Science Threads
Introduction
Beginners should start here. The Introductory threads provide an overview of the main components (GUI applications, parameter files) and concepts (the Data Model, filtering) in the CIAO data analysis software.
General:
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 newer files available. Similarly, some science decisions are made during SDP; every user has the option to reprocess the data with different parameters.
Analysis Guides:
ACIS:
- Check the ACIS Data Caveats
- Why topic: -110 C Observations
- Why topic: Continuous Clocking Mode Data
- Reprocessing Data to Create a New Level=2 Event File
- Customizing an ACIS Bad Pixel File
- Removing ACIS Background Flares
- Analysing the ACIS Background with the "Blank-Sky" Files
- Remove the ACIS Readout Streak
- Removing Warm ACIS Data
HRC:
- Check the HRC Data Caveats
- New Observation-Specific HRC Bad Pixel File
-
The chandra_repro script may be used to easily reprocess Chandra datasets.
To reprocess your data step-by-step, follow the Reprocessing Data to Create a New Level=2 Event File thread.
- Computing Average HRC Dead Time Corrections
- The HRC-I Background Event Files
- The HRC-I Background Spectra Files
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:
General:
- Analysing the ACIS Background with the "Blank-Sky" Files
- The HRC-I Background Event Files
- The HRC-I Background Spectra Files
- Match the Binning of an Image
- An Estimated Background Image
- True Color Images
- True Color Images in ds9
- An Image of Diffuse Emission
-
Creating mean energy maps (aka pseudo temperature maps)
![[New]](../imgs/new.gif)
(05 Jan 2023)
- Using Data Cubes
- Using Contrib Color Look-Up Tables
Coordinates, Astrometry, & Spatial Filtering:
Source Characteristics:
- Estimate Source Counts in an Event File
- Obtain and Fit a Radial Profile
- Calculate source count rates and fluxes
- Calculate source count rates and fluxes for combined datasets
-
Using srcflux plugins
(14 Dec 2022)
- Compute Net Counts, Rate, or Flux for Point Sources
-
Computing the Intensity Upper Limit and
Upper Value for Flux Uncertainty for an Unresolved Source
![[Updated]](../imgs/updated.gif)
(10 May 2023)
- Calculate a Flux for a Position
- Measuring Source Extent
- Search for Variability in a Source
- Determining Exposed Region Area
Exposure Maps:
- Using merge_obs to combine observations and create exposure-corrected images
- Calculating Spectral Weights for mkinstmap
- Single Chip ACIS Exposure Map and Exposure-corrected Image
- Multiple Chip ACIS Exposure Map and Exposure-corrected Image
- HRC-I Exposure Map and Exposure-corrected Image
- HRC-S Exposure Map and Exposure-Corrected Image
- Match the Binning of an Image
Modeling & Fitting Imaging Data with Sherpa
(from the Sherpa analysis threads):
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, a weighted ARF and RMF are built for the spectral analysis.
Modeling & Fitting Spectral Data with Sherpa
(from the Sherpa analysis threads):- Introduction to Fitting PHA Spectra
- Changing the grouping scheme of a data set within Sherpa
- Introduction to Fitting ASCII Data with Errors: Single-Component Source Models
- Simultaneously Fitting Two Data Sets
- Simulating 1-D Data: the Sherpa FAKE_PHA Command
- Simulating Chandra ACIS-S Spectra with Sherpa
- Fitting PHA Data with Multi-Component Source Models
- Independent Background Responses
- Using A Pileup Model
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.
- Chandra Grating Analysis Page
- WebGUIDE: Interactive GUIDE for ATOMDB
- Chandra Grating Data Archive and Catalog (TGCat): a browsable interface to analysis-quality spectral products.
-
The chandra_repro script may be
used to easily reprocess Chandra datasets.
Problems with the Zero Order:
LETG/HRC-S:
- LETG/HRC-S Grating Spectra
- Applying Customized Background Regions to LETG/HRC-S Observations
- Grating Spectra for Multiple Sources - HRC
- Higher-order Responses for HRC-S/LETG Spectra
- HRC Grating RMFs
- LETG/HRC-S Grating ARFs
- Grouping a Grating Spectrum
- The calibration page Optimized LETG/HRC-S Extraction Region and Recalibrated EEFRACs contains information needed to use the detilt, dewiggle, and symmetrize scripts.
Combining Spectra & Preparation for Fitting:
Modeling & Fitting Grating Data with Sherpa
(from the Sherpa analysis threads):
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. These same tools and threads work equally well with 0th order grating data.
General:
Analyzing Lightcurves:
- See the S-lang/ISIS Timing Analysis Routines (SITAR) package which provides a set of functions and subroutines for timing analysis within ISIS.
PSF Simulations
ChaRT is easily run with a few input parameters, producing output data files that contain the simulated HRMA PSF. The following threads illustrate collecting the necessary input for ChaRT, unpacking and identifying the output files and the final step of projecting the HRMA PSF onto the detector-plane.
Steps to Run ChaRT Simulations
Using ChaRT Outputs
-
After running ChaRT, the simulated PSF must be projected onto
onto the detector-plane—this is done with
MARX,
which includes the detector response—and an image file may
be created from the projected event file.
- Using MARX to Create an Event File from ChaRT Rays
- Creating an Image of the PSF
MARX Spectrum
-
It is also possible to use the intrinsic MARX instrument and HRMA
models to perform raytracing. If a PSF with a source spectrum
is desired, then a MARX-compatible input spectrum may be created.
- Creating an Input Spectrum for Running MARX Simulations
MARX Examples
-
The internal MARX HRMA model may also be used to run raytracing
simulations, and two use-cases are described.
- Using MARX to Simulate an Existing Observation
- Using MARX to Simulate a Planned Observation
Data Analysis Threads
-
The PSF effects may also be accounted for during 2D image
fitting.
- Using a PSF Image as the Convolution Kernel
Tips, Tricks, and Techniques
Most of the analysis threads are focused on a particular science goal or objective : instrument, grating, point source vs. extended, etc. They present the best path to reduce the data for those specific criteria. However, there are many kinds of analysis techniques that apply to general data reduction that can be performed with CIAO -- on Chandra data or other missions. There are far too many to have individual threads for all possible scenarios.
The threads presented in this section will focus on how to accomplish a particular task and the options available. When one should use these technique and why one would want to do such a thing are up to the user. The emphasis here is to highlight the functionality available. It is expected users will find uses for CIAO that the CXC might not have anticipated.