Viewing missing methods/software, part VII: PHP+GD

I was getting dissatisfied with Processing for visualizing missing methods. It was nice to have animation of the diagrams, but it was just too brittle: it would only work in certain browsers, it stopped working sometimes when you moved between tabs or windows, it was hard to update and keep working. This is probably more due to my lack of experience in the language and the odd way I was using it (read a variable stored in Javascript on a page to talk to a PHP script to talk to a Postgres database and display the results in real time) than any inherent flaws in it. I had thought about going to Flash, but that also involved learning a new programming language. I had recently started using PHP with GD to visualize progress of my jobs on Duke's computing cluster and found it easy to use (though I'm having issues with transparency). I decided to try this with the method visualization (I wanted to get TreeTapper cleaned up a bit more before a job interview next week). I wrote a script that reads information stored in GET variables and saves an image and image map. In front of this I wrote a controller script that only calls the drawing script when an entry in the database is newer than the saved image and image map (using ideas from my Google Summer of Code student Paul McMillan, who put sophisticated caching in his DBGraphNav). The image and image map are displayed in an iframe in the calling page. There's a Javascript function that calls the controller script as a user chooses which options to display. There's also a Javascript function that uses a Panel object from YUI to display a lot of information about each node on the diagram on mouseover in a floating panel. This is a lot more flexible than the Processing implementation. For example, you can now go to a summary page for each node or click on an entry in the floating panel to go to an info page on just that item (such as a program).  Caching the images makes display a lot faster, though only a subset of possible combinations can be cached. The cache of images also provides some nice pictures for screen savers or talks.

You can try out the new interface here.

Here's a picture of the new display:

And some of the cached images:

dbgraphnav up

Paul McMillan has been working hard at his dbgraphnav Google Summer of Code project, and it's now pretty much ready to use. I've installed it on TreeTapper (see an example here). This allows navigation of author and reference relationships, a visual complement to the coauthor and reference tables already present. It's a general tool allowing navigation of relational databases with a lot of user configuration options. After all Paul's work, and our frequent IRC conversations, it's good to see it running. One nice aspect of it is caching: GraphViz takes a long time to draw graphs, and there's a user-set option to cache by time or by using diff to only update graphs that have changed (the latter works remarkably fast). I'll be firing off a few scripts tonight to generate cached files for all the people and references in the database to make it easier for people to use.

One aspect of the project I've been disappointed by is GraphViz itself. When I proposed this project, it seemed like the logical choice to use, but I've been amazed at some of its limitations. For example, on graphs with many nodes, using "neato" layout (an undirected graph layout), some nodes are far from the rest of the graph (see Michael Donoghue's TreeTapper page for an example). This results in nodes in the center being tightly clumped while nodes at the edges have far too much whitespace around them. No matter what options we've tried for desired edge length, spring parameter, etc., we just can't make GraphViz pull those far off nodes in. Any suggestions? Other than that sort of annoyance, though, this should be a very useful addition to TreeTapper and perhaps other websites as well.