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Im2P_CollectDataVR_New.m
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Im2P_CollectDataVR_New.m
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%Parameters
TopFolder = 'Z:\Dudi\Imaging\2Photon\Dudi_setup\';
Folders = {[TopFolder, 'DSX_VR2P_Auditory']};
SaveTo = fullfile(Folders{1},'mAllData_VR_New.mat');
mAllData = cell2table(cell(1,16),'VariableNames',...
{'StimName', 'Folder', 'Gender', 'StimNumber', 'FramesPerSecond', 'SamplesPerSeconds', 'FrameStartStim', 'ROIname','ROISide',...
'GreenSignal_FinROI','GreenSignal_DFFinROI','RedSignal','GreenSignal_MaxDFF','GreenSignal_SumDFF','MaxDFFAllStim','MaxSumDFFAllStim'});
nLine = 1;
for nFolder = 1:size(Folders,2)
MasterFolder = Folders{nFolder};
CurrDir = cd(MasterFolder);
XLSfile = dir('DSX*.xlsx*');
if isempty(XLSfile) || size(XLSfile,1)>1
disp('Need exactly 1 excell file in the master folder. Returning.')
cd(CurrDir), return
end
XLSfile = fullfile(MasterFolder,XLSfile(1).name);
Table = readtable(XLSfile);
vSessions = find(Table.USE==1);%number of session in the table to go over
for nSession = vSessions'
Use = Table.USE(nSession);
Date = Table.Date(nSession);
Session = Table.Session(nSession);
Folder = fullfile(MasterFolder,num2str(Date),[num2str(Date),'_',num2str(Session)]);
cd(Folder)
File_OneSession = dir('*OneSession*'); File_OneSession = File_OneSession(1).name;
if ~exist(File_OneSession,'file')
disp(['No structure sOneSession for folder ',Folder,' . Skipping.'])
cd(MasterFolder), continue
end
nGender = Table.Gender{nSession};
if any(strcmp(Table.Properties.VariableNames,'Housed')) && ~isempty(Table.Housed{nSession})
nHoused = Table.Housed{nSession};
else%default
nHoused = 'S';
end
load(File_OneSession)
%Check that all the relevant fields exist and not empty
IsAllFields(1) = isfield(sOneSession,'stimAll') && ~isempty(sOneSession.stimAll);
IsAllFields(2) = isfield(sOneSession,'stimOrder') && ~isempty(sOneSession.stimOrder);
IsAllFields(3) = isfield(sOneSession,'StimParams') && ~isempty(sOneSession.StimParams);
IsAllFields(4) = isfield(sOneSession,'GreenSignal') && ~isempty(sOneSession.GreenSignal);
if ~all(IsAllFields)
disp(['Missing fields in sOneSession in folder ',Folder,' . Skipping.'])
cd(MasterFolder), continue
end
disp(['Extracting data from session ',Folder])
%Speeds from FicTrac
x = sOneSession.FicTracOUT(:,1);
y = sOneSession.FicTracOUT(:,1:4);
qx = 1:sOneSession.FicTracOUT(end,1);
SPEEDS_FromFicTrac = interp1(x,y,qx);
%Find number of stimuli types and how many trials to take
AllStim = size(sOneSession.stimAll,2);
sOneSession.LastStimToUse = min(size(sOneSession.GreenSignal{1}.DFFinROI,2), Use*AllStim);
%Frames per second
SamplesPerSeconds = sOneSession.LOGfile{2,2};
FramesPerSecond = SamplesPerSeconds/median(diff(sOneSession.SamplesStart_ImFrames(:,1)));
for ROItoUSE = 1:size(sOneSession.GreenSignal,2)
%Find max DFF for normalization
MaxDFF = 0;
for nStim = 1:sOneSession.LastStimToUse
if MaxDFF < sOneSession.GreenSignal{ROItoUSE}.MaxDFF{nStim}, MaxDFF = sOneSession.GreenSignal{ROItoUSE}.MaxDFF{nStim};end
end
%find MaxSum_DFF
MaxSumDFF = 0;
for nStim = 1:sOneSession.LastStimToUse
StartStim = floor(sOneSession.LOGfile{nStim,4}/1000*FramesPerSecond);
if MaxSumDFF < sum(sOneSession.GreenSignal{ROItoUSE}.DFFinROI{nStim}(StartStim:end))
MaxSumDFF = sum(sOneSession.GreenSignal{ROItoUSE}.DFFinROI{nStim}(StartStim:end));
end
end
for nStim = 1:sOneSession.LastStimToUse
FrameStartStim = floor(sOneSession.LOGfile{nStim,4}/1000*FramesPerSecond);
ROIname = sOneSession.ROIname{1};
if strcmp(ROIname,'LPC'), ROIname = 'Ring';end
mAllData.Folder{nLine,1} = sOneSession.Folder;
mAllData.StimName{nLine,1} = sOneSession.LOGfile{nStim,1}{1};
mAllData.Intensity{nLine,1} = sOneSession.LOGfile.intensity{nStim,1};
mAllData.Gender{nLine,1} = nGender;
mAllData.Housed{nLine,1} = nHoused;
mAllData.StimNumber{nLine,1} = nStim;
mAllData.FramesPerSecond{nLine,1} = FramesPerSecond;
mAllData.SamplesPerSeconds{nLine,1} = SamplesPerSeconds;
mAllData.FrameStartStim{nLine,1} = FrameStartStim;
mAllData.ROIname{nLine,1} = ROIname;
mAllData.ROISide{nLine,1} = sOneSession.ROISide{1};
mAllData.Stim{nLine,1} = sOneSession.stimAll{sOneSession.stimOrder(nStim)}(:,1);
mAllData.GreenSignal_FinROI{nLine} = sOneSession.GreenSignal{ROItoUSE}.FinROI{nStim};
mAllData.GreenSignal_DFFinROI{nLine} = sOneSession.GreenSignal{ROItoUSE}.DFFinROI{nStim};
mAllData.RedSignal{nLine} = sOneSession.RedSignal{ROItoUSE}.FinROI{nStim};
mAllData.GreenSignal_MaxDFF{nLine,1} = sOneSession.GreenSignal{ROItoUSE}.MaxDFF{nStim};
mAllData.GreenSignal_SumDFF{nLine,1} =...
sum(sOneSession.GreenSignal{ROItoUSE}.DFFinROI{nStim}(FrameStartStim:end));
mAllData.MaxDFFAllStim{nLine,1} = MaxDFF;
mAllData.MaxSumDFFAllStim{nLine,1} = MaxSumDFF;
%% Add stim ON/OFF times
STIMON_sample = find(sOneSession.stimAll{nStim}(:,1)>0,1);
STIMOFF_sample = find(sOneSession.stimAll{nStim}(STIMON_sample:end,1)>0,1,'Last')+STIMON_sample;
%Find the ImFrame number when StimOn
SamplesStart_ImFrames_OneSession = sOneSession.SamplesStart_ImFrames(sOneSession.SamplesStart_ImFrames(:,2)==nStim,:);
%stim ON
SampleFromStimON = abs((SamplesStart_ImFrames_OneSession(:,1) - SamplesStart_ImFrames_OneSession(1,1)) - STIMON_sample);
STIMON_ImFrame = find(SampleFromStimON == min(SampleFromStimON),1);
%stim OFF
SampleFromStimOFF = abs((SamplesStart_ImFrames_OneSession(:,1) - SamplesStart_ImFrames_OneSession(1,1)) - STIMOFF_sample);
STIMOFF_ImFrame = find(SampleFromStimOFF == min(SampleFromStimOFF),1);
%Find the frames in the fictrac output [OneSession.FicTracOUT(:,1)] that correspont to STIMON / STIMOFF
%fictrac frame at Start session
SampleAtStartTrial = sOneSession.StartStim(nStim);
temp = abs(SampleAtStartTrial - sOneSession.Samples_AVIFrames(:,2));
StartTrial_FicTracFrame = sOneSession.Samples_AVIFrames(find(temp == min(temp),1),1);
%fictrac frame at End Session
SampleAtEndTrial = sOneSession.StartStim(nStim) + size(sOneSession.stimAll{sOneSession.stimOrder(nStim)},1);
temp = abs(SampleAtEndTrial - sOneSession.Samples_AVIFrames(:,2));
EndTrial_FicTracFrame = sOneSession.Samples_AVIFrames(find(temp == min(temp),1),1);
%Stim ON
SampleAtStartStim = sOneSession.StartStim(nStim)+STIMON_sample;
temp = abs(SampleAtStartStim - sOneSession.Samples_AVIFrames(:,2));
STIMON_FicTracFrame = sOneSession.Samples_AVIFrames(find(temp == min(temp),1),1);
%Stim OFF
SampleAtEndStim = sOneSession.StartStim(nStim)+STIMOFF_sample;
temp = abs(SampleAtEndStim - sOneSession.Samples_AVIFrames(:,2));
STIMOFF_FicTracFrame = sOneSession.Samples_AVIFrames(find(temp == min(temp),1),1);
mAllData.STIMON_sample{nLine,1} = STIMON_sample;
mAllData.STIMOFF_sample{nLine,1} = STIMOFF_sample;
mAllData.STIMON_ImFrame{nLine,1} = STIMON_ImFrame;
mAllData.STIMOFF_ImFrame{nLine,1} = STIMOFF_ImFrame;
mAllData.StartTrial_FicTracFrame{nLine,1} = StartTrial_FicTracFrame;
mAllData.EndTrial_FicTracFrame{nLine,1} = EndTrial_FicTracFrame;
mAllData.STIMON_FicTracFrame{nLine,1} = STIMON_FicTracFrame;
mAllData.STIMOFF_FicTracFrame{nLine,1} = STIMOFF_FicTracFrame;
START = find(sOneSession.FicTracOUT(:,1)>=StartTrial_FicTracFrame,1);
END = find(sOneSession.FicTracOUT(:,1)<=EndTrial_FicTracFrame,1,'Last');
mAllData.FicTracSpeed{nLine,1} = SPEEDS_FromFicTrac(START:END,:);
%%
nLine = nLine + 1;
end
cd(MasterFolder)
end
end
cd(MasterFolder)
%if ~exist('./res','dir'), mkdir('res'),end
%cd('res')
save(SaveTo,'mAllData')
cd(CurrDir)
end