function varargout = mergeRoiTool(varargin)
% ROITOOL MATLAB code for mergeRoiTool.fig
%      ROITOOL, by itself, creates a new ROITOOL or raises the existing
%      singleton*.
%
%      H = ROITOOL returns the handle to a new ROITOOL or the handle to
%      the existing singleton*.
%
%      ROITOOL('CALLBACK',hObject,eventData,handles,...) calls the local
%      function named CALLBACK in ROITOOL.M with the given input arguments.
%
%      ROITOOL('Property','Value',...) creates a new ROITOOL or raises the
%      existing singleton*.  Starting from the left, property value pairs are
%      applied to the GUI before roiTool_OpeningFcn gets called.  An
%      unrecognized property name or invalid value makes property application
%      stop.  All inputs are passed to roiTool_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 roiTool

% Last Modified by GUIDE v2.5 12-Dec-2014 13:48:37

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

% Choose default command line output for roiTool
handles.output = hObject;
handles.needsReload = 1;
handles.roi = struct;
handles.roiCoords = struct;
% Update handles structure
guidata(hObject, handles);

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


% --- Outputs from this function are returned to the command line.
function varargout = roiTool_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)
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);
        imagesc([0 0; 0 0]);
        handles.needsReload = 1;
        msgbox('ROI Saved Successfully')
    catch
        h = warndlg('Save failed.  Nothing saved');
    end
end
guidata(hObject, handles);
%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

axes(handles.axes1);
imagesc([0 0; 0 0]);

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;
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);
imagesc(images(:,:,1,1));
tsize = size(images);
display("matrix size");
display(tsize);
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.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


% --- 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)

% 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;
    imagesc(images(:,:,1,get(handles.slider2,'Value')));
end


% --- 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