analyse_saved_track.m

%% 1. Load tracking
%Open FreezingAnalysis folder
addpath(genpath('.'));

% Load video and tracking
g = mbvid.mbVideoReader('wt80_test_1-10-14.mp4');
load 'wt80_test_1-10-14_tracking.mat' 
tracking.video = g; 
%(you can ignore the following error message: "Warning: While loading an
%object of class 'VideoReader': The filename specified was not found in the
%MATLAB path." - the following steps should still work!)
%% 2. Check tracking parameters
% This is to check that the mouse was successfully tracked (ensure that the mouse is in each of the frames displayed). The montage
% displays every 500th frame between frame 1 and frame 27000.
gpatch = mbvid.patchReader(g,'track',tracking);
gpatch.patchWidth   = 128;
gpatch.patchHeight  = 128;
gpatch.montage('frames',1:500:27000);
%% 3. Compute and plot pixel changes between frames 
% Compute pixel changes between frames. 'compareWith' parameter corresponds
% to the number of frames between the two frames that are being compared
% (i.e. it should be 30 when video is 30 frames per second).
magnitudes = blobTrackMotionVector(tracking.getArray,'compareWith',30);
trackMagnitudes = mbvid.videotrack.scalar('video',g,'data',magnitudes);

% Make interactive plot of pixels changed (y axis) x frame number (x axis).
trackMagnitudes.plot();

%The plot displays pixel changes relative to the frame 30 frames beforehand
%on the y axis and frame number on the x axis. That is, low plateaus
%correspond to little pixel change (= little movement of the mouse).
%It is possible to double click anywhere on the plot, and this will display
%the frame corresponding to the location on which you clicked
%% 4. Find and plot freezing episodes and stimulus trials
% Find all freezing episodes
r = mbvid.freezing.findRegions('videotrack',trackMagnitudes,'addDelay',30,'maxScore',5,'minimumLength',30);

% Plot freezing episodes. Freezing episodes can be inspected (double clicking on the region) and are
% displayed at the frame rate defined by 'r.depictionIntervalInFrames'
r.depictionIntervalInFrames = 10;

% Freezing episodes are classified as a maximum of 5 pixels ('maxScore')
% changing over 30 consecutive frames compared to the preceding 30 consecutive 
%frames (since our frame rate is 30 frames per second, this corresponds to
%a period of 2 seconds - hence when freezing is defined as the absence of
%movement for minimum of 2 seconds, the 'minimumLength' should be equal to the frame
%rate, and the 'compareWith' value and the section above)
% to a frame 30 frames [1 second] beforehand, 30 consecutive frames
% corresponds to a period of 2 seconds. 
% Plot freezing episodes, displayed as red bars. Freezing episodes can be inspected by double clicking on the red bars and are
% displayed at the frame rate defined by 'r.depictionIntervalInFrames'. In
% this way one can check whether the mouse is actually freezing during the
% detected freezing episodes.

% Plot freezing episodes alongside trials
rtrials = mbvid.videotrack.fragmentSet('video',g,'fragmentsAsPartitionInSeconds','trialmatrix_test_basic.dlm');
rtrials.depictionIntervalInFrames = 15;
mbvid.videotrack.fragmentSet.comparePlotFragments({rtrials,r},'colors',{'g','r'},'nfig',2);

% Plot freezing episodes alongside trials. Trial times are obtained from
% the 'trialmatrix_test_basic.dlm' file. Trials are displayed as the green
% bars. In this case, the first four green bars are four 30 second baseline
% periods, the next four green bars are the CS- trials, and the last four
% green bars are the CS+ trials. If changes are made to the fear
% conditioning test protocol (e.g. the inter-trial intervals, number of
% trials, then a new trialmatrix.dlm file must be generated to be able to
% calculate the freezing percentages. It is also possible to double click on the 
%green bars, and this displays every 15th frame
%(rtrials.depictionIntervalInFrames = 15). This can be done to check
%whether any potential freezing episodes could have been missed (e.g. if
%the pixel change threshold was too stringent).
%% 5. Obtain freezing percentages
o = trialPercentages(r,rtrials);
bar(o.percentage);
%Gives the percentage of time spent freezing in each trial ("fraction of active frames"), also plots a
%rudimentary bar graph.