jaxspec 0.0.7__py3-none-any.whl → 0.0.8__py3-none-any.whl

jaxspec/model/additive.py

@@ -3,13 +3,17 @@ from __future__ import annotations
 import astropy.constants
 import astropy.units as u
 import haiku as hk
+import interpax
 import jax
 import jax.numpy as jnp
 import jax.scipy as jsp
+import numpy as np
 
+from astropy.table import Table
 from haiku.initializers import Constant as HaikuConstant
 
 from ..util.integrate import integrate_interval
+from ..util.online_storage import table_manager
 
 # from ._additive.apec import APEC
 from .abc import AdditiveComponent
@@ -28,8 +32,8 @@ class Powerlaw(AdditiveComponent):
     """
 
     def continuum(self, energy):
-        alpha = hk.get_parameter("alpha", [], init=HaikuConstant(1.3))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1e-4))
+        alpha = hk.get_parameter("alpha", [], float, init=HaikuConstant(1.3))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1e-4))
 
         return norm * energy ** (-alpha)
 
@@ -45,12 +49,12 @@ class AdditiveConstant(AdditiveComponent):
     """
 
     def continuum(self, energy):
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
 
         return norm * jnp.ones_like(energy)
 
     def primitive(self, energy):
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
 
         return norm * energy
 
@@ -68,9 +72,9 @@ class Lorentz(AdditiveComponent):
     """
 
     def continuum(self, energy):
-        line_energy = hk.get_parameter("E_l", [], init=HaikuConstant(1))
-        sigma = hk.get_parameter("sigma", [], init=HaikuConstant(1))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
+        line_energy = hk.get_parameter("E_l", [], float, init=HaikuConstant(1))
+        sigma = hk.get_parameter("sigma", [], float, init=HaikuConstant(1))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
 
         return norm * sigma / (2 * jnp.pi) / ((energy - line_energy) ** 2 + (sigma / 2) ** 2)
 
@@ -93,9 +97,9 @@ class Logparabola(AdditiveComponent):
 
     # TODO : conform with xspec definition
     def continuum(self, energy):
-        a = hk.get_parameter("a", [], init=HaikuConstant(11 / 3))
-        b = hk.get_parameter("b", [], init=HaikuConstant(0.2))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
+        a = hk.get_parameter("a", [], float, init=HaikuConstant(11 / 3))
+        b = hk.get_parameter("b", [], float, init=HaikuConstant(0.2))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
 
         return norm * energy ** (-(a + b * jnp.log(energy)))
 
@@ -113,8 +117,8 @@ class Blackbody(AdditiveComponent):
     """
 
     def continuum(self, energy):
-        kT = hk.get_parameter("kT", [], init=HaikuConstant(11 / 3))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
+        kT = hk.get_parameter("kT", [], float, init=HaikuConstant(11 / 3))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
 
         return norm * 8.0525 * energy**2 / ((kT**4) * (jnp.exp(energy / kT) - 1))
 
@@ -132,8 +136,8 @@ class Blackbodyrad(AdditiveComponent):
     """
 
     def continuum(self, energy):
-        kT = hk.get_parameter("kT", [], init=HaikuConstant(11 / 3))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
+        kT = hk.get_parameter("kT", [], float, init=HaikuConstant(11 / 3))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
 
         return norm * 1.0344e-3 * energy**2 / (jnp.exp(energy / kT) - 1)
 
@@ -152,9 +156,9 @@ class Gauss(AdditiveComponent):
     """
 
     def continuum(self, energy) -> (jax.Array, jax.Array):
-        line_energy = hk.get_parameter("E_l", [], init=HaikuConstant(1))
-        sigma = hk.get_parameter("sigma", [], init=HaikuConstant(1))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
+        line_energy = hk.get_parameter("E_l", [], float, init=HaikuConstant(1))
+        sigma = hk.get_parameter("sigma", [], float, init=HaikuConstant(1))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
 
         return norm * jsp.stats.norm.pdf(energy, loc=line_energy, scale=sigma)
 
@@ -200,9 +204,9 @@ class APEC(AdditiveComponent):
         )
 
     def mono_fine_structure(self, e_low, e_high) -> (jax.Array, jax.Array):
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
-        kT = hk.get_parameter("kT", [], init=HaikuConstant(1))
-        Z = hk.get_parameter("Z", [], init=HaikuConstant(1))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
+        kT = hk.get_parameter("kT", [], float, init=HaikuConstant(1))
+        Z = hk.get_parameter("Z", [], float, init=HaikuConstant(1))
 
         idx = jnp.searchsorted(self.kT_ref, kT, side="left") - 1
 
@@ -231,9 +235,9 @@ class APEC(AdditiveComponent):
 
     @partial(jnp.vectorize, excluded=(0,))
     def continuum(self, energy):
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
-        kT = hk.get_parameter("kT", [], init=HaikuConstant(1))
-        Z = hk.get_parameter("Z", [], init=HaikuConstant(1))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
+        kT = hk.get_parameter("kT", [], float, init=HaikuConstant(1))
+        Z = hk.get_parameter("Z", [], float, init=HaikuConstant(1))
 
         idx = jnp.searchsorted(self.kT_ref, kT, side="left") - 1  # index of left value
 
@@ -271,9 +275,9 @@ class Cutoffpl(AdditiveComponent):
     """
 
     def continuum(self, energy):
-        alpha = hk.get_parameter("alpha", [], init=HaikuConstant(1.3))
-        beta = hk.get_parameter("beta", [], init=HaikuConstant(15))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1e-4))
+        alpha = hk.get_parameter("alpha", [], float, init=HaikuConstant(1.3))
+        beta = hk.get_parameter("beta", [], float, init=HaikuConstant(15))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1e-4))
 
         return norm * energy ** (-alpha) * jnp.exp(-energy / beta)
 
@@ -298,9 +302,9 @@ class Diskpbb(AdditiveComponent):
     """
 
     def continuum(self, energy):
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
-        p = hk.get_parameter("p", [], init=HaikuConstant(0.75))
-        tin = hk.get_parameter("Tin", [], init=HaikuConstant(1))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
+        p = hk.get_parameter("p", [], float, init=HaikuConstant(0.75))
+        tin = hk.get_parameter("Tin", [], float, init=HaikuConstant(1))
 
         # Tout is set to 0 as it is evaluated at R=infinity
         def integrand(kT, energy):
@@ -326,8 +330,8 @@ class Diskbb(AdditiveComponent):
     def continuum(self, energy):
         p = 0.75
         tout = 0.0
-        tin = hk.get_parameter("Tin", [], init=HaikuConstant(1))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
+        tin = hk.get_parameter("Tin", [], float, init=HaikuConstant(1))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
 
         # Tout is set to 0 as it is evaluated at R=infinity
         def integrand(kT, e, tin, p):
@@ -360,9 +364,9 @@ class Agauss(AdditiveComponent):
 
     def continuum(self, energy) -> (jax.Array, jax.Array):
         hc = (astropy.constants.h * astropy.constants.c).to(u.angstrom * u.keV).value
-        line_wavelength = hk.get_parameter("Lambda_l", [], init=HaikuConstant(hc))
-        sigma = hk.get_parameter("sigma", [], init=HaikuConstant(0.001))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
+        line_wavelength = hk.get_parameter("Lambda_l", [], float, init=HaikuConstant(hc))
+        sigma = hk.get_parameter("sigma", [], float, init=HaikuConstant(0.001))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
 
         return norm * jsp.stats.norm.pdf(hc / energy, loc=line_wavelength, scale=sigma)
 
@@ -384,10 +388,10 @@ class Zagauss(AdditiveComponent):
 
     def continuum(self, energy) -> (jax.Array, jax.Array):
         hc = (astropy.constants.h * astropy.constants.c).to(u.angstrom * u.keV).value
-        line_wavelength = hk.get_parameter("Lambda_l", [], init=HaikuConstant(hc))
-        sigma = hk.get_parameter("sigma", [], init=HaikuConstant(0.001))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
-        redshift = hk.get_parameter("redshift", [], init=HaikuConstant(0))
+        line_wavelength = hk.get_parameter("Lambda_l", [], float, init=HaikuConstant(hc))
+        sigma = hk.get_parameter("sigma", [], float, init=HaikuConstant(0.001))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
+        redshift = hk.get_parameter("redshift", [], float, init=HaikuConstant(0))
 
         return (
             norm
@@ -411,11 +415,132 @@ class Zgauss(AdditiveComponent):
     """
 
     def continuum(self, energy) -> (jax.Array, jax.Array):
-        line_energy = hk.get_parameter("E_l", [], init=HaikuConstant(1))
-        sigma = hk.get_parameter("sigma", [], init=HaikuConstant(1))
-        norm = hk.get_parameter("norm", [], init=HaikuConstant(1))
-        redshift = hk.get_parameter("redshift", [], init=HaikuConstant(0))
+        line_energy = hk.get_parameter("E_l", [], float, init=HaikuConstant(1))
+        sigma = hk.get_parameter("sigma", [], float, init=HaikuConstant(1))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1))
+        redshift = hk.get_parameter("redshift", [], float, init=HaikuConstant(0))
 
         return (norm / (1 + redshift)) * jsp.stats.norm.pdf(
             energy * (1 + redshift), loc=line_energy, scale=sigma
         )
+
+
+class NSatmos(AdditiveComponent):
+    r"""
+    A neutron star atmosphere model based on the `NSATMOS` model from `XSPEC`. See [this page](https://heasarc.gsfc.nasa.gov/docs/xanadu/xspec/manual/node205.html)
+
+    !!! warning
+        The boundary case of $R_{\text{NS}} < 1.125 R_{\text{S}}$ is handled with a null flux instead of a constant value as in `XSPEC`.
+
+    ??? abstract "Parameters"
+        * $T_{eff}$ : Effective temperature at the surface in K (No redshift applied)
+        * $M_{ns}$ : Mass of the NS in solar masses
+        * $R_∞$ : Radius at infinity (modulated by gravitational effects) in km
+        * $D$ : Distance to the neutron star in kpc
+        * norm : fraction of the neutron star surface emitting
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        entry_table = Table.read(table_manager.fetch("nsatmosdata.fits"), 1)
+
+        # Extract the table values. All this code could be summarize in two lines if we reformat the nsatmosdata.fits table
+        self.tab_temperature = np.asarray(entry_table["TEMP"][0], dtype=float)  # Logarithmic value
+        self.tab_gravity = np.asarray(entry_table["GRAVITY"][0], dtype=float)  # Logarithmic value
+        self.tab_mucrit = np.asarray(entry_table["MUCRIT"][0], dtype=float)
+        self.tab_energy = np.asarray(entry_table["ENERGY"][0], dtype=float)
+        self.tab_flux_flat = Table.read(table_manager.fetch("nsatmosdata.fits"), 2)["FLUX"]
+
+        tab_flux = np.empty(
+            (
+                self.tab_temperature.size,
+                self.tab_gravity.size,
+                self.tab_mucrit.size,
+                self.tab_energy.size,
+            )
+        )
+
+        for i in range(len(self.tab_temperature)):
+            for j in range(len(self.tab_gravity)):
+                for k in range(len(self.tab_mucrit)):
+                    tab_flux[i, j, k] = np.array(
+                        self.tab_flux_flat[
+                            i * len(self.tab_gravity) * len(self.tab_mucrit)
+                            + j * len(self.tab_mucrit)
+                            + k
+                        ]
+                    )
+
+        self.tab_flux = np.asarray(tab_flux, dtype=float)
+
+    def interp_flux_func(self, temperature_log, gravity_log, mu):
+        # Interpolate the tables to get the flux on the tabulated energy grid
+
+        return interpax.interp3d(
+            10.0**temperature_log,
+            10.0**gravity_log,
+            mu,
+            10.0**self.tab_temperature,
+            10.0**self.tab_gravity,
+            self.tab_mucrit,
+            self.tab_flux,
+            method="linear",
+        )
+
+    def continuum(self, energy):
+        temp_log = hk.get_parameter(
+            "Tinf", [], float, init=HaikuConstant(6.0)
+        )  # log10 of temperature in Kelvin
+
+        #         'Tinf': temp_log, # 5 to 6.5
+        #         'M': mass, # 0.5 to 3
+        #         'Rns': radius, # 5 to 30
+
+        mass = hk.get_parameter("M", [], float, init=HaikuConstant(1.4))
+        radius = hk.get_parameter("Rns", [], float, init=HaikuConstant(10.0))
+        distance = hk.get_parameter("dns", [], float, init=HaikuConstant(10.0))
+        norm = hk.get_parameter("norm", [], float, init=HaikuConstant(1.0))
+
+        # Derive parameters usable to retrive value in the flux table
+        Rcgs = 1e5 * radius  # Radius in cgs
+        r_schwarzschild = 2.95e5 * mass  # Schwarzschild radius in cgs
+        r_normalized = Rcgs / r_schwarzschild  # Ratio of the radius to the Schwarzschild radius
+        r_over_Dsql = 2 * jnp.log10(
+            Rcgs / (3.09e21 * distance)
+        )  # Log( (R/D)**2 ), 3.09e21 constant transforms radius in cgs to kpc
+        zred1 = 1 / jnp.sqrt(1 - (1 / r_normalized))  # Gravitational redshift
+        gravity = (6.67e-8 * 1.99e33 * mass / Rcgs**2) * zred1  # Gravity field g in cgs
+        gravity_log = jnp.log10(
+            gravity
+        )  # Log gravity because this is the format given in the table
+
+        # Not sure about mu yet, but it is linked to causality
+        cmu = jnp.where(
+            r_normalized < 1.5, jnp.sqrt(1.0 - 6.75 / r_normalized**2 + 6.75 / r_normalized**3), 0.0
+        )
+
+        # Interpolate the flux table to get the flux at the surface
+
+        flux = jax.jit(self.interp_flux_func)(temp_log, gravity_log, cmu)
+
+        # Rescale the photon energies and fluxes back to the correct local temperature
+        Tfactor = 10.0 ** (temp_log - 6.0)
+        fluxshift = 3.0 * (temp_log - 6.0)
+        E = self.tab_energy * Tfactor
+        flux += fluxshift
+
+        # Rescale applying redshift
+        fluxshift = -jnp.log10(zred1)
+        E = E / zred1
+        flux += fluxshift
+
+        # Convert to counts/keV (which corresponds to dividing by1.602e-9*EkeV)
+        # Multiply by the area of the star, and calculate the count rate at the observer
+        flux += r_over_Dsql
+        counts = 10.0 ** (flux - jnp.log10(1.602e-9) - jnp.log10(E))
+
+        true_flux = norm * jnp.exp(
+            interpax.interp1d(jnp.log(energy), jnp.log(E), jnp.log(counts), method="linear")
+        )
+
+        return jax.lax.select(r_normalized < 1.125, jnp.zeros_like(true_flux), true_flux)

jaxspec/model/multiplicative.py

@@ -37,9 +37,9 @@ class Expfac(MultiplicativeComponent):
     """
 
     def continuum(self, energy):
-        amplitude = hk.get_parameter("A", [], init=HaikuConstant(1))
-        factor = hk.get_parameter("f", [], init=HaikuConstant(1))
-        pivot = hk.get_parameter("E_c", [], init=HaikuConstant(1))
+        amplitude = hk.get_parameter("A", [], float, init=HaikuConstant(1))
+        factor = hk.get_parameter("f", [], float, init=HaikuConstant(1))
+        pivot = hk.get_parameter("E_c", [], float, init=HaikuConstant(1))
 
         return jnp.where(energy >= pivot, 1.0 + amplitude * jnp.exp(-factor * energy), 1.0)
 
@@ -63,12 +63,14 @@ class Tbabs(MultiplicativeComponent):
 
     """
 
-    table = Table.read(table_manager.fetch("xsect_tbabs_wilm.fits"))
-    energy = jnp.asarray(np.array(table["ENERGY"]), dtype=np.float64)
-    sigma = jnp.asarray(np.array(table["SIGMA"]), dtype=np.float64)
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        table = Table.read(table_manager.fetch("xsect_tbabs_wilm.fits"))
+        self.energy = jnp.asarray(np.array(table["ENERGY"]), dtype=np.float64)
+        self.sigma = jnp.asarray(np.array(table["SIGMA"]), dtype=np.float64)
 
     def continuum(self, energy):
-        nh = hk.get_parameter("N_H", [], init=HaikuConstant(1))
+        nh = hk.get_parameter("N_H", [], float, init=HaikuConstant(1))
         sigma = jnp.interp(energy, self.energy, self.sigma, left=1e9, right=0.0)
 
         return jnp.exp(-nh * sigma)
@@ -84,12 +86,14 @@ class Phabs(MultiplicativeComponent):
 
     """
 
-    table = Table.read(table_manager.fetch("xsect_phabs_aspl.fits"))
-    energy = jnp.asarray(np.array(table["ENERGY"]), dtype=np.float64)
-    sigma = jnp.asarray(np.array(table["SIGMA"]), dtype=np.float64)
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        table = Table.read(table_manager.fetch("xsect_phabs_aspl.fits"))
+        self.energy = jnp.asarray(np.array(table["ENERGY"]), dtype=np.float64)
+        self.sigma = jnp.asarray(np.array(table["SIGMA"]), dtype=np.float64)
 
     def continuum(self, energy):
-        nh = hk.get_parameter("N_H", [], init=HaikuConstant(1))
+        nh = hk.get_parameter("N_H", [], float, init=HaikuConstant(1))
         sigma = jnp.interp(energy, self.energy, self.sigma, left=jnp.inf, right=0.0)
 
         return jnp.exp(-nh * sigma)
@@ -105,12 +109,14 @@ class Wabs(MultiplicativeComponent):
 
     """
 
-    table = Table.read(table_manager.fetch("xsect_wabs_angr.fits"))
-    energy = jnp.asarray(np.array(table["ENERGY"]), dtype=np.float64)
-    sigma = jnp.asarray(np.array(table["SIGMA"]), dtype=np.float64)
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        table = Table.read(table_manager.fetch("xsect_wabs_angr.fits"))
+        self.energy = jnp.asarray(np.array(table["ENERGY"]), dtype=np.float64)
+        self.sigma = jnp.asarray(np.array(table["SIGMA"]), dtype=np.float64)
 
     def continuum(self, energy):
-        nh = hk.get_parameter("N_H", [], init=HaikuConstant(1))
+        nh = hk.get_parameter("N_H", [], float, init=HaikuConstant(1))
         sigma = jnp.interp(energy, self.energy, self.sigma, left=1e9, right=0.0)
 
         return jnp.exp(-nh * sigma)
@@ -136,9 +142,9 @@ class Gabs(MultiplicativeComponent):
     """
 
     def continuum(self, energy):
-        tau = hk.get_parameter("tau", [], init=HaikuConstant(1))
-        sigma = hk.get_parameter("sigma", [], init=HaikuConstant(1))
-        center = hk.get_parameter("E_0", [], init=HaikuConstant(1))
+        tau = hk.get_parameter("tau", [], float, init=HaikuConstant(1))
+        sigma = hk.get_parameter("sigma", [], float, init=HaikuConstant(1))
+        center = hk.get_parameter("E_0", [], float, init=HaikuConstant(1))
 
         return jnp.exp(
             -tau / (jnp.sqrt(2 * jnp.pi) * sigma) * jnp.exp(-0.5 * ((energy - center) / sigma) ** 2)
@@ -160,8 +166,8 @@ class Highecut(MultiplicativeComponent):
     """
 
     def continuum(self, energy):
-        cutoff = hk.get_parameter("E_c", [], init=HaikuConstant(1))
-        folding = hk.get_parameter("E_f", [], init=HaikuConstant(1))
+        cutoff = hk.get_parameter("E_c", [], float, init=HaikuConstant(1))
+        folding = hk.get_parameter("E_f", [], float, init=HaikuConstant(1))
 
         return jnp.where(energy <= cutoff, 1.0, jnp.exp((cutoff - energy) / folding))
 
@@ -182,9 +188,9 @@ class Zedge(MultiplicativeComponent):
     """
 
     def continuum(self, energy):
-        E_c = hk.get_parameter("E_c", [], init=HaikuConstant(1))
-        D = hk.get_parameter("D", [], init=HaikuConstant(1))
-        z = hk.get_parameter("z", [], init=HaikuConstant(0))
+        E_c = hk.get_parameter("E_c", [], float, init=HaikuConstant(1))
+        D = hk.get_parameter("D", [], float, init=HaikuConstant(1))
+        z = hk.get_parameter("z", [], float, init=HaikuConstant(0))
 
         return jnp.where(energy <= E_c, 1.0, jnp.exp(-D * (energy * (1 + z) / E_c) ** 3))
 
@@ -207,13 +213,34 @@ class Tbpcf(MultiplicativeComponent):
 
     """
 
-    table = Table.read(table_manager.fetch("xsect_tbabs_wilm.fits"))
-    energy = jnp.asarray(np.array(table["ENERGY"]), dtype=np.float64)
-    sigma = jnp.asarray(np.array(table["SIGMA"]), dtype=np.float64)
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        table = Table.read(table_manager.fetch("xsect_tbabs_wilm.fits"))
+        self.energy = jnp.asarray(np.array(table["ENERGY"]), dtype=np.float64)
+        self.sigma = jnp.asarray(np.array(table["SIGMA"]), dtype=np.float64)
 
     def continuum(self, energy):
-        nh = hk.get_parameter("N_H", [], init=HaikuConstant(1))
-        f = hk.get_parameter("f", [], init=HaikuConstant(0.2))
+        nh = hk.get_parameter("N_H", [], float, init=HaikuConstant(1))
+        f = hk.get_parameter("f", [], float, init=HaikuConstant(0.2))
         sigma = jnp.interp(energy, self.energy, self.sigma, left=1e9, right=0.0)
 
         return f * jnp.exp(-nh * sigma) + (1 - f)
+
+class FDcut(MultiplicativeComponent):
+    r"""
+    A Fermi-Dirac cutoff model.
+
+    $$
+        \mathcal{M}(E) = \left( 1 + \exp \left( \frac{E - E_c}{E_f} \right) \right)^{-1}
+    $$
+
+    ??? abstract "Parameters"
+        * $E_c$ : Cutoff energy $\left[\text{keV}\right]$
+        * $E_f$ : Folding energy $\left[\text{keV}\right]$
+    """
+
+    def continuum(self, energy):
+        cutoff = hk.get_parameter("E_c", [], init=HaikuConstant(1))
+        folding = hk.get_parameter("E_f", [], init=HaikuConstant(1))
+
+        return (1 + jnp.exp((energy - cutoff)/folding)) ** -1

jaxspec/util/online_storage.py

@@ -11,5 +11,18 @@ table_manager = pooch.create(
         "xsect_tbabs_wilm.fits": "sha256:3cf45e45c9d671c4c4fc128314b7c3a68b30f096eede6b3eb08bf55224a44935",
         "xsect_phabs_aspl.fits": "sha256:3eaffba2a62e3a611e0a4e1ff4a57342d7d576f023d7bbb632710dc75b9a5019",
         "xsect_wabs_angr.fits": "sha256:9b3073a477a30b52e207f2c4bf79afc6ae19abba8f207190ac4c697024f74073",
+        "nsatmosdata.fits": "sha256:faca712f87710ecb866b4ab61be593a6813517c44f6e8e92d689b38d42e1b6dc",
+        "example_data/NGC7793_ULX4/MOS2background_spectrum.fits": "sha256:5387923be0bf39229f4390dd5e85095a3d534b43a69d6d3179b832ebb366d173",
+        "example_data/NGC7793_ULX4/MOS1background_spectrum.fits": "sha256:265fd7465fb1a355f915d9902443ba2fd2be9aface04723056a8376971e3cf14",
+        "example_data/NGC7793_ULX4/MOS2.rmf": "sha256:b6af00603dece33dcda35d093451c947059af2e1e45c31c5a0ffa223b7fb693d",
+        "example_data/NGC7793_ULX4/PN.arf": "sha256:0ee897a63b6de80589c2da758d7477c54ba601b788bf32d4d16bbffa839acb73",
+        "example_data/NGC7793_ULX4/MOS1.rmf": "sha256:2d1138d22c31c5398a4eed1170b0b88b07350ecfec7a7aef4f550871cb4309ae",
+        "example_data/NGC7793_ULX4/PN_spectrum_grp20.fits": "sha256:a985e06076bf060d3a5331f20413afa9208a8d771fa6c671e8918a1860577c90",
+        "example_data/NGC7793_ULX4/MOS2_spectrum_grp.fits": "sha256:dccc7eda9d3d2e4aac2af4ca13d41ab4acc621265004d50a1586a187f7a04ffc",
+        "example_data/NGC7793_ULX4/MOS1_spectrum_grp.fits": "sha256:7e1ff664545bab4fdce1ef94768715b4d87a39b252b61e070e71427e5c8692ac",
+        "example_data/NGC7793_ULX4/MOS1.arf": "sha256:9017ada6a391d46f9b569b8d0338fbabb62a5397e7c29eb0a16e4e02d4868159",
+        "example_data/NGC7793_ULX4/PN.rmf": "sha256:91ba9ef82da8b9f73e6a799dfe097b87c68a7020ac6c5aa0dcd4067bf9cb4287",
+        "example_data/NGC7793_ULX4/MOS2.arf": "sha256:a126ff5a95a5f4bb93ed846944cf411d6e1c448626cb73d347e33324663d8b3f",
+        "example_data/NGC7793_ULX4/PNbackground_spectrum.fits": "sha256:55e017e0c19b324245fef049dff2a7a2e49b9a391667ca9c4f667c4f683b1f49",
     },
 )

{jaxspec-0.0.7.dist-info → jaxspec-0.0.8.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: jaxspec
-Version: 0.0.7
+Version: 0.0.8
 Summary: jaxspec is a bayesian spectral fitting library for X-ray astronomy.
 License: MIT
 Author: sdupourque
@@ -10,21 +10,22 @@ 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,<0.19.0)
+Requires-Dist: arviz (>=0.17.1,<0.20.0)
 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)
 Requires-Dist: dm-haiku (>=0.0.11,<0.0.13)
 Requires-Dist: gpjax (>=0.8.0,<0.9.0)
-Requires-Dist: jax (>=0.4.29,<0.5.0)
-Requires-Dist: jaxlib (>=0.4.29,<0.5.0)
+Requires-Dist: interpax (>=0.3.3,<0.4.0)
+Requires-Dist: jax (>=0.4.30,<0.5.0)
+Requires-Dist: jaxlib (>=0.4.30,<0.5.0)
 Requires-Dist: jaxns (>=2.5.1,<3.0.0)
 Requires-Dist: jaxopt (>=0.8.1,<0.9.0)
 Requires-Dist: matplotlib (>=3.8.0,<4.0.0)
-Requires-Dist: mendeleev (>=0.15,<0.17)
+Requires-Dist: mendeleev (>=0.15,<0.18)
 Requires-Dist: mkdocstrings (>=0.24,<0.26)
 Requires-Dist: networkx (>=3.1,<4.0)
-Requires-Dist: numpy (>=1.26.1,<2.0.0)
+Requires-Dist: numpy (<2.0.0)
 Requires-Dist: numpyro (>=0.15.0,<0.16.0)
 Requires-Dist: optimistix (>=0.0.7,<0.0.8)
 Requires-Dist: pandas (>=2.2.0,<3.0.0)

{jaxspec-0.0.7.dist-info → jaxspec-0.0.8.dist-info}/RECORD

@@ -1,46 +1,42 @@
 jaxspec/__init__.py,sha256=Sbn02lX6Y-zNXk17N8dec22c5jeypiS0LkHmGfz7lWA,126
 jaxspec/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 jaxspec/analysis/compare.py,sha256=g2UFhmR9Zt-7cz5gQFOB6lXuklXB3yTyUvjTypOzoSY,725
-jaxspec/analysis/results.py,sha256=58IM_HS3q8xgW0espGgh11eBdIJYa-m2XccW_-pO2to,24495
+jaxspec/analysis/results.py,sha256=mTSPPzKVsZ-yaz-BZvGRw195S9542VZb0kR1vv4np6Y,26541
 jaxspec/data/__init__.py,sha256=aantcYKC9kZFvaE-V2SIwSuLhIld17Kjrd9CIUu___Y,415
 jaxspec/data/example_data/MOS1.arf,sha256=kBetpqOR1G-bVpuNAzj7q7YqU5fnwp6woW5OAtSGgVk,34560
-jaxspec/data/example_data/MOS1.pha,sha256=fh_2ZFRbq0_c4e-UdocVtNh6ObJSth4HDnFCflyGkqw,83520
 jaxspec/data/example_data/MOS1.rmf,sha256=LRE40iwxxTmKTu0RcLC4iwc1Ds_senrvT1UIcctDCa4,14846400
 jaxspec/data/example_data/MOS1_spectrum_grp.fits,sha256=fh_2ZFRbq0_c4e-UdocVtNh6ObJSth4HDnFCflyGkqw,83520
 jaxspec/data/example_data/MOS1background_spectrum.fits,sha256=Jl_XRl-xo1X5FdmQJEO6L9K-mvrOBHIwVqg3aXHjzxQ,69120
 jaxspec/data/example_data/MOS2.arf,sha256=oSb_WpWl9LuT7YRpRM9BHW4cRIYmy3PTR-MzJGY9iz8,34560
-jaxspec/data/example_data/MOS2.pha,sha256=3Mx-2p09LkqsKvTKE9QatKzGISZQBNUKFYahh_egT_w,89280
 jaxspec/data/example_data/MOS2.rmf,sha256=tq8AYD3s4z3No10JNFHJRwWa8uHkXDHFoP-iI7f7aT0,14783040
 jaxspec/data/example_data/MOS2_spectrum_grp.fits,sha256=3Mx-2p09LkqsKvTKE9QatKzGISZQBNUKFYahh_egT_w,89280
 jaxspec/data/example_data/MOS2background_spectrum.fits,sha256=U4eSO-C_OSKfQ5DdXoUJWj1TS0OmnW0xebgy67Nm0XM,77760
 jaxspec/data/example_data/PN.arf,sha256=DuiXpjtt6AWJwtp1jXR3xUumAbeIvzLU0Wu_-oOay3M,31680
-jaxspec/data/example_data/PN.pha,sha256=qYXgYHa_Bg06UzHyBBOvqSCKjXcfpsZx6JGKGGBXfJA,138240
 jaxspec/data/example_data/PN.rmf,sha256=kbqe-C2oufc-anmd_gl7h8aKcCCsbFqg3NQGe_nLQoc,3962880
 jaxspec/data/example_data/PN_spectrum_grp20.fits,sha256=qYXgYHa_Bg06UzHyBBOvqSCKjXcfpsZx6JGKGGBXfJA,138240
 jaxspec/data/example_data/PNbackground_spectrum.fits,sha256=VeAX4MGbMkJF_vBJ3_KnouSbmjkWZ8qcT2Z8T2g7H0k,120960
-jaxspec/data/example_data/fakeit.pha,sha256=IhkeWkE-b3ELECd_Uasjo9h3cXgcjCYH20wDpXJ8LMk,60480
 jaxspec/data/grouping.py,sha256=hhgBt-voiH0DDSyePacaIGsaMnrYbJM_-ZeU66keC7I,622
 jaxspec/data/instrument.py,sha256=0pSf1p82g7syDMmKm13eVbYih-Veiq5DnwsyZe6_b4g,3890
 jaxspec/data/obsconf.py,sha256=0X9jR-pV-Pk4-EVuUdlVWgl_gBx8ZurVkRNrfKQWdC4,8663
 jaxspec/data/observation.py,sha256=1UnFu5ihZp9z-vP_I7tsFY8jhhIJunv46JyuE-acrg0,6394
 jaxspec/data/ogip.py,sha256=sv9p00qHS5pzw61pzWyyF0nV-E-RXySdSFK2tUavokA,9545
-jaxspec/data/util.py,sha256=TZg_zrH2qk3LiPmn7yw5nMN-XT3z23R9pq8HMYBB_uE,8231
-jaxspec/fit.py,sha256=yfP1INuHYfjpXvZfmkgJ84TbeGWuFg1nvkXduMfxgyk,22057
+jaxspec/data/util.py,sha256=ycLPVE-cjn6VpUWYlBU1BGfw73ANXIBilyVAUOYOSj0,9540
+jaxspec/fit.py,sha256=4rJ8Zcv-CGwjAEKQ5r6bKD4Abw9OMcZd__rns6S4fto,21375
 jaxspec/model/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 jaxspec/model/_additive/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 jaxspec/model/_additive/apec.py,sha256=r7CQqscAgR0BXC_AJqF6B7CPq3Byoo65Z-h9XgACZeU,12460
 jaxspec/model/_additive/apec_loaders.py,sha256=jkUoH0ezeYdaNw3oV10V0L-jt848SKp2thanLWLWp9k,2412
 jaxspec/model/abc.py,sha256=SWjKOOsqU5UJsVy63Tt9dDq8H2eTIbvK2C9iqgiR0cY,19817
-jaxspec/model/additive.py,sha256=ayGkL0ftmK-MVndYoHorPZVpNopi1MyyEtymLlBRl-o,16885
+jaxspec/model/additive.py,sha256=CT2K2DVVeHKN1tee9-J3MYdEPqEOolLB2E7HU-RJKZw,22485
 jaxspec/model/background.py,sha256=QSFFiuyUEvuzXBx3QfkvVneUR8KKEP-VaANEVXcavDE,7865
 jaxspec/model/list.py,sha256=0RPAoscVz_zM1CWdx_Gd5wfrQWV5Nv4Kd4bSXu2ayUA,860
-jaxspec/model/multiplicative.py,sha256=8S7_agz32fdX-qxYnkL7fGXW2CnuwRGBZ5pYV4-b_5k,7194
+jaxspec/model/multiplicative.py,sha256=TG3PCgS7oCuHwJ4TM4whw6pz318oo9MVvjSs4sQZVPc,8300
 jaxspec/util/__init__.py,sha256=vKurfp7p2hxHptJjXhXqFAXAikAGXAqISMJUqPeiGTw,1259
 jaxspec/util/abundance.py,sha256=fsC313taIlGzQsZNwbYsJupDWm7ZbqzGhY66Ku394Mw,8546
 jaxspec/util/integrate.py,sha256=_Ax_knpC7d4et2-QFkOUzVtNeQLX1-cwLvm-FRBxYcw,4505
-jaxspec/util/online_storage.py,sha256=cJGHsgPh3CukRwwlOcxV9eGvrainDOIP5AQP60tWLN4,818
+jaxspec/util/online_storage.py,sha256=vm56RfcbFKpkRVfr0bXO7J9aQxuBq-I_oEgA26YIhCo,2469
 jaxspec/util/typing.py,sha256=qwZMKHivZlozoo0ESsiaQNkG99Dh3PE2Z-5aOQD9zc0,1650
-jaxspec-0.0.7.dist-info/LICENSE.md,sha256=2q5XoWzddts5IqzIcgYYMOL21puU3MfO8gvT3Ype1eQ,1073
-jaxspec-0.0.7.dist-info/METADATA,sha256=MX7-CIwPDBVjZtjRP3BMQnm0gKEcN5Z91yYW4n5PvXA,3375
-jaxspec-0.0.7.dist-info/WHEEL,sha256=d2fvjOD7sXsVzChCqf0Ty0JbHKBaLYwDbGQDwQTnJ50,88
-jaxspec-0.0.7.dist-info/RECORD,,
+jaxspec-0.0.8.dist-info/LICENSE.md,sha256=2q5XoWzddts5IqzIcgYYMOL21puU3MfO8gvT3Ype1eQ,1073
+jaxspec-0.0.8.dist-info/METADATA,sha256=vRPdPEBjgjTjvYpff1w-O7yTlcdAaoFF_jNTDst7P-M,3407
+jaxspec-0.0.8.dist-info/WHEEL,sha256=sP946D7jFCHeNz5Iq4fL4Lu-PrWrFsgfLXbbkciIZwg,88
+jaxspec-0.0.8.dist-info/RECORD,,

{jaxspec-0.0.7.dist-info → jaxspec-0.0.8.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 1.7.0
+Generator: poetry-core 1.9.0
 Root-Is-Purelib: true
 Tag: py3-none-any