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

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

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

Effective programming principles: – Language?

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.

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 new functions –Make yourself understood: keep it easy and explain things to yourself in comments.

Effective programming principles: – Language? – Modelling

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“.

MODELLING - WEB Examples:

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

Effective programming principles: – Language? – Modelling –Readability

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.

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(); 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. 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. Effective programming - READABILITY

Effective programming principles: – Language? – Modelling –Readability – Reusability

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.

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)

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 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. Effective programming - REUSEABILITY

Effective programming principles: – Language? – Modelling –Readability – Reusability – Divide & Conquer

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

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

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’); Variables at start, Sounding names Readability, Comments, Short & easy loops Different grammar, same function Using stucts to group data

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

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]);

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Thank you…