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Last modified: 12 November 2010

URL: http://cxc-newtest.cfa.harvard.edu/ciao4.2/download/scripts/index.html

CIAO 4.2 Contributed Scripts and Modules


The CIAO contributed tarfile contains analysis scripts and modules written by scientists at the CXC. The contributed scripts and modules automate repetitive tasks and extend the functionality of the CIAO software package by filling specific analysis needs.

These scripts and modules are not official CIAO tools. The user is responsible for the validity of any scientific results obtained from the analysis. Known issues with the scripts and modules are included in the CIAO bug pages.


Installation

The contributed tarfile can be installed and updated with the ciao-install script. There are also installation instructions for manually adding the scripts package to your CIAO installation.

In CIAO 4.2, the CIAO contributed tarfile unpacks in the same manner as the CIAO software. The tarfile should be unpacked from the directory which contains the root on the CIAO installation. For instance, if CIAO is installed in /soft/ciao-4.2/, the contributed tarfile should be unpacked in /soft. (Prior to CIAO 4.2, the tarfile had to be unpacked in /soft/ciao-4.2/.)


Download the Script Package

ciao-4.2-contrib-15Nov2010.tar.gz All the scripts listed on this page, packaged for seamless integration with CIAO.
Last Updated: 15 Nov 2010

A VERSION.CIAO_scripts file is included in the scripts package. This allows you to check if you are working with the newest set of scripts:

unix% cat $ASCDS_CONTRIB/VERSION.CIAO_scripts 
15 Nov 2010

The VERSION.CIAO_scripts file is updated when you install a newer scripts package.

Recent Changes

Package Version Name Changes
15 Nov 2010 ciao_contrib.runtool

The ciao_contrib.runtool module has been updated to include support for the chandra_repro, combine_spectra and make_psf_asymmetry_region tools, as well as fix an issue that could occur when setting parameters to floating-point values.

sherpa_contrib.profiles

The sherpa_contrib.profiles module has been updated so that the routines (e.g. prof_data, prof_fit and prof_fit_delchi) will work with models created using the set_full_model command.

26 Oct 2010 download_chandra_obsid

The download_chandra_obsid tool provides easy command-line downloads of public Chandra data.

make_psf_asymmetry_region

The make_psf_asymmetry_region tool creates a region file indicating the location of the PSF asymmetry found in HRC and ACIS data, as discussed in the Probing higher resolution: an asymmetry in the Chandra PSF.

12 Oct 2010 chandra_repro
  • Support for HRC imaging data has been added.
  • The default value of the pix_adj parameter is set to "default" to accommodate ACIS and HRC default parameter settings.
  • A HISTORY entry for chandra_repro is added to the header of the level=1 and level=2 event files. Use the dmhistory tool to view the entry.
  • additional updates are listed in the "CHANGES IN THE OCTOBER 2010 RELEASE" section of the help file
combine_spectra
  • Bug fix: the SPECRESP column values in the combined ARF were not scaled by the number of files that were combined. Users who combined an ARF with an earlier version of the script should remake it to get the correct output values.

  • The RESPFILE keyword value in the header of combined background spectrum is set to "NONE" if the background RMFs were not combined. Previously, the keyword value was left blank.

The Script Update History has a record of all changes made to the scripts package since the most recent CIAO release.


Scripts and Modules (by category)

Installation
Name Associated thread(s) Language Last update
check_ciao_caldb What CALDB version are you using? Python 2-Jun-2010
A tool to test the installation of the CIAO Calibration Database (CALDB); check_ciao_caldb help page
Data Preparation and Analysis
Name Associated thread(s) Language Last update
download_chandra_obsid How to Download Chandra Data from the Archive Python 26-Oct-2010
Provides easy command-line downloads of public Chandra data; download_chandra_obsid help page
acis_bkgrnd_lookup The ACIS "Blank-Sky" Background Files (S-Lang or Python) Python 2-Jun-2010
Find the ACIS "blank-sky" datasets in the CALDB matching your observation; acis_bkgrnd_lookup help page
acis_set_ardlib Setting the Observation-specific Bad Pixel Files Python 2-Jun-2010
Update ardlib.par files to find bad pixel lists; acis_set_ardlib help page
chandra_repro Python 12-Oct-2010
Data reprocessing script that runs all the recommended analysis threads for a given observation.
check_ctiapp.sh See the ACIS CTI correction documentation. sh 9-Dec-2008
Adds the CTI_APP header keyword to a file, using the value of the CTI_CORR header keyword to set the correct value.
deflare Filtering lightcurves (S-Lang or Python) Python 2-Jun-2010

The deflare script allows the user to run either lc_clean() or lc_sigma_clip() from the command line to filter flares from a lightcurve. These lightcurve routines are called from the CIAO contributed lightcurves package.

hrc_bkgrnd_lookup The HRC-I Background Event Files, The HRC-I Background Spectra Files Python 2-Jun-2010
Find the HRC-I background event and spectrum files in the CALDB matching your observation; hrc_bkgrnd_lookup help page
lightcurves Filtering Lightcurves (S-Lang or Python)
The ACIS "Blank-Sky" Background Files (S-Lang or Python)
S-Lang,Python 17-Feb-2010

The lightcurves (S-Lang or Python help) module contains two routines for identifying flares in lightcurves:

  1. lc_clean (S-Lang or Python help): clean a lightcurve to match the ACIS "blank-sky" datasets;
  2. lc_sigma_clip (S-Lang or Python help): an alternative algorithm for cleaning lightcurves that uses sigma clipping to reject outliers. Prior to CIAO 4.1 this routine was called analyze_ltcrv and only available in S-Lang.
ciao_utils ciao_contrib.utils S-Lang,Python 11-Dec-2009

The ciao_utils (S-Lang or Python help) module contains simple data-analysis routines: simple_stats (S-Lang or Python help) and simple_hist (S-Lang or Python help).

Imaging
Name Associated thread(s) Language Last update
get_sky_limits Match the Binning of an Image Python 2-Jun-2010
Find the required binning to match two images; get_sky_limits help page
make_psf_asymmetry_region Python -Oct-2010
Creates a region file indicating the location of the PSF asymmetry found in HRC and ACIS data, as discussed in the Probing higher resolution: an asymmetry in the Chandra PSF; make_psf_asymmetry_region help page
make_instmap_weights Python 2-Jun-2010

The make_instmap_weights script allows users to create the spectral weights file used by the spectrumfile parameter of mkinstmap from the command line.

merge_all Using merge_all to Compute ACIS Exposure Maps and Fluxed Images; Merging Data from Multiple Imaging Observations Perl 1-Jun-2009
Combine arbitrary number of ObsIDs, create exposure maps and fluxed images; merge_all help page
mkBgReg.pl, mkSubBgReg.pl An Image of Diffuse Emission Perl 11-Oct-2002
Create a smoothed, exposure-corrected image of diffuse emission; mkBgReg.pl help page, mkSubBgReg.pl help page
sherpa_utils sherpa_contrib.utils Calculating the Spectral Weights for mkinstmap S-Lang,Python 11-Dec-2009

The sherpa_utils module contains routines for calculating the weights file for mkinstmap.

Imaging Spectroscopy
Name Associated thread(s) Language Last update
acis_fef_lookup Extract ACIS Spectra for Pointlike Sources and Make RMFs and ARFs and Step-by-Step Guide to Creating ACIS Spectra (among others) Python 2-Jun-2010
Find the FITS Embedded Function file for use by mkrmf; acis_fef_lookup help page
acisspec Coadding Spectra and Weighted Responses sh 07-Feb-2007
Extract point-like and extended ACIS spectra with weighted responses or coadd acis spectra; acisspec help page
combine_spectra Python 12-Oct-2010
Sums multiple imaging source PHA spectra, and (optionally) the associated background PHA spectra and source and background ARF files; combine_spectra help page
psextract Extract ACIS Spectra for Pointlike Sources and Make RMFs and ARFs sh 30-May-2008
Extract source and background ACIS spectra for point-like sources and build associated ARFs and RMFs; psextract help page
Grating Spectroscopy

A number of scripts for grating data analysis which use ISIS, the Interactive Spectral Interpretation System, are available from the MIT/CXC S-Lang Packages webpage. Note that ISIS is not packaged with CIAO; users have to download and install it separately.

Name Associated thread(s) Language Last update
add_grating_orders Extract Coadded and Grouped Nth-Order Source & Background Spectra and ARFs sh 30-May-2008
Add positive and negative diffraction orders of a grating PHA spectra and the corresponding ARFs; add_grating_orders help page
add_grating_spectra Add Grating Spectra and Average ARFs sh 30-May-2008
Add two source and background grating PHA spectra, average the corresponding ARFs, and group the coadded spectrum; add_grating_spectra help page
fullgarf Create Grating ARFs for HETG/ACIS-S and LETG/ACIS-S data sh 1-Jun-2009
Create a grating ARF for a particular order; fullgarf help page
tg_bkg PHA Background File for XSPEC sh 11-Dec-2009
Create PHA background file for use in XSPEC; tg_bkg help page
Sherpa
Name Associated thread(s) Language Last update
SherpaCL Python 2-Jun-2010
An interactive interface that allows users to use CIAO 3.4 syntax for Sherpa and ChIPS commands in CIAO 4. The language that can be used is currently limited. Refer to "ahelp sherpacl" and the SherpaCL page on the Sherpa website for more information and usage examples.
sherpa_profiles sherpa_contrib.profiles Radial and elliptical profiles of Image Data S-Lang,Python 15-Nov-2010
Allows users to create radial (or elliptical) profiles of 2D imaging data, including model fits, from within Sherpa to allow users to visually inspect the quality of the results; see sherpa_profiles.
sherpa_flux_dist sherpa_contrib.flux_dist Calculating Uncertainties by Simulating Flux Distributions S-Lang,Python 11-Dec-2009
Create and plot the distribution of flux values due to the uncertainties on model parameters; see sherpa_flux_dist.
sherpa_utils sherpa_contrib.utils Radial and elliptical profiles of Image Data S-Lang,Python 1-Apr-2010
Utility routines for Sherpa users; see sherpa_utils.
chart_spectrum Preparing to Run ChaRT S-Lang,Python 02-Mar-2009
Create a source spectrum for which you would like a PSF to be simulated; the spectrum is used as input to ChaRT
ChIPS
Name Associated thread(s) Language Last update
chips_utils chips_contrib.utils See the ChIPS gallery for examples, such as the FOV examples in the Annotations section (Python or S-Lang). S-Lang,Python 1-Mar-2010
Utility routines for ChIPS users; see chips_contrib (S-Lang or Python help).
Crates
Name Associated thread(s) Language Last update
crates_utils crates_contrib.utils S-Lang,Python 11-Dec-2009
Utility routines for Crates users; see crates_utils (S-Lang or Python help).
CIAO
Name Associated thread(s) Language Last update
ciao_contrib S-Lang,Python 15-Nov-2010
The ciao_contrib (S-Lang or Python help) module loads in all the routines from the sherpa_contrib, chips_contrib (S-Lang or Python help), and crates_contrib (S-Lang or Python help) modules.

The Python version includes the ciao_contrib.runtool module for running CIAO tools as if they were Python functions and the ciao_contrib.caldb module for access to version information of the installed CALDB.

ISIS

A number of scripts for data analysis which use ISIS, the Interactive Spectral Interpretation System, are available from the MIT/CXC S-Lang Packages webpage. Note that ISIS is not packaged with CIAO; users have to download and install it separately.


Last modified: 12 November 2010