saltjax 0.1.0__tar.gz

saltjax-0.1.0/LICENSE

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saltjax-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: saltjax
+Version: 0.1.0
+Summary: Fast batched SALT2 lightcurve fitting with JAX, reproducing sncosmo
+Author-email: Mickael Rigault <m.rigault@ipnl.in2p3.fr>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/MickaelRigault/saltjax
+Keywords: astronomy,astrophysics,supernovae,jax
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.26
+Requires-Dist: pandas
+Requires-Dist: scipy
+Requires-Dist: jax
+Requires-Dist: sncosmo
+Requires-Dist: extinction
+Provides-Extra: docs
+Requires-Dist: myst-nb; extra == "docs"
+Requires-Dist: sphinx-book-theme; extra == "docs"
+Requires-Dist: sphinx_copybutton; extra == "docs"
+Requires-Dist: sphinx-design; extra == "docs"
+Provides-Extra: tests
+Requires-Dist: pytest; extra == "tests"
+Requires-Dist: coverage; extra == "tests"
+Requires-Dist: iminuit; extra == "tests"
+Provides-Extra: progress
+Requires-Dist: tqdm; extra == "progress"
+Dynamic: license-file
+
+# saltjax
+
+Fast, batched SALT2 lightcurve fitting with [JAX](https://docs.jax.dev), reproducing
+[sncosmo](https://sncosmo.readthedocs.io)'s `fit_lc`.
+
+`saltjax` fits SALT2 to thousands of lightcurves at once. It uses the same model as sncosmo
+(same interpolation kernel, model covariance and Milky Way dust), and gives the same
+parameters and errors (to ~1e-2 sigma at worst) one to two orders of magnitude faster.
+
+## Install
+
+```bash
+git clone https://github.com/MickaelRigault/saltjax.git
+cd saltjax
+pip install .
+```
+
+## Quick start
+
+```python
+import saltjax
+
+# data: lightcurves, indexed by (target, observation), with columns
+#       time (or mjd), band, flux, fluxerr, zp [, zpsys]
+# targets: one row per target with z [, t0, x1, c, mwebv]
+results = saltjax.fit_salt(data, targets, modelcov=True, progress_bar=True)
+results[["t0", "x0", "x1", "c", "t0_err", "x0_err", "x1_err", "c_err"]]
+```
+
+`saltjax` is used by [skysurvey](https://github.com/MickaelRigault/skysurvey) through
+`skysurvey.lcfit.fit_salt_jax(dataset)`.
+
+## How it reproduces sncosmo
+
+* **Interpolation.** sncosmo interpolates the SALT2 surfaces with a separable bicubic-convolution kernel. Band
+  integration is linear, so `saltjax` band-integrates the surfaces at the native phase nodes
+  and applies the *same* kernel in phase. This is exact.
+* **Colour and dust.** The colour law and the Milky Way extinction (CCM89, observer frame) are written as an exact
+  band-mean factor times power series truncated below machine precision.
+* **Redshift tables.** The band integrals are tabulated on a fine redshift grid. This is the only approximation:
+  relative flux differences are below 1e-6.
+* **Model covariance.** `modelcov=True` follows `sncosmo.fit_lc`. The model covariance (a diagonal plus one block
+  per band) is inverted exactly with the Woodbury identity.
+* **Errors.** Errors are `2 H^-1`, with `H` the exact Hessian of the chi2 (as Minuit HESSE).
+
+## Limitations
+
+* SALT2 sources only (`sncosmo.SALT2Source`).
+* The only effect supported is Milky Way CCM89 dust in the observer frame.
+* AB magnitude system only.
+* No parameter bounds.
+* Fixed redshift.

saltjax-0.1.0/README.md

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+# saltjax
+
+Fast, batched SALT2 lightcurve fitting with [JAX](https://docs.jax.dev), reproducing
+[sncosmo](https://sncosmo.readthedocs.io)'s `fit_lc`.
+
+`saltjax` fits SALT2 to thousands of lightcurves at once. It uses the same model as sncosmo
+(same interpolation kernel, model covariance and Milky Way dust), and gives the same
+parameters and errors (to ~1e-2 sigma at worst) one to two orders of magnitude faster.
+
+## Install
+
+```bash
+git clone https://github.com/MickaelRigault/saltjax.git
+cd saltjax
+pip install .
+```
+
+## Quick start
+
+```python
+import saltjax
+
+# data: lightcurves, indexed by (target, observation), with columns
+#       time (or mjd), band, flux, fluxerr, zp [, zpsys]
+# targets: one row per target with z [, t0, x1, c, mwebv]
+results = saltjax.fit_salt(data, targets, modelcov=True, progress_bar=True)
+results[["t0", "x0", "x1", "c", "t0_err", "x0_err", "x1_err", "c_err"]]
+```
+
+`saltjax` is used by [skysurvey](https://github.com/MickaelRigault/skysurvey) through
+`skysurvey.lcfit.fit_salt_jax(dataset)`.
+
+## How it reproduces sncosmo
+
+* **Interpolation.** sncosmo interpolates the SALT2 surfaces with a separable bicubic-convolution kernel. Band
+  integration is linear, so `saltjax` band-integrates the surfaces at the native phase nodes
+  and applies the *same* kernel in phase. This is exact.
+* **Colour and dust.** The colour law and the Milky Way extinction (CCM89, observer frame) are written as an exact
+  band-mean factor times power series truncated below machine precision.
+* **Redshift tables.** The band integrals are tabulated on a fine redshift grid. This is the only approximation:
+  relative flux differences are below 1e-6.
+* **Model covariance.** `modelcov=True` follows `sncosmo.fit_lc`. The model covariance (a diagonal plus one block
+  per band) is inverted exactly with the Woodbury identity.
+* **Errors.** Errors are `2 H^-1`, with `H` the exact Hessian of the chi2 (as Minuit HESSE).
+
+## Limitations
+
+* SALT2 sources only (`sncosmo.SALT2Source`).
+* The only effect supported is Milky Way CCM89 dust in the observer frame.
+* AB magnitude system only.
+* No parameter bounds.
+* Fixed redshift.

saltjax-0.1.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "saltjax"
+description = "Fast batched SALT2 lightcurve fitting with JAX, reproducing sncosmo"
+authors = [
+    {name = "Mickael Rigault", email = "m.rigault@ipnl.in2p3.fr"},
+]
+readme = "README.md"
+requires-python = ">=3.10"
+license = "Apache-2.0"
+keywords = ["astronomy", "astrophysics", "supernovae", "jax"]
+classifiers = [
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: 3",
+    "Topic :: Scientific/Engineering :: Astronomy",
+    "Topic :: Scientific/Engineering :: Physics",
+]
+dependencies = [
+    # basic
+    "numpy >=1.26",
+    "pandas",
+    "scipy",
+    # jax
+    "jax",
+    # Astro
+    "sncosmo",
+    "extinction",
+]
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/MickaelRigault/saltjax"
+
+[project.optional-dependencies]
+docs = [
+    "myst-nb",
+    "sphinx-book-theme",
+    "sphinx_copybutton",
+    "sphinx-design",
+]
+tests = ["pytest", "coverage", "iminuit"]
+progress = ["tqdm"]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.dynamic]
+version = {attr = "saltjax.__version__"}
+
+
+# RUFF
+[tool.ruff]
+exclude = ["tests", "docs"]
+include = ["*.py"]
+
+[tool.ruff.lint]
+select = [
+  "E", "F", # flake8
+  "NPY",         # numpy
+]
+ignore = [
+  "E501",  # line-too-long
+]
+unfixable = [
+  "F841", # Removes unused variables
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["saltjax"]
+
+[tool.pytest.ini_options]
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+testpaths = ["tests"]
+
+[tool.coverage.run]
+source = ["saltjax"]
+omit = ["tests/*"]
+branch = true
+
+[tool.coverage.report]
+exclude_lines = [
+  "pragma: no cover",
+  "except ImportError",
+  "raise AssertionError",
+  "raise NotImplementedError",
+  "if __name__ == .__main__.:",
+]

saltjax-0.1.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

saltjax-0.1.0/src/saltjax/__init__.py

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+"""Fast batched SALT2 lightcurve fitting with JAX, reproducing sncosmo."""
+
+__version__ = "0.1.0"
+
+from .fit import fit_salt # noqa: F401, E402
+from .tables import build_tables, get_tables, get_salt2_source # noqa: F401, E402
+from .data import pack_lightcurves # noqa: F401, E402
+from .model import get_model_functions # noqa: F401, E402
+from .kernel import kernel_weights # noqa: F401, E402

saltjax-0.1.0/src/saltjax/data.py

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+"""Pack lightcurves and per-target tables into padded arrays for the fit."""
+
+import warnings
+
+import numpy as np
+import jax
+import jax.numpy as jnp
+
+from .kernel import kernel_weights
+
+__all__ = ["pack_lightcurves"]
+
+LC_KEYS = ("t", "flux", "err", "zpn", "band", "mask")
+FIT_KEYS = ("K", "Ke", "CLb", "Tmw", "F", "Fe", "V", "Ve", "CD", "z") + LC_KEYS
+
+
+def get_time_key(data, time_key=None):
+    """Get the time column of the lightcurves.
+
+    Parameters
+    ----------
+    data : pandas.DataFrame
+        Lightcurve data.
+
+    time_key : str or None, optional
+        Time column. If None, the first of 'time', 'mjd' or 'jd' found.
+        The default is None.
+
+    Returns
+    -------
+    str
+        Name of the time column.
+
+    Raises
+    ------
+    ValueError
+        If `time_key` is None and no time column is found.
+    """
+    if time_key is not None:
+        return time_key
+    time_key = next((k for k in ("time", "mjd", "jd") if k in data.columns), None)
+    if time_key is None:
+        raise ValueError("cannot parse the time column, provide time_key.")
+    return time_key
+
+
+@jax.jit
+def _interp_contract(K, idx, w, epow):
+    """Interpolate K in redshift and contract the dust series, per target."""
+    def one(i, ww, e):
+        return jnp.einsum("j,m,jbkcmp->bkcp", ww, e, K[i])
+    return jax.vmap(one)(idx, w, epow)
+
+
+def pack_lightcurves(data, targets, tables, indexes=None, phase_range=(-10, 40),
+                     mwebv_key="mwebv", time_key=None, pad_to=16):
+    """Pack the lightcurves and the per-target tables into padded arrays.
+
+    Parameters
+    ----------
+    data : pandas.DataFrame
+        Lightcurves, with a (target, observation) multi-index and columns
+        time (see `time_key`), 'band', 'flux', 'fluxerr', 'zp' and optionally
+        'zpsys'.
+
+    targets : pandas.DataFrame
+        Targets, indexed as the first level of `data`, with a 'z' column, a
+        't0' column if `phase_range` is given and a `mwebv_key` column for the
+        Milky Way extinction.
+
+    tables : dict
+        Output of :func:`saltjax.tables.build_tables`.
+
+    indexes : list or None, optional
+        Targets to pack. If None, all those of `targets`. The default is None.
+
+    phase_range : list or None, optional
+        Rest-frame phase range (relative to the targets' t0) of the data used.
+        The default is (-10, 40).
+
+    mwebv_key : str or None, optional
+        Column of `targets` with the Milky Way E(B-V). If None or absent, no
+        Milky Way extinction. The default is 'mwebv'.
+
+    time_key : str or None, optional
+        Time column of the lightcurves. If None, the first of 'time', 'mjd' or
+        'jd' found. The default is None.
+
+    pad_to : int, optional
+        The number of points per lightcurve is padded to a multiple of
+        `pad_to`. The default is 16.
+
+    Returns
+    -------
+    dict
+        Arrays used by the fit (one row per target).
+
+    Raises
+    ------
+    NotImplementedError
+        If a magnitude system other than 'ab' is used.
+    """
+    indexes = list(targets.index if indexes is None else indexes)
+    truth = targets.loc[indexes]
+    z = truth["z"].to_numpy(float)
+    has_mw = mwebv_key is not None and mwebv_key in truth
+    ebv = truth[mwebv_key].to_numpy(float) if has_mw else np.zeros(len(z))
+    zg = tables["zgrid"]
+    idx, w = kernel_weights((z - zg[0]) / (zg[1] - zg[0]), len(zg))
+
+    def zi(table):
+        return np.einsum("sj,sj...->s...", w, table[idx])
+    epow = ebv[:, None] ** np.arange(tables["nm"])
+    with jax.enable_x64(True):
+        K, Ke = (np.asarray(_interp_contract(jnp.asarray(tables[key]), jnp.asarray(idx),
+                                             jnp.asarray(w), jnp.asarray(epow)))
+                 for key in ("K", "Ke"))
+
+    data = data.loc[indexes]
+    time_key = get_time_key(data, time_key)
+    if "zpsys" in data.columns and not data["zpsys"].str.lower().eq("ab").all():
+        raise NotImplementedError("only the 'ab' magnitude system is supported")
+    lut = {k: j for j, k in enumerate(indexes)}
+    pos = np.fromiter((lut[v] for v in data.index.get_level_values(0)), int, len(data))
+    # as sncosmo.fit_lc: drop the points whose band is out of the model wavelength range
+    bandid = {b: j for j, b in enumerate(tables["bands"])}
+    bid = data["band"].map(bandid).to_numpy()
+    wmin, wmax = tables["wave_range"]
+    brange = tables["band_range"][bid]
+    covered = (brange[:, 0] >= wmin * (1 + z[pos])) & (brange[:, 1] <= wmax * (1 + z[pos]))
+    if not np.all(covered):
+        warnings.warn(f"{np.sum(~covered)} points dropped: band out of the model wavelength range "
+                      f"({', '.join(sorted(data['band'][~covered].unique()))})")
+        data, pos = data[covered], pos[covered]
+    if phase_range is not None:
+        ph = (data[time_key].to_numpy() - truth["t0"].to_numpy(float)[pos]) / (1 + z[pos])
+        keep = (ph >= phase_range[0]) & (ph <= phase_range[1])
+        data, pos = data[keep], pos[keep]
+    order = np.argsort(pos, kind="stable")
+    ps = pos[order]
+    starts = np.r_[0, np.flatnonzero(np.diff(ps)) + 1]
+    slot = np.empty(len(ps), int)
+    slot[order] = np.arange(len(ps)) - np.repeat(starts, np.diff(np.r_[starts, len(ps)]))
+    nsn = len(indexes)
+    nobs = int(np.ceil((slot.max() + 1) / pad_to) * pad_to) if len(slot) else pad_to
+    out = {k: np.zeros((nsn, nobs)) for k in LC_KEYS}
+    out["t"][pos, slot] = data[time_key]
+    out["flux"][pos, slot] = data["flux"]
+    out["err"][pos, slot] = data["fluxerr"]
+    out["zpn"][pos, slot] = 10 ** (0.4 * data["zp"].to_numpy(float))
+    out["band"][pos, slot] = data["band"].map(bandid)
+    out["mask"][pos, slot] = 1.
+    out["err"][out["mask"] == 0] = 1.
+    out["band"] = out["band"].astype(int)
+    # exact band-mean dust factor
+    Tmw = 10 ** (-0.4 * ebv[:, None] * tables["Kb"][None, :])
+    return out | dict(K=K, Ke=Ke, CLb=zi(tables["CLb"]), Tmw=Tmw,
+                      F=zi(tables["F"]), Fe=zi(tables["Fe"]),
+                      V=zi(tables["V"]), Ve=zi(tables["Ve"]), CD=zi(tables["CD"]), z=z,
+                      ebv=ebv, index=np.asarray(indexes))