cosmicfishpie.fishermatrix package

Submodules

cosmicfishpie.configs.config module

cosmicfishpie.configs.config.init(options={}, specifications={}, observables=None, freepars=None, extfiles=None, fiducialpars=None, photobiaspars=None, photopars=None, IApars=None, PShotpars=None, spectrobiaspars=None, spectrononlinearpars=None, IMbiaspars=None, surveyName='Euclid', cosmoModel='w0waCDM', latexnames=None)[source]

This class is to handle the configuration for the fishermatrix computation as well as the fiducial parameters. It then gives access to all global variables

Parameters:

options (dict, optional) – A dictionary that contains the global options for the calculation of the fishermatrix. A list of all possible keys are found below
specifications (dict, optional) – A dictionary containing the survey specifications. Defaults to the specifications in the .yaml of the survey specifications
observables (list, optional) – A list of strings for the different observables
freepars (dict, optional) – A dictionary containing all cosmological parameters to be varied and their corresponding rel. step sizes
extfiles (dict, optional) – A dictionary containing the path to the external files as well as how all the names of the files in the folder correspond to the cosmological quantities, units etc.
fiducialpars (dict, optional) – A dictionary containing the fiducial cosmological parameters
photobiaspars (dict, optional) – A dictionary containing the specifications for the galaxy biases of the photometric probe
photopars (dict, optional) – A dictionary containing specifications for the window function’s galaxy distribution
IApars (dict, optional) – A dictionary containing the specifications for the intrinsic alignment effect in cosmic shear
PShotpars (dict, optional) – A dictionary containing the values of additional shotnoise of the spectroscopic probes
spectrobiaspars (dict, optional) – A dictionary containing the specifications for the galaxy biases of the spectroscopic probe
spectrononlinearpars (dict, optional) – A dictionary containing the values of the non linear modeling parameters of the spectroscopic probe
IMbiaspars (dict, optional) – A dictionary containing the specifications for the galaxy biases of the spectroscopic intensity mapping probe
surveyName (str, optional) – String of the name of the survey for which the forecast is done. Defaults to Euclid with optimistic specifications
cosmoModel (str, optional) – A string of the name of the cosmological model used in the calculations. Defaults to flat “w0waCDM” cosmology
latexnames (dict, optional) – A dictionary that contains the Latex names of the cosmological parameters
Options
-------
camb_path (str) – Path to camb. Defaults to the camb in your current environment
specs_dir (str) – Path to the survey specifications. Defaults to the specs_dir_default
specs_dir_default (str) – Path to the default survey specifications. Defaults to the survey_specifications folder in the config directory of cosmicfishpie
survey_name (str) – String of the names of the survey. Defaults to the name passed in the parameter surveyName
survey_name_photo (str) – Name of the survey specifications file for a photometric probe
survey_name_spectro (str) – Name of the survey specifications file for a spectrocopic probe
survey_name_radio_IM (str) – Name of the survey specifications file for a line intensity mapping probe
derivatives (str) – String of the name of the derivative method. Either 3PT, 4PT_FWD, STEM or POLY. Defaults to 3PT
nonlinear (bool) – If True will do nonlinear corrections in the computation of the different observables. Defaults to True
nonlinear_photo (bool) – If True will use the nonlinear power spectrum when calculation the angular power spectrum of the photometric probe. Defaults to True
bfs8terms (bool) – If True will expand the observed power spectrum with \(\sigma_8\) to match the IST:F recipe. Defaults to True
vary_bias_str (str) – The root of the name of the bias parameters that should be varied in the spectroscopic probe. Defaults to ‘lnb’
AP_effect (bool) – If True the Alcock-Paczynsk effect will be considered in the spectroscopic probe. Defaults to True
FoG_switch (bool) – If True the finger of god effect will be modelled in the observed power spectrum of the spectroscopic probe. Defaults to True
GCsp_linear (bool) – If True there will be no nonlinear modelling used in the spectroscopic probe. Defaults to False
fix_cosmo_nl (bool) – If True and the nonlinear modeling parameters are not varied, then they will be fixed to the values computed in the fiducial cosmology. Else they will be recomputed in each sample cosmology. Defaults to True
Pshot_nuisance_fiducial (float) – Value of the fiducial additional shotnoise of the spectroscopic probe. Defaults to 0.0
pivot_z_IA (float) – Redshift on which the power law dependance in the eNLA model of intrinsic alignment should be normalized to. Defaults to 0.0
accuracy (int) – Global rescaling of the amount of points that are used in internal calculations or interpolations for the probes. Defaults to 1
feedback (int) – Number indicating the verbosity of the output. Higher numbers generally mean more output. Defaults to 2
activateMG (bool) – If True will also consider modified gravity in the calculations of the observables. Defaults to False
external_activateMG (bool) – If True while reading the external Files will also look for files specific to modified gravity models
cosmo_model (str) – A string of the name of the cosmological model used in the calculations. Defaults to what was passed in the parameter cosmoModel
outroot (str) – The name of the output files are always starting with CosmicFish_Version number_outroot. Defaults to ‘default_run’
code (str) – String of the method to obtain the cosmological functions such as the power spectrum. Either ‘camb’, ‘class’ or ‘external’. Defaults to ‘camb’
memorize_cosmo (bool) – If True will save and load cosmologies that have already been computed in the cache. Defaults to False
results_dir (str) – Name of the folder in which the results should be saved. If the folder does not exist will create a new one. Defaults to ‘./results’
boltzmann_yaml_path (str) – Path to the configurations for the Einstein-Boltzmann solvers. Defaults to the boltzmann_yaml_files folder in the home directory of cosmicfishpie
class_config_yaml (str) – Path to the configurations for class. Defaults to ‘boltzmann_yaml_path/class/default.yaml’
camb_config_yaml (str) – Path to the configurations for camb. Defaults to ‘boltzmann_yaml_path/camb/default.yaml’
fishermatrix_file_extension (str) – Specifies in what kind of file the result Fisher matrix should be saved. Defaults to ‘.txt’
savgol_polyorder (float) – Order of the Savitzky-Golay filter. Defaults to 3 matching the IST:F recipe
savgol_width (float) – Width of the Savitzky-Golay filter. Defaults to ~1.359
savgol_internalsamples (float) – How many points on a logarithmic k axis should be taken to apply the Savitzky-Golay filter to. Defaults to 800
savgol_internalkmin (float) – Lowest wavenumber that should be used when calculating when applying the Savitzky-Golay filter. Defaults to 1e-3. Together with the other defaults this is matching the IST:F recipe
eps_cosmopars (float) – The default rel. step size of the cosmological parameters if none have been passed. Defaults to 1e-2
eps_gal_nuispars (float) – The default rel. step size of the bias parameters if none have been passed. Defaults to 1e-4
GCsp_Tracer (str) – What power spectrum should be used as the underlying power spectrum the spectroscopic probe’s galaxy clustering traces. Either ‘matter’ for the total matter spectrum or ‘clustering’ for CDM+baryons. Defaults to ‘matter’
GCph_Tracer (str) – What power spectrum should be used as the underlying power spectrum the photometric probe’s galaxy clustering traces. Either ‘matter’ for the total matter spectrum or ‘clustering’ for CDM+baryons. Defaults to ‘matter’
ShareDeltaNeff (bool) – If True, the variation of the cosmological parameter Neff is understood as a rescaling of the decoupling temperature of neutrinos. If False any additional Neff is accounted for as additional massless relics.
kh_rescaling_bug (bool) – If true, the internal wavenumber in the computation of the spectroscopic probe’s power spectrum computation will be rescaled by an adtional factor h/hfid. Default False
kh_rescaling_beforespecerr_bug (bool) – If True, the internal scales in the computation of the spectroscopic probe’s resolution error will be rescaled by an adtional factor h/hfid. Default False

cosmicfishpie.configs.config.settings

A dictionary containing all the global options passed as well as the default values of the ones not passed

Type:: dict, global

cosmicfishpie.configs.config.external

A dictionary containing all paths to the external files, how all the names of the files in the folder correspond to the cosmological quantities, the units etc. Will be None if no external files are given

Type:: dict, global

cosmicfishpie.configs.config.input_type

String of the method to obtain the cosmological functions such as the power spectrum. Either ‘camb’, ‘class’ or ‘external’

Type:: str, global

cosmicfishpie.configs.config.specs

A dictionary containing the survey specifications

Type:: dict, global

cosmicfishpie.configs.config.boltzmann_classpars

A dictionary containing the configuration, precision parameters, and fixed cosmological parameters for class

Type:: dict, global

cosmicfishpie.configs.config.boltzmann_cambpars

A dictionary containing the configuration, precision parameters, and fixed cosmological parameters for camb

Type:: dict, global

cosmicfishpie.configs.config.survey_equivalence

Part of the Parser, will correspond the passed survey to the name of a specifications file

Type:: callable, global

cosmicfishpie.configs.config.obs

A list of strings for the different observables

Type:: list, global

cosmicfishpie.configs.config.freeparams

A dictionary containing all names and the corresponding rel. step size for all parameters

Type:: dict, global

cosmicfishpie.configs.config.fiducialparams

A dictionary containing all fiducial values for the cosmological parameters

Type:: dict, global

cosmicfishpie.configs.config.fiducialcosmo

An instance of cosmo_functions of the fiducial cosmology, this contains all the cosmological functions and quantities computed from them

Type:: cosmicfishpie.cosmology.cosmology.cosmo_functions, global

cosmicfishpie.configs.config.biasparams

a dictionary containing the specifications for the galaxy biases of the photometric probe

Type:: dict, global

cosmicfishpie.configs.config.photoparams

A dictionary containing specifications for the window function’s galaxy distribution of the photometric probe

Type:: dict, global

cosmicfishpie.configs.config.IAparams

A dictionary containing the specifications for the intrinsic alignment effect in cosmic shear of the photometric probe

Type:: dict, global

cosmicfishpie.configs.config.PShotparams

A dictionary containing the values of the additional shot noise per bin dictionary containing the values of the additional shot noise per bin for the spectroscopic probe

Type:: dict, global

cosmicfishpie.configs.config.Spectrobiasparams

A dictionary containing the specifications for the galaxy biases of the spectroscopic probe

Type:: dict, global

cosmicfishpie.configs.config.Spectrononlinearparams

A dictionary containing the values of the non linear modeling parameters entering FOG and the dewiggling weight per bin for the spectroscopic probe

Type:: dict, global

cosmicfishpie.configs.config.IMbiasparams

A dictionary containing the specifications for the line intensity biases of the spectroscopic probe

Type:: dict, global

cosmicfishpie.configs.config.latex_names

A dictionary with all cosmological + nuisance parameters and their corresponding name for the LaTeX labels.

Type:: dict, global

cosmicfishpie.fishermatrix.cosmicfish module

MAIN

This is the main engine of CosmicFish.

class cosmicfishpie.fishermatrix.cosmicfish.FisherMatrix(options={}, specifications={}, observables=None, freepars=None, extfiles=None, fiducialpars=None, photobiaspars=None, photopars=None, spectrononlinearpars=None, spectrobiaspars=None, IApars=None, IMbiaspars=None, PShotpars=None, surveyName='Euclid', cosmoModel='w0waCDM', latexnames=None, parallel=False, parallel_cpus=4)[source]

Bases: object

CMB_fishermatrix(noisy_cls=None, covmat=None, derivs=None, cmb_obj=None)[source]

compute(max_z_bins=None)[source]

This function will compute the Fisher information matrix and export using the specified settings.

Parameters:: max_z_bins (int) – For the spectroscopic probe what the highest redshift bin that should be considered in the computation of the Fisher
Returns:: A instance of fisher_matrix containing the calculated Fisher matrix as well as parameter names, settings, etc
Return type:: cosmicfishpie.analysis.fisher_matrix

compute_binned_derivs(z_arr)[source]

This computes the derivatives of the observed power spectrum for all redshift bins

Parameters:: z_arr (list, numpy.ndarray) – List of the redshift bin centers of the probe
Returns:: A dictionary containing lists of derivatives of the observed power spectrum for each redshift bin and varied parameter
Return type:: dict

eliminate_zbinned_freepars(nmax)[source]

This helper function is there to find any parameters passed that correspond to no zbin. It will then remove them from the varied parameters list

Parameters:: nmax (int) – Index of the highest redshift bin that should be considered

export_fisher(fishmat, totaltime=None)[source]

Will print the fisher matrix as well as specifications and the parameter names to files. To change location and filenames for this check the settings dictionary of cosmicfishpie.configs.config

Parameters:

fishmat (numpy.ndarray) – Computed Fisher matrix
totaltime (float, optional) – Total time needed to compute the fisher. Will print time information if passed

Returns:

A instance of fisher_matrix containing the calculated Fisher matrix as well as parameter names, settings, etc

Return type:

cosmicfishpie.analysis.fisher_matrix

fish_integrand(zi, k, mu, pi, pj)[source]

Helper function to calculate the integrand that enters the computation of the Fisher elements.

Parameters:

zi (int) – index of the redshift bin
k (numpy.ndarray) – grid of wavenumbers used in the calculation. Has to be the internal kmesh
mu (numpy.ndarray) – grid of observation angles used in the calculation. Has to be the internal mumesh
pi (str) – name of the first parameter
pj (str) – name of the second parameter

Returns:

Integrant that enters the Fisher matrix element computation. The shape matches ( shape of the kmesh ) x ( shape of mumesh)

Return type:

numpy.ndarray

fisher_calculation(zi, p_i, p_j)[source]

This helper function calculates a singular element of the fisher matrix

Parameters:

zi (int) – index of the redshift bin
p_i (str) – name of the first parameter
p_j (str) – name of the second parameter

Returns:

The Fisher matrix element computed from the derivative with respect to two parameters and a given redshift bin for a spectroscopic probe

Return type:

float

fisher_integral(integrand)[source]

Function to calculate the integral that enters the computation of the Fisher elements. Uses a simpson integration on the mu and k grid

Parameters:: integrand (numpy.ndarray) – Integrant that enters the Fisher matrix element computation. The shape needs to match ( shape of the kmesh ) x ( shape of mumesh)
Returns:: The Fisher matrix element computed from the derivative with respect to two parameters at a given redshift bin for a spectroscopic probe
Return type:: float

fisher_per_bin(ibin)[source]

This helper function contains the Fisher matrix of a spectroscopic probe for a single redshift bin

Parameters:: ibin (int) – index of the redshift bin
Returns:: Fisher matrix of a spectroscopic probe for a single redshift bin
Return type:: numpy.ndarray

photo_LSS_fishermatrix(noisy_cls=None, covmat=None, derivs=None, lss_obj=None)[source]

Compute the Fisher matrix of a photometric probe.

Parameters:

noisy_cls (dict, optional) – a dictionary with all the auto and cross correlation fiducial angular power spectra with noise added to it. Will recompute from lss_obj when not passed
covmat (list, optional) – A list of pandas.DataFrame objects that store the covariance matrix for each multipole. Will recompute from lss_obj when not passed
derivs (dict, optional) – A dictionary containing the derivatives of the angular power spectrum at the fiducial for all free parameters. Will recompute from lss_obj when not passed
lss_obj (cosmicfishpie.LSSsurvey.photo_cov.PhotoCov, optional) – This object is used to compute the ingredients of the Fisher matrix if they were not passed

Returns:

The full fisher matrix for the photometric probe

Return type:

numpy.ndarray

photo_LSS_fishermatrix_einsum(noisy_cls=None, covmat=None, derivs=None, lss_obj=None)[source]

Compute the Fisher matrix of a photometric probe.

Parameters:

noisy_cls (dict, optional) – a dictionary with all the auto and cross correlation fiducial angular power spectra with noise added to it. Will recompute from lss_obj when not passed
covmat (list, optional) – A list of pandas.DataFrame objects that store the covariance matrix for each multipole. Will recompute from lss_obj when not passed
derivs (dict, optional) – A dictionary containing the derivatives of the angular power spectrum at the fiducial for all free parameters. Will recompute from lss_obj when not passed
lss_obj (cosmicfishpie.LSSsurvey.photo_cov.PhotoCov, optional) – This object is used to compute the ingredients of the Fisher matrix if they were not passed

Returns:

The full fisher matrix for the photometric probe

Return type:

numpy.ndarray

pk_LSS_Fisher(nbins)[source]

This computes the Fisher matrix of a spectroscopic probe for all redshift bins

Parameters:: nbins (int) – number of redshift bins the spectroscopic probe has
Returns:: A list of Fisher matrices for each redshift bin
Return type:: numpy.ndarray

recap_options()[source]: This will print all the selected options into the standard output

set_pk_settings()[source]: Function to define grids of the internal wavenumber and observation angle

Note

This is not a setter function. Rather the internal grids are constructed from the passed options and then they are stored in the attributes Pk_kgrid and Pk_mugrid as well as the combined meshes Pk_kmesh and Pk_mumesh.

cf_version = 'CosmicFish_v1.3.0'

cosmicfishpie.fishermatrix.cosmicfish.ray_session(num_cpus=4, restart=True, shutdown=False)[source]

cosmicfishpie.fishermatrix.derivatives module

DERIVATIVES

This is the derivatives engine of CosmicFish.

class cosmicfishpie.fishermatrix.derivatives.derivatives(observable, fiducial, special_deriv_function=None, derivatives_type='3PT', freeparams={}, observables_type=None, external_settings=None, feed_lvl=None)[source]

Bases: object

der_3pt_stencil(fwd, bwd, step)[source]

Helper function to compute the 3PT symmetrical finite step size derivative

Parameters:

fwd (float, numpy.ndarray) – Observable computed at the forward step
fwd – Observable computed at the backwards step
step (float) – Absolute step size of the numerical derivative

Returns:

Numerical derivative using the a 3 point stencil

Return type:

float, numpy.ndarray

der_fwd_4pt(fwdi, step)[source]

Helper function to compute the 4PT forward finite step size derivative

Parameters:

fwdi (list, numpy.ndarray) – Observable computed at the fiducial and at equally spaced points in the forward direction
step (float) – Absolute distance between the size of the numerical derivative

Returns:

Numerical derivative using the a 4 point forward stencil

Return type:

float, numpy.ndarray

derivative_3pt()[source]

One of the possible derivative methods. Computes the numerical derivative using a finite differences 3 point symmetrical derivative

Returns:: A dictionary containing the derivative of the observable for each varied parameter.
Return type:: dict

Note

Implements the following equation:

\[\frac{\mathrm{d} \mathcal{O}}{\mathrm{d} \theta} = \frac{\mathcal{O}(\theta+h)-\mathcal{O}(\theta-h)}{2\,h}\]

derivative_forward_4pt()[source]

One of the possible derivative methods. Computes the numerical derivative using a finite differences one-sided 4 point forward derivative. Taken from: https://web.media.mit.edu/~crtaylor/calculator.html @misc{fdcc, title={Finite Difference Coefficients Calculator}, author={Taylor, Cameron R.}, year={2016}, howpublished=”url{https://web.media.mit.edu/~crtaylor/calculator.html}” }

Returns:: A dictionary containing the derivative of the observable for each varied parameter.
Return type:: dict

Note

Implements the following equation:

\[\begin{split}\\frac{\\mathrm{d} \\mathcal{O}}{\\mathrm{d} \\theta} = \\frac{-11\\,\\mathcal{O}(\\theta)+18\\,\\mathcal{O}(\\theta+h)-9\\,\\mathcal{O}(\\theta+2\\,)+2\\,\\mathcal{O}(\\theta+3\\,h)}{6\\,h}\end{split}\]

derivative_poly()[source]

One of the possible derivative methods. Computes the numerical derivative using a polynomial derivative method

Returns:: A dictionary containing the derivative of the observable for each varied parameter.
Return type:: dict

derivative_stem()[source]

One of the possible derivative methods. Computes the numerical derivative using the SteM derivative method

Returns:: A dictionary containing the derivative of the observable for each varied parameter.
Return type:: dict