AnalysisMain.m

%% Description of Tetrodes
% From tetinfo files
%
% -----------------------
% ANIMAL, HPa
% -----------------------
% Tetrodes			Area
% -----------------------
% 1-7		...		CA1
% 8-14		...		iCA1
% 15-20		...		PFC
%
% -----------------------
% ANIMAL, HPb
% -----------------------
% Tetrodes			Area
% -----------------------
% 1-7		...		CA1
% 8-14		...		PFC
% 15-20		...		iCA1
%
% ----------------------
% Best for HPb
% ----------------------
% 
%  1,3,4,6 for CA1; 9 for PFC

%% Putting Data Files on Path and Clearing Variables

% if files.brandeis.edu is in the file system, then add data to path
d = filesep;

if ispc; files_dot_brandeis_edu = '\\files.brandeis.edu\jadhav-lab';
elseif ismac; files_dot_brandeis_edu = '/Volumes/jadhav-lab';
elseif isunix; files_dot_brandeis_edu = '/Volumes/jadhav-lab';
else files_dot_brandeis_edu = '/home/mcz/DataShare'; end;
path_str = [d 'DATA' d 'sjadhav' d 'HPexpt' d];
path_added = false;


if path_added || (~path_added && exist(files_dot_brandeis_edu, 'dir'))
	
	disp('Adding animal folders to path! ...');
	
	% Adds all data folders to path and subfolders. For now this is
	% how functions will find data.
	path(path,genpath([files_dot_brandeis_edu path_str 'HPa_direct'])) 
	path(path,genpath([files_dot_brandeis_edu path_str 'HPb_direct']))
	path(path,genpath([files_dot_brandeis_edu path_str 'HPc_direct']))
    
     clear all;
    
    path_added = true;
end
    
clear sampleParams acquisition acquisition2 grams avg_grams paramSet

%% Parameter Section

% This is where we specifiy which parameters we're interested ... which
% animals, which days/epochs, which tetrodes, and what types of maze and
% electrophysiology parameters to select for.

% ----------------------------------------------------------
% Parameters for circumscribing sample around a point
% --------------------------------------------------------
% How large of radius should we sample
% sampleParams.circleParams.radius = 20;       % 20 pixel radius
% % % Where to sample
% sampleParams.circleParams.segment = {1, 'final'}; % end of segment 1


% ----------------------------------------------------------
% Parameters for controlling which segment transitions to sample 
% ----------------------------------------------------------
% In most cases, we trigger either on segment transitions (e.g. segment 1
% to 4) or we trigger on radii around points. If you uncomment the line 
% below, it triggers based on segment transition. Both circle and segment
% triggers could be used together in theory, but it hasn't been debugged
% yet.
% 
sampleParams.segmentTransition = [1 4; 1 2];

% ----------------------------------------------------------
% Parameters for selecting trajectory type to sample
% ---------------------------------------------------------
% Which trajectory type to sample?
sampleParams.trajbound_type = 1 ;            % 0 denotes outbound


% ---------------------------------------------------------------------
% Pameters for controlling edge mode, i.e. triggering on entrance/exit
% ----------------------------------------------------------------------
% Edge mode refers to a mode where we sample from the edges of a choice
% region. Adding it into the struct activates it. Placing a window subfield
% controlls the size of the window in front and behind sample region
% entrance or exit. Its unit is frames.  For 30hz sample rate, [15 15]
% grabs 15 frames in front and behind boundary crossing. entranceOrExit
% subfield controls whether to sample entrance or exit.
 sampleParams.edgeMode.window = [120 120];
 
 sampleParams.edgeMode.entranceOrExit = 'entrance';
 

 % --------------------------------------------------------------------
 % Parmeters for controlling which data to acquire spec or coheregrams
 % ------------------------------------------------------------------------

animal_set = {'HPa'};       
day_set = 1:8;			% set of days to analyze for all animals ...
epoch_set = [2 4];		% set of epochs, except exceptions described in EnforceException
tetrode_set = [1];
tetrode_set2 = [9];

averaged_trials = 'both';

% ----------------------------------------------------------------------
% Parameters for controlling what data to window, and how to pad samples
% -----------------------------------------------------------------------

% specify which electrophysiology data to window!
paramSet.datType = 'eeggnd';	% this can read any wave data type

% specify padding if any. gatherWindowsOfData requires NaN padding right
% now, as this tells lets downstream code quickly ignore parts of the eeg
% data that are not relevant to sampling above.
processOpt.windowPadding = NaN;

%%%%%%%% PRE-PROCESSING SUB-SECTION %%%%%%%%%
paramSet.sampleParams = sampleParams;
% set .animals field to contain who, which day, which epoch, and which
% tetrodes
for a = 1:numel(animal_set)
	paramSet.animals.(animal_set{a}).days = day_set;
	paramSet.animals.(animal_set{a}).epochs = epoch_set;
	paramSet.animals.(animal_set{a}).tetrodes = tetrode_set;
    if exist('tetrode_set2','var')
        paramSet.animals.(animal_set{a}).tetrodes2 = tetrode_set2;
	end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% ---------------------
% Where to save data
% ---------------------
saveFolder = ['./'];

% ---------------------
% Processing options -- whether to output to file, to RAM, or plot
% ---------------------

processOpt.output = true; processOpt.save = false;
processOpt.plot = false;					% Controls plotting during spectrogram extraction -- Section D plots now, so this is an easter egg.
paramSet.processOpt = processOpt;


 

%% A. Gather Windows of Data

disp('Acquiring windows of data at requested sample points...');

% Acquire from first set of tetrodes

paramSet.processOpt.otherTetrodes = false;
[acquisition beh_data]= gatherWindowsOfData(saveFolder, paramSet);

if exist('tetrode_set2','var')		% Acquire for TetrodeY Set, if user asked for it
    paramSet.processOpt.otherTetrodes = true;
    [acquisition2 beh_data2] = gatherWindowsOfData(saveFolder, paramSet);
end

%% B.1 Generate Spectrograms

disp('Generating spec- or coherograms...');

if exist('tetrode_set2','var')		% TETRODE PAIRS - Coherence
    grams = generate_xGrams(acquisition,paramSet,acquisition2);
else								% TETRODE SET	- Spectrogram
    grams = generate_xGrams(acquisition,paramSet);
end

%% B.2 Clear RAM after Spectrogram Creation
clear acquisition acquisition2;


%% C. Average Spectrograms/Coherograms

disp('Averaging data...');

if exist('tetrode_set2','var')
    paramSet.coherograms=true;
end

paramSet.average = {'trial'};

avg_grams = averageAcross(grams,paramSet);

%% E. Analyze Spectrograms/Coherograms Components
% This script in this section are temporary and will be replaced by a
% better-designed, more well-commented function.

disp('Grouping desired frequencies and averaging per day...');

% Place desired bandwidth here
paramSet.lower_freq = 6;
paramSet.upper_freq = 12;
paramSet.estimate_best_freq = true;

[grams S_summary C_summary] = ...
	meanInFreqBand(grams, paramSet);
[avg_grams] = ...
	meanInFreqBand(avg_grams, paramSet);


%% D. Plot and Save Spectrograms/Coherograms

disp('Plotting and saving data...');

% --------------
% Select plot types ... comment out unwanted types
% ---------------
paramSet.coherograms		= true;
paramSet.plotAvgVelocity	= true;
paramSet.plotPositions		= true;
paramSet.plotStrongestBand	= true;
% ---------------
    
for trials = [true false]
	paramSet.trials = trials;
	if trials; dataToPlot = grams; else; dataToPlot = avg_grams; end
	plotAndSave2(dataToPlot,paramSet,beh_data);
end


disp('FINISHED DAY');