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Thesis Overview and Design Organizer (TODO 😝)

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Useful Thesis Links

This file stands to track any minor improvements (at least I think they would be) or final edits needed before the submission of my thesis, my local setup (In case, I don't know, my laptop is stolen 🙄), any styles and style preferences to keep the file/document structure neat and logical, as well as any useful external references.

To any reading, I hope this document serves to improve your write-up experience. ❤️

Worm Regards, 🪱

Justin Cooper

Minor TODOs

  • Much empty,
    • such wow

Final TODOs

  • General
    • SALT RSS → SALT/RSS, etc.
    • Footnotes
  • Pre-3.4.3/3.4.2 end/POLSALT pre-reductions
    • spacing

At Submission

From General Academic Rules:

  • Submitted material must contain:
    • Style:
      • There is no standard format for the submission of a dissertation or thesis and formatting is at the candidate's discretion.
      • Reasonable-width margins ($2 - 2.5$ cm)
      • 1,5 line spacing are desirable to ensure comfortable reading of the text.
      • Consistent referencing should be applied, according to departmental styling
      • PDF format (for electronic submission)
        • embedded fonts
    • Abstract (<600 words)
    • ~10 key terms, no less than 5(keywords)
      • Title page:
        • Registered research title
        • Student's Full names
        • Declaration:
          • “Submitted in fulfillment of the requirements in respect of the Master’s Degree Master of Science in Astrophysics in the Department of Physics in the Faculty of Natural and Agricultural Sciences at the University of the Free State”
        • Submission date
        • Names of Supervisor(s) (and co-supervisor(s) / Mentor(s))
  • Submitted alongside material:
    • A summary report compiled in the Turnitin plagiarism search engine
    • A written declaration of approval by the supervisor
    • “I, Justin Cooper, declare that the Master’s Degree research dissertation that I herewith submit for the Master’s Degree qualification Master of Science in Astrophysics at the University of the Free State is my independent work, and that I have not previously submitted it for a qualification at another institution of higher education” (See GAR)
  • Provided by Supervisor(s):
    • A letter that they approve the submission for assessment and that the submitted work has not previously, either in part or in its entirety, been submitted to the examiners or moderators
    • Proof of the title registration, and
    • proof of appointment of the examiners, with their acceptance of appointment and their addresses for the dispatching of the examination copy.
  • Provided for graduation ceremony programme:
    • Date of birth
    • Place of birth
    • School of matriculation
    • Professional career
    • Exceptional achievements
    • Marital and familial details
  • And Finally:

VSCode

This section contains the setup I've found irreplaceable while writing my thesis in VSCode, or anything useful in general.

General setup

  1. My Python setup includes the full Python and Jupyter Notebook extensions as well as the Black and autopep8 formatting extensions.
    • Python must still be installed locally.
  2. I use a private GitHub repo, shared with my supervisor, for backing up and version control of my thesis, as well as for my developed software, in a separate repo (goodbye backup_thesis_(copy)_v1 folders).
    • Look up GitHub Education if you are a registered student. It provides both a pro version of GitHub (Private repository advanced features, such as sharing) as well as access to GitHub's Copilot (You're welcome).
  3. I use the Latex Workshop and the LTex - LanguageTool grammar/spell chacking extensions to use $\LaTeX$ in VSCode.
    • $\LaTeX$ must still be installed locally (I use Tex Live as recommended by Latex Workshop).
  4. I use GitHub Copilot for its predictive text and as a first stop for problem shooting as the currently open file is included in its context.
  5. I use markdownlint for linting Markdown documents.

Useful shortcuts

Keyboard Shortcut Use
Ctrl+k, v VSCode View rendered markdown
Ctrl+Shift+P Open Command Palette
Ctrl+k, Ctrl+s View VSCode shortcuts
Ctrl+` Open Terminal
Ctrl+k, z Zen mode
(Hold) Alt, Click(s) Multiple cursors
Alt+(↑|↓) Move line up/down
Ctrl+Shift+(↑|↓) Insert cursor above/below
Ctrl+Click SyncTex: Link from PDF to source
Ctrl+Alt+j SyncTex: Link from source to PDF
Ctrl+,, Search: invert Latex Workshop: Invert PDF color scheme

VSCode also includes the ability to insert code snippets. I've set up a few frequently used code snippets, but there is, as always, much to be improved upon. See this file for where to implement them as well as my code snippets.1

Useful RegEx patterns

RegEx allows for complex find and replace functionality. It may also be used in the VSCode Search tab in the primary sidebar (Ctrl+Shift+F)

  • () represent capture groups in find which may be referred to later in replace using $1, etc.
  • [] represent character groups in find.
  • Quantifiers such as +, *, etc. allow for more complex behavior, especially combined with greedy and lazy quantifiers.

Here are some useful RegEx patterns I have needed:

Regex use Find Replace
John {Smith} → {Smith}, J. ([A-Z])[a-z]*?\s(\{[A-Z].+?\}) $2, $1.
E. J {Powell} → {Powell}, E. J. (?<=and\s)([A-Z]\.|[A-Z]\.\s[A-Z]\.)\s(\{.+?\}) $2, $1
1 | 1.1 → $1$ | $1.1$ \s([0-9][\.]*[0-9]*)\s* $$$1$
.../:version: ... → version: ... ^[^:]*:\s*

I have also made use of grep for finding RegEx patterns within files using a CLI:

grep -ri 'version: ' > version.txt

where the r flag is used for a recursive search in the working directory, and the i flag ignores the RegEx case. Combining this with the VSCode `find and replace', `delete duplicates', and `sort lines ascending' results in a sanitized version list of all polsalt/pysalt software.

Markdown

Useful Links

This section contains any markdown not used in this document but deemed useful nonetheless.

  • Use [//]: # (Comment) or <!-- Comment --> on a separate line for comments not meant for rendering.
  • Use [^end_text]: A comment that renders as an endnote.
    • Only works in some Markdown viewers (I.E. GitHub)
  • Comments that link to a separate file may link to a specific line within the file using the #L suffix.

Tips and Tricks

Here are some general tips and tricks related to VSCode that do not fit neatly into any of the other sections.

  • MARK: Heading within a comment of a document allows for headings in the VSCode code map, allowing for navigation at a glance.

$\LaTeX$ Style guides

Useful Links

Included herein are the style guides I have followed during the course of writing my thesis. Custom styles (my*.sty files) have been included to both simplify the preamble (located in Thesis.tex) and to create a more homogeneous styling throughout when dealing with the relevant packages contained in the style files.

General Notes:

  • Inline values with units should be formatted as: $val$~unit
    • If the value is a quantifier, consider writing it out
      • i.e. ... 7 filters ... becomes ... seven filters ...
  • labels are defined using \label{}
  • Commands may be defined with \def but may also be defined using \newcommand\eg{}, \renewcommand\eg{}, or \providescommand\eg{}, which all define new commands that may be used, with differing failure states
    • \newcommand crashes when overwriting
    • \renewcommand crashes when not overwriting, and
    • \providescommand attempts to create a new command (I believe exclusively in meta files, I.E. .sty, etc.)

hyperref

$\LaTeX$'s hyperref package allows for linking within a PDF as well as setting up the document's metadata properties. The hyperref.cfg file is where the metadata is stored.

Link Types Description
\autoref{label} internal reference to label, prefixed with (I.E. $\S$, etc.)
\ref{label} internal reference to label, no prefix text
autopageref{label} internal reference to page of label, prefixed with (I.E. p.)
\pageref{label} internal reference to page of label, no prefix text
\href{URL}{text} any URL's with anchor text
\url{URL} any raw URL
\hyperref{URL}{category}{name}{text} text link to URL
\hyperref[label]{text} text link to label

See also the documentation using: texdoc hyperref

Glossary and Acronyms

$\LaTeX$'s glossaries-extra allow keywords and acronyms to be defined and used and stated in full on first use. Note that acronyms used for software use a display text in the small caps font.

% Glossary entries
\newglossaryentry{maths}
{%
    name=mathematics,
    description={Mathematics is what mathematicians do}
}

\gls{maths} -> mathematics
\Gls{maths} -> Mathematics
\glspl{maths} -> mathematics
\Glspl{maths} -> Mathematics

% Acronym entries
\newacronym{gcd}{GCD}{Greatest Common Divisor}

\acrlong{} -> Greatest Common Divisor
\acrshort{} -> GCD
\acrfull{} -> Greatest Common Divisor (GCD)

New commands for the most common glossary/acronym keys may improve 'writability' (\acr{POLSALT} vs \polsalt). This was implemented for all software acronyms. See also the documentation using: texdoc glossaries-extra

Headings

My headings use Title Case.2 Generally, labels are only included when necessary and are not compulsory when creating a new section, etc.

% Note case is `Title Case`
\chapter{Chapter Title}
\section{Section Title} \label{sec:sec_title}
\dots

Equations

Equations are written in-text and are a part of sentences unless otherwise indicated. To this end, there is no new line before \begin or after \end (unless the sentence ends with the equation and the equation is punctuated) and multiple equations in a single environment are properly punctuated.

Note: multi-line, or continued, equations are aligned by the = symbol while related equations within one environment are aligned by centering.

% Align center
\begin{equation} \label{eq:name}
    eq \,[,|.]
\end{equation}

% Align center, ignore end text
\begin{equation} \label{eq:name}
    \begin{gathered}
        eq1 = ... \,,\\
        eq2 = ... \rlap{\,,\ and}\\
        eq3 = ...
    \end{gathered}
\end{equation}

% Align by `=', ignore end text
\begin{equation} \label{eq:name}
    \begin{aligned}
      eq1 &= ... \,,\\
      eq2 &= ... \rlap{\,,\ and}\\
      eq3 &= ...
    \end{aligned}
\end{equation}

See references (Wikibooks) for more configurations of equations.

Figures

Figures are located in their relevant chapter (chapter_*/figures/) and have the chapter number, $i$, prepended to their name (<i>_<name>.[pdf|svg]).

The figures included in the document are pdf's, but it is useful to save a copy of self-generated figures as svg's for when edits to the figure will naturally arise. See 'Custom Figures' for further constraints on generated figures. FITS images are also saved as pdf, but may have a lower dpi as compared to other figures when not much detail is needed for the figure.

To use the figures in the $\LaTeX$ document, use:

\begin{figure}[t]
    \centering
    \includegraphics[width = 1.0\textwidth]{'<i>_<name>.[pdf|png]'}
    \caption{Include a suitable caption here. Figure (if cited: 'adapted from', if own: 'created using') 'source'.(if link: \protect\footnotemark)}
    \label{fig:'suitable_label'}
\end{figure}
\footnotetext{\protect\url{(link)}}

or, for sub-figures, use:

\begin{figure}[t]
    \centering
    \begin{subfigure}[b]{0.49\textwidth}
        \centering
        \includegraphics[width = 1.0\textwidth]{fig1.extension}
        \caption{fig1 caption}
        \label{subfig:fig1_label}
    \end{subfigure}
    \hfill
    \begin{subfigure}[b]{0.49\textwidth}
        \centering
        \includegraphics[width = 1.0\textwidth]{fig2.extension}
        \caption{fig2 caption}
        \label{subfig:fig2_label}
    \end{subfigure}
    \caption{Overall caption}
    \label{fig:fig_caption}
\end{figure}

Custom Figures

Figures created by myself are (generally) made using Inkscape. To keep line widths / text size / etc. consistent the following document properties are used:

  • Document properties

    • $6.28$ ($160mm$) x ? inches
      • $x$-size set to the $\LaTeX$ \textwidth (usually in inches)
        • (\textwidth found by using \the\textwidth anywhere in the $\LaTeX$ document)
        • $6.28$ inches == $A4$ page with uniform $1$ inch border.
      • $y$-size depends on figure aspect ratio, usually left undefined
    • Before saving, use resize to content (if no text included in custom figure)
    • scale = $0.1$

  • Grid properties

    • $s_x$, $s_y$ = $1$ mm
    • Major Grid every $5$

  • Fill properties

    • Lightness = $66$
    • (I.E. $0$, $0$, $66$, $100$)

  • Font properties

    • CMU Serif for text
    • CMU Serif Italics for symbols
    • weight = normal
    • size = $12$ pt

  • Stroke properties

    • width = $1$ px

See also: https://jwalton.info/Matplotlib-latex-PGF/

Figures are first saved as an svg before being exported as either a png or pdf to 'play well' with the $\LaTeX$ \includegraphics[]{} command.

$TikZ$ Figures

Useful Links

$TikZ$ refers to the tikz package (which may include libraries) which can generate figures and diagrams, etc. The relevant preamble commands are:

\usepackage{tikz}
\usetikzlibrary{shapes.geometric, arrows} % specifically for flowcharts

The preamble must also include the definitions of any required tikzstyle definitions. Styles may include nodes and lines:

\tikzstyle{ends} = [rectangle, draw, text centered, rounded corners, minimum height=2em]
\tikzstyle{step} = [rectangle, draw, text centered, minimum height=2em]
\tikzstyle{choice} = [diamond, draw, text centered, minimum height=2em]
\tikzstyle{data}=[trapezium, draw, text centered, trapezium left angle=60, trapezium right angle=120, minimum height=2em]
\tikzstyle{to} = [draw, -latex']

and may be included in a document using:

\begin{figure}[t]
    \centering
    \begin{tikzpicture}
        \node (name) [type, right of=(name), below of=(name), xshift=2cm, yshift=2cm] {text};
        \draw [to] (name_from) -- (name_to);
        \draw [arrow] (name_from) -- node[anchor=east] {yes} (name_to_yes);
        \draw [arrow] (name_from) -- node {no} (name_to_no);
    \end{tikzpicture}
    \caption{File caption}
    \label{fig:file_label}
\end{figure}

Tables

Tables can be generated using a $\LaTeX$ Table Generator. Tables are located in their relevant chapter (chapter_*/tables/) and have the chapter number, $i$, prepended to their name (<i>_<name>.tex). The contents of the file are structured similar to:

\begin{table}[t]
    \centering
    \begin{tabular}{c(* the amount of columns)}
        ...
    \end{tabular}
    \caption{A suitable caption and relevant reference.\protect\footnotemark}
    \label{table:'suitable_label'}
\end{table}
\footnotetext{Link or further description of reference or discussion of footnotemark in text.}

To insert a table within the document, use the command:

\input{chapter_<i>/tables/table_name.tex}

Useful external References

See 'preamble' of references.bib for further useful links relevant to specific chapters of thesis.

Footnotes

  1. If the relative link breaks due to the .gitignore file, see this page for more information on VSCode code snippets. ↩

  2. Sentence case may also be used, just stick to whichever style is chosen. ↩

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Keeping track of my Masters thesis, safely and securely.

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pipeline thesis astronomy-astrophysics spectropolarimetry

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