% Supplemental Item 1 for Spagna, J.C. et al., "PHYLOGENY, SCALING, AND THE GENERATION OF 
%								EXTREME FORCES IN TRAP-JAW ANTS"
% Code written by:  Antonis Vakis
% Tracing rotating appendages in MATLAB				
% Revision #5 - Comments edited by 	J. Spagna
% 11/28/2007

clear all;
close all;
clc;

% Zooming in at 150% of the original image size and showing axes
iptsetpref('ImshowInitialMagnification',150)
iptsetpref('ImshowAxesVisible','on')

% Specifying the name of the image set (same as the folder name);
% Note: the individual images should have an extension of TIF, not TIFF
filename = input('Input the folder name (case-sensitive): ','s');

% Specifying number of frames per second
fps = input('Frames per second: ');

% Specifying the width of the video
width = input('Width of the video (pixels): ');

% Specifying the height of the video
height = input('Height of the video (pixels): ');

% Specifying the dpi of the images
dpi = input('Input the image resolution (dpi): ');

% Specifying/ creating image directory
% Note: Change the name of the directory shown between quotation marks to
% correspond to the path where captured images are saved!
dir1 = ['C:\Documents and Settings\Antonis Vakis\My Documents\Biomechanics Research\Work\Velocities & Accelerations\Revision 5\Images\'];
dir2 = [dir1,filename,'\'];
addpath(dir1,dir2)                  % Adding paths

% Specifying & displaying frames of interest
% i.e. the frames where the strike is occuring
disp('Please examine the images to determine the first and last frames of interest!')
first = input('First frame of interest: ');
last = input('Last frame of interest: ');
NEWframenum = last - first + 1;     % Number of frames of interest

% Specify whether to trace both mandibles, only the left or only the right
which = input('Select 0 to trace both mandibles; 1 to trace the left only; 2 trace the right only: ');

if (which == 1)
    % Left mandible only
    % Identifying & recording mandible tip coordinates
    coords = zeros(NEWframenum,4);      % Mandible coordinates
    base = zeros(2,2);                  % Mandible BASE coordinates
    
    figure(2)
    % Mandible base
    if (first <= 9)
        imshow([filename,'00',num2str(first),'.tif'])
    elseif (first <= 99)
        imshow([filename,'0',num2str(first),'.tif'])
    elseif (first <= 999)
        imshow([filename,num2str(first),'.tif'])
    end
    title('Select the approximate location of the mandible BASE')
    disp('Select the approximate location of the mandible BASE')
    [base(1,1),base(1,2)] = ginput(1);

    % Right mandible
    title('Select the RIGHT mandible tip')
    disp('Select the RIGHT mandible tip')
    dummycoords = zeros(1,2);
    [dummycoords(1,3),dummycoords(1,4)] = ginput(1);
    for k = 1:NEWframenum
        coords(k,3) = dummycoords(1,3);
        coords(k,4) = dummycoords(1,4);
    end

    % Left mandible
    for j = 1:NEWframenum
        figure(j + 2)                   % Displaying frames of interest
        if ((first - 1 + j) <= 9)
            imshow([filename,'00',num2str(first - 1 + j),'.tif'])
        elseif ((first - 1 + j) <= 99)
            imshow([filename,'0',num2str(first - 1 + j),'.tif'])
        elseif ((first - 1 + j) <= 999)
            imshow([filename,num2str(first - 1 + j),'.tif'])
        end
        title('Select the LEFT mandible tip')
        disp('Select the LEFT mandible tip')
        if (j > 1)
            hold on
            plot(coords(j - 1,1),coords(j - 1,2),'b*')
            plot(coords(j - 1,3),coords(j - 1,4),'r*')
            hold off
        end
        [coords(j,1),coords(j,2)] = ginput(1);
    end

    % Mandible base
    figure(NEWframenum + 3)
    if (last <= 9)
        imshow([filename,'00',num2str(last),'.tif'])
    elseif (last <= 99)
        imshow([filename,'0',num2str(last),'.tif'])
    elseif (last <= 999)
        imshow([filename,num2str(last),'.tif'])
    end
    title('Select the approximate location of the mandible BASE')
    [base(2,1),base(2,2)] = ginput(1);
    
elseif (which == 2)
    % Right mandible only
    % Identifying & recording mandible tip coordinates
    coords = zeros(NEWframenum,4);      % Mandible coordinates
    base = zeros(2,2);                  % Mandible BASE coordinates
    
    figure(2)
    % Mandible base
    if (first <= 9)
        imshow([filename,'00',num2str(first),'.tif'])
    elseif (first <= 99)
        imshow([filename,'0',num2str(first),'.tif'])
    elseif (first <= 999)
        imshow([filename,num2str(first),'.tif'])
    end
    title('Select the approximate location of the mandible BASE')
    disp('Select the approximate location of the mandible BASE')
    [base(1,1),base(1,2)] = ginput(1);
    
    % Left mandible
    title('Select the LEFT mandible tip')
    disp('Select the LEFT mandible tip')
    dummycoords = zeros(1,2);
    [dummycoords(1,1),dummycoords(1,2)] = ginput(1);
    for k = 1:NEWframenum
        coords(k,1) = dummycoords(1,1);
        coords(k,2) = dummycoords(1,2);
    end

    % Right mandible
    for j = 1:NEWframenum
        figure(j + 2)                   % Displaying frames of interest
        if ((first - 1 + j) <= 9)
            imshow([filename,'00',num2str(first - 1 + j),'.tif'])
        elseif ((first - 1 + j) <= 99)
            imshow([filename,'0',num2str(first - 1 + j),'.tif'])
        elseif ((first - 1 + j) <= 999)
            imshow([filename,num2str(first - 1 + j),'.tif'])
        end
        title('Select the RIGHT mandible tip')
        disp('Select the RIGHT mandible tip')
        if (j > 1)
            hold on
            plot(coords(j - 1,1),coords(j - 1,2),'b*')
            plot(coords(j - 1,3),coords(j - 1,4),'r*')
            hold off
        end
        [coords(j,3),coords(j,4)] = ginput(1);
    end

    % Mandible base
    figure(NEWframenum + 3)
    if (last <= 9)
        imshow([filename,'00',num2str(last),'.tif'])
    elseif (last <= 99)
        imshow([filename,'0',num2str(last),'.tif'])
    elseif (last <= 999)
        imshow([filename,num2str(last),'.tif'])
    end
    title('Select the approximate location of the mandible BASE')
    [base(2,1),base(2,2)] = ginput(1);

else
    % Both mandibles
    % Identifying & recording mandible tip coordinates
    coords = zeros(NEWframenum,4);      % Mandible coordinates
    base = zeros(2,2);                  % Mandible BASE coordinates
    
    figure(2)
    % Mandible base
    if (first <= 9)
        imshow([filename,'00',num2str(first),'.tif'])
    elseif (first <= 99)
        imshow([filename,'0',num2str(first),'.tif'])
    elseif (first <= 999)
        imshow([filename,num2str(first),'.tif'])
    end
    title('Select the approximate location of the mandible BASE')
    disp('Select the approximate location of the mandible BASE')
    [base(1,1),base(1,2)] = ginput(1);

    % Mandible tips
    for j = 1:NEWframenum
        figure(j + 2)                   % Displaying frames of interest
        if ((first - 1 + j) <= 9)
            imshow([filename,'00',num2str(first - 1 + j),'.tif'])
        elseif ((first - 1 + j) <= 99)
            imshow([filename,'0',num2str(first - 1 + j),'.tif'])
        elseif ((first - 1 + j) <= 999)
            imshow([filename,num2str(first - 1 + j),'.tif'])
        end
        title('Select the LEFT and RIGHT mandible tips')
        if (j > 1)
            hold on
            plot(coords(j - 1,1),coords(j - 1,2),'b*')
            plot(coords(j - 1,3),coords(j - 1,4),'r*')
            hold off
        end
        disp('Select the LEFT mandible tip')
        [coords(j,1),coords(j,2)] = ginput(1);
        disp('Select the RIGHT mandible tip')
        [coords(j,3),coords(j,4)] = ginput(1);
    end

    % Mandible base
    figure(NEWframenum + 3)
    if (last <= 9)
        imshow([filename,'00',num2str(last),'.tif'])
    elseif (last <= 99)
        imshow([filename,'0',num2str(last),'.tif'])
    elseif (last <= 999)
        imshow([filename,num2str(last),'.tif'])
    end
    title('Select the approximate location of the mandible BASE')
    [base(2,1),base(2,2)] = ginput(1);
end

% Averaging mandible base location
base_coords = [((base(1,1) + base(2,1))/2) ((base(1,2) + base(2,2))/2)];

% Correcting the coordinates in terms of the origin (i.e. setting the
% origin to be at the lower left instead of the upper left
coords_new(:,1) = coords(:,1);
coords_new(:,2) = height - coords(:,2);
coords_new(:,3) = coords(:,3);
coords_new(:,4) = height - coords(:,4);
base_coords_new(:,1) = base_coords(:,1);
base_coords_new(:,2) = height - base_coords(:,2);

% Specifying the image magnification
mag = input('Select 0 to use a magnification of 10x; 1 to specify other value: ');
if (mag == 0)
    zoom = 10;
else
    know = input('Select 0 if you know the value of the magnification; 1 if not: ');
    if (know == 0)
        zoom = input('Input the image magnification: ');
    else
        % Default image to be loaded
        manddefault = input('Specify the frame to be used for the calculation: ');

        % Mandible length from known data
        mandlength = input('Input the pre-measured mandible length: ');

        % Measuring the mandible size from the image
        figure(1)
        if (manddefault <= 9)
            imshow([filename,'00',num2str(manddefault),'.tif'])
        elseif (manddefault <= 99)
            imshow([filename,'0',num2str(manddefault),'.tif'])
        elseif (manddefault <= 999)
            imshow([filename,num2str(manddefault),'.tif'])
        end
        title('Select the start and end points of the mandible')
        disp('Select the start and end points of the mandible')

        % Calculating the magnification from the known and measured mandible
        % sizes
        mandcoords = zeros(2,2);
        [mandcoords(:,1),mandcoords(:,2)] = ginput(2);
        mandsize = sqrt((mandcoords(2,2) - mandcoords(1,2))^2 +...
            (mandcoords(2,1) - mandcoords(1,1))^2);
        zoom = (mandsize*0.0254)/dpi/mandlength;

        % Displaying the mangification factor
        disp('The magnification factor was calculated to be: ');
        zoom
    end
end

% Exporting the data necessary for the solution
save([filename,'_data'],...
    'NEWframenum','base_coords_new','coords_new','dir1','dir2',...
    'dpi','first','fps','last','which','zoom');