sed-model 0.1.7__tar.gz

sed_model-0.1.7/LICENSE

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+SED_Model License
+
+Copyright (c) 2026 Niall Miller
+
+This repository uses a mixed-license structure:
+
+1. The Python source code, documentation, examples, tests, and packaging files
+   are distributed under the MIT License.
+
+2. The Fortran numerical kernels in the `fortran/` directory are distributed
+   under the GNU Lesser General Public License v3.0 or later (LGPL-3.0-or-later),
+   as indicated in their source headers.
+
+MIT License
+-----------
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of the MIT-licensed portions of this software and associated documentation
+files (the "Software"), to deal in those portions of the Software without
+restriction, including without limitation the rights to use, copy, modify,
+merge, publish, distribute, sublicense, and/or sell copies of those portions
+of the Software, and to permit persons to whom those portions of the Software
+are furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the MIT-licensed portions of the Software.
+
+THE MIT-LICENSED PORTIONS OF THE SOFTWARE ARE PROVIDED "AS IS", WITHOUT
+WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
+FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT,
+TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+THE USE OR OTHER DEALINGS IN THE MIT-LICENSED PORTIONS OF THE SOFTWARE.
+
+LGPL Notice
+-----------
+
+The Fortran kernels in `fortran/` are licensed under LGPL-3.0-or-later. See
+the source file headers for the applicable license notice. The full text of
+the LGPL-3.0 license is available from the Free Software Foundation:
+https://www.gnu.org/licenses/lgpl-3.0.html

sed_model-0.1.7/MANIFEST.in

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+recursive-include fortran *.f90

sed_model-0.1.7/PKG-INFO

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+Metadata-Version: 2.1
+Name: sed-model
+Version: 0.1.7
+Summary: Forward and inverse stellar photometry from SED grids.
+Author-email: Niall Miller <niall.j.miller@gmail.com>
+Project-URL: Homepage, https://github.com/nialljmiller/SED_Model
+Project-URL: Repository, https://github.com/nialljmiller/SED_Model
+Project-URL: Issues, https://github.com/nialljmiller/SED_Model/issues
+Keywords: astronomy,astrophysics,stellar astronomy,synthetic photometry,spectral energy distributions,sed,stellar parameters,bayesian inference,mcmc
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Fortran
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.22
+Requires-Dist: pandas>=1.5
+Requires-Dist: emcee>=3.1
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Provides-Extra: demo
+Requires-Dist: matplotlib; extra == "demo"
+
+# SED_Model
+
+**MESA-free synthetic photometry and stellar parameter inference.**
+
+SED_Model is a Python package for computing observer-ready synthetic spectral energy distributions (SEDs) and broadband magnitudes from stellar atmosphere grids, and for recovering stellar parameters from observed photometry via Bayesian MCMC inference. It is designed to work directly downstream of `SED_Tools` and as a standalone drop-in for workflows that use MESA-style atmosphere grids and filter transmission curves.
+
+Version: `0.1.0`
+
+---
+
+## Overview
+
+SED_Model provides two paired models that share the same parameter language:
+
+- **Forward model** — maps `(Teff, logg, [M/H], R, d)` to an interpolated SED, bolometric flux and magnitude, and synthetic magnitudes in any set of loaded filters.
+- **Inverse model** — maps observed magnitudes with uncertainties to a posterior distribution over `(Teff, logg, [M/H])`, and optionally over `Av` and distance, via `emcee` MCMC sampling.
+
+Both directions operate through a shared `FitParams` object. The same parameter specification flows from the forward model to the likelihood evaluator inside the sampler and back out again.
+
+---
+
+## Features
+
+- Hermite and linear interpolation over 3D atmosphere grids `(Teff, logg, [M/H])`.
+- Photon-counting filter convolution in Vega, AB, and ST photometric systems.
+- Precomputed zero-points matching MESA `colors/private/synthetic.f90` conventions.
+- Pure-NumPy interstellar dust extinction with multiple supported laws.
+- Bayesian stellar-parameter inference via `emcee` with fixed, bounded, and fully free parameter modes.
+- Structured result containers with summaries, persistence to CSV and NPZ, and interpolation diagnostics.
+- Fortran kernels for performance-critical paths, compiled via `f2py`/Meson.
+- Forward tests validated against MESA colors reference outputs; inverse tests verified by self-consistent synthetic recovery.
+
+---
+
+## Installation
+
+### From source
+
+```bash
+git clone https://github.com/nialljmiller/SED_Model.git
+cd SED_Model
+python -m pip install -e .
+````
+
+### Build the Fortran extension
+
+```bash
+python setup.py build_ext --inplace
+```
+
+or:
+
+```bash
+make
+```
+
+The build compiles:
+
+```text
+fortran/cc_kernels.f90
+fortran/cc_api.f90
+```
+
+into the `sed_model.cc_api` extension module.
+
+### Requirements
+
+* Python >= 3.10
+* `numpy`
+* `pandas`
+* `emcee`
+* `gfortran`
+* `meson`
+* `ninja`
+
+`matplotlib` is only needed for plotting/demo workflows.
+
+---
+
+## Quick Start
+
+```python
+from sed_model import load_grid, load_filters, run_forward, run_inverse
+
+grid = load_grid("/path/to/Kurucz2003all/")
+filters = load_filters([
+    "/path/to/filters/GAIA/G.dat",
+    "/path/to/filters/2MASS/J.dat",
+])
+
+# Forward model
+result = run_forward(
+    teff=5777,
+    logg=4.44,
+    meta=0.0,
+    R=6.957e10,
+    d=3.086e19,
+    grid=grid,
+    filters=filters,
+    mag_system="Vega",
+)
+
+print(result.magnitudes)
+
+# Inverse model
+posterior = run_inverse(
+    obs_magnitudes=[5.03, 4.17],
+    obs_uncertainties=[0.01, 0.02],
+    filter_names=["G", "J"],
+    R=6.957e10,
+    d=3.086e19,
+    grid=grid,
+    filters=filters,
+    mag_system="Vega",
+)
+
+posterior.print_summary()
+```
+
+---
+
+## Grid Loading
+
+```python
+from sed_model import load_grid
+
+grid = load_grid("/path/to/Kurucz2003all/")
+```
+
+`load_grid()` expects a MESA/SED_Tools-style atmosphere grid containing a `flux_cube.bin`, with optional validation against a co-located `lookup_table.csv`.
+
+The returned `AtmosphereGrid` exposes:
+
+* `teff_grid`, `logg_grid`, `meta_grid`
+* `teff_bounds`, `logg_bounds`, `meta_bounds`
+* `wavelengths`
+* `in_bounds(teff, logg, meta)`
+* `clamp(teff, logg, meta)`
+* `interp_radius(teff, logg, meta)`
+
+---
+
+## Filter Loading
+
+```python
+from sed_model import load_filters, load_filters_from_instrument_dir
+
+filters = load_filters([
+    "/path/to/filters/Generic/Johnson/B.dat",
+    "/path/to/filters/Generic/Johnson/V.dat",
+])
+
+filters = load_filters_from_instrument_dir(
+    "/path/to/filters/Generic/Johnson"
+)
+```
+
+Each `Filter` stores:
+
+* `name`
+* `wavelengths`
+* `transmission`
+* Vega, AB, and ST zero-points
+* `zero_point(system)`
+
+Supported systems are:
+
+```text
+Vega
+AB
+ST
+```
+
+---
+
+## Forward Model
+
+```python
+from sed_model import run_forward
+
+result = run_forward(
+    teff=5778.0,
+    logg=4.44,
+    meta=0.0,
+    R=6.957e10,
+    d=3.086e19,
+    grid=grid,
+    filters=filters,
+    mag_system="Vega",
+    interp_method="hermite",
+)
+```
+
+`ForwardResult` contains:
+
+* `wavelengths`
+* `surface_flux`
+* `observed_flux`
+* `magnitudes`
+* `band_fluxes`
+* `bol_flux`
+* `bol_mag`
+* `interp_radius`
+* `clamped`
+* `teff`, `logg`, `meta`, `R`, `d`, `a_v`
+* `mag_system`
+* `extinction_applied`
+
+---
+
+## Inverse Model
+
+```python
+from sed_model import run_inverse
+
+result = run_inverse(
+    obs_magnitudes=[5.03, 4.17],
+    obs_uncertainties=[0.01, 0.02],
+    filter_names=["G", "J"],
+    R=6.957e10,
+    d=3.086e19,
+    grid=grid,
+    filters=filters,
+    n_walkers=32,
+    n_steps=1000,
+    n_burn=300,
+    seed=42,
+)
+```
+
+`InverseResult` contains:
+
+* `samples`
+* `log_prob`
+* `filter_names`
+* `obs_magnitudes`
+* `obs_uncertainties`
+* `R`, `d`, `mag_system`
+* `n_walkers`, `n_steps`, `n_burn`, `n_thin`
+* `acceptance_fraction`
+* `autocorr_time`
+
+It also provides:
+
+```python
+result.summary()
+result.print_summary()
+result.save("posterior.npz")
+```
+
+---
+
+## Parameter Modes
+
+`FitParams` and `ParamSpec` define the shared parameter language used by the forward and inverse models.
+
+```python
+from sed_model import fit_params_from_grid, fixed, free, bounded
+
+params = fit_params_from_grid(
+    grid,
+    a_v=(0.0, 2.0),   # free Av
+    d_cm=3.086e19,    # fixed distance
+)
+```
+
+Available modes:
+
+```python
+fixed(value)
+free(lo, hi)
+bounded(lo, hi)
+```
+
+Example:
+
+```python
+from sed_model import FitParams, fixed, free
+
+params = FitParams(
+    teff=free(5000.0, 6500.0),
+    logg=fixed(4.44),
+    meta=free(-1.0, 0.5),
+    a_v=fixed(0.0),
+    d=fixed(3.086e19),
+)
+```
+
+---
+
+## Extinction
+
+```python
+from sed_model import make_extinction_model, run_forward
+
+ext = make_extinction_model(
+    enabled=True,
+    law="fitzpatrick99",
+    a_v=0.3,
+    r_v=3.1,
+)
+
+result = run_forward(
+    teff=5778,
+    logg=4.44,
+    meta=0.0,
+    R=6.957e10,
+    d=3.086e19,
+    grid=grid,
+    filters=filters,
+    extinction=ext,
+)
+```
+
+Supported extinction-law keys include:
+
+```text
+ccm89
+odonnell94
+fitzpatrick99
+fm07
+calzetti00
+gordon23
+```
+
+---
+
+## Output and I/O
+
+```python
+from sed_model import save_sed, save_magnitudes
+
+save_sed(result, "forward_sed.csv")
+save_magnitudes(result, "forward_magnitudes.csv")
+```
+
+Inverse results can be saved directly:
+
+```python
+posterior.save("posterior_samples.npz")
+```
+
+---
+
+## Relationship to SED_Tools
+
+SED_Model sits directly downstream of `SED_Tools`.
+
+`SED_Tools` handles acquisition, standardization, filter downloads, grid construction, and SED completion/generation. SED_Model uses the resulting atmosphere grids and filter files for forward synthetic photometry and Bayesian stellar-parameter inference.
+
+A typical workflow is:
+
+```text
+SED_Tools  ->  build/download SED grids and filters
+SED_Model  ->  generate synthetic magnitudes and infer stellar parameters
+```
+
+---
+
+## Testing
+
+```bash
+pytest tests/test_forward.py
+pytest tests/test_inverse.py
+```
+
+The forward tests verify grid loading, bounds checking, interpolation, filter loading, zero-points, bolometric quantities, and synthetic magnitudes.
+
+The inverse tests verify self-consistent posterior recovery and `InverseResult` persistence.
+
+---
+
+## Repository Structure
+
+```text
+sed_model/
+  __init__.py
+  grid.py
+  filters.py
+  forward.py
+  inverse.py
+  params.py
+  io.py
+  sed_extinction.py
+
+fortran/
+  cc_kernels.f90
+  cc_api.f90
+
+demos/
+tests/
+Makefile
+meson.build
+pyproject.toml
+setup.py
+```
+
+---
+
+## License
+
+SED_Model uses a mixed-license structure. The Python source code, documentation, examples, tests, and packaging files are distributed under the MIT License. The Fortran numerical kernels in `fortran/` are distributed under LGPL-3.0-or-later. See `LICENSE` and source file headers for details.