Effective Programming Tips for Cogent

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Effective Programming Tips for Cogent

• Session 10, 27.3.2008
• Christian Kaul

MATLAB for Cognitive Neuroscience
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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

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Effective programming
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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

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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

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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.

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Effective programming the most important

• 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, its likely you can then reuse it
  in another script.

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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.

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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.

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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

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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.

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handling files
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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

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handling files

• Saving data results within your stimulus script
  
• outputPath 'c\home\ckaul\'
• cd(outputPath)
• subjectname input('Please enter subject name
  ','s')
• subjectnuminput('Please enter subject run
  number ')
• subjectnamerunsubjectname, int2str(subjectnum)
  
• filenamesubjectnamerun, 'AttentionChoice_behav_r
  es' data file name (one per trial)
• datafilenamesubjectnamerun, '_AttentionChoice_b
  ehav_data.mat' results file name (one per
  scipt execution)
• if exist(filename,'file')
• error('Results file already exists!')
• end
• For trial 1NoOfTrials
• script main body here
• Datafilename datafilename int2str(trial)
  .mat
• save(datafilename, 'data') save data(!)
  after EACH trial
• End trial

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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, ''
  subjectss0,4 '.\.img')
• add folder name to filenames
• fs cellstr(repmat(epiDir
  '\',size(f,1),1) f)
• clear temporary variables for next run
• f fs
• end

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Peripheral devices
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Peripheral devices

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

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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.

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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

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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 pinsendreturn

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Thank you