% PLI across trials and relative change in envelope amplitude time-locked to the bumps, for paper figure
%addpath('/home/p277634/Documents/MATLAB/eeglab14_1_2b/')

clear all
close all
clc

bln     = 40;
nroi    = 68;
win = [100,100]; % time window on the left and right of the stage onset on samples

dataPath = './data';
dataFile = '/hmmBu4RroiAveMap3StagBL.mat';

load('./data/mapFS2DTI.mat')
load('./data/FCstages_R.mat', 'fcTh')
fcTh = logical(fcTh ~= 0 );

load([dataPath dataFile],'proBump', 'x','y','cond', 'subj')
load('./data/thetaROIs_R.mat', 'roiaveR',  'yR','xR')
% get bump locations
[mOnset, onset, stages, mStage] = getDurations(proBump,x,y); % proBump cell(3,3)
cond = cond;
duraByCond = cell(4,1);
for i = 1:4
    duraByCond{i} = stages(cond==i,:);
end
info = {'from: saveAcrossTrialsPLI4paper.m, stage duration by conditions'};

%save('/dataSave/stageDurationByCondition.mat','duraByCond','info')

onsetN = round(onset/10+bln);
lens = y - x + 1;
lensR = yR - xR + 1;
nroi = 68;
nTr  = length(xR);
nSj  = max(subj);
nStg = size(onsetN,2)-1;
stageIXs = [2,3,4,5];
pairs = combnk([1:nroi],2);

enveZS = zeros(sum(lensR),nroi,'single');

phase = zeros(sum(lensR),nroi,'single');

for tr = 1:nTr
    data_   = padHilbert(roiaveR(xR(tr):yR(tr),:),40);
    phase(xR(tr):yR(tr),:)   = angle(data_);
    % enelope
    envelope = abs(data_);
    envMean = mean(envelope(40+1:end-40,:),1);
    envSTD = std(envelope(40+1:end-40,:),[],1);
    enveZS(xR(tr):yR(tr),:) = (envelope - envMean) ./ envSTD;
end
%% FC, PLI
phZ = exp(1i* single(phase) );
phFC = sign( imag( phZ(:, pairs(:,1)) .* conj(phZ(:, pairs(:,2))) )) ;


[pliW, pliWsd]=getERP_SUBJwindow(phFC,stageIXs,win, onsetN, xR, yR,subj);

vis1ERPFCwindows(pliW, fcTh(stageIXs+1,:), win(1),1)
vis1ERPFCwindows(pliW, ~fcTh(stageIXs+1,:), win(1),1)


[envZSW, envZSWsd]=getERP_SUBJwindow(enveZS,stageIXs,win, onsetN, xR, yR,subj);
visERPwindows(envZSW(:,map.raw2cross,:), win(1),1)

envZSW = envZSW(:,map.raw2cross,:);
envZSWsd = envZSWsd(:,map.raw2cross,:);

info = {'from: saveAcrossTrialsPLI4paper.m, PLI and z-scored envelopes like an erp'};

%save('/dataSave/PLI8ENVbumperp.mat','win','pliW','pliWsd','fcTh','envZSW', 'info')

% save('/dataSave/PLIacrossTials.mat','phFC','stageIXs','onsetN','xR','yR','subj','-v7.3')