This repository contains notes & scripts for reduction and analysis of the JWST Cycle 1 project 2221 GO that observed the Brick and Cloud C in NIRCAM narrow-band filters and the MIRI F2550W filter.

While some aspects of this repository are well-organized, the notebooks are not: they often include asides and experiments that lead to dead ends or just got dropped. There are a lot of 'notes in the margins'. Most of them should work if you have the directory structure set up right and the right files in place, but I haven't put in the time needed to make clear what that structure should be.

Reduction process

1. Pipeline files are in reduction/.

• PipelineRerunNIRCAM-LONG.py run the JWST pipeline with modifications to the tweakwcs stage
• destreak.py runs "Massimo's Destriper", which is a simple percentile-subtraction across the X-axis of each horizontal quadrant of each detector (this is run by the pipeline)
• align_to_catalogs.py includes some post-facto re-alignment tools. One function runs only on the final processed data & matches it to VVV. (this is run by the pipeline)
• saturated_star_finding.py performs PSF fitting on saturated stars and removes them. (this is run by the pipeline)
• crowdsource_catalogs_long.py runs the crowsource extraction algorithm. This must be run on the long-wavelength channels before running the short-wavelength pipeline to provide the reference catalog we use for the shortwave data.
• merge_catalogs.py merges the multiwavelength catalogs.
• make_reftable.py makes the reference table from the long-wavelength (F410M) data to be used on the short-wavelength data (this is run by merge_catalogs) - note that this is in analysis/
• PipelineRerunNIRCAM-SHORT.py run the JWST pipeline with modifications to the tweakwcs stage including a reference catalog generated from F410M
• crowdsource_catalogs_long.py on the short data (it has _long in the name, but I merged both into this one; the _short version is deprecated) - note that this is in analysis/
• merge_catalogs.py again to finally merge wavelengths - note that this is in analysis/

2. Notebooks. There are a lot of these.

• BrA_separation_nrc{a,b}.ipynb should be run after the pipeline. They subtract BrA from F410M, then subtract the rescaled continuum from the BrA image.
• F466_separation_nrc{a,b}.ipynb does the same thing, but for the F466 filter. It doesn't work as well because of the wavelength difference.
• StarKILLER_nrc{a,b}.ipynb manually remove stars from the images, only for display purposes!
• Stitch_A_to_B.ipynb pulls the two modules together. It makes the "star-free" three-color merged image
• nrca_contsub_colorimages.ipynb and BrickImages.ipynb make 3-color images.

Most of the rest are test / WIP things.

Analysis

The analysis has been done haphazardly in notebooks, but then I tried to reconcile different notebooks and merge them.

• analysis_setup.py - loads the latest versions of 3-color images and catalogs. Meant to be called before running plotting things.
• co_fundamental_modeling.py - extracts from the CO2_PhoenixModel.ipynb, CO2_Phoenix_Example.ipynb, and COFundamentalModeling_and_IceModeling.ipynb notebooks. This script produces a wider range of models than those notebooks
• plot_tools.py - contains many plot templates for color-color, color-magnitude, etc.
• selections.py - downselects from the full merged catalog of NIRCAM data of the brick, in all 6 filters, to the subset(s) that are reliable
• ColorVsCOIceAnalysis.ipynb - makes several color-color plots