps for region "0.2-0.5 R500", and update
the values of 'T(0.2-0.5 R500)' and 'Z(0.2-0.5 R500)'.
## --------------------------------------------------------
(44) $ cd ../..; # in 'repro' dir
$ cp -a mass lxfx; cd lxfx;
(45) $ calclxfx global.cfg c 500 200 # 'c' for center values
$ calclxfx global.cfg 500 200 # calc 'errors'
(46) $ getlxfx . c 500 200 # for center results
$ getlxfx . 500 200 # for all results (with errors)
## --------------------------------------------------------
(47) $ cd ..; cd spc/profile
(48) Calculate cooling time:
$ ciao_calc_ct.sh
check results in file 'cooling_results.txt'
(49) Calculate Csb (surface brightness concentration):
$ ciao_calc_csb.sh
(it will open ds9 to show the regions, modify the regions if necessary;
and answer y/n/m to continue)
check results in file 'csb_results.txt'
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