How to Think through your program

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How to Think through your program

• Session 5, 4.12.2008
• Christian Kaul

MATLAB for Cognitive Neuroscience
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How to Think through your program

• How can I spend LESS time in front of MATLAB?
• the key to effective programming

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

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• Effective programming principles
• Language?

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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.

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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.

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• Effective programming principles
• Language?
• Modelling

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Effective programming - MODELLING

• Do you know what you want?
• --gt 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.

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MODELLING - WEB Examples
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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
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• Effective programming principles
• Language?
• Modelling
• Readability

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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.

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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, its likely you can then reuse it
  in another script setupValues
  getSetupValues()

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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.

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Effective programming - READABILITY

• commenting,
• Comment WHILE you write
• --gtIt 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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• Effective programming principles
• Language?
• Modelling
• Readability
• Reusability

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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.

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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 its on the matlab path)

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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

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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.

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• Effective programming principles
• Language?
• Modelling
• Readability
• Reusability
• Divide Conquer

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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

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

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• 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 1NoOfTrials
• stim presentation here
• Datafilename datafilename int2str(trial)
  .mat
• Eval(save datafilename 'data) save
  data(!) after EACH trial
• End trial
• For trial 1NoOfTrials

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

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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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Struggling with Errorbars?

• Struggling to place your errorbars at the right
  point?
• Instead of endless trial error, search web for
  a better functionBarweb.m (http//www.mathworks.c
  om/matlabcentral/fileexchange/10803)

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Thank you