lilrig video alignment is 1-2 s delayed

[takacsflora]

Any data coming from the lilrig has some delays compared to the correct alignement. I believe it is correct because of the aud evoked movement is apparent only if i align with the lilrig code.

Example dataset: \\znas\FT009\2021-01-20\8
Lilrig time alignement: face_timeStamps.mat

lilrig alignment code:

function alignVideo_lilrig(mouseName, thisDate, expNum, movieName, varargin)
% function alignVideo(mouseName, thisDate, expNum, movieName[, params])
% reposName = 'master';
% timelineExpNums = expNum;
% tlSyncName = 'camSync';
% silentMode = true;
% recompute = false;
% nFramesToLoad = 3000;
% 
switch movieName
    case 'eye'
        strobeName = 'eyeCamStrobe';
    case 'face'
        strobeName = 'faceCamStrobe';
    case 'fastface'
        strobeName = 'faceCamStrobe';
    otherwise
        strobeName = 'unknown';
end
% 
% if ~isempty(varargin)
%     params = varargin{1};
%     if isfield(params, 'reposName')
%         reposName = params.reposName;
%     end
%     if isfield(params, 'timelineExpNums')
%         timelineExpNums = params.timelineExpNums;
%     end
%     if isfield(params, 'strobeName')
%         strobeName = params.strobeName;
%     end
%     if isfield(params, 'tlSyncName')
%         tlSyncName = params.tlSyncName;
%     end
%     if isfield(params, 'silentMode')
%         silentMode = params.silentMode;
%     end
%     if isfield(params, 'recompute')
%         recompute = params.recompute;
%     end
%     if isfield(params, 'nFramesToLoad')
%         nFramesToLoad = params.nFramesToLoad;
%     end
% end
% 
% assert(~strcmp(strobeName, 'unknown'), 'please provide params.strobeName');
% 
% %%
% 
% % mouseName = 'Dam';
% % thisDate = '2016-08-26';
% % expNum = 1;
% % movieName = 'eye';
% 
% movieDir = fileparts(dat.expFilePath(mouseName, thisDate, expNum, 'eyetracking', reposName));
% intensFile = fullfile(fileparts(dat.expFilePath(mouseName, thisDate, expNum, 'eyetracking', reposName)), ...
%     [movieName '_avgIntensity.mat']);
% 
% 
% if recompute && exist(intensFile, 'file')
%     delete(intensFile);
% end
%%
% expNum=7;
% mouseName='FT009'; 
% thisDate='2021-01-20'; 
%movieName='face'; 

%%
timelineExpNums = expNum;
tlSyncName = 'camSync';
recompute = false;
nFramesToLoad = 3000;
%%

% if isfield(params, 'recompute')
%     recompute = params.recompute;
% end
% if isfield(params, 'nFramesToLoad')
%     nFramesToLoad = params.nFramesToLoad;
% end
%%
folderTools = 'C:\Users\Flora\Documents\Github';
addpath(genpath(fullfile(folderTools, 'AV_passive')));
addpath(genpath(fullfile(folderTools, 'npy-matlab')));
addpath(genpath(fullfile(folderTools, 'kilotrodeRig')));
addpath(genpath(fullfile(folderTools, 'spikes')));
%%
% should have a way to generalize (dat.expFilePath should be helpful,
% but isn't working with the current split in servers...
% Should insist a bit more though)
server = '\\znas.cortexlab.net\Subjects\';
if ~exist(fullfile(server,mouseName, thisDate, num2str(expNum)),'dir')
    server = '\\128.40.224.65\Subjects\';
end
movieDir = fullfile(server, mouseName, thisDate, num2str(expNum));
intensFile = fullfile(server, mouseName, thisDate, num2str(expNum), ...
    [movieName '_avgIntensity.mat']);
% have to deal with the "lastFrames" file. Pretty annoying.
intensFile_lastFrames = fullfile(server, mouseName, thisDate, num2str(expNum), ...
    [movieName '_lastFrames_avgIntensity.mat']);

if recompute && exist(intensFile, 'file')
    delete(intensFile);
end
if recompute && exist(intensFile_lastFrames, 'file')
    delete(intensFile_lastFrames);
end
%%


% if ~exist(intensFile, 'file')            
%     fprintf(1, 'computing average intensity of first/last frames...\n');
%     if silentMode
%         ROI = avgMovieIntensity(movieDir, movieName, [], true, [], [], nFramesToLoad);
%     else
%         ROI = avgMovieIntensity(movieDir, movieName, [], true, 'ask', [], nFramesToLoad);
%     end
% end
if ~exist(intensFile, 'file')
    fprintf(1, 'computing average intensity of first/last frames...\n');
    ROI = avgMovieIntensity(movieDir, movieName, [], true, [], [], nFramesToLoad);
end

fprintf(1, 'loading avg intensity\n');
load(intensFile)

%% first detect the pulses in the avgIntensity trace

expectedNumSyncs = numel(timelineExpNums)*2; % one at the beginning and end of each timeline file

vidIntensThresh = [15 20];
[intensTimes, intensUp, intensDown] = schmittTimes(1:numel(avgIntensity), avgIntensity, vidIntensThresh);
attemptNum = 1; loadAttemptNum = 1;
while(numel(intensDown)~=expectedNumSyncs)
    % try some different approaches to get the right threshold
    % automatically...
    switch attemptNum
        case 1
            vidIntensThresh = min(avgIntensity)*[1.2 1.4];
        case 2
            intensMed = median(avgIntensity);
            intensMin = min(avgIntensity);
            vidIntensThresh = intensMin+(intensMed-intensMin)*[0.4 0.6];
        case 3
            vidIntensThresh = intensMin+(intensMed-intensMin)*[0.15 0.25];
        otherwise
            switch loadAttemptNum
                case 1
                    fprintf(1, 'trying to load more frames...\n')
                    avgMovieIntensity(movieDir, movieName, [], true, ROI, [], 10000);
                    load(intensFile)
                    attemptNum = 0;
                case 2
                    fprintf(1, 'trying to load all frames...\n')
                    avgMovieIntensity(movieDir, movieName, [], true, ROI);
                    load(intensFile)
                    attemptNum = 0;
                otherwise
                    fprintf(1, 'cannot find a threshold that works. You tell me...\n');
                    figure; plot(avgIntensity);
                    keyboard
            end
            loadAttemptNum = loadAttemptNum+1;
    end
    
    [intensTimes, intensUp, intensDown] = schmittTimes(1:numel(avgIntensity), avgIntensity, vidIntensThresh);
    attemptNum = attemptNum +1;
end
assert(numel(intensDown)==expectedNumSyncs, 'could not find correct number of syncs');
fprintf(1, 'found the sync pulses in the video\n');

%%
% usually these are TTL and pretty much anything between 0 adn 5 will work
% but here I use a small value because for the whisker camera I didn't have
% TTL so this works for that too.

% need to search for this in a more complex manner - maybe kmeans see at
% the bottom


%tlStrobeThresh = [0.08 0.25]; 


tlSyncThresh = [2 2.5];


tVid = NaN(size(avgIntensity));

for tInd = 1:numel(timelineExpNums)
    
    fprintf(1, 'loading timeline\n');
    %load(dat.expFilePath(mouseName, thisDate, timelineExpNums(tInd), 'Timeline', reposName));
    % load the timeline in another way.... 
    ops.root=sprintf('%s\\%s\\%s',server,mouseName,thisDate);

    load(fullfile(ops.root,sprintf('%.0f\\%s_%.0f_%s_Timeline.mat',expNum,thisDate,expNum,mouseName)));


    %check strobe counts against the number of frames between sync events that
    %were actually in the video

    % find the timeline samples where cam sync pulses started (went
    % from 0 to 5V)
    syncIndex = find(strcmp({Timeline.hw.inputs.name}, tlSyncName));
    tlSync = Timeline.rawDAQData(:,syncIndex);
    [~, tlSyncOnSamps, ~] = schmittTimes(1:numel(tlSync), tlSync, tlSyncThresh);

    % find the strobe times for the camera
    strobeIndex = find(strcmp({Timeline.hw.inputs.name}, strobeName));
    tlStrobe = Timeline.rawDAQData(:,strobeIndex);
    
    %%
    [~,thresh]=kmeans(tlStrobe,5); 
    tlStrobeThresh = [min(thresh) + range(thresh)*0.2;  max(thresh) - range(thresh)*0.2];
    %%
    [~,strobeSamps,~] = schmittTimes(1:numel(tlStrobe), tlStrobe, tlStrobeThresh);
    
    vidSyncOnFrames = intensUp([1 2]+(tInd-1)*2);

    numStrobesFoundBetweenSyncs = sum(strobeSamps>=tlSyncOnSamps(1) & strobeSamps<tlSyncOnSamps(2));
    numFramesFoundBetweenSyncs = diff(vidSyncOnFrames);

    framesMissed = numStrobesFoundBetweenSyncs-numFramesFoundBetweenSyncs;

    %unique(diff(strobeSamps))/Timeline.hw.daqSampleRate

    framesMissedPerSec = framesMissed/(diff(tlSyncOnSamps)/Timeline.hw.daqSampleRate);
    
    fprintf(1, 'missed %d frames, for %.2f frames missed/sec\n', framesMissed, framesMissedPerSec);
    if abs(framesMissed)<=2 && abs(framesMissed)>0
        fprintf(1, 'values of +/-2 are normal, can happen when you get exposures across part of the cam sync onsets\n');
    elseif abs(framesMissed)>2
        fprintf(1, 'too many missed frames! Figure out how to reduce it. Will interpolate frame times linearly.\n');
    end
    
    % get the actual timestamps for the video in question. 
    % need to make this a function

    tt = Timeline.rawDAQTimestamps;
    
    if framesMissed==0
        % best case, use the strobe times exactly
        tVid(vidSyncOnFrames(1)+1:vidSyncOnFrames(2)) = ...
            tt(strobeSamps(strobeSamps>=tlSyncOnSamps(1) & strobeSamps<tlSyncOnSamps(2)));
    else
        % otherwise interpolate from first to last
        tVid(vidSyncOnFrames(1)+1:vidSyncOnFrames(2)) = ...
            linspace(tt(strobeSamps(find(strobeSamps>=tlSyncOnSamps(1),1))), ...
            tt(strobeSamps(find(strobeSamps<tlSyncOnSamps(2),1, 'last'))), ...
            numel(vidSyncOnFrames(1)+1:vidSyncOnFrames(2)));
    end
    
    % fill in the timestamps before and after sync pulses
    vidFs = 1/(mean(diff(strobeSamps))/Timeline.hw.daqSampleRate);
    
    if tInd==1
        % only fill in before sync pulses if it's the first timeline file,
        % otherwise we'll overwrite the previous timestamps.
        tVid(1:vidSyncOnFrames(1)) = (-vidSyncOnFrames(1):-1)/vidFs+tVid(vidSyncOnFrames(1)+1);
    end
    tVid(vidSyncOnFrames(2)+1:end) = (1:numel(tVid(vidSyncOnFrames(2)+1:end)))/vidFs+tVid(vidSyncOnFrames(2));
    
end


exploc=sprintf('%s\\%.0f',ops.root,expNum); 

saveName = fullfile(exploc, ...
    [movieName '_timeStamps.mat']);

fprintf(1, 'saving to %s\n', saveName)

save(saveName, 'tVid', 'vidFs');

[takacsflora]

this is hacked currently by running the lilrig alingment directly on the lilrig videos