Initial commit

Added files:
  * mass_profile: developed by Junhua GU, modified by Weitian LI
  * opt_utilities: developed by Junhua GU
  * tools/cosmo_calc: originated from 'calc_distance', modified
  * scripts: scripts used to process Chandra ACIS data
  * files: useful files used in processing
  * HOWTO_chandra_acis_process.txt
  * README.md

1 files changed, 150 insertions, 0 deletions

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+###########################################################
+## HOWTO
+## Processing Chandra ACIS data
+##
+## Weitian LI <liweitianux@gmail.com>
+## Last updated: 2014/06/18
+###########################################################
+
+### Settings: {{{
+## directory:
+# chandra scripts:
+CHANDRA_SCRIPT_DIR="${HOME}/bin/chandra/scripts"
+# mass program dir:
+MASS_PROFILE_DIR="${HOME}/bin/chandra/mass_profile"
+
+## aliases:
+# ciao scripts
+alias chcld="${CIAO_SCRIPT_DIR}/chandra_collect_data_v3.sh"
+alias chr500="${CIAO_SCRIPT_DIR}/ciao_r500avgt_v3.sh"
+# mass_profile related
+alias fitmass="${MASS_PROFILE_DIR}/fit_mass.sh"
+alias fitnfw="${MASS_PROFILE_DIR}/fit_nfw_mass mass_int.dat"
+alias fitsbp="${MASS_PROFILE_DIR}/fit_sbp.sh"
+alias fitwang="${MASS_PROFILE_DIR}/fit_wang2012_model tcl_temp_profile.txt"
+alias calclxfx="${MASS_PROFILE_DIR}/calc_lxfx_simple.sh"
+alias getlxfx="${MASS_PROFILE_DIR}/get_lxfx_data.sh"
+### Settings: }}}
+
+### Websites: {{{
+NED: http://ned.ipac.caltech.edu/forms/byname.html
+Chandra Chaser: http://cda.harvard.edu/chaser/dispatchOcat.do
+SIMBAD: http://simbad.u-strasbg.fr/simbad/
+nH tool: https://heasarc.gsfc.nasa.gov/cgi-bin/Tools/w3nh/w3nh.pl
+### }}}
+
+### Process step-guide: {{{
+ (1) $ chandra_repro indir=. outdir=repro verbose=2
+ (2) $ cd repro; mkdir -p evt bkg img spc/profile mass;
+ (3) $ cd evt; ln -s ../acis*evt2.fits .;
+ (4) $ ciao_procevt2.sh
+ (5) $ cd ../bkg; ln -s ../evt/evt2*_clean.fits .;
+ (6) $ ciao_blanksky_v4.sh
+ (7) ds9 open 'evt2*_clean.fits'; select edge region as the
+     *local background*, save as 'lbkg.reg';
+     and estimate the phonton counts:
+ (8) $ dmlist "evt2_clean.fits[sky=region(lbkg.reg)][energy=400:8000]" blocks
+ (9) $ ciao_bkg_spectra_v4.sh reg="lbkg.reg" basedir=.. nh=<nh> z=<z>
+(10) $ xspec
+(11) xspec> @xspec_lbkg_model.xcm
+     xspec> fit
+     xspec> cpd /xs
+     xspec> pl l del
+     xspec> @~/astro/scripts/xspec_bkgcorr_v2.tcl
+(12) cd ../img; ln -s ../evt/evt2*_clean.fits .;
+(13) ds9 open 'evt2*_clean.fits', select the center of cluster,
+     save the region as 'center.reg'
+(14) $ ciao_genregs_v1.sh reg_in=center.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 conf file '<NAME>_spec.conf' like:
+     basedir    ../..
+     reg        rspec.reg
+     bkgd       bkgcorr_blanksky_lbkg.pi | lbkg.pi
+     nh         <nh>
+     z          <redshift>
+(18) $ ciao_deproj_spectra_v8.sh reg="rspec.reg" bkgd=<bkgd> basedir="../.." nh=<nh> z=<z>
+(19) $ xspec
+     xspec> @xspec_deproj.xcm
+     xspec> fit
+     xspec> @~/astro/scripts/xspec_coolfunc_v2.tcl
+     (input 1)
+     xspec> exit
+(20) fix 'NULL' values in 'tcl_temp_profile.qdp' & 'tcl_temp_profile.txt'
+(21) $ xspec
+     xspec> newpar <..>=<..> (bind all kT's and Abundanc's)
+     xspec> fit (get avarage Temp and Abund)
+     xspec> exit
+(22) $ cd ../../img;
+     create '<NAME>_expcorr.conf' with contents:
+     basedir    ..
+     reg        sbprofile.reg
+     nh         <nh>
+     z          <redshift>
+     temp       <avg_temp>
+     abund      <avg_abund>
+(23) $ ciao_expcorr_sbp_v4.sh basedir=.. nh=<nh> z=<redshift> temp=<avg_temp> abund=<avg_abund>
+## --------------------------------------------------------
+
+(24) $ cd ../mass; clean_massdir.sh;
+(25) check needed linked files:
+     sbprofile.txt, flux_sbp.txt, radius_sbp.txt, tcl_temp_profile.txt
+(26) check needed config files:
+     wang2012_param.txt,
+     fitting_mass.conf, fitting_sbp.conf,
+     fitting_dbeta_mass.conf, fitting_dbeta_sbp.conf,
+     global.cfg
+(27) $ fitwang wang2012_param.txt
+(28) $ qdp fit_result.qdp   # check fitted temperature profile
+(29) $ fitsbp fitting_mass.conf   # single-beta sbp
+     $ fitsbp fitting_dbeta_mass.conf    # double-beta sbp
+(30) $ qdp sbp_fit.qdp   # check fitted sbp
+(31) $ ln -s fitting_mass.conf global.cfg   # use single-beta
+     $ ln -s fitting_dbeta_mass.conf global.cfg   # use double-beta
+(32) $ fitnfw <z> [rmin_kpc]
+(33) $ qdp nfw_fit_result.qdp   # check fitted nfw profile, and ajust 'rmin_kpc'
+(34) add 'nfw_rmin_kpc' to 'global.cfg'
+(35) $ fitmass global.cfg c    # calculate the center values
+(36) $ fitmass global.cfg 2>&1 | tee global_<date>.log    # calculate mass data
+(37) $ chandra_collect_data_v3.sh
+(38) $ cd ../img;
+     $ chandra_update_xcentroid.sh
+(39) $ cd ../spc/profile;
+(40) $ chr500 inner=0.1 outer=0.5   # check 0.5R500 range
+     $ chr500 inner=0.2 outer=0.5
+(41) $ xspec
+     xspec> @xspec_r500avgt_0.1-0.5.xcm
+     xspec> fit; fit;
+     xspec> cpd /xs; pl l del;
+     xspec> error 1. 2 3    # calc errors (68%) of kT and Abundanc
+(42) update the data of 'T(0.1-0.5 R500)', 'Z(0.1-0.5 R500)' ...
+
+## --------------------------------------------------------
+(43) $ cd ../..;  # in 'repro' dir
+     $ cp -a mass lxfx; cd lxfx;
+(44) $ calclxfx global.cfg c 500 200  # 'c' for center values
+     $ calclxfx global.cfg 500 200  # calc 'errors'
+(45) $ getlxfx . c 500 200  # for center results
+     $ getlxfx . 500 200  # for all results (with errors)
+
+## --------------------------------------------------------
+(46) $ 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'
+     ---
+### process }}}
+
+
+# vim: set ts=8 sw=4 tw=0 fenc=utf-8 ft=txt: #