function varargout = airwaySegmenter(varargin)
% AIRWAYSEGMENTER MATLAB code for airwaySegmenter.fig
%      AIRWAYSEGMENTER, by itself, creates a new AIRWAYSEGMENTER or raises the existing
%      singleton*.
%
%      H = AIRWAYSEGMENTER returns the handle to a new AIRWAYSEGMENTER or the handle to
%      the existing singleton*.
%
%      AIRWAYSEGMENTER('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in AIRWAYSEGMENTER.M with the given input arguments.
%
%      AIRWAYSEGMENTER('Property','Value',...) creates a new AIRWAYSEGMENTER or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before airwaySegmenter_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to airwaySegmenter_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES

% Edit the above text to modify the response to help airwaySegmenter

% Last Modified by GUIDE v2.5 21-Nov-2017 16:25:09

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
    'gui_Singleton',  gui_Singleton, ...
    'gui_OpeningFcn', @airwaySegmenter_OpeningFcn, ...
    'gui_OutputFcn',  @airwaySegmenter_OutputFcn, ...
    'gui_LayoutFcn',  [] , ...
    'gui_Callback',   []);
if nargin && ischar(varargin{1})
    gui_State.gui_Callback = str2func(varargin{1});
end

if nargout
    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
else
    gui_mainfcn(gui_State, varargin{:});
end
% End initialization code - DO NOT EDIT


% --- Executes just before airwaySegmenter is made visible.
function airwaySegmenter_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
% varargin   command line arguments to airwaySegmenter (see VARARGIN)

% Choose default command line output for airwaySegmenter
handles.output = hObject;

handles = instantiate(handles);

% Update handles structure
guidata(hObject, handles);

% UIWAIT makes airwaySegmenter wait for user response (see UIRESUME)
% uiwait(handles.figure1);


% --- Outputs from this function are returned to the command line.
function varargout = airwaySegmenter_OutputFcn(hObject, eventdata, handles)
% varargout  cell array for returning output args (see VARARGOUT);
% hObject    handle to figure
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Get default command line output from handles structure
varargout{1} = handles.output;


% --- Executes on button press in generate.
function generate_Callback(hObject, eventdata, handles)
% hObject    handle to generate (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if(isfield(handles, 'generatedObjectHandle'))
    delete(handles.generatedObjectHandle);
end

[col, row] = ginput(1);
col = round(col);
row = round(row);

h = waitbar(0, 'Regiongrowing');

handles.bw(:,:,1:3) = 0;
handles.bw(:,:,end-3:end) = 0;

handles.bw(row, col, handles.cp)
objectRegionGrowed = regiongrowing(handles.bw, 0.5, [row col handles.cp]);

waitbar(0.5, h, 'Reducing  Mesh');
sum(objectRegionGrowed(:))
if(sum(objectRegionGrowed(:)) < 10000000)
    objectRegionGrowedReduced = objectRegionGrowed(1:1:end, 1:1:end, 1:1:end);
    
    waitbar(0.5, h, 'Generating Surface');
    handles.objectGenerated = isosurface(objectRegionGrowedReduced(:,:,end:-1:1), 0.5);
    
    waitbar(0.8, h, 'Smoothing Surface');
    handles.objectGeneratedSmooth = smoothpatch(handles.objectGenerated);
    axes(handles.secScreen);
    
    waitbar(0.9, h, 'Plotting Surface');
    handles.generatedObjectHandle = patch(handles.objectGeneratedSmooth, 'edgecolor','none' ,'facecolor', 'b');
    
else
    msgbox('Too much attached to the object, please cuttoff more');
    
end
close(h);
guidata(hObject,handles);

function handles =instantiate(handles)
axes(handles.mainScreen)
handles.mainImage = imshow([0 0], [0 1]);
handles.press = false;
axes(handles.secScreen)
handles.cp = 1;
camlight('left')
camlight('right')
daspect([1 1 1])
lighting phong;


% --- Executes on button press in loadData.
function loadData_Callback(hObject, eventdata, handles)
% hObject    handle to loadData (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

pathName = uigetdir('C:\Users\RB\Desktop\1.2.826.0.1.3680043.2.594.28972.3299.6332.20534.12470');
[handles.volume, handles.info] = loadDicom(pathName, true);

handles.bw = handles.volume < 1300;

handles = startMainViewer(handles);

assignin('base', 'h' , handles);

guidata(handles.figure1, handles)


function handles = startMainViewer(handles)

axes(handles.mainScreen)
delete(handles.mainImage);
handles.cp = round(size(handles.bw,3) / 2);
handles.mainImage = imshow(handles.bw(:,:,handles.cp), [0 1]);

set(handles.mainScreen, 'clim', [0 1]);

guidata(handles.figure1, handles)

function handles = updateScrollScreen(handles, amount)

if(handles.cp + amount < 1)
    handles.cp = 1;
elseif(handles.cp + amount > size(handles.bw,3))
    handles.cp = size(handles.bw,3);
else
    handles.cp = handles.cp + amount;
end


set(handles.mainImage, 'cdata', handles.bw(:,:,handles.cp));


% --- Executes on scroll wheel click while the figure is in focus.
function figure1_WindowScrollWheelFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  structure with the following fields (see MATLAB.UI.FIGURE)
%	VerticalScrollCount: signed integer indicating direction and number of clicks
%	VerticalScrollAmount: number of lines scrolled for each click
% handles    structure with handles and user data (see GUIDATA)
handles = updateScrollScreen(handles, eventdata.VerticalScrollCount);
guidata(hObject, handles);


% --- Executes on mouse press over figure background.
function figure1_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

handles.press = true;
guidata(hObject, handles);

% --- Executes on mouse motion over figure - except title and menu.
function figure1_WindowButtonMotionFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if(handles.press)
    currentPosition = get (gca, 'CurrentPoint');
    b = get(gcf,'selectiontype');
    
    color = 0;
    
    if(strcmpi(b,'normal'))
        color = 0;
    elseif(strcmpi(b,'alt'))
        color = 1;
    else
        return;
    end
    
    dx = round(currentPosition(1,1)); dy = round(currentPosition(1,2));
    
    if(dx > 0 && dx < size(handles.bw,1) && dy > 0 && dy < size(handles.bw,2) )
        
        radius = 2;
        
        % Paint
        if(get(handles.maxDepthToggle, 'value') == 1)
            handles.bw(dy - radius: dy + radius,dx - radius : dx + radius, :) = color;
        else
            handles.bw(dy - radius: dy + radius,dx - radius : dx + radius,handles.cp) = color;
        end
        
        handles = updateScrollScreen(handles,0);
        
    end
    
    guidata(hObject, handles);
end


% --- Executes on mouse press over figure background, over a disabled or
% --- inactive control, or over an axes background.
function figure1_WindowButtonUpFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
handles.press = false;
guidata(hObject, handles);


% --- Executes on mouse press over figure background, over a disabled or
% --- inactive control, or over an axes background.
function figure1_WindowButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to figure1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

handles.press = true;
guidata(hObject, handles);


% --- Executes on button press in maxDepthToggle.
function maxDepthToggle_Callback(hObject, eventdata, handles)
% hObject    handle to maxDepthToggle (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: get(hObject,'Value') returns toggle state of maxDepthToggle


% --- Executes on button press in removeEthmoid.
function removeEthmoid_Callback(hObject, eventdata, handles)
% hObject    handle to removeEthmoid (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

h = figure,
imshow(imrotate(squeeze(handles.volume(:,round(end/2),:)),-90),[-1200 3000]);
[col, row] = ginput(3);

xVals = 1:1:size(handles.bw,2);
res = round(spline(col, row, xVals));
resCompensated = size(handles.bw,3) - res;
hold on;
plot(xVals, res, 'r');

% Construct a questdlg with three options
choice = questdlg('Is this correct?', ...
    'Question', ...
    'Yes','No','No');

% Handle response
switch choice
    case 'Yes'
        tic
        mask = ones(size(handles.bw));
        for i = 1:size(handles.bw,2)
            
            mask(size(handles.bw,1) - i + 1,:,1:res(i)) = 0;
        end
        handles.bw = handles.bw .* mask;
        toc
        
    case 'No'
end



close(h)
guidata(hObject, handles);


% --- Executes on button press in export.
function export_Callback(hObject, eventdata, handles)
% hObject    handle to export (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
[fileName, filePath] = uiputfile('*.stl');

stlwrite([filePath fileName], handles.objectGenerated.faces, handles.objectGenerated.vertices);

fileName = strrep(fileName, '.stl', '_smooth.stl');
stlwrite([filePath fileName], handles.objectGeneratedSmooth.faces, handles.objectGeneratedSmooth.vertices);

msgbox('write completed');


% --- Executes on button press in belowVert.
function belowVert_Callback(hObject, eventdata, handles)
% hObject    handle to belowVert (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

h = figure,
imshow(imrotate(squeeze(handles.volume(:,round(end/2),:)),-90),[-1200 3000]);
[col, row] = ginput(2);

xVals = 1:1:size(handles.bw,2);
res = round(spline(col, row, xVals));
resCompensated = res;
hold on;
plot(xVals, res, 'r');




% Construct a questdlg with three options
choice = questdlg('Is this correct?', ...
    'Question', ...
    'Yes','No','No');

% Handle response
switch choice
    case 'Yes'
              
        
        tic
        mask = ones(size(handles.bw));
        for i = 1:size(handles.bw,2)
            mask(size(handles.bw,1) - i + 1,:,res(i):end) = 0;
        end
        handles.bw = handles.bw .* mask;
        handles.volume = handles.volume .* mask;
        toc
        
    case 'No'
end



close(h)
guidata(hObject, handles);


% --- Executes on button press in threshold.
function threshold_Callback(hObject, eventdata, handles)
% hObject    handle to threshold (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
predicted{1} = num2str(0.5*mode(handles.volume(:), 1))
answer = inputdlg('New threshold', 'Change threshold', 1, predicted);
newThreshold = str2num(answer{1})

handles.bw  = handles.volume < newThreshold;


handles = updateScrollScreen(handles, 0);
guidata(hObject, handles);