jaxspec 0.0.4__py3-none-any.whl → 0.0.6__py3-none-any.whl

jaxspec/util/abundance.py

@@ -0,0 +1,111 @@
+import importlib.resources
+import pandas as pd
+from mendeleev.fetch import fetch_table
+from astropy.io import ascii
+
+abundance_table: pd.DataFrame = ascii.read(importlib.resources.files("jaxspec") / "tables/abundances.dat").to_pandas()
+element_data: pd.DataFrame = fetch_table("elements")[0:30][
+    ["symbol", "atomic_number", "atomic_radius", "atomic_volume", "atomic_weight"]
+].rename(columns={"symbol": "Element"})
+
+abundance_table: pd.DataFrame
+"""
+Dataframe containing various abundances that can be used in `jaxspec`. It is adapted from
+[XSPEC's abundance table](https://heasarc.gsfc.nasa.gov/xanadu/xspec/manual/node116.html). The following table are available:
+
+| Name   | Reference                                                                                      | Note                         |
+| :----: | :--------------------------------------------------------------------------------------------- | :--------------------------- |
+| `angr` | [Anders & Gevresse (1989)](https://ui.adsabs.harvard.edu/abs/1989GeCoA..53..197A/abstract)     | Photospheric, using Table 2. |
+| `aspl` | [Asplund et al. (2009)](https://ui.adsabs.harvard.edu/abs/2009ARA%26A..47..481A/abstract)      | Photospheric, using Table 1. |
+| `feld` | [Feldman (1992)](https://ui.adsabs.harvard.edu/abs/1992PhyS...46..202F/abstract)               |
+| `aneb` | [Anders & Ebihara (1982)](https://ui.adsabs.harvard.edu/abs/1982GeCoA..46.2363A/abstract)      |
+| `grsa` | [Grevesse & Sauval (1998)](https://ui.adsabs.harvard.edu/abs/1998SSRv...85..161G/abstract)     |
+| `wilm` | [Wilms et al. (2000)](https://ui.adsabs.harvard.edu/abs/2000ApJ...542..914W/abstract)          |
+| `lodd` | [Lodders (2003)](https://ui.adsabs.harvard.edu/abs/2003ApJ...591.1220L/abstract)               | Photospheric, using Table 1. |
+| `lgpp` | [Lodders, Palme & Gail (2009)](https://ui.adsabs.harvard.edu/abs/2009LanB...4B..712L/abstract) | Photospheric, using Table 4. |
+| `lgps` | [Lodders, Palme & Gail (2009)](https://ui.adsabs.harvard.edu/abs/2009LanB...4B..712L/abstract) | Proto-solar, using Table 10. |
+
+
+The table is a `pandas.Dataframe` object, and can be accessed as such. For example, to get the abundance of iron in the `aspl` table, one can do:
+
+```python
+from jaxspec.util.abundance import abundance_table
+assert abundance_table['Element'][ 26 - 1] == 'Fe'
+print(abundance_table['aspl'][ 26 - 1]) # 3.16e-05
+```
+
+The full table is displayed below:
+
+| Element | angr | aspl | feld | aneb | grsa | wilm | lodd | lgpp | lgps |
+|:---:|---:|---:|---:|---:|---:|---:|---:|---:|:---:|
+| H | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 | 1.0 |
+| He | 0.0977 | 0.0851 | 0.0977 | 0.0801 | 0.0851 | 0.0977 | 0.0792 | 0.0841 | 0.0969 |
+| Li | 1.45e-11 | 1.12e-11 | 1.26e-11 | 2.19e-09 | 1.26e-11 | 0.0 | 1.9e-09 | 1.26e-11 | 2.15e-09 |
+| Be | 1.41e-11 | 2.4e-11 | 2.51e-11 | 2.87e-11 | 2.51e-11 | 0.0 | 2.57e-11 | 2.4e-11 | 2.36e-11 |
+| B | 3.98e-10 | 5.01e-10 | 3.55e-10 | 8.82e-10 | 3.55e-10 | 0.0 | 6.03e-10 | 5.01e-10 | 7.26e-10 |
+| C | 0.000363 | 0.000269 | 0.000398 | 0.000445 | 0.000331 | 0.00024 | 0.000245 | 0.000245 | 0.000278 |
+| N | 0.000112 | 6.76e-05 | 0.0001 | 9.12e-05 | 8.32e-05 | 7.59e-05 | 6.76e-05 | 7.24e-05 | 8.19e-05 |
+| O | 0.000851 | 0.00049 | 0.000851 | 0.000739 | 0.000676 | 0.00049 | 0.00049 | 0.000537 | 0.000606 |
+| F | 3.63e-08 | 3.63e-08 | 3.63e-08 | 3.1e-08 | 3.63e-08 | 0.0 | 2.88e-08 | 3.63e-08 | 3.1e-08 |
+| Ne | 0.000123 | 8.51e-05 | 0.000129 | 0.000138 | 0.00012 | 8.71e-05 | 7.41e-05 | 0.000112 | 0.000127 |
+| Na | 2.14e-06 | 1.74e-06 | 2.14e-06 | 2.1e-06 | 2.14e-06 | 1.45e-06 | 1.99e-06 | 2e-06 | 2.23e-06 |
+| Mg | 3.8e-05 | 3.98e-05 | 3.8e-05 | 3.95e-05 | 3.8e-05 | 2.51e-05 | 3.55e-05 | 3.47e-05 | 3.98e-05 |
+| Al | 2.95e-06 | 2.82e-06 | 2.95e-06 | 3.12e-06 | 2.95e-06 | 2.14e-06 | 2.88e-06 | 2.95e-06 | 3.27e-06 |
+| Si | 3.55e-05 | 3.24e-05 | 3.55e-05 | 3.68e-05 | 3.55e-05 | 1.86e-05 | 3.47e-05 | 3.31e-05 | 3.86e-05 |
+| P | 2.82e-07 | 2.57e-07 | 2.82e-07 | 3.82e-07 | 2.82e-07 | 2.63e-07 | 2.88e-07 | 2.88e-07 | 3.2e-07 |
+| S | 1.62e-05 | 1.32e-05 | 1.62e-05 | 1.89e-05 | 2.14e-05 | 1.23e-05 | 1.55e-05 | 1.38e-05 | 1.63e-05 |
+| Cl | 3.16e-07 | 3.16e-07 | 3.16e-07 | 1.93e-07 | 3.16e-07 | 1.32e-07 | 1.82e-07 | 3.16e-07 | 2e-07 |
+| Ar | 3.63e-06 | 2.51e-06 | 4.47e-06 | 3.82e-06 | 2.51e-06 | 2.57e-06 | 3.55e-06 | 3.16e-06 | 3.58e-06 |
+| K | 1.32e-07 | 1.07e-07 | 1.32e-07 | 1.39e-07 | 1.32e-07 | 0.0 | 1.29e-07 | 1.32e-07 | 1.45e-07 |
+| Ca | 2.29e-06 | 2.19e-06 | 2.29e-06 | 2.25e-06 | 2.29e-06 | 1.58e-06 | 2.19e-06 | 2.14e-06 | 2.33e-06 |
+| Sc | 1.26e-09 | 1.41e-09 | 1.48e-09 | 1.24e-09 | 1.48e-09 | 0.0 | 1.17e-09 | 1.26e-09 | 1.33e-09 |
+| Ti | 9.77e-08 | 8.91e-08 | 1.05e-07 | 8.82e-08 | 1.05e-07 | 6.46e-08 | 8.32e-08 | 7.94e-08 | 9.54e-08 |
+| V | 1e-08 | 8.51e-09 | 1e-08 | 1.08e-08 | 1e-08 | 0.0 | 1e-08 | 1e-08 | 1.11e-08 |
+| Cr | 4.68e-07 | 4.37e-07 | 4.68e-07 | 4.93e-07 | 4.68e-07 | 3.24e-07 | 4.47e-07 | 4.37e-07 | 5.06e-07 |
+| Mn | 2.45e-07 | 2.69e-07 | 2.45e-07 | 3.5e-07 | 2.45e-07 | 2.19e-07 | 3.16e-07 | 2.34e-07 | 3.56e-07 |
+| Fe | 4.68e-05 | 3.16e-05 | 3.24e-05 | 3.31e-05 | 3.16e-05 | 2.69e-05 | 2.95e-05 | 2.82e-05 | 3.27e-05 |
+| Co | 8.32e-08 | 9.77e-08 | 8.32e-08 | 8.27e-08 | 8.32e-08 | 8.32e-08 | 8.13e-08 | 8.32e-08 | 9.07e-08 |
+| Ni | 1.78e-06 | 1.66e-06 | 1.78e-06 | 1.81e-06 | 1.78e-06 | 1.12e-06 | 1.66e-06 | 1.7e-06 | 1.89e-06 |
+| Cu | 1.62e-08 | 1.55e-08 | 1.62e-08 | 1.89e-08 | 1.62e-08 | 0.0 | 1.82e-08 | 1.62e-08 | 2.09e-08 |
+| Zn | 3.98e-08 | 3.63e-08 | 3.98e-08 | 4.63e-08 | 3.98e-08 | 0.0 | 4.27e-08 | 4.17e-08 | 5.02e-08 |
+"""
+
+element_data: pd.DataFrame
+"""
+Dataframe containing various properties of the 30 first elements. It is adapted from
+[`mendeleev`](https://mendeleev.readthedocs.io/en/stable/). The full table is displayed below:
+
+| Element   |   atomic_number |   atomic_radius |   atomic_volume |   atomic_weight |
+|:----------|----------------:|----------------:|----------------:|----------------:|
+| H         |               1 |              25 |           14.1  |         1.008   |
+| He        |               2 |             120 |           31.8  |         4.0026  |
+| Li        |               3 |             145 |           13.1  |         6.94    |
+| Be        |               4 |             105 |            5    |         9.01218 |
+| B         |               5 |              85 |            4.6  |        10.81    |
+| C         |               6 |              70 |            5.3  |        12.011   |
+| N         |               7 |              65 |           17.3  |        14.007   |
+| O         |               8 |              60 |           14    |        15.999   |
+| F         |               9 |              50 |           17.1  |        18.9984  |
+| Ne        |              10 |             160 |           16.8  |        20.1797  |
+| Na        |              11 |             180 |           23.7  |        22.9898  |
+| Mg        |              12 |             150 |           14    |        24.305   |
+| Al        |              13 |             125 |           10    |        26.9815  |
+| Si        |              14 |             110 |           12.1  |        28.085   |
+| P         |              15 |             100 |           17    |        30.9738  |
+| S         |              16 |             100 |           15.5  |        32.06    |
+| Cl        |              17 |             100 |           18.7  |        35.45    |
+| Ar        |              18 |              71 |           24.2  |        39.948   |
+| K         |              19 |             220 |           45.3  |        39.0983  |
+| Ca        |              20 |             180 |           29.9  |        40.078   |
+| Sc        |              21 |             160 |           15    |        44.9559  |
+| Ti        |              22 |             140 |           10.6  |        47.867   |
+| V         |              23 |             135 |            8.35 |        50.9415  |
+| Cr        |              24 |             140 |            7.23 |        51.9961  |
+| Mn        |              25 |             140 |            7.39 |        54.938   |
+| Fe        |              26 |             140 |            7.1  |        55.845   |
+| Co        |              27 |             135 |            6.7  |        58.9332  |
+| Ni        |              28 |             135 |            6.6  |        58.6934  |
+| Cu        |              29 |             135 |            7.1  |        63.546   |
+| Zn        |              30 |             135 |            9.2  |        65.38    |
+
+"""

jaxspec/util/integrate.py

@@ -11,11 +11,12 @@ It mainly relies on tanh-sinh (or double exponential) quadrature to perform the
 
 import jax
 import jax.numpy as jnp
+from jax import Array
 from jax.scipy.integrate import trapezoid
 from typing import Callable
 
 
-def interval_weights(a, b, n):
+def interval_weights(a: float, b: float, n: int) -> tuple[Array, Array, Array]:
     """
     Return the weights for the tanh-sinh quadrature over the interval [a, b].
     """
@@ -28,7 +29,7 @@ def interval_weights(a, b, n):
     return t, x, dx
 
 
-def positive_weights(n):
+def positive_weights(n: int) -> tuple[Array, Array, Array]:
     """
     Return the weights for the tanh-sinh quadrature over the positive real line.
     """
@@ -39,7 +40,7 @@ def positive_weights(n):
     return t, x, dx
 
 
-def integrate_interval(integrand, n: int = 51) -> Callable:
+def integrate_interval(integrand: Callable, n: int = 51) -> Callable:
     r"""
     Build a function which can compute the integral of the provided integrand over the interval $[a, b]$ using
     the tanh-sinh quadrature. Returns a function $F(a, b, \pmb{\theta})$ which takes the limits of the interval and
@@ -100,7 +101,7 @@ def integrate_interval(integrand, n: int = 51) -> Callable:
     return f
 
 
-def integrate_positive(integrand, n: int = 51) -> Callable:
+def integrate_positive(integrand: Callable, n: int = 51) -> Callable:
     r"""
     Build a function which can compute the integral of the provided integrand over the positive real line using
     the tanh-sinh quadrature. Returns a function $F(\pmb{\theta})$ which takes the parameters of the integrand

{jaxspec-0.0.4.dist-info → jaxspec-0.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: jaxspec
-Version: 0.0.4
+Version: 0.0.6
 Summary: jaxspec is a bayesian spectral fitting library for X-ray astronomy.
 License: MIT
 Author: sdupourque
@@ -10,7 +10,7 @@ Classifier: License :: OSI Approved :: MIT License
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Dist: arviz (>=0.17.1,<0.18.0)
+Requires-Dist: arviz (>=0.17.1,<0.19.0)
 Requires-Dist: astropy (>=6.0.0,<7.0.0)
 Requires-Dist: chainconsumer (>=1.0.0,<2.0.0)
 Requires-Dist: cmasher (>=1.6.3,<2.0.0)
@@ -20,11 +20,13 @@ Requires-Dist: jax (>=0.4.23,<0.5.0)
 Requires-Dist: jaxlib (>=0.4.23,<0.5.0)
 Requires-Dist: jaxopt (>=0.8.1,<0.9.0)
 Requires-Dist: matplotlib (>=3.8.0,<4.0.0)
+Requires-Dist: mendeleev (>=0.15.0,<0.16.0)
 Requires-Dist: mkdocstrings (>=0.24.0,<0.25.0)
 Requires-Dist: networkx (>=3.1,<4.0)
 Requires-Dist: numpy (>=1.26.1,<2.0.0)
 Requires-Dist: numpyro (>=0.13.2,<0.15.0)
 Requires-Dist: pandas (>=2.2.0,<3.0.0)
+Requires-Dist: pyzmq (<26)
 Requires-Dist: scipy (<1.13)
 Requires-Dist: seaborn (>=0.13.1,<0.14.0)
 Requires-Dist: simpleeval (>=0.9.13,<0.10.0)
@@ -50,7 +52,7 @@ Documentation : https://jaxspec.readthedocs.io/en/latest/
 
 ## Installation
 
-We recommend the users to start from a fresh Python 3.10 [conda environment](https://conda.io/projects/conda/en/latest/user-guide/install/index.html). 
+We recommend the users to start from a fresh Python 3.10 [conda environment](https://conda.io/projects/conda/en/latest/user-guide/install/index.html).
 
 ```
 conda create -n jaxspec python=3.10

{jaxspec-0.0.4.dist-info → jaxspec-0.0.6.dist-info}/RECORD

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