function varargout = imageviewer(varargin)
% IMAGEVIEWER - GUI for interactive image browsing
%               (M-file for imageviewer.fig)
%
%      IMAGEVIEWER, by itself, creates a new IMAGEVIEWER or raises the existing
%      singleton*.
%
%      H = IMAGEVIEWER returns the handle to a new IMAGEVIEWER or the handle to
%      the existing singleton*.
%
%  Notes:
%  ------
%    1.) IMAGEVIEWER is based on several other routines developed at PSI:
%          - imageread.m
%          - medianfilter.m
%          - pilatus.m
%          - setroi.m
%          - readscanlog.m
%        In order for IMAGEVIEWER to run properly, all the above routines
%        must be available and accessible through MATLABS working path.
%        Use 'addpath' to add the corresponding directory where the files
%        are saved to MATLAB's current working path.
%
%    2.) IMAGEVIEWER was developed and tested using MATLAB R2006a.
%        Backwards compatibility is neither expected nor guaranteed.
%        
%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one
%      instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
%           IMAGEREAD, MEDIANFILTER, PILATUS, SETROI, READSCANLOG
%           ADDPATH

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

% Last Modified by GUIDE v2.5 18-Oct-2006 14:56:02

%==========================================================================
% Further info for function IMAGEVIEWER
% -------------------------------------
%
% CVS-Info:
% ---------
% $Date: 2006/12/05 16:57:16 $
% $Author: schlepuetz $
% $Revision: 1.3 $
% $Source: /import/cvs/X/PILATUS/X04SA/App/lib/X_PILATUS_X04SA_Matlab/imageviewer.m,v $
% $Tag: $
% 
% Author(s):            C.M. Schlepuetz (CS)
% Address:              Surface Diffraction Station
%                       Materials Science Beamline X04SA
%                       Swiss Light Source (SLS)
%                       Paul Scherrer Institut
%                       CH - 5232 Villigen PSI
% Created:              2006/10/17
% 
% Change Log:
% -----------
% 
% 2006/10/17 (CS):
% - first version of this file
%
% 2006/10/18 (CS):
% - implemented separated autoscaling for min, max, gamma
% - fixed bug in edit_image_depth
% - fixed bug with rescaling the image when changing the image dimensions.

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

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

% ------------------------------------------------------------------
% add some struct arrays to store handle data in an organized manner
handles.data = struct(...
    'image_dim',{[487 195]},...
    'image',{''},...
    'filter_image',{''},...
    'disp_image',{''},...
    'image_cdepth',{32},...
    'scanlog',{''},...
    'scanlogheader',{''},...
    'npoints',{0});

handles.files = struct(...
    'image',{''},...
    'imagepath',{''},...
    'image_file_format',{'image_%05d.img'},...
    'scanlogfile',{''},...
    'scanlogpath',{''},...
    'list_scan_files',{0},...
    'file_filter',{'*.img'},...
    'cwdir',{''});

handles.image_control = struct(...
    'gamma',{1},...
    'max',{56535},...
    'min',{0},...
    'caxis',{''},...
    'colormap',{'jet'},...
    'filter',{'none'},...
    'autoscale_max',{1},...
    'autoscale_min',{1},...
    'autoscale_gamma',{0},...
    'slider_max',{56535},...
    'slider_min',{0});

handles.roi = struct(...
    'roi',{ones([handles.data.image_dim(2) handles.data.image_dim(1)])},...
    'roi_color',{[1 0 0]});

handles.figures.view_scanlogfile.text_scanlog = struct(...
    'figure',{0},...
    'text_scanlog',{0});

handles.data.image = ones([handles.data.image_dim(2) handles.data.image_dim(1)]);

%-------------------------------------

% populate the axes with image objects.
ydim = handles.data.image_dim(1);
xdim = handles.data.image_dim(2);

handles.image_zoom_image = image(zeros([xdim ydim]),...
    'Tag','image_zoom_image',...
    'CDataMapping','scaled',...
    'Parent', handles.axes_zoom_image);
handles.image_colorbar = imagesc(ones([1024 1]),...
    'Tag','image_colorbar',...
    'CDataMapping','direct',...
    'Parent', handles.axes_colorbar);
set(handles.axes_colorbar,'YDir','normal');


% prepare the image scroll panel and set magnification to 400%
handles.zoom_image_scrollpanel = imscrollpanel(handles.uipanel_zoom_image,...
    handles.image_zoom_image);
set(handles.zoom_image_scrollpanel,...
    'Clipping','on',...
    'Units','normalized',...
    'Position',[0 .1 1 .9])
scrollapi = iptgetapi(handles.zoom_image_scrollpanel);
handles.zoom_image_scrollpanel_api = scrollapi;
scrollapi.setMagnification(4);


% create the image magnification box
axes(handles.axes_zoom_image);
handles.zoom_image_magbox = immagbox(handles.uipanel_zoom_image,...
    handles.image_zoom_image);
set(handles.zoom_image_magbox,...
    'Units','normalized',...
    'Position',[0.1 0 0.2 0.1]);


% create the pixel information tool
handles.zoom_image_pixinf = impixelinfoval(handles.uipanel_zoom_image,...
    [handles.image_zoom_image]);
set(handles.zoom_image_pixinf,...
    'Units','normalized',...
    'FontSize',12,...
    'Position',[0.41 0 0.5 0.08]);


% create the image overview panel inside the Image Overview uipanel
handles.uipanel_image_overview = imoverviewpanel(handles.uipanel_original_image,...
    handles.image_zoom_image);
set(handles.uipanel_image_overview,'Units','Normalized',...
    'Position',[0.015 0 0.8 1]);


% get handles of axis and image object inside the overview panel
% 1) axis
handles.axes_original_image = findobj(handles.uipanel_image_overview,...
    'Type','axes');
set(handles.axes_original_image,'Tag','axes_original_image');
% 2) image
handles.image_original_image = findobj(handles.axes_original_image,...
    'Type','image');
set(handles.image_original_image,'Tag','image_original_image');


% Update handles structure
guidata(hObject, handles);


% make sure that a colormap is ready at startup
popupmenu_colormap_Callback(handles.popupmenu_colormap, eventdata, handles)


% position figure at upper left corner of screen
set(0,'Units','Pixels')
screen_pos = get(0,'ScreenSize');
set(hObject,'Units','Pixels')
fig_pos = get(hObject,'Position');
set(hObject,'Position',[10 screen_pos(4)-fig_pos(4)-50 fig_pos(3) fig_pos(4)])

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

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

%=========================================================================
% Object callbacks, CreateFcn, etc.
%=========================================================================

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

% Hint: place code in OpeningFcn to populate axes_original_image


%-------------------------------------------------------------------------
function edit_scanlogfile_Callback(hObject, eventdata, handles)
% hObject    handle to edit_scanlogfile (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 edit_scanlogfile as text
%        str2double(get(hObject,'String')) returns contents of edit_scanlogfile as a double

[path,base,ext] = fileparts(get(hObject,'String'));

% check if directory exists
if ~isdir(strcat(path,filesep))
    errordlg('directory does not exist','Directory error','on');
    return
end
handles.files.scanlogpath = strcat(path,filesep);

% check if scanlogfile exists
if ~exist(strcat(path,filesep,base,ext),'file')
    errordlg('file does not exist','File error','on')
    return
end
handles.files.scanlogfile = strcat(base,ext);

scanlog = strcat(path,filesep,base,ext);
[handles.data.scanlog,handles.data.scanlogheader]=readscanlog(scanlog);

data_dim = size(handles.data.scanlog);
handles.data.npoints = data_dim(1);

set(handles.popupmenu_image_column,'String',handles.data.scanlogheader')

% try to guess correct values for image data column
if any(strcmp('ID', handles.data.scanlogheader))
    set(handles.popupmenu_image_column,'Value',...
        find(strcmp('ID', handles.data.scanlogheader)));
elseif any(strcmp('image', handles.data.scanlogheader))
    set(handles.popupmenu_image_column,'Value',...
        find(strcmp('image', handles.data.scanlogheader)));
end

% update handles
guidata(handles.figure_imageviewer,handles)

% try to guess image path based on standard directory structure
if ~isdir(handles.files.imagepath)
    imdir = fileparts(fileparts(fileparts(handles.files.scanlogpath)));
    imdir = strcat(imdir,filesep,'pixel',filesep,'images');
    if isdir(imdir)
        set(handles.edit_imagepath,'String',imdir)  
        edit_imagepath_Callback(handles.edit_imagepath, eventdata, handles)
    end
end

% update handles structure, otherwise the one passed to this function
% will be used which does not contain the changes made by
% fcn_image_autoscale.
handles = guidata(handles.figure_imageviewer);
    
% call the rescan pushbutton callback function to update imagelist.
pushbutton_rescan_images_Callback(handles.pushbutton_rescan_images, ...
    eventdata, handles)

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_scanlogfile_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_scanlogfile (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 pushbutton_browse_scanlogfile.
function pushbutton_browse_scanlogfile_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton_browse_scanlogfile (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if isdir(handles.files.scanlogpath)
    uigetfile_filter = strcat(handles.files.scanlogpath,'*.dat');
elseif isdir(handles.files.imagepath)
    scanlogdir = fileparts(fileparts(handles.files.imagepath));
    scanlogdir = [scanlogdir filesep 'spec' filesep 'scanlogs' filesep];
    if isdir(scanlogdir)
        uigetfile_filter = strcat(scanlogdir,'*.dat');
    else
        uigetfile_filter = '*.dat'; 
    end
else
    uigetfile_filter = '*.dat';
end
[filename, path] = uigetfile(uigetfile_filter);

% don't do anything if user clicked Cancel
if isequal(filename,0)
    return
end

set (handles.edit_scanlogfile,'String',strcat(path,filename));
edit_scanlogfile_Callback(handles.edit_scanlogfile,eventdata,handles)

%-------------------------------------------------------------------------
% --- Executes on selection change in listbox_select_scanimage.
function listbox_select_scanimage_Callback(hObject, eventdata, handles)
% hObject    handle to listbox_select_scanimage (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 listbox_select_scanimage contents as cell array
%        contents{get(hObject,'Value')} returns selected item from listbox_select_scanimage

contents = get(hObject,'String');
imagename = contents(get(hObject,'Value'),:);
imagefile = strcat(handles.files.imagepath,imagename);

% retrieve file format
[pathstr, name, ext] = fileparts(imagefile);
switch ext
    case '.img'
        imageformat = 'img';
    case {'.tif','.tiff'}
        imageformat = 'tif';
    case '.edf'
        imageformat = 'edf';
    case '.ff'
        imageformat = 'ff';
    otherwise
        errordlg('image has invalid extension','File format error','on');
        return
end

imagedata = imageread(imagefile, imageformat,...
    handles.data.image_dim,handles.data.image_cdepth);

handles.data.image = imagedata;

% update navigation tools:
set(handles.edit_nofm,'String',...
    sprintf('%d',get(hObject,'Value')));

% update handles
guidata(handles.figure_imageviewer,handles)

popupmenu_filter_Callback(handles.popupmenu_filter, eventdata, handles)
fcn_update_image_info(handles.figure_imageviewer, eventdata, handles)
fcn_update_roi_info(handles.figure_imageviewer, eventdata, handles)

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function listbox_select_scanimage_CreateFcn(hObject, eventdata, handles)
% hObject    handle to listbox_select_scanimage (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



%-------------------------------------------------------------------------
function edit_image_xdim_Callback(hObject, eventdata, handles)
% hObject    handle to edit_image_xdim (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 edit_image_xdim as text
%        str2double(get(hObject,'String')) returns contents of edit_image_xdim as a double

xdim = str2double(get(hObject,'String'));

if xdim ~= floor(xdim)
    errordlg('xdim must be integer number','Value error','on');
    return
else
    handles.data.image_dim(1) = uint32(xdim);
    guidata(handles.figure_imageviewer,handles)
end


%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_image_xdim_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_image_xdim (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



%-------------------------------------------------------------------------
function edit_image_ydim_Callback(hObject, eventdata, handles)
% hObject    handle to edit_image_ydim (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 edit_image_ydim as text
%        str2double(get(hObject,'String')) returns contents of edit_image_ydim as a double

ydim = str2double(get(hObject,'String'));

if ydim ~= floor(ydim)
    errordlg('ydim must be integer number','Value error','on');
    return
else
    handles.data.image_dim(2) = uint32(ydim);
    guidata(handles.figure_imageviewer,handles)
end

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_image_ydim_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_image_ydim (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



%-------------------------------------------------------------------------
function edit_image_depth_Callback(hObject, eventdata, handles)
% hObject    handle to edit_image_depth (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 edit_image_depth as text
%        str2double(get(hObject,'String')) returns contents of edit_image_depth as a double

depth = str2double(get(hObject,'String'));

if ~(any(depth == [8 16 32 64]))
    errordlg('color depth can only be: 8, 16, 32, or 64','Value error','on');
    return
else
    handles.data.image_cdepth = uint32(depth);
    guidata(handles.figure_imageviewer,handles)
end


%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_image_depth_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_image_depth (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 pushbutton_navigation_begin.
function pushbutton_navigation_begin_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton_navigation_begin (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

set(handles.listbox_select_scanimage,'Value',1);

% call listbox callback
listbox_select_scanimage_Callback(handles.listbox_select_scanimage,...
                                  eventdata,handles);


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

currentpoint = get(handles.listbox_select_scanimage,'Value');
point = currentpoint - ...
        int32(str2double(get(handles.edit_navigation_stepn,'String')));

% restrict to allowed values if out of bounds
if point < 1
    point =1;
elseif point > handles.data.npoints
    point = handles.data.npoints;
end
    
set(handles.listbox_select_scanimage,'Value',point);

% call listbox callback
listbox_select_scanimage_Callback(handles.listbox_select_scanimage,...
                                  eventdata,handles);


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

currentpoint = get(handles.listbox_select_scanimage,'Value');
point = currentpoint - 1;

% restrict to allowed values if out of bounds
if point < 1
    point =1;
elseif point > handles.data.npoints
    point = handles.data.npoints;
end
    
set(handles.listbox_select_scanimage,'Value',point);

% call listbox callback
listbox_select_scanimage_Callback(handles.listbox_select_scanimage,...
                                  eventdata,handles);


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

currentpoint = get(handles.listbox_select_scanimage,'Value');
point = currentpoint + 1;

% restrict to allowed values if out of bounds
if point < 1
    point =1;
elseif point > handles.data.npoints
    point = handles.data.npoints;
end
    
set(handles.listbox_select_scanimage,'Value',point);

% call listbox callback
listbox_select_scanimage_Callback(handles.listbox_select_scanimage,...
                                  eventdata,handles);


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

currentpoint = get(handles.listbox_select_scanimage,'Value');
point = currentpoint + ...
        int32(str2double(get(handles.edit_navigation_stepn,'String')));

% restrict to allowed values if out of bounds
if point < 1
    point =1;
elseif point > handles.data.npoints
    point = handles.data.npoints;
end
    
set(handles.listbox_select_scanimage,'Value',point);

% call listbox callback
listbox_select_scanimage_Callback(handles.listbox_select_scanimage,...
                                  eventdata,handles);


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

set(handles.listbox_select_scanimage,'Value',handles.data.npoints);

% call listbox callback
listbox_select_scanimage_Callback(handles.listbox_select_scanimage,...
                                  eventdata,handles);

%-------------------------------------------------------------------------
function edit_navigation_stepn_Callback(hObject, eventdata, handles)
% hObject    handle to edit_navigation_stepn (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 edit_navigation_stepn as text
%        str2double(get(hObject,'String')) returns contents of edit_navigation_stepn as a double


%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_navigation_stepn_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_navigation_stepn (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 slider movement.
function slider_gamma_Callback(hObject, eventdata, handles)
% hObject    handle to slider_gamma (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

slipos = get (hObject, 'Value');
gamma = 10^slipos;
set (handles.edit_gamma, 'String', num2str (gamma, '% 2.4g'));
edit_gamma_Callback(handles.edit_gamma,eventdata,handles);

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function slider_gamma_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider_gamma (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_intensity_max_Callback(hObject, eventdata, handles)
% hObject    handle to slider_intensity_max (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

slipos = get (hObject, 'Value');
set (handles.edit_intensity_max, 'String', num2str (slipos, '%.0f'));
edit_intensity_max_Callback(handles.edit_intensity_max,eventdata,handles);


%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function slider_intensity_max_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider_intensity_max (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_intensity_min_Callback(hObject, eventdata, handles)
% hObject    handle to slider_intensity_min (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

slipos = get (hObject, 'Value');
set (handles.edit_intensity_min, 'String', num2str (slipos, '%.0f'));
edit_intensity_min_Callback(handles.edit_intensity_min,eventdata,handles);

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function slider_intensity_min_CreateFcn(hObject, eventdata, handles)
% hObject    handle to slider_intensity_min (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 selection change in popupmenu_filter.
function popupmenu_filter_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu_filter (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 popupmenu_filter contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu_filter

contents = get(hObject, 'String');
imagefilter = contents{get(hObject, 'Value')};

% apply ff-data to the original image

% do that here...
% handles.data.filter_image = handles.data.image * ffdata;
handles.data.filter_image = handles.data.image;

% then apply filter
switch imagefilter
    case '3x3 median'
        handles.data.filter_image = medianfilter(handles.data.filter_image, ...
            [3 3], -1, [], [], 'median');
    case '3x3 mean'
        handles.data.filter_image = medianfilter(handles.data.filter_image, ...
            [3 3], -1, [], [], 'mean');
    case 'no filter'
        % don't do anything...
end


% update handles
guidata(handles.figure_imageviewer,handles)

% call function to display the image
fcn_image_display(handles.figure_imageviewer, eventdata, handles)

% apply image control parameters
fcn_image_control(hObject, eventdata, handles);

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function popupmenu_filter_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu_filter (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


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

auto = get(hObject,'Value');

% update handles
handles.image_control.autoscale_max = auto;
guidata(handles.checkbox_autoscale_max,handles)

if auto
    fcn_image_control(handles.checkbox_autoscale_max, eventdata, handles)
end

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

auto = get(hObject,'Value');

% update handles
handles.image_control.autoscale_gamma = auto;
guidata(handles.checkbox_autoscale_gamma,handles)

if auto
    fcn_image_control(handles.figure_imageviewer, eventdata, handles)
end


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

auto = get(hObject,'Value');

% update handles
handles.image_control.autoscale_min = auto;
guidata(handles.checkbox_autoscale_min,handles)

if auto
    fcn_image_control(handles.figure_imageviewer, eventdata, handles)
end


%-------------------------------------------------------------------------
function edit_intensity_range_min_Callback(hObject, eventdata, handles)
% hObject    handle to edit_intensity_range_min (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 edit_intensity_range_min as text
%        str2double(get(hObject,'String')) returns contents of edit_intensity_range_min as a double

slider_range_min = str2double(get(hObject,'String'));

% make sure slider_range_min is lower than value of min-slider and bigger
% than zero
slider_min_val = str2double(get(handles.edit_intensity_min,'String'));
slider_range_min = max([0 slider_range_min]);
slider_range_min = min([slider_min_val slider_range_min]);

% update string and slider ranges
set (hObject,'String',slider_range_min);
set (handles.slider_intensity_min,'Min',slider_range_min)
set (handles.slider_intensity_max,'Min',slider_range_min)

% update handles
handles.image_control.slider_min = slider_range_min;
guidata(handles.edit_intensity_range_min,handles)


%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_intensity_range_min_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_intensity_range_min (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



%-------------------------------------------------------------------------
function edit_intensity_range_max_Callback(hObject, eventdata, handles)
% hObject    handle to edit_intensity_range_max (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 edit_intensity_range_max as text
%        str2double(get(hObject,'String')) returns contents of edit_intensity_range_max as a double

slider_range_max = str2double(get(hObject,'String'));

% make sure slider_range_max is higher than value of max-slider
slider_max_val = str2double(get(handles.edit_intensity_max,'String'));
slider_range_max = max([slider_range_max slider_max_val]);

% update string and slider ranges
set(hObject,'String',slider_range_max);
set (handles.slider_intensity_min,'Max',slider_range_max);
set (handles.slider_intensity_max,'Max',slider_range_max);

% update handles
handles.image_control.slider_max = slider_range_max;
guidata(handles.edit_intensity_range_max,handles)


%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_intensity_range_max_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_intensity_range_max (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


%-------------------------------------------------------------------------
function edit_gamma_Callback(hObject, eventdata, handles)
% hObject    handle to edit_gamma (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 edit_gamma as text
%        str2double(get(hObject,'String')) returns contents of edit_gamma as a double

% deactivate auto-scaling
set(handles.checkbox_autoscale_gamma,'Value',0);
checkbox_autoscale_gamma_Callback(handles.checkbox_autoscale_gamma, ...
    eventdata, handles)

gamma = str2double(get(hObject,'String'));

% restrict to values between 0.1 and 10
gamma = max([gamma 0.1]);
gamma = min([gamma 10]);
set(hObject,'String',gamma)

handles.image_control.gamma = gamma;

% update slider value
set(handles.slider_gamma,'Value',log10(gamma));

% update handles
guidata(handles.figure_imageviewer,handles)

% redisplay image
fcn_image_control(handles.figure_imageviewer, eventdata, handles);

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_gamma_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_gamma (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


%-------------------------------------------------------------------------
function edit_intensity_max_Callback(hObject, eventdata, handles)
% hObject    handle to edit_intensity_max (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 edit_intensity_max as text
%        str2double(get(hObject,'String')) returns contents of edit_intensity_max as a double

% deactivate auto-scaling
set(handles.checkbox_autoscale_max,'Value',0);
checkbox_autoscale_max_Callback(handles.checkbox_autoscale_max, ...
    eventdata, handles)

int_max = str2double(get(hObject,'String'));
int_min_val = str2double(get(handles.edit_intensity_min,'String'));

% make sure int_max is larger than the value for int_min
int_max = max([int_min_val+1 int_max]);

% adjust slider ranges if value is out of bounds
slider_min = str2double(get(handles.edit_intensity_range_min,'String'));
slider_max = str2double(get(handles.edit_intensity_range_max,'String'));
if int_max < slider_min
    set(handles.edit_intensity_range_min,'String',int_max)
    edit_intensity_range_min_Callback(handles.edit_intensity_range_min,...
        eventdata,handles)
elseif int_max > slider_max
    set(handles.edit_intensity_range_max,'String',int_max)
    edit_intensity_range_max_Callback(handles.edit_intensity_range_max,...
        eventdata,handles)
end

handles.image_control.max = int_max;

% update strint and slider value
set(handles.edit_intensity_max,'String',int_max);
set(handles.slider_intensity_max,'Value',int_max);

% update handles
guidata(handles.figure_imageviewer,handles)

% redisplay image
fcn_image_control(handles.figure_imageviewer, eventdata, handles);


%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_intensity_max_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_intensity_max (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



%-------------------------------------------------------------------------
function edit_intensity_min_Callback(hObject, eventdata, handles)
% hObject    handle to edit_intensity_min (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 edit_intensity_min as text
%        str2double(get(hObject,'String')) returns contents of edit_intensity_min as a double

% deactivate auto-scaling
set(handles.checkbox_autoscale_min,'Value',0);
checkbox_autoscale_min_Callback(handles.checkbox_autoscale_min, ...
    eventdata, handles)

int_min = str2double(get(hObject,'String'));
int_max_val = str2double(get(handles.edit_intensity_max,'String'));

% make sure int_min is between 0 and the value for int_max
int_min = max([0 int_min]);
int_min = min([int_min int_max_val-1]);

% adjust slider ranges if value is out of bounds
slider_min = str2double(get(handles.edit_intensity_range_min,'String'));
slider_max = str2double(get(handles.edit_intensity_range_max,'String'));
if int_min < slider_min
    set(handles.edit_intensity_range_min,'String',int_min)
    edit_intensity_range_min_Callback(handles.edit_intensity_range_min,...
        eventdata,handles)
elseif int_min > slider_max
    set(handles.edit_intensity_range_max,'String',int_min)
    edit_intensity_range_max_Callback(handles.edit_intensity_range_max,...
        eventdata,handles)
end

handles.image_control.min = int_min;

% update slider and string value
set(handles.edit_intensity_min,'String',int_min);
set(handles.slider_intensity_min,'Value',int_min);

% update handles
guidata(handles.figure_imageviewer,handles)

% redisplay image
fcn_image_control(handles.figure_imageviewer, eventdata, handles);

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_intensity_min_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_intensity_min (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 pushbutton_zoom_out.
function pushbutton_zoom_out_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton_zoom_out (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

scrollapi = handles.zoom_image_scrollpanel_api;
mag = scrollapi.getMagnification();
mag = max([0.25 mag/2]);
scrollapi.setMagnification(mag);

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

scrollapi = handles.zoom_image_scrollpanel_api;
mag = scrollapi.getMagnification();
mag = min([100 mag*2]);
scrollapi.setMagnification(mag);

%-------------------------------------------------------------------------
% --- Executes on button press in pushbutton_zoom_area.
function pushbutton_zoom_area_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton_zoom_area (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 popupmenu_colormap.
function popupmenu_colormap_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu_colormap (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 popupmenu_colormap contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu_colormap

contents = get(hObject,'String');
cmap = contents{get(hObject,'Value')};
cmap = [cmap '(1024)'];
handles.image_control.colormap = colormap(cmap);

% adjust colorbar
gamma = handles.image_control.gamma;
cmap_dim = size(handles.image_control.colormap);
set(handles.axes_colorbar,'YLim',[0 cmap_dim(1)]);
cbardata = (0:1:cmap_dim(1))';
cbardata = cbardata;%.^(gamma);
set(handles.image_colorbar,'CData',cbardata,'CDataMapping','scaled');

% update handles
guidata(hObject,handles)


%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function popupmenu_colormap_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu_colormap (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

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function pushbutton_navigation_begin_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_navigation_begin (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 pushbutton_navigation_minusn_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_navigation_minusn (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 pushbutton_navigation_previous_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_navigation_previous (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 pushbutton_navigation_next_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_navigation_next (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 pushbutton_navigation_plusn_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_navigation_plusn (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 pushbutton_navigation_end_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_navigation_end (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called



%-------------------------------------------------------------------------
function edit_nofm_Callback(hObject, eventdata, handles)
% hObject    handle to edit_nofm (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 edit_nofm as text
%        str2double(get(hObject,'String')) returns contents of edit_nofm as a double

point = int32(str2double(get(hObject,'String')));

% restrict to allowed values if out of bounds
if point < 1
    point =1;
elseif point > handles.data.npoints
    point = handles.data.npoints;
end
    
set(handles.listbox_select_scanimage,'Value',point);

% call listbox callback
listbox_select_scanimage_Callback(handles.listbox_select_scanimage,...
                                  eventdata,handles);


%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_nofm_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_nofm (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



%-------------------------------------------------------------------------
function edit_imagepath_Callback(hObject, eventdata, handles)
% hObject    handle to edit_imagepath (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 edit_imagepath as text
%        str2double(get(hObject,'String')) returns contents of edit_imagepath as a double

imagepath = get(hObject,'String');

% check if directory exists
if ~isdir(imagepath)
    errordlg('directory does not exist','Directory error','on');
    return
end

if ~strcmp(imagepath(length(imagepath)),filesep)
    imagepath = strcat(imagepath,filesep);
    set(hObject,'String',imagepath);
end

handles.files.imagepath = imagepath;

% update handles
guidata(handles.figure_imageviewer,handles)

pushbutton_rescan_images_Callback(handles.pushbutton_rescan_images, eventdata, handles)

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_imagepath_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_imagepath (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 pushbutton_browse_imagepath.
function pushbutton_browse_imagepath_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton_browse_imagepath (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

if isdir(handles.files.imagepath) && ...
        (strcmp(handles.files.imagepath,filesep)==0)
    uigetdir_startpath = handles.files.imagepath;
elseif isdir(handles.files.scanlogpath)
    imagedir = fileparts(fileparts(fileparts(handles.files.scanlogpath)));
    imagedir = [imagedir filesep 'pixel' filesep 'images' filesep];
    if isdir(imagedir)
        uigetdir_startpath = imagedir;
    else
        uigetdir_startpath = handles.files.scanlogpath;
    end
else
    uigetdir_startpath = pwd;
end

imagepath = uigetdir(uigetdir_startpath,'Select image path');

% don't do anything if user clicked Cancel
if isequal(imagepath,0)
    return
else
    imagepath = strcat(imagepath,filesep);
    set (handles.edit_imagepath,'String',imagepath)
    edit_imagepath_Callback(handles.edit_imagepath,eventdata,handles)
end

%-------------------------------------------------------------------------
function edit_image_file_format_Callback(hObject, eventdata, handles)
% hObject    handle to edit_image_file_format (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 edit_image_file_format as text
%        str2double(get(hObject,'String')) returns contents of edit_image_file_format as a double

image_file_format = get(hObject,'String');

%
% here we should check whether syntax is valid...
% i.e. whether it contains a %0Xd string.
%

handles.files.image_file_format = image_file_format;

% update handles
guidata(handles.figure_imageviewer,handles)

% call the rescan pushbutton callback function to update filelist.
pushbutton_rescan_images_Callback(handles.pushbutton_rescan_images, eventdata, handles)

%-------------------------------------------------------------------------
% --- Executes during object creation, after setting all properties.
function edit_image_file_format_CreateFcn(hObject, eventdata, handles)
% hObject    handle to edit_image_file_format (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 pushbutton_show_scanlog.
function pushbutton_show_scanlog_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton_show_scanlog (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    structure with handles and user data (see GUIDATA)

handles.figures.view_scanlogfile.figure = ...
    figure('Name','view_scanlogfile',...
    'ResizeFcn',@fcn_view_scanlogfile_ResizeFcn);
pos = get(handles.figures.view_scanlogfile.figure,'Position');
text_handle = uicontrol(handles.figures.view_scanlogfile.figure,...
    'style','listbox','Position',[0 0 pos(3) pos(4)],...
    'horizontalAlignment','left',...
    'FontName', 'FixedWidth',...
    'FontSize',9,...
    'Tag','text_view_scanlogfile',...
    'max',20,'min',1);
handles.figures.view_scanlogfile.text_scanlog = text_handle;

%-------------------------------
% find out maximum column widths
col_width = zeros(size(handles.data.scanlogheader));
data_dim = size(handles.data.scanlog);

% 1. header line
for i=1:length(handles.data.scanlogheader)
    col_width(i) = length(handles.data.scanlogheader{i});
end

% 2. data section
for i=1:data_dim(2)
    data_string = [];
    for j=1:data_dim(1)
        data_string = strvcat(data_string,...
            sprintf('%g ',handles.data.scanlog(j,i)));
    end
    data_string_size = size(data_string);
    col_width(i) = max([col_width(i) data_string_size(2)]);
end

%----------------------------
% build formatted data string

% build header line from handles.data.scanlogheader char array
header_string = '';
for i=1:length(handles.data.scanlogheader)
    format_tag = sprintf('%%%ds ',col_width(i));
    header_string = [header_string sprintf(format_tag,...
        handles.data.scanlogheader{i})];
end
header_string = char(header_string);

% print formatted data lines from handles.data.scanlog
data_string = [];
for i=1:data_dim(2)
    data_string_col = [];
    for j=1:data_dim(1)
        format_tag = sprintf('%%%dg ',col_width(i));
        data_string_col = strvcat(data_string_col,...
            sprintf(format_tag,handles.data.scanlog(j,i)));
    end
    data_string = [data_string data_string_col];
end

% display scanlogfile in the text field
set(handles.figures.view_scanlogfile.text_scanlog,...
    'String',strvcat(header_string, data_string));

%-------------------------------------------------------------------------
% --- Resize function for the scanlog preview window.
function fcn_view_scanlogfile_ResizeFcn(hObject, eventdata, handles)
pos=get(gcbo,'Position');
set(findobj('Tag','text_view_scanlogfile'),'Position',[0 0 pos(3) pos(4)]);


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

imagepath = handles.files.imagepath;
image_file_format = handles.files.image_file_format;
image_list_string = [];
listbox_ok = 1;

% rescale image axes in case image dimension changed
set(handles.axes_original_image,'Xlim',[1 handles.data.image_dim(1)])
set(handles.axes_original_image,'Ylim',[1 handles.data.image_dim(2)])
set(handles.axes_zoom_image,'Xlim',[1 handles.data.image_dim(1)])
set(handles.axes_zoom_image,'Ylim',[1 handles.data.image_dim(2)])

% scan image directory or scanlogfile for images
switch handles.files.list_scan_files

    % display all images in image directory
    case 0
        
        file_list = dir(fullfile(imagepath,handles.files.file_filter));
        npoints = length(file_list);
        handles.data.npoints = npoints;
        
        if npoints < 1
            image_list_string = sprintf('Could not find any images: %s',...
                fullfile(imagepath,handles.files.file_filter));
            npoints = 1;
            listbox_ok = 0;
            errmsg = sprintf('No image files found in directory\n%s',...
                fullfile(imagepath,handles.files.file_filter));
        else

            for i=1:npoints
                image_list_string = ...
                    strvcat(image_list_string, file_list(i).name);
            end
        end
        
    % display only images in scanlog
    case 1
        
        npoints = handles.data.npoints;
        imagecol = get(handles.popupmenu_image_column,'Value');
        imagenumbers = handles.data.scanlog(:,imagecol);
        for i=1:npoints
            imagefilename = sprintf(image_file_format,imagenumbers(i));

            % check whether file exists, then add to list.
            if ~exist(strcat(imagepath,imagefilename),'file')
                image_list_string = sprintf('Could not find image: %s',...
                    strcat(imagepath,imagefilename));
                listbox_ok = 0;
                errmsg = ...
                    sprintf('Error reading images in scanlog\n%s%s',...
                    handles.files.scanlogpath, handles.files.scanlogfile);
            else
                image_list_string = ...
                    strvcat(image_list_string, imagefilename);
            end
        end
        
        
end

set(handles.listbox_select_scanimage,'String',...
    image_list_string);

% update handles
guidata(handles.figure_imageviewer,handles)

% set new listbox value if current one is out of bounds.
if get(handles.listbox_select_scanimage,'Value') > npoints
    set(handles.listbox_select_scanimage,'Value',npoints);
end

% update navigation tools:
set(handles.text_nimages,'String',sprintf('of %d',npoints));
set(handles.edit_nofm,'String',...
    sprintf('%d',get(handles.listbox_select_scanimage,'Value')));

% display current image
if listbox_ok
    listbox_select_scanimage_Callback(handles.listbox_select_scanimage,...
        eventdata, handles);
else
    errordlg(errmsg,'Image file error','on');
end

%=========================================================================
% Additional functions
%=========================================================================

%-------------------------------------------------------------------------
% --- apply changes to the displayed image.
function fcn_image_control(hObject, eventdata, handles)

% perform auto-scaling if selected
auto = [get(handles.checkbox_autoscale_min,'Value'),...
    get(handles.checkbox_autoscale_max,'Value'),...
    get(handles.checkbox_autoscale_gamma,'Value')];
if any(auto)
    fcn_image_autoscale(handles.figure_imageviewer, eventdata, handles)
    
    % update handles structure, otherwise the one passed to this function
    % will be used which does not contain the changes made by
    % fcn_image_autoscale.
    handles = guidata(hObject);
end

gamma = handles.image_control.gamma;
int_min = handles.image_control.min;
int_max = handles.image_control.max;

cmap = handles.image_control.colormap;

cmap_dim = size(cmap);
cind = ((1:cmap_dim(1))-1)./(cmap_dim(1)-1);
cind = cind.^gamma;
cind = round(cind.*(cmap_dim(1)-1))+1;
cmap = handles.image_control.colormap(cind,:);
colormap(cmap);

% change caxis of colorbar
nticks = length(get(handles.axes_colorbar,'YTick'));
ticks = linspace(int_min,int_max,nticks);
ticks = ((((ticks-int_min)./(int_max-int_min)).^(1/gamma)).*...
        (int_max-int_min))+int_min;
set(handles.axes_colorbar,'YTickLabel',ticks);

% adjust colorbar
cmap_dim = size(handles.image_control.colormap);
set(handles.axes_colorbar,'YLim',[0 cmap_dim(1)]);
cbardata = (0:1:cmap_dim(1))';
cbardata = cbardata.^(1/gamma);

set(handles.image_colorbar,'CData',cbardata,'CDataMapping','scaled');

% change caxis of overview image
axes(handles.axes_original_image);
caxis([int_min int_max]);

% change caxis of zoom image
axes(handles.axes_zoom_image);
caxis([int_min int_max]);

% update handles
guidata(handles.figure_imageviewer,handles)

%-------------------------------------------------------------------------
% --- display the entire image.
function fcn_image_display(hObject, eventdata, handles)

set(handles.image_original_image,'CData',handles.data.filter_image);
set(handles.image_zoom_image,'CData',handles.data.filter_image);


%-------------------------------------------------------------------------
% --- perform autoscaling of image.
function fcn_image_autoscale(hObject, eventdata, handles)

auto_max = get(handles.checkbox_autoscale_max,'Value');
auto_min = get(handles.checkbox_autoscale_min,'Value');
auto_gamma = get(handles.checkbox_autoscale_gamma,'Value');

int_min = handles.image_control.min;
int_max = handles.image_control.max;
gamma = handles.image_control.gamma;

I = handles.data.filter_image;
scale = max(max(I));
I = I./scale;
int_lim = stretchlim(I,[0.00005 0.99995]);

if auto_min
    int_min = floor(int_lim(1)*scale);
end

if auto_max
    int_max = ceil(int_lim(2)*scale);
end

if auto_gamma
    temp_img = imadjust(I,int_lim);
    [temp_img2,Ty] = histeq(temp_img);
    Tx = (1:length(Ty))./length(Ty);

    % fit gamma value to the equalized histogram
    optimset('Display','off','LargeScale','off','TolFun',1e-4);
    minfunc = @(g,x,y)sum(((x.^g)-y).^2);
    gamma = fminsearch(@(g) minfunc(g,Tx,Ty),0.5);

    % restrict gamma to values between 0.1 and 10
    gamma = max([gamma 0.1]);
    gamma = min([gamma 10]);
end

%----------------------------------------
% update all slider and edit text values:
slider_min = str2double(get(handles.edit_intensity_range_min,'String'));
slider_max = str2double(get(handles.edit_intensity_range_max,'String'));

% 1. Intensity minimum:
% adjust slider ranges if value is out of bounds
if int_min < slider_min
    set(handles.edit_intensity_range_min,'String',int_min)
    edit_intensity_range_min_Callback(handles.edit_intensity_range_min,...
        eventdata,handles)
elseif int_min > slider_max
    set(handles.edit_intensity_range_max,'String',int_min)
    edit_intensity_range_max_Callback(handles.edit_intensity_range_max,...
        eventdata,handles)
end
% update string and slider values
handles.image_control.min = int_min;
set(handles.edit_intensity_min,'String',int_min);
set(handles.slider_intensity_min,'Value',int_min);
guidata(handles.figure_imageviewer,handles);

% 2. Intensity maximum:
% adjust slider ranges if value is out of bounds
if int_max < slider_min
    set(handles.edit_intensity_range_min,'String',int_max)
    edit_intensity_range_min_Callback(handles.edit_intensity_range_min,...
        eventdata,handles)
elseif int_max > slider_max
    set(handles.edit_intensity_range_max,'String',int_max)
    edit_intensity_range_max_Callback(handles.edit_intensity_range_max,...
        eventdata,handles)
end
% update string and slider value
handles.image_control.max = int_max;
set(handles.edit_intensity_max,'String',int_max);
set(handles.slider_intensity_max,'Value',int_max);
guidata(handles.figure_imageviewer,handles);

% 3. gamma value:
% update string and slider value
handles.image_control.gamma = gamma;
set(handles.edit_gamma,'String',gamma)
set(handles.slider_gamma,'Value',log10(gamma));
guidata(handles.figure_imageviewer,handles);


% --- Executes during object creation, after setting all properties.
function text_label_intensity_min_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_intensity_min (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 text_label_intensity_max_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_intensity_max (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 text_label_gamma_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_gamma (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 checkbox_autoscale_max_CreateFcn(hObject, eventdata, handles)
% hObject    handle to checkbox_autoscale_max (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 text_image_info_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_image_info (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 uipanel_imagecontrol_CreateFcn(hObject, eventdata, handles)
% hObject    handle to uipanel_imagecontrol (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 uipanel_zoom_image_CreateFcn(hObject, eventdata, handles)
% hObject    handle to uipanel_zoom_image (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 axes_zoom_image_CreateFcn(hObject, eventdata, handles)
% hObject    handle to axes_zoom_image (see GCBO)
% eventdata  reserved - to be defined in a future version of MATLAB
% handles    empty - handles not created until after all CreateFcns called

% Hint: place code in OpeningFcn to populate axes_zoom_image


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

% Hint: place code in OpeningFcn to populate axes_colorbar


% --- Executes during object creation, after setting all properties.
function uipanel_original_image_CreateFcn(hObject, eventdata, handles)
% hObject    handle to uipanel_original_image (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 pushbutton_zoom_out_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_zoom_out (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 pushbutton_zoom_in_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_zoom_in (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 text_navigation_n_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_navigation_n (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 text_nimages_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_nimages (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 uipanel_navigation_CreateFcn(hObject, eventdata, handles)
% hObject    handle to uipanel_navigation (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 text_label_scanlog_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_scanlog (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 pushbutton_browse_scanlogfile_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_browse_scanlogfile (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 pushbutton_show_scanlog_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_show_scanlog (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 text_label_imagepath_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_imagepath (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 pushbutton_browse_imagepath_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_browse_imagepath (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 text_label_image_file_format_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_image_file_format (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 text_label_horiz_size_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_horiz_size (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 text_label_vet_size_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_vet_size (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 text_label_bit_depth_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_bit_depth (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 pushbutton_rescan_images_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_rescan_images (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 text_label_imagelist_CreateFcn(hObject, eventdata, handles)
% hObject    handle to text_label_imagelist (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 selection change in popupmenu_image_column.
function popupmenu_image_column_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu_image_column (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 popupmenu_image_column contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu_image_column


% --- Executes during object creation, after setting all properties.
function popupmenu_image_column_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu_image_column (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


% --- Executes on selection change in popupmenu_select_roi.
function popupmenu_select_roi_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu_select_roi (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 popupmenu_select_roi contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu_select_roi

contents = get(hObject,'String');
method = contents{get(hObject,'Value')};

switch method
    case 'none'

        if isfield(handles,'line_roi') && ishandle(handles.line_roi)
            delete(handles.line_roi);
        end
        if isfield(handles,'line_roi_overview') && ...
                ishandle(handles.line_roi_overview)
            delete(handles.line_roi_overview);
        end
        
    otherwise
        [MaskImage,x,y] = setroi(handles.axes_zoom_image,method);
        handles.roi.roi = MaskImage;
        lineColor = handles.roi.roi_color;
        
        % draw line in zoom image
        axes(handles.axes_zoom_image);
        hold on;
        if isfield(handles,'line_roi') && ishandle(handles.line_roi)
            set(handles.line_roi,'xdata',x,'ydata',y);
            set(handles.line_roi,'Color',lineColor);
        else
            handles.line_roi = plot(x,y,'Color',lineColor,'LineWidth',2);
        end

        % draw line in overview image
        axes(handles.axes_original_image);
        hold on;
        if isfield(handles,'line_roi_overview') && ...
                ishandle(handles.line_roi_overview)
            set(handles.line_roi_overview,'xdata',x,'ydata',y);
            set(handles.line_roi_overview,'Color',lineColor);
        else
            handles.line_roi_overview = plot(x,y,'Color',lineColor,'LineWidth',2);
        end
end

% update handles
guidata(handles.figure_imageviewer,handles)

fcn_update_roi_info(handles.figure_imageviewer, ...
    eventdata, handles);

% --- Executes during object creation, after setting all properties.
function popupmenu_select_roi_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu_select_roi (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


% --- Executes on selection change in pushbutton_roi_color.
function pushbutton_roi_color_Callback(hObject, eventdata, handles)
% hObject    handle to pushbutton_roi_color (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 pushbutton_roi_color contents as cell array
%        contents{get(hObject,'Value')} returns selected item from pushbutton_roi_color

color = uisetcolor(handles.roi.roi_color,'Select ROI color');

if isequal(color,0)
    return
end

if isfield(handles,'line_roi')
    set(handles.line_roi,'Color',color);    
end
if isfield(handles,'line_roi_overview')
    set(handles.line_roi_overview,'Color',color);    
end
handles.roi.roi_color = color;

% update handles
guidata(handles.figure_imageviewer,handles)

% --- Executes during object creation, after setting all properties.
function pushbutton_roi_color_CreateFcn(hObject, eventdata, handles)
% hObject    handle to pushbutton_roi_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: 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


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

selected = get(handles.uipanel_files_and_paths,'SelectedObject');

if selected == handles.radiobutton_files_all
   handles.files.list_scan_files = 0;
   set(handles.popupmenu_file_filter,'Enable','on');
   set(handles.edit_scanlogfile,'Enable','off');
   set(handles.pushbutton_browse_scanlogfile,'Enable','off');
   set(handles.text_label_image_col,'Enable','off');   
   set(handles.popupmenu_image_column,'Enable','off');  
   set(handles.pushbutton_show_scanlog,'Enable','off');
   if isdir(handles.files.imagepath)
       edit_imagepath_Callback(handles.edit_imagepath,...
           eventdata,handles);
   end
elseif selected == handles.radiobutton_files_scanlog
   handles.files.list_scan_files = 1;
   set(handles.popupmenu_file_filter,'Enable','off');
   set(handles.edit_scanlogfile,'Enable','on');
   set(handles.pushbutton_browse_scanlogfile,'Enable','on');
   set(handles.text_label_image_col,'Enable','on');   
   set(handles.popupmenu_image_column,'Enable','on');  
   set(handles.pushbutton_show_scanlog,'Enable','on');
   if exist(strcat(handles.files.scanlogpath,handles.files.scanlogfile),...
           'file')
       edit_scanlogfile_Callback(handles.edit_scanlogfile,...
           eventdata,handles);
   end
end

% update handles
guidata(handles.figure_imageviewer,handles)


% --- Executes on selection change in popupmenu_file_filter.
function popupmenu_file_filter_Callback(hObject, eventdata, handles)
% hObject    handle to popupmenu_file_filter (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 popupmenu_file_filter contents as cell array
%        contents{get(hObject,'Value')} returns selected item from popupmenu_file_filter

contents = get(hObject,'String');
handles.files.file_filter = contents{get(hObject,'Value')};

% update handles
guidata(handles.figure_imageviewer,handles)

pushbutton_rescan_images_Callback(hObject,eventdata, handles)


% --- Executes during object creation, after setting all properties.
function popupmenu_file_filter_CreateFcn(hObject, eventdata, handles)
% hObject    handle to popupmenu_file_filter (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

%-------------------------------------------------------------------------
% --- update the image information text upon change of image info file.
function fcn_update_image_info(hObject, eventdata, handles)

im_image = handles.data.image;
im_counts = sum(im_image(:));
im_npix = numel(im_image);
[im_min, min_ind] = min(im_image(:));
[im_min_y, im_min_x] = ind2sub(size(im_image), min_ind);
[im_max, max_ind] = max(im_image(:));
[im_max_y, im_max_x] = ind2sub(size(im_image), max_ind);
im_avg = mean(im_image(:));
[im_cen_x im_cen_y] = centroid(im_image);

infoStr1 = sprintf('counts=%.3e',im_counts);
infoStr2 = sprintf('#pix=%-7d avg=%.2f',im_npix,im_avg);
infoStr3 = sprintf('cen=(%.1f,%.1f)',im_cen_x,im_cen_y);
infoStr4 = sprintf('min=%-7d @ (%d,%d)', im_min, im_min_x, im_min_y);
infoStr5 = sprintf('max=%-7d @ (%d,%d)', im_max, im_max_x, im_max_y);
infoStr = {infoStr1;infoStr2;infoStr3;infoStr4;infoStr5};

set(handles.text_image_info,'String',infoStr)

%-------------------------------------------------------------------------
% --- update the image information text upon change of image info file.
function fcn_update_roi_info(hObject, eventdata, handles)

roi_contents = get(handles.popupmenu_select_roi,'String');
roi_method = roi_contents{get(handles.popupmenu_select_roi,'Value')};

switch roi_method

    case 'none'

        set(handles.text_image_roi_info,'String',...
            'No region of interest defined');

    otherwise
        Mask = handles.roi.roi;
        ind = find(Mask);
        im_image = handles.data.image.*Mask;
        im_counts = sum(im_image(:));
        im_npix = sum(Mask(:));
        [im_min, min_ind] = min(im_image(ind));
        min_ind = ind(min_ind);
        [im_min_y, im_min_x] = ind2sub(size(im_image), min_ind);
        [im_max, max_ind] = max(im_image(ind));
        max_ind = ind(max_ind);
        [im_max_y, im_max_x] = ind2sub(size(im_image), max_ind);
        im_avg = mean(im_image(ind));
        [im_cen_x im_cen_y] = centroid(im_image);

        infoStr1 = sprintf('counts=%.3e',im_counts);
        infoStr2 = sprintf('#pix=%d avg=%.2f',im_npix,im_avg);
        infoStr3 = sprintf('cen=(%.1f,%.1f)',im_cen_x,im_cen_y);
        infoStr4 = sprintf('min=%-7d @ (%d,%d)', ...
            im_min, im_min_x, im_min_y);
        infoStr5 = sprintf('max=%-7d @ (%d,%d)', ...
            im_max, im_max_x, im_max_y);
        infoStr = {infoStr1;infoStr2;infoStr3;infoStr4;infoStr5};

        set(handles.text_image_roi_info,'String',infoStr)

end


%-------------------------------------------------------------------------
% --- calculate the centroid of image data.
function [x,y] = centroid(I)

    
[x,y,z] = size(I);          % Checking whether the picture is colored or monochromatic, if colored then converting to gray.
if ~(z==1)
    I = rgb2gray(I);
end

[rows,cols] = size(I);
x = ones(rows,1)*(1:cols);    % Matrix with each pixel set to its x coordinate
y = (1:rows)'*ones(1,cols);   %   "     "     "    "    "  "   "  y    "

area = sum(I(:));
if area > 0
    x = sum(sum(double(I).*x))/area;
    y = sum(sum(double(I).*y))/area;
else
    x = NaN;
    y = NaN; 
end


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


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


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


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


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

close(handles.figure_imageviewer)

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

I = handles.data.filter_image;

printfig = fcn_open_print_window(I, [0 0], hObject, eventdata, handles);

F = getframe(printfig);

[outfile, outpath] = uiputfile({'*.jpg';'*.tif'},...
                                'Export file');
% don't do anything if user clicked Cancel
if isequal(outfile,0)
    close(printfig)
    return
end

filename = fullfile(outpath, outfile);
[pathstr, name, ext] = fileparts(fullfile(outpath,outfile));

cmd = 'imwrite(F.cdata,filename';
switch ext
    case {'.jpg','.jpeg'}
        cmd = [cmd ',''Quality'',100'];     
end
cmd = [cmd ')'];

eval(cmd)
close(printfig)

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

rect = handles.zoom_image_scrollpanel_api.getVisibleImageRect();
ImPrint = imcrop(handles.data.filter_image,rect);

printfig = fcn_open_print_window(ImPrint, ...
    [rect(1) rect(2)], hObject, eventdata, handles);

F = getframe(printfig);

[outfile, outpath] = uiputfile({'*.jpg';'*.tif'},...
                                'Export file');
                            
% don't do anything if user clicked Cancel
if isequal(outfile,0)
    close(printfig)
    return
end                            
                            
filename = fullfile(outpath, outfile);
[pathstr, name, ext] = fileparts(fullfile(outpath,outfile));

cmd = 'imwrite(F.cdata,filename';
switch ext
    case {'.jpg','.jpeg'}
        cmd = [cmd ',''Quality'',100'];     
end
cmd = [cmd ')'];

eval(cmd)
close(printfig)


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

F = getframe(handles.figure_imageviewer);

[outfile, outpath] = uiputfile({'*.jpg';'*.tif'},...
                                'Export file');
% don't do anything if user clicked Cancel
if isequal(outfile,0)
    return
end

filename = fullfile(outpath, outfile);
[pathstr, name, ext] = fileparts(fullfile(outpath,outfile));

cmd = 'imwrite(F.cdata,filename';
switch ext
    case {'.jpg','.jpeg'}
        cmd = [cmd ',''Quality'',100'];
end
cmd = [cmd ')'];

eval(cmd)

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

I = handles.data.filter_image;
printfig = fcn_open_print_window(I, [0 0], hObject, eventdata, handles);

try
    printdlg('-crossplatform',printfig);

catch
    err = lasterror;
    if (strcmp(computer,'GLNX86') == 0)
        try
            F = getframe(printfig);
            imwrite(F.cdata,'/tmp/imageviewerfig.jpg','Quality',90);
            unix('chmod 777 /tmp/imageviewerfig.jpg');
            unix('lpr /tmp/imageviewerfig.jpg');
        catch
            err2 = lasterror;
            rethrow(err);
            rethrow(err2);
        end
    else
        rethrow(err);
    end
end

close(printfig)


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

rect = handles.zoom_image_scrollpanel_api.getVisibleImageRect();
ImPrint = imcrop(handles.data.filter_image,rect);
printfig = fcn_open_print_window(ImPrint, ...
    [rect(1) rect(2)], hObject, eventdata, handles);

try
    printdlg('-crossplatform',printfig);

catch
    err = lasterror;
    if (strcmp(computer,'GLNX86') == 0)
        try
            F = getframe(printfig);
            imwrite(F.cdata,'/tmp/imageviewerfig.jpg','Quality',90);
            unix('chmod 777 /tmp/imageviewerfig.jpg');
            unix('lpr /tmp/imageviewerfig.jpg');
        catch
            err2 = lasterror;
            rethrow(err);
            rethrow(err2);
        end
    else
        rethrow(err);
    end
end

close(printfig)


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

try
    printdlg('-crossplatform',handles.figure_imageviewer);
    
catch
    err = lasterror;
    if (strcmp(computer,'GLNX86') == 0)
        try
            F = getframe(handles.figure_imageviewer);
            imwrite(F.cdata,'/tmp/imageviewerfig.jpg','Quality',90);
            unix('chmod 777 /tmp/imageviewerfig.jpg');
            unix('lpr /tmp/imageviewerfig.jpg');
        catch
            err2 = lasterror;
            rethrow(err);
            rethrow(err2);
        end
    else
        rethrow(err);
    end
end

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

helpfig = figure('Name','About ImageViewer...','Resize','off');

textfield = uicontrol(helpfig,...
    'style','text',...
    'Units','normalized',...
    'Position',[0 0 1 1],...
    'horizontalAlignment','center',...
    'FontSize',14,...
    'Tag','text_about');
about_string = {' ';...
    'IMAGE VIEWER';...
    '==========';...
    ' ';...
    '$Revision: 1.3 $';'$Date: 2006/12/05 16:57:16 $';'$Tag: $';...
    '$Source: /import/cvs/X/PILATUS/X04SA/App/lib/X_PILATUS_X04SA_Matlab/imageviewer.m,v $';
    ' ';...
    'Author(s):';
    'C.M. Schlepuetz';...
    'Surface Diffraction Station';...
    'Materials Science Beamline X04SA';...
    'Swiss Light Source (SLS)';...
    'Paul Scherrer Institut';...
    'CH - 5232 Villigen PSI';...
    ' '};

 [about_string, pos] = textwrap(textfield,about_string);

 fig_pos = get(helpfig,'Position');
 fig_pos(3) = fig_pos(3)*pos(3);
 fig_pos(4) = fig_pos(4)*pos(4);
 set(helpfig,'Position',fig_pos);
 
 % display scanlogfile in the text field
set(textfield,'String',about_string);


% --------------------------------------------------------------------
% opens a new figure with image to be printed
function printfig = fcn_open_print_window(I, zeroOff, hObject, eventdata, handles)

printfig = figure;
pos = get(printfig,'Position');
[ydim xdim] = size(I);
imagedim = handles.data.image_dim;
while (xdim < imagedim(1)) && (ydim < imagedim(2))
    xdim = xdim*2;
    ydim = ydim*2; 
end

set(printfig,'Position',[pos(1) pos(2) xdim ydim])
printaxes = axes('Units','normalized','Position',[0 0 1 1],...
                 'Parent',printfig);

imagesc(I,'Parent',printaxes);

cmap = handles.image_control.colormap;
cmap_dim = size(cmap);
cind = ((1:cmap_dim(1))-1)./(cmap_dim(1)-1);
cind = cind.^handles.image_control.gamma;
cind = round(cind.*(cmap_dim(1)-1))+1;
cmap = handles.image_control.colormap(cind,:);
colormap(cmap);

caxis([handles.image_control.min handles.image_control.max])
axis equal
axis off