STAMP: Spectral Time-series Analysis and Mapping Program

STAMP is a browser-based tool for exploring JWST spectral time-series observations. It ingests FITS x1dints files or HDF5 spectral cubes from MAST, generates interactive 3D surface plots and 2D heatmaps, and fits model atmosphere grids to individual or time-resolved spectra. Designed for brown dwarf and exoplanet atmosphere characterization, it runs as a Flask web application with Plotly visualizations.

Demo

STAMP_demo_video.mp4

Features

• MAST data ingestion — Query and download JWST spectral time-series directly from MAST, or upload local FITS/HDF5 files
• Interactive 3D surface plots — Flux vs. wavelength vs. time rendered as rotatable Plotly surfaces
• 2D heatmaps — Wavelength-time heatmaps with configurable color scales
• Spectral band filtering — Restrict wavelength, time, and variability ranges interactively
• Time-series video generation — Animate spectra frame-by-frame as MP4 (requires ffmpeg)
• Model atmosphere fitting — Chi-squared grid fitting against 12 synthetic spectral libraries (see Model Grids)
• Chunked spectral fitting — Fit independent wavelength segments to detect spatially-varying atmospheric properties
• Parameter sweeps — Fit all time-steps against a grid to track Teff, log g, and metallicity evolution
• Sinusoidal light-curve fitting — Fit single or multi-component sinusoids to extracted light curves, with amplitude-vs-wavelength sweeps
• Data export — Download standalone HTML plots, CSV tables, and combined ZIP archives with embedded video
• Interactive guided tour — Step-by-step walkthrough of the interface for new users

Live Instance

https://stamp.us.reclaim.cloud

Quick Start

git clone https://github.com/munozcar/SA3D.git
cd SA3D
python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

# Download at least one model grid (optional, for fitting)
python scripts/download_all_grids.py

# Run the development server
python app.py

The app will be available at http://localhost:5000.

For production deployment, use gunicorn:

gunicorn wsgi:application --bind 0.0.0.0:8080

Supported Data Formats

FITS (JWST x1dints)

STAMP reads multi-integration JWST spectral files (_x1dints.fits). Each file must contain:

• One or more EXTRACT1D HDUs with columns WAVELENGTH (microns) and FLUX (Jy)
• An INT_TIMES HDU with column int_mid_MJD_UTC for time-axis registration

Multiple files are sorted by observation time and concatenated into a single spectral time-series cube.

HDF5

HDF5 files (.h5) are supported with datasets:

• wavelength — 1D array of wavelength values (microns)
• flux — 2D array of shape (n_times, n_wavelengths)
• time — 1D array of timestamps

Model Grids

STAMP ships download scripts for 12 model atmosphere grids. After downloading, grids are stored under model_grids/ with a standardized index.csv + spectra/ layout.

Grid	Teff Range (K)	log g	Metallicity	Source	Reference
ATMO 2020 CEQ	200 -- 3000	2.5 -- 5.5	Solar	SVO	Phillips et al. (2020)
ATMO 2020 NEQ Strong	200 -- 1800	2.5 -- 5.5	Solar	SVO	Phillips et al. (2020)
ATMO 2020 NEQ Weak	200 -- 1800	2.5 -- 5.5	Solar	SVO	Phillips et al. (2020)
BT-Settl CIFIST	1200 -- 7000	2.5 -- 5.5	0.0	Zenodo	Allard et al. (2012)
DRIFT-PHOENIX	1000 -- 3000	3.0 -- 6.0	-0.6 to +0.3	SVO	Helling et al. (2008)
Exo-REM	Varies	Varies	Varies (+ C/O)	LESIA	Charnay et al. (2018)
Morley 2012	400 -- 1300	4.0 -- 5.5	Solar (+ f_sed)	Morley et al. (2012)	Morley et al. (2012)
Phoenix-ACES	2500 -- 5000	3.5 -- 5.5	-1.0 to +0.5	Goettingen	Husser et al. (2013)
Sonora Bobcat	200 -- 2400	3.25 -- 5.5	-0.5 to +0.5	Zenodo	Marley et al. (2021)
Sonora Diamondback	900 -- 2400	3.5 -- 5.5	-0.5 to +0.5 (+ f_sed)	Zenodo	Morley et al. (2024)
Sonora Elf Owl (Y)	Varies	Varies	Varies	Zenodo	Mukherjee et al. (2024)
Sonora Elf Owl (T, L)	Varies	Varies	Varies	Zenodo	Mukherjee et al. (2024)

To download all grids:

python scripts/download_all_grids.py

Individual grids can be downloaded separately (e.g., python scripts/download_phoenix_grid.py).

Project Structure

SA3D/
├── app.py                  # Flask application factory
├── config.py               # Configuration (BASE_DIR, COLOR_SCALES, GRIDS_DIR)
├── wsgi.py                 # WSGI entry point for production servers
├── state.py                # Shared mutable state (progress tracking, results cache)
├── data_io.py              # FITS and HDF5 file readers
├── processing.py           # Binning, smoothing, regridding, variability analysis
├── plotting.py             # Plotly figure builders (3D surface + 2D heatmap)
├── fitting.py              # Chi-squared grid fitting + sinusoidal fitting
├── model_grids.py          # Grid loader with caching and unit conversion
├── cache_manager.py        # Disk-based dataset cache
├── routes/
│   ├── main.py             # Index page, static plot serving
│   ├── upload.py           # File upload and MAST query endpoints
│   ├── jobs.py             # Background job processing and progress tracking
│   └── fitting.py          # Model fitting API endpoints
├── templates/
│   └── index.html          # Single-page application template
├── static/
│   ├── css/                # Stylesheets (Tailwind, tour overlay)
│   ├── js/                 # Frontend modules (state, plots, fitting, export, tour)
│   └── demo_data/          # Bundled demo dataset
├── model_grids/            # Downloaded spectral grids (gitignored spectra)
├── scripts/                # Grid download utilities and fitting validation
└── requirements.txt

Deployment

STAMP is deployed on Reclaim Cloud with gunicorn as the WSGI server. Key environment variables:

Variable	Default	Description
GRIDS_DIR	model_grids/	Path to model grid directory
DEMO_DATA_DIR	static/demo_data/	Path to bundled demo dataset

An optional config.yaml in the project root can set data_dir for uploaded file storage.

References

• Allard, F., Homeier, D., & Freytag, B. (2012). Models of very-low-mass stars, brown dwarfs and exoplanets. Phil. Trans. R. Soc. A, 370, 2765.
• Charnay, B., et al. (2018). A self-consistent cloud model for brown dwarfs and young giant exoplanets. ApJ, 854, 172.
• Helling, Ch., et al. (2008). A comprehensive nomenclature for brown dwarf and extrasolar giant planet atmosphere models. A&A, 485, 547.
• Husser, T.-O., et al. (2013). A new extensive library of PHOENIX stellar atmospheres and synthetic spectra. A&A, 553, A6.
• Marley, M. S., et al. (2021). The Sonora Brown Dwarf Atmosphere and Evolution Models. ApJ, 920, 85.
• Morley, C. V., et al. (2012). Neglected clouds in T and Y dwarf atmospheres. ApJ, 756, 172.
• Morley, C. V., et al. (2024). The Sonora Substellar Atmosphere Models. IV. Diamondback. arXiv:2402.00758.
• Mukherjee, S., et al. (2024). The Sonora Substellar Atmosphere Models. III. Elf Owl. ApJ, 963, 73.
• Phillips, M. W., et al. (2020). A new set of atmosphere and evolution models for cool T-Y brown dwarfs and giant exoplanets. A&A, 637, A38.