How to Think through your program

1. How to Think through your program Session 5, 4.12.2008 Christian Kaul MATLAB for Cognitive Neuroscience

2. How to Think through your program “How can I spend LESS time in front of MATLAB?” … the key to effective programming…

3. Effective programming principles: • Language? • Modelling • Readability • Reusability • Divide & Conquer • A few exemplary pieces of code

4. Effective programming principles: • Language?

5. Effective programming - LANGUAGE? • Why is it called a programming language? • Matlab is a very powerful programming language with which you can achieve nearly everything! • important to understand its grammar & using it • Important to constantly learn new vocabulary & grammar • Important to use your language understandable • … because leaning programming is just like learning a language.

6. Effective programming - LANGUAGE? • … so you must keep learning: • Grammar: statements can be coded in different ways - learn new stuff all the time • New Vocabulary: constantly check out help & the internet for newfunctions • Make yourself understood: keep it easy and explain things to yourself in comments.

7. Effective programming principles: • Language? • Modelling

8. Effective programming - MODELLING • Do you know what you want? --> The Modelling step! • Modeling = • Drawing a flowchart listing the steps we want to achieve. • Defining a model first makes it easier to break up a task into discrete, simple pieces. • We can then focus more easily on the smaller parts of a system and then understand the "big picture“.

9. MODELLING - WEB Examples:

10. MODELLING - Examples: Start Stim program Type in subject number Produce moving dots for backgroud, 100 frames Load main task images Start presentation Repeat 4 times, Record response Repeat again, Calculate mean over last 5 trials no Higher than alpha lower than alpha Go the next image Increase image contrast End of images? yes Calculate overall time, save result, end

11. Effective programming principles: • Language? • Modelling • Readability

12. Effective programming - READABILITY • Readability • brings clarity — ease of understanding. Understanding a program is the first step in either building or enhancing it. It makes it easy to document.

13. Effective programming - READABILITY • avoiding lists: • Many lists can be avoided. • Lists clutter your code and make it hard to read. • Therefore: • Consider the use of matrices & loops whenever you see a list. • Consider structs to group variables & information • If you really need a list have it in a separate file/function, it’s likely you can then reuse it in another script: setupValues = getSetupValues();

14. Effective programming - READABILITY • sounding variables, • Call your variables names that tell you what they stand for: Instead: I = j - mean(f1), have names like: MeanBaselineCorrectedValue = result - mean(baseline) • Define & assign your variables ONLY at the beginning of your script. • Never “hard code” numbers and values inside the main body of your script.

15. Effective programming - READABILITY • commenting, • Comment WHILE you write • -->It will take you twice the time one day after, four times the time one month later • Group your comments neatly away to a common indent, this way you avoid “cluttering” your code and ensure readability. • Have a short explanatory commented out section at the beginning of your script. Explain in simple terms what you code is doing there.

16. Effective programming principles: • Language? • Modelling • Readability • Reusability

17. Effective programming - REUSEABILITY • Reusability • After a system has been modeled to make it easy to understand, we tend to identify similarities or redundancy in the smaller steps involved.

18. Effective programming - REUSEABILITY Identify bits of your code that do stuff over and over again. Write a simple function with inputs & outputs How? Write a file ‘fnname.m’, starting with function [output1,… N] = fnname(input1,…N) Matlab will automatically recognize your function (as long as it’s on the matlab path)

19. Effective programming - REUSEABILITY • control variables, • Define control variables at the beginning of your program (& comment them) • control variables help you to keep your script flexible and are a good tool to avoid hard-coding data in your code. • Give them sounding name

20. Effective programming - REUSEABILITY • loop structures, • Keep your loops small and readable • Whenever you find a line of code inside a loop that does not contain a variable used in that loop put it outside the loop immediately. • Use CTRL-i to automatically indent your script and your loops for better readability.

21. Effective programming principles: • Language? • Modelling • Readability • Reusability • Divide & Conquer

22. Effective programming - DIVIDE & CONQUER • Divide & Conquer, • Is the principle to break large tasks up into small sub-units to be able to compute / understand them. • Is achieved by deciding to put simple units of your code in separate functions. • Ideally, these functions can be reused

23. Effective programming principles: • Language? • Modelling • Readability • Reusability • Divide & Conquer • A few exemplary pieces of code

24. Variables at start, Sounding names Readability, Comments, Short & easy loops • Collecting & Saving data in your stimulus script • outputPath = 'c:\home\ckaul\'; • Subjectname = input('Please enter subject name: ','s'); • Subjectnum =input('Please enter subject run number: '); • Subjectnamerun =[subjectname, int2str(subjectnum)]; • Filename =[subjectnamerun, exp_behav_res.mat']; % data file name (one per trial) • NoOfTrials = 10; • if exist([ outputPath filename],'file') • error('Results file already exists!'); • end • For trial = 1:NoOfTrials • %stim presentation here • Datafilename = [datafilename int2str(trial) ‘.mat’]; • Eval([‘save ‘ datafilename 'data‘]); % save data(!) after EACH trial • End % trial • For trial = 1:NoOfTrials • Result(trial) = eval(['load ' datafilename int2str(trial) ‘.mat’]); • end • Final.result =Result; • Final.NoOfTrials = NoOfTrials; • … • Save([ outputPath filename],’final’); Different grammar, same function Using stucts to group data

25. Effective programming - EXAMPLES • Everybody knows the endless boredom of copying loads of files from one into the other directory for many subjects, runs, etc. • Why not have it done automatically! • Example: sorting raw fMRI data • File: sort_raw_fMRI_data.m

26. Prewritten functions often make life much easier: • Selecting many files with SPM-select • Many SPM functions require long long list of filenames as input. This can be very tedious to program. • The SPM-select function helps! • % define epi files in the run • epiDir = [origDir dataFolder]; • % select scans and assign to all_files • f = spm_select('List', epiDir, ['^' MAO5675'.*\.img$']); • % add folder name to filenames • fs = cellstr([repmat([epiDir '\'],size(f,1),1) f]);

27. Struggling with Errorbars? • Struggling to place your errorbars at the right point? • Instead of endless trial & error, search web for a better function:Barweb.m (http://www.mathworks.com/matlabcentral/fileexchange/10803)

28. Thank you…