generic_segmentation_gui.m

function generic_segmentation_gui
% ***********************************************************************
% Description : A MATLAB based Graphical User Interface to load medical
% images, stored as mat files, to annotate labels
% UNIVERSITY OF ARIZONA
%
% Author      : LU
% Date        : 2021
%
% Creates a GUI window to load a mat file containing 3D image data in a
% variable called img (HxWxD). Uses information from config file to determine the
% number of ROIs that need to be annotated and their colors. Saves a
% variable called masks (HxWxDxC) where the channel dimension consists of
% masks that were annotated for each label.
% ***********************************************************************

clear; clc;

% ***********************************************************************
% Configuration variables for customizing annotation interface
cfg = readstruct('config.json');

% ***********************************************************************


% Check for compatibility. Works only if MATLAB 2017 and above
if(verLessThan('matlab','9.3'))
    error('Matlab version needs to be 2017b or higher');
%     return;
end

% Variables with global scope
global gui_elements gui_params gui_data

% Initialize structs for GUI
gui_params = {};
gui_elements = {};
gui_data = {};

gui_params.cfg = cfg;
% Create a figure container for the GUI
% Get current monitor screen size to display the main fig window
Current_scr_size = get(0,'ScreenSize');

% % Positioning the window
mf_frmLft = Current_scr_size(1);
mf_frmBtm = Current_scr_size(2);
mf_wt = Current_scr_size(3);
mf_ht = Current_scr_size(4);
gui_elements.main_fig = figure('Visible','off','Position',[mf_frmLft,mf_frmBtm,mf_wt,mf_ht]);

% Assign a name to appear in the window title.
gui_elements.main_fig.Name = cfg.gui_name;

% ***********************************************************************
% Create a panel to display the main push-button to load input file
% ***********************************************************************

disp_str = 'Select input';
h_panel_select_ip= uipanel('FontSize',14,'Position',[0.82,0.85,0.15,0.1]);

uicontrol('Parent',h_panel_select_ip,'Style','pushbutton',...
    'Units','normalized','Position',[0.2 0.6 0.6 0.3],'FontSize',12,...
    'String',disp_str,...
    'FontWeight','bold','Callback',{@select_ip_Callback,cfg});

% Move the window to the center of the screen.
movegui(gui_elements.main_fig,'center')

% Make the UI visible.
gui_elements.main_fig.Visible = 'on';

% ***********************************************************************
% Create a panel to display the axial image : Main figure
% ***********************************************************************

gui_elements.h_panel_axialImage= uipanel('Title','Display Panel','FontSize',12,...
    'Position',[0.2,0.05,0.6,0.9],'FontWeight','bold');

% ***********************************************************************
% Create a panel to control zoom level in the image
% ***********************************************************************

% Initialize the limits for zoom window
gui_params.limits = [];
h_panel_zoom = uipanel('Title','Zoom Settings','FontSize',12,...
    'Position',[0.82,0.75,0.15,0.1]);

uicontrol('Parent',h_panel_zoom,'Style','pushbutton',...
    'Units','normalized','Position',[0.2 0.3 0.3 0.4],...
    'String','Zoom in','FontName','Arial','FontSize',11,...
    'HorizontalAlignment','left','Callback',@createZoomInLims);

uicontrol('Parent',h_panel_zoom,'Style','pushbutton',...
    'Units','normalized','Position',[0.6 0.3 0.3 0.4],...
    'String','Zoom out','FontName','Arial','FontSize',11,...
    'HorizontalAlignment','left','Callback',@createZoomOutLims);

% ***********************************************************************
% Create a panel to control opacity of the overlays
% ***********************************************************************
slider_incr = 0.1;
slider_range = 1;
slider_step = slider_incr/slider_range;

h_panel_opacity = uipanel('Title','Opacity Control','FontSize',12,...
    'Position',[0.82,0.55,0.15,0.1]);

gui_elements.h_panel_opacity_slider = uicontrol('Parent',h_panel_opacity,'Style','slider',...
    'Units','normalized','Position',[0.1 0.2 0.8 0.3],...
    'SliderStep',[slider_step,slider_step],'Min',0,'Max',1,...
    'Value',0.5,'Callback',{@display_slider_img});

opacity_dispStr = ['Value: ',num2str(0.5)];
gui_elements.h_panel_opacity_txt = uicontrol('Parent',h_panel_opacity,'Style','text',...
    'Units','normalized','Position',[0.1 0.7 0.8 0.2],...
    'String',opacity_dispStr,'FontName','Arial','FontSize',10);

% ***********************************************************************
% Create a panel to adjust Window and level in the image
% ***********************************************************************

h_panel_adjWL = uipanel('Title','Adjust Window and Level','FontSize',12,...
    'Position',[0.82,0.65,0.15,0.1]);
uicontrol('Parent',h_panel_adjWL,'Style','pushbutton',...
    'Units','normalized','Position',[0.2 0.3 0.3 0.4],...
    'String','Adjust','FontName','Arial','FontSize',11,...
    'HorizontalAlignment','left','Callback',@adjust_windowLevel);
uicontrol('Parent',h_panel_adjWL,'Style','pushbutton',...
    'Units','normalized','Position',[0.6 0.3 0.3 0.4],...
    'String','Done','FontName','Arial','FontSize',11,...
    'HorizontalAlignment','left','Callback',@close_windowLevel);

% ***********************************************************************
% Create a panel and text box to display informational messages.
% ***********************************************************************
% Create a panel to display user messages
h_user_info_txt_0 = uipanel('Title','Message to User','FontSize',12,...
    'Position',[0.82,0.35,0.15,0.2]);
% The panel acts as a container for other uicontrol buttons for which it is
% a parent!
disp_str = 'Click select input button to load a new image volume';
gui_elements.h_user_info_txt = uicontrol('Parent',h_user_info_txt_0,'Style','text',...
    'Units','normalized','Position',[0.1 0.1 0.8 0.8],...
    'String',disp_str,...
    'FontName','Arial','FontSize',12,'HorizontalAlignment','Center');
 
end

function select_ip_Callback(source,eventdata, cfg)
% ***********************************************************************
% Open a dialog-box to select the nifti file of interest.
% ***********************************************************************

global gui_params gui_elements gui_data

try
    % ***********************************************************************
    % Load a h5 file for a subject
    % ***********************************************************************

    [data_file,directory]= uigetfile({'*.mat'},'Select a file',pwd);
    gui_data.dataPath = [directory data_file];
    gui_data.data_file = data_file;
    gui_data.directory = directory;
    file_disp_name = strsplit(gui_data.dataPath, filesep);
    file_disp_name = [file_disp_name{end-1} filesep data_file];
    
    % Adding data directory to path to make it saving easier.
    addpath(genpath(directory));

    % Load the data
    temp = load(gui_data.dataPath);
    img = temp.img;   
    [xdim,ydim,zdim] = size(img);
    
    % Rescale img intensities to [0,255] for ease
    max_ = max(img(:));
    min_ = min(img(:));
    gui_data.origImg = cfg.img_max_intensity * ((img - min_)./(max_ - min_));
    
    % Check if masks exist. If not, create a new mask with label dimension
    % equal to the number of labels defined in cfg
    
    if(isfield(temp,'masks'))
        gui_data.UserMask = temp.masks;
    else
        
        gui_data.UserMask = zeros(xdim,ydim,zdim,cfg.num_labels);
    end

    gui_params.max_slideNum = zdim;
    gui_params.slideNum = round(gui_params.max_slideNum/2);  % Load first image of the slide    
    disp_str = ['Current file : ',file_disp_name];

    % ***********************************************************************
    % Create a text box to display the current .mat file loaded
    % ***********************************************************************
    uicontrol('Parent',source.Parent,'Style','text',...
        'Units','normalized','Position',[0.01 0.01 0.95 0.5],...
        'String',disp_str,'FontName','Arial','FontSize',10.5, ...
        'FontAngle','italic', 'HorizontalAlignment','left');


    % Load the data corresponding to the current slide number on the GUI
    img = gui_data.origImg(:,:,gui_params.slideNum);
    mask = squeeze(gui_data.UserMask(:,:,gui_params.slideNum,:));

    % Set variables to display the initial image in GUI
    gui_params.min_val = double(prctile(gui_data.origImg(:),0));
    gui_params.max_val = double(prctile(gui_data.origImg(:),99));

    % Create figure axis handle. This will be used by all functions to make
    % edits to this axis

    gui_elements.axial_fig = subplot(1,1,1,'Parent',gui_elements.h_panel_axialImage);
    gui_elements.axial_fig.CLim = [gui_params.min_val gui_params.max_val];
    set(gui_elements.axial_fig,'position',[.05 .01 .9 .9])
    temp_im = getImageWithMaskOverlay(img,mask);
   
    % generate pixelwise alphadata
%     alpha = 0.5;
    alpha = max(0,gui_elements.h_panel_opacity_slider.Value);
    overlay_mask = logical(squeeze(mask(:,:,1)));
    for label_idx = 2 : gui_params.cfg.num_labels
        overlay_mask = overlay_mask | logical(squeeze(mask(:,:,label_idx)));
    end
    overlay_mask = alpha .* overlay_mask;
    imagesc(img);colormap gray;axis image off;
    hold on;
    gui_elements.h_img_fig = imagesc(temp_im,'Parent',gui_elements.axial_fig);
    axis image off;
    hold off;

    set(gui_elements.h_img_fig,'AlphaData', overlay_mask);
    gui_elements.axial_fig.CLim = [gui_params.min_val gui_params.max_val];
      
    % ***********************************************************************
    % Create a slider for the user to move across the different slices
    % ***********************************************************************
    slider_incr = 1;
    slider_range = gui_params.max_slideNum - 1;
    slider_step = slider_incr/slider_range;

    % Display the slider to change the image
    gui_elements.h_img_slider = uicontrol('Parent',gui_elements.h_panel_axialImage,'Style','slider',...
        'Units','normalized','Position',[0.05 0.93 0.9 0.04],...
        'SliderStep',[slider_step,slider_step],'Min',1,'Max',gui_params.max_slideNum,...
        'Value',gui_params.slideNum,'String','Slider','Callback',{@display_slider_img});

    gui_elements.h_img_slider_txt = uicontrol('Parent',gui_elements.h_panel_axialImage,'Style','text',...
        'Units','normalized','Position',[0.3 0.97 0.3 0.02],...
        'String',['Slide #: ',num2str(gui_params.slideNum)],'FontName','Arial','FontSize',12);

    % ***********************************************************************
    % Create a panel to edit annotations
    % ***********************************************************************  

    h_panel_ROI = uipanel('Title','ROI Annotation Tools','FontSize',12,...
        'Position',[0.02,0.6,0.142,0.25], 'FontWeight','bold');
    
    annotation_label_list = cfg.label_names + " labels";
    gui_elements.h_listROI_popmenu = uicontrol('Parent',h_panel_ROI,'Style','popupmenu',...
    'Units','normalized','Position',[0.2 0.85 0.5 0.1],...
    'FontSize',10,'FontWeight','bold',...
    'String',annotation_label_list,'Callback',@change_annotation_label);
    
    gui_params.mask_type = cfg.label_names{cfg.default_label};
  
    [edit_ROI,del_ROI,draw_ROI,save_ROI ] = createROIbuttons(h_panel_ROI);
    gui_elements.edit_ROI = edit_ROI;
    gui_elements.del_ROI = del_ROI;
    gui_elements.draw_ROI = draw_ROI;
    gui_elements.save_ROI = save_ROI;
   
        % Copy original limits for zoom-out function
    gui_params.limits(1,:) = gui_elements.axial_fig.XLim;
    gui_params.limits(2,:) = gui_elements.axial_fig.YLim;
catch
    fprintf('Exception occured. Load an image file.\n');
end
end


% ***********************************************************************
% Callback for the image slider. Based on the current location of the
% slider, the image in the figure window as well as its caption is updated.
% ***********************************************************************

function display_slider_img(source,eventdata)
global gui_elements gui_params gui_data

% Based on the current value of the slider the following updates are made:
gui_params.slideNum = max(1,round(gui_elements.h_img_slider.Value));

% Update slider text
set(gui_elements.h_img_slider_txt,'String',['Slide #: ',num2str(gui_params.slideNum)]);
gui_elements.h_user_info_txt.String = 'No message to display now!';

% Opacity slider updates
alpha = max(0,gui_elements.h_panel_opacity_slider.Value);

% Update slider text
opacity_dispStr = ['Value: ',num2str(alpha)];
gui_elements.h_panel_opacity_txt.String = opacity_dispStr;

% Copy limits so that they can be applied again.
tempXLimits = gui_elements.axial_fig.XLim;
tempYLimits = gui_elements.axial_fig.YLim;

% Create figure handle
figure(gui_elements.main_fig);
axes(gui_elements.axial_fig);
gui_elements.axial_fig.CLim = [gui_params.min_val gui_params.max_val];


img = gui_data.origImg(:,:,gui_params.slideNum);
mask = squeeze(gui_data.UserMask(:,:,gui_params.slideNum,:));

% generate pixelwise alphadata
overlay_mask = logical(squeeze(mask(:,:,1)));
for label_idx = 2 : gui_params.cfg.num_labels
    overlay_mask = overlay_mask | logical(squeeze(mask(:,:,label_idx)));
end
overlay_mask = alpha .* overlay_mask;

temp_im = getImageWithMaskOverlay(img,mask);

imagesc(img);colormap gray;axis off;
hold on;
% Create figure handle
gui_elements.h_img_fig = imagesc(temp_im,'Parent',gui_elements.axial_fig);
axis image off;
hold off;
 
set(gui_elements.h_img_fig,'AlphaData', overlay_mask);
 
gui_elements.axial_fig.XLim = tempXLimits;
gui_elements.axial_fig.YLim = tempYLimits;
gui_elements.axial_fig.CLim = [gui_params.min_val gui_params.max_val];


end


% ***********************************************************************
% Callback for the draw mask pushbutton.The current mask is deleted and a
% user draws the new mask using freehand
% ***********************************************************************
function draw_img_Callback(source,eventdata)
global gui_elements gui_data gui_params

source.Interruptible = 'off';
% Disable other editing tools till this action is completed
gui_elements.edit_ROI.Enable = 'off';
gui_elements.del_ROI.Enable = 'off';
gui_elements.save_ROI.Enable = 'off';

% Based on the current value of the slider the following updates are made:
slideNum = max(1,round(gui_elements.h_img_slider.Value));

% Identify which label type is this function drawing based on the value of
% gui element in roi list
label_num = gui_elements.h_listROI_popmenu.Value;

% binary mask
BW = squeeze(gui_data.UserMask(:,:,slideNum,label_num));
disp_color = gui_params.cfg.roi_display_colors{label_num};

gui_elements.h_user_info_txt.String = 'Trace the mask outline.Use add roi button to add new regions of interest to mask.';

% This is to ensure that the draw command works on the main window
axes(gui_elements.axial_fig);
mask_Main = imfreehand;
setColor(mask_Main,disp_color);
bw_use = createMask(mask_Main,gui_elements.h_img_fig);
BW = logical(BW) | logical(bw_use);

gui_data.UserMask(:,:,slideNum,label_num)= BW;

% Enable other editing tools after this action is completed
gui_elements.edit_ROI.Enable = 'on';
gui_elements.del_ROI.Enable = 'on';
gui_elements.save_ROI.Enable = 'on';

% Display the new annotations
display_slider_img(gui_elements.h_img_slider,eventdata);

end

% ***********************************************************************
% Callback for the delete mask pushbutton. The mask on the current slice of
% the image will be deleted. Based on tha value of label being edited, the
% corresponding mask would be deleted.
% ***********************************************************************
function del_img_Callback(source,eventdata)
global gui_data gui_elements gui_params

% Based on the current value of the slider the following updates are made:
slideNum = max(1,round(gui_elements.h_img_slider.Value));

% Identify which label type is this function editing based on the value of
% gui element in roi list
label_num = gui_elements.h_listROI_popmenu.Value;
label_name = gui_params.cfg.label_names{label_num}; 
% binary mask
BW = squeeze(gui_data.UserMask(:,:,slideNum,label_num));

if(nnz(BW)==0)
    gui_elements.h_user_info_txt.String = 'No mask to delete here. Use draw option to first generate a mask.';
else
    BW = zeros(size(BW));
end

gui_data.UserMask(:,:,slideNum,label_num)= BW;
disp_str = [label_name ,' mask deleted from current slice'];
gui_elements.h_user_info_txt.String = disp_str;  
 
% Update the display figure
display_slider_img(gui_elements.h_img_slider,eventdata);

end


% ***********************************************************************
% Callback for the save mask pushbutton. Based on the mask Type, the
% corresponding label is saved
% ***********************************************************************
function save_img_Callback(~,eventdata)
global gui_data gui_elements
 
fileName = [gui_data.directory filesep gui_data.data_file];
masks = gui_data.UserMask;
save(fileName,'-append','masks');
gui_elements.h_user_info_txt.String = 'Masks successfully saved to mat file!';
end

% ***********************************************************************
% Callback for the edit mask pushbutton. The mask on the current slice of
% the image can be altered, based on the label type
% ***********************************************************************

function edit_img_Callback(source,eventdata)
global gui_params gui_data gui_elements

% Disable other editing tools till this action is completed
gui_elements.draw_ROI.Enable = 'off';
gui_elements.del_ROI.Enable = 'off';
gui_elements.save_ROI.Enable = 'off';

% Based on the current value of the slider the following updates are made:
slideNum = max(1,round(gui_elements.h_img_slider.Value));

% Identify which label type is this function editing based on the value of
% gui element in roi list
label_num = gui_elements.h_listROI_popmenu.Value;

% load mask from current slice and label
curr_mask = squeeze(gui_data.UserMask(:,:,slideNum,label_num));
disp_color = gui_params.cfg.roi_display_colors{label_num};

if(nnz(curr_mask)==0)
    gui_elements.h_user_info_txt.String = 'No mask for this label to edit here. Use draw option first.';
else
    gui_elements.h_user_info_txt.String = 'Trace the exclusion mask to exclude pixels without lifting the pen.';

    % This is to ensure that the draw command works on the main window
    axes(gui_elements.axial_fig);
    mask_Main = imfreehand;   
    setColor(mask_Main,disp_color);
    excl_mask = createMask(mask_Main,gui_elements.h_img_fig);
    curr_mask = logical(curr_mask) & (~logical(excl_mask));    
    gui_data.UserMask(:,:,slideNum,label_num)= curr_mask;
    
    % Enable other editing tools till this action is completed
    gui_elements.draw_ROI.Enable = 'on';
    gui_elements.del_ROI.Enable = 'on';
    gui_elements.save_ROI.Enable = 'on';
    display_slider_img(gui_elements.h_img_slider,eventdata);
end
end


% ***********************************************************************
% Callback for when the user presses zoom in push button. It lets the user
% zoom into the image once and saves the axes and pplies it to all
% subsequent images.
% ***********************************************************************
function createZoomInLims(source,eventdata)
global gui_elements
gui_elements.h_user_info_txt.String = 'Drag the mouse to select a region to zoom in.';
zoomObj = zoom(gui_elements.main_fig);
set(zoomObj,'ActionPostCallback', @storelimits);
zoomObj.Direction = 'in';
zoomObj.Enable = 'on';
uiwait(gui_elements.main_fig);
zoomObj.Enable = 'off';
end

% ***********************************************************************
% Callback for when the user presses zoom out push button. It resets the
% zoom level to original settings
% ***********************************************************************
function createZoomOutLims(source,eventdata)
global gui_elements gui_params
gui_elements.axial_fig.XLim = gui_params.limits(1,:);
gui_elements.axial_fig.YLim = gui_params.limits(2,:);
display_slider_img(gui_elements.h_img_slider,eventdata);
gui_elements.h_user_info_txt.String= 'Zoom reset.';
end

function storelimits(source,eventdata)
global gui_elements
uiresume(gui_elements.main_fig);
end


% ***********************************************************************
% This function is to create ROI editting buttons 
% Given a parent panel, the buttons correspond to draw, edit, delete &
% save.
%*********************************************************************
function [edit_btn, del_btn, draw_btn, save_btn ] = createROIbuttons(parent_panel)
% set the foreground and background colors
bg_col = 'b';
fg_col = 'y';

% Panel Functionality edits:
draw_btn = uicontrol('Parent',parent_panel,'Style','pushbutton',...
    'Units','normalized','Position',[0.05 0.5 0.3 0.25],...
    'String','Draw','FontName','Arial','FontSize',12,...
    'HorizontalAlignment','left','Callback',{@draw_img_Callback},...
    'BackgroundColor',bg_col,'ForegroundColor',fg_col,...
    'FontAngle','italic', 'FontWeight','bold');

edit_btn = uicontrol('Parent',parent_panel,'Style','pushbutton',...
    'Units','normalized','Position',[0.55 0.5 0.3 0.25],...
    'String','Edit','FontName','Arial','FontSize',12,...
    'HorizontalAlignment','left','Callback',{@edit_img_Callback},...
    'BackgroundColor',bg_col,'ForegroundColor',fg_col,...
    'FontAngle','italic', 'FontWeight','bold');

del_btn = uicontrol('Parent',parent_panel,'Style','pushbutton',...
    'Units','normalized','Position',[0.05 0.1 0.3 0.25],...
    'String','Delete','FontName','Arial','FontSize',12,...
    'HorizontalAlignment','left','Callback',{@del_img_Callback},...
    'BackgroundColor',bg_col,'ForegroundColor',fg_col,...
    'FontAngle','italic', 'FontWeight','bold');

save_btn = uicontrol('Parent',parent_panel,'Style','pushbutton',...
    'Units','normalized','Position',[0.55 0.1 0.3 0.25],... 
    'String','Save','FontName','Arial','FontSize',12,...
    'HorizontalAlignment','left','Callback',{@save_img_Callback},...
    'BackgroundColor',bg_col,'ForegroundColor',fg_col,...
    'FontAngle','italic', 'FontWeight','bold');

end


% ***********************************************************************
% This is the function that converts the image into RGB channels to overlay
% the mask boundaries on the image. Therefore, colormaps other than gray
% would not work here. I could make it to work with other colormaps, if
% required. For now, grayscale should be okay.
% ***********************************************************************
function opImg = overlayMaskOnImage(ipImg,mask,color)
if(nargin<3)
    color = [255 0 0]; % Default red color
end
if max(color) <= 1
    color = normalize_ipImg(color,255); % Change to uint8.
end

% Check if the image has 3-bands (RGB image).
if size(ipImg,3) == 1 % Create grayscale image.
    ipImg(:,:,2) = ipImg(:,:,1);
    ipImg(:,:,3) = ipImg(:,:,1);
end

% Find the outline of the mask.
[indx] = find(mask);
% Take those pixels and change their color
for i = 1:size(ipImg,3)
    temp_im = ipImg(:,:,i);
    temp_im(indx) = color(i);
    ipImg(:,:,i) = temp_im;
end
opImg = uint8(ipImg);

end

function opImg = normalize_ipImg(ipImg,ref_val,min_val,max_val)
%**********************************************************************
% Function to normalize an input image so that the intensities are rescaled
% to 0-reference value. Here the reference value is 255
%*********************************************************************
ipImg = double(ipImg);
if(nargin < 3)
    min_ = min(ipImg(:));
    max_ = max(ipImg(:));
else
    min_ = min_val;
    max_ = max_val;
end
opImg = ref_val .* ((ipImg - min_)./(max_ - min_));
end

function op_Img = getImageWithMaskOverlay(ip_Img,ip_Mask)
global gui_params
num_labels = gui_params.cfg.num_labels;
label_colors = gui_params.cfg.roi_display_colors;
img_max_intensity = gui_params.cfg.img_max_intensity;

% Using red color for WMH lesions
ip_Img = normalize_ipImg(squeeze(ip_Img), img_max_intensity,gui_params.min_val,gui_params.max_val);
for label_idx = 1:num_labels
    label_mask = ip_Mask(:,:,label_idx);
    label_color = img_max_intensity * label_colors{label_idx};
    op_Img = overlayMaskOnImage(ip_Img,label_mask,label_color); 
    ip_Img = op_Img;
end

end

% ***********************************************************************
% Callback to adjust window and level in the image displayed. This callback
% uses matlab's imcontrast tool to let the user adjust the image and saves
% the minimum and the maximum image intensities on exit. The image
% intensities for all subsequent images is also adjusted. While adjusting
% the images, MATLAB shows a new figure.Therefore, ROIs will not be visible
% until the slider is moved, such that the display slider function is
% called again.
% ***********************************************************************

function adjust_windowLevel(source,~)
global gui_elements gui_params gui_data
gui_elements.h_user_info_txt.String = 'Drag the mouse (left-right) to change window width and (up-down) to change window center. Click Done once finished';
slc_num = max(1,round(gui_elements.h_img_slider.Value));
ipImg = gui_data.origImg(:,:,slc_num);

% figure(main_fig);
% Only show contrast edits on the main window
tempXLimits = gui_elements.axial_fig.XLim;
tempYLimits = gui_elements.axial_fig.YLim;

gui_elements.h_img_fig = imshow(ipImg,[0,gui_params.cfg.img_max_intensity],'Parent',gui_elements.axial_fig);
if(~isempty(gui_params.limits))
    gui_elements.axial_fig.XLim = tempXLimits;
    gui_elements.axial_fig.YLim = tempYLimits;
end
gui_elements.axial_fig.CLim = [min(ipImg(:)) max(ipImg(:))];
gui_elements.hfig_contrast = imcontrast(gui_elements.h_img_fig);
set(gui_elements.hfig_contrast, 'CloseRequestFcn', @(s,e)getValues(s));
gui_elements.hfig_contrast.Visible = 'off';

end

% ***********************************************************************
% This function is to get the min and the max values from the imcontrast
% tool. This is used to set the window and the level option.
% ***********************************************************************
function getValues(hfig)
global gui_params
gui_params.min_val = str2double(get(findobj(hfig, 'tag', 'window min edit'), 'String'));
gui_params.max_val = str2double(get(findobj(hfig, 'tag', 'window max edit'), 'String'));
end

% ***********************************************************************
% Callback for closing imcontrast tool and saving the minimum and maximum
% image intensities.
% ***********************************************************************
function close_windowLevel(source,eventdata)
global gui_elements;
try
    close(gui_elements.hfig_contrast);
    delete(gui_elements.hfig_contrast);
    gui_elements.h_user_info_txt.String = 'Contrast adjusted.';
catch
end
end

% ***********************************************************************
% This function changes the annotation label based on the value selected in
% the list window
% ***********************************************************************
function change_annotation_label(source,eventdata)
global gui_params
gui_params.mask_type = gui_params.cfg.label_names{source.Value};
end