8 files changed, 617 insertions, 0 deletions
diff --git a/tex/src/delete-me-demo.tex b/tex/src/delete-me-demo.tex
new file mode 100644
index 0000000..8174bc8
--- /dev/null
+++ b/tex/src/delete-me-demo.tex
@@ -0,0 +1,34 @@
+\begin{tikzpicture}
+
+  %% The displayed WFPC2 image.
+  \node[anchor=south west] (img) at (0,0)
+       {\includegraphics[width=0.5\linewidth]
+         {tex/pipeline/delete-me-demo/wfpc2.pdf}};
+
+  %% Its label
+  \node[anchor=south west] at (0.45\linewidth,0.45\linewidth)
+       {\textcolor{white}{a}};
+
+  %% This histogram.
+  \begin{axis}[at={(0.52\linewidth,0.1\linewidth)},
+      no markers,
+      axis on top,
+      xmode=normal,
+      ymode=normal,
+      yticklabels={},
+      scale only axis,
+      xlabel=Pixel value,
+      width=0.5\linewidth,
+      height=0.412\linewidth,
+      enlarge y limits=false,
+      enlarge x limits=false,
+      ]
+    \addplot [const plot mark mid, fill=red]
+    table [x index=0, y index=1]
+    {tex/pipeline/delete-me-demo/wfpc2-hist.txt}
+    \closedcycle;
+  \end{axis}
+
+  %% The histogram's label
+  \node[anchor=south west] at (0.95\linewidth,0.45\linewidth) {b};
+\end{tikzpicture}
diff --git a/tex/src/delete-me.tex b/tex/src/delete-me.tex
new file mode 100644
index 0000000..fc1a1f9
--- /dev/null
+++ b/tex/src/delete-me.tex
@@ -0,0 +1,17 @@
+%% PGFPlots code to plot a random set of numbers as demo
+
+\begin{tikzpicture}
+
+  %% Settings of the plotted axis
+  \begin{axis}[
+      width=\linewidth,
+      xlabel=$X$,
+      ylabel=$X^2$,
+    ]
+
+    %% A particular plot.
+    \addplot+[scatter, only marks]
+    table {tex/pipeline/delete-me/data.txt};
+
+  \end{axis}
+\end{tikzpicture}
diff --git a/tex/src/preamble-biblatex.tex b/tex/src/preamble-biblatex.tex
new file mode 100644
index 0000000..bd99502
--- /dev/null
+++ b/tex/src/preamble-biblatex.tex
@@ -0,0 +1,116 @@
+%% Biblatex settings.
+%%
+%% Settings necessary to make the bibliography with Biblatex. Keeping all
+%% BibLaTeX settings in a separate preamble was done in the spirit of
+%% modularity to 1) easily managable, 2) If a similar BibLaTeX
+%% configuration is necessary in another LaTeX compilation, this file can
+%% just be copied there and used.
+%%
+%% USAGE:
+%%  - `tex/src/references.tex': the file containing Bibtex source of each
+%%     reference. The file suffix doesn't have to be `.bib'. This naming
+%%     helps in clearly identifying the files and avoiding places that
+%%     complain about `.bib' files.
+
+
+
+
+
+%% To break up highlighted text (for example texttt when some it is on the
+%% line break) and also to no underline emphasized words (like journal
+%% titles in the references).
+\usepackage[normalem]{ulem}
+
+
+
+
+
+% Basic BibLaTeX settings
+\usepackage[
+    doi=false,
+    url=false,
+    dashed=false,
+    eprint=false,
+    maxbibnames=4,
+    minbibnames=1,
+    hyperref=true,
+    maxcitenames=2,
+    mincitenames=1,
+    style=authoryear,
+    uniquelist=false,
+    backend=biber,natbib]{biblatex}
+\DeclareFieldFormat[article]{pages}{#1}
+\DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}}
+\addbibresource{tex/src/references.tex}
+\renewbibmacro{in:}{}
+\renewcommand*{\bibfont}{\footnotesize}
+\DefineBibliographyStrings{english}{references = {References}}
+
+%% Include the adsurl field key into those that are recognized:
+\DeclareSourcemap{
+  \maps[datatype=bibtex]{
+    \map{
+      \step[fieldsource=adsurl,fieldtarget=iswc]
+      \step[fieldsource=gbkurl,fieldtarget=iswc]
+    }
+  }
+}
+
+%% Set the color of the doi link to mymg (magenta) and the ads links
+%% to mypurp (or purple):
+\definecolor{mypurp}{cmyk}{0.75,1,0,0}
+\newcommand{\doihref}[2]{\href{#1}{\color{magenta}{#2}}}
+\newcommand{\adshref}[2]{\href{#1}{\color{mypurp}{#2}}}
+\newcommand{\blackhref}[2]{\href{#1}{\color{black}{#2}}}
+
+%% Define a format for the printtext commands in
+%% DeclareBibliographyDriver to make links for the doi, ads link and
+%% arxiv link:
+\DeclareFieldFormat{doilink}{
+  \iffieldundef{doi}{#1}{\doihref{http://dx.doi.org/\thefield{doi}}{#1}}}
+\DeclareFieldFormat{adslink}{
+    \iffieldundef{iswc}{#1}{\adshref{\thefield{iswc}}{#1}}}
+\DeclareFieldFormat{arxivlink}{
+  \iffieldundef{eprint}{#1}{\href{http://arxiv.org/abs/\thefield{eprint}}{#1}}}
+
+\DeclareListFormat{doiforbook}{
+  \iffieldundef{doi}{#1}{\doihref{http://dx.doi.org/\thefield{doi}}{#1}}}
+\DeclareFieldFormat{googlebookslink}{
+    \iffieldundef{iswc}{#1}{\adshref{\thefield{iswc}}{#1}}}
+
+%% Set the formatting to make the last three values into the
+%% appropriate link. Note that the % signs are necessary. Without
+%% them, the items will be indented.
+\DeclareBibliographyDriver{article}{%
+  \usebibmacro{bibindex}%
+  \usebibmacro{begentry}%
+  \usebibmacro{author/translator+others}%
+  \newunit%
+  \ifdefined\makethesis\printtext{\usebibmacro{title}}\fi%
+  \newunit%
+  \printtext[doilink]{\usebibmacro{journal}}%
+  \addcomma%
+  \printtext[adslink]{\printfield{volume}}%
+  \addcomma%
+  \printtext[arxivlink]{\printfield{pages}}%
+  \addperiod%
+}
+
+\DeclareBibliographyDriver{book}{%
+  \usebibmacro{bibindex}%
+  \usebibmacro{begentry}%
+  \usebibmacro{author/translator+others}%
+  \newunit%
+  \printtext{\usebibmacro{title}}%
+  \addperiod%
+  \addspace%
+  \printlist[doiforbook]{publisher}%
+  \addcomma%
+  \addspace%
+  \printfield[googlebookslink]{edition}%
+  \printtext{ ed.}%
+  \addperiod%
+}
+
+%% In order to have et al. instead of et al.,:
+\renewcommand*{\nameyeardelim}{\addspace}
diff --git a/tex/src/preamble-header.tex b/tex/src/preamble-header.tex
new file mode 100644
index 0000000..eb83c27
--- /dev/null
+++ b/tex/src/preamble-header.tex
@@ -0,0 +1,86 @@
+%% The headers: title, authors, top of pages and section title formatting
+%% of the final LaTeX file are configured here.
+
+
+
+
+
+%% General page header settings.
+\usepackage{fancyhdr}
+\pagestyle{fancy}
+\lhead{\footnotesize{\scshape Draft paper}, {\footnotesize nnn:i (pp), Year Month day}}
+\rhead{\scshape\footnotesize YOUR-NAME et al.}
+\cfoot{\thepage}
+\setlength{\voffset}{0.75cm}
+\setlength{\headsep}{0.2cm}
+\setlength{\footskip}{0.75cm}
+\renewcommand{\headrulewidth}{0pt}
+
+
+
+
+
+%% Specific style for first page.
+\fancypagestyle{firststyle}
+{
+  \lhead{\footnotesize{\scshape Draft paper}, nnn:i (pp), YYYY Month day\\
+  \scriptsize \textcopyright YYYY, Your name. All rights reserved.}
+  \rhead{\footnotesize \footnotesize \today, \currenttime\\}
+}
+
+
+
+
+
+%To set the style of the titles:
+\usepackage{titlesec}
+\titleformat{\section}
+  {\centering\normalfont\uppercase}
+  {\thesection.}
+  {0em}
+  { }
+\titleformat{\subsection}
+  {\centering\normalsize\slshape}
+  {\thesubsection.}
+  {0em}
+  { }
+\titleformat{\subsubsection}
+  {\centering\small\slshape}
+  {\thesubsubsection.}
+  {0em}
+  { }
+
+
+
+
+
+% Basic Document information that goes into the PDF meta-data.
+\hypersetup
+{
+    pdfauthor={YOUR NAME},
+    pdfsubject={A SHORT DESCRIPTION OF THE WORK},
+    pdftitle={THE TITLE OF THIS PROJECT},
+    pdfkeywords={SOME, KEYWORDS, FOR, THE, PDF}
+}
+
+
+
+
+
+%% Title and author information
+\usepackage{authblk}
+\renewcommand\Authfont{\small\scshape}
+\renewcommand\Affilfont{\footnotesize\normalfont}
+\setlength{\affilsep}{0.2cm}
+
+\title{\large \uppercase{The paper's title goes here}}
+
+\author[1]{Your name}
+\author[2]{Coauthor one}
+\author[1,3]{Coauthor two}
+
+\affil[1]{The first affiliation in the list.; \url{your@email.address}}
+\affil[2]{Another affilation can be put here.}
+\affil[3]{And generally as many affiliations as you like.
+\par \emph{Received YYYY MM DD; accepted YYYY MM DD; published YYYY MM DD}}
+\date{}
diff --git a/tex/src/preamble-necessary.tex b/tex/src/preamble-necessary.tex
new file mode 100644
index 0000000..e6ac18e
--- /dev/null
+++ b/tex/src/preamble-necessary.tex
@@ -0,0 +1,75 @@
+%% Necessary (independent of style) macros for this project.
+%%
+%% These are a set of packages that have been commonly necessary in most
+%% LaTeX usages. However, if any are not needed in your work, please feel
+%% free to remove them.
+
+
+
+
+
+%% Values from the analysis.
+\input{tex/pipeline/macros/pipeline.tex}
+
+
+
+
+
+% Macros for to help in typing, remove them if you don't need them, but
+% this can help as a demo on how you can simply writing of commonly used
+% words that need special formatting (like software names).
+\newcommand{\snsign}{{\small S}/{\small N}}
+\newcommand{\originsoft}{\textsf{ORIGIN}}
+\newcommand{\sextractor}{\textsf{SE\-xtractor}}
+\newcommand{\noisechisel}{\textsf{Noise\-Chisel}}
+\newcommand{\makecatalog}{\textsf{Make\-Catalog}}
+
+
+
+
+
+%% For highlighting updates. When this is set, text marked as \new
+%% will be colored in dark green and text that is marked wtih \tonote
+%% will be marked in dark red.
+\ifdefined\highlightchanges
+\newcommand{\new}[1]{\textcolor{green!60!black}{#1}}
+\newcommand{\tonote}[1]{\textcolor{red!60!black}{[#1]}}
+\else
+\newcommand{\new}[1]{\textcolor{black}{#1}}
+\newcommand{\tonote}[1]{{}}
+\fi
+
+
+
+
+
+% Better than verbatim for displaying typed text.
+\usepackage{alltt}
+
+
+
+
+
+% For arithmetic opertions within LaTeX
+\usepackage[nomessages]{fp}
+
+
+
+
+
+%To add a code font to the text:
+\usepackage{courier}
+
+
+
+
+
+%To add some enumerating styles
+\usepackage{enumerate}
+
+
+
+
+
+%Including images if necessary
+\usepackage{graphicx}
diff --git a/tex/src/preamble-pgfplots.tex b/tex/src/preamble-pgfplots.tex
new file mode 100644
index 0000000..4999656
--- /dev/null
+++ b/tex/src/preamble-pgfplots.tex
@@ -0,0 +1,107 @@
+%% PGFPlots settings
+%% -----------------
+%%
+%% PGFPLOTS is a package in (La)TeX for making plots internally. It fits
+%% nicely with the purpose of a reproduction pipeline. But it isn't
+%% mandatory. Therefore if you don't need it, just comment/delete the line
+%% that includes this file in the top LaTeX source (`paper.tex').
+%%
+%% However, TiKZ and PGFPlots are the recommended way to include figures
+%% and plots in your paper. There are two main reasons: 1) it follows the
+%% same LaTeX settings as the text of the paper, so the figures will be in
+%% the exact same settings (for example font or lines) as the main body of
+%% the papers. 2) It doesn't require any extra dependency (it is
+%% distributed as part of TeX-live). Adding specific programs/libraries for
+%% plots can greatly increase the number of dependencies for the
+%% pipeline. For example Python's Matplotlib library is indeed very good,
+%% but it requires Python and Numpy. The latter is not easy to build from
+%% source, so after a few years, installing the required version can be
+%% very frustrating.
+%%
+%% Keeping all BibLaTeX settings in a separate preamble was done in the
+%% spirit of modularity to 1) easily managable, 2) If a similar BibLaTeX
+%% configuration is necessary in another LaTeX compilation, this file can
+%% just be copied there and used.
+%%
+%% PGFPlots uses the (La)TeX TiKZ package to build plots. So we will first
+%% do the settings that are necessary in TiKZ, and then go onto the actual
+%% PGFPlots package.
+%%
+%% USAGE:
+%%
+%%  - All plots are made within a `tikz' directory (that must already be
+%%    present in the location LaTeX is run).
+%%
+%%  - Use `\includetikz{XXXX}' to make/use the figure. If a `makepdf' LaTeX
+%%    macro is not defined, then \includetikz will assume a `XXXX.pdf' file
+%%    exists in `tex/tikz' and simply import it. If `makepdf' is defined,
+%%    then TiKZ/PGFPlot will be called to (possibly) build the plot based
+%%    on `tex/XXXX.tex'. Note that if the contents of `tex/src/XXXX.tex'
+%%    hasn't changed since the last build. TiKZ/PGFPlots won't rebuild the
+%%    plot.
+
+
+
+
+
+%% Very general TiKZ settings. In particular, to allow faster processing
+%% (not having to re-build the plots on every run), we are using the
+%% externalization feature of TiKZ. With this option, TiKZ will build every
+%% figure independently in a special directory afterwards it will include
+%% the built figure in the final file. This has many advantages: 1) if the
+%% code for the plot hasn't changed, then the plot won't be re-made (can be
+%% slow with detailed plots). 2) You can use the PDFs of the individual
+%% plots for other purposes (for example to include in slides) cleanly.
+\usepackage{tikz}
+\usetikzlibrary{external}
+\tikzexternalize
+\tikzsetexternalprefix{tikz/}
+
+
+
+
+
+%% The following rule will cause the name of the files keeping a figure's
+%% external PDF to be set based on the file that the TiKZ commands are
+%% from. Without this, TiKZ will use numbers based on the order of
+%% figures. These numbers can be hard to manage and they will also depend
+%% on order in the final PDF, so it will be very buggy to manage them.
+\newcommand{\includetikz}[1]{%
+  \ifdefined\makepdf%
+    \tikzsetnextfilename{#1}%
+    \input{tex/src/#1.tex}%
+  \else
+    \includegraphics[width=\linewidth]{tex/tikz/#1.pdf}
+  \fi
+}
+
+
+
+
+
+%% Uncomment the following lines for EPS and PS images. Note that you still
+%% have to use the `pdflatex' executable and also add a `[dvips]' option to
+%% graphicx.
+
+%% \tikzset{external/system call={rm -f "\image".eps "\image".ps
+%% "\image".dvi; latex \tikzexternalcheckshellescape -halt-on-error
+%% -interaction=batchmode -jobname "\image" "\texsource";
+%% dvips -o "\image".ps "\image".dvi;
+%% ps2eps "\image.ps"}}
+
+
+
+
+
+%% Inport and configure PGFPlots.
+\usepackage{pgfplots}
+\pgfplotsset{compat=newest}
+\usepgfplotslibrary{groupplots}
+\pgfplotsset{
+  axis line style={thick},
+  tick style={semithick},
+  tick label style = {font=\footnotesize},
+  every axis label = {font=\footnotesize},
+  legend style = {font=\footnotesize},
+  label style = {font=\footnotesize}
+  }
diff --git a/tex/src/preamble-style.tex b/tex/src/preamble-style.tex
new file mode 100644
index 0000000..fb08df7
--- /dev/null
+++ b/tex/src/preamble-style.tex
@@ -0,0 +1,137 @@
+%% General paper's style settings.
+%%
+%% This preamble can be completely ignored when including this TeX file in
+%% another style. This is done because this LaTeX build is meant to be an
+%% initial/internal phase or part of a larger effort, so it has a basic
+%% style defined here as a preamble. To ignore it, uncomment or delete the
+%% respective line in `paper.tex'.
+
+
+
+
+
+%% Font.
+\usepackage[T1]{fontenc}
+\usepackage{newtxtext}
+\usepackage{newtxmath}
+
+
+
+
+
+%% Print size
+\usepackage[a4paper, includeheadfoot, body={18.7cm, 24.5cm}]{geometry}
+
+
+
+
+
+%% Set the distance between the columns if two columns:
+\setlength{\columnsep}{0.75cm}
+
+
+
+
+
+% To allow figures to take up more space on the top of the page:
+\renewcommand{\topfraction}{.99}
+\renewcommand{\bottomfraction}{.7}
+\renewcommand{\textfraction}{.05}
+\renewcommand{\floatpagefraction}{.99}
+\renewcommand{\dbltopfraction}{.99}
+\renewcommand{\dblfloatpagefraction}{.99}
+\setcounter{topnumber}{1}
+\setcounter{bottomnumber}{0}
+\setcounter{totalnumber}{2}
+\setcounter{dbltopnumber}{1}
+
+
+
+
+
+%% Color related settings:
+\usepackage{xcolor}
+\color{black}                   % Text color
+\definecolor{DarkBlue}{RGB}{0,0,90}
+
+
+
+
+
+
+% figure and figure* ordering correction:
+\usepackage{fixltx2e}
+
+
+
+
+
+%% For editing the caption appearence. The `setspace' package defines
+%% the `stretch' variable. `abovecaptionskip' is the distance between
+%% the figure and the caption.
+\usepackage{setspace, caption}
+\captionsetup{font=footnotesize, labelfont={color=DarkBlue,bf}, skip=1pt}
+\captionsetup[figure]{font={stretch=1, small}}
+\setlength{\abovecaptionskip}{3pt plus 1pt minus 1pt}
+\setlength{\belowcaptionskip}{-1.25em}
+
+
+
+
+
+
+%% To make the footnotes align:
+\usepackage[hang]{footmisc}
+\setlength\footnotemargin{10pt}
+
+
+
+
+
+%For including time in the title:
+\usepackage{datetime}
+
+
+
+
+
+%To make links to webpages and include document information in the
+%properties of the PDF
+\usepackage[
+  colorlinks,
+  urlcolor=blue,
+  citecolor=blue,
+  linkcolor=blue,
+  linktocpage]{hyperref}
+\renewcommand\UrlFont{\rmfamily}
+
+
+
+
+
+%% Define the abstract environment
+\renewenvironment{abstract}
+ {\vspace{-0.5cm}\small%
+  \list{}{%
+    \setlength{\leftmargin}{2cm}%
+    \setlength{\rightmargin}{\leftmargin}%
+  }%
+  \item\relax}
+ {\endlist}
+
+
+
+
+
+%% To keep the main page's code clean.
+\newcommand{\includeabstract}[1]{%
+\twocolumn[%
+  \begin{@twocolumnfalse}%
+    \maketitle%
+    \begin{abstract}%
+    #1%
+    \end{abstract}%
+    \vspace{1cm}%
+  \end{@twocolumnfalse}%
+  ]%
+}
diff --git a/tex/src/references.tex b/tex/src/references.tex
new file mode 100644
index 0000000..b3998a2
--- /dev/null
+++ b/tex/src/references.tex
@@ -0,0 +1,45 @@
+@ARTICLE{bacon17,
+   author = {{Bacon}, R. and {Conseil}, S. and {Mary}, D. and {Brinchmann}, J. and
+	{Shepherd}, M. and {Akhlaghi}, M. and {Weilbacher}, P.~M. and
+	{Piqueras}, L. and {Wisotzki}, L. and {Lagattuta}, D. and {Epinat}, B. and
+	{Guerou}, A. and {Inami}, H. and {Cantalupo}, S. and {Courbot}, J.~B. and
+	{Contini}, T. and {Richard}, J. and {Maseda}, M. and {Bouwens}, R. and
+	{Bouch{\'e}}, N. and {Kollatschny}, W. and {Schaye}, J. and
+	{Marino}, R.~A. and {Pello}, R. and {Herenz}, C. and {Guiderdoni}, B. and
+	{Carollo}, M.},
+    title = "{The MUSE Hubble Ultra Deep Field Survey. I. Survey description, data reduction, and source detection}",
+  journal = {A\&A},
+archivePrefix = "arXiv",
+   eprint = {1710.03002},
+ keywords = {galaxies: distances and redshifts, galaxies: high-redshift, cosmology: observations, methods: data analysis, techniques: imaging spectroscopy, galaxies: formation},
+     year = 2017,
+    month = nov,
+   volume = 608,
+      eid = {A1},
+    pages = {A1},
+      doi = {10.1051/0004-6361/201730833},
+   adsurl = {http://adsabs.harvard.edu/abs/2017A\%26A...608A...1B},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
+
+
+
+
+@ARTICLE{ai15,
+   author = {{Akhlaghi}, M. and {Ichikawa}, T.},
+    title = "{Noise-based Detection and Segmentation of Nebulous Objects}",
+  journal = {ApJS},
+archivePrefix = "arXiv",
+   eprint = {1505.01664},
+ primaryClass = "astro-ph.IM",
+ keywords = {galaxies: irregular, galaxies: photometry, galaxies: structure, methods: data analysis, techniques: image processing, techniques: photometric},
+     year = 2015,
+    month = sep,
+   volume = 220,
+      eid = {1},
+    pages = {1},
+      doi = {10.1088/0067-0049/220/1/1},
+   adsurl = {http://adsabs.harvard.edu/abs/2015ApJS..220....1A},
+  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}