All Threads - CIAO 3.3

Introduction

Beginners should start here. The Introductory threads provide an overview of the main components (GUI applications, plotting) and concepts (the Data Model, filtering) in the CIAO data analysis software.

Getting Started:
Chandra Data:
General:
- Introduction to the Data Model
- Introduction to Plotting Using ChIPS
- Using CIAO Region Files
- Using SAOImage ds9
  Uses: the getcounts.sl S-Lang script
- Using Parameter Files
GUIs:
A Complete List of CIAO tools can be found at the Introduction to Tools page.
If you are looking for a general topic, try the CXC Search at the top of the page.

Data Preparation

When Chandra data goes through Standard Data Processing (SDP), the most recently available calibration is applied to it. Since this calibration is continuously being improved, one should check whether there are currently newer files available. Similarly, some science decisions are made during SDP; every user has the option to reprocess the data with different parameters.

See the current Calibration Status Report
Analysis Guides:
- ACIS Data Preparation
- HRC Data Preparation
General:
- Use Observation-specific Bad Pixel Files
  Uses: the acis_set_ardlib script
- Filtering Data
- Filtering Lightcurves
  Uses: the analyze_ltcrv.sl S-Lang script
- Create a New Level=2 Event File
Coordinates, Astrometry, & Spatial Filtering:
ACIS:
- Check the ACIS Data Caveats
- Why topic: Continuous Clocking Mode
- Calculate CC-mode Times of Arrival
  (25 Apr 2006)
- acis_process_events:
  - The Create a New Level=2 Event File thread simplifies reprocessing data by combining all the acis_process_events options into one run of the tool.
  - Apply the Time-Dependent ACIS Gain Correction
    (7 Nov 2006)
  - Apply the ACIS CTI Correction
  - Apply an ACIS Gain Map
  - Remove ACIS Pixel Randomization
  - Apply/Remove ACIS PHA Randomization
  - Clean ACIS Background in VFAINT Mode
- Remove the acis_detect_afterglow Correction
- Identify ACIS Hot Pixels and Cosmic Ray Afterglows
- Using the ACIS "Blank-Sky" Background Files
  Uses: the acis_bkgrnd_lookup script; the lc_clean.sl S-Lang script
- Destreak the ACIS-S4 Chip
- Remove the ACIS Readout Streak
HRC:
ACA Monitor Window Data:
- Processing ACA Monitor Window Data

Timing Analysis

In order to perform absolute timing analysis on a dataset, a barycenter correction must first be applied to the data. One may then create lightcurves and phase-binned spectra to look for variability in the source. These threads also provide information on working with data taken in the ACIS continuous clocking (CC) mode.

General:
- Why topic: Continuous Clocking Mode
- Calculate CC-mode Times of Arrival
  (25 Apr 2006)
- Apply Barycenter Correction
- Create a Phase-binned Spectrum
Analyzing Lightcurves:
- Why topic: Timing Analysis with Lightcurves
- Basic Lightcurves
- Filtering Lightcurves
  Uses: the analyze_ltcrv.sl S-Lang script
See the S-lang/ISIS Timing Analysis Routines (SITAR) package which provides a set of functions and subroutines for timing analysis within ISIS.

Imaging

The Imaging threads cover a wide range of topics that include source detection, creating exposure maps and normalized images, and calculating image statistics. How to create color images for publication is addressed, as well as merging data from multiple observations.

Analysis Guides:
- HRC Imaging
- Extended Sources
General:
- Using the ACIS "Blank-Sky" Background Files
  Uses: the acis_bkgrnd_lookup script; the lc_clean.sl S-Lang script
- Updating dmgroup Syntax for CIAO 3
- Match the Binning of an Image
  Uses: the get_sky_limits script
- Create A True Color Image
  Uses: the color_image script
- Create an Image of Diffuse Emission
  Uses: the mkBgReg.pl script; the mkSubBgReg.pl script
- Using Data Cubes
Reprojecting Data:
- Merging Data from Multiple Imaging Observations
  Uses: the merge_all script
  (6 Jun 2006)
- Overview: Reprojecting Files
- Correcting Absolute Astrometry with reproject_aspect
  (24 Apr 2006)
- Reprojecting Images: Making an Exposure-corrected Mosaic
  (23 May 2006)
- Reprojecting Coordinates of a Solar System Object
Coordinates, Astrometry, & Spatial Filtering:
- Notes on Chandra Astrometric Accuracy
- Using SAOImage ds9
  Uses: the getcounts.sl S-Lang script
- Using CIAO Region Files
- Creating Source and Background Files
- Using dmcoords to Convert between CHIP and SKY Coordinates
Source Counts, Surface Brightness, & Statistics:
- Estimate Source Counts in an Image
- Obtain and Fit a Radial Profile
- Calculating Statistics of Images
  Uses: the sstats.sl S-Lang script
PSFs:
Detect:
- Overview: Detecting Sources in Imaging Observations
- Running celldetect
  Uses: the acis_expmap script
- Running vtpdetect
- Running wavdetect
- Using the Output of Detect Tools
Exposure Maps:
- Use merge_all Script to Compute ACIS Exposure Maps and Fluxed Images
  Uses: the merge_all script
- Compute Single Chip ACIS Exposure Map and Fluxed Image Step-by-Step
- Compute Multiple Chip ACIS Exposure Map and Fluxed Image Step-by-Step
- Compute an HRC-I Exposure Map and Build Fluxed Image
- Match the Binning of an Image
  Uses: the get_sky_limits script
- Calculating Spectral Weights
  Uses: the spectrum.sl S-Lang script

Imaging Spectroscopy

After extracting source and background PI or PHA spectra from an imaging observation, the appropriate response files (ARF, RMF) are created so that the data may be modeled and fit. In the case of multiple or extended sources, weighted ARF and RMF are built for the spectral analysis.

Extracting Spectra and Creating Response Files:

The recommended use for the specextract script has been changed. It has been determined that the mkwarf tool, which is used for ARF generation by specextract, may not produce accurate results for point sources. The mkarf tool, used by psextract, is preferred for point source extraction.

specextract should be used for the analysis of extended sources only. Users working with point sources should instead use the psextract script. Analysis of point sources that was done with mkwarf/specextract should be redone with mkarf/psextract for the most accurate results, e.g. taking bad columns into account.

In certain cases, the mkacisrmf tool will need to be run separately to create the best possible RMFs for ACIS observations; see the thread for details.
- Using specextract to Extract ACIS Spectra and Response Files
- Using psextract to Extract ACIS Spectra and Response Files for Pointlike Sources
  Uses: the psextract script; the acis_fef_lookup script
- Coadding Spectra and Weighted Responses
  Uses: the acisspec script
- Creating ACIS RMFs with mkacisrmf
Step-by-step Analyses:

These threads give step-by-step instructions for creating spectra and response files. Note that all of the tasks described here are executed automatically by the specextract script.
- Weighting ARFs and RMFs: multiple sources
  Uses: the show_wgt.sl S-Lang script
- Step-by-Step Guide to Creating ACIS Spectra for Pointlike Sources
  Uses: the acis_fef_lookup script
Deprecated Threads:

The analyses shown in this thread should now be done with the specextract script instead. The thread will be removed in a future CIAO release.
- Extracting Extended Source Spectra and Responses
  Uses: the acisspec script
General:
- A Note on HRC Spectra
- Displaying the FEF Regions Covered by a Source
  Uses: the regions.sl S-Lang script
- Why topic: ACIS QE Degradation
- Correcting Responses for ACIS Contamination
See the Sherpa threads for information on fitting spectral data.

Grating Spectroscopy

If new calibration has been applied to the event file, the grating spectrum should be re-extracted as well. It is then possible to build grating response files (gARF, gRMF) in order to model and fit the data in Sherpa.

Visit the Chandra Grating Analysis Page
ATOMDB: CIAO's spectroscopic library
WebGUIDE: Interactive GUIDE for ATOMDB version 1.3
General:
- Examining Grating Spectra and Regions: PHA2 files
- Updating dmgroup Syntax for CIAO 3
- Why topic: ACIS QE Degradation
- Correcting Responses for ACIS Contamination
- Measure Grating Dispersion Distance
  Uses: the tg_scale_reg S-Lang script
- Create an Order-Sorting Image
  Uses: the tg_osort_img S-Lang script
- Create a Color Spectrum
Problems with the Zero Order:
- Correcting a Misplaced Zero-order Source Position
- Source Position for Grating Data with a Piled or Blocked Zero Order
HETG/ACIS:
- Obtain Grating Spectra from HETG/ACIS-S Data
- Obtain Grating Spectra for Multiple Sources - ACIS
- Create Grating RMFs for ACIS-S Observations
- Compute HETG/ACIS-S Grating ARFs
  Uses: the fullgarf script
- Grouping a Grating Spectrum
LETG/ACIS:
- Obtain Grating Spectra from LETG/ACIS Data
- Obtain Grating Spectra for Multiple Sources - ACIS
- Create Grating RMFs for ACIS-S Observations
- Compute LETG/ACIS-S Grating ARFs
  Uses: the fullgarf script
- Grouping a Grating Spectrum
LETG/HRC-S:
LETG/HRC-I:
Combining Spectra & Fitting:
- Extract Coadded and Grouped Nth-Order Source & Background Spectra and ARFs
  Uses: the add_grating_orders script
- Add Grating Spectra and Average ARFs
  Uses: the add_grating_spectra script
- Sherpa: Fitting Grating Data
- Create PHA Background File for Use in XSPEC
  Uses: the tg_bkg script
- Sherpa: GUIDE: Fitting and Identifying Spectral Lines

S-Lang

A list of threads that use S-Lang, the CIAO Scripting Language, to automate a variety of tasks.

Why topic: S-Lang as the CIAO Scripting Language
Threads using S-Lang:
- Using SAOImage ds9
  Uses: the getcounts.sl S-Lang script
- Filtering Lightcurves
  Uses: the analyze_ltcrv.sl S-Lang script
- Using the ACIS "Blank-Sky" Background Files
  Uses: the acis_bkgrnd_lookup script; the lc_clean.sl S-Lang script
- Calculating Statistics of Images
  Uses: the sstats.sl S-Lang script
- Calculating Spectral Weights
  Uses: the spectrum.sl S-Lang script
- Displaying the FEF Regions Covered by a Source
  Uses: the regions.sl S-Lang script
- Weighting ARFs and RMFs: multiple sources
  Uses: the show_wgt.sl S-Lang script
- Measure Grating Dispersion Distance
  Uses: the tg_scale_reg S-Lang script
- There are also several Sherpa threads that use S-Lang

Science Threads for CIAO 3.3

Introduction

Getting Started:

Chandra Data:

General:

GUIs:

Data Preparation

Analysis Guides:

General:

Coordinates, Astrometry, & Spatial Filtering:

ACIS:

acis_process_events:

HRC:

ACA Monitor Window Data:

Timing Analysis

General:

Analyzing Lightcurves:

Imaging

Analysis Guides:

General:

Reprojecting Data:

Coordinates, Astrometry, & Spatial Filtering:

Source Counts, Surface Brightness, & Statistics:

PSFs:

Detect:

Exposure Maps:

Imaging Spectroscopy

Extracting Spectra and Creating Response Files:

Step-by-step Analyses:

Deprecated Threads:

General:

Grating Spectroscopy

General:

Problems with the Zero Order:

HETG/ACIS:

LETG/ACIS:

LETG/HRC-S:

LETG/HRC-I:

Combining Spectra & Fitting:

S-Lang

Threads using S-Lang: