JWST Post-Pipeline Data Analysis
JWST post-pipeline data analysis tools will be used for viewing and analyzing JWST data. While its development is still ongoing, overviews, software installation, and training materials are currently available for interested users.
JWST post-pipeline data analysis tools are distributed as part of AstroConda to assist observers in viewing and analyzing their JWST data. The tools are generally written in Python and work with Astropy. Development is ongoing1.
The suite of post-pipeline data analysis tools is intended to help astronomers with the often iterative and interactive workflow involved in converting these calibration pipeline data products into meaningful scientific results. This involves tasks such as:
- inspecting data and data quality information;
- masking or flagging data and using those annotations to guide later steps in the analysis;
- using the results of interactive analysis to guide a custom run of the pipeline (e.g., tweaking spectral extraction parameters or background estimates);
- combining data sets in various ways, with careful attention to astrometry, PSF matching, and other issues;
- source detection and photometry using different choices or algorithms than those used in the pipeline;
- measuring lines and continuum in spectral data;
- fitting models to data or otherwise testing hypotheses.
A typical workflow involves highly interactive exploratory analysis on small portions of the data, followed by the development of custom scripts to automate the analysis on larger data sets.
1 All software is open source and community contributions are welcome in the form of suggestions, bug reports, or actual code. Further details on how to contribute can be found at the Data Analysis Tools Development Forum.
The recommended way to install stable versions of the JWST data analysis tools is to use AstroConda.
There are development versions of many of the tools linked in the "Repository" column in Table 1 that link to the open-source development locations on Github. Contributions to these developments are welcomed via bug reports (most effectively filed as github issues, but the JWST help desk is fine as well), or by code contributions through github pull requests. Use of the development versions of the code straight from github comes with the following caveats: at any given time, the code may not actually run or return correct results, and the documentation may be inconsistent with the code. Users who are not interested in contributing to the development software should use the versions in AstroConda.
Table 1 provides links to further information about the tools. User training workshops are being offered to help new users familiarize themselves with these tools.
Table 1. Software tools information
A Python library to explore relationships within and among related datasets.
A toolkit designed for building viewers for scientific image data in Python.
Tools for detecting and performing photometry of astronomical sources.
Convenience tools for working with astronomical images.
Tool for simple image examination, and plotting, with similar functionality to IRAF's imexamine.
An interactive astronomical 1D spectra analysis tool with similar functionality to IRAF's splot.
A quick-look analysis and visualization tool for multi-object spectroscopy.
Interactive analysis tool for 3D spectroscopy (coming soon)
Advanced Scientific Data Format is a next generation interchange format for scientific data (docs)
Generalized World Coordinate System tools for dealing with image and spectral geometries (docs)
Synthetic photometry toolkit for building model spectra and estimating count-rates. (docs)
Levels of maturity run from prototypes with little or no documentation, symbolized by buds,, progressing through various levels: to .
The exact meanings of these icons are a bit hard to quantify, but the flowers will tend to be still lacking in documentation and important features. The cherries are generally quite robust and well documented. The cherry pies are ready to be baked into your day-to-day workflow.
Be aware that all of the packages above are in very active stages of development, including Astropy and glue. For the ones at the cherry pie level, there is significant attention given to backwards compatibility as the APIs of the different modules evolve.
There are many resources available for learning Python and for using Python for astronomical data analysis. This section provides pointers to astronomy-focused materials and to more JWST-specific training materials.
General python astronomical data analysis training
Table 2. List of training resources for python astronomical data analysis
Using Python for Astronomical Data Analysis
January 2017 American Astronomical Society Special Session
Scientific Python Course at STScI
Notebooks are from 2015 version of course; videos from 2012-13
Practical Python for Astronomers
2011, 2012, 2013 Smithsonian Astrophysical Observatory
JWST focused training materials
Training materials for JWST data analysis will eventually include worked examples of common workflows, using outputs from the JWST calibration pipeline. Currently the materials are more general than that, and make use example data sets from other observatories. Table 3 provides links to these materials.
Table 3. List of JWST focused training materials
|JWST User Training in Data Analysis||Notebooks||Webcast||2016 Workshop at STScI|
Table 4 shows a more topic-oriented map of the materials from the 2016 Workshop.
Table 4. Introductory material
|Tables, I/O and FITS||Notebooks||Webcast|
Table 5. More specialized material
|JWST user training|
|JWST calibration pipeline overview||Webcast starts at 50:00|
|Astropy & JWST tools overview||Webcast|
|Image examination (imexam)||Notebooks||Webcast|
|Image display toolkit (ginga)||Ginga embedded in a Jupiter Notebook|
|Photometry (photutils)||Webcast starts at 55:30|
PSF-fitting Webcast 46:00
|Data exploration (glue)|
|Interactive spectral analysis (SpecViz, MosViz, CubeViz)||Webcast starts at 1:01:30|
|NIRCam Data Reduction||Webcast|
|Advanced Astropy Tables||Notebook||Webcast|
|Generalized World Coordinate System (gwcs)||Notebook||Webcast|