%% muscleContours

% This script allows to select the contours on Tiff images of the four  
% cuff rotator muscles: Supraspinatus (SS), Infraspinatus (IS), Subscapularis (SC)
% and Teres Minor (TM).
% 

% INPUT: 
% subject: ### subject number
% type: 'normal' or 'pathologic'

% Author: EPFL-LBO
% Date: 2016-09-05
%%

function [] = muscleContours(subject,type)

directory = '../../../data'; % Location of the CT database
location = 'P';
CTn = sprintf('P%03d',subject);

listDirInCurrDir = dir([directory '/' CTn(1) '/' CTn(2) '/' CTn(3)]);
listDirInCurrDir = listDirInCurrDir(3:end);

for i=1:length(listDirInCurrDir)
        if ~isempty(regexp(listDirInCurrDir(i).name,['^[PN]\d{0,2}[' CTn(4) '][-]\w*'], 'once'))
              
            listDirInCaseFolder = dir([listDirInCurrDir(i).folder '\' listDirInCurrDir(i).name]);
            listDirInCaseFolder = listDirInCaseFolder(3:end);
            
            % In all CT folders in the current Case Folder, find CT #1
            for j=1:length(listDirInCaseFolder)
                if ~isempty(regexp(listDirInCaseFolder(j).name,'^[C][T][-][PN]\d{1,3}[-]\d*[-][1]', 'once'))
                    outputPath = [listDirInCaseFolder(j).folder '\' listDirInCaseFolder(j).name];
                end
            end            
        end
end


pathologic_list = dir(sprintf('%s/%s/P*', directory, location)); %Create the case list
for i = 1:1:numel(pathologic_list)  % Loop over the list of patients and extract the complete name of the specific patient
    name = pathologic_list(i).name;
    t = strfind(name,CTn);
    if t == 1;
        patient_name = name;
    end
end

finaldirectory = [outputPath '\amira\*tif'];
muscleName = cellstr(['SS';'IS';'SC';'TM']);

close all; % Close all figure windows except those created by imtool.
imtool close all; % Close all figure windows created by imtool.
workspace; % Make sure the workspace panel is showing.
fontSize = 16;
imageWindow = [-100 200];

% Choose file
[inputFile, inputPath] = uigetfile(finaldirectory,'Select the image for muscle atrophy measurement');
whereisp = strfind(inputFile, 'P');
if isempty(whereisp)
    whereisp = strfind(inputFile, 'N');
    if isempty(whereisp)
        return
    end
end
subject = inputFile(whereisp:whereisp+3);

% Read gray scale image.
inputImage = imread(sprintf('%s%s',inputPath,inputFile));

if size(inputImage,3) == 3
% Calculate the monochrome luminance by combining the RGB values according to the NTSC standard
    inputImage = 0.2989*inputImage(:,:,1)...
        +0.5870*inputImage(:,:,2)...
        +0.1140*inputImage(:,:,3);
end

for i=1:4;
    
    finished = 'Redo';
    while strcmp('Redo',finished)
        msg = 0; % 0 = no message
        %         clc; % Clear command window.
        close all; % Close all figure windows except those created by imtool.
        imtool close all; % Close all figure windows created by imtool.
        imshow(inputImage,imageWindow);
        imagetitle = sprintf('Select %s ideal section', char(muscleName(i)));
        title(imagetitle, 'FontSize', fontSize);
        set(gcf, 'Position', get(0,'Screensize')); % Maximize figure.
        
        if msg == 1
            message = sprintf('Select the ideal section of your muscle in the image. \nLeft click to place points and draw a polygon. Click again on the first point to close the shape.\nYou can move the points once the line is closed. Double-click or right-click and "Create Mask" to finish.');
            msg = 0;
            uiwait(msgbox(message));
        end
        
        binaryImage1 = roipoly();
        
        if isempty(binaryImage1)
            error('Invalid selection or interface closed')
        end
        
        binaryImage1 = bwmorph(binaryImage1,'majority');
        % Get coordinates of the boundary of the polygonal drawn region.
        structBoundaries1 = bwboundaries(binaryImage1);
        xy1 = structBoundaries1{1}; % Get n by 2 array of x,y coordinates.
        x1 = xy1(:, 2); % Columns.
        y1 = xy1(:, 1); % Rows.
        hold on
        plot(x1, y1, 'color','green');
        
        % check contours
        finished = questdlg('Please verify the contours. Press "Save" if they are satisfactory or "Redo" if you would like to redo the selection. ',...
            'Contour verification','Save','Redo','Save');
    end
    
    %% Report results
    % mkdir('./results',subject);
    if exist([outputPath '\muscles'],'dir') == 0
        mkdir(outputPath,'muscles');
    end
    
    outputPath2 = [outputPath '\muscles\' char(muscleName(i)) '\'];
    mkdir(outputPath2);
    outputFile = sprintf('ssContours%s',subject);
    
    % Check for overwriting
    overwrite = exist(sprintf('%s%s.mat',outputPath2,outputFile), 'file');
    switch overwrite
        case 2
            isoverwrite = questdlg('Overwrite existing file ?', 'Warning', 'No', 'Yes', 'No');
            switch isoverwrite
                case 'Yes'
                    save(sprintf('%s%s.mat',outputPath2,outputFile), 'inputImage','binaryImage1')
                    saveas(gcf,sprintf('%s%s.tif',outputPath2,outputFile))
                    fprintf('%s%s.mat\n%s%s.tif\n',outputPath2,outputFile,outputPath2,outputFile);
            end
            
        case 0
            save(sprintf('%s%s.mat',outputPath2,outputFile), 'inputImage','binaryImage1')
            saveas(gcf,sprintf('%s%s.tif',outputPath2,outputFile))
            fprintf('%s%s.mat\n%s%s.tif\n',outputPath2,outputFile,outputPath2,outputFile);
    end
end
close all;
end