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Flipse R&D - World, meet my alpha version (part III)

World, meet my alpha version (part III)

Mon, 28 Jan 2013

On the top of my bucket list is fixing a ton of bugs or issues with regards to the workflow, that should make the app run more stable. A lot of things I want to change are caused by common beginner mistakes. Even though I’ve read the Pragmatic Programmer and tried to take a lot of their comments to heart, it’s funny how poorly I understood what it all meant until I really encountered a situation where it applied. Jeff Atwood posted a nice summary of the book here.

Some of the things I’d like to fix are:

  • Refactoring my early code to be more up to date based on my current experience. This applies to much of the main panel and how the GUI is controlled by PubSub.
  • Make the code more self-contained. Even though I tried to apply MVC by separating the GUI from the calculations and the database, when I started out a lot of database functions would pass along a message back to the GUI. You can imagine that later on when you want to reuse the same database functions, the GUI got called as well creating all sorts of nasty side effects.
  • Because I didn’t fully understand how to use debugging, I cheated by simply adding print statements to each function. Obviously that doesn’t scale (though it helped me understand my workflow tremendously), so instead I’d like critical functions to send a PubSub message to which I can subscribe. Then I can simply add a Settings option to print these messages from one central location or simply unsubscribe from them.
  • Currently when I change the database, I manually change my own MySQL database and then figure out how to replicate it. Up until now I’d advise my one user not to invest large amount of time in annotating contacts, because she’d risk having all that effort go to waste when I decided to update her table. In the future I’d like to make this more easier for the user, especially the non-technical ones, by only dropping tables if its trivial to compute the results again or update the database (rather than dropping it) when it’s an important table.
  • Interface several database action/settings and more general settings, like making a backup of the database, tweak the ratios of the color map or change the default location where the measurement data can be found.
  • Add exceptions or make sure the code doesn’t have any expectations about the data. A good example was that my results first required each subject to have 4 paws, else the code wouldn’t run. But some dogs or cats are amputees and humans obviously only have 2 feet, so I did my best to remove any of these expectations. However, I’m sure there are still some of these assumptions hidden in the code waiting to come across a trial that doesn’t meet them.
  • Document more! This is one major area where I’ve slacked off, telling myself that it’s just a waste of time and didn’t feel like wasting it. However, after spending several days trying to hunt down obscure bugs, because I didn’t fully remember what function triggered what other functions, I’ve definitely changed my mind. Another great advantage I’ve found was that when I write out what I want the code to do, I spot errors in my thinking much faster and get a much better grasp of what I actually want the code to achieve. On top of all this, I want to look into a library that takes all my doc strings and uses that to create proper documentation.

Furthermore, I’d like to keep adding features that either improve the usability or that make the app more useful. Examples of this are:

  • Allow the user to edit objects, rather than requiring them to delete it and create a new one. This applies to simple things adding measurements after a session has been saved, tweaking a single zone location or even being able to redo it without having to recalculate all the results.
  • Allow the user to drag the zone’s square to the right position rather than requiring to use the directional keys on the keyboard. Not everyone prefers using a keyboard, so they shouldn’t be forced to use it.
  • Make it easier to annotate the contacts when the keyboard lacks a numpad. While the numpad is definitely the fastest way to annotate them, laptops generally lack one and pressing Fn while trying to find the keys isn’t as easy. I used to have a version where you could click on the average contacts, but the event required to do so (EVTCHILDFOCUS) had the nasty habit of not being very reliable and getting called more often. One ‘shortcut’ would be to make a button and display the imshow() image as the face of the button.
  • Create a function to manually override the paw detection in a given slice of the entire plate, so if the automagic detection fails enabled the user to try and fix it.
  • Allow different shapes, sizes and number of zones. This should make the application more flexible for measuring other kinds of data, such as humans, horses or elephants (you have to think big!).

There are also features I’d like to add that allow for more data exploration and analysis:

  • Currently I don’t remove any outliers (other than ignoring incomplete contacts or those that didn’t get recognized properly), so it would be helpful if before calculating all the definitive results you could clean up the results. For example by displaying histograms with the distribution of certain variables or plotting all contacts in one graph. By listing all contacts in a list and allow the user to delete them if necessary they can perform any required data cleaning.
  • At the moment you can only analyze one protocol at a time (while the graphs do allow you to plot both at the same time), but obviously comparing them would be very interesting. As I’ve experienced in the past, just displaying two graphs next to each other is not comparing. It takes a lot of experience to interpret the differences especially without a clear frame of reference.
  • Another thing that I’d like to analyze are differences on a population level. Even though I already experimented with this, I wasn’t happy with the end result. Simply displaying multiple graphs over one another wasn’t really useful and since the dogs were subdivided into weight groups there was a lot of variety in numbers. Another issue was averaging dogs with a ‘normal’ and amble gait pattern. As you can see in this figure, the step lengths between the left front and right hind paw (bottom right) were either negative (right hind being behind the left front paw) or positive. However, when you calculate an average, you get a value around -10 which doesn’t really describe either pattern. Clearly there’s a need for some more diligence when segmenting the data.
  • I don’t only want to display the population data alone, but rather compare any dog with the ‘normal’ values based on the medical history of the dog. That way its results are much easier to quantify, because you get a sense of what they should be, so spotting abnormalities should be a lot easier.

Lastly there are several things that I’d like to work on in the future, but that will me require me to learn a lot more. First on the bucket list is: - Reading more books, first of all finishing Code Complete. I’ve got plenty of interesting books, I just haven’t had the time the past few months to try and read them. On top of that, in most cases its best to have a small pet project to try out all the news things you’re trying to learn. This obviously doesn’t go so well if you’re under any time constraints. - Experiment with OpenGL, because though I have an animation working, that library doesn’t work with wxPython. So I’d love to learn some OpenGL so I can learn how to draw to a Canvas myself, without the need of a library to do the heavy lifting. - I’d love to mess around with Microsoft’s Kinect. Not only because it’s a fun gadget, but also because the kinematic data could be a great asset to the gait analysis. First off, it allows me to measure the angles and make estimations about the moments around the joints. Second, it tells me which paw is where at what point in time, so a synchronized Kinect + pressure measurement would make it much easier to automate the paw detection. But obviously Kinect requires some OpenGL knowledge (for performant displaying), OpenCV knowledge for interpreting the image data and brushing up on my old courses on Inverse Kinematics... So I’m still a long way off ever getting this to work. - Try out if sorting results is any better when using MongoDB. Now I know that NoSQL isn’t the solution to all my database problems, but the problem I have with MySQL is how it requires me to break my data into pieces and stitch them back together when I need them again. I’d much rather leave things as they are and skip tedious parsing loops every time I need a different result. Furthermore, requiring a schema is an absolute pain in the ass when your design isn’t set in stone. I’ve spend nearly as much time writing code to ‘build’ a database as I needed to put things in the database. Off course, I don’t intend to break something that’s already working, so I’m probably going to work on a small pet project to see if I like this any better. - Given that I’m writing scientific software I need to be pretty darn sure whether the results are correct. I’d love to build in a dummy data set that can function as a ‘Mock’ object and allow me to check whether the results are correct. This should allow me to catch errors with my calculations that aren’t detectable with the human eye. Especially when you have highly dimensional data, errors easily slip in without a good way to spot them early on. - Above all else, I desperately want to be able to manage measuring myself! Currently I first need to do measurements in the vendor’s software, without any way to tell if the measurement went ok, then export it from their software and import it into mine. You can understand that most clinicians would find this process far too laborious and decide not to use my app. On top of that, the new drivers allow for continuous measuring in contrast to the 2 second limit of the current software version. This would allow me to greatly increase the pace at which the measurements can be performed and analyzed. However, I first need to convince the vendor to give me this access…

As you can see there’s more than enough work for me in store! On top of all this I have to await what the clinic thinks of my first version and how useful they find it. But I’ll be sure to keep you guys up to date on any progress I’m making. If you have any questions on how or why I did something a certain way, be sure to drop a comment!