%% Summary:
% 
% This script opens and updates all selected files to contain the correct
% Ca2+ transient frequencies during rest for motor trials.
% 
% Inputs:
% 
% User-selected .mat file names
%
% Outputs:
% 
% Updated data structure, re-saved under its original name in the .mat file
% 
% Author: Jeffrey March, 2018

%% Main Code

[trials, pathname] = uigetfile('*.mat','MultiSelect','on');

if ~iscell(trials)
    tempTrials = trials;
    trials = cell(1);
    trials{1} = tempTrials;
end

cd(pathname)
totalFiles = 0;

MINW = 4;
noiseThresh = 0.4;
stdAway = 5;
isMoving = 0;

roi = {};

for trial = 1:length(trials);
	load(trials{trial});
	totalFiles = totalFiles + 1
    
    if isfield(data, 'subVideoRestOnsets')
    
    roi{1} = data.dF1;
    roi{2} = data.dF2;
      
    for cellType = 1:2;
        if isempty(roi{cellType}.dF)
            continue
        end

        roi2 = zeros(size(roi{cellType}.dF));
        % Z-scoring Cells
        for nCell = 1:size(roi{cellType}.dF,1)
            roi2(nCell,:) = smooth(roi{cellType}.dF(nCell,:),5)';
        end
        
        roi{cellType}.motorFreqRest = zeros(size(roi{cellType}.dF,1),1);
        numSpikesCell = zeros(size(roi{cellType}.dF,1),2);
           
        roiData = data;
        roiData.indOnsets = data.subVideoRestOnsets;
        roiData.indOffsets = data.subVideoRestOffsets;
        
        totalTime = sum(roiData.indOffsets-roiData.indOnsets)/roiData.framerate;
        
        for onset = 1:length(roiData.indOnsets)
            onsetMat = roi2(:,roiData.indOnsets(onset):roiData.indOffsets(onset));
            for nCell = 1:size(onsetMat,1)
                warning('OFF');
                MPP = mean(roi2(nCell,roi2(nCell,:) < noiseThresh)) + stdAway*std(roi2(nCell,roi2(nCell,:) < noiseThresh));
                MPH = MPP;
                [tempPKS, tempLOCS] = findpeaks(onsetMat(nCell,:),'MinPeakProminence', MPP, 'MinPeakHeight', MPH, 'MinPeakWidth', MINW);
                numSpikesCell(nCell, isMoving + 1) =  numSpikesCell(nCell, isMoving + 1) + length(tempLOCS);
            end
        end
        
        roi{cellType}.motorFreqRest(:,isMoving + 1) = numSpikesCell(:,isMoving + 1)/totalTime;
        
    end
    
    data.dF1 = roi{1};
    data.dF2 = roi{2};
    
    save(trials{trial},'data')
    end
                    
end