From 30733df5d30e150a26d53173d14bf941f179f6f5 Mon Sep 17 00:00:00 2001 From: Mohammad Akhlaghi Date: Tue, 27 Feb 2018 14:48:02 +0100 Subject: Default PDF now uses PGFPlots and BibLaTeX Making plots and including references are integral parts of a scientific paper. Therefore to demonstrate how cleanly they can be used within the pipeline, they are now used to produce the final PDF. To use PGFPlots a random dataset is made (using AWK's random function) and is plotted using PGFPlots. The minimum and maximum values of the dataset are also included in the text to further show how such calculations can go into the macros and text. For the references, the NoiseChisel paper was added as a reference to cite when using this pipeline along with the MUSE UDF paper I, which uses this pipeline for two sections. Following this discussion, citation is also discussed in `README.md` and the NoiseChisel paper is also added as a published work with a reproduction pipeline. --- tex/delete-me.tex | 17 +++++++++++++++++ tex/preamble-biblatex.tex | 2 +- tex/preamble-pgfplots.tex | 4 ++++ tex/preamble-style.tex | 2 +- tex/references.tex | 45 +++++++++++++++++++++++++++++++++++++++++++++ 5 files changed, 68 insertions(+), 2 deletions(-) create mode 100644 tex/delete-me.tex create mode 100644 tex/references.tex (limited to 'tex') diff --git a/tex/delete-me.tex b/tex/delete-me.tex new file mode 100644 index 0000000..495333a --- /dev/null +++ b/tex/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=Counter, + ylabel=Random value, + ] + + %% A particular plot. + \addplot+[scatter, only marks] + table {\bdir/tex/delete-me/data.txt}; + + \end{axis} +\end{tikzpicture} diff --git a/tex/preamble-biblatex.tex b/tex/preamble-biblatex.tex index 757f007..869d3d5 100644 --- a/tex/preamble-biblatex.tex +++ b/tex/preamble-biblatex.tex @@ -40,7 +40,7 @@ backend=biber,natbib]{biblatex} \DeclareFieldFormat[article]{pages}{#1} \DeclareFieldFormat{pages}{\mkfirstpage[{\mkpageprefix[bookpagination]}]{#1}} -\addbibresource{./tex/ref.tex} +\addbibresource{tex/references.tex} \renewbibmacro{in:}{} \renewcommand*{\bibfont}{\footnotesize} \DefineBibliographyStrings{english}{references = {References}} diff --git a/tex/preamble-pgfplots.tex b/tex/preamble-pgfplots.tex index c2a7f14..78937a7 100644 --- a/tex/preamble-pgfplots.tex +++ b/tex/preamble-pgfplots.tex @@ -37,8 +37,12 @@ %% 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/#1.tex}% + \else + \includegraphics[width=\linewidth]{\bdir/tex/build/tikz/#1.pdf} + \fi } diff --git a/tex/preamble-style.tex b/tex/preamble-style.tex index d794ac1..228cd10 100644 --- a/tex/preamble-style.tex +++ b/tex/preamble-style.tex @@ -128,7 +128,7 @@ % Title, author, pipeline info and date as they appear on the output PDF. -\title{THE TITLE OF THIS PROJECT} +\title{THE TITLE OF YOUR PROJECT} \author{YOUR NAME, COLLEAGE1 NAME, ETC} \date{\small Reproduction pipeline \pipelineversion{} and Gnuastro \gnuastroversion\\on \today, \currenttime} diff --git a/tex/references.tex b/tex/references.tex new file mode 100644 index 0000000..b3998a2 --- /dev/null +++ b/tex/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} +} -- cgit v1.2.1