extract_time_trace_mp_template.m

%% Add path
addpath('../../neuRoi')
%% Clear variables
clear all
close all
%%
% Step01 Load experiment configuration from file
expName = '20221026_NT0012_f3_13dpf_testNTvsRModors';
resultDir = fullfile(pwd,'results');
expFilePath = fullfile(resultDir,sprintf('experimentConfig_%s.mat',expName));
foo = load(expFilePath);
myexp = foo.myexp;
nTrials = length(myexp.rawFileList);
disp(myexp.expInfo)

%% Step02 (optional) Sepcify options for opening a trial
myexp.roiDir = myexp.getDefaultDir('roi');

myexp.loadFileType = 'binned';
myexp.trialOptionRaw = struct('process',true,...
                              'noSignalWindow',[1 6],...
                              'intensityOffset',-30);
myexp.trialOptionBinned = struct('process',false,...
                                 'noSignalWindow',[],...
                                 'intensityOffset',-10);

myexp.responseOption = struct('offset',-10,...
                        'fZeroWindow',[1 9],...
                        'responseWindow',[12 20]);
myexp.responseMaxOption = struct('offset',-10,...
                           'fZeroWindow',[3 7],...
                           'slidingWindowSize',5);
myexp.mapsAfterLoading = {'response','responseMax'};
% myexp.mapsAfterLoading = {};

myexp.alignToTemplate = false;


%%  Step03 Open neuRoi GUI
myexp.planeNum = 2;
myexp.mapsAfterLoading = {'response'};
mycon = NrController(myexp);

%% Add local correlation (optional)
mapType = 'localCorrelation';
mapOption = struct('tileSize',32);
trial = myexp.getCurrentTrial();
trial.calculateAndAddNewMap(mapType,mapOption);
%% Copy ROI
trial = myexp.getCurrentTrial();
idx = trial.findRoiByTag(trial.selectedRoiTagArray(1))
roiClipboard = trial.roiArray(idx)

%% Paste ROI
trial = myexp.getCurrentTrial();
trial.addRoi(roiClipboard);

%% Remove very small ROIs generated by false clicking
%% Delete point ROIs
%% Delete ROIs with only one point
% Get current trial
trial = myexp.getCurrentTrial();
roiArray = trial.roiArray;
deleteTagArray = {};
for k = 1:length(roiArray)
    roi = roiArray(k);
    if size(roi.position,1)<2
        deleteTagArray{end+1} = roi.tag;
    end
end
% Delete point ROIs
for k=1:length(deleteTagArray)
    tag = deleteTagArray{k};
    trial.deleteRoi(tag);
end


%% Step04 Extract time trace with template ROI in all trials
% Apply template ROI map and correct ROIs in each trial
% If you accidentally closed the GUI, the following code might
% throw an error. In that case, just run Step01, then continue with
% Step04

for planeNum = 1
    myexp.alignToTemplate = false;
    myexp.trialOptionRaw = struct('process',true,...
                                  'noSignalWindow',[1 6]);
    
    fileIdxList = 1:nTrials;
%     planeNum = myexp.planeNum;
    
    prefix = '';
    appendix = '';
    
    load(strcat(resultDir,'\BUnwarpj\','plane0',num2str(planeNum),'\',strcat(prefix,'Rois',appendix,'.mat')));
    roiFileList=squeeze(struct2cell(RoiArray))';
    plotTrace = true;
    myexp.extractTimeTraceBatch(fileIdxList, ...
                                roiFileList,planeNum, ...
                                plotTrace);
end
% %% Save ROI tags and results directories for each roi to pool later
% planeString = NrModel.getPlaneString(myexp.planeNum);
% resultDirSave= fullfile(myexp.resultDir,'time_trace',planeString); 
% expID = repmat(cellstr(resultDirSave),length(roiArray),1);
% for roiroi=1:length(roiArray)
%     roiID {roiroi,1} = roiArray (roiroi).tag;
% end
% 
% 
% roiIDFilePath = fullfile(resultDirSave, ...
%                            'roiID.mat');
% %save(roiIDFilePath,'roiID','expID','category')
% save(roiIDFilePath,'roiID','expID')
disp("****** done! ********")