Usage

This is a basic walkthrough of how to do a Fisher matrix analysis with 21cmFAST and 21cmfish.

Creating lightcones for your analysis

Start by creating a .config file for your runs. Have a look in 21cmFAST_config_files/ for examples.

You can add any of the usual 21cmFAST AstroParams, UserParams and FlagOptions.

At the end of the config file list the AstroParams you want to vary

You will need to change the output_dir to the full path to where you want to save lightcones all other 21cmfish outputs.

To make the lightcones run:

python make_lightcones_for_fisher.py PATH_TO_YOUR_CONFIG_FILE.config --dry_run

I advise adding the –dry_run flag the first time you run to check the lightcones it will make before it tries to run 21cmFAST! 21cmfish can also create lightcones using multiprocessing and multithreading, which you can specify via (–num_cores and –N_THREADS. By default, 21cmfish will run on n_cpus - 1.

Process lightcones for each parameter

The py21cmfish.Parameter() class loads lightcones for each parameter and exports the 21cm global signal and power spectra for each lightcones, and then calculates the derivatives of these quantities needed for the Fisher matrix analysis.

Start by importing 21cmfish.

import py21cmfish

Parameters are loaded from the config file

astro_params_vary, astro_params_fid = p21fish.get_params_fid(config_file=data_dir+'21cmFAST_config_files/EoS_mini.config')

Each parameter is loaded as a separate py21cmfish.Parameter() object into a parameters dictionary. For example:

output_dir_Park19 = data_dir+'examples/EoS_mini/'
params_EoS = {}
for param in astro_params_vary:
    params_EoS[param] = p21fish.Parameter(param=param, output_dir=output_dir)

If you are adding a new parameter from new lightcones, add new=True to generate new global signals and power spectra.

Create Fisher matrix

The Fisher matrix and its inverse are generated from the parameters dictionary:

Fij_matrix_PS, Finv_PS= p21fish.make_fisher_matrix(params_EoS,
                                                    fisher_params=astro_params_vary,
                                                    hpeak=0.0, obs='PS',
                                                    k_min=0.1, k_max=1,
                                                    z_min=5.7, z_max=30.,
                                                    sigma_mod_frac=0.2,
                                                    add_sigma_poisson=True)

For more details see the examples notebook #TODO