From e623102768c426e86b0ed73904168006dfea2af9 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sun, 25 Nov 2018 15:22:48 +0000
Subject: Pipeline now downloads and uses an input dataset

In most analysis situations (except for simulations), an input dataset is
necessary, but that part of the pipeline was just left out and a general
`SURVEY' variable was set and never used. So with this commit, we actually
use a sample FITS file from the FITS standard webpage, show it (as well as
its histogram) and do some basic calculations on it.

This preparation of the input datasets is done in a generic way to enable
easy addition of more datasets if necessary.
---
 paper.tex | 86 ++++++++++++++++++++++++++++++++++++++++++---------------------
 1 file changed, 57 insertions(+), 29 deletions(-)

(limited to 'paper.tex')

diff --git a/paper.tex b/paper.tex
index 53176cd..32a3465 100644
--- a/paper.tex
+++ b/paper.tex
@@ -53,7 +53,9 @@
 
   \textsl{Keywords}: Add some keywords for your research here.
 
-  \textsl{Reproducible paper}: Reproduction pipeline \pipelineversion{}
+  \textsl{Reproducible paper}: All quantitave results (numbers and plots)
+  in this paper are exactly reproducible with reproduction pipeline
+  \pipelineversion{}
   (\url{https://gitlab.com/makhlaghi/reproducible-paper}).}
 
 %% To add the first page's headers.
@@ -69,8 +71,8 @@ Congratulations on running the reproduction pipeline! You can now follow
 the checklist in the \texttt{README.md} file to customize this pipeline to
 your exciting research project.
 
-Just don't forget to \emph{never} use any numbers or fixed strings (for
-example database urls like \url{\websurvey}) directly within your \LaTeX{}
+Just don't forget to \emph{never} use numbers or fixed strings (for example
+database urls like \url{\wfpctwourl}) directly within your \LaTeX{}
 source. Read them directly from your configuration files or outputs of the
 programs as part of the reproduction pipeline and import them into \LaTeX{}
 as macros through the \texttt{tex/pipeline.tex} file. See the several
@@ -83,14 +85,12 @@ or
 in this way, will let you focus clearly on your science and not have to
 worry about fixing this or that number/name in the text.
 
-Just as a demonstration of creating plots within \LaTeX{} (using the
-{\small PGFP}lots package), in Figure \ref{deleteme} we show a simple
-plot, where the Y axis is the square of the X axis. The minimum value
-in this distribution is $\deletememin$, and $\deletememax$ is the
-maximum. Take a look into the \LaTeX{} source and you'll see these
-numbers are actually macros that were calculated from the same dataset
-(they will change if the dataset, or function that produced it,
-changes).
+Figure \ref{deleteme} shows a simple plot as a demonstration of creating
+plots within \LaTeX{} (using the {\small PGFP}lots package). The minimum
+value in this distribution is $\deletememin$, and $\deletememax$ is the
+maximum. Take a look into the \LaTeX{} source and you'll see these numbers
+are actually macros that were calculated from the same dataset (they will
+change if the dataset, or function that produced it, changes).
 
 The individual {\small PDF} file of Figure \ref{deleteme} is available
 under the \texttt{tex/build/tikz/} directory of your build directory. You
@@ -100,15 +100,6 @@ progress or after publishing the work). If you want to directly use the
   KZ} decide if it should be remade or not, you can also comment the
 \texttt{makepdf} macro at the top of this \LaTeX{} source file.
 
-{\small PGFP}lots is a great tool to build the plots within \LaTeX{} and
-removes the necessity to add further dependencies (to create the plots) to
-your reproduction pipeline. High-level language libraries like Matplotlib
-do exist to also generate plots. However, bare in mind that they require
-many dependencies (Python, Numpy and etc). Installing these dependencies
-from source (after several years when the binaries are no longer available
-in common repositories), is not easy and will harm the reproducibility of
-your paper.
-
 \begin{figure}[t]
   \includetikz{delete-me}
 
@@ -116,10 +107,39 @@ your paper.
     demonstration.}
 \end{figure}
 
+Figure \ref{deleteme-wfpc2} is another demonstration of showing images
+(datasets) using PGFPlots. It shows a small crop of an image from the
+Wide-Field Planetary Camera 2, on board the Hubble Space Telescope from
+1993 to 2009. This cropped image is one of the sample FITS files from the
+FITS file standard
+webpage\footnote{\url{https://fits.gsfc.nasa.gov/fits_samples.html}}. Just
+as another basic reporting of measurements on this dataset within the paper
+without using numbers in the \LaTeX{} source, the mean is
+$\deletemewfpctwomean$ and the median is $\deletemewfpctwomedian$. The
+skewness in the histogram of Figure \ref{deleteme-wfpc2}(b) explains this
+difference between the mean and median. Also, the value of quantile
+$\deletemewfpcquantile$ (set in the pipeline configuration file
+\texttt{delete-me-wfpc2-quant.mk}) is $\deletemewfpctwoquantile$. The
+dataset was prepared for demonstration here with Gnuastro's
+\textsf{Convert\-Type} program and the histogram and basic statstics were
+generated with Gnuastro's \textsf{Statistics} program.
+
+{\small PGFP}lots\footnote{\url{https://ctan.org/pkg/pgfplots}} is a great
+tool to build the plots within \LaTeX{} and removes the necessity to add
+further dependencies (to create the plots) to your reproduction
+pipeline. There are high-level language libraries like Matplotlib which
+also generate plots. However, the problem is that they require many
+dependencies (Python, Numpy and etc). Installing these dependencies from
+source, is not easy and will harm the reproducibility of your paper. Note
+that after several years, the binary files of these high-level libraries,
+that you easily install today, will no longer be available in common
+repositories. Therefore building the libraries from source is the only
+option to reproduce your results.
+
 Furthermore, since {\small PGFP}lots is built by \LaTeX{} it respects all
-the properties of your text (for example line width and fonts and etc), so
-the final plot blends in your paper much more nicely. It also has a
-wonderful
+the properties of your text (for example line width and fonts and
+etc). Therefore the final plot blends in your paper much more nicely. It
+also has a wonderful
 manual\footnote{\url{http://mirrors.ctan.org/graphics/pgf/contrib/pgfplots/doc/pgfplots.pdf}}.
 
 This pipeline also defines two \LaTeX{} macros that allow you to mark text
@@ -135,7 +155,15 @@ existing coauthors (who are just interested in the new parts or notes) and
 new co-authors (who don't want to be distracted by these issues in their
 first time reading).
 
+\begin{figure}[t]
+  \includetikz{delete-me-wfpc2}
 
+  \captionof{figure}{\label{deleteme-wfpc2} (a) An example image of the
+    Wide-Field Planetary Camera 2, on board the Hubble Space Telescope from
+    1993 to 2009. This is one of the sample images from the FITS standard
+    webpage, kept as examples for this file format. (b) Histogram of pixel
+    values in (a).}
+\end{figure}
 
 
 
@@ -177,12 +205,12 @@ SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness
 
 The following free software tools were also critical component of this
 research (in alphabetical order): Bzip2 \bziptwoversion, CFITSIO
-\cfitsioversion, CMake \cmakeversion, cURL \curlversion, Git \gitversion,
-GNU Bash \bashversion, GNU Coreutils \coreutilsversion, GNU AWK
-\gawkversion, GNU Grep \grepversion, GNU Libtool \libtoolversion, GNU Make
-\makeversion, GNU Sed \sedversion, GNU Scientific Library (GSL)
-\gslversion, GNU Tar \tarversion, GNU Which \whichversion, Lzip
-\lzipversion, GPL Ghostscript \ghostscriptversion, Libgit2
+\cfitsioversion, CMake \cmakeversion, cURL \curlversion, Discoteq flock
+\flockversion, Git \gitversion, GNU Bash \bashversion, GNU Coreutils
+\coreutilsversion, GNU AWK \gawkversion, GNU Grep \grepversion, GNU Libtool
+\libtoolversion, GNU Make \makeversion, GNU Sed \sedversion, GNU Scientific
+Library (GSL) \gslversion, GNU Tar \tarversion, GNU Which \whichversion,
+Lzip \lzipversion, GPL Ghostscript \ghostscriptversion, Libgit2
 \libgitwoversion, Libtiff \libtiffversion, WCSLIB \wcslibversion, XZ Utils
 \xzversion, and ZLib \zlibversion. The final paper was produced with \TeX{}
 Live \texliveversion, using the following packages: \TeX{} \textexversion,
-- 
cgit v1.2.1

