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How to hack conditional branching in the PsychoPy builder

Regular readers will know that I’m a big fan of PsychoPy, which (for non-regular readers; *tsk*) is a piece of free, open-source software for designing and programming experiments, built on the Python language. I’ve been using it a lot recently, and I’m happy to report my initial ardour for it is still lambently undimmed.

The PsychoPy ‘builder’ interface (a generally brilliant, friendly, GUI front-end) does have one pretty substantial drawback though; it doesn’t support conditional branching. In programming logic, a ‘branch’ is a point in a program which causes the computer to start executing a different set of instructions. A ‘conditional branch’ is where the computer decides what to do out of two of more alternatives (i.e. which branch to follow) based on some value or ‘condition’. Essentially the program says, ‘if A is true: do X, otherwise (or ‘else’ in programming jargon) if B is true; do Y’. One common use of conditional branching in psychology experiments is to repeat trials that the subject got incorrect; for instance, one might want one’s subjects to achieve 90% correct on a block of trials before they continue to the next one, so the program would have something in it which said ‘if (correct trials > 90%); then continue to the next block, else if (correct trials < 90%); repeat the incorrect trials’.

At the bottom of the PsychoPy builder is a time-line graphic (the ‘flow panel’) which shows the parts of the experiment:

PsychoPy_builderThe experiment proceeds from left to right, and each part of the flow panel is executed in turn. The loops around parts of the flow panel indicate that the bits inside the loops are run multiple times (i.e. they’re the trial blocks). This is an extremely powerful interface, but there’s no option to ‘skip’ part of the flow diagram – everything is run in the order in which it appears from left-to-right.

This is a slight issue for programming fMRI experiments that use block-designs. In block-design experiments, typically two (or more) blocks of about 15-20 seconds are alternated. They might be a ‘rest’ block (no stimuli) alternated with a visual stimulus, or two different kinds of stimuli, say, household objects vs. faces. For a simple two-condition-alternating experiment one could just produce routines for two conditions, and throw a loop around them for as many repeats as needed. The problem arises when there are more than two block-types in your experiment, and you want to randomise them (i.e. have a sequence which goes ABCBCACAB…etc.). There’s no easy way of doing this in the builder. In an experiment lasting 10 minutes one might have 40 15-second blocks, and the only way to produce the (psuedo-random) sequence you want is with 40 separate elements in the flow panel that all executed one-by-one (with no loops). Building such a task would be very tedious, and more importantly, crashingly inelegant. Furthermore, you probably wouldn’t want to use the same sequence for every participant, so you’d have to laboriously build different versions with different sequences of the blocks. There’s a good reason for why this kind of functionality hasn’t been implemented; it would make the builder interface much more complicated and the PsychoPy developers are (rightly) concerned with keeping the builder as clean and simple as possible.

Fortunately, there’s an easy little hack which was actually suggested by Jon Peirce (and others) on the PsychoPy users forum. You can in fact get PsychoPy to ‘skip’ routines in the flow panel, by the use of loops, and a tiny bit of coding magic. I thought it was worth elaborating the solution on here somewhat, and I even created a simple little demo program which you can download and peruse/modify.

So, this is how it works. I’ve set up my flow panel like this:

flow

So, there are two blocks, each of which have their own loop, a ‘blockSelect’ routine, and a ‘blockSelectLoop’ enclosing the whole thing. The two blocks can contain any kind of (different) stimulus element; one could have pictures, and one could have sounds, for instance – I’ve just put some simple text in each one for demo purposes. The two block-level loops have no condition files associated with them, but in the ‘nReps’ field of their properties box I’ve put a variable ‘nRepsblock1’ for block1 and ‘nRepsblock2’ for block2. This tells the program how many times to go around that loop. The values of these variables are set by the blockSelect routine which contains a code element, which looks like this:

Screen Shot 2013-11-12 at 09.58.02

The full code in the ‘Begin Routine’ box above is this:

if selectBlock==1:
 nRepsblock1=1
 nRepsblock2=0
elif selectBlock==2:
 nRepsblock1=0
 nRepsblock2=1

This is a conditional branching statement which says ‘if selectBlock=1, do X, else if selectBlock=2, do Y’. The variable ‘selectBlock’ is derived from the conditions file (an excel workbook) for the blockSelectLoop, which is very simple and looks like this:

Screen Shot 2013-11-12 at 10.06.36

So, at the beginning of the experiment I define the two variables for the number of repetitions for the two blocks, then on every go around the big blockSelectLoop, the code in the blockSelect routine sets one of the number of repetitions of each of the small block-level loops to 0, and the other to 1. Setting the number of repetitions for a loop to 0 basically means ‘skip that loop’, so one is always skipped, and the other one is always executed. The blockSelectLoop sequentially executes the conditions in the excel file, so the upshot is that this program runs block1, then block2, then block1 again, then block2 again. Now all I have to do if I want to create a different sequence of blocks is to edit the column in the conditions excel file, to produce any kind of sequence I want.

Hopefully it should be clear how to extend this very simple example to use three (or more) block/trial types. I’ve actually used this technique to program a rapid event-related experiment based on this paper, that includes about 10 different trial types, randomly presented, and it works well. I also hope that this little program is a good example of what can be achieved by using code-snippets in the builder interface; this is a tremendously powerful feature, and really extends the capabilities of the builder well beyond what’s achievable through the GUI. It’s a really good halfway step between relying completely on the builder GUI and the scaryness of working with ‘raw’ python code in the coder interface too.

If you want to download this code, run it yourself and poke it with a stick a little bit, I’ve made it available to download as a zip file with everything you need here. Annoyingly, WordPress doesn’t allow the upload of zip files to its blogs, so I had to change the file extension to .pdf; just download (right-click the link and ‘Save link as…’) and then rename the .pdf bit to .zip and it should work fine. Of course, you’ll also need to have PsychoPy installed as well. Your mileage may vary, any disasters that occur as a result of you using this program are your own fault, etc. etc. blah blah.

Happy coding! TTFN.

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Programming experiments using PsychoPy – first impressions

Links to PsychoPy websiteI wrote a tiny post about PsychoPy a little while ago and it’s something I’ve been meaning to come back to since then. I’ve recently been tasked with an interesting problem; I need an experimental task for a bunch of undergrads to use in a ‘field study’ – something that they can run on their personal laptops, and test people in naturalistic environments (i.e. the participants’ homes). The task is based on a recent paper (Rezlescu et al., 2012) in PLoS One, and involves presenting face stimuli that vary in facial characteristics associated with trustworthiness, in a ‘game’ where the participant  plays the role of an investor and has to decide how much money they would invest in each person’s business. I was actually given a version of the experiment programmed (by someone else) in Matlab using the Psychtoolbox system. However, using this version seemed impractical for a number of reasons; firstly Matlab licences are expensive and getting a licenced version of Matlab on every student’s computer would have blown the budget available. Secondly, in my (admittedly, limited) experience with Matlab and Psychtoolbox, I’ve always found it to be a little… sensitive. What I mean is that whenever I’ve tried to transfer a (working) program onto another computer, I’ve generally run into trouble. Either the timing goes to hell, or  a different version of Matlab/Psychtoolbox is needed, or (in the worst cases) the program just crashes and needs debugging all over again. I could foresee getting this Matlab code working well on every single students’ laptop would be fraught with issues – some of them might be using OS X, and some might be using various versions of Windows – this is definitely going to cause problems.*

Somewhat counterintuitively therefore, I decided that the easiest thing to do was start from scratch and re-create the experiment using something else entirely. Since PsychoPy is a) entirely free, b) cross-platform (meaning it should work on any OS), and c) something I’d been meaning to look at seriously for a while anyway, it seemed like a good idea to try it out.

I’m happy to report it’s generally worked out pretty well. Despite being a complete novice with PsychoPy, and indeed the Python programming language, I managed to knock something reasonably decent together within a few hours. At times it was frustrating, but that’s always the case when programming experiments (at least, it’s always the case for a pretty rubbish programmer like me, anyway).

So, there are two separate modules to PsychoPy – the ‘Builder’ and the ‘Coder’. Since I’m a complete novice with Python, I steered clear of the Coder view, and pretty much used the Builder, which is a really nice graphical interface where experiments can be built up from modules (or ‘routines’) and flow parameters (i.e. ‘loop through X number of trials’) can be added. Here’s a view of the Builder with the main components labelled (clicky for bigness):


At the bottom is the Flow panel, where you add new routines or loops into your program. The large main Routine panel shows a set of tabs (one for each of your routines) where the events that occur in each of the routines can be defined on a timeline-style layout. At the right is a panel containing a list of stimuli (pictures, videos, random-dot-kinematograms, gratings etc.) and response types (keyboard, mouse, rating scales) that can be added to the routines. Once a stimulus or response is added to a routine, a properties box pops up which allows you to modify basic  (e.g. position, size, and colour of text) and some advanced (through the ‘modify everything’ field in some of the dialog boxes) characteristics.

It seems like it would be perfectly possible to build some basic kinds of experiments (e.g. a Stroop task) through the builder without ever having to look at any Python code. However, one of the really powerful features of the Builder interface is the ability to insert custom code snippets (using the ‘code’ component). These can be set to execute at the beginning or end of the experiment, routine, or on every frame. This aspect of the Builder really extends its capabilities and makes it a much more flexible, general-purpose tool. Even though I’m not that familiar with Python syntax, I was fairly easily able to get some if/else functions incorporating random number generation that calculated the amount returned to the investor on a trial, and to use those variables to display post-trial feedback. Clearly a bit of familiarity with the basics of programming logic is important to use these functions though.

This brings me to the Coder view – at any point the ‘Compile Script’ button in the toolbar can be pushed, which opens up the Coder view and displays a script derived from the current Builder view. The experiment can then be run either from the Builder or the Coder. I have to admit, I didn’t quite understand the relationship between the two at first –  I was under the impression that these were two views of the same set of underlying data, and changes in either one would be reflected in the other (a bit like the dual-view mode of HTML editors like Dreamweaver) but it turns out that’s not the case, and in fact, once I thought about it, that would be very difficult to implement with a ‘proper’ compiled language like Python. So, a script can be generated from the Builder, and the experiment can then be run from that script, however, changes made to it can not be propagated back to the Builder view. This means that unless you’re a serious Python ninja, you’re probably going to be doing most of the work in the Builder view. The Coder view is really good for debugging and working out how things fit together though – Python is (rightly) regarded as one of the most easily human-readable languages and if you’ve got a bit of experience with almost any other language, you shouldn’t find it too much of a problem to work out what’s going on.

Another nice feature is the ability of the ‘loop’ functions to read in the data it needs for each repeat of the loop (e.g. condition codes, text to be presented, picture filenames, etc.) from a plain text (comma separated) file or Excel sheet. Column headers in the input file become variables in the program and can then be referenced from other components. Data is also saved by default in the same two file formats – .csv and .xls. Finally, the PsychoPy installation comes with a set of nine pre-built demo experiments which range from the basic (Stroop) to more advanced ones (BART) which involve a few custom code elements.

There’s a couple of features that it doesn’t have which I think would be really useful – in particular in the Builder view it would be great if individual components could be copied and pasted between different routines. I found myself adding in a number of text elements and it was a bit laborious to go through them all and change the font, size, position etc. on each one so they were all the same. Of course ‘proper’ programmers working in the Coder view would be able to copy/paste these things very easily…

So, I like PsychoPy; I really do. I liked it even more when I transferred my program (written on a MacBook Air running OS X 10.8) onto a creaky old Windows XP desktop and it ran absolutely perfectly, first time. Amazing! I’m having a little bit of trouble getting it running well on a Windows Vista laptop (the program runs slowly and has some odd-looking artefacts on some of the pictures) but I’m pretty sure that’s an issue with the drivers for the graphics card and can be relatively easily fixed. Of course, Vista sucks, that could be the reason too.

So, I’d recommend PsychoPy to pretty much anybody – the Builder view makes it easy for novices to get started, and the code components and Coder view means it should keep seasoned code-warriors happy too. Plus, the holy trinity of being totally free, open-source, and cross-platform are huge advantages. I will definitely be using it again in future projects, and recommending it to students who want to learn this kind of thing.

Happy experimenting! TTFN.

*I don’t mean to unduly knock Matlab and/or Psychtoolbox – they’re both fantastically powerful and useful for some applications.

Guest post by Hayley Thair: A student’s perspective on learning to program

Hayley, hard at work on her programming project.

deeply exciting day for this blogger today, as I’m excited to put up my first guest post. After writing my earlier piece on why (psychology) students should learn to code  I was interested in getting a current student’s perspective on the topic, and the delightful Hayley Thair was kind enough to write me a piece about her experience. I first met Hayley while she was working at the Science Museum on this project and she subsequently moved to Bangor to pursue a MSc in Clinical Neuropsychology. I hope this will help to further convince any other students who might be reading that it really is worthwhile putting a bit of time into learning a bit of coding. Here then is Hayley’s experiences of learning to program and what she feels she’s gained from it:

Something else to do with your PC…

Programming – yet another excuse I now have to spend even more time at my computer. Something that initially sounded rather scary, in a “I have no idea what I’m doing” kind of way, has become something incredibly useful that I am now confident in.I am currently completing my Masters in Clinical Neuropsychology and opted for a module called “practical programming.” Knowing that I have a huge research thesis to run and write up I figured knowing something about how to program would be invaluable! Unfortunately my thesis requires the use of Matlab, and the module taught me Visual Basic. However, I soon realised the fundamentals are the same and even if I couldn’t write Matlab code alone, I could certainly understand what was going on with the assistance of my supervisor.

I saw recently on the news that even primary school children are learning to code… this makes me hesitant to admit it was tricky to start with! However, once I learnt the basics I could design anything I wanted. Being short on ideas and running out of time to complete my mini-project I only managed to come up with a times-table game. It’s actually pretty cool, in a nerdy sort of way! I had two numbers being randomly generated to create the questions; a timer to make it more interesting; a scoring system so you can improve; and a fat robin as the loveable character to save!

Although what I made was simple, I felt a great sense of accomplishment in that I made and coded something from scratch without any help. This was a much greater feeling than anything I had at school in IT lessons. These, as far as I recall, were essentially “today let’s open Word.” I honestly can’t recall where I learnt my basic PC knowledge from, but it certainly wasn’t IT lessons at school. I think these lessons would be more engaging and fun if you were making something, like with programming. Being able to create something that’s yours and personalised would be far more entertaining than just being shown how to use something.

Either way, I’m glad I took the module as so many research assistant jobs ask that you be able to program. I think this puts me ahead of other applicants just because I’ll be able to design experiments and run them independently without needing someone else to come in and build my behavioural task for me.

What surprised me about programming, was that even though at first it was tricky, it suddenly became easy once you got the basics. Even if a piece of code doesn’t run (any programmer will be all too familiar with error messages!) you can continue to try to fix it and think of another way to word it. Essentially it’s all logic. You think what you want a button to do, and about how to break that down into simple step-by-step instructions, and weyhey it works! (Sometimes…) I like to think all those years of playing logic based games like Myst have finally proved useful! For people who enjoy learning something new, and constructing things it’s definitely worth a go. I didn’t find a textbook useful at all, but rather preferred viewing online YouTube tutorials for ideas once you have the basics. Visual Basic is free to download online and it easy to have a play around with as everything is clearly labelled, so I would suggest VB is a good starting point.

If you need another incentive, I’ve learnt to code to a confident level in just 10 lessons. It doesn’t take long to pick it up, and it’s now an invaluable skill that I can mention at interviews that (luckily for me) not everyone has!

More on coding for students, plus a teeny bit of recursive self-indulgence

My lovely, lovely friends at TheNeuronClub have just put up a new post, where they say some very kind things about this blog – thanks guys! However, this post is not just about a bit of self-back-slappery – they also mention a few really great-looking resources to help you get started with programming using Python – if you’re interested in coding, this would be a great place to start. Check out their piece here. You can also (*ahem* self-promotion *ahem*), if you felt so inclined, read my previous guest piece on their site (on whether to average functionally or anatomically in fMRI) here.

TTFN.

Why every (psychology) student should learn to code

Why should you, as a psychology student, or indeed any other kind of student, need to learn computer programming? My position on this is that the basics of computer programming should be taught to everyone, preferably in schools, at a young age. I think the benefits of this could be enormous – programming (just like learning any other language) expands the mind, and teaches you to think in new ways. In particular programming languages force the user to think algorithmically, and by their very nature instantiate the basics of formal logic. Unfortunately, a recent report by the Royal Society (Guardian write-up here) has highlighted the deficiencies in the UK’s teaching of IT in schools; despite the best computer:student ratio in primary schools in Europe, there is a massive lack of well-qualified and competent teachers. This is somewhat understandable; a competent programmer can easily make much more money actually being a programmer than teaching kids. It’s difficult to know how to effectively address this issue, but it would definitely be a shame if the UK starts to fall behind in its computer industry because of a lack of quality teaching staff.

So, assuming you didn’t learn to program at school, and you’re now a university student, why should you learn now? Wouldn’t it be better to spend your time learning the material you need to know for whatever course you’re doing, than learning some kind of esoteric skill that you might not ever need? The answer, is, emphatically, no. Programming is about as essential a skill as it’s possible to conceive of. As the world moves towards a knowledge and tech-based economy a lot of traditional skills are becoming more and more automated. Vast industries have been created in the last 20 years, focussed around building the systems which make this transition possible – and that means coding. Read the rest of this entry