TrackLegAngle4_withComments.m

%Track tibia angle for each frame in the .avi file.
%
%InFile: .avi file that contains the tibia image.
%Threshold: Pixels less (darker) than this value will be used to fit the angle.
%
%It also reads in "...DrawMaskAndBackground.mat" file made by another
%script, "DrawMaskAndBackground3". This file specifies the area in the image
%that will be used for tracking (in case there are dark or bright spots in
%the image that you want to ignore), and the background image.
%

function []=TrackLegAngle4_withComments(InFile,Threshold)

%Find the output file from DrawMaskAndBackground and load it.
%Thre should be only one file in the directory.
MaskFile=dir('*DrawMaskAndBackground.mat');
load(MaskFile(1).name);

%Specify the input video file
ExampleVid=VideoReader(InFile);

%Read up till 1 second (in video replay time) before the end of the video
%to avoid possible artifact at the end.
FramesToRead=floor((ExampleVid.Duration-1)*ExampleVid.FrameRate);
LegAngleArea=zeros(FramesToRead,4);

k=1;
while k<=FramesToRead
    vidFrame=readFrame(ExampleVid);
    %Chose the area of the video image previously selected in MaskRegion and
    %subtract the Background from them. If not using MaskRegion and
    %Background image, just keep vidFrame.
    MaskedBGImage=double(vidFrame).*MaskRegion-BackgroundAll;

    %Select the pixels that are darker than "Threshold".
    Mask=MaskedBGImage<Threshold;
    
    TestRegion=regionprops(Mask,'orientation','area','centroid');
    %"regionprops" will provide the specified properties for each group of
    %contiguous pixels. Depending on the threshold setting, there may be
    %mulitple pixel groups, but the tibia should be the biggest one.
    %Find the group with largest area and use its orientation as "tibia
    %orientation" in the image.
    allArea=[TestRegion.Area];%Concatinate all the area information.
    [MaxArea, Index]=max(allArea);
    LegAngleArea(k,1)=TestRegion(Index).Orientation;
    %Also save the area, and the centroid of the tibia.
    LegAngleArea(k,2)=MaxArea;
    LegAngleArea(k,3)=TestRegion(Index).Centroid(1);
    LegAngleArea(k,4)=TestRegion(Index).Centroid(2);
    
    k=k+1;
end


position=strfind(InFile,'.'); %gives the position of the "period" in the string FileName
NewName=InFile(1:position-1); %string NewName has the file name without the ".avi".
Outfile=strcat(NewName,'TrackLegAngle4');

save(Outfile,'Threshold','LegAngleArea');

clear