%% SIMPoly Matlab Code
clearvars, clc, close all

[file, p] = uigetfile('*.*');
R=['File name:', file];
disp(R)
I = imread(fullfile(p,file));
% I = imread('C:\Users\Leo\Documents\MATLAB\Large_Fiber_Images\LX1000.jpg');

warning off
ftitle = 'Converstion Ratio Question';
quest = '\fontsize{10}Do you know the pixel converstion ratio (\mum/pixel)?';
btn1 = 'Yes'; btn2 = 'No, but I want to measure it'; btn3 = 'There is no scale bar';
opts.Interpreter = 'tex'; opts.Default = 'Yes';
answer = questdlg(quest,ftitle,btn1,btn2,btn3,opts);
switch answer
    case 'Yes'
        dessert = 2;
    case 'No, but I want to measure it'
        dessert = 1;
    case 'There is no scale bar'
        dessert = 0;
end
if dessert == 2
    
    prompt = {'\fontsize{10}What is the pixel converstion ratio (\mum/pixel)?'};
    dlgtitle = 'Input';
    dims = [1 65];
    definput = {''};
    opts.Interpreter = 'tex';
    conv = inputdlg(prompt,dlgtitle,dims,definput,opts);
    conv = string(conv);
    conv = str2double(conv);
    
elseif dessert == 1
    conv = 0;
    while conv == 0 
        togglefig('Original Image')
        imshow(I)
        h = imdistline;
        fcn = makeConstrainToRectFcn('imline',get(gca,'XLim'),get(gca,'YLim'));
        setDragConstraintFcn(h,fcn); 
        prompt = {'\fontsize{10}What is the length of the scale (\mum)?     This will be the number next to the scale.','\fontsize{10}What is the pixel length of the scale bar? Use the distance tool over the image.'};
        dlgtitle = 'Input';
        dims = [1 58];
        definput = {'',''};
        opts.WindowStyle = 'normal';
        opts.Interpreter = 'tex';
        answer = inputdlg(prompt,dlgtitle,dims,definput,opts);
        scale = answer(1); scale = string (scale); scale = str2double(scale);
        measure = answer(2); measure = string (measure); measure = str2double(measure);
        conv = scale / measure;
    end
    close all
  
elseif dessert == 0
    conv = 0;
end

I = I(1:end-90,:,1);
%Removes SEM information (e.g. scale bar, magnification, etc)

togglefig('Original Image')
imshow(I)
drawnow

Ihist = adapthisteq(I); 
Ihist = histeq(Ihist);
%Enhances contract using histogram equalization

marker = imerode(Ihist, strel('disk', 5));
%Erodes the grayscape image I and returns the eroded image
Iobr = imreconstruct(marker, Ihist);
%Performs morphological reconstruction of the image 

min_area = 20;
E = edge(Iobr, 'Canny', [0.2 0.4]);
%Finds edges in intensity image
E = bwareaopen(E, min_area);
%Removes small objects with less than 20 pixels
E = bwmorph(E, 'thicken', 1);
OL = imoverlay(Ihist, E, 'red');

%%
level = graythresh(I) + 0.1;
BW = imbinarize(Ihist,level);
%Creates a binary image from 2D grayscale by replacing all values above a
%globally determined threshold with 1s

BW = imclose(BW, strel('disk', 1));
%Performs morphological closing on the image, returning the closed image. 

BW = bwmorph(BW, 'clean', 100000);
BW = bwmorph(BW, 'fill', 5000);
BW = bwmorph(BW, 'majority', 500);
BW = bwmorph(BW, 'thin', 4);

%Applies a specific morphological operation to the binary image BW

BWf = medfilt2(BW);
i = 0;
while sum(sum(BWf)) ~= sum(sum(BW))
    i = i + 1;
    BW = BWf;
    BWf = medfilt2(BW);
end

%median filter than cleans image, stops when loop no longer changes image
%%
BW = bwmorph(BW, 'thicken', 4);

SK = bwskel(BW);
%Reduces all objects in the 2D binary image to 1 pixel wide curved lines
branchpoints = bwmorph(SK, 'branchpoints', 1);
branchpoints = imdilate(branchpoints, strel('disk', 3, 0));
SK = SK & ~branchpoints;
SK = bwmorph(SK, 'spur', 1);

[m,n] = size(SK);
F=bwdist(E);
for i = 1:m
    for j = 1:n
        if SK(i,j)==1
            Ry=F(i,j);
            if Ry > 55
                SK(i,j) = 0;
            end
        end
    end
end
%Uses edge overlay to filter out background noise
togglefig('Segmented Image')
imshow(BW)
drawnow

togglefig('Overlay')
OL = imoverlay(Ihist, SK, 'red');
imshow(OL)
showMaskAsOverlay(0.3, BW, 'c')
%%
Dist = 2*bwdist(~BW);
%Calculates distance between a pixel and the nearest nonzero pixel;
%chessboard, cityblock, euclidean, quasi-euclidean
diameters = Dist(SK);

togglefig('Data')
if conv > 0
    h = histogram(diameters*conv);
else
    h = histogram(diameters);
end
hold on
findpeaks(h.Values, h.BinEdges(1:end-1), 'Threshold', 0.01*max(h.Values))
[pks, loc] = findpeaks(h.Values, h.BinEdges(1:end-1), 'Threshold', 0.01*max(h.Values),'Annotate', 'peaks');
[~,i] = max(pks);


y = [0 0 h.Values];
x = [h.BinEdges(1)-2 h.BinEdges(1)-1 h.BinEdges(1:end-1)];
f = fit(x',y','gauss1');

hold on
plot(f,x,y)
ylim([0 inf]);
ylabel('Frequency');
if conv > 0
    xlabel('Diameter (µm)');
    disp('Average Diameter (pixels)')
    ave = f.b1;
    avep = ave / conv;
    disp(avep)
    disp('Standard Deviation (pixels)')
    stdev = f.c1/2;
    stdevp = stdev / conv;
    disp(stdevp)
    disp('Average Diameter (µm)')
    disp(ave)
    disp('Standard Deviation (µm)')
    disp(stdev)
    dia_img = Dist.*SK * conv;
else
    xlabel('Diameter (pixels)');
    disp('Average Diameter (pixels)')
    ave = f.b1;
    disp(ave)
    disp('Standard Deviation (pixels)')
    stdev = f.c1/2;
    disp(stdev) 
    dia_img = Dist.*SK;
end

dia_img(dia_img == 0) = NaN;
%%
color = 0.05:0.05:0.95;
len = length(color);
RED = [1 0 0;
       ones(len,1) color' zeros(len,1)];
YELLOW = [1 1 0;
          flip(color)' ones(len,1) zeros(len,1)];
GREEN = [0 1 0];
     
%      flip(YELLOW);
%          flip(RED)]

map = [0 0 0;
       RED;
       YELLOW;
       GREEN];

togglefig('Diameter map')
imshow(dia_img);
colormap(map)
caxis([(ave - (3.35*stdev)), (ave + (3*stdev))])
colorbar('FontSize',14,'Ticks',[ave - (3*stdev), ave - (2*stdev), ave - stdev, ave,...
                  ave + stdev, ave + (2*stdev), ave + (3*stdev)],...
         'TickLabels',{'-3\sigma', '-2\sigma', '-1\sigma', 'Average',...
                       '+1\sigma', '+2\sigma', '+3\sigma'});  
%% End of SIMPoly Matlab Method Code
                   
%Note: It is recommended to move the "togglefig" and "showMaskAsOverlay" functions to seperate .m
%files in the same folder as the main Matlab Code. Save the file as "togglefig.m" and "showMaskAsOverlay.m" respectively. 
%Alternatively, download the togglefig and showMaskASOverlay functions online. 
%This will increase the Matlab method speed significantly. 
                   
function fig = togglefig(name, clearfig)
if ~nargin
    tmp = get(findall(0,'type','figure'),'name');
    if isempty(tmp)
        tmp = 0;
    elseif ischar(tmp)
        tmp = 1;
    else 
        tmp = sum(cell2mat(regexp(tmp,'untitled')));
    end
    name = ['untitled',num2str(tmp+1)];
    clearfig = 0;
elseif nargin == 1
    clearfig = 0;
end

fig = findall(0,'type','figure','name',name);
if isempty(fig)
    fig = figure('numbertitle','off','name',name);shg;
else
    set(0,'currentfigure',fig)
end
drawnow;
figure(fig)
if clearfig
    clf
end
if ~nargout
    clear fig
end
end

%Note: This is the endpoint for the "togglefig" function and the start of
%the "showMaskAsOverlay" function. Recommendation is to copy and save both
%of these files in a seperate .m file for increased code speed. 

function varargout = showMaskAsOverlay(opacity, mask, overlaycolor, varargin)
error(nargchk(1,5,nargin));
if nargin >= 4
    if ~isempty(varargin{1})
        if ishandle(varargin{1})
            imgax = varargin{1};
        else
            figure;
            imshow(varargin{1});
            imgax = imgca;
        end
    else
        imgax = imgca;
    end
    fig = get(imgax,'parent');
    axes(imgax);
else
    fig = gcf;
end

if nargin == 5
    deleMasks = logical(varargin{2});
else
    deleMasks = true;
end

iptcheckinput(opacity, {'double'},{'scalar'}, mfilename, 'opacity', 1);
iptcheckinput(deleMasks, {'logical'}, {'nonempty'}, mfilename, 'deleMasks', 5);

if nargin == 1
    overlay = findall(gcf,'tag','opaqueOverlay');
    if isempty(overlay)
        error('SHOWMASKASOVERLAY: No opaque mask found in current figure.');
    end
    mask = get(overlay,'cdata');
    newmask = max(0,min(1,double(any(mask,3))*opacity));
    set(overlay,'alphadata',newmask);
    figure(fig);
    return
else
    iptcheckinput(mask, {'double','logical'},{'nonempty'}, mfilename, 'mask', 2);
end

DEFAULT_COLOR = [1 0 0];
if nargin < 3
    overlaycolor = DEFAULT_COLOR;
elseif ischar(overlaycolor)
    switch overlaycolor
        case {'y','yellow'}
            overlaycolor = [1 1 0];
        case {'m','magenta'}
            overlaycolor = [1 0 1];
        case {'c','cyan'}
            overlaycolor = [0 1 1];
        case {'r','red'}
            overlaycolor = [1 0 0];
        case {'g','green'}
            overlaycolor = [0 1 0];
        case {'b','blue'}
            overlaycolor = [0 0 1];
        case {'w','white'}
            overlaycolor = [1 1 1];
        case {'k','black'}
            overlaycolor = [0 0 0];
        otherwise
            disp('Unrecognized color specifier; using default.');
            overlaycolor = DEFAULT_COLOR;
    end
end

figure(fig);
tmp = imhandles(fig);
if isempty(tmp)
    error('There doesn''t appear to be an image in the current figure.');
end
try
    a = imattributes(tmp(1));
catch %#ok
    error('There doesn''t appear to be an image in the current figure.');
end
imsz = [str2num(a{2,2}),str2num(a{1,2})]; 

if ~isequal(imsz,size(mask(:,:,1)))
    error('Size mismatch');
end
if deleMasks
    delete(findall(fig,'tag','opaqueOverlay'))
end

overlaycolor = im2double(overlaycolor);
mask = logical(mask);

if size(mask,3) == 1
    newmaskR = zeros(imsz);
    newmaskG = newmaskR;
    newmaskB = newmaskR;
    newmaskR(mask) = overlaycolor(1);
    newmaskG(mask) = overlaycolor(2);
    newmaskB(mask) = overlaycolor(3);
elseif size(mask,3) == 3
    newmaskR = mask(:,:,1);
    newmaskG = mask(:,:,2);
    newmaskB = mask(:,:,3);
else
    beep;
    disp('Unsupported masktype in showImageAsOverlay.');
    return
end
newmask = cat(3,newmaskR,newmaskG,newmaskB);
hold on;
h = imshow(newmask);
try
    set(h,'alphadata',double(mask)*opacity,'tag','opaqueOverlay');
catch %#ok
    set(h,'alphadata',opacity,'tag','opaqueOverlay');
end
if nargout > 0
    varargout{1} = imhandles(imgca);
end
if nargout > 1
    varargout{2} = getframe;
    varargout{2} = varargout{2}.cdata;
end
end