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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) $ chandra_repro indir=. outdir=repro verbose=2
+ (2) $ cd repro
+     $ mkdir -p evt bkg img spc/profile mass
+ (3) $ cd evt
+     $ ln -s ../*_repro_evt2.fits .
+ (4) $ ciao_procevt.sh
+ (5) $ cd ../bkg
+     $ ln -s ../evt/evt2*_clean.fits .
+ (6) $ ciao_blanksky.sh
+ (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]" blocks
+     Enlarge the regions if the total photon counts are too small
+     (e.g., say 2,000).
+ (9) Query the redshift from NED and nH from the HEASARC nH tool
+(10) $ ciao_bkg_spectra.sh reg="lbkg.reg" basedir=.. nh=<nh> z=<z>
+(11) $ xspec
+     xspec> @xspec_lbkg_model.xcm
+     xspec> fit
+     xspec> cpd /xs
+     xspec> pl l del
+     xspec> @<path>/xspec_bkgcorr.tcl
+(12) $ cd ../img
+     $ ln -s ../evt/evt2*_clean.fits .
+     $ ln -s ../bkg/bkgcorr_blanksky_lbkg.pi .  # maybe 'lbkg.pi'
+     $ ln -s ../pcadf*_asol1.fits .
+(13) $ ds9 evt2*_clean.fits
+     Roughly select the source center and save the region as 'center.reg'
+(14) $ ciao_genregs.sh reg_in=center.reg bkgd=<bkgd>
+     Check whether the calculated centroid is OK; if not, manually
+     adjust the centroid position, and save & overwrite the
+     'centroid_phy.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'
+(17) create a config file '<NAME>_spec.conf' looks like (for batch process):
+     basedir    ../..
+     reg        rspec.reg
+     bkgd       bkgcorr_blanksky_lbkg.pi | lbkg.pi
+     nh         <nh>
+     z          <redshift>
+(18) $ ciao_deproj_spectra.sh reg="rspec.reg" bkgd=<bkgd> basedir="../.." nh=<nh> z=<z>
+(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;
+     calculate cooling time and Csb value:
+     $ ciao_calc_ct_csb.sh
+     check the region whether exceeds ccd edge, and answer y/n
+     check results in file 'ct_csb_results.txt'
+     ---
+     Alternatively:
+     $ ciao_calc_ct.sh
+     $ ciao_calc_csb.sh
+     check the region whether exceeds ccd edge, and answer y/n
+     check results in file 'cooling_results.txt' and 'csb_results.txt'
+     ---