fake-spectra 1.0

= Flux extractor =

This is a small code for generating and analyzing simulated spectra from Arepo/Gadget HDF5 simulation output. It is fast, parallel and written in C++ and Python 3. It really has two parts: 1) a C++/python 3 code which generates and analyses arbitrary spectra 2) A (slightly) maintained C++ command line program, extract, that generates Lyman-alpha spectra and outputs them to a binary file.

If you are reading these instructions, I will assume you are using the first part: the second program is for compatibility with older spectral extraction codes, of which this is a rewrite, and so anyone who wants it should already know how to use it.

== Installation ==

This is a python 3 code Make sure you install the python 3 libraries!

Required Python libraries: - numpy (core functionality) - h5py (for saving)

Optional libraries: - matplotlib (if you want to plot) - cloudy_tables (scripts for finding an ionisation fraction from a cloudy table): this is required to generate metal line absorption. - bigfile (to install, do ‘pip install –user bigfile’) for reading BigFile snapshot outputs from Yu Feng’s MP-Gadget. - spb_common (used only to read halo catalogues)

All these libraries should be in your $PYTHONPATH

At time of writing, the code should compile with python2, once python3-config in the Makefile is replaced with python2-config. However, I do not guarantee bug-free operation, and strongly recommend using python 3.

To make the C module, type: “make” On some systems you may have to set PYINC in the Makefile to the location of your python include headers.

The test suite for the C++ module requires Boost::Test and can be used with “make test”

== Usage == The main spectral generation routines are used can be called with:

import spectra spectra.Spectra(…)

However, this requires you to specify the positions of each sightline. I have created a number of convenient wrappers for common configurations. Two of these are:

randspectra.py - Generate spectra at random locations. Can optionally discard spectra that do not meet an HI column density threshold. halospectra.py - Generate spectra through the center of halos.

Spectral generation routines take two arguments, base and num, which specify where they should look for snapshot output. They will search: $(base)/snapdir_$(num)/snap_$(num).hdf5 Note that num is padded with zeros to three characters, so passing ‘40’ will result in ‘040’.

Column densities can be generated for arbitrary ions with the method get_col_density(elem, ion) For neutral gas, pass ion 1. For the sum of all ionic species, pass ion -1.

Optical depths can be generated for arbitrary lines with the method get_tau(elem, ion, line) Line data is loaded from a copy of atom.dat taken from VPFIT.

Thus, to generate randomly positioned Lyman-series spectra and associated HI column densities, one would use this script:

from randspectra import RandSpectra

rr = RandSpectra(5, “MySim”, thresh=0.) rr.get_tau(“H”,1,1215) #Lyman-beta rr.get_tau(“H”,1,1026) rr.get_col_density(“H”,1) #Save spectra to file rr.save_file()

Generated spectra will be saved into HDF5 files, for ease of later analysis. Each spectral generation routine saves spectra to a differently named file.

To load them again, use the PlottingSpectra routines:

from plot_spectra import PlottingSpectra

ps = PlottingSpectra(5,”MySim”, savefile=”mysavefile.hdf5”) ps.plot_cddf(“H”,1)