Institute of Omniscience in Institute of Omniscience

Sns

Mon, 01 Jan 0001 00:00:00 UTC

Institute of Omniscience

Mon, 01 Jan 0001 00:00:00 UTC

Cruz vs Sanders

Mon, 01 Jan 0001 00:00:00 UTC

On CNN’s Cruz-Sander health-care debate Long talk, no real debate. Cruz talks about the “average family” and Sanders the “cancer patients”, two different things. Cancer happens to a small portion of the population, and an “average family” is unlikely to have to deal with it.

Thesis

Mon, 01 Jan 0001 00:00:00 UTC

Template

Mon, 01 Jan 0001 00:00:00 UTC

Template

Mon, 01 Jan 0001 00:00:00 UTC

Resources

Mon, 01 Jan 0001 00:00:00 UTC

Phd Tips

Mon, 01 Jan 0001 00:00:00 UTC

Latex

Mon, 01 Jan 0001 00:00:00 UTC

Latex

Mon, 01 Jan 0001 00:00:00 UTC

Academia

Mon, 01 Jan 0001 00:00:00 UTC

Academia

Mon, 01 Jan 0001 00:00:00 UTC

Doctoral/Master Dissertation Template - Massey University

Mon, 01 Jan 0001 00:00:00 UTC

This is the template for doctoral/master thesis. It’s my thesis still in writing with all the content removed. I also populate it with LaTex tips and tricks that you might find useful. The template is not an official one but it complies with all requirements regarding layout, font typeface and appearance. It compiles with PdfLaTeX and biber. XeTeX and LuaTeX are also tested and confirmed working.

Source code in Tex: thesis-template.zip

Poster

Mon, 01 Jan 0001 00:00:00 UTC

Scientific Poster Template - Massey University

Mon, 01 Jan 0001 00:00:00 UTC

This is my poster at the Image and Vision Computing New Zealand (IVCNZ) 2016 held at Massey’s Manawatu campus. It’s the visualisation of the paper I submitted to that conference. I’m too lazy to remove the actual content so you have to do that yourself.

To change the background image, find line

\includegraphics[width=\paperwidth,height=\paperheight]{bird3.jpg}

and change bird3.jpg to anything you want.

The poster is A0 size, but temporarily resized to A4 when editing, so that the size stays manageable and you don’t have to zoom in everytime it’s recompiled. This is thank to package pgfpage and its command \pgfpagesuselayout{resize to}[a4paper]. When you send the poster for printing, remember to uncomment that line and compile again. I’m sure the printery knows how to resize A4 to A0, but it’s better to provide the right size right away, so the bitmap background doesn’t become pixelated.

Source code in Tex: poster-template.zip

New Zealand

Mon, 01 Jan 0001 00:00:00 UTC

Graphics

Mon, 01 Jan 0001 00:00:00 UTC

Graphics

Mon, 01 Jan 0001 00:00:00 UTC

Academic Report Template - Massey University

Mon, 01 Jan 0001 00:00:00 UTC

This is the template for academic report at university level. It’s basically my PhD Confirmation Report with all the content removed. I also populate it with LaTex tips and tricks that you might find useful. The template is not an official one but it complies with all requirements regarding layout, font typeface and appearance. It compiles with PdfLaTeX and biber. XeTeX and LuaTeX are also tested and confirmed working.

Source code in Tex: report-template.zip

Conference

Mon, 01 Jan 0001 00:00:00 UTC

Conference Presentation Template - Massey University

Mon, 01 Jan 0001 00:00:00 UTC

This is the presentation I gave at the INMS PostGraduate Conference 2016. You are welcome to use it as template for your own presentation A nice thing I did in this document is to embed presenter’s note in it. Several software like MS Powerpoint are able to detect these notes and show them as cues on the screen facing the presenters. Not only that, after compiling all the notes will be extracted to a .pdfpc file for an easy print-out. Because I couldn’t guarantee that the computer on which I presented my talk would show the notes for me, I needed this fail-safe measure.

The theme is based on Goddard

Source code in Tex: inms-pgconf-2016-texsrc.zip

Overleaf

Mon, 01 Jan 0001 00:00:00 UTC

Mendeley

Mon, 01 Jan 0001 00:00:00 UTC

Git

Mon, 01 Jan 0001 00:00:00 UTC

Blogs

Mon, 01 Jan 0001 00:00:00 UTC

LaTeX with Overleaf

Mon, 01 Jan 0001 00:00:00 UTC

L^aT_eX has been around for 30+ years (first release was in 1985) and is still the champion of typesetting, especially scientific typesetting. The language itself is fixed but the framework has undergone many expansion by third-party packages. So when people talk about L^aT_eX they usually mean the whole framework with all the packages without which you can’t even compile the most basic papers. This is a burden especially for academic novice like myself one year ago. Lucky me I’m a computer geek so learning how to install, upgrade and use L^aT_eX was a matter of a few hours Googling. But even within academics, sharing a L^aT_eX document remains a pain in the arse.

Overleaf is an online compiler that solves all those problems. When combined with Mendeley and Git they form a “dream team” that can significcantly improve your productivity. This article will show you how to set them up and and work with them in the most effective way.

Full disclosure: I am an official Overleaf advisor of Massey University (you can find me here). This is a voluntary role and I don’t get any financial incentive to advertise for Overleaf. I also tried other similar services (such as ShareLaTeX and Papeeria) but eventually settle at Overleaf. You should try all other options as well, but I have no in-depth experience to talk about them.

An online tool for offline work

Overleaf is more than just an online L^aT_eX compiler (a computer geek can create one with Gitlab’s pipeline as described here), it is foremost a repository for L^aT_eX documents with links you can quickly share. Secondly, it allows real-time collaboration between multiple users, similar to what Google Drive or Office 365 provide. This feature once allow me and my supervisor to finish a paper moment before the submission closed. Third, its incorporation of Git allows you to version control your writing. And finally, Overleaf can access a reference managing service such as Mendeley, Zotero and CiteULike via API calls, so you don’t have to manage your bib file manually.

These features are very useful when collaborating with another writers. However, most of the time I write stuff alone and working online is an unnecessary complication. First, Overleaf compiles your writing every few seconds, it’s pretty troublesome when you are in the middle of writing an unfinished piece of code and it gets compiled, which certainly will result in an error. This can be overcome by selecting manual compilation instead of automatic. Second, the web-based editor of Overleaf is far from perfect. It lacks a lot of features that a proper Tex editor provides, such as auto completing user-defined code, complicated math equations and table edition. Third, the integration of Overleaf with Mendeley is not automatic: first you have to sync the Mendeley application with its online repository, then you have to refresh Overleaf to update the bib file. That’s too many steps compare to what you can do following my article here, which doesn’t require you to do anything. And finally, everytime overleaf compiles your document it’ll make a commit to the Git repository. This is fine if you don’t care about Git, but if you do, it’ll clutter your repository with lots of “Updated on Overleaf” commits. In contrast, I want to have total control of the commits, such as having meaningful commit message and make commit only when reaching a milestone.

In this article I’ll only write about using Overleaf together with offline tools. Its online interface remains essential for sharing and collaborating when needed, but most of the time when writing alone, you should do so offline, and occasionally commit your change to Overleaf.

Tools that you need

You will need an account on Overleaf, obviously. Check with your university if they have agreement with Overleaf to provide free Pro accounts for students and faculty members. In case they don’t, you can always sign up for a free account with 100 MB storage and then earn your way for larger space (See here for details).
You need Mendeley (forget Zotero, and CiteULike, they aren’t even close) and set it up according this article.
Install a TeX compiler (Follow the instructions here) as well as a TeX editor (I highly recommend TeXStudio).
Install Git
On Windows, use Git Bash for command line interface - Don’t torture yourself with Windows’ built-in console (CMD). Git Bash is available after installing Git and you can open a Git Bash window by right-clicking on an empty place on the desktop and choose Git Bash.

Alternatively, install

The pipeline

Initiate a new document

It is imperative that you initiate a L^aT_eX document from Overleaf first, so that the repository gets set up correctly at the beginning. Otherwise, you’ll regret it. Navigate to Overleaf.com and click on “New Project”, as following:

Clone the project to your computer

Then, open the new document, click on “Share”, you’ll see the link to it’s Git repository.

Now, open a console window and clone the repository to your computer with the following command:

git clone https://git.overleaf.com/7969959psbvhptbrmmw my-new-document

Of course you’ll have to replace https://git.overleaf.com/7969959psbvhptbrmmw with the actual link and my-new-document with any name you want. Essentially the new document will be cloned into folder my-new-document. When you open it, you’ll see the following content:

my-new-document/
|-- .git/
`-- main.tex

Some housekeeping to keep it clean

Now, if you set up Mendeley correctly, then there will be a library.bib file in that folder as well. You might not see the .git folder because it is hidden. But don’t worry about that. What you need to do immediately is to create a file named .gitignore which tells Git not to care about certain files, because the compilation of L^aT_eX creates a lot of temporary files.

*.acn
*.acr
*.alg
*.aux
*.bbl
*.bcf
*.blg
*.dvi
*.fdb_latexmk
*.fls
*.glg
*.glo
*.gls
*.idx
*.ilg
*.ind
*.ist
*.lof
*.log
*.lot
*.maf
*.mtc
*.mtc0
*.nav
*.nlo
*.out
*.pdfsync
*.ps
*.run.xml
*.snm
*.synctex.gz
*.toc
*.vrb
*.xdy
*.tdo
.DS_Store
*-blx.bib
tmp/
*.upa
*.upb
cleanup.sh
*.dpth
*.auxlock
*.markdown.*
_markdown_main/

That’s a huge list isn’t it? Now, once you do this, Git will ignore them, but they’re still there. You can also ignore them but I find it annoying to have all those temporary files sitting there contaminating my folder’s structure. Temporary files can also mess up with the compilation process, so I suggest you create a script that cleans them up for you automatically. Here’s the content of my cleanup.sh

#! /bin/bash
find . -name "*.aux" | xargs rm -rf
find . -name "*.bbl" | xargs rm -rf
find . -name "*.bcf" | xargs rm -rf
find . -name "*.blg" | xargs rm -rf
find . -name "*.log" | xargs rm -rf
find . -name "*.run.xml" | xargs rm -rf
find . -name "*.synctex.gz" | xargs rm -rf
find . -name "*.fdb_latexmk" | xargs rm -rf
find . -name "*.toc" | xargs rm -rf
find . -name "*.out" | xargs rm -rf
find . -name "*.fls" | xargs rm -rf
find . -name "*.dpth" | xargs rm -rf
find . -name "*.auxlock" | xargs rm -rf
find . -name "*.lof" | xargs rm -rf
find . -name "*.dvi" | xargs rm -rf
find . -name "*.markdown.*" | xargs rm -rf
rm -rf main.synctex.gz\(busy\)
rm -rf _markdown_main

The optimal project structure

Now, you’re all set to get your document compiled and committed. If it’s a big document, such as a thesis, you might want to set it up in a more organising way than having everything inside main.tex. My typical project structure will be as following:

my-new-document/
|-- .git/
|-- chapters/
|   |-- chapter-1.tex
|   `-- chapter-2.tex
|-- figures/
|   |-- figure1.pdf
|   |-- figure1.pdf_tex
|   |-- figure2.pdf
|   `-- figure2.pdf_tex
|-- .gitignore
|-- main.tex
|-- setup.tex
`-- library.bib

setup.tex is where you put the preamble, which include all the packages, configurations, and custom commands/definitions.

main.tex is where you setup the overall structure. The first two lines are compilation directives that instruct the editor to compile with pdflatex and biber

% !TEX program = pdflatex
% !BIB program = biber
\input{setup}
\title{My Thesis}
\author{John Doe}
\begin{document}
 \include{chapters/chapter-1}
 \include{chapters/chapter-2}
 \printbibliography
\end{document}

chapter-xxx.tex is the actual content of the chapter. All the chapters should begin with this directive:
```
   % !TEX root = ../main.tex
```
so that you can compile from any place, otherwise you’ll need to go back to main.tex to recompile the project.
figures/ is where you put all your graphics, logos, figures

An actual project that follows this structure is given in this article.

So, how does that fit together?

On a typical day you will edit your document in your favourite TeX editor. You add more chapters to chapters and graphics to figures, compile and enjoy the flashy result. In the end of the day, you can commit all the change to Overleaf with a few simple commands:

./cleanup.sh # To remove all temporary files
git add -A # Add all the changes to the local git
git commit -m "Finish chapter 1 and a bit of chapter 2" # Store the change locally
git push # Deliver the change to Overleaf

The git push command might fail if someone whom you share your project with modify the document during the day (simply clicking on the document on Overleaf.com somehow will also create an empty commit - this is very annoying and I hope they fix it soon), in which case you need to git pull to get the changes on the remote server, then git push again. After setting all this up, you will be using Overleaf as an online repository instead of say, Github. But it preserves the ability to share and collaborate with other people if necessary. This is now I wrote my papers: mostly by myself offline, commit it online so that my supervisor can view and fix my writing. When necessary (such as before a submission deadline), we both sit down with our own computer and write the document simultaneously.

Compare Overleaf and other services

Both ShareLaTeX and Papeeria provide pretty much the same services as Overleaf, but the knock-out feature that draws me to Overleaf is that it provides Git integration for free accounts. With ShareLaTeX you have to pay for it and with Papeeria you can link to a public repository, which I really don’t like. For all fairness, Overleaf’s Git repos for free accounts are also public, but they’re not indexed and there is no way one can find it from a search engine.

Vector logos of New Zealand's universities

Mon, 01 Jan 0001 00:00:00 UTC

Most universities won’t make their logos available in scalable, vectorised version, for unspecified reasons (some universities do, so obviously security/forgery is not the concern). Uni such as Victoria or Cantebury supply their logo in rasterised form with different sizes, colours and the contexts where they should be used. Massey Uni for one, does not. Students and staff have to take a screenshot of the uni’s website and do manual cut paste. Regardless, rasterised logos make a document look much less professional & appealing because of pixelation and inconsistency with the overall design. Luckily, I was able to get my hands on the vector logos of all NZ universities. I share them here along with the technique that allows you to do the same to almost any large institution you want.

Wait, what the hell is vector/scalable graphics?

The pictures you take with your camera (even DSLR with photographic film) are all rasterised, which means they will look blurrier and blurrier when you zoom in, or even out. This is because when you zoom in, you practically ask for more information. Two pixels originally next to each other now 1,2 or 3 pixels apart and the computer needs to interpolate or “make a guess” to fill in the gap. New pixels are added to the bigger sized picture by deducing their colour values from the neigbouring pixels, usually the new pixels will have values equivalent to an average or median value of the neighbourhood.

Vector graphics on the other hand, are not defined by pixel values at all, but instead as functions of lines, shapes and colours in space. For example: line from point A(0.1, 0.2) to point B(0.8,0.9) colour red means: when rendering, define point A at position x=10% the width and y=20% of the height, point B at position x=80% the width and y=90% the height, draw a line from A to B with colour red. This way, the rendering process is the same no matter what the actual size of the graphic is, so it will always look sharp.

If you’re writing an important document (thesis, report, essay…) and wants to make it look as shinny as possible, then you will make sure that the university’s logo displayed sharp and fine to the details. And this cannot be done without scalable graphics, which can be in quite a number of formats, such as SVG, PDF, AI (Adobe Illustrator), EPS (which can be read/saved by many software), WPF (Microsoft’s proprietary), etc,… If you see these extension, then the file is most certainly vector. PNG, GIF, JPEG, BMP, … are not. Don’t use them for your thesis.

Below is a screenshot of my thesis’s front page (yes I actually research how to annihilate mankind using AI ). What happens here is that I changed the logo to unfill the shapes and remove colours, keeping only the strokes (borders) in plain black. It looks perfect when printed. The reason why I removed the fill is because as I explain later, I use the logo without any text to support it so it has to be quite big. The filled shapes emphasises the logo too much that the whole front page is out of balance. Keeping only the strokes makes it look much lighter without loosing its significance.

Where were the treasures hidden?

Just Google “University X svg logo” or go to their Wikipedia page, you might get the vector logo ready made for your convenience. But trust me it is hardly the case for most unis. The place where it is hidden is no other than the university’s website itself, right under your nose. Most universities produce tons and tons of brochures, maps and booklets and most are in PDF format. Of course the institution will make sure that their documents look appealing by using vector logos, so we just need to reverse engine the PDF files to get them. I’ll show you how it’s done in details below. The whole procedure takes about 1-5 minutes if you have the right tool.

What tool?

You need a vector graphic software. I prefer Adobe Illustrator since it has the most user friendly interface of all software out there, and most importantly, I can afford it. However, you should have no problem with Corel Draw and the likes. Even the freeware Inkscape can do it at the same level of ease. The process is basically the same for all of them:

Go to the university’s website and search for “pdf”, it should give you a ton of documents. A sure place to get one is at the “Campus map” section. Make sure the logo is vector, not bitmap, by zooming in as much as you can and see if it still appear sharp.
Use Illustrator, Corel or Inkscape to open the page that has the logo.
Sometimes the logo is right there to grab. The screenshot below was taken after I opened a booklet found on the website of the University of Cantebury in Inkscape. You can see that the logo is right there when I click on it. Sometimes it might be a bit tricky if the logo is on top of a complicated background, or if it has many layers. Some graphic skills are required to take the logo out neatly. In my experience, rather than trying to get it out, the easier way is to remove other objects in the document until only the logo is left.
Now you can copy and paste the logo to another document and resize it to fit the boundary. You should save one original version of the logo, and then if you want to mess with it (change colours, remove fill, add strokes, …), make a copy and go nuts!

Logos of NZ Universities

If you’re from NZ, you’re in luck. I already extracted all the logos of 8 universities, plus Unitec (they’re pretty big & their logo looks cool). To demonstrate the scalability of vector graphics, I’m using svg-pan-zoom to display a small controller in the corner of each image here. You can zoom in and out too see that the pictures look sharp at any scale.

If the text in those logos appear deformed, don’t worry. Many browsers don’t support SVG very well at the moment. They will look good on paper.