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# F. Salesa, Sep 26, 2017  #
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This are the steps to follow to reproduce the results from the "Extended TeV gamma-Ray Sources Around Pulsars Constrain the Origin of the Positron Flux at Earth" paper:

1) 3ML and LiFF installation (only for Linux, not Mac yet):
# 3ML is a multi-wavelength/multi-messenger analysis framework that provides a
# unified interface to software from many different instruments. It is 
# available as open-source code under: https://github.com/giacomov/3ML . 
# LiFF is the HAWC analysis software (compatible with 3ML) that is used to 
# study HAWC sky maps. It is available as open source code under:
# https://github.com/rjlauer/aerie-liff .
# Both frameworks can be installed via conda:

# Install miniconda
wget -q https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O ~/miniconda.sh

# This will install conda in ~/miniconda . If you want to put it somewhere else change accordingly these 3 lines
bash ~/miniconda.sh -b -p $HOME/miniconda
export PATH="$HOME/miniconda/bin:$PATH"
source ~/miniconda/bin/activate

# Create a test environment (to avoid playing with the root conda installation)
conda create --name hawc_test -y python

# Activate environment
source activate hawc_test

# install liff and threeml
conda install -c giacomov -c hawc -y liff threeml

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2) Reproduce Table results:
# After activating the 3ML environment, run the 3ML script in the '3ML_fit' directory 
python paper_3ML_script.py

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3) Reproduce Fig.1:
# To obtain the significance map (in FITS format) assuming a point source hypothesis run the following
liff-HealpixSigFluxMap -m maptree.root -e response.root -r 102 -d 16 --edgeRA 32 --edgeDec 32 --binStart 1 --binStop 9 --nside 512 --padding 1 -o fig1map.fits.gz

# To obtain the significance map, assuming a diffusion model emission, follow the README file instructions in 'Fig1_diffusion'

#Outputs are regular FITS files. This is a list of viewers able to display FITS files: 
https://fits.gsfc.nasa.gov/fits_viewer.html
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4) Reproduce Fig.2
# Follow the README file instructions in 'Fig2'

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5) Reproduce Fig.3
#Install EDGE from: https://github.com/rlopezcoto/EDGE

#Follow the README included in the folder 'Science_paper'

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If you have question you can reach us by email:
fsalesa@ifj.edu.pl
hao@lanl.gov
rlopez@mpi-hd.mpg.de
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