JWST Data Analysis Tool Notebooks#

The jdat_notebooks repository contains notebooks illustrating workflows for post-pipeline analysis of JWST data. Some of the notebooks also illustrate generic analysis workflows that are applicable to data from other observatories as well. This repository and the notebooks are one component of STScI’s larger Data Analysis Tools Ecosystem.

Installation Instructions#

Please see the installation instructions for details on how to download, install, and run your notebooks.

Summary of Notebooks#

The table below summarizes the notebooks currently available. The Table of Contents on the left of this page will take you to rendered versions of the notebooks, which require no special tools beyond your web browser. If you do not see an expected notebook listed in the left-hand column, it is not currently rendered. The links in the table will take you to the GitHub repository location of the notebooks for you to download.

Table 1 JWST Science Analysis Notebooks#

Notebook

Description

Cross-Instrument

asdf

  • Use case: create ASDF (Advanced Scientific Data) file from FITS file.

  • Data: CANDELS image of the COSMOS field.

  • Tools: asdf, gwcs, astrocut.

  • Cross-instrument: All.

Background Estimation

  • Use case: estimate the sk background in complex scenes.

  • Data: images with pathological background pattern created in the notebook.

  • Tools: photutils

  • Cross-instrument: All.

Querying MAST

  • Use case: How to submit NIRSpec MAST Query using python.

  • Data:

  • Tools: mast, astroquery

  • Cross-instrument: All.

Specviz GUI

  • Use case: How to inspect and export spectra in Specviz GUI.

  • Data: NIRISS simulation generated with MIRAGE.

  • Tools: specutils, jdaviz.

  • Cross-instrument: All.

Composite Model Fitting

  • Use case: Fitting the complex continuum around Lyman-alpha in the spectrum of an active galaxy NGC 5548.

  • Data: 3-column ECSV file with units for each column.

  • Tools: specutils, numpy.

  • Cross-instrument: All.

Redshift Cross-Correlation

  • Use case: Reproduce the workflow of the IRAF task XCORFIT to measure redshfit.

  • Data: LEGA-C spectra and galaxy template spectra; optical rest frame.

  • Tools: specutils

  • Cross-instrument: All.

IFU Cube Fitting

  • Use case: Continuum and emission-line modeling of galaxy IFU spectra.

  • Data: Spitzer/IRS on M58.

  • Tools: specutils, custom functions

  • Cross-instrument: MIRI, NIRSpec

MIRI

MRS Cube Pipeline, Optimal Extraction, Analysis

  • Use case: For MIRI MRS, run the JWST pipeline, optimal extraction of point source, and analysis in Cubeviz.

  • Data: Simulated MIRI MRS spectrum of AGB star.

  • Tools: jdaviz, specutils, jwst, photutils, astropy, scipy

  • Cross-instrument:

IFU of YSO’s in LMC

  • Use case: Automatically detect point sources and extract photometry in a 3D cube. Analyze spectral lines.

  • Data: ALMA 13CO data cubes.

  • Tools: specutils, photutils, astropy.

  • Cross-instrument:

LRS Optimal Extraction

  • **Use case:**Optimal spectral extraction.

  • Data: MIRISim simulated LRS spectrum.

  • Tools: jwst pipeline, gwcs.

  • Cross-instrument: NIRSpec, NIRISS, MIRI

NIRCam

Point Source Aperture Photometry

  • Use case: Crowded field imaging with Aperture-fitting photometry.

  • Data: Simulated NIRCam images of LMC astrometric calibration field.

  • Tools: jwst pipeline, photutils

  • Cross-instrument: MIRI, NIRCam

Multiband Extended Aperture Photometry

  • Use case: measure extended galaxy galaxy photomtery in a field.

  • Data: Simulated NIRCam images from JADES GTO extragalactic blank field.

  • Tools: photutils

  • Cross-instrument: MIRI, NIRCam

Cross-Filter PSF-Matched Aperture Photometry

  • Use case: A more advanced version of the above notebook that uses PSF corrections, but still performs aperture photometry.

  • Data: Simulated NIRCam images from JADES GTO extragalactic blank field.

  • Tools: photutils

  • Cross-instrument: MIRI, NIRCam

PSF Photometry

  • Use case: Crowded field imaging with PSF-fitting photomtery.

  • Data: Simulated NIRCam images of LMC astrometric calibration field.

  • Tools: webbpsf, photutils

  • Cross-instrument: MIRI, NIRCam

MIRAGE Simulations

  • Use case: Putting together simulations and running the NIRCam Imaging JWST Calibration Pipeline.

  • Data: Simulated NIRCam images of LMC astrometric calibration field.

  • Tools: webbpsf, jwst

  • Cross-instrument:

NIRISS

WFSS Spectra

  • Use case: Optimal Extraction and analysis of grism spectra.

  • Data: Simulated NIRISS spectra of galaxy center.

  • Tools: specutils

  • Cross-instrument: NIRSpec, NIRISS

WFSS MOS Spectra

  • Use case: Emission-line measurements and template matching on 1D spectra.

  • Data: LEGA-C spectra and agalxy template spectra; optical rest frame

  • Tools: specutils

  • Cross-instrument: NIRSpec, NIRISS

AMI Binary Star

  • Use case: Find the binary parameters of AB Dor.

  • Data: Simulated MIRAGE data for a binary point source.

  • Tools: jwst pipeline, nrm_analysis

  • Cross-instrument:

SOSS Transiting Exoplanet

  • Use case: Primary transit of an exoplanet.

  • Data: Simulated transit using awesomesoss.

  • Tools: jwst pipeline, juliet

  • Cross-instrument:

NIRSpec

IFU Cube Modeling

  • Use case: Continuum and emission line modeling of AGN; 1.47-1.87um.

  • Data: NIFS on Gemini; NGC 4151

  • Tools: specutils, cubeviz

  • Cross-instrument: MIRI, NIRSpec

IFU Optimal Extraction

  • Use case: Optimal spectral extraction.

  • Data: Simulated data of a faint (quasar) point source.

  • Tools: jwst pipeline, scipy, specutils, jdaviz, photutils, astropy.io astropy.wcs

  • Cross-instrument:

MOS Optimal Extraction

  • Use case: Optimal spectral extraction.

  • Data: Simulated NIRSpec MOS data; point sources.

  • Tools: jwst pipeline

  • Cross-instrument:

BOTS Transiting Exoplanet

  • Use case: Primary transit of an exoplanet.

  • Data: Simulated NIRSpec data from ground-based campaign.

  • Tools:

  • Cross-instrument:

Help#

If you uncover any issues or bugs, you can open a GitHub issue. For faster responses, however, we encourage you to submit a JWST Help Desk Ticket.

Contributing#

Contributions are welcome from both the scientist and developer community. If you wish to contribute fixes or clarifications to existing notebooks, feel free to do so directly to this repository. If you wish to contribute new notebooks or major reworks of existing notebooks, we refer you to dat_pyinthesky.

For details on how to provide such contributions, see the contributing instructions. The notebooks attempt to utilize a number of software packages supported by STScI, including Astropy, glue, ginga, photutils, specutils, astroimtools, imexam, jdaviz, asdf, gwcs, and synphot. Note jdaviz is STScI’s JWST Data Analysis Visualization Tool, designed to be used with spectra, IFU cubes, and multi-object spectroscopy (MOS).