TeXworks shortcuts

I use TeXworks as my LaTeX editor currently and I recently discovered a few shortcuts that I'm finding really handy in the preview window:

Shift + click = Zoom in
Alt + click = Zoom out
Ctrl + click = Find paragraph in source code

Hope those few are helpful to someone. Let me know if there are any others that I might find useful!


Adding bzr files through the cb2bib

I recently described my referencing process where I simultaneously hold reference pdf files in a version control system and keep track of their details in bibtex file. I have also described a problem I've been having with my version control system of choice, Bazaar.

Based on these I decided that there might be a better (more automated) way of adding my references. After a very useful email exchange with the author of cb2bib they confirmed that this should be possible. Now, after a day of messing around and learning about various command-line tools that I hadn't used before, I think I've got it working. Here's how...

First I created a new batch file that I called "bzrAddRef.bat". Here are its contents:

@echo OFF

rem --------------------------------------------------------------------------
rem cb2Bib Tools addition by J. Welford
rem --------------------------------------------------------------------------

echo   bzrAddRef:
echo   cb2Bib script for adding BibTeX files to a Bazaar repository
echo   Using sed and xargs utilities from:
echo   http://gnuwin32.sourceforge.net
echo   Path below may need changing to be within the repository

echo   Processing:
cd "C:\Users\welf\Documents\literatureReview"
sed -n -e "s|.*file.*=.*{\(.*\)}.*|\"\1\"|p" %1 > bzrRefs.tmp
xargs bzr add <bzrRefs.tmp
del bzrRefs.tmp

Only the last 4 lines are really important. The first one sets the working directory, I don't think it matters what you use as long as you have write access and it is within the repository you want to add to. The next line runs through the current bibtex file and extracts the location of all the references to a temporary file. The next line adds all these files to Bazaar repository. The final line deletes the temporary file. (maybe I could have used a pipe between commands so that the temporary file was not required?)

Some special commands are used that will need to be installed, what you need are: sed.exe (and its dependencies:  regex2.dll, libintl3.dll, libiconv2.dll) and xargs.exe.

Within the settings of cb2bib this batch file can now be pointed at under the "Configure BibTeX" - "External BibTeX Postprocessing" - "Command:" section. Once that is done simply hitting "Alt"+"p" in the cb2bib window should run the batch file and add all the references to version control.

I hope the helps someone! (I presume it could be altered for other version control systems or be called from other applications.)


My referencing process

I suspect everyone has a subtly different way of doing this, depending on the tools they prefer and the way they like to work. I thought I would document my process as I think it's pretty efficient and has some real advantages, I'm sure there is still plenty of room for improvement though.

Overall aim

As an academic I often need to refer to work done by others, this normally done by noting their published work as a list of references or bibliography at the end of my documents. The most basic way of achieving this would be to have a stack of published books and papers in my drawer that I can refer to and then type in the reference details at the end of the each document I want to write. I'm sure that plenty of people do work this way, but from my point of view I see it as pretty inefficient (lots of printing, lots of sorting, lots of typing, not very portable, an awful pain to change reference styles, etc).

I manage my references entirely in software using a few specific tools. I've mentioned most of them in other posts but I'll go into a bit more detail here on the actual process I use. 

I'm going to split referencing into two separate processes. Firstly, as I'm researching a topic, I tend to gather references to get an idea what I'm doing. Secondly, when I come to document my work I need to search and cite the references I've found.


Google Scholar is generally my primary resource for finding papers and documents. I also rely on standard Google searches a massive amount and I have a Google alert set up to email me when a few key phrases appear in new articles added to the web.
IEEExplore generally has most of the published work (in terms of papers, Journal articles, etc) that I need to refer to. The University has a subscription to this that allows me to download what I need (otherwise I'd have to pay!).
Pdf format is generally how almost all papers are delivered and the format that I keep them in. I use Foxit reader to read pdf documents. I keep all my reference documents in one big folder rather than worrying about any kind of complex filing system.
I use Bazaar to version control my folder of pdf documents. I've previously discussed how this works and how it allows me to work between different computers, even without installing any software on them.
I use a tool called cb2bib to maintain a list of references in bibtex format. I started off just using this to add references to my bibtex file, but I've found it to also be really good for browsing references and citing whilst writing a document. I changed some of the default setup to help it retrieve data from the net.
I use Latex to typeset most of my work. Within this I can simply point it at the bibtex file for all the details of the references. I have previously mentioned how to use a bibtex file that is not in the same place as the rest latex document.

Gathering references

  1. Search for the document that I need to find using Google, Google Scholar or general web browsing.
  2. Open and read the document to see if it looks relevant and useful. Assuming that it does...
  3. Download the document to my big folder of "third party" references. I tend to use the full title of the work as the save name of the document - this can lead to quite long file names, but it makes it a lot easier to find things!
  4. Add the saved file to my bazaar version control system. This only takes a couple of clicks through  tortoiseBzr menus in windows explorer.
  5. Add the document to my bibtex file using cb2bib. This is a pretty straightforward process:
    1. Open cb2bib, I have a keyboard shortcut setup for this (it should also remember what bibtex file is being used)
    2. Click "import from pdf file"
    3. Click "select files"
    4. Select pdf files saved previously (hold ctrl to select a bunch at once)
    5. Click "process"
    6. The software will try to extract as much info as possible from the pdf file, this probably won't be enough so...
    7. Click Network query to retrieve all the info about the file from the web (this usually works fine, but it's worth checking the results, you may need to give it the right title to start it off)
    8. Click save to add the reference to the bibtex file
  6. The changed bibtex file and added references will need to be "commited" to the version control repository.
UPDATE: I have added now made a batch file that effectively takes the place of step 4 and occurs after step 5 - it can be run after a whole set of references have been input through cd2bib and adds them all to my version control repository using "Alt"+"p".

Citing references

  1. With a Latex document that has a pointer to the bibtex file within it.
  2. Open cb2bib citer (I use a keyboard shortcut) and select the reference(s) required:
    1. [optional] Select the way I want my reference list displayed by pressing "a" (author), "j" (journal), "t" (title) or "y" (year). I find author is usually best.
    2. [optional] Filter the reference list by pressing "f" and then typing what you want to search for ("d" clears the search)
    3. Click on a chosen reference
    4. [optional] Press "o" to open the reference and read it
    5. Press "enter" to cite the reference, a small pen marker will appear next to it (in author view it will appear next to each author for the same paper). Multiple references may be cited by selecting them and pressing "enter". "delete" clears all the selected references.
    6. Press "c" once all the references for citing are selected, this will close the citer window and copy the latex text for the references to the clipboard.
  3. Paste the text into the latex file to include the references at that point in the document.
Although those might seem like a lot of steps it's really pretty straightforward once you get used to it. The only real difficulty is remembering the keyboard commands for cb2bib citer. With this setup I can take all my references with me between machines (even between Linux and Windows) and use the same process everywhere.

Bazaar GUI issue on Windows 7 - adding files using the commandline GUI interface

Due to an unfortunate hard drive issue I recently had cause to swap to a new drive. Along with this came an upgrade from XP to Windows7 (64bit). This was not a real issue, just a bit of hassle moving everything over and re-installing all my applications.

As part of the process I had to re-install Bazaar which I'm using to version control all my work. This appeared to go fine, including the addition of tortoiseBzr to integrate the Bazaar commands into the windows explorer GUI. Unfortunately when I came to use it with my work it gave me an error, I think due to the "special" folders structure in windows7. Here is a copy of the message I posted to the Bazaar user group:

Hi everyone, I hope someone can help me out.

I'm using Bazaar to version control a whole set of different files between a few different machines. On a previous windows XP machine I was able to use the whole user area as my repository and only add the files that I wanted to control.

I have just upgraded to a windows 7 machine (64bit) and there seem to be some issues with the preconfigured folders not being accessible by Bazaar. I have been able to commit files fine, but when I try to open a window to add new files it crashes as it tries to display them, with the error:

bzr: ERROR: [Error 5] Access is denied: u'C:/Users/welf/AppData/Local/Application Data\\*.*'
(It also seems to have issues with "My Music" and similar)

Any thoughts on why it's happening or a way round the problem?

(I suspect that it would work if I had the repository at a lower level without any "windows" folders, but that is not really the way I'd like to work. I don't actually need to version control anything in these folders, so if they can be skipped in some way that would be fine.)

It seems suspiciously similar to an outstanding bug here:

The general upshot is that I can't add new files to version control using the GUI, although I seem to be able to do pretty much everything else. I thought I would detail the workaround I'm currently using. It isn't too bad, but wasn't totally obvious, so I thought I would document it in case it was of use to anyone else:
  1. Right click in the folder containing the files and select the "Tortoise Bazaar" menu item, then select "Run command". A GUI window to allow you to run a command will open.
  1. Select "Core" after "Category"
  2. Select "add" after "Command"
  3. Click "Insert filenames...", a file selecting window will open.
  4. Select the files you wish to add (hold 'Ctrl' to select multiple files) and click "Open"
  1. Click "OK" and the status window should tell you that the files have been added
You're now at the same stage as if you'd added the files using the standard GUI. Of course you will still need to perform a commit before the files are part of the repository.

Hope that's useful to someone.

UPDATE: Discussion on a Bazaar email list confirms that the problem I'm seeing is due to the error linked above. Unfortunately a fix does not look imminent therefore I'll have to continue using the command-line method described.


Bazaar revert only one file to previous version

So this was the situation I was recently in:

  • I found that a simulation I was running in Simulink was giving me results that seemed to be wrong
  • I was sure that previously it had given me the right results
  • Therefore I wanted to "roll-back" to the previous version of that Simulink model

I thought this would be a simple and easy thing to do as I have all my files under version control. This sort of procedure is termed "reverting" in version control lingo. It was certainly possible, however it wasn't quite as easy as I expected, so I'll detail the process required.

As noted previously I'm using Bazaar for version control, through both the TortoiseBzr windows interface and also the Bazaar Explorer GUI. Bazaar supports several different methods of undoing mistakes. Through either method of accessing Bazaar you can get at a log of all the commits done on a certain file. From this window you have the option of either "Revert to this revision" or "Update to this revision". Either of these will give you the previous version (although the first one will not count the changes as committed); however they will give you whole of the repository at that revision. This might be useful for pulling out a whole set of software that works together, or establishing the state of an entire project at a particular point, but this is not what I needed.

It is possible to get at an individual file, but it involves a little bit more work. It may also be worth ensuring that the current version is committed in case you later decide that reverting was a mistake. Here is the process:
  1. Look at the log of file to determine what revision number contains the version you want (this is where having written good commit messages will help!)
  2. Make a note of the revision number that you require
  3. Highlight the address of the folder you are in and copy it
  4. Open a command line (on windows go to start - run... - "cmd")
  5. Change to the directory you require by typing "cd " and then pasting the folder address you copied before
  6. Type in the Bazaar revert command as follows:
bzr revert -r num file.ext
num is the revision number that you require (as noted from the log)
file.ext is the filename and extension that you wish to revert to (this could be a list of files if you prefer)

This should give you the previous version of only that file. It will not be committed so you can check that it is the right version and make any changes you want before recommitting.

Matlab figures in Powerpoint

I've just been putting together a presentation in which I wanted to include a set of Matlab plots. Whilst there are plenty of ways to do this I thought I would detail the way I managed it...

I've mentioned before about maintaining quality by using vector graphics. Previously I've used .eps format for this, but I don't think it's well supported in Powerpoint (I did consider using alternative presentation software but I was pressed for time and this seemed like the easiest option). Instead I used .emf format which seems pretty well supported by Matlab. This is a Windows specific format so I can't say I'm particularly keen on it for general use, but it served a purpose here.

I saved my figures as separate images from Matlab and then imported into Powerpoint, but I think the same result can be achieved if you simply copy and paste between the two.

One of the benefits of having the plots in vector format is the ability to manipulate them within Powerpoint itself. For the unscrupulous this could be a good technique for "adjusting" a few points here and there to improve  your results - but obviously I didn't do that! What I did do was separate out several lines that were on the same plot, so that I could make them appear (using Powerpoint's animation features) gradually. This made the plots (which were a comparison of the results of several different simulations) much cleaner.

It was a little bit of a hassle to do this, but not awful, and I think worthwhile as it made the results much easier to present. When the .emf file is initially imported it is handled as an image; however, if you right click on it you will find that it can be "ungrouped". You might have to repeat this process a few times as the image seems to be built up of several sub-groups, but once you're done you'll find that individual lines are available to be manipulated. Unfortunately I then had to go through and "regroup" some of them manually to reform complete lines, which involved a bit of 'Ctrl' clicking - this was the tedious bit. I guess it depends how complicated the lines in your plots are as to how long this will take (and whether it is worthwhile or not).

Another benefit was being able to alter the font of my axes to match my presentation style. A trivial point perhaps, but it all goes to improve the overall appearance.

So to summarise:

  1. Copy figure in Matlab
  2. Paste in Powerpoint
  3. Right click and "ungroup"
  4. Repeat 3. until you get to a  level that you can manipulate the objects that you want
  5. You may find there are a few large white squares that form the background of the plot - these can be deleted (it will make things easier when you come to regrouping things in step 7.)
  6. 'ctrl'+'a' to select everything and then change the font to match your presentation
  7. 'ctrl' and click on objects to collect all the ones that should be in a group (you may need to zoom in on your slides to do this accurately)
  8. right click and "group" them
  9. move/recolour/animate/resize the objects as you desire to suit your presentation!

Hope that is of help to someone!?


IET conference paper reference style

I've recently prepared a paper for a forthcoming IET conference in which I cited references.
Whilst the template for the paper provided an example of the format it would like references to journals to be included in, it gave no further advice.

Assuming that there would be a standard format for all IET conference papers I went a-googling - with very little success. My next option was to ask on the IET forums here. Unfortunately this didn't turn up any standard formats either. Therefore my conclusion is that a "standard" doesn't exit.

This isn't a major issue as I think you'd have to work quite hard to contrive an example where a reader wouldn't be able to decipher a reference due to the use of an obtuse format. However I think it would be good practice to document the format I've used here...

The conference template suggests (for a journal article):
[1]    A. B. Author, C. D. Author. “Title of the article”, The Journal, volume, pp. 110-120, (2000).

Surprisingly this differs from the IET advice for research journal citations and the two documents on IEEE reference formats.

Therefore the style I decided to use is:

Journal article
  •  A. B. Author, C. D. Author. “Title of the article”, The Journalvolume, pp. 110  120, (year).
Conference paper
  •  A. B. Author, C. D. Author. The title of the conference paper”, The Conference, Location City, Location Country, pp. 1-7, (Month year).
Book, book chapter and manual
  • A. B. Author, C. D. Author. The title of the book chapter”, in D. Editor (Ed.), The title of the book (Publisher, year, 1st edn.), pp. 1 – 7.
           A. B. Author, C. D. Author. The title of the book (Publisher, year, 2nd edn. 2006).
  • A. B. Author.  The title of the patent, British Patent 123456, (Month year).
  • A. B. Author, C. D. Author. British Patent Application 98765, (Month year).
  • A. B. Author.  The title of the thesis”, PhD thesis, XYZ University, year.
  • BS1234:  The title of the standard, year.
  • http://www.theiet.org, accessed Month year.

As I prepared the paper using LaTeX, all my referencing was done using BibTeX. I therefore needed to create a custom bibliography style file. I did this using the custom-bib package. This a fairly straightforward process once it's figured out, roughly consisting of:
  1. run latex on "username"\Application Data\MikTeX\2.8\tex\latex\custom-bib\makebst.tex
  2. answer questions appearing in the output window
  3. get *.dbj file produced at the end
  4. run latex on that file to produce *.bst file (I found that the full path to the file was required at this step, so it needed to be run from the command line rather than through an editor)
There is a fairly large set of questions that allow you to customise the style through this process, so I ended up with a style that was pretty close to what I wanted. Unfortunately there were a few niggling differences in the output. Most significantly custom-bib does not allow the option of changing the comma between the author list and title to a period. To rectify this I had to dive into the .bst file and start hacking!

Now I wouldn't recommend this if it can be avoided as the language used is pretty obscure, however I eventually got something that looked about right.

If you want to use my style file it's here. Obviously it comes with no warranty and no official backing from the IET. It looked ok for the paper I submitted but I'd recommend thorough checking of the output if you do use it.

Please let me know if this is of use to you, or if you have any comments on my chosen style, using custom-bib or any other part of my process.