models

Module contents

xga.models.convert_to_odr_compatible(model_func, new_par_name='β', new_data_name='x_values')[source]

This is a bit of a weird one; its meant to convert model functions from the standard XGA setup (i.e. pass x values, then parameters as individual variables), into the form expected by Scipy’s ODR. I’d recommend running a check to compare results from the original and converted functions where-ever this function is called - I don’t completely trust it.

Parameters

  • model_func (FunctionType) – The original model function to be converted.

  • new_par_name (str) – The name we want to use for the new list/array of fit parameters.

  • new_data_name (str) – The new name we want to use for the x_data.

Returns

A successfully converted model function (hopefully) which can be used with ODR.

Return type

FunctionType

models.base module

class xga.models.base.BaseModel1D(x_unit, y_unit, start_pars, par_priors, model_name, model_pub_name, par_pub_names, describes, info, x_lims=None)[source]

Bases: object

The superclass of XGA’s 1D models, with base functionality implemented, including the numerical methods for calculating derivatives and abel transforms which can be overwritten by subclasses if analytical solutions are available. The BaseModel class shouldn’t be instantiated by itself, as it won’t do anything.

Parameters

  • x_unit (Unit/str) – The unit of the x-axis of this model, kpc for instance. May be passed as a string representation or an astropy unit object.

  • y_unit (Unit/str) – The unit of the output of this model, keV for instance. May be passed as a string representation or an astropy unit object.

  • start_pars (List[Quantity]) – The start values of the model parameters for any fitting function that used start values.

  • Quantity/str]] par_priors (List[Dict[str,) – The priors on the model parameters, for any fitting function that uses them.

  • model_name (str) – The simple name of the particular model, e.g. ‘beta’.

  • model_pub_name (str) – A smart name for the model that might be used in a publication plot, e.g. ‘Beta Profile’

  • par_pub_names (List[str]) – The names of the parameters of the model, as they should be used in plots for publication. As matplotlib supports LaTeX formatting for labels these should use $$ syntax.

  • describes (str) – An identifier for the type of data this model describes, e.g. ‘Surface Brightness’.

  • info (dict) – A dictionary with information about the model, used by the info() method. Can hold a general description, reference, authors etc.

  • x_lims (Quantity) – Upper and lower limits outside of which the model may not be valid, to be passed as a single non-scalar astropy quantity, with the first entry being the lower limit and the second entry being the upper limit. Default is None.

get_realisations(x)[source]

This method uses the parameter distributions added to this model by a fitting process to generate random realisations of this model at a given x-position (or positions).

Parameters

x (Quantity) – The x-position(s) at which realisations of the model should be generated from the associated parameter distributions. If multiple, non-distribution, radii are to be used, make sure to pass them as an (M,), single dimension, astropy quantity, where M is the number of separate radii to generate realisations for. To marginalise over a radius distribution when generating realisations, pass a multi-dimensional astropy quantity; i.e. for a single set of realisations pass a (1, N) quantity, where N is the number of samples in the parameter posteriors, for realisations for M different radii pass a (M, N) quantity.

Returns

The model realisations, in a Quantity with shape (len(x), num_samples) if x has multiple radii in it (num_samples is the number of samples in the parameter distributions), and (num_samples,) if only a single x value is passed.

Return type

Quantity

abstract static model(x, pars)[source]

This is where the model function is actually defined, this MUST be overridden by every subclass model, hence why I’ve used the abstract method decorator.

Parameters

  • x (Quantity) – The x-position at which the model should be evaluated.

  • pars (List[Quantity]) – The parameters of model to be evaluated.

Returns

The y-value of the model at x.

derivative(x, dx, use_par_dist=False)[source]

Calculates a numerical derivative of the model at the specified x value, using the specified dx value. This method will be overridden in models that have an analytical solution to their first derivative, in which case the dx value will become irrelevant.

Parameters

  • x (Quantity) – The point(s) at which the slope of the model should be measured.

  • dx (Quantity) – The dx value to use during the calculation.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a derivative distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

Returns

The calculated slope of the model at the supplied x position(s).

Return type

Quantity

nth_derivative(x, dx, order, use_par_dist=False)[source]

A method to calculate the nth order derivative of the model using a numerical method.

Parameters

  • x (Quantity) – The point(s) at which the slope of the model should be measured.

  • dx (Quantity) – The dx value to use during the calculation.

  • order (int) – The order of the desired derivative.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a derivative distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

Returns

The value(s) of the nth order derivative of the model at x, either calculated from the current best fit parameters, or a distribution.

Return type

Quantity

inverse_abel(x, use_par_dist=False, method='direct')[source]

This method uses numerical methods to generate the inverse abel transform of the model. It may be overridden by models that have analytical solutions to the inverse abel transform. All numerical inverse abel transform methods are from the pyabel module, and please be aware that in my (limited) experience the numerical solutions tend to diverge from analytical solutions at large radii.

Parameters

  • x (Quantity) – The x location(s) at which to calculate the value of the inverse abel transform.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a inverse abel transform distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

  • method (str) – The method that should be used to calculate the values of this inverse abel transform. You may pass ‘direct’, ‘basex’, ‘hansenlaw’, ‘onion_bordas’, ‘onion_peeling’, ‘two_point’, or ‘three_point’.

Returns

The inverse abel transform result.

Return type

Quantity

volume_integral(outer_radius, inner_radius=None, use_par_dist=False)[source]

Calculates a numerical value for the volume integral of the function over a sphere of radius outer_radius. The scipy quad function is used. This method can either return a single value calculated using the current model parameters, or a distribution of values using the parameter distributions (assuming that this model has had a fit run on it).

This method may be overridden if there is an analytical solution to a particular model’s volume integration over a sphere.

The results of calculations with single values of outer and inner radius are stored in the model object to reduce processing time if they are needed again, but if a distribution of radii are passed then the results will not be stored and will be re-calculated each time.

Parameters

  • outer_radius (Quantity) – The radius to integrate out to. Either a single value or, if you want to marginalise over a radius distribution when ‘use_par_dist=True’, a non-scalar quantity of the same length as the number of samples in the parameter posteriors.

  • inner_radius (Quantity) – The inner bound of the radius integration. Default is None, which results in an inner radius of 0 in the units of outer_radius being used.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a volume integral distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value

Returns

The result of the integration, either a single value or a distribution.

Return type

Quantity

allowed_prior_types(table_format='fancy_grid')[source]

Simple method to display the allowed prior types and their expected formats. :param str table_format: The desired format of the allowed models table. This is passed to the

tabulate module (allowed formats can be found here - https://pypi.org/project/tabulate/), and alters the way the printed table looks.

static compare_units(check_pars, good_pars)[source]

Simple method that will be used in the inits of subclasses to make sure that any custom start values passed in by the user match the expected units of the default start parameters for that model.

Parameters

  • check_pars (List[Quantity]) – The first list of parameters, these are being checked.

  • good_pars (List[Quantity]) – The second list of parameters, these are taken as having ‘correct’ units.

Returns

Only if the check pars pass the tests. We return the check pars list but with all elements converted to EXACTLY the same units as good_pars, not just equivelant.

Return type

List[Quantity]

info(table_format='fancy_grid')[source]

A method that gives some information about this particular model. :param str table_format: The desired format of the allowed models table. This is passed to the

tabulate module (allowed formats can be found here - https://pypi.org/project/tabulate/), and alters the way the printed table looks.

predicted_dist_view(radius, bins='auto', colour='lightslategrey', figsize=6, 5)[source]

A simple view method, to visualise the predicted value distribution at a particular radius. Only usable if this model has had parameter distributions assigned to it.

Parameters

  • radius (Quantity) – The radius at which you wish to evaluate this model and view the predicted distribution.

  • int] bins (Union[str,) – Equivelant to the plt.hist bins argument, set either the number of bins or the algorithm to decide on the number of bins.

  • colour (str) – Set the colour of the histogram.

  • figsize (tuple) – The desired dimensions of the figure.

par_dist_view(bins='auto', colour='lightslategrey')[source]

Very simple method that allows you to view the parameter distributions that have been added to this model. The model parameter and uncertainties are indicated with red lines, highlighting the value and enclosing the 1sigma confidence region.

Parameters

  • int] bins (Union[str,) – Equivelant to the plt.hist bins argument, set either the number of bins or the algorithm to decide on the number of bins.

  • colour (str) – Set the colour of the histogram.

view(radii=None, xscale='log', yscale='log', figsize=8, 8, colour='black')[source]

Very simple view method to visualise XGA models with the current parameters.

Parameters

  • radii (Quantity) – Radii at which to calculate points to plot, doesn’t need to be set if the model has x limits defined.

  • xscale (str) – The scale to apply to the x-axis, default is log.

  • yscale (str) – The scale to apply to the y-axis, default is log.

  • figsize (tuple) – The size of figure to be set up.

  • colour (str) – The colour that the line in the plot should be.

property model_pars

Property that returns the current parameters of the model, by default they are the same as the parameter start values.

Returns

A list of astropy quantities representing the values of the parameters of this model.

Return type

List[Quantity]

property model_par_errs

Property that returns the uncertainties on the current parameters of the model, by default these will be zero as the default model_pars are the same as the start_pars.

Returns

A list of astropy quantities representing the uncertainties on the parameters of this model.

Return type

List[Quantity]

property start_pars

Property that returns the current start parameters of the model, by which I mean the values that certain types of fitting function will use to start their fit.

Returns

A list of astropy quantities representing the values of the start parameters of this model.

Return type

List[Quantity]

property unitless_start_pars

Returns sanitised start parameters which are floats rather than astropy quantities, sometimes necessary for fitting methods.

Returns

Array of floats representing model start parameters.

Return type

np.ndarray

property par_priors

Property that returns the current priors on parameters of the model, these will be used by any fitting function that sets priors on parameters. Each entry in this list will be a dictionary with two keys ‘prior’ and ‘type’. The value for prior will be an astropy quantity, and the value for type will be a prior type (so uniform, gaussian, etc.)

Returns

A list of astropy quantities representing the values of the start parameters of this model.

Return type

List[Quantity]

property x_unit

Property to access the expected x-unit of this model.

Returns

Astropy unit of the x values of the model.

Return type

Unit

property y_unit

Property to access the expected y-unit of this model.

Returns

Astropy unit of the y values of the model.

Return type

Unit

property x_lims

Property to access the x limits within which the model is considered valid, the default is None if no x limits were set for the model on instantiation.

Returns

A non-scalar astropy quantity with two entries, the first is a lower limit, and the second an upper limit. The default is None if no x limits were set.

Return type

Quantity

property par_units

A list of units for the parameters of this model.

Returns

A list of astropy units.

Return type

List[Unit]

property name

Property getter for the simple name of the model, which the user would enter when requesting a particular model to be fit to a profile, for instance.

Returns

String representation of the simple name of the model.

Return type

str

property publication_name

Property getter for the publication name of the model, which is what would be added in a plot meant for publication, for instance.

Returns

String representation of the publication (i.e. pretty) name of the model.

Return type

str

property par_publication_names

Property getter for the publication names of the model parameters. These would be used in a plot for instance, and so can make use of Matplotlib’s ability to render LaTeX math code.

Returns

List of string representation of the publication (i.e. pretty) names of the model parameters.

Return type

List[str]

property describes

A one or two word description of the type of data this model describes.

Returns

A string description.

Return type

str

property num_pars

Property getter for the number of parameters associated with this model.

Returns

Number of parameters.

Return type

int

property par_dists

A property that returns the currently stored distributions for the model parameters, by default these will be empty quantities as no fitting will have occurred. Once a fit has been performed involving the model however, the distributions can be set externally.

Returns

A list of astropy quantities containing parameter distributions for all model parameters.

Return type

List[Quantity]

property fit_warning

Returns any warnings generated by a fitting function that acted upon this model.

Returns

A string containing warnings.

Return type

str

property acceptance_fraction

Property getter for the acceptance fraction of an MCMC fit (if one has been associated with this model).

Returns

The acceptance fraction.

Return type

int

property emcee_sampler

Property getter for the emcee sampler used to fit this model, if applicable. By default this will be None, as the it has to be set externally, as the model won’t necessarily be fit by emcee

Returns

The emcee sampler used to fit this model.

Return type

em.EnsembleSampler

property cut_off
Property getter for the number of steps that an MCMC fitting method decided should be removed for burn-in.

By default this will be None, as the it has to be set externally, as the model won’t necessarily be fit by emcee

Returns

The number of steps to be removed for burn-in.

Return type

int

property fit_method

Property getter for the method used to fit the model instance, this will be None if no fit has been run using this model.

Returns

The fit method.

Return type

str

property par_names

The names of the parameters as they appear in the signature of the model python function.

Returns

A list of parameter names.

Return type

List[str]

property success

If an fit has been run using this model then this property will tell you whether the fit method considered it to be ‘successful’ or not. If no fit has been run using this model then the value is None.

Returns

Was the fit successful?

Return type

bool

property profile

The profile that this model has been fit to.

Returns

The profile object that this has been fit to, if no fit has been performed then this property will return None.

Return type

BaseProfile1D

models.density module

class xga.models.density.KingProfile1D(x_unit='kpc', y_unit=Unit('solMass / Mpc3'), cust_start_pars=None)[source]

Bases: xga.models.base.BaseModel1D

An XGA model implementation of the King profile, describing an isothermal sphere. This describes a radial density profile and assumes spherical symmetry.

Parameters

  • x_unit (Unit/str) – The unit of the x-axis of this model, kpc for instance. May be passed as a string representation or an astropy unit object.

  • y_unit (Unit/str) – The unit of the output of this model, keV for instance. May be passed as a string representation or an astropy unit object.

  • cust_start_pars (List[Quantity]) – The start values of the model parameters for any fitting function that used start values. The units are checked against default start values.

static model(x, beta, r_core, norm)[source]

The model function for the king profile.

Parameters

  • x (Quantity) – The radii to calculate y values for.

  • beta (Quantity) – The beta slope parameter of the model.

  • r_core (Quantity) – The core radius.

  • norm (Quantity) – The normalisation of the model.

Returns

The y values corresponding to the input x values.

Return type

Quantity

derivative(x, dx=<Quantity 0.>, use_par_dist=False)[source]

Calculates the gradient of the king profile at a given point, overriding the numerical method implemented in the BaseModel1D class, as this simple model has an easily derivable first derivative.

Parameters

  • x (Quantity) – The point(s) at which the slope of the model should be measured. If multiple, non-distribution, radii are to be used, make sure to pass them as an (M,), single dimension, astropy quantity, where M is the number of separate radii to generate realisations for. To marginalise over a radius distribution when generating realisations, pass a multi-dimensional astropy quantity; i.e. for a single set of realisations pass a (1, N) quantity, where N is the number of samples in the parameter posteriors, for realisations for M different radii pass a (M, N) quantity.

  • dx (Quantity) – This makes no difference here, as this is an analytical derivative. It has been left in so that the inputs for this method don’t vary between models.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a derivative distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

Returns

The calculated slope of the model at the supplied x position(s).

Return type

Quantity

class xga.models.density.DoubleKingProfile1D(x_unit='kpc', y_unit=Unit('solMass / Mpc3'), cust_start_pars=None)[source]

Bases: xga.models.base.BaseModel1D

An XGA model implementation of the double King profile, simply the sum of two King profiles. This describes a radial density profile and assumes spherical symmetry.

Parameters

  • x_unit (Unit/str) – The unit of the x-axis of this model, kpc for instance. May be passed as a string representation or an astropy unit object.

  • y_unit (Unit/str) – The unit of the output of this model, keV for instance. May be passed as a string representation or an astropy unit object.

  • cust_start_pars (List[Quantity]) – The start values of the model parameters for any fitting function that used start values. The units are checked against default start values.

static model(x, beta_one, r_core_one, norm_one, beta_two, r_core_two, norm_two)[source]

The model function for the double King profile.

Parameters

  • x (Quantity) – The radii to calculate y values for.

  • beta_one (Quantity) – The beta slope parameter of the first King model.

  • r_core_one (Quantity) – The core radius of the first King model.

  • norm_one (Quantity) – The normalisation of the first King model.

  • beta_two (Quantity) – The beta slope parameter of the second King model.

  • r_core_two (Quantity) – The core radius of the second King model.

  • norm_two (Quantity) – The normalisation of the second King model.

Returns

The y values corresponding to the input x values.

Return type

Quantity

derivative(x, dx=<Quantity 0.>, use_par_dist=False)[source]

Calculates the gradient of the double King profile at a given point, overriding the numerical method implemented in the BaseModel1D class, as this simple model has an easily derivable first derivative.

Parameters

  • x (Quantity) – The point(s) at which the slope of the model should be measured. If multiple, non-distribution, radii are to be used, make sure to pass them as an (M,), single dimension, astropy quantity, where M is the number of separate radii to generate realisations for. To marginalise over a radius distribution when generating realisations, pass a multi-dimensional astropy quantity; i.e. for a single set of realisations pass a (1, N) quantity, where N is the number of samples in the parameter posteriors, for realisations for M different radii pass a (M, N) quantity.

  • dx (Quantity) – This makes no difference here, as this is an analytical derivative. It has been left in so that the inputs for this method don’t vary between models.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a derivative distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

Returns

The calculated slope of the model at the supplied x position(s).

Return type

Quantity

class xga.models.density.SimpleVikhlininDensity1D(x_unit='kpc', y_unit=Unit('solMass / Mpc3'), cust_start_pars=None)[source]

Bases: xga.models.base.BaseModel1D

An XGA model implementation of a simplified version of Vikhlinin’s full density model. Used relatively recently in https://doi.org/10.1051/0004-6361/201833325 by Ghirardini et al., a simplified form of Vikhlinin’s full density model, which can be found in https://doi.org/10.1086/500288.

Parameters

  • x_unit (Unit/str) – The unit of the x-axis of this model, kpc for instance. May be passed as a string representation or an astropy unit object.

  • y_unit (Unit/str) – The unit of the output of this model, keV for instance. May be passed as a string representation or an astropy unit object.

  • cust_start_pars (List[Quantity]) – The start values of the model parameters for any fitting function that used start values. The units are checked against default start values.

static model(x, beta, r_core, alpha, r_s, epsilon, norm)[source]

The model function for the simplified Vikhlinin density profile.

Parameters

  • x (Quantity) – The radii to calculate y values for.

  • beta (Quantity) – The beta parameter of the model.

  • r_core (Quantity) – The core radius of the model.

  • alpha (Quantity) – The alpha parameter of the model.

  • r_s (Quantity) – The radius near where a change of slope by epsilon occurs.

  • epsilon (Quantity) – The epsilon parameter of the model.

  • norm (Quantity) – The overall normalisation of the model.

Returns

The y values corresponding to the input x values.

Return type

Quantity

derivative(x, dx=<Quantity 0.>, use_par_dist=False)[source]

Calculates the gradient of the simple Vikhlinin density profile at a given point, overriding the numerical method implemented in the BaseModel1D class.

Parameters

  • x (Quantity) – The point(s) at which the slope of the model should be measured. If multiple, non-distribution, radii are to be used, make sure to pass them as an (M,), single dimension, astropy quantity, where M is the number of separate radii to generate realisations for. To marginalise over a radius distribution when generating realisations, pass a multi-dimensional astropy quantity; i.e. for a single set of realisations pass a (1, N) quantity, where N is the number of samples in the parameter posteriors, for realisations for M different radii pass a (M, N) quantity.

  • dx (Quantity) – This makes no difference here, as this is an analytical derivative. It has been left in so that the inputs for this method don’t vary between models.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a derivative distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

Returns

The calculated slope of the model at the supplied x position(s).

Return type

Quantity

class xga.models.density.VikhlininDensity1D(x_unit='kpc', y_unit=Unit('solMass / Mpc3'), cust_start_pars=None)[source]

Bases: xga.models.base.BaseModel1D

An XGA model implementation of Vikhlinin’s full density model for galaxy cluster intra-cluster medium, which can be found in https://doi.org/10.1086/500288. It is a radial profile, so an assumption of spherical symmetry is baked in.

Parameters

  • x_unit (Unit/str) – The unit of the x-axis of this model, kpc for instance. May be passed as a string representation or an astropy unit object.

  • y_unit (Unit/str) – The unit of the output of this model, keV for instance. May be passed as a string representation or an astropy unit object.

  • cust_start_pars (List[Quantity]) – The start values of the model parameters for any fitting function that used start values. The units are checked against default start values.

static model(x, beta_one, r_core_one, alpha, r_s, epsilon, gamma, norm_one, beta_two, r_core_two, norm_two)[source]

The model function for the full Vikhlinin density profile.

Parameters

  • x (Quantity) – The radii to calculate y values for.

  • beta_one (Quantity) – The beta parameter of the model.

  • r_core_one (Quantity) – The core radius of the model.

  • alpha (Quantity) – The alpha parameter of the model.

  • r_s (Quantity) – The radius near where a change of slope by epsilon occurs.

  • epsilon (Quantity) – The epsilon parameter of the model.

  • gamma (Quantity) – Width of slope change transition region.

  • norm_one (Quantity) – The normalisation of the model first part of the model.

  • beta_two (Quantity) – The beta parameter slope of the small core part of the model.

:param Quantity r_core_two:The core radius of the small core part of the model. :param Quantity norm_two: The normalisation of the additive, small core part of the model.

derivative(x, dx=<Quantity 0.>, use_par_dist=False)[source]

Calculates the gradient of the full Vikhlinin density profile at a given point, overriding the numerical method implemented in the BaseModel1D class.

Parameters

  • x (Quantity) – The point(s) at which the slope of the model should be measured. If multiple, non-distribution, radii are to be used, make sure to pass them as an (M,), single dimension, astropy quantity, where M is the number of separate radii to generate realisations for. To marginalise over a radius distribution when generating realisations, pass a multi-dimensional astropy quantity; i.e. for a single set of realisations pass a (1, N) quantity, where N is the number of samples in the parameter posteriors, for realisations for M different radii pass a (M, N) quantity.

  • dx (Quantity) – This makes no difference here, as this is an analytical derivative. It has been left in so that the inputs for this method don’t vary between models.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a derivative distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

Returns

The calculated slope of the model at the supplied x position(s).

Return type

Quantity

models.fitting module

xga.models.fitting.log_likelihood(theta, r, y, y_err, m_func)[source]

Uses a simple Gaussian likelihood function, returns the logged value.

Parameters

  • theta (np.ndarray) – The knowledge we have (think theta in Bayesian parlance) - gets fed into the model we’ve chosen.

  • r (np.ndarray) – The radii at which we have measured profile values.

  • y (np.ndarray) – The values we have measured for the profile.

  • y_err (np.ndarray) – The uncertainties on the measured profile values.

  • m_func – The model function that is being fit to.

Returns

The log-likelihood value.

Return type

np.ndarray

xga.models.fitting.log_uniform_prior(theta, pr)[source]

This function acts as a uniform prior. Using the limits for the parameters in the chosen model (either user defined or default), the function checks whether the passed theta values sit within those limits. If they do then of course probability is 1, so we return the natural log (as this is a log prior), otherwise the probability is 0, so return -infinity.

Parameters

  • theta (np.ndarray) – The knowledge we have (think theta in Bayesian parlance) - gets fed into the model we’ve chosen.

  • pr (List) – A list of upper and lower limits for the parameters in theta, the limits of the uniform, uninformative priors.

Returns

The log prior value.

Return type

float

xga.models.fitting.log_prob(theta, r, y, y_err, m_func, pr)[source]

The combination of the log prior and log likelihood.

Parameters

  • theta (np.ndarray) – The knowledge we have (think theta in Bayesian parlance) - gets fed into the model we’ve chosen.

  • r (np.ndarray) – The radii at which we have measured profile values.

  • y (np.ndarray) – The values we have measured for the profile.

  • y_err (np.ndarray) – The uncertainties on the measured profile values.

  • m_func – The model function that is being fit to.

  • pr (List) – A list of upper and lower limits for the parameters in theta, the limits of the uniform, uninformative priors.

Returns

The log probability value.

Return type

np.ndarray

models.misc module

xga.models.misc.straight_line(x_values, gradient, intercept)[source]

As simple a model as you can get, a straight line. Possible uses include fitting very simple scaling relations.

Parameters

  • x_values (np.ndarray/float) – The x_values to retrieve corresponding y values for.

  • gradient (float) – The gradient of the straight line.

  • intercept (float) – The intercept of the straight line.

Returns

The y values corresponding to the input x values.

Return type

Union[np.ndarray, float]

xga.models.misc.power_law(x_values, slope, norm)[source]

A simple power law model, with slope and normalisation parameters. This is the standard model for fitting cluster scaling relations in XGA.

Parameters

  • x_values (np.ndarray/float) – The x_values to retrieve corresponding y values for.

  • slope (float) – The slope parameter of the power law.

  • norm (float) – The normalisation parameter of the power law.

Returns

The y values corresponding to the input x values.

Return type

Union[np.ndarray, float]

models.sb module

class xga.models.sb.BetaProfile1D(x_unit='kpc', y_unit=Unit('ct / (s arcmin2)'), cust_start_pars=None)[source]

Bases: xga.models.base.BaseModel1D

An XGA model implementation of the beta profile, essentially a projected isothermal king profile, it can be used to describe a simple galaxy cluster radial surface brightness profile.

Parameters

  • x_unit (Unit/str) – The unit of the x-axis of this model, kpc for instance. May be passed as a string representation or an astropy unit object.

  • y_unit (Unit/str) – The unit of the output of this model, keV for instance. May be passed as a string representation or an astropy unit object.

  • cust_start_pars (List[Quantity]) – The start values of the model parameters for any fitting function that used start values. The units are checked against default start values.

static model(x, beta, r_core, norm)[source]

The model function for the beta profile.

Parameters

  • x (Quantity) – The radii to calculate y values for.

  • beta (Quantity) – The beta slope parameter of the model.

  • r_core (Quantity) – The core radius.

  • norm (Quantity) – The normalisation of the model.

Returns

The y values corresponding to the input x values.

Return type

Quantity

derivative(x, dx=<Quantity 0.>, use_par_dist=False)[source]

Calculates the gradient of the beta profile at a given point, overriding the numerical method implemented in the BaseModel1D class, as this simple model has an easily derivable first derivative.

Parameters

  • x (Quantity) – The point(s) at which the slope of the model should be measured.

  • dx (Quantity) – This makes no difference here, as this is an analytical derivative. It has been left in so that the inputs for this method don’t vary between models.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a derivative distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

Returns

The calculated slope of the model at the supplied x position(s).

Return type

Quantity

inverse_abel(x, use_par_dist=False, method='analytical')[source]

This overrides the inverse abel method of the model superclass, as there is an analytical solution to the inverse abel transform of the single beta model. The form of the inverse abel transform is that of the king profile, but with an extra transformation applied to the normalising parameter. This method can either return a single value calculated using the current model parameters, or a distribution of values using the parameter distributions (assuming that this model has had a fit run on it).

Parameters

  • x (Quantity) – The x location(s) at which to calculate the value of the inverse abel transform.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a inverse abel transform distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

  • method (str) – The method that should be used to calculate the values of this inverse abel transform. Default for this overriding method is ‘analytical’, in which case the analytical solution is used. You may pass ‘direct’, ‘basex’, ‘hansenlaw’, ‘onion_bordas’, ‘onion_peeling’, ‘two_point’, or ‘three_point’ to calculate the transform numerically.

Returns

The inverse abel transform result.

Return type

Quantity

class xga.models.sb.DoubleBetaProfile1D(x_unit='kpc', y_unit=Unit('ct / (s arcmin2)'), cust_start_pars=None)[source]

Bases: xga.models.base.BaseModel1D

An XGA model implementation of the double beta profile, a summation of two single beta models. Often thought to deal better with peaky cluster cores that you might get from a cool-core cluster, this model can be used to describe a galaxy cluster radial surface brightness profile.

Parameters

  • x_unit (Unit/str) – The unit of the x-axis of this model, kpc for instance. May be passed as a string representation or an astropy unit object.

  • y_unit (Unit/str) – The unit of the output of this model, keV for instance. May be passed as a string representation or an astropy unit object.

  • cust_start_pars (List[Quantity]) – The start values of the model parameters for any fitting function that used start values. The units are checked against default start values.

static model(x, beta_one, r_core_one, norm_one, beta_two, r_core_two, norm_two)[source]

The model function for the double beta profile.

Parameters

  • x (Quantity) – The radii to calculate y values for.

  • norm_one (Quantity) – The normalisation of the first beta profile.

  • beta_one (Quantity) – The beta slope parameter of the first component beta profile.

  • r_core_one (Quantity) – The core radius of the first component beta profile.

  • norm_two (Quantity) – The normalisation of the second beta profile.

  • beta_two (Quantity) – The beta slope parameter of the second component beta profile.

  • r_core_two (Quantity) – The core radius of the second component beta profile.

Returns

The y values corresponding to the input x values.

Return type

Quantity

derivative(x, dx=<Quantity 0.>, use_par_dist=False)[source]

Calculates the gradient of the double beta profile at a given point, overriding the numerical method implemented in the BaseModel1D class, as this simple model has an easily derivable first derivative.

Parameters

  • x (Quantity) – The point(s) at which the slope of the model should be measured.

  • dx (Quantity) – This makes no difference here, as this is an analytical derivative. It has been left in so that the inputs for this method don’t vary between models.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a derivative distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

Returns

The calculated slope of the model at the supplied x position(s).

Return type

Quantity

inverse_abel(x, use_par_dist=False, method='analytical')[source]

This overrides the inverse abel method of the model superclass, as there is an analytical solution to the inverse abel transform of the double beta model. The form of the inverse abel transform is that of two summed king profiles, but with extra transformations applied to the normalising parameters. This method can either return a single value calculated using the current model parameters, or a distribution of values using the parameter distributions (assuming that this model has had a fit run on it).

Parameters

  • x (Quantity) – The x location(s) at which to calculate the value of the inverse abel transform.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a inverse abel transform distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

  • method (str) – The method that should be used to calculate the values of this inverse abel transform. Default for this overriding method is ‘analytical’, in which case the analytical solution is used. You may pass ‘direct’, ‘basex’, ‘hansenlaw’, ‘onion_bordas’, ‘onion_peeling’, ‘two_point’, or ‘three_point’ to calculate the transform numerically.

Returns

The inverse abel transform result.

Return type

Quantity

models.temperature module

class xga.models.temperature.SimpleVikhlininTemperature1D(x_unit='kpc', y_unit=Unit('keV'), cust_start_pars=None)[source]

Bases: xga.models.base.BaseModel1D

An XGA model implementation of the simplified version of Vikhlinin’s temperature model. This is for the description of 3D temperature profiles of galaxy clusters.

Parameters

  • x_unit (Unit/str) – The unit of the x-axis of this model, kpc for instance. May be passed as a string representation or an astropy unit object.

  • y_unit (Unit/str) – The unit of the output of this model, keV for instance. May be passed as a string representation or an astropy unit object.

  • cust_start_pars (List[Quantity]) – The start values of the model parameters for any fitting function that used start values. The units are checked against default start values.

static model(x, r_cool, a_cool, t_min, t_zero, r_tran, c_power)[source]

The model function for the simplified Vikhlinin temperature profile.

Parameters

  • x (Quantity) – The radii to calculate y values for.

  • r_cool (Quantity) – Parameter describing the radius of the cooler core region.

  • a_cool (Quantity) – Power law parameter for the cooler core region.

  • t_min (Quantity) – A minimum temperature parameter for the model.

  • t_zero (Quantity) – A normalising temperature parameter for the model.

  • r_tran (Quantity) – The radius of the transition region of this broken power law model.

  • c_power (Quantity) – The power law index for the part of the model which describes the outer region of the cluster.

Returns

The y values corresponding to the input x values.

Return type

Quantity

derivative(x, dx=<Quantity 0.>, use_par_dist=False)[source]

Calculates the gradient of the simple Vikhlinin temperature profile at a given point, overriding the numerical method implemented in the BaseModel1D class.

Parameters

  • x (Quantity) – The point(s) at which the slope of the model should be measured.

  • dx (Quantity) – This makes no difference here, as this is an analytical derivative. It has been left in so that the inputs for this method don’t vary between models.

  • use_par_dist (bool) – Should the parameter distributions be used to calculate a derivative distribution; this can only be used if a fit has been performed using the model instance. Default is False, in which case the current parameters will be used to calculate a single value.

Returns

The calculated slope of the model at the supplied x position(s).

Return type

Quantity

class xga.models.temperature.VikhlininTemperature1D(x_unit='kpc', y_unit=Unit('keV'), cust_start_pars=None)[source]

Bases: xga.models.base.BaseModel1D

An XGA model implementation of the full version of Vikhlinin’s temperature model. This is for the description of 3D temperature profiles of galaxy clusters.

Parameters

  • x_unit (Unit/str) – The unit of the x-axis of this model, kpc for instance. May be passed as a string representation or an astropy unit object.

  • y_unit (Unit/str) – The unit of the output of this model, keV for instance. May be passed as a string representation or an astropy unit object.

  • cust_start_pars (List[Quantity]) – The start values of the model parameters for any fitting function that used start values. The units are checked against default start values.

static model(x, r_cool, a_cool, t_min, t_zero, r_tran, a_power, b_power, c_power)[source]

The model function for the full Vikhlinin temperature profile.

Parameters

  • x (Quantity) – The radii to calculate y values for.

  • r_cool (float) – Parameter describing the radius of the cooling region (I THINK - NOT CERTAIN YET).

  • a_cool (float) – Power law parameter for the cooling region (I THINK - NOT CERTAIN YET).

  • t_min (float) – A minimum temperature parameter for the model (I THINK - NOT CERTAIN YET).

  • t_zero (float) – A normalising temperature parameter for the model (I THINK - NOT CERTAIN YET).

  • r_tran (float) – The radius of the transition region of this broken power law model.

  • a_power (float) – The first power law index.

  • b_power (float) – The second power law index.

  • c_power (float) – the third power law index.

Returns

The y values corresponding to the input x values.

Return type

Quantity