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 Journal, volume, 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.

Book

           A. B. Author, C. D. Author. The title of the book (Publisher, year, 2nd edn. 2006).

Patent

• 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).

Thesis

• A. B. Author.  “The title of the thesis”, PhD thesis, XYZ University, year.

Standard

• BS1234:  “The title of the standard”, year.

Website

• 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.

Weather in iGoogle

I've been using iGoogle for a while now. For those not in the know, this personalises the Google homepage and allows you to add "gadgets". Since I've started using Chrome as my browser I tend to Google search from the address bar anyway, but I still find iGoogle pretty handy.

I use it as a way to amass all the stuff I tend to look at in one session. Currently I have three different tabs:

• News - Local and world affairs and specific technology news
• Comics - Webcomics that I like to read
• Weather - Local weather forecasts so I know if I need a coat

These are all areas that I tend to want to update myself on regularly - approximately once a day. So instead of trawling through various bookmarked pages I can accumulate all the info in one convenient page.

This works out really well and I've found there are specific gadgets for most of the pages the I want to visit. Some of the news related ones didn't have gadgets but I was able to use use their RSS feed to display them in an RSS reader gadget.

The only real pain was the some of the weather forecast sites that I wanted to look at didn't have gadgets - most notably Metcheck.com. I really like the way they display the forecast so I set about trying to get it onto an iGoogle page. The 'official' way to do this I guess would be to make a specific gadget; however this seemed like it would be a lot of effort and learning time. So I went with a different option.

I used a gadget that allows the inclusion of html. Then I wrote some HTML to include a portion of another website. This allowed me to trim the site down to just the specific window I wanted. For example:
<style type="text/css"> #container{ width: 0px; height: 0px;} #container iframe {width: 780px;   height: 590px;   margin: -180px 0px 0px -240px; }   </style> <div id="container"> <iframe scrolling="no" width="0" height="0" src="https://www.netweather.tv/index.cgi?action=uk7dayx7;page=1;ct=19121~Manchester;sess=#forecast></iframe></div>

This includes the portion of netweather.tv for my specific region. I was previously using metcheck but have recently switched as their results page seems to regularly give errors at the moment.

There might be an easier way of doing things, and for other websites the numbers in the HTML will need fiddling with so that the right portion of the page is in the window, but this technique seems to work pretty well for now.

Future documentation methods

Coming towards the end of the first year of my PhD and spending some time writing up my progress so far has led me to muse over the nature of report writing and ask the question: "surely there must be something better"...

Whilst the old adage "if it ain't broke don't fix it" might well apply here, I can't help but think that in the 21st century of immersive 3D virtual reality game playing, home 3D printing, and everyone carrying at least one state of the art electronic device about their person at all times, the concept of a paper report seems a little dated.

Here are a few examples to try to illustrate my point:

• If there is a book and a film of the same story (or even a webpage and a youtube video) I will inevitably look at the the film first as it will convey the information to me far faster, and with less effort than reading the book.
• If I have a choice between a photo or drawing of an object and a 3D model (either manipulable on screen or available to touch) I would get a better understanding of it from the 3D.
• If I want information on a specific subject then I turn to Google/Wikipedia before I head off to the library.

I don't think these are examples of me being weird, they are simply illustrations of modern life making information more readily accessible. I'm sure you could argue over semantics ("the book contains more detail than the film", "library books have a more systematic review process than google hits", etc) but I hope you can accept my general point.

It therefore seems strange to me that a piece of work, perhaps costing thousands of pounds and many hundreds of man hours, should be presented in such a one dimensional format as a printed report. Here is a summary of what I see as the limitations to a printed report:

1. One dimensionality - sure pictures might take this up to 2D, but all too often there aren't enough of these!
2. Lack of user interaction - I can't search for a keyword, interactively link to source, or request further detail on a topic.
3. Page constrained format - diagrams need to fit within a certain width, zooming in is limited by your eyes and printer resolution and page breaks artificially chop things up.
4. Visual sense only - My other senses are put on hold, and only serve as a distraction.

So what have people done to improve on this? Here're a few examples that I can think of:

• Video - a good recent example is this guys youtube CV
• Hyperlinking - within sections of a document or out to other documents or web sites
• Wiki formats - taking linking between sections to the extreme and making progress through the information less linear
• 3D graphics - starting to be seen more in web pages, an excellent example is Google body
• Powerpoint - a format often used in place of a standard document, it has many of the same issues, however users often seem to feel a little less constrained in terms of layout (perhaps this is only due to convention?)
• Computable document format - this is a really exciting new development that reflects a lot of what I'm describing here

This last concept may or may not take off but I can see what they are hoping it will achieve. Some of its functionality can already be achieved in a pdf (details of how to achieve a lot of them through LaTeX are here) and almost all of it could also be done through HTML and javascript. An interesting discussion on this is given here. In fact the recently developed HTML5, in combination with javascript programming, offers a whole mass of interesting possibilities for the presentation of information. A step towards using HTML5 for what I'm talking about here is Tangle. This is a javascript library that supports the production of "reactive documents", allowing a reader to play with the content of the document.

Another alternative format with a lot of capability is Flash animation, these animations are typically web-based and often allow user interaction. Some basic options for creating these are given here. Although it is a very widely used format it requires a good level of experience to be able to code it. It has also faced quite widespread criticism recently, the most high profile of which came from Apple, and therefore there is speculation about whether HTML5 will ultimately replace it.

An obvious downside to these types of advanced documentation method is the length of time it takes to actually produce a document. Even when the author has a good knowledge of the specific tool they're using I think it's safe to say that nothing I've mentioned above will be as quick to produce as a simple text document. In fact the more advanced the documentation method - the longer it's likely to take to produce.

I'd love to be able to round off with a recommendation of the ultimate tool or combination of tools that can be used to create the perfect document, but as far as I've seen it doesn't yet exist. Lots of things seem to offer at least part of the solution I'm looking for, but none pull it all together into one great package. So instead I'll do two things, firstly I'll make a few plain points in summary/prediction, then I'll put together a set of use cases that I'd like to see available to the end user of my "ultimate document".

Summary/Predictions

• The plain printed word document is currently in the process of being overtaken by more electronic forms of documentation, inherently bringing a lot more potential to the document itself (hyperlinking and embedded video being two major ones). I would expect this to be a continuing trend (that may eventually even reach formal engineering reporting or even academia!).
• There is the potential for this to go a lot further than the type of electronic documents seen today with the addition of 3D effects, audio tracks and similar.
• HTML5 currently seems to offer the most potential for supporting this type of advanced documentation (although the computable document format may also be a candidate if it manages to pickup much of a user base).
• Very little progress towards this end goal will be achieved until there are good tools for authoring the type of document I'm discussing here.
• It seems highly likely that viewing of any document of this type will be through a web browser or similar.

Use cases - scenarios that I, as an end 'reader', would like to see supported in this ultimate document format.

1. User managed detail level - I'd like to be able to look in more detail at sections I'm interested in or know little about, whilst invisibly skipping over the mundane or tedious stuff.
2. Unconstrained document flow - If I want to read summary, then the contents, then the conclusions, then methods, it should be easy for me to work through that way.
3. Recommended document flow - If I simply want to be guided through the document ensuring that I pick up all the important information then this should also be easy
4. User interaction - Where more information could be made available then I should be able to access it. For example I should be able to zoom in on a waveform or rotate a 3D model.
5. Multiple sense stimulation - practically this is likely to be limited to visual and audio currently (at least until we develop smell-o-vision and feel-o-vision...)
6. Portability - I want this document to be viewable in as many places as possible, consequently it must be compact and easily openable on a variety of devices (laptops, mobiles, touchpads, e-readers, etc). This might even extend to alternative language/disability support and (somewhat ironically) the ability to print onto plain old paper.

So what have I missed? I'd love to discuss this topic and related areas more so please leave me a comment.
I'd also love to have the time, skills and supervisor buy-in to trying to present my thesis in the manner I've outlined; however I suspect that that will remain a pipe-dream...

Creating Gantt charts

I've had this issue before and it annoyed me. It's still annoying me now!
Gantt charts are one of the types of chart that I have come to accept as a part of life that's not going away, and actually they're not all that bad. They are however difficult to draw.

I (like plenty of other people I've seen) have tried kludging together a Gantt chart in an Excel spreadsheet and it always seems to come out looking pretty horrific. I've also seen them drawn freehand in paint or Powerpoint or similar. Obviously these aren't really a proper solution, so I had a look round to try to find something that would let me manage a simple Gantt chart to plan and track my PhD progress.

Two options looked promising:
Gnome Planner - part of the gnome desktop but also usable under Windows
GanttProject - another open source cross platform piece of software

I started out with the latter and then switched to the former, but to be honest I don't find either that useful. I think the primary issue is that I'm not looking for a tool to perform PERT or CPM or do resource levelling for me. All I want is something that will accept all of my task details in a well contained format and produce a vector graphic of the chart that I can include in a LaTeX document. It's this last part where both of these tools fall down.

The output of these tools is much more of a formal report than it is a nice image. They also seem to really struggle with the multi-year duration of my work. With planner I've had to resort to taking screenshots of the window and including those in reports!

There are packages for LaTeX that support drawing of Gantt charts, but they're a bit too fiddly for the kind of quick changes that I'd like to be able to make. As Planner saves in XML format there must be a method of auto-converting to the LaTeX code...

Any solutions or alternatives out there that I'm missing?

UPDATE: In the end I went with drawing it out using one of the Latex packages. This used all the same data that the planner XML file had in it but in a different format - I was sorely tempted to put together a script to do the conversion for me but in the end I couldn't justify the time required and did it manually. I also had to meddle around a bit to get the gantt to fit on an A4 page - in the end I made it landscape and adjusted the page margins. I think the output from Latex looked a lot more professional and it would be really useful to have a conversion tool. If there is any interest in how I put the latex code together then leave a comment and I'll write a bit more about it...

Using a remote Bibtex file

As mentioned previously:

1. I am using version control software to backup my work
2. I'm using LaTeX
3. I don't like duplicating files around my system
4. I'm working between both Windows and Linux

So I've found myself today writing an end of year report (housed within its own folder in my filesystem) and wanting to pull in some references from my bibtex file (housed within the literature review folder in my filesystem). I could use the copying hack that I previously devised for figures, but that wasn't very elegant.

There are plenty of questions about this out there in internetland, mostly with the following suggestions:

• Move your bibtex file to within the tex installation root - I can't really do this because of 1. above.
• Use symbolic links to the original in the local folder - I can't do this becuase of 4. (windows doesn't support them)
• Give a relative filename reference e.g. '\bibiography{../literatureReview/references}'
• Adding the location as an environment variable as described here.

Both of these later two methods seemed to work for me. I went with the relative referencing for portability between systems. Odd that such a straightforward solution works for references but not for figures!?

Making a bibtex file from a folder of pdf files

The issue
As I'm going to be writing some big documents with lots of references I'd be a fool to try to manage these manually, I therefore needed to pick a reference management piece of software. After some browsing I settled on JabRef because: it's free, it's open source, it's lightweight, it's cross-platform and it handles bibtex format natively (which is what I need for it to integrate with latex). It should also link nicely into the Sciplore mind mapping software which I'm using (more about that some other time).

JabRef is basically a database management tool for references that stores its database in bibtex format. It  looks like it will work rather well, but unfortunately my first stumbling block is that I already have a folder full of my references in pdf format (~200). This means that I'm immediately faced with the big task of going through and adding the details of each pdf individually. There must be a better way...

Someone else asked the same question here. The answer seemed to be that there was no easy way in JabRef, but it could be done in some other reference management software - such as Mendeley. So I could install that as well and export from there to use JabRef, that seemed like a pain though, especially as you need log in details and all sorts for Mendeley.

The solution
Somewhere else cb2Bib was suggested. This looks like an awesome piece of software, almost to the point that I could use it instead of JabRef, although I don't think it does quite the same job. It's designed as a bibtex database manager, however it is more tailored towards reference entry than editing or final use (e.g. citations) - although it can do this. Its method of adding a new reference is based on what's currently in the clipboard - thats whatever you most recently 'cut' or 'copied' in your operating system. This can either be a piece of text or a pdf file.

Files from the system can also be queued up to be added to the clipboard for addition to the bibtex database - in this manner a folders worth of pdf files can be added. Once the file is in the clipboard the software interrogates it to try to extract the right details for the bibtex reference entry. It is also able to do some other clever things like search the web and find a web reference for it that matches only one of the pieces of data it has extracted. There is also the option to manually edit the fields or to set off a whole run of files to add automatically.

My implementation
In practice the software took a little while to get used to; the buttons aren't in quite the locations I'd expect, there seem to be about 3 different windows that are independent but interrelated and the method of specifying a bibtex file and then successively saving additions to it felt a little odd (rather than running through to create a file and then saving it all at once). But once I was used to it at that level it all worked.

When I came to actually try to add all of my pre-saved pdfs however, I hit problems. Whilst automatic extraction usually managed to pull out a few nuggets of useful data, it rarely found enough for a complete entry. Hitting the button to search the web didn't seem to give much assistance. So it was time to dig a little deeper.

Probing through the website there is quite a lot of useful information on how to configure the software to do what you want. What I needed to do was look into where was being searched on the web for my articles. This is all setup in a configuration file located at:
C:\Program Files\cb2bib\data\netqinf.txt (windows)
or
/usr/share/cb2bib/data/netqinf.txt (linux) (you'll need permissions or to be root to edit)

Wading into there you can find out where is being searched and in what order. What would have been ideal for me would have been a search of the IEEE Xplore site, as that would have turned up most of my papers. Unfortunately it was not in there. Second best was google scholar, sitting at the bottom of the list of options. The documentation in the file wasn't brilliant, but with a bit of trial and error I was able to work out what was going on.

The major change I made to the file was to add this at the top of the queries list:

# QUERY INFO FOR Google Scholar
journal=
query=http://scholar.google.com/scholar?hl=en&lr=&ie=UTF-8&q=<<title>>&btnG=Search
capture_from_query=info:(.+):scholar
referenceurl_prefix=http://scholar.google.com/scholar.bib?hl=en&lr=&ie=UTF-8&q=info:
referenceurl_sufix=:scholar.google.com/&output=citation&oe=ASCII&oi=citation
pdfurl_prefix=
pdfurl_sufix=
action=


journal=
query=http://scholar.google.com/scholar?hl=en&lr=&ie=UTF-8&q=<<excerpt>>&btnG=Search
capture_from_query=info:(.+):scholar
referenceurl_prefix=http://scholar.google.com/scholar.bib?hl=en&lr=&ie=UTF-8&q=info:
referenceurl_sufix=:scholar.google.com/&output=citation&oe=ASCII&oi=citation
pdfurl_prefix=
pdfurl_sufix=
action=

The important changes here are the <<title>> and <<excerpt>> search strings, and the change from capture_from_query=info:(\w+):scholar in the existing scholar searches to capture_from_query=info:(.+):scholar in my search. I'm not too sure what the latter change did, but its effect was that it found the details - where previously it was often missing them!

The other change I made was to untick the option "Set 'title' in double braces" box in the configuration window. After I'd made these changes it worked a lot more consistently.

Some of the time it still pulled out the wrong details if it mis-extracted the article title, however I'd named all my pdfs with the title of the paper, therefore it was simply a case of copying and pasting the filename into the title field and rerunning. It would have been really nice to be able to use the title of my pdf as part of the search but unfortunately I couldn't find a way of doing that.

The only other issue I'm having is that although cb2bib adds in the link to the pdf file, JabRef wont understand it as it uses a very slightly different bibtex format for it. The cb2bib format seems to be:

file = {location}

whereas the JabRef format seems to be:

file = {description:location:type}

There is a comment here by a Mendeley admin that suggests that there is no prescribed format for this aspect of a bibtex file, so I guess it's to be expected. I should be able to work around it with a bit of clever find/replace, but it's an annoyance.
ACTUALLY - this seems to be working under windows! It looks like a different version of JabRef has gotten around this issue.

UPDATE: After a couple of months of getting used to cb2bib and using it to produce a document I'm not really finding the need to use JabRef at all! The 'citer' facility of cb2bib is actually really good.

UPDATE: I hadn't previously gotten round to extracting from IEEE Xplore, as almost everything is on Google Scholar. However I've just tried to set it up and found that the IEEE pages use javascript buttons to produce the citation. This makes it difficult to fully automate.

If you add the following to netqinf.txt then it should search IEEE Xplore for the title, you can then manually click the "download citation" button, select BibTeX format and then copy the BibTeX citation into cb2bib:

# QUERY INFO FOR IEEEXplore
journal=
query=http://ieeexplore.ieee.org/search/searchresult.jsp?newsearch=true&queryText=<<title>>&x=35&y=7
capture_from_query=arnumber=(\d+)&contentType
referenceurl_prefix=http://ieeexplore.ieee.org/xpl/articleDetails.jsp?tp=&arnumber=
referenceurl_sufix=
pdfurl_prefix=
pdfurl_sufix=
action=browse_referenceurl

Latex \psfragfig of figures in other folders

What I've spent part of today wrestling with...

I've detailed previously how I'm exporting Matlab plots and including them in Latex documents. This works very well for figure files in the same directory - which is kind of the way Latex is set up. Unfortunately I'd like to maintain my folder structure in a different manner, for example, I have a "results" folder and a "thesis" folder both at the same level. Within "results" I have my Matlab plotting scripts and the images that are automatically saved by them. In my "thesis" folder I have my Latex files, in which I would like to include my results images.

Ideally I would be able to simply reference the image in my Latex document but that's not quite how it worked out. Let me explain what I tried...

Using \graphicspath
This is the most obvious way of doing things as noted here, and it works fine for graphics inserted with the \includegraphics command. I was also able to reference relatively like this: \graphicspath{{../results/}} and apparently it would also look in all the subdirectories if I put a double slash on the end: \graphicspath{{../results//}}.

This would be a great solution if I were using the \includegraphics command - but I'm not. I'm using \psfragfig and it doesn't work with this command, I guess because it's not set up to?

There is also a suggestion here that this method shouldn't be used, in favour of adding the images directory within your Latex compiler setup - although I'm not sure this would be appropriate for what I was trying to do.

Using \input, \include or \import
These all do similar things, in that they allow you to bring in latex documents from elsewhere in a folder structure. Only some of them will allow relative linking via higher level directories (rather than just subdirectories). \import seemed to be what I needed (or rather the \subimport variant of it did), so I set up a .tex file containing only my \psfragfig command within the "results" folder and imported that into my document. This got the figure into the document, but it didn't do all the nice text replacement that it was supposed to. In this respect it was no better than the previous technique.

After some experimentation it seems that \psfragfig only looks locally to the master document for the .tex files that it uses to include text with the figures.

Using \write18
So it appeared that the only way I was going to get the \psfragfig command to work properly was by having both the "figure.eps" file and the "figure.tex" file local to the master document. I'm not keen on the unnecessary duplication involved in this, so at the very least I decided to make it automatic. I therefore set it up so that these two files are automatically copied to the local directory during compile. This means that I always have the most up to date version of them in my document, and everything stays nice and automatic.

I think the only way to copy a file around between directories from within a Latex document is by issuing a system level command using \write18. This is usually disabled by default in Latex as it has the possibility of really mucking things up in your system if you were compiling 3rd party code. Therefore I had to compile my code with the extra argument '--shell-escape' as detailed here.

So I want to use the Latex \write18 command to execute a DOS copy command, that's fine; but there is also the tricky issue of needing to use backslashes for the path in the DOS copy command - these are obviously reserved in Latex. Therefore I had to use the technique outlined here to get around this.

So finally I managed to put together a Latex command that works, and it looks like this:
\def\psfragfigremote{\begingroup\catcode 92 12 \execB}
\def\execB#1#2%

{\immediate

\write18{copy #1#2.eps}%

\write18{copy #1#2.tex}%

\psfragfig*{#2}

\endgroup

}

So after including that in my header I can reference figures in other directories in my document like so:
\psfragfigremote{..\results\}{figure}
This copies both figure.eps and figure.tex (generated from Matlab with the matlabfrag command) from the results folder into the current folder and then includes them in the document.

It works fairly well, but not the first time it is run. I'm not sure why this is, possibly it hasn't finished copying the .tex file before starting to execute the next command. Therefore two compiles may be necessary to get all the labels sorted out.

I'm sure there must be a better way of doing this, possibly modifying the \graphicspath and \psfragfig commands so that they play well together would be a neater solution, but this works ok for now.

I hope this is of use to someone. Any improvements or suggestions then please comment.

UPDATE: Replacing the \write18 commands with:
\write18{robocopy #1 . #2.tex #2.eps}%
and removing the star after \psfragfig will only copy the files if they have changed, speeding up processing significantly.