function varargout = mergeRoiTool(varargin)
% ROITOOL MATLAB code for mergeRoiTool.fig
%      ROITOOL, by itself, creates a new ROITOOL or raises the existing
%      singleton*.
%      
%      H = mergeRoiTool returns the handle to a new mergeRoiTool or the handle to
%      the existing singleton*.
%
%      mergeRoiTool('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in mergeRoiTool.M with the given input arguments.
%
%      mergeRoiTool('Property','Value',...) creates a new mergeRoiTool or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before mergeRoiTool_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to mergeRoiTool_OpeningFcn via varargin.
%
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
%      set global variable mergeDebugVerbosity to >0 if you want more debug
%
% See also: GUIDE, GUIDATA, GUI

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

% Last Modified by GUIDE v2.5 10-Apr-2024 08:12:13

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @mergeRoiTool_OpeningFcn, ...
                   'gui_OutputFcn',  @mergeRoiTool_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 mergeRoiTool is made visible.
function mergeRoiTool_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 mergeRoiTool (see VARARGIN)

% Choose default command line output for mergeRoiTool
global mergeDebugVerbosity
if isempty(mergeDebugVerbosity)
    handles.debug=0;
else
    handles.debug=mergeDebugVerbosity;
end
handles.output = hObject;
handles.needsReload = 1;
handles.roi = struct;
handles.roiCoords = struct;
handles.lungGridSize = -1;
% Update handles structure
guidata(hObject, handles);

% This sets up the initial plot - only do when we are invisible
% so window can get raised using mergeRoiTool.
set(handles.progressAxes,'XTick',0,'YTick',0);
%{
if strcmp(get(hObject,'Visible'),'off')
    plot(rand(5));
end
%}
% UIWAIT makes mergeRoiTool wait for user response (see UIRESUME)
% uiwait(handles.figure1);


% --- Outputs from this function are returned to the command line.
function varargout = mergeRoiTool_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 pushbutton_save.
function pushbutton_save_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton_save (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
lungMatrix = handles.lungMatrix;

savePath = [handles.path '/mergeLungROI'];
fname = handles.curName;
if exist(savePath,'dir') ~= 7
    mkdir(savePath);
end
try
    save([savePath '/mergeLung-' fname '.mat'],'lungMatrix')
    set(handles.checkbox_saved,'Value',1,'BackgroundColor','g');
    axes(handles.axes1);
    %warn('here')
    h = imagesc([0 0; 0 0]);
    
    %set(h,'HitTest','off')
    %get(h);
    %set(h,'ButtonDownFcn',@axes1_ButtonDownFcn)
    handles.needsReload = 1;
    
    msgbox('ROI Saved Successfully');
catch
    h = warndlg('Save failed.  Nothing saved');
end

guidata(hObject, handles);
%% old save function
%{
roi = handles.roi;

roiCoords = handles.roiCoords;
if (~checkReload(hObject,handles))
    
elseif (max(roi.liver(:)) == 0 ...
        || max(roi.muscle(:)) == 0 ...
        || get(handles.checkbox_liver,'Value') == 0 ...
        || get(handles.checkbox_musc,'Value') == 0 )
    h = warndlg('One of the ROIs is all zero or hasn''t been performed.  Nothing saved');

else
    savePath = [handles.path '/ROI'];
    fname = handles.curName;
    if exist(savePath,'dir') ~= 7
        mkdir(savePath);
    end
    try
        save([savePath '/liver-' fname '.mat'],'roi','roiCoords')
        set(handles.checkbox_saved,'Value',1,'BackgroundColor','g');
        axes(handles.axes1);
        warn('here')
        h = imagesc([0 0; 0 0])
        
        %set(h,'HitTest','off')
        get(h)
        %set(h,'ButtonDownFcn',@axes1_ButtonDownFcn)
        handles.needsReload = 1;
        
        msgbox('ROI Saved Successfully')
    catch
        h = warndlg('Save failed.  Nothing saved');
    end
end
guidata(hObject, handles);
%}
% end old save function
%popup_sel_index = get(handles.popupmenu1, 'Value');
%{
switch popup_sel_index
    case 1
        plot(rand(5));
    case 2
        plot(sin(1:0.01:25.99));
    case 3
        bar(1:.5:10);
    case 4
        plot(membrane);
    case 5
        surf(peaks);
end
%}

% --------------------------------------------------------------------
function FileMenu_Callback(hObject, eventdata, handles)
% hObject    handle to FileMenu (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


% --------------------------------------------------------------------
function OpenMenuItem_Callback(hObject, eventdata, handles)
% hObject    handle to OpenMenuItem (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
%[file, path] = uigetfile('*');
%try
%    img = dicomread([path file]);
%    nfo = dicominfo([path file]);
%catch
%    disp('Not a dicom');
%end


if( ~isfield(handles, 'path') )
    path = uigetdir();
else
    path = uigetdir(handles.path);
end
handles.path = path;
handles.needsReload = 1;
files = dir(path);
dcmlist = struct;
setProgress(hObject, eventdata, handles,0,'Loading...');
for n=3:length(files);
fp = [path '/' files(n).name];
    if ~files(n).isdir && isdicom(fp) && (isempty(strfind(files(n).name,'XX')) && isempty(strfind(files(n).name,'PS')))
        nfo=dicominfo(fp);
        dcmlist(end+1).path = fp;
        dcmlist(end).fname = files(n).name;
        dcmlist(end).protocol = nfo.ProtocolName;     
    end
    setProgress(hObject, eventdata, handles,n/length(files),[]);
end
setProgress(hObject, eventdata, handles,1,'Finished');

if length(dcmlist) < 1
    error('no dicoms found');
else
    dcmlist = dcmlist(2:end);
end

% prep the listbox
for n=1:length(dcmlist)
    fileStrings{n} = dcmlist(n).protocol;
end
set(handles.listbox1,'String',fileStrings);
handles.roi.liver = 0;
handles.roi.muscle = 0;
set(handles.checkbox_liver,'Value',0,'BackgroundColor','r');
set(handles.checkbox_musc,'Value',0,'BackgroundColor','r');
set(handles.checkbox_saved,'Value',0,'BackgroundColor','r');
handles.dcmlist = dcmlist;
handles.needsReload = 1;

%ha = axes(handles.axes1);
ha = handles.axes1;
h = imagesc(ha,zeros(330));
colormap('gray');
%get(h)
set(h,'HitTest','off');
set(h,'PickableParts','none');
%get(ha);
set(ha,'ButtonDownFcn',@axes1_ButtonDownFcn);
handles.imageHandle = h;

guidata(hObject,handles);


% --------------------------------------------------------------------
function PrintMenuItem_Callback(hObject, eventdata, handles)
% hObject    handle to PrintMenuItem (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
printdlg(handles.figure1)

% --------------------------------------------------------------------
function CloseMenuItem_Callback(hObject, eventdata, handles)
% hObject    handle to CloseMenuItem (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
selection = questdlg(['Close ' get(handles.figure1,'Name') '?'],...
                     ['Close ' get(handles.figure1,'Name') '...'],...
                     'Yes','No','Yes');
if strcmp(selection,'No')
    return;
end

delete(handles.figure1)


% --- Executes on selection change in popupmenu1.
function popupmenu1_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = get(hObject,'String') returns popupmenu1 contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu1


% --- Executes during object creation, after setting all properties.
function popupmenu1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: popupmenu controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
     set(hObject,'BackgroundColor','white');
end

set(hObject, 'String', {'plot(rand(5))', 'plot(sin(1:0.01:25))', 'bar(1:.5:10)', 'plot(membrane)', 'surf(peaks)'});


% --- Executes on button press in buttonLiverROI.
function buttonLiverROI_Callback(hObject, eventdata, handles)
% hObject    handle to buttonLiverROI (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if checkReload(hObject,handles)
    [a x y] = roipoly();
    imageNum = get(handles.slider2,'Value');
    handles.roi.liver(:,:,imageNum) = a;
    handles.roiCoords.liver(imageNum).x = x;
    handles.roiCoords.liver(imageNum).y = y;
    guidata(hObject,handles);
    set(handles.checkbox_liver,'Value',1,'BackgroundColor','g');
end
% --- Executes on button press in buttonLiverROI.
function buttonMuscROI_Callback(hObject, eventdata, handles)
% hObject    handle to buttonLiverROI (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
if checkReload(hObject,handles)
    [a x y] = roipoly();
    imageNum = get(handles.slider2,'Value');
    handles.roi.muscle(:,:,imageNum) = a;
    handles.roiCoords.muscle(imageNum).x = x;
    handles.roiCoords.muscle(imageNum).y = y;
    guidata(hObject,handles);
    set(handles.checkbox_musc,'Value',1,'BackgroundColor','g');
end
% --- If Enable == 'on', executes on mouse press in 5 pixel border.
% --- Otherwise, executes on mouse press in 5 pixel border or over buttonLiverROI.
function buttonLiverROI_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to buttonLiverROI (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)


% --- Executes on selection change in listbox1.
function listbox1_Callback(hObject, eventdata, handles)
% hObject    handle to listbox1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: contents = cellstr(get(hObject,'String')) returns listbox1 contents as cell array
%        contents{get(hObject,'Value')} returns selected item from listbox1


% --- Executes during object creation, after setting all properties.
function listbox1_CreateFcn(hObject, eventdata, handles)
% hObject    handle to listbox1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: listbox controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes on button press in buttonLoad.
function buttonLoad_Callback(hObject, eventdata, handles)
% hObject    handle to buttonLoad (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
set(handles.checkbox_liver,'Value',0,'BackgroundColor','r');
set(handles.checkbox_musc,'Value',0,'BackgroundColor','r');
set(handles.checkbox_saved,'Value',0,'BackgroundColor','r');

imagenum = get(handles.listbox1,'Value');
path = handles.dcmlist(imagenum).path;

axes(handles.axes1);
images = dicomread(path);
dcminfo = dicominfo(path);
%h = imagesc(images(:,:,1,1),'HitTest','off');\
handles.dcminfo = dcminfo;
set(handles.imageHandle,'CData',images(:,:,1,1));
%h = imagesc(images(:,:,1,1));
set(handles.sliceCount,'String',sprintf('/ %i',size(images,4)));
%get(gca,'HitTest')
%get(gca,'Children')
%get(h)
%set(h,'HitTest','off')
%set(h,'ButtonDownFcn',@axes1_ButtonDownFcn)
tsize = size(images);
if handles.debug
    display("matrix size");
    display(tsize);
end
if max(size(tsize)) > 2
tsize = tsize([1:2 4]);
end
roi = zeros(tsize);
if size(images,4) > 1
    sliderVal = size(images,4);
    sH = handles.slider2;
    set(sH, 'SliderStep',[1/(sliderVal-1) 1], 'Min', 1, 'Max', sliderVal, 'Value', 1);
else
    sH = handles.slider2;
    set(sH, 'SliderStep',[.1 1], 'Min', 1, 'Max', 1.1, 'Value', 1);
end
handles.curName = handles.dcmlist(imagenum).fname;
handles.roiCoords = struct;
handles.roi.liver = roi;
handles.roi.muscle = roi;
handles.imageMat = images;
handles.currentSlice = 1;
handles.needsReload = 0;
handles.climval = get(handles.axes1,'CLim');
set(handles.slider_color,'Value',1);
guidata(hObject,handles);



function setProgress(hObject, eventdata, handles,value,text)

if ~isempty(value)
    axes(handles.progressAxes);
    vxlow=0;
    vxhigh = value;
    vylow = 0;
    vyhigh = 1;
    fillhandle = fill([vxlow,vxlow,vxhigh,vxhigh], [vyhigh,vylow,vylow,vyhigh],[.3,.4,0]); %creates the plot of a box.  If you reverse the order of one of the sets of points, you get an hourglass shape
    set(fillhandle,'FaceAlpha',.2,'EdgeAlpha',.2);%set edge color
    set(gca,'Ylim',[0,1],'Xlim',[0,1],'XTick',0,'YTick',0);
end

if ~isempty(text)
    set(handles.progressText,'String',text);
end


function redrawImage(hObject, eventdata, handles)
axes(handles.axes1);
images = handles.imageMat;
%h = imagesc(images(:,:,1,1),'HitTest','off');
cs = handles.currentSlice;
gridsize = handles.lungGridSize;
newim = repmat(images(:,:,1,cs),1,1,3);
newim = double(newim);
newim = newim ./ max(newim(:));
lms = handles.lungGridSize;
imsize = size(images);
overlay = zeros(size(newim));

if lms > -1
    for n=1:size(handles.lungMatrix,1)-1
        for m=1:size(handles.lungMatrix,2)-1
            xx = n*lms;
            yy = m*lms;
            switch handles.lungMatrix(m,n,1,handles.currentSlice)
                case 1
                    cd = [0.2, 0.2, 0.0];
                case 2
                    cd = [0.4,0,0];
                case 3
                    cd = [0,0.4,0];
                case 4
                    cd = [0.1,0.1,0.5];
                otherwise
                    cd = [0 0 0];
            end
    
                
            overlay(yy:yy+lms, xx:xx+lms,1)=cd(1);
            overlay(yy:yy+lms, xx:xx+lms,2)=cd(2);
            overlay(yy:yy+lms, xx:xx+lms,3)=cd(3);
        end
    end
end
%size(newim)
%size(overlay)
newim = newim + overlay;
%set(handles.imageHandle,'CData',newim)
h = imagesc(newim);
set(h,'HitTest','off')
set(h,'PickableParts','none')
set(handles.sliceNum, 'String', num2str(handles.currentSlice));
set(handles.sliceCount,'String',sprintf('/ %i',size(images,4)));
if lms > -1
    hold on; for n=0:gridsize:imsize(1); 
        h = plot([n,n],[0,imsize(2)],'g'); 
        set(h,'HitTest','off')
        set(h,'PickableParts','none')
        %set(h,'ButtonDownFcn',@axes1_ButtonDownFcn)
    end
    for n=0:gridsize:imsize(2); 
        h = plot([0,imsize(1)],[n,n],'g');
        set(h,'HitTest','off')
        set(h,'PickableParts','none')
        %set(h,'ButtonDownFcn',@axes1_ButtonDownFcn)
    end
%handles
end





% --- Executes on slider movement.
function slider2_Callback(hObject, eventdata, handles)
% hObject    handle to slider2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

sv = round(get(handles.slider2,'Value'));
set(handles.slider2,'Value',sv);
handles.currentSlice = sv;
% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider
if get(handles.slider2,'Max') ~= 1.1
    axes(handles.axes1);
    images = handles.imageMat;
    h = imagesc(images(:,:,1,get(handles.slider2,'Value')));
    colormap('gray')
    set(h,'ButtonDownFcn',@axes1_ButtonDownFcn);
    redrawImage(hObject,eventdata,handles);
end

guidata(hObject,handles);



% --- Executes during object creation, after setting all properties.
function slider2_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end

% --- Executes on slider movement.
function slider_color_Callback(hObject, eventdata, handles)
% hObject    handle to slider2 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'Value') returns position of slider
%        get(hObject,'Min') and get(hObject,'Max') to determine range of slider


%handles.climval
%get(handles.slider_color,'Value')

set(handles.axes1,'CLim',handles.climval .* [1 get(handles.slider_color,'Value')]);




function out = checkReload(hObject,handles)
    if handles.needsReload ~= 0
        warndlg('Please load an image');
        out = 0;
    else
        out = 1;
    end


% --- Executes during object creation, after setting all properties.
function slider_color_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider_color (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: slider controls usually have a light gray background.
if isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor',[.9 .9 .9]);
end


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

axes(handles.axes1);

[x_coord, y_coord]=ginput(2);

gridsize = sqrt((x_coord(2)-x_coord(1)).^2 + (y_coord(2)-y_coord(1)).^2);
gridsize = ceil(gridsize);
imsize = size(handles.imageMat);
lungMatrix = zeros(floor(imsize(1)./gridsize),floor(imsize(2)./gridsize),imsize(3),imsize(4));
handles.lungMatrix = lungMatrix;
handles.lungGridSize = gridsize;
hold on; for n=0:gridsize:imsize(1); 
    h = plot([n,n],[0,imsize(2)],'g'); 
    %set(h,'HitTest','off')
    set(h,'ButtonDownFcn',@axes1_ButtonDownFcn)
end
for n=0:gridsize:imsize(2); 
    h = plot([0,imsize(1)],[n,n],'g'); 
    set(h,'HitTest','off')
    set(h,'ButtonDownFcn',@axes1_ButtonDownFcn)
end
%handles

guidata(hObject,handles);
redrawImage(hObject,eventdata,handles);
%set(gca, 'ButtonDownFcn', @axes1_ButtonDownFcn);
%ax = gca;
%im.PickableParts = 'none';
%ax.ButtonDownFcn = @mouseClick;

% --- Executes on mouse press over axes background.
function axes1_ButtonDownFcn(hObject, eventdata, handles)
% hObject    handle to axes1 (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
%gca;

drawnow
handles = guidata(hObject);
%colormap('gray');
if handles.debug > 3
    disp('yes it ran')
    datetime
end
currentPoint = get(gca, 'currentpoint');
currentBox = currentPoint(1,1:2);
if handles.debug > 3
    currentPoint
    currentBox
    handles
end
%handles2 = guihandles(hObject)
%handles2
%size(handles.lungMatrix)
lungGridSize = handles.lungGridSize;
lungGridMatSize = size(handles.lungMatrix);
lungMatLoc = floor(currentBox);
lmy = floor(lungMatLoc(1)./size(handles.imageMat,2)*lungGridMatSize(2));
lmx = floor(lungMatLoc(2)./size(handles.imageMat,1)*lungGridMatSize(1));
currentSlice = get(handles.slider2,'Value');
if handles.debug > 3
    lungGridMatSize
    lungMatLoc
    lmy
    lmx
    currentSlice
end
handles.lungMatrix(lmx,lmy,1,currentSlice) = mod(handles.lungMatrix(lmx,lmy,1,currentSlice)+1,5);

handles.lungMatrix(:,:,1,currentSlice);
guidata(hObject, handles);

redrawImage(hObject, eventdata, handles);
%r = rectangle('Position',[lungMatLoc.*lungGridSize lungMatLoc.*lungGridSize+[lungGridSize,lungGridSize]],'FaceColor',[0.5 0.5 0.5] )

%SliderLocation = round(get(handles.slider1,'Value'));
%[xlist ylist]=ginput(5);
%tableData = {xlist(1),ylist(1),SliderLocation};
%set(handles.CoordinateTable,'Data',tableData)
% Update handles structure
guidata(hObject, handles);

function mouseClick(~,~)
    disp('yep')
    get(gca,'CurrentPoint')



function clicker(h,~)


    get(h, 'selectiontype')
    % 'normal' for left moue button
    % 'alt' for right mouse button
    % 'extend' for middle mouse button
    % 'open' on double click

    get(h, 'currentpoint')
    % Current mouse location, in pixels from the lower left.
    % When the units of the figure are 'normalized', the
    % coordinates will be [0 0] inb lower left, and [1 1] in
    % the upper right.



function sliceNum_Callback(hObject, eventdata, handles)
% hObject    handle to sliceNum (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hints: get(hObject,'String') returns contents of sliceNum as text
%        str2double(get(hObject,'String')) returns contents of sliceNum as a double


% --- Executes during object creation, after setting all properties.
function sliceNum_CreateFcn(hObject, eventdata, handles)
% hObject    handle to sliceNum (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: edit controls usually have a white background on Windows.
%       See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end


% --- Executes on key press with focus on sliceNum and none of its controls.
function sliceNum_KeyPressFcn(hObject, eventdata, handles)
% hObject    handle to sliceNum (see GCBO)
% eventdata  structure with the following fields (see MATLAB.UI.CONTROL.UICONTROL)
%	Key: name of the key that was pressed, in lower case
%	Character: character interpretation of the key(s) that was pressed
%	Modifier: name(s) of the modifier key(s) (i.e., control, shift) pressed
% handles    structure with handles and user data (see GUIDATA)

set(handles.slider2,'Value',get(handles.sliceNum,'Value'));


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

%stats text variable
st = "Statistics";

lungVoxels = size(find(handles.lungMatrix),1);
lungNormal = size(find(handles.lungMatrix==1),1);
lungHypo = size(find(handles.lungMatrix==2),1);
lungHyper = size(find(handles.lungMatrix==3),1);
lungBronchodyslasia = size(find(handles.lungMatrix==4),1);
lungVol = -1;
if strcmp(handles.dcminfo.SOPClassUID,'1.2.840.10008.5.1.4.1.1.4.1')
    %this is an enhanced dicom
    d = handles.dcminfo;
    sliceThickness = d.PerFrameFunctionalGroupsSequence.Item_1.PixelMeasuresSequence.Item_1.SliceThickness;
    sliceSpacing = d.PerFrameFunctionalGroupsSequence.Item_1.PixelMeasuresSequence.Item_1.SpacingBetweenSlices;
    if sliceThickness ~= sliceSpacing
        warndlg("Slice thickness does not equal slice spacing, lung volume may be very wrong");
    end
    pixelSpacing = d.PerFrameFunctionalGroupsSequence.Item_1.PixelMeasuresSequence.Item_1.PixelSpacing;
    pixelsPerLungMatVox = handles.lungGridSize^2;
    lmVoxVol = pixelSpacing(1)*pixelSpacing(2)*sliceThickness*pixelsPerLungMatVox;
    lungVol = lungVoxels * lmVoxVol;
    
elseif strcmp(handles.dcminfo.SOPClassUID,'1.2.840.10008.5.1.4.1.1.4')
    % this is a classic dicom
    warndlg('Classic dicom does not compute lung volume stats yet');
else
    error('SOPClassUID %s not equal to MR Classic or Enhance DICOM SOPClassUID',handles.dcminfo.SOPClassUID );
end

st = st + sprintf("Counts:\n");
st = st + sprintf(" Total Lung Voxels:   %d (%03.2f%%)\n",lungVoxels, 100*lungVoxels/lungVoxels);
st = st + sprintf(" Normal Lung Voxels:   %d (%03.2f%%)\n",lungNormal, 100*lungNormal/lungVoxels);
st = st + sprintf(" Hypointense Voxels:   %d (%03.2f%%)\n",lungHypo, 100*lungHypo/lungVoxels);
st = st + sprintf(" Hyperintense Voxels:   %d (%03.2f%%)\n",lungHyper, 100*lungHyper/lungVoxels);
st = st + sprintf(" Bronchodyspl Voxels:   %d (%03.2f%%)\n",lungBronchodyslasia, 100*lungBronchodyslasia/lungVoxels);
st = st + sprintf("\nVolumes:\n");
st = st + sprintf(" Estimated Total Lung Volume:   %06.1f cc", lungVol);


set(handles.statsTextbox,'String',st);