ImageSectionGenerator(varargin)

%--------------------------------------------------------------------%
%	    Alison Chaiken, sole author and maintainer     			     %
%        ------------------------------------------------------      %
%	    GUI-based Matlab and FEMLAB data analysis, instrument	     %
%	    control, statistical analysis, finite-element modelling,     %
%	    image acquisition and analysis          				     %
%       -------------------------------------------------------      %
%	    [e-mail]			                    		     %
%	    http://www.exerciseforthereader.org/         			     %
%	    [phone]-5600					                         %
%--------------------------------------------------------------------%

function varargout = ImageSectionGenerator(varargin)
% Main file for Image Section Generator application


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

% Last Modified by GUIDE v2.5 27-May-2009 18:25:28

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

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

%these statements must be in the opening function to create the new handles
handles.ImageSectionGenerator = hObject;
handles.ImageWidth = -1;
handles.ImageHeight = -1;
handles.ScaleMax = -1;
handles.ImageType = 'none';
handles.rcflag='h';
handles.ScaleFactor=-1;
handles.Image = -1;
handles.SectionPlot = -1;

%the color that buttons have when they aren't highlighted
global DEFAULT_BACKGROUND_COLOR;
DEFAULT_BACKGROUND_COLOR = [0.8706    0.9216    0.9804];
global GRAY;
GRAY=[0.9 0.9 0.9];

initialize_gui(hObject, handles, false);

% Update handles structure
guidata(hObject, handles);



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


% --- Outputs from this function are returned to the command line.
function varargout = ImageSectionGenerator_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;



% --------------------------------------------------------------------
function initialize_gui(fig_handle, handles, isreset)
% If the metricdata field is present and the QuitButton flag is false, it means
% we are we are just re-initializing a GUI by calling it from the cmd line
% while it is up. So, bail out as we dont want to QuitButton the data.
%if isfield(handles, 'metricdata') && ~isreset
%    return;
%end

set(gcf,'Name','Section-plot generator for TIFF and JPEG images')
set(handles.SelectionMethodGroup, 'SelectedObject', handles.RowColumnChoiceButton);
set(handles.SectionOrientationGroup, 'SelectedObject', handles.HorizontalButton);
set(handles.HorizontalPresets,'Visible','on')
set(handles.VerticalPresets,'Visible','off')
set(handles.ImageFileName,'string','')
set(handles.NumericSectionLocation,'value',-1);
set(handles.Magnification,'value',20);
set(handles.Magnification,'string',20);
set(handles.DisplayScaleBar,'value',0);
set(fig_handle,'UserData',[])

% user start-up cues
%global GRAY
set(handles.LoadNewImageButton,'BackgroundColor','green')
%set(handles.DisplayImage,'ForegroundColor',GRAY)
%set(handles.MakeSectionPlot, 'ForegroundColor',GRAY)

CenterCurrentWindow

% Update handles structure
guidata(fig_handle,handles)


% --- Executes on button press in HorizontalButton.
function HorizontalButton_Callback(hObject, eventdata, handles)
% hObject    handle to HorizontalButton (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 HorizontalButton

SectionOrientationGroup_SelectionChangeFcn(hObject, eventdata, handles)


% --- Executes on button press in HorizontalButton.
function VerticalButton_Callback(hObject, eventdata, handles)
% hObject    handle to VerticalButton (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 HorizontalButton

SectionOrientationGroup_SelectionChangeFcn(hObject, eventdata, handles)

% --- Executes on button press in LoadNewImageButton.
function LoadNewImageButton_Callback(hObject, eventdata, handles)
% hObject    handle to LoadNewImageButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global DEFAULT_BACKGROUND_COLOR;
set(handles.LoadNewImageButton,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SaveSectionDataButton,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.MakeSectionPlot,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SelectionMethodGroup,'ForegroundColor','black')
set(handles.SelectionMethodGroup,'Shadow','black')
set(handles.SelectionMethodGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ForegroundColor','black')
set(handles.SectionOrientationGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'Shadow','black')


%both lbox2 and ReloadImageButton_Callback change handle values
lbox2('ImageSectionGenerator',handles.ImageSectionGenerator);

if (~isempty(get(handles.ImageFileName,'string')))
    ReloadImageButton_Callback(hObject, eventdata, handles)
else
    %errordlg('Empty filename','Empty filename')
end


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


function NumericSectionLocation_Callback(hObject, eventdata, handles)
% hObject    handle to NumericSectionLocation (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 NumericSectionLocation as text
%        str2double(get(hObject,'String')) returns contents of NumericSectionLocation as a double
global DEFAULT_BACKGROUND_COLOR;
set(handles.NumericSectionLocation,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SelectionMethodGroup,'ForegroundColor','black')
set(handles.SelectionMethodGroup,'ShadowColor','black')
set(handles.SelectionMethodGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ForegroundColor','black')
set(handles.SectionOrientationGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ShadowColor','black')

location = str2double(get(handles.NumericSectionLocation,'string'));
%location is empty if the string contains non-numeric characters
if (isempty(location) || ~isfinite(location))
    set(handles.NumericSectionLocation,'string','')
    set(handles.NumericSectionLocation,'value',-1)
else
    set(handles.NumericSectionLocation,'value',location)
end
guidata(hObject,handles)



% --- Executes during object creation, after setting all properties.
function NumericSectionLocation_CreateFcn(hObject, eventdata, handles)
% hObject    handle to NumericSectionLocation (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 button press in SetCenterButton.
function SetCenterButton_Callback(hObject, eventdata, handles)
% hObject    handle to SetCenterButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

global DEFAULT_BACKGROUND_COLOR
set(handles.NumericSectionLocation,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SelectionMethodGroup,'ForegroundColor','black')
set(handles.SelectionMethodGroup,'ShadowColor','black')
set(handles.SelectionMethodGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ForegroundColor','black')
set(handles.SectionOrientationGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ShadowColor','black')

set(handles.NumericSectionLocation,'value',.5*handles.ImageHeight)
set(handles.NumericSectionLocation,'string',num2str(0.5*handles.ImageHeight))
guidata(hObject,handles)


% --- Executes on button press in SetBottomButton.
function SetBottomButton_Callback(hObject, eventdata, handles)
% hObject    handle to SetBottomButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global DEFAULT_BACKGROUND_COLOR
set(handles.NumericSectionLocation,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SelectionMethodGroup,'ForegroundColor','black')
set(handles.SelectionMethodGroup,'ShadowColor','black')
set(handles.SelectionMethodGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ForegroundColor','black')
set(handles.SectionOrientationGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ShadowColor','black')

set(handles.NumericSectionLocation,'value',handles.ImageHeight)
set(handles.NumericSectionLocation,'string',num2str(handles.ImageHeight))
guidata(hObject,handles)


% --- Executes on button press in SetTopButton.
function SetTopButton_Callback(hObject, eventdata, handles)
% hObject    handle to SetTopButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global DEFAULT_BACKGROUND_COLOR
set(handles.NumericSectionLocation,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SelectionMethodGroup,'ForegroundColor','black')
set(handles.SelectionMethodGroup,'ShadowColor','black')
set(handles.SelectionMethodGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ForegroundColor','black')
set(handles.SectionOrientationGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ShadowColor','black')

set(handles.NumericSectionLocation,'value',1)
set(handles.NumericSectionLocation,'string',num2str(1));
guidata(hObject,handles)

% --- Executes when selected object is changed in SectionOrientationGroup.
function SectionOrientationGroup_SelectionChangeFcn(hObject, eventdata, handles)
% hObject    handle to the selected object in SectionOrientationGroup
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if (get(handles.VerticalButton,'Value') == 1.0)
    set(handles.HorizontalPresets,'Visible','off')
    set(handles.VerticalPresets,'Visible','on')
    handles.rcflag = 'v';
else
    set(handles.HorizontalPresets,'Visible','on')
    set(handles.VerticalPresets,'Visible','off')
    handles.rcflag = 'h';
end

set(handles.SectionOrientationGroup,'ForegroundColor','black')
set(handles.SectionOrientationGroup,'Fontweight','normal')
set(handles.SectionOrientationGroup,'ShadowColor','black')
if ((~(get(handles.NumericSectionLocation,'value'))) > 0)
    set(handles.NumericSectionLocation,'BackgroundColor','green')
end
% Update handles structure
guidata(hObject,handles)




% --- Executes when selected object is changed in SelectionMethodGroup.
function SelectionMethodGroup_SelectionChangeFcn(hObject, eventdata, handles)
% hObject    handle to the selected object in SectionOrientationGroup
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if (get(handles.RowColumnChoiceButton,'Value') == 1.0)
    set(handles.NumericControlsPanel,'Visible','on')
else
    set(handles.NumericControlsPanel,'Visible','off')
end

set(handles.SelectionMethodGroup,'ForegroundColor','black')
set(handles.SelectionMethodGroup,'FontWeight','normal')
set(handles.SelectionMethodGroup, 'Shadow','black')
set(handles.SectionOrientationGroup,'ForegroundColor','green')
set(handles.SectionOrientationGroup,'Fontweight','bold')

% Update handles structure
guidata(hObject,handles)


% --- Executes on button press in SetLeftButton.
function SetLeftButton_Callback(hObject, eventdata, handles)
% hObject    handle to SetLeftButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global DEFAULT_BACKGROUND_COLOR
set(handles.NumericSectionLocation,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SelectionMethodGroup,'ForegroundColor','black')
set(handles.SelectionMethodGroup,'ShadowColor','black')
set(handles.SelectionMethodGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ForegroundColor','black')
set(handles.SectionOrientationGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ShadowColor','black')

set(handles.NumericSectionLocation, 'value',1)
set(handles.NumericSectionLocation,'string',num2str(1))
guidata(hObject,handles)


% --- Executes on button press in SetMiddleButton.
function SetMiddleButton_Callback(hObject, eventdata, handles)
% hObject    handle to SetMiddleButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global DEFAULT_BACKGROUND_COLOR
set(handles.NumericSectionLocation,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SelectionMethodGroup,'ForegroundColor','black')
set(handles.SelectionMethodGroup,'ShadowColor','black')
set(handles.SelectionMethodGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ForegroundColor','black')
set(handles.SectionOrientationGroup,'FontWeight','normal')
set(handles.SectionOrientationGroup,'ShadowColor','black')

middle = 0.5*handles.ImageWidth;
set(handles.NumericSectionLocation, 'value',middle)
set(handles.NumericSectionLocation,'string',num2str(middle))
guidata(hObject,handles)


% --- Executes on button press in SetRightButton.
function SetRightButton_Callback(hObject, eventdata, handles)
% hObject    handle to SetRightButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global DEFAULT_BACKGROUND_COLOR
set(handles.NumericSectionLocation,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.NumericSectionLocation, 'value',handles.ImageWidth)
set(handles.NumericSectionLocation,'string',num2str(handles.ImageWidth))
guidata(hObject,handles)

% --- Executes on button press in DisplayImage.
function DisplayImage_Callback(hObject, eventdata, handles)
% hObject    handle to DisplayImage (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
%show image with selected linescan
tiffarray = [];
tiffarray = get(handles.ImageSectionGenerator,'UserData');
if (~isempty(tiffarray))
    handles.Image = figure;
    UpperRightCurrentWindow
    lineshow=axes();
    imshow(tiffarray,'Parent',lineshow)
    if (get(handles.DisplayScaleBar,'value'))
        DrawScaleBar
    end
    BetterWindowTitle
else
    errordlg('No image data.   Load a new image first.')
    set(handles.LoadNewImageButton,'BackgroundColor','green')
    guidata(hObject,handles)
end


function Magnification_Callback(hObject, eventdata, handles)
% hObject    handle to Magnification (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 Magnification as text
%        str2double(get(hObject,'String')) returns contents of Magnification as a double
%Image is 200 microns high for 20x and 640x480
%SCALEFACTOR=(20*200)/(imageheight*Magnification);
%for better agreement with image of ruler
%SCALEFACTOR=1.163*(20*200)/(imageheight*Magnification);
%1.2011 comes analysis of gaertner4x.tif, a calibrated scale
%SCALEFACTOR=1.2011*(20*200)/(imageheight*Magnification);
%For 37x SEM image, 210 pixels = 1 mm = 1000 microns
%SCALEFACTOR=(1000*double(imagewidth)*37)/(double(Magnification)*210)

global DEFAULT_BACKGROUND_COLOR

magn = str2double(get(handles.Magnification,'string'));
%magnification is empty if the string contains non-numeric characters
if (isempty(magn) || ~isfinite(magn))
    set(handles.Magnification,'string','')
    set(handles.Magnification,'BackgroundColor','green')
else
    set(handles.Magnification,'value',magn)
    set(handles.Magnification,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
    set(handles.SelectionMethodGroup,'ForegroundColor','green')
    set(handles.SelectionMethodGroup,'FontWeight','bold')
    set(handles.SelectionMethodGroup, 'Shadow','green')
end
handles.ScaleFactor=37000.0/(magn*210);
guidata(hObject,handles)


% --- Executes during object creation, after setting all properties.
function Magnification_CreateFcn(hObject, eventdata, handles)
% hObject    handle to Magnification (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 button press in ReloadImageButton.
function ReloadImageButton_Callback(hObject, eventdata, handles)
% hObject    handle to ReloadImageButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
filename=get(handles.ImageFileName,'string');
if isempty(filename)
    errordlg('Empty filename','Empty filename')
    set(handles.LoadNewImageButton,'BackgroundColor','green')
    guidata(hObject,handles)
else
    %retrieve path name stored by lbox2 'Done' button in ImageFileName's
    %appdata
    filepath=getappdata(handles.ImageFileName,'ImageFileDirectory');
    ImageFileName=fullfile(filepath,filename);
    set(handles.ImageSectionGenerator,'UserData', []);
    tiffarray = [];
    if ((~isempty(findstr('tif',ImageFileName))) || (~isempty(findstr('TIF',ImageFileName))))
        tiffarray = imread(ImageFileName,'tiff');
    elseif ((~isempty(findstr('jpg',ImageFileName))) || (~isempty(findstr('JPG',ImageFileName) >0)))
        tiffarray = imread(ImageFileName,'jpg');
    else errordlg('Please load a TIFF or JPEG file.','Input file selection error.')
    end
    
    if size(tiffarray)
        set(handles.ImageSectionGenerator,'UserData',tiffarray)
        
        [handles.ImageHeight,handles.ImageWidth,imagecolored]=size(tiffarray);
        imagedepth=get_image_depth(tiffarray);
        
        switch (imagecolored)
            case 3
                handles.ImageType='color';
                set(handles.ForceGray,'Visible','on')
            case 1
                handles.ImageType='grayscale';
                set(handles.ForceGray,'Visible','off')
            otherwise
                error('Unknown image type.')
        end
        handles.ScaleMax=2^imagedepth;
        
        %paramstring=sprintf('%d-bit %s image of size %dx%d.',imagedepth,handles.ImageType,handles.ImageHeight,handles.ImageWidth);
        %disp(paramstring);
        
        set(handles.Magnification,'BackgroundColor','green')
        %set(handles.DisplayImage,'ForegroundColor','black')
        %set(handles.MakeSectionPlot, 'ForegroundColor','black')
                
    end
    guidata(hObject,handles)
end



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


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


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


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




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

SelectionMethodGroup_SelectionChangeFcn(hObject, eventdata, handles)


% --- Executes on button press in MakeSectionPlot.
function MakeSectionPlot_Callback(hObject, eventdata, handles)
% hObject    handle to MakeSectionPlot (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global DEFAULT_BACKGROUND_COLOR;
set(handles.MakeSectionPlot,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SelectionMethodGroup,'FontWeight','normal')
set(handles.SelectionMethodGroup,'ForegroundColor','black')
set(handles.SelectionMethodGroup,'Shadow','black')
Magnification_Callback(hObject, eventdata, handles)
%handles is changed in Magnification_Callback, so we must reread them
%Without this statement, the changes in Magnification_Callback don't get
%passed along to MakeSectionPlot
handles=guidata(hObject);

if isempty(get(handles.ImageFileName,'string'))
    set(handles.LoadNewImageButton,'BackgroundColor','green')
    errordlg('Please designate an image file and a section location before creating a plot.')
elseif ((get(handles.RowColumnChoiceButton,'value')==1)&& ...
        (get(handles.NumericSectionLocation,'value') == -1))
    set(handles.NumericSectionLocation,'BackgroundColor','green')
    errordlg('Please designate a section location before creating a plot.')
else
    MakeSectionPlot
    
    %only turn SaveSectionData button green if data to save is available in
    %the handles of the figures.    Numeric-choice data needs only the
    %section plot; cursor-drawn data needs both the section plot and the
    %image window.
    if (ishandle(handles.SectionPlot))
        if (get(handles.RowColumnChoiceButton,'value')==1)
            set(handles.SaveSectionDataButton,'BackgroundColor','green')
        % if(get(handles.CursorChoiceButton,'value)==1)
        elseif (ishandle(handles.Image))
            set(handles.SaveSectionDataButton,'BackgroundColor','green')
        end
    end            
end


% --- Executes on key press with focus on NumericSectionLocation and no controls selected.
function NumericSectionLocation_KeyPressFcn(hObject, eventdata, handles)
% hObject    handle to NumericSectionLocation (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

%I had hoped that this function would prevent non-numeric characters from
%appearing in the text box as they are typed, but non-numeric characters
%are only cleared by loss of focus through NumericSectionLocation_Callback.
%This function never appears to be invoked, probably because the textboxes
%properties aren't updated until focus is transferred.

%location = str2num(get(handles.NumericSectionLocation,'string'));
%if isempty(location)
%    set(handles.NumericSectionLocation,'string','')
%end
%guidata(hObject,handles)


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

ImageSectionGenerator_CloseRequestFcn(handles.ImageSectionGenerator, eventdata, handles)

% --- Executes when user attempts to close main figure.
function ImageSectionGenerator_CloseRequestFcn(hObject, eventdata, handles)
% hObject    handle to main figure (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

% Hint: delete(hObject) closes the figure
delete(hObject);


% --- Executes on button press in ForceGray.
function ForceGray_Callback(hObject, eventdata, handles)
% hObject    handle to ForceGray (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 ForceGray


% --- Executes on button press in CursorChoiceButton.
function CursorChoiceButton_Callback(hObject, eventdata, handles)
% hObject    handle to CursorChoiceButton (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 CursorChoiceButton
set(handles.RowColumnChoiceButton,'ForegroundColor','black')
set(handles.CursorChoiceButton,'ForegroundColor','black')
set(handles.RowColumnChoiceButton,'FontWeight','normal')
set(handles.CursorChoiceButton,'FontWeight','normal')
set(handles.MakeSectionPlot,'BackgroundColor','green')
guidata(hObject,handles)

SelectionMethodGroup_SelectionChangeFcn(hObject, eventdata, handles)


% --- Executes on button press in DisplayScaleBar.
function DisplayScaleBar_Callback(hObject, eventdata, handles)
% hObject    handle to DisplayScaleBar (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 DisplayScaleBar

if (get(handles.DisplayScaleBar,'value') == 1)
    DrawScaleBar
else %redisplay image without scalebar by closing current image and then opening a new one
   % close(handles.Image)
   % DisplayImage_Callback(hObject, eventdata, handles)
   % This re-display works, but it prevents the user from later saving the
   % data in a file.
end


% --- Executes on button press in HelpButton.
function HelpButton_Callback(hObject, eventdata, handles)
% hObject    handle to HelpButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
web('http://www.exerciseforthereader.org/ISGdocs/index.html','-browser')


% --- Executes on button press in DemoButton.
function DemoButton_Callback(hObject, eventdata, handles)
% hObject    handle to DemoButton (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)
global DEFAULT_BACKGROUND_COLOR
%initialize_gui(handles.ImageSectionGenerator,handles,false)
set(handles.ImageFileName,'string','TestImage.jpg')
guidata(hObject,handles)
ReloadImageButton_Callback(hObject,eventdata,handles)
%handles is changed in ReloadImageButton_Callback, so we must reread them
%Without this statement, the changes in ReloadImageButton_Callback don't get
%passed along to MakeSectionPlot
handles=guidata(hObject);
%DisplayImage_Callback(hObject,eventdata,handles)
SetCenterButton_Callback(hObject, eventdata, handles)
set(handles.LoadNewImageButton,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.Magnification,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.NumericSectionLocation,'BackgroundColor',DEFAULT_BACKGROUND_COLOR)
set(handles.SaveSectionDataButton, 'BackgroundColor','green')
guidata(hObject,handles)
MakeSectionPlot