V1-V4-LFPs-and-Visual-Attention/Code/getSubjectData.m

function [subjectData] = getSubjectData (sSubjectName, sVisualArea, sPenNumber, sDataType, sSelectedTimeWins)

% varargin = sSubjectName, sVisualArea, sPenNumber, sDataType, sSelectedTimeWins, sSorted,
%                                                                                               sSNRThreshold)
% gets all of the data you may want for a selected subject
% DEPENDS ON getSubjectInfos
%
% sSubjectName      [Jones, Wyman, Taylor] *REQUIRED FIELD
% sVisualArea       [V1, V4] *REQUIRED FIELD
% sPenNumber        [double, GOOD, ALL] ALL is default
% sDataType         [LFPs, MUAEs, ALL] ALL is default 
% sSelectedTimeWins [PreStim, PostStim, Stationary, PostCue, PeFirstDim, PreSecondDim, PreThirdDim, ALL] MUTUALLY EXCLUSIVE, ALL is default

%% PARSING INPUT PARAMETERS AND DEFAULT ASSIGNMENTS

if nargin<5
    if nargin<4
        if nargin<3
            if nargin<2
                error('You should at least select a Subject Name and a Visual Area.');
            end
            sPenNumber='ALL';
        end
        sDataType='ALL';
    end
    sSelectedTimeWins='ALL';
end

%% CHECKING SUBJECT NAME
if ~sum(cellfun(@(x) strcmp(sSubjectName,x),{'Wyman','Taylor','monkey 1','monkey 2'}))
    error(['The selected Subject Name "' sSubjectName '" is not valid.']);
elseif strcmpi(sSubjectName,'monkey 1'); sSubjectName='Wyman'; 
elseif strcmpi(sSubjectName,'monkey 2'); sSubjectName='Taylor'; 
end
%% CHECKING VISUAL AREA
if ~sum(cellfun(@(x) strcmp(sVisualArea,x),{'V1','V4'}))
    error(['The selected Visual Area "' sVisualArea '" is not valid.']);
end

%% PARSING PEN NUMBERS
subjectInfos=getSubjectInfos(sSubjectName);

if strcmp(sPenNumber,'ALL')
    penValues=subjectInfos.penIDs;
    penIndices=1:length(penValues);
elseif strcmp(sPenNumber,'GOOD')
    penVec=subjectInfos.penIDs;
    px=1;
    for pp=1:length(penVec)
        if strcmp(subjectInfos.penInfos(pp).([sVisualArea 'Contacts']).Quality,'BAD')
            warning(['PEN ID ' num2str(penVec(pp)) ' was discarded, ' sSubjectName ' ' sVisualArea ' data have BAD quality.']);
        else
            penIndices(px)=pp;
            penValues(px)=penVec(pp);
            px=px+1;
        end
    end
else % if you provide a penID or interval of penIDs
    penVec=str2num(sPenNumber);
    
    px=1;
    penIndices=[];
    
    for pv=1:length(penVec)
        penIndex=find(subjectInfos.penIDs==penVec(pv));
        if isempty(penIndex)
            warning(['PEN ID ' num2str(penVec(pv)) ' was discarded, not valid for ' sSubjectName ' ' sVisualArea '.']);
        else
            penIndices(px)=penIndex;
            penValues(px)=penVec(pv);
            px=px+1;
        end
    end
end

%% CHECKING PEN NUMBERS - DISCARDING NO V1/V4 DATA
if ~isempty(penIndices)
    rmPenIndices=zeros(1,length(penIndices));
    for pv=1:length(penIndices)
        if strcmp(subjectInfos.penInfos(penIndices(pv)).([sVisualArea 'Contacts']).Quality,['NO ' sVisualArea ' DATA']) % REJECT (MAY BE IMPROVED)
            warning(['NO ' sVisualArea ' DATA for ' sSubjectName ' PEN ' num2str(penValues(pv))]);
            rmPenIndices(pv)=1;
        end
    end
    penIndices(logical(rmPenIndices))=[];
    penValues(logical(rmPenIndices))=[];
    if isempty(penIndices)
        error(['None of the selected PEN IDs "' sPenNumber '" is valid for ' sSubjectName ' ' sVisualArea '.']);
    end
else
    error(['None of the selected PEN IDs "' sPenNumber '" is valid for ' sSubjectName ' ' sVisualArea '.']);
end

%% CHECKING DATATYPE
if ~sum(cellfun(@(x) strcmp(sDataType,x),{'LFPs','iCSDs','MUAes','ALL'}))
    error(['The selected Data Type "' sDataType '" is not valid.']);
end

%% CHECKING THE TIME WINDOWS
allTimeWins={'PreStim','PostStim','Stationary','PostCue','PreFirstDim','PreSecondDim','PreThirdDim','ALL'};
% Parsing selected time windows
if ~strcmp(sSelectedTimeWins,'ALL')
    error('Selecting a single timewin is not supported yet, write some code');
end
if ~sum(cellfun(@(x) strcmp(sSelectedTimeWins,x),allTimeWins)) 
    error(['The selected Time Window "' sSelectedTimeWins '" is not valid.']);
end

%% INITIALIZE THE DATA STRUCTURE
subjectData.subjectName=sSubjectName;
subjectData.penIDs=subjectInfos.penIDs(penIndices);

for pp=1:length(penIndices)
    
    %% PARSING LAYERS TO GET DATA FROM OR PARSING SNRs - EVENTUALLY LATER
    
    %% GETTING LFPs
    if  strcmp(sDataType,'LFPs') || strcmp(sDataType,'ALL')
        disp(['Loading ' sSelectedTimeWins ' LFPs for ' sSubjectName ' ' sVisualArea ' PEN ' num2str(penValues(pp))]);
        LLStr=load(subjectInfos.penInfos(penIndices(pp)).selectedTimeWinsFilePaths.([sVisualArea 'Contacts']).LFPs);
        if ~isempty(LLStr.LfpStruct)
            subjectData.LfpStruct(pp).Sorted=LLStr.LfpStruct.Sorted;
        end
        subjectData.LfpStruct(pp).penNum=subjectInfos.penIDs(penIndices(pp));
        clear LLStr
    end
    
    
    %% GETTING MUAes
    if  strcmp(sDataType,'MUAEs') || strcmp(sDataType,'ALL')
        disp(['Loading ' sSelectedTimeWins ' MUAs for ' sSubjectName ' ' sVisualArea ' PEN ' num2str(penValues(pp))]);
        MMstr=load(subjectInfos.penInfos(penIndices(pp)).selectedTimeWinsFilePaths.([sVisualArea 'Contacts']).MUAs);
        if ~isempty(MMstr.MUAStruct)
            subjectData.MUAStruct(pp).Sorted=MMstr.MUAStruct.Sorted;
        end
        subjectData.MUAStruct(pp).penNum=subjectInfos.penIDs(penIndices(pp));
        clear MMstr
    end
    
        
    %% Appending penInfos
    subjectData.penInfos(pp)=subjectInfos.penInfos(penIndices(pp));
     
end




end