Added a simplified generalised NFW pressure profile. For issue #1272 …

…(indirectly)

xga/models/pressure.py

@@ -0,0 +1,112 @@
+#  This code is a part of X-ray: Generate and Analyse (XGA), a module designed for the XMM Cluster Survey (XCS).
+#  Last modified by David J Turner (turne540@msu.edu) 22/11/2024, 14:26. Copyright (c) The Contributors
+
+from typing import Union, List
+
+from astropy.units import Quantity, Unit, UnitConversionError, kpc
+
+from .base import BaseModel1D
+from ..utils import r200, r500, r2500
+
+
+class SimpleGNFWThermalPressure(BaseModel1D):
+    """
+    A model to fit galaxy cluster radial thermal pressure profiles, based on the generalized NFW profile equation
+    proposed by https://ui.adsabs.harvard.edu/abs/2007ApJ...668....1N/abstract and used
+    in https://ui.adsabs.harvard.edu/abs/2010A%26A...517A..92A/abstract - this one has had several parameters removed
+    or frozen.
+
+    :param Unit/str x_unit: The unit of the x-axis of this model, kpc for instance. May be passed as a string
+        representation or an astropy unit object.
+    :param Unit/str y_unit: The unit of the output of this model, keV/cm^3 for instance. May be passed as a string
+        representation or an astropy unit object.
+    :param List[Quantity] cust_start_pars: The start values of the model parameters for any fitting function that
+        used start values. The units are checked against default start values.
+    """
+    def __init__(self, x_unit: Union[str, Unit] = 'kpc', y_unit: Union[str, Unit] = Unit('keV cm^-3'),
+                 cust_start_pars: List[Quantity] = None):
+        """
+        The init of a subclass of the XGA BaseModel1D class, describing a model of how thermal pressure changes
+        with radius.
+        """
+        # If a string representation of a unit was passed then we make it an astropy unit
+        if isinstance(x_unit, str):
+            x_unit = Unit(x_unit)
+        if isinstance(y_unit, str):
+            y_unit = Unit(y_unit)
+
+        poss_y_units = [Unit('keV cm^-3')]
+        y_convertible = [u.is_equivalent(y_unit) for u in poss_y_units]
+        if not any(y_convertible):
+            allowed = ", ".join([u.to_string() for u in poss_y_units])
+            raise UnitConversionError("{p} is not convertible to any of the allowed units; "
+                                      "{a}".format(p=y_unit.to_string(), a=allowed))
+        else:
+            yu_ind = y_convertible.index(True)
+
+        poss_x_units = [kpc]
+        x_convertible = [u.is_equivalent(x_unit) for u in poss_x_units]
+        if not any(x_convertible):
+            allowed = ", ".join([u.to_string() for u in poss_x_units])
+            raise UnitConversionError("{p} is not convertible to any of the allowed units; "
+                                      "{a}".format(p=x_unit.to_string(), a=allowed))
+        else:
+            xu_ind = x_convertible.index(True)
+
+        p_zero_starts = [Quantity(0.1, 'keV cm^-3')]
+        r_scale_starts = [Quantity(100, 'kpc'), Quantity(0.2, 'deg'), Quantity(0.05, r200), Quantity(0.1, r500),
+                          Quantity(0.5, r2500)]
+        alpha = Quantity(1, '')
+        beta = Quantity(1, '')
+
+        start_pars = [p_zero_starts[yu_ind], r_scale_starts[xu_ind], alpha, beta]
+
+        if cust_start_pars is not None:
+            # If the custom start parameters can run this gauntlet without tripping an error then we're all good
+            # This method also returns the custom start pars converted to exactly the same units as the default
+            start_pars = self.compare_units(cust_start_pars, start_pars)
+
+        pz_priors = [{'prior': Quantity([0.0001, 10], 'keV cm^-3'), 'type': 'uniform'}]
+        r_scale_priors = [{'prior': Quantity([0, 2000], 'kpc'), 'type': 'uniform'},
+                         {'prior': Quantity([0, 1], 'deg'), 'type': 'uniform'},
+                         {'prior': Quantity([0, 1], r200), 'type': 'uniform'},
+                         {'prior': Quantity([0, 1], r500), 'type': 'uniform'},
+                         {'prior': Quantity([0, 1], r2500), 'type': 'uniform'}]
+        alpha_priors = {'prior': Quantity([-4, 4], ''), 'type': 'uniform'}
+        beta_priors = {'prior': Quantity([-4, 4], ''), 'type': 'uniform'}
+
+        priors = [pz_priors[yu_ind], r_scale_priors[xu_ind], alpha_priors, beta_priors]
+
+        nice_pars = [r"P$_{0}$", r"$R_{s}$", r"$\alpha$", r"$\beta$"]
+        info_dict = {'author': 'Arnaud et al.', 'year': 2010,
+                     'reference': 'https://ui.adsabs.harvard.edu/abs/2007ApJ...668....1N/abstract',
+                     'general': "A model to fit galaxy cluster radial thermal pressure profiles, \n"
+                                "based on the generalized NFW profile equation, but with gamma fixed."}
+
+        super().__init__(x_unit, y_unit, start_pars, priors, 'simple_gnfw_pressure',
+                         'Simplified gNFW Pressure Profile', nice_pars, 'Thermal Pressure', info_dict)
+
+    @staticmethod
+    def model(x: Quantity, p_zero: Quantity, r_scale: Quantity, alpha: Quantity, beta: Quantity) -> Quantity:
+        """
+        The model function for the simplified generalized NFW pressure profile.
+
+        :param Quantity x: The radii to calculate y values for.
+        :param Quantity p_zero: The pressure normalization for the model.
+        :param Quantity r_scale: The scale radius for the radial pressure profile.
+        :param Quantity alpha: The alpha slope parameter, for the intermediate slope.
+        :param Quantity beta: The beta slope parameter, for the outer slope.
+        :return: The y values corresponding to the input x values.
+        :rtype: Quantity
+        """
+        gamma = 0.31
+        rad_rat = x/r_scale
+
+        result = p_zero * (1/(rad_rat**gamma * (1 + rad_rat**alpha)**((beta - gamma)/alpha)))
+
+        return result
+
+# So that things like fitting functions can be written generally to support different models
+PRESSURE_MODELS = {"simple_gnfw_pressure": SimpleGNFWThermalPressure}
+PRESSURE_MODELS_PUB_NAMES = {n: m().publication_name for n, m in PRESSURE_MODELS.items()}
+PRESSURE_MODELS_PAR_NAMES = {n: m().par_publication_names for n, m in PRESSURE_MODELS.items()}