Effective Programming Tips for Cogent

Session 10, 27.3.2008

Christian Kaul

MATLAB for Cognitive Neuroscience

A collection of useful things

• Effective programming– Why does Peter only need 30 lines to achieve the same

than I do with 300 lines?– Readability & Reusability

• A few exemplary pieces of code (to reuse)– Handling files– Peripheral devices with Cogent

Effective programming

Effective programming

• Why is it called a programming language?

– Matlab is a very powerful programming language with which you can achieve nearly everything you ever want on a PC.

• important to understand its grammar & using it• Important to constantly learn new vocabulary &

grammar• Important to use your language understandable

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“. Hence, the reasons behind modeling can be summed up in two words:

– Readability

– Reusability

Effective programming - Modelling

• Readability brings clarity — ease of understanding. Understanding a system is the first step in either building or enhancing it. It makes it easy to document.

• 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.

• 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. – If you really need a list have it in a separate

file/function, it’s likely you can then reuse it in another script.

Effective programming – the most important

• sounding variables, – Call your variables names that tell you what they stand

for. – A script with variables i, j, a, f1, etc. becomes very hard

to understand. – 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 – the most important

• loop structures, – 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.

– This way any loop or nested loops remain small and readable.

– Use CTRL-i to automatically indent your script and your loops for better readability.

Effective programming – the most important

• control variables, – To switch things on/off – To switch between conditions – control variables help you to keep your script flexible

and are a good tool to avoid hard-coding data in your code.

– Define control variables at the very beginning of your script

– Give them sounding name to increase readablity

Effective programming – the most important

• commenting,– Comment your script WHILE you write it. – 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 – the most important

handling files

handling files

• 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

handling files• Saving data & results within your stimulus script

– outputPath = 'c:\home\ckaul\';– cd(outputPath);– subjectname= input('Please enter subject name: ','s');– subjectnum=input('Please enter subject run number: ');– subjectnamerun=[subjectname, int2str(subjectnum)];– filename=[subjectnamerun, 'AttentionChoice_behav_res']; % data file name (one per trial)– datafilename=[subjectnamerun, '_AttentionChoice_behav_data.mat']; % results file name (one per scipt execution)– if exist(filename,'file')– error('Results file already exists!');– end

– For trial = 1:NoOfTrials – % script main body here– Datafilename = [datafilename int2str(trial) ‘.mat’];– save(datafilename, 'data'); % save data(!) after EACH trial– End % trial– Clear data % clear data after saving, no memory-overflow

– % with all data at hand calculate behavioural results(!) at the end of your script – – For trial = 1:NoOfTrials– eval(['load ' datafilename]);– end

– final.result=[results.mean_p_hits results.mean_N_false_alarms results.mean_RTs];– eval(['save ' filename ' results data vectors final']);

handling files

• Selecting many files with SPM-select– Many SPM functions require long long list of filenames as

input. This can be vary tedious to program.– The SPM-select function helps!

– for run = 1 : runs– % define epi files in the run– epiDir = [origDir '\s' int2str(subjNo) '\' dataFolder int2str(run)];– % select scans and assign to all_files– f = spm_select('List', epiDir, ['^' subjects{s0,4} '.*\.img$']);– % add folder name to filenames– fs = cellstr([repmat([epiDir '\'],size(f,1),1) f]); – % clear temporary variables for

next run– f = []; fs = [];– end

Peripheral devices

Peripheral devices

• Cogent has very easy-to-use functions that allow handling all kinds of peripheral devices on– Parallel ports– Serial ports– USB ports

Peripheral devices – examples

• VETcontrol.m

• Written by Elliot Freeman to • Control the eyetracker system in room 101.

• uses simple command strings to operate the

eyetracker.

Peripheral devices – examples

• fMRI Scanner environment, controlling the scanner with your stimulus script

• Additionally you might want to control the eyetracker within the scanner in the same script.

• Important Cogent-functions:– getslice, Waitslice, – get_current_slice, get_current_volume– waitserialbite– cgTracker

Peripheral devices – examples

• set_parallel_port.m• Download “startportb.m” und “outportb.m” at featherstobe • For more detailed information please email me or Christian Ruff.

• function set_parallel_port(action,pattern)% pattern is an 8-bit binary string, e.g. '01010101'

switch action    case 'initialise'        startportb(888); wait(20);        outportb(888, 0);    case 'set'        outportb(888, bin2dec(pattern)); % set pins        wait(10)        outportb(888, 0); % set pinsend

return;

Thank you…