Chandra ACIS analysis tools and documents
=========================================

Weitian (Aaron) LI, Junhu GU, and Zhenghao ZHU


Introduction
------------
This repository currently contains the following tools:
+ Chandra ACIS data reduction
+ Point source and flares removal
+ Blanksky reprojection
+ Background spectrum correction
+ Source spectra extraction and deprojection analysis (temperature profile)
+ Surface brightness profile extraction
+ Gravitational mass profile calculation (NFW profile extrapolation)
+ Luminosity and flux calculation

These tools are developed to help and automate our batch analysis of the
big galaxy groups and clusters sample observed by Chandra ACIS.
Therefore, there are many assumptions and hacks in these tools, and many
cleanups are needed.  Last but not least, documents are badly needed.

These tools are tested with:
+ CIAO v4.4 (support will be dropped)
+ CIAO v4.6
+ HEASoft v6.12
+ HEASoft v6.16


TODO
----
+ drop ``calc_distance`` in favor of ``cosmo_calc``
+ add arguments to control the ``cosmo_calc`` output for easier use in scripts
+ integrate the memos/docs for Chandra data analysis
+ integrate the ``chandra_guide`` doc


Installation
------------
Dependencies:
+ GSL
+ a working HEASoft installation (for ``libpgplot.a`` and ``libcpgplot.a``)

1. ``mass_profile``
```
$ cd mass_profile
$ make clean
$ heainit   # initilize heasoft, to link libpgplot.a and libcpgplot.a
$ ./init.sh
$ make
```

2. ``cosmo_calc``
Get from repository [atoolbox](https://github.com/liweitianux/atoolbox),
under the directory ``astro/cosmo_calc``.


Settings
--------
Add the following settings to your shell's initialization file
(e.g., ``~/.bashrc`` or ``~/.zshrc``).
```
# environment variables:
export MASS_PROFILE_DIR="/path/to/mass_profile"
export CHANDRA_SCRIPT_DIR="/path/to/script"
# aliaes
# 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"
```


Usage
-----
See the doc ``HOWTO_chandra_acis_analysis.txt``


License
-------
The tools are distributed under the **MIT license** unless otherwise declared.
The documents are distributed under the ??? License (coming...).