Functions
Check if fileName is a path or a simple file name if	isempty (strfind(fileName,'\'))%only filename if exist(fullfile(dirs.DataIn
else	warning ('File%s does not exist in the specified path', fileName)
end else complete path if	exist (fullfile(fileName),'file') diodeData
else	warning ('File%s does not exist in the%s folder', fileName, dirs.DataIn)%end end%Checking rows are for channels and create[d1
else end Getting the stim frequencies if	strfind (fileName,'DiodeData_15') stimFreq
elseif	strfind (fileName,'DiodeData_sweep') stimFreq
	title (fileName,'FontWeight','Bold') xlabel('Sec'
	ylabel ('PhotoDiode State','FontWeight','Bold') xRange
Get start of	stimulation (flickering) fprintf('Get ''start''of stimulation for freq.%i\n'
Get start of	stimFreq (1))[xRange(1)
Get start of Extract sections for each	freq (time boundaries) if strfind(fileName
	SweepTimes (iFreq-1,:)
end else	fprintf ('Get ''end''of stimulation/flickering for freq.%i\n', stimFreq(1))[xRange(1
	plot (f, 10 *log10(pxx)) plot(f
pxx	xlabel ('Frequency')
	ylabel ('dB')
	title (sprintf('Periodogram of photodiode%s', titleStr))
end Matlab	save (sprintf('%s.mat', fullfile(dirs.DataOut, saveFilename)),'ptData','ptTime','ptInfo')
Comma Separated	Values (CSV) photoDiode
Putting files in one for time another for	photodiode (so Excel can open it) csvwrite(sprintf('%s.csv'
Putting files in one for time another for	fullfile (dirs.DataOut, saveFilename))
Putting files in one for time another for photoDiode	fprintf ('\nSuccessfully saved all the files to%s as%s\n', dirs.DataOut, saveFilename) end function dirs
id	C: (id Unlock)
Add path to chronux toolbox otherwise	disp ('No paths have been estalished') end%Set up path so code is accessible to Matlab addpath(dirs.helpers)
Add dir w my helpers	addpath (dirs.DataIn)
Add dir w your Data path	addpath (genpath(dirs.Code))
Add dir w your code path	addpath (genpath(dirs.PTB))
Add dir w PsychToolbox code	addpath (genpath(dirs.chronux))
Variables
	function [ptData, ptTime, ptInfo]
creates photo diode and time vector0 Also a structure with info regarding smapling	frequency
creates photo diode and time vector0 Also a structure with info regarding smapling flickering stimulation freq and times for sweep analysis INPUT	fileName = 'C:\Users\Administrator\Documents\BU\Speechlab\Unlock\Data\raw\20131211-photodiode\DiodeData_15.mat'
Check if fileName is a path or a simple file name if file	diodeData = load(fullfile(dirs.DataIn,fileName))
else	d2 = size(diodeData.y)
if d1 d2 diodeData	y = diodeData.y'
	titleStr = '15'
Get name of file to save it	strIndx = strfind(fileName,'DiodeData_15')
end	saveStr = fileName(strIndx(end)+10:end-4)
	ptTime = diodeData.y(1,:)
Sampling frequency	Fs = 1/(ptTime(3) - ptTime(2))
Extra analysis Plot data	hFig = plot(ptTime, ptData)
	FontWeight
	Bold
	SweepTimes = zeros(length(stimFreq),2)
Get start of Extract sections for each DiodeData_sweep Get right most boundary for	iFreq
end Filter the data Filter params	smpRate = Fs
	freqBand = [1 Fs/2]
	filterOrder = 2
	filterType = 'butter'
Filtering	dataFiltered = setFilterParams(freqBand, filterType, filterOrder, smpRate) true
	ptData = filtfilt(filtParams.b,filtParams.a,ptData)
Running	periodogram [pxx, f] = periodogram(ptData,[],[],Fs)
Info structure with info required for analysis	ptInfo = struct('nameFile',fileName,'HighStates',8,'LowStates',0,'sampFreq',Fs,'StimTimeSec',3,'StimRestTimeSec',3','StimFreq',stimFreq,'SweepTimes',SweepTimes)
Saving files if~dataFiltered	saveFilename = ['PhotoDiodeDataAndTimes-',saveStr]
Putting files in	column
Putting files in one for time	vector
Putting files in one for time another for photoDiode data input and	output
Putting files in one for time another for photoDiode data input and based on system	hostname [~, host] = system('hostname')
	host = deblank(host)
Dir w data analysis Code dirs	helpers = 'C:\Users\salacho\Documents\Code\helpers'
Dir w helpers analysis Code dirs	DataIn = 'C:\Users\salacho\Documents\Analysis\unlock'
Local Dir to output analyzed datafiles and figures too dirs	BCIparams = ''
Add path where all BCIparams are located dirs	PTB = 'C:\Users\salacho\Documents\MATLAB\toolbox\Psychtoolbox'
Add path to PsychToolbox dirs	chronux = 'C:\Users\salacho\Documents\MATLAB\toolbox\chronux'

Function Documentation

Add dir w my helpers addpath ( dirs. DataIn )

Add dir w your Data path addpath ( genpath(dirs.Code) )

Add dir w your code path addpath ( genpath(dirs.PTB) )

Add dir w PsychToolbox code addpath ( genpath(dirs.chronux) )

id C: ( id Unlock ) [virtual]

Add path to chronux toolbox otherwise disp ( 'No paths have been estalished' )

end else complete path if exist	(	fullfile(fileName)	,
		'file'
	)

Putting files in one for time another for photoDiode fprintf	(	'\nSuccessfully saved all the files to%s as%s\n'	,
		dirs.	DataOut,
		saveFilename
	)

end else fprintf	(	'Get ''end''of stimulation/flickering for freq.%i\n'	,
		stimFreq(1)
	)

Get start of Extract sections for each freq ( time boundaries )

Putting files in one for time another for fullfile	(	dirs.	DataOut,
		saveFilename
	)

Check if fileName is a path or a simple file name if isempty ( strfind(fileName,'\') )

Putting files in one for time another for photodiode ( so Excel can open it )

plot	(	f	,
		10 *	log10pxx
	)

end Matlab save	(	sprintf('%s.mat', fullfile(dirs.DataOut, saveFilename))	,
		'ptData'	,
		'ptTime'	,
		'ptInfo'
	)

Get start of stimFreq ( 1 )

Get start of stimulation ( flickering )

elseif strfind	(	fileName	,
		'DiodeData_sweep'
	)

else end Getting the stim frequencies if strfind	(	fileName	,
		'DiodeData_15'
	)

SweepTimes	(	iFreq-	1,
		:
	)

title	(	fileName	,
		'FontWeight'	,
		'Bold'
	)

title ( sprintf('Periodogram of photodiode%s', titleStr) )

Comma Separated Values ( CSV )

else warning	(	'File%s does not exist in the%s folder'	,
		fileName	,
		dirs.	DataIn
	)

else warning	(	'File%s does not exist in the specified path'	,
		fileName
	)

pxx xlabel ( 'Frequency' )

ylabel ( 'dB' )

ylabel	(	'PhotoDiode State'	,
		'FontWeight'	,
		'Bold'
	)

Variable Documentation

Local Dir to output analyzed datafiles and figures too dirs BCIparams = ''

Bold

Add path to PsychToolbox dirs chronux = 'C:\Users\salacho\Documents\MATLAB\toolbox\chronux'

Putting files in column

else d2 = size(diodeData.y)

Filtering dataFiltered = setFilterParams(freqBand, filterType, filterOrder, smpRate) true

Dir w helpers analysis Code dirs DataIn = 'C:\Users\salacho\Documents\Analysis\unlock'

Check if fileName is a path or a simple file name if file diodeData = load(fullfile(dirs.DataIn,fileName))

Check if fileName is a path or a simple file name if fileName = 'C:\Users\Administrator\Documents\BU\Speechlab\Unlock\Data\raw\20131211-photodiode\DiodeData_15.mat'

filterOrder = 2

filterType = 'butter'

FontWeight

freqBand = [1 Fs/2]

creates photo diode and time vector0 Also a structure with info regarding smapling frequency

Sampling frequency Fs = 1/(ptTime(3) - ptTime(2))

function[ptData, ptTime, ptInfo]

Initial value:

 photodiodeMain(fileName)
% [ptData,ptTime,ptInfo] = photodiodeMain(fileName)
%
% Loads and parses data

Dir w data analysis Code dirs helpers = 'C:\Users\salacho\Documents\Code\helpers'

Extra analysis Plot data hFig = plot(ptTime, ptData)

host = deblank(host)

Putting files in one for time another for photoDiode data input and based on system hostname[~, host] = system('hostname')

Get start of Extract sections for each DiodeData_sweep Get right most boundary for iFreq

Initial value:

 2:length(stimFreq)+1
        fprintf('Get ''end'' of stimulation for freq. %i\n',stimFreq(iFreq-1))
        [xRange(iFreq),~] = ginput(1)

Putting files in one for time another for photoDiode data input and output

Running periodogram[pxx, f] = periodogram(ptData,[],[],Fs)

Add path where all BCIparams are located dirs PTB = 'C:\Users\salacho\Documents\MATLAB\toolbox\Psychtoolbox'

ptData = filtfilt(filtParams.b,filtParams.a,ptData)

Info structure with info required for analysis ptInfo = struct('nameFile',fileName,'HighStates',8,'LowStates',0,'sampFreq',Fs,'StimTimeSec',3,'StimRestTimeSec',3','StimFreq',stimFreq,'SweepTimes',SweepTimes)

ptTime = diodeData.y(1,:)

else saveFilename = ['PhotoDiodeDataAndTimes-',saveStr]

end saveStr = fileName(strIndx(end)+10:end-4)

end Filter the data Filter params smpRate = Fs

strIndx = strfind(fileName,'DiodeData_15')

end else SweepTimes = zeros(length(stimFreq),2)

titleStr = '15'

Putting files in one for time vector

if d1 d2 diodeData y = diodeData.y'

unlock/analysis/andres/Code/photodiodeMain.m File Reference

Functions

Variables

Function Documentation

Variable Documentation