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 v4.6
+ CIAO v4.9 (testing ...)
+ HEASoft v6.16
+ HEASoft v6.19


WARNING
-------
Our Chandra sample has been finished for a period of time, and we at the moment
have no plan to re-process/update the results.
In consequence, these tools/scripts are currently **untested** and very likely have
some **bugs**.


TODO
----
+ drop ``calc_distance`` in favor of ``cosmo_calc``
+ use JSON as the output format (for easier parse and conversion)
+ use python (instead of shell) to manipulate JSON data files
+ 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
------------
1. Clone this repository with ``opt_utilities``:

   ```
   $ git clone --recursive https://github.com/liweitianux/chandra-acis-analysis.git
   ```

   or in this way:

   ```
   $ git clone https://github.com/liweitianux/chandra-acis-analysis.git
   $ cd chandra-acis-analysis
   $ git submodule update --init --recursive
   ```

2. Build ``mass_profile`` tools:

   ```
   $ cd mass_profile
   $ make clean
   $ make
   (or use this to enable OpenMP)
   $ make OPENMP=yes
   ```

3. Get and build ``cosmo_calc``:

   Get it from repository [atoolbox](https://github.com/liweitianux/atoolbox),
   under the directory ``astro/cosmo_calc``.
   Then place the built binary to where can be searched by shell
   (e.g., ``~/bin``, and add ``~/bin`` to ``$PATH``).

4. Install the following runtime dependencies:

   * Python (>=3.5)
   * [ruamel.yaml](https://bitbucket.org/ruamel/yaml)
   * [numpy](http://numpy.org/)
   * [scipy](https://scipy.org/)
   * [astropy](http://www.astropy.org/)


Settings
--------
Add the following settings to your shell's initialization file
(e.g., ``~/.bashrc`` or ``~/.zshrc``).
```
# Environment variables:
export MASS_PROFILE_DIR="<path>/chandra-acis-analysis/mass_profile"
export CHANDRA_SCRIPT_DIR="<path>/chandra-acis-analysis/scripts"

# Handy aliases:
alias fitmass="${MASS_PROFILE_DIR}/fit_mass.sh"
alias fitnfw="${MASS_PROFILE_DIR}/fit_nfw_mass mass_int.dat"
alias fitsbp="${MASS_PROFILE_DIR}/fit_sbp.sh"
alias fittp="${MASS_PROFILE_DIR}/fit_wang2012_model"
alias calclxfx="${MASS_PROFILE_DIR}/calc_lxfx_wrapper.sh"
alias getlxfx="${MASS_PROFILE_DIR}/get_lxfx_data.sh"
```


Usage
-----
See the documentations located in the ``doc`` directory,
especially the [``HOWTO_chandra_acis_analysis.txt``](doc/HOWTO_chandra_acis_analysis.txt)

NOTE: complete and detailed documentations are badly needed!


Useful Links
------------
* [CIAO](http://cxc.cfa.harvard.edu/ciao/)
* [Chandra CALDB](http://cxc.cfa.harvard.edu/ciao/download/caldb.html)
* [Chandra Data Archive](http://cda.harvard.edu/chaser/)
* [NED search by name](http://ned.ipac.caltech.edu/forms/byname.html)
* [NED search near position](https://ned.ipac.caltech.edu/forms/nearposn.html)
* [SIMBAD](http://simbad.u-strasbg.fr/simbad/)
* [HEASoft](https://heasarc.gsfc.nasa.gov/lheasoft/)
* [XSPEC](https://heasarc.gsfc.nasa.gov/lheasoft/xanadu/xspec/index.html)
* [QDP/PLT User's Guide](https://heasarc.gsfc.nasa.gov/ftools/others/qdp/qdp.html)
* [FTOOLS](https://heasarc.gsfc.nasa.gov/ftools/)
* [HEASARC nH tool](https://heasarc.gsfc.nasa.gov/cgi-bin/Tools/w3nh/w3nh.pl)


License
-------
Unless otherwise declared:

* Codes developed by us are distributed under the
  [MIT License](https://opensource.org/licenses/MIT);
* Documentations and products generated by us are distributed under the
  [Creative Commons Attribution 3.0 License](https://creativecommons.org/licenses/by/3.0/us/deed.en_US).