This repository contains the code used for calculations and simulations
for the paper "Peeling off the late Universe: Reconstructing the ISW map with 
galaxy surveys," by Jessica Muir and Dragan Huterer.

Most of the files in it were used to produce the results in the paper, though
some were used for testing. Comments in each file should be somewhat self-explanatory
but brief descriptions of the various files are below.

README written 3/18/16 - Jessie Muir

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run scripts contain functions which run specific analysis and make plots.
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run_euclidlike_analysis.py - the main script for our paper's analysis.
    The name refers to the fact that we model our fiducial survey on Euclid's dn/dz.
    Has functions defined for the various studies we ran (roughly corresponding to
    paper sections). At the bottom, it contains  a number of functions calls with
    if statements set up as switches and some  explanatory comments. These are the
    function calls used to get our results. Changes switches to 1 and execute file
    to run. 
    >Depends on all the scripts listed in the 'utilities' section below
    >Assumes you have an output directory set up for each test, not included in repo.

run_MDcrosscheck_analysis.py - contains calculations used to check our ISW rec
    pipeline against paper by Manzotti and Dodelson. Uses some functions defined in
    run_euclidlike_analysis.py.

genplots_forpaper.py - either calls functions of run_euclidlike_analysis or has them
    rewritten in a way that allows greater control of formatting. Contains function
    callsed used to generate plots for our paper.

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output directory
--------------------------
contains data files for Cl used for depth test, bin test, and z distribution tests,
but no map or plot output. The files in the run scripts will assume t0hat there exist
some subdirectories in this which you will have to make manually. Contact me
if you'd like more information about that. 

==========================================
utility scripts containing functions and class definitions used for various calcs
--------------------------
ClRunUtils - contains some classes used in Cl calculations
   -KData - bundles together info about wave number k used in Cl computation
   -RunData - keeps track directories where results go, tags to add to output files,
       where file of cosmological parameters used is and the relevent Cosmology object
       but not specific info about Cl clculation
   -ClRunData - inherits from RunData, cotains additional info needed for Cl integrals
   
CosmParams.py - containts class and function which bundles info about cosmology, P(k)
   -Cosmology - reads in and keeps track of cosmological paramters, can run camb to
       compute P(k) tabulates background cosmology functions or reads them in
       
MapParams.py - contains classes and functions used to model LSS surveys
   -MapWrapper - contains some string tags identifying maps + bools isISW, isGal
   -MapType - inherits from MapWrapper, still a pretty general class which keeps
     track of some general info about a map, its redshift distribution and # of bins
     Creates a list of BinMap objects for each associated Bin
   -SurveyType - inherits from MapType, is specific to galaxy surveys, contains info
     about dn/dz, b(z), nbar, fraction of catastrophic photo z erorrs. When initialized
     computes appropriate dn/dz for each bun and normalizes them before creating
     list of associated SurveyBinMap objects
   -BinMap - inherits from MapWraper, contains info for a map that has a tophat z range
   -SurveyBinMap - object containing info about a single bin of a galaxy survey  

genCrossCor.py - contains classes and functions used to compute, read in, store Cl data
   -ClData - class bundling array of Cl data together with tags for the input maps
      ell values, shot noise levels, and tranlastions between map and crosscorr indices
   - functions to compute Cl using Limber approx
   - functions used to compute and tabulate I_l(k) transfer functions
   - functions for computing, tabulating, and reading in Cl
   >Depends on the ClRunUTils, CosmParams, MapParams.
   >Note that Ilk and Cl integrals are set up to use python multiprocessing, but
    that due to some issue with the linear algebra module of numpy, running both
    of these at once cause errors on macs. I usually just run these on a cluster
    to avoid this problem. There are hardcoded "DOPARALLEL" booleans which can be used
    to switch multiprocessing on and off for these calculations.
   >I have not done this, but one could feasibly write a function that reads Cl output
    from CLASS into my ClData object format, so some utilities here can be used
    independently of the actual integral calculations
   
genMapsfromCor.py - contains classes and functions used to generate and store map info
   -glmData - classes that holds g_lm (and a_lm) data in an array of size
     Nrealizations x Nmaps x Nlm, as well as info about the associated maps
     and a bunch of functions that keep track of where the fits files for the maps go
     Becasue of this, it is useful even if you don't want the g_lm data; if you
     set this up with Nreal=0, can use it as a way to keep track of map info and
     filenames
   -functions to generate glm from Cl, read in glm from files, or extract glm from maps
   -functions for generate calibration error or shot noise maps, adding noise to
     existing galaxy maps
   >Depends on all utilities functions above
   
mapdef_utils.py - contains some functions used to generate maptypes used in our survey
    as well as those used to get teh RunData object used in our analysis.
    >Depends on above utilties functions

AnalysisUtils.py - contains functions and class defs used to do+analyze ISW rec
   -RecData - class that holds info about an ISW reconstruction: what input LSS maps,
     to use for maps and model Cl's, what ell values, info for output map files
   -functions for fitting for constant bias
   -funcitons which extract info from a ClData object and convert into an
     NellxNmapxNmap array used to make ISW estimator, with ISW map at index 0
   -functions which extract and order glm data from glmData objects to make it
     consistant with Dl matrix used in reconstruction
   -functions which compute ISW estimator for one or many maps or reconstruction
     setupts described using RecData objects
   -functions used to compute reconstruction quality statistics from maps or theory
     in our paper we only looked at rho and s, there are some functions here for other
     stats that we didn't end up using; code has been edited since we last used these
     so they may not work without some tweaking.
   -a few plotting functions, though most of the work for this will be in the 'run'
     scripts described at the top of this README.

==========================================
test scripts used in early stages of the project
  These have not been run in a while, and so may not be compatible with all
  changes that have since been made to the utility scripts.
--------------------------
testmapmaking.py - used to run intial tests of map making and reconstruction utilities
test_integrals.py - used to test accuracy/convergence of Cl calculations
testscript.py - used to test that some features of the utility scripts can run