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Astro Scripts

A collection of Python scripts and notebooks for retrieving astronomical imaging and catalog data from major surveys (DECaLS, SDSS, and LS DR10).

Table of Contents

Setup

Use Python 3.11 in a dedicated environment, especially for the DESI workflow:

python3.11 -m venv .venv
source .venv/bin/activate
python -m pip install --upgrade pip
python -m pip install -r requirements.txt

The scripts validate coordinates and retry remote requests where supported, but survey services can still be temporarily unavailable. Outputs are intentionally ignored by Git so that large downloads do not enter the repository.

1. LS DR10 Photometry Downloader (ls_dr10_catalog_download.py)

Queries the Legacy Surveys DR10 Tractor catalog via the NOIRLab TAP service to extract multi-band photometry (optical + WISE) within a user-defined sky box.

More Information about LS DR10: https://datalab.noirlab.edu/data/legacy-surveys

Requirements

  • astroquery

Search Method

This script intentionally performs a fast RA/Dec box search instead of a true cone search. The returned table may include some sources near the corners of the box that fall outside a circular radius, which can be filtered manually afterward if needed.

Usage

python ls_dr10_catalog_download.py --ra <ra> --dec <dec> --name <name> --radius <radius> --output-dir <output_dir>

Arguments

  • --ra: Right Ascension of the target center (in degrees).
  • --dec: Declination of the target center (in degrees).
  • --name: Label for the output CSV file.
  • --radius: Half-width of the search box in degrees (default: 0.0166667, approximately 1 arcmin).
  • --output-dir: Directory where the CSV file will be written (default: current directory).
  • --extra-columns: Comma-separated list of additional ls_dr10.tractor columns to append to the default export.
  • --list-columns: Query TAP_SCHEMA.columns, print the currently available ls_dr10.tractor columns, and exit.

Example

Query sources around a target galaxy cluster:

python ls_dr10_catalog_download.py --ra 64.3950417 --dec -11.9110306 --name macs0417 --radius 0.02

Save the result to a specific directory:

python ls_dr10_catalog_download.py --ra 64.3950417 --dec -11.9110306 --name macs0417 --radius 0.02 --output-dir output_catalogs

Inspect which other columns can be downloaded:

python ls_dr10_catalog_download.py --list-columns

Append a few extra Tractor columns to the default CSV:

python ls_dr10_catalog_download.py --ra 64.3950417 --dec -11.9110306 --name macs0417 --radius 0.02 --extra-columns objid,brickid,ebv

Output

The script writes a CSV file named like:

ls_dr10_<name>_ra<ra>_dec<dec>_r<radius>.csv

It also prints the RA/Dec bounds of the search box and the number of sources returned.

Output Columns

The script returns a CSV file containing:

  • Astrometry: ra, dec
  • Photometry: Native observed fluxes (flux_*), observed magnitudes (mag_*), dereddened fluxes (dered_flux_*), and dereddened magnitudes (dered_mag_*)
  • Uncertainties / Quality: Flux inverse variances (flux_ivar_*) and signal-to-noise ratios (snr_*)
  • Metadata: Galactic transmission factors, morphology types, and quality flags

If --extra-columns is used, those columns are appended after the default set. The script validates requested names against the live ls_dr10.tractor schema before running the science query.

SED Photometry Calculations

For each filter band (g, r, i, z, w1, w2, ...), the script converts Tractor catalog parameters using the following formulas:

# 1. Use dereddened flux for SED
dered_flux = flux / mw_transmission

# 2. Flux error
sigma_flux = 1 / sqrt(flux_ivar)
sigma_dered_flux = sigma_flux / mw_transmission

# 3. AB Magnitude
mag = 22.5 - 2.5 * log10(dered_flux)

# 4. Magnitude error
mag_err = (2.5 / ln(10)) / (flux * sqrt(flux_ivar))

2. DESI Spectra Downloader (desi_download_spectra.py)

Queries the SPARCL catalog for DESI spectra around one sky position or a batch of positions, downloads the spectra, and saves both data products and diagnostic plots.

The script now uses a two-step metadata workflow:

  1. Cone search in sparcl.main to find nearby spectra and collect sparcl_id / targetid
  2. Join richer DESI metadata from desi_dr1.zpix, desi_dr1.photometry, and desi_dr1.target

The spectra themselves are still downloaded from SPARCL using sparcl_id.

Requirements

The DESI script is heavier than the other scripts in this repository because it depends on two astronomy-specific client packages:

  • sparclclient: provides from sparcl.client import SparclClient
  • astro-datalab: provides from dl import queryClient as qc

These packages can be harder to install into an existing Python environment because they bring in a fairly specific scientific Python stack.

At the time of writing:

  • astro-datalab 2.24.0 declares Requires-Python: >=3.9,<3.12
  • astro-datalab 2.24.0 also pins versions of core packages such as numpy, astropy, pandas, matplotlib, scipy, specutils, pyvo, and pycurl
  • sparclclient 1.3.0 depends on numpy, pandas, requests, specutils, spectres, and pyjwt

Because of that, the safest approach is to install this script in its own clean conda environment instead of mixing it with unrelated packages.

Recommended Conda Setup

Recommended starting point:

conda create -n desi python=3.11 pip
conda activate desi
python -m pip install --upgrade pip
python -m pip install astro-datalab==2.24.0 sparclclient==1.3.0

A tested working environment on this project used:

  • Python 3.11.15
  • astro-datalab 2.24.0
  • sparclclient 1.3.0
  • numpy 1.26.3
  • astropy 5.3.4
  • pandas 2.1.4
  • matplotlib 3.8.4
  • specutils 1.13.0

If you already have a complicated astronomy or machine-learning environment, it is strongly recommended not to install these DESI dependencies into that same environment.

Single-Target Usage

python desi_download_spectra.py --ra <ra> --dec <dec> --radius <radius> --output <output_dir>

Example:

python desi_download_spectra.py --ra 64.3950417 --dec -11.9110306 --radius 0.02 --output macs0417

Batch Usage With CSV

Use --csv to run the same workflow for many targets at once.

python desi_download_spectra.py --csv targets.csv

The included example file targets.csv uses this format:

name,ra,dec,radius,output
macs0417,64.3950417,-11.9110306,0.02,macs0417

Required CSV columns:

  • name
  • ra
  • dec
  • radius

Optional CSV column:

  • output: Output directory name for that row. If omitted, the script uses name.

Useful Options

  • --overwrite: Re-run a target even if download_complete.txt already exists.
  • --no-plots: Save only the catalog and .npz spectra, without PNG plots.
  • --show-model: Overlay the SPARCL model spectrum when available.
  • --no-smooth: Disable the smoothed spectrum overlay.
  • --smooth-sigma: Change the Gaussian smoothing width for plots.
  • --no-absorption-lines: Do not draw common absorption lines on the plot.
  • --catalog-columns default: Write a compact everyday catalog.
  • --catalog-columns duplicates: Write a catalog aimed at investigating repeated rows and target-level duplicates.
  • --catalog-columns full: Write every fetched join column from the DESI tables.

Duplicate Handling

If multiple rows share the same targetid, the script keeps only one row before downloading spectra.

The current preference order is:

  • smaller redshift_err
  • smaller chi2
  • larger deltachi2

This helps reduce obvious repeated entries while keeping the better-fit DESI solution.

Replot Existing Directories

If you already have output directories with object_catalog.csv and spectrum_*.npz, you can regenerate the PNG plots without doing the cone search, DESI joins, or SPARCL download again.

python desi_download_spectra.py --replot-dirs macs0417

This mode also works with plot options such as:

python desi_download_spectra.py --replot-dirs macs0417 --show-model --no-smooth

Output

For each target, the script writes:

  • object_catalog.csv: Final catalog after SPARCL cone search, DESI table joins, and optional column filtering
  • spectrum_<sparcl_id>.npz: Saved spectrum arrays and metadata
  • spectrum_<sparcl_id>.png: Plot of the spectrum, unless --no-plots is used
  • download_complete.txt: Sentinel file marking the target as complete

3. DECaLS Image Downloader (decal_image_download.py)

Downloads optical images directly from the DECaLS servers.

Requirements

  • numpy
  • matplotlib
  • astropy

Usage

python decal_image_download.py <index> <ra> <dec> <name> <redshift> <fraction_size>

Both <redshift> and <fraction_size> are optional:

  • default redshift: 0.2
  • default fraction size: 1

Arguments

  • <index>: Identifier index or row number.
  • <ra>: Right Ascension (in degrees).
  • <dec>: Declination (in degrees).
  • <name>: Output file name/prefix.
  • <redshift>: Target redshift used for the physical scale label (default: 0.2). Set to 0 if unknown.
  • <fraction_size>: Resolution scaling factor (default: 1).
  • --fits: Download a FITS cube instead of an annotated JPEG.
  • --keep-raw-fits: Keep the original downloaded FITS file alongside the reordered output.
  • --desi-csv: Path to object_catalog.csv from desi_download_spectra.py. When provided, the JPEG output marks those catalog objects on the image. If the flag is provided without a value, the script tries to auto-create the default DESI catalog in <name>/.
  • --ls10-csv: Path to a CSV from ls_dr10_catalog_download.py. When provided, the JPEG output marks the brightest LS objects using mag_i. If the flag is provided without a value, the script auto-creates the default LS catalog in <name>/.
  • --brightest-count: Number of brightest LS objects to mark from --ls10-csv (default: 5).
  • --label-chars: Number of leading sparcl_id characters to display beside each marker (default: 3).
  • --overwrite: Recreate the final JPEG even if it already exists.

fraction_size examples: 1 = 2048 px 2 = 2048 / 2 px 4 = 2048 / 4 px (Increase value to zoom in and reduce file size)

Examples

  • Download JPEG:
python decal_image_download.py 1 64.3950417 -11.9110306 macs0417 0.44 4
  • Download JPEG using the default redshift (0.2) and default image size:
python decal_image_download.py 1 64.3950417 -11.9110306 macs0417
  • Download FITS file:
python decal_image_download.py 1 64.3950417 -11.9110306 macs0417 0.44 4 --fits
  • Download FITS file and keep the original raw download too:
python decal_image_download.py 1 64.3950417 -11.9110306 macs0417 0.44 4 --fits --keep-raw-fits
  • Download a JPEG and overlay DESI catalog objects from an existing catalog CSV:
python decal_image_download.py 1 64.3950417 -11.9110306 macs0417 0.44 4 --desi-csv macs0417/object_catalog.csv
  • Download a JPEG and overlay the 5 brightest LS DR10 sources from a photometry CSV:
python decal_image_download.py 1 64.3950417 -11.9110306 macs0417 0.44 4 --ls10-csv macs0417/ls_dr10_macs0417_ra64.39504_dec-11.91103_r0.02000.csv
  • Download a JPEG with both DESI and LS overlays at the same time:
python decal_image_download.py 1 64.3950417 -11.9110306 macs0417 0.44 4 --desi-csv macs0417/object_catalog.csv --ls10-csv macs0417/ls_dr10_macs0417_ra64.39504_dec-11.91103_r0.02000.csv
  • Download a JPEG and auto-create both overlay catalogs in <name>/ when needed:
python decal_image_download.py 1 64.3950417 -11.9110306 macs0417 0.44 4 --desi-csv --ls10-csv
  • Force regeneration of an existing JPEG output:
python decal_image_download.py 1 64.3950417 -11.9110306 macs0417 0.44 4 --overwrite

Output

  • JPEG mode writes an annotated image named like img_ix00001_annoted_test.jpg
  • JPEG mode adds suffixes when overlays are used: ..._desi.jpg, ..._lsbright.jpg, or ..._desi_lsbright.jpg
  • FITS mode writes a reordered FITS cube named like img_ix00001_annoted_test.fits

The original FITS cube downloaded from the DECaLS server has the band order wrong for SAOImage DS9 RGB display. This script automatically reorders the downloaded cube before saving the final FITS output, so no second fix-up script is needed.

The JPEG annotation includes a real 1 arcmin scale bar computed from the DECaLS pixel scale (0.262 arcsec/px), plus a physical-size label in kpc at the chosen redshift.

DESI Marker Overlay

When --desi-csv is used, the script reads that object_catalog.csv file and overlays the catalog objects on the JPEG cutout.

If --desi-csv is passed without a value, the script tries to run desi_download_spectra.py automatically to create the default object_catalog.csv inside <name>/.

If that helper times out while contacting the remote SPARCL/NOIRLab service, the script now prints a message explaining that this is sometimes a temporary remote-service problem and that you can try the same command again. If the DESI search completes but finds no matching objects within the default 0.02 deg radius, the script reports that too. In both cases, if no DESI catalog file is created, the JPEG is still produced without DESI markers.

Each DESI marker is drawn as a hollow cyan circle and labeled with:

  • the first --label-chars characters of sparcl_id
  • the object redshift as z=... with 2 decimal places, when the redshift column is available in object_catalog.csv

The marker positions are computed using:

  • the input ra and dec as the image center
  • the DECaLS JPEG pixel scale of 0.262 arcsec/px

This mode does not use WCS; it uses sky-coordinate offsets from the image center and converts them directly into pixel offsets.

LS Brightest Overlay

When --ls10-csv is used, the script reads the LS DR10 CSV, sorts by mag_i, and marks the brightest rows on the JPEG cutout.

If --ls10-csv is passed without a value, the script runs ls_dr10_catalog_download.py automatically to create the default LS catalog inside <name>/ before drawing the markers.

Each LS marker is drawn as a hollow yellow circle and labeled with mag_i to 1 decimal place.

DS9 Note

If you want to open the FITS cube in SAOImage DS9 as an RGB image, first go to Frame -> RGB, then choose File -> Open As -> RGB Cube.

4. SDSS Catalog Downloader (download_SDSS_catalog_withSciServer.ipynb)

A Jupyter Notebook designed to query and download SDSS catalog data using the SciServer environment.

Important

This notebook relies on SciServer internal libraries and cannot be run locally. It must be executed within the SciServer Compute environment.

Setup Instructions

  1. Create an account at the SciServer Login Portal.
  2. Follow the setup steps in the SciServer Example-Notebooks Installation Guide.
  3. Create a persistent directory under /Storage/<username>/persistent/.
  4. Upload this notebook into that folder and run it within a SciServer Compute container.

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Various astronomy scripts

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