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aedes/aedes.m

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function aedes(DATA,ROI,inputOverlay)
% AEDES - Graphical user interface for analyzing MRI images
%
%
% Synopsis:
% aedes(InArg)
%
% or
%
% aedes
%
% Description:
% AEDES is a graphic user interface (GUI) based tool for region
% of interest (ROI) analysis of (mainly) MRI images.
%
% The input argument InArg is optional. If the function is called
% without input arguments, an empty GUI window is initialized. InArg
% can be a DATA structure, containing at least the FTDATA and HDR
% fields, and a string or a cell array of strings containing the full
% path(s) to supported data file(s). Input argument can also be a 2D,
% 3D, or 4D-matrix containing image slices and possibly volumes in the
% 4th dimension.
%
% Examples:
% %% Example 1
% aedes % Initialize an empty GUI window
%
% %% Example 2
% DataMtx = rand(100); % Generate a 100x100 random matrix
% aedes(DataMtx) % Open the data in Aedes
%
% %% Example 3
% DATA=aedes_data_read; % Read various image data to a DATA-structure
% aedes(DATA) % Open data in Aedes
%
% %% Example 4
% % Read data from file with path given as a string
% aedes('C:\MyDataDirectory\MyDataFiles\MyData.fid')
%
% %% Example 5
% % Read data from multiple files given as a cell
% % array. Each file has to contain only one slice.
% files={'C:\MyData\MyDataFile1.nii','C:\MyData\MyDataFile1.nii'};
% aedes(files)
%
% See also:
% AEDES_DATA_READ, AEDES_READFID, AEDES_RESVIEWER, AEDES_JUIGETFILES
% Aedes - A graphical tool for analyzing medical images
%
% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka.Niskanen@uku.fi>
%
% Department of Physics, Department of Neurobiology
% University of Eastern Finland, Kuopio, FINLAND
%
% This program may be used under the terms of the GNU General Public
% License version 2.0 as published by the Free Software Foundation
% and appearing in the file LICENSE.TXT included in the packaging of
% this program.
%
% This program is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
% WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
% Define "public" variables. Since Aedes utilizes nested functions,
% these variables will be visible to all the subfunctions.
H = []; % Handles structure. Contains all handles to figure,
% uicontrols, axes, etc...
Dat = []; % Internal data structure for exchanging information between
% functions
switch nargin
case 0;
DATA = []; % The data structure containing image data and header
ROI = []; % The ROI structure
inputOverlay = [];
case 1
ROI = [];
inputOverlay = [];
case 2
inputOverlay = [];
end
% % Auto-check for updates ------------------------------
% try
% if getpref('Aedes','AutoCheckUpdates')
% Dat=aedes_update('semiprompt');
% if Dat
% return
% else
% Dat = [];
% end
% end
% catch
% % pass
% end
% Detect Matlab version
[Dat.MatlabVersion,Dat.isImageProc] = aedes_getmatlabversion;
% Show license and warranty notification ----------------
%
% NOTE: You can disable this license notification using the following
% command: setpref('Aedes','ShowLicenseAtStartUp',false)
if ~ispref('Aedes','ShowLicenseAtStartUp') || ...
getpref('Aedes','ShowLicenseAtStartUp')
l_PrintLicense([],[]);
end
%% Parse input arguments -------------------------
if nargin>0
if ischar(DATA) %% String input
tmp_filename = DATA;
DATA = [];
% Draw blank GUI
H=l_draw_gui();
% Read data and initialize
l_OpenFile([],[],'single',tmp_filename)
% Initialize GUI
%l_Initialize([],[])
elseif iscell(DATA) %% Cell input
if ischar(DATA{1})
tmp_filename = DATA;
DATA = [];
% Draw blank GUI
H=l_draw_gui();
% Read data and initialize
l_OpenFile([],[],'multi',tmp_filename)
% Initialize GUI
%l_Initialize([],[])
elseif ~isstruct(DATA{1})
error('Invalid type for input argument!')
else
% Draw blank GUI
H=l_draw_gui();
% Initialize GUI
l_Initialize([],[])
end
else
if isstruct(DATA) %% Structure input
DATA = {DATA};
% Check if kspace should be viewed
if isfield(DATA{1},'KSPACE') && ...
(isempty(DATA{1}.FTDATA) & ~isempty(DATA{1}.KSPACE))
resp=questdlg(['The inputted DATA structure contains only k-space',...
' information. Do you want to view real, imaginary, or absolute',...
' part of the complex k-space?'],...
'Complex data inputted',...
'Real','Imaginary','Absolute','Absolute');
if strcmpi(resp,'Real')
DATA{1}.FTDATA = real(DATA{1}.KSPACE);
elseif strcmpi(resp,'Imaginary')
DATA{1}.FTDATA = imag(DATA{1}.KSPACE);
elseif strcmpi(resp,'Absolute')
DATA{1}.FTDATA = abs(DATA{1}.KSPACE);
else
% Canceled
return
end
%DATA{1}.FTDATA = abs(DATA{1}.KSPACE);
end
elseif isnumeric(DATA) || islogical(DATA)
if isreal(DATA)
DATA_tmp=DATA;
else
resp=questdlg(['The inputted data is complex. Do you want ' ...
'to view real, imaginary, or absolute part of the data?'],...
'Complex data inputted',...
'Real','Imaginary','Absolute','Absolute');
if strcmpi(resp,'Real')
DATA_tmp = real(DATA);
elseif strcmpi(resp,'Imaginary')
DATA_tmp = imag(DATA);
else
DATA_tmp = abs(DATA);
end
end
DATA=[];
DATA.FTDATA = DATA_tmp;
DATA.HDR.fpath = '';
DATA.HDR.fname = '';
DATA={DATA};
clear DATA_tmp
else
error('Invalid type for input argument')
end
% Draw blank GUI
H=l_draw_gui();
% Initialize GUI
l_Initialize([],[])
end
% Load ROI if given as input argument
if nargin>1
if ~isempty(ROI)
l_RoiLoad([],[],'');
end
if nargin==3 && ~isempty(inputOverlay)
% Load overlay
l_LoadImageOverlay([],[],'inputarg')
end
end
else
% Open an empty GUI window, if called without input arguments
H=l_draw_gui;
end
% Build plugins menu
l_BuildPluginsMenu();
% Wait for quit in standalone
if isdeployed
waitfor(H.FIG)
end
% Debug function - paste debug information into workspace...
function l_debug(h,evd)
assignin('base','DATA',DATA);
assignin('base','H',H);
assignin('base','ROI',ROI);
assignin('base','Dat',Dat);
end
%%%%%%%%%%%%%%%%%%%%%%%%%%
% CHECK FOR UPDATES
%%%%%%%%%%%%%%%%%%%%%%%%%%
function l_CheckUpdates(h,evd)
done = aedes_update('prompt');
end
%%%%%%%%%%%%%%%%%%%%%%%%%%
% DRAW GUI
%%%%%%%%%%%%%%%%%%%%%%%%%%
function H=l_draw_gui()
%% Toggle debug on/off
debug=true;
%% Determine paths
tmp=which('aedes');
[fp,fn,fe]=fileparts(tmp);
Dat.AedesFolder = [fp,filesep];
Dat.PluginsFolder = [Dat.AedesFolder,'plugins',filesep];
Dat.IconsFolder = [Dat.AedesFolder,'icons',filesep];
Dat.TablibFolder = [Dat.AedesFolder,'tablib',filesep];
%% Figure Size Definitions ----------------
taskbar_sz = 70; % The windows taskbar height in pixels
fig_w = 1000; % Screen width in pixels
fig_h = 661;%768-taskbar_sz; % Screen height in pixels
dx = 1/fig_w; % Horizontal space
dy = 1/fig_h; % Vertical space
dxx = 5*dx; % Horizontal big space
dyy = 5*dy; % Vertical big space
btn_h = 25/fig_h; % Push button height
btn_w = 75/fig_w; % Push button width
btns_w = 25/fig_w;
popup_h = 25/fig_h; % Popup menu height
popup_w = 100/fig_w; % Popup menu width
edit_w = 45/fig_w; % Edit box width
edit_h = 20/fig_h; % Edit box height
%% Load default font and colors
if isunix
DefaultColor = [239 235 222]/255;
else
DefaultColor=get(0,'DefaultUicontrolBackgroundcolor');
end
GD=aedes_gui_defaults;
GD.col.frame = DefaultColor;
Dat.HG2graphics = GD.HG2graphics;
% Calculate default position for Aedes window
try
% If multiple monitors are connected, draw Aedes on the monitor where the
% mouse cursor is located
scrsz = get(0,'MonitorPositions');
ind = aedes_getcurrentmonitor;
fig_pos = [scrsz(ind,3)/2-fig_w/2 scrsz(ind,4)/2-fig_h/2-20 fig_w fig_h];
fig_pos(1) = fig_pos(1)+scrsz(ind,1);
catch
% Get screen size
scrsz=get(0,'ScreenSize');
% Calculate gui position on the center of the screen
fig_pos = [scrsz(3)/2-fig_w/2 scrsz(4)/2-fig_h/2-20 fig_w fig_h];
end
%% Check if other Aedes windows exist
figs=findall(0,'tag','aedes_main_fig');
if ~isempty(figs)
tmp_pos=get(figs(1),'position');
fig_pos(1)=tmp_pos(1)+15;
fig_pos(2)=tmp_pos(2)-15;
end
%% Draw main figure
H.FIG=figure('Position',fig_pos, ...
'Units','Pixel', ...
'Name','Aedes 1.0', ...
'Numbertitle','off', ...
'Tag','aedes_main_fig', ...
'Color',GD.col.mainfig, ...
'Toolbar','none', ...
'Menubar','none', ...
'DockControls','off',...
'renderer','OpenGL',...
'KeyPressFcn',@l_KeyPressFcn,...
'CloseRequestFcn',@l_quit,...
'Handlevisibility','off');
if ~Dat.HG2graphics
set(H.FIG,'DoubleBuffer','on')
end
% File Uimenu ---------------------------
file_h = uimenu('Label','File','Accelerator','F', ...
'Parent',H.FIG);
H.FILEMENU_NEW = uimenu(file_h,'Label','New window',...
'Callback','aedes');
H.FILEMENU_OPEN_SINGLE = uimenu(file_h,'Label','&Open File',...
'Accelerator','O', ...
'Callback',{@l_OpenFile,'single'},'Tag', ...
'open_single_file',...
'separator','on');
H.FILEMENU_OPEN_MULTI = uimenu(file_h,'Label','Open &Multiple Files',...
'Callback',{@l_OpenFile,'multi'},'Tag', ...
'open_multiple_file');
H.FILEMENU_OPEN_RECENT = uimenu(file_h,'Label','Open Recent',...
'Tag','open_recent',...
'separator','on');
l_BuildRecentFilesMenu([],[],H.FILEMENU_OPEN_RECENT);
H.FILEMENU_SAVE_IMAGE = uimenu(file_h,'Label','Save Image Data as', ...
'Callback',@l_SaveImageData, ...
'Separator','on','userdata','','enable','off');
H.FILEMENU_SAVERES = uimenu(file_h,'Label','Save results as','Accelerator','S', ...
'Callback',{@l_SaveResults,[]}, ...
'Separator','off','userdata','','enable','off');
H.FILEMENU_EXPORT = uimenu(file_h,'Label','Export Image Data...', ...
'Callback',@l_ExportImages, ...
'Separator','on','userdata','','enable','off');
% $$$ H.FILEMENU_PRINT = uimenu(file_h,'Label','Print...', ...
% $$$ 'Callback',@l_Print, ...
% $$$ 'Separator','on','userdata','','enable','off');
closefile_h = uimenu(file_h,'Label','Close File', ...
'Callback',@l_CloseFile, ...
'Separator','on','userdata','','enable','off');
H.FILEMENU_QUIT = uimenu(file_h,'Label','Exit Aedes','Accelerator','Q', ...
'Callback',@l_quit,'Separator','on');
% Edit Uimenu ---------------------------------
edit_h = uimenu('Label','Edit', ...
'Parent',H.FIG,...
'enable','off');
H.UIEDIT_IMSTACK = uimenu(edit_h,'Label','&Image Stack',...
'Callback',@l_EditImageStack,...
'separator','off',...
'enable','off');
% Unfold data
H.UNFOLD_DATA = uimenu(edit_h,'Label','Unfold data',...
'Callback',@l_UnfoldData,...
'separator','on',...
'enable','off');
% Rotate/flip view
rotate_h=uimenu(edit_h,'Label','Rotate/Flip Images','separator','on',...
'enable','off');
H.UIMENU_ROTATEFLIP = rotate_h;
rot_h=uimenu(rotate_h,'Label','Rotate Current Slice');
tmp_str={'90','180','270'};
for ii=1:3
H.ROTATE(ii) = uimenu(rot_h,'Label',[tmp_str{ii},char(176)],...
'callback',...
{@l_RotateFlip,tmp_str{ii}});
end
flip_h=uimenu(rotate_h,'Label','Flip Current Slice');
tmp_str={'FlipLR','FlipUD'};
for ii=1:2
H.FLIP(ii) = uimenu(flip_h,'Label',tmp_str{ii},...
'callback',...
{@l_RotateFlip,tmp_str{ii}});
end
rotcustom_h = uimenu(rotate_h,'Label','Rotate/Flip Custom...',...
'callback',...
{@l_RotateFlip,'custom'},...
'separator','on');
H.UIROTRESET = uimenu(rotate_h,'Label','Reset Rotation/Flip',...
'callback',...
{@l_RotateFlip,'reset'},...
'separator','on');
% Rotate/Flip volumes ----------------------------------------
rotate3d_h=uimenu(edit_h,'Label','Rotate/Flip Volumes','separator','off',...
'enable','off');
H.UIMENU_ROTATEFLIP3D = rotate3d_h;
rot3d_h=uimenu(rotate3d_h,'Label','Rotate');
flip3d_h=uimenu(rotate3d_h,'Label','Flip');
tmpx_h = uimenu(rot3d_h,'Label','X-dir');
tmpy_h = uimenu(rot3d_h,'Label','Y-dir');
tmpz_h = uimenu(rot3d_h,'Label','Z-dir');
tmp_str={'90','180','270'};
tmp_h = [tmpx_h,tmpy_h,tmpz_h];
tmp_str2 = {'X','Y','Z'};
for kk=1:3
for ii=1:3
H.ROTATE3D(kk,ii) = uimenu(tmp_h(kk),'Label',[tmp_str{ii},char(176)],...
'callback',...
{@l_RotateFlip,['3d',tmp_str2{kk},'_',tmp_str{ii}]});
end
end
H.FLIP3D_X = uimenu(flip3d_h,'Label','X-dir',...
'callback',{@l_RotateFlip,'flipX'});
H.FLIP3D_Y = uimenu(flip3d_h,'Label','Y-dir',...
'callback',{@l_RotateFlip,'flipY'});
H.FLIP3D_Z = uimenu(flip3d_h,'Label','Z-dir',...
'callback',{@l_RotateFlip,'flipZ'});
H.FLIP3D_V = uimenu(flip3d_h,'Label','V-dir',...
'callback',{@l_RotateFlip,'flipV'},...
'enable','off');
% View Uimenu ------------------------------
view_h = uimenu('Label','View', ...
'Parent',H.FIG,...
'enable','off');
% View XYZ (3D) direction (default)
H.UIVIEW_3D = uimenu(view_h,'Label','View 3D',...
'callback',{@l_ChangeView,0},...
'checked','on');
% View only X direction
H.UIVIEW_X = uimenu(view_h,'Label','View X direction',...
'callback',{@l_ChangeView,1},...
'separator','on');
% View only X direction
H.UIVIEW_Y = uimenu(view_h,'Label','View Y direction',...
'callback',{@l_ChangeView,2});
% View only X direction
H.UIVIEW_Z = uimenu(view_h,'Label','View Z direction',...
'callback',{@l_ChangeView,3});
% View axes ticks and grid
H.UIVIEW_GRID = uimenu(view_h,'Label','Show Grid',...
'callback',{@l_ViewAxesUnits,'pixel'},...
'separator','on',...
'checked','off');
% View Header in aedes_headerbrowser
H.viewheader_h = uimenu(view_h,'Label','File Header',...
'callback',@l_LaunchHeaderBrowser,...
'enable','on','Accelerator','H',...
'separator','on');
% Show Info text background
H.UIVIEW_INFOTXTBACKGROUND = uimenu(view_h,'Label','Info/ROI Text Background',...
'callback',@l_InfoTextBackground,...
'separator','on',...
'checked','off');
% View Voxel Time Series
H.UIVIEW_TIMESERIES = uimenu(view_h,'Label','Voxel time-series',...
'callback',{@l_ShowTimeSeries,'toggle'},...
'separator','on',...
'checked','off');
% % Volume menu
% H.UIVIEW_VOL = uimenu(view_h,'Label','Select volume',...
% 'separator','on');
%
% $$$ H.UIVIEW_FOV_UNITS = uimenu(view_h,'Label','View FOV units',...
% $$$ 'callback',{@l_ViewAxesUnits,'FOV'},...
% $$$ 'checked','off');
% $$$ flipcustom_h=uimenu(rotate_h,'Label','Flip Custom',...
% $$$ 'callback',...
% $$$ {@l_RotateZoom,'flip','custom'},...
% $$$ 'separator','off');
% % Zoom view
% tmp_str={'normalized',...
% '0.5x',...
% '1x',...
% '2x',...
% '3x',...
% '4x',...
% '5x',...
% '6x',...
% '7x',...
% '8x',...
% '9x',...
% '10x',...
% '11x',...
% '12x',...
% '13x',...
% '14x',...
% '15x',...
% '16x',...
% '17x',...
% '18x',...
% '19x',...
% '20x'};
% tmp_fact = [0 0.5 1 2 3 4 5 6 7 8 9 10 ...
% 11 12 13 14 15 16 17 18 19 20];
% zoom_h=uimenu(view_h,'Label','Zoom',...
% 'separator','on');
% for ii=1:length(tmp_str)
% H.UIZOOM(ii)=uimenu(zoom_h,'Label',tmp_str{ii},...
% 'callback',{@l_Zoom,tmp_fact(ii)},...
% 'tag',['uizoom_' num2str(tmp_fact(ii))],...
% 'userdata',tmp_fact(ii));
% if ii==2
% set(H.UIZOOM(ii),'separator','on')
% end
% end
% set(H.UIZOOM(3),'checked','on')
% TOOLS UIMENU -------------------------------------
tools_h = uimenu('Label','Tools', ...
'Parent',H.FIG,...
'enable','on');
vnmredit_h = uimenu(tools_h,'Label','Edit VNMR defaults', ...
'callback','aedes_readfidprefs',...
'enable','on');
resview_h = uimenu(tools_h,'Label','Results Viewer', ...
'callback','aedes_resviewer',...
'enable','on',...
'separator','on');
% update_h = uimenu(tools_h,'Label','Check for updates', ...
% 'callback',@l_CheckUpdates,...
% 'enable','on',...
% 'separator','on');
% Overlay menu ---------------------------------------
H.UIOVERLAY = uimenu('Label','Overlay', ...
'Parent',H.FIG,...
'enable','off');
load_overlay_h = uimenu(H.UIOVERLAY,'Label','Load Image Overlay', ...
'separator','off',...
'enable','on');
uimenu(load_overlay_h,'Label','From File', ...
'callback',{@l_LoadImageOverlay,'file'},...
'separator','off',...
'enable','on');
uimenu(load_overlay_h,'Label','From Variable', ...
'callback',{@l_LoadImageOverlay,'var'},...
'separator','on',...
'enable','on');
H.UIOVERLAY_SAVE = uimenu(H.UIOVERLAY,'Label','Save Overlay to file', ...
'callback',{@l_OverlayControls,'save'},...
'separator','on',...
'enable','off');
H.UIOVERLAY_CONTROLS = uimenu(H.UIOVERLAY,'Label','Show Overlay Controls', ...
'callback',{@l_OverlayControls,'show'},...
'separator','on',...
'enable','off');
H.UIOVERLAY_DELETE = uimenu(H.UIOVERLAY,'Label','Delete Image Overlay', ...
'callback',{@l_OverlayControls,'delete'},...
'separator','on',...
'enable','off');
% ROI Tools ------------------------------------------
roi_tools_h = uimenu('Label','ROI', ...
'Parent',H.FIG,...
'enable','off');
% $$$ H.UIROITOOLS_AUTOCLOSE = uimenu(roi_tools_h,'Label','Autoclose',...
% $$$ 'callback',...
% $$$ ['if strcmp(get(gcbo,''checked''),''on''),' ...
% $$$ 'set(gcbo,''checked'',''off''),else,' ...
% $$$ 'set(gcbo,''checked'',''on''),end'],...
% $$$ 'checked','off');
H.UIROITOOLS_LOAD = uimenu(roi_tools_h,'Label','Load ROI(s)',...
'callback',{@l_RoiLoad,'interactive'},...
'separator','off');
H.UIROITOOLS_SAVE = uimenu(roi_tools_h,'Label','Save ROI(s)',...
'callback',@l_RoiSave,...
'separator','off',...
'enable','off');
H.UIROITOOLS_SAVETEMPLATE = uimenu(roi_tools_h,'Label','Save ROI template',...
'callback',{@l_RoiSave,'template'},...
'separator','off',...
'enable','off');
H.UIROISTATS = uimenu(roi_tools_h,'Label','View/Export ROI Statistics',...
'callback',@l_RoiViewStats,...
'separator','on',...
'enable','off');
H.UIROITOOLS_COPY = uimenu(roi_tools_h,'Label','Copy ROI',...
'separator','on',...
'enable','off');
H.UIROITOOLS_COPYSLICES = uimenu(H.UIROITOOLS_COPY,'Label','Copy ROI to slices/volumes',...
'callback',@l_RoiCopy,...
'separator','off',...
'enable','on');
H.UIROITOOLS_COPYADD = uimenu(H.UIROITOOLS_COPY,'Label','Copy current ROI to new',...
'callback',{@l_RoiAdd,'copy'},...
'separator','off',...
'enable','on');
H.UIROITOOLS_FLIP = uimenu(roi_tools_h,'Label','Flip current ROI',...
'separator','off',...
'enable','off');
tmp_str={'FlipLR','FlipUD'};
for ii=1:2
H.ROIFLIP(ii) = uimenu(H.UIROITOOLS_FLIP,'Label',tmp_str{ii},...
'callback',...
{@l_RoiFlip,tmp_str{ii}});
end
H.UIROITOOLS_COMP = uimenu(roi_tools_h,'Label','Boolean operations',...
'callback',@l_RoiBooleanOperations,...
'separator','off',...
'checked','off',...
'enable','off');
H.UIROISHOWEDGES = uimenu(roi_tools_h,'Label','Show ROI edges',...
'callback',@l_UiRoiEdgesCB,...
'separator','off',...
'checked','off',...
'enable','off');
H.UIROIRENAME = uimenu(roi_tools_h,'Label','Rename current ROI',...
'callback',@l_RoiRename,...
'separator','off',...
'checked','off',...
'enable','off');
H.UIROISETCOLOR = uimenu(roi_tools_h,'Label','Set current ROI color',...
'callback',@l_RoiSetColor,...
'separator','off',...
'checked','off',...
'enable','off');
H.UIROITOOLS_UNDO = uimenu(roi_tools_h,'Label','Undo draw (0)',...
'callback',@l_RoiUndo,...
'separator','on',...
'enable','off',...
'accelerator','z');
%% Plugins menu --------------------------------------------------------
%% DO NOT ADD/REMOVE PLUGINS FROM HERE.
% Construct plugins uimenu
H.UIPLUGINS = uimenu('Label','Plugins', ...
'Parent',H.FIG,...
'enable','off');
%% ----------------------------------------------------------------------
%% Help uimenu
help_h = uimenu('Label','Help', ...
'Parent',H.FIG,...
'enable','on');
help_about_h = uimenu(help_h,...
'Label','About Aedes', ...
'enable','on',...
'callback','eval(get(gcbo,''userdata''))');
set(help_about_h,'userdata',...
'aedes_helpabout');
if debug
debug_h=uimenu('Label','Debug', ...
'Parent',H.FIG,...
'enable','on',...
'callback',@l_debug);
end
%% Uitoolbar controls --------------------------------
H.UITOOLBAR = uitoolbar('parent',H.FIG);
%% load CData for buttons
btn_cdata = load('aedes_cdata.mat');
H.btn_cdata = btn_cdata;
%tmp=NaN(18,20,3);
%tmp(:,3:end,:)=btn_cdata.cdata.open;
% Open file
H.UIPUSH_OPEN = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.open2,...
'ClickedCallback',{@l_OpenFile,'single'},...
'TooltipString','Open a new data file');
% Open multiple files
H.UIPUSH_OPENMULTI = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.openmulti,...
'ClickedCallback',{@l_OpenFile,'multi'},...
'TooltipString',...
'Open multiple single-slice data files');
% Save file
H.UIPUSH_SAVE = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.save2_small,...
'ClickedCallback',{@l_SaveResults,[]},...
'TooltipString','Save',...
'enable','off');
% Print
% $$$ H.UIPUSH_PRINT = uipushtool('parent',H.UITOOLBAR,...
% $$$ 'CData',btn_cdata.cdata.print2,...
% $$$ 'ClickedCallback','',...
% $$$ 'TooltipString','Print',...
% $$$ 'enable','off');
% Zoom Normalized
H.UITOGGLE_ZOOMNORM = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.fitheight,...
'separator','on',...
'ClickedCallback',{@l_Zoom,'normalize'},...
'TooltipString','Fit to Window Height',...
'enable','off');
% Zoom in
H.UIPUSH_ZOOMIN = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.zoomin,...
'separator','off',...
'ClickedCallback',{@l_Zoom,'+'},...
'TooltipString','Zoom In',...
'enable','off');
% Zoom out
H.UIPUSH_ZOOMOUT = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.zoomout,...
'ClickedCallback',{@l_Zoom,'-'},...
'TooltipString','Zoom Out',...
'enable','off');
% Show/hide crosshairs
H.UITOGGLE_CROSSHAIRS = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.crosshairs_small,...
'ClickedCallback',@l_ShowHideCrossbars,...
'TooltipString','Show/Hide Crosshairs',...
'enable','off',...
'state','off',...
'separator','on');
% Show Grid
H.UITOGGLE_GRID = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.grid,...
'ClickedCallback',{@l_ViewAxesUnits,'pixel'},...
'TooltipString','Show/Hide Grid',...
'enable','off',...
'state','off',...
'separator','on');
% Show/hide colorbar
H.UITOGGLE_COLORBAR = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.colorbar,...
'ClickedCallback',@l_ShowColorbar,...
'TooltipString','Show/Hide Colorbar',...
'enable','off',...
'state','off',...
'separator','off');
% Show Info Text
H.UITOGGLE_INFO = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.about,...
'ClickedCallback',@l_UpdateInfoText,...
'TooltipString','Show/Hide Info Text',...
'enable','off',...
'state','on',...
'separator','off');
% Show image stack
H.UIPUSH_IMSTACK = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.editimagestack,...
'ClickedCallback',@l_EditImageStack,...
'TooltipString','Edit Image Stack',...
'enable','off',...
'separator','on');
% Show rotate/flip custom menu
H.UIPUSH_ROTATE = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.rotateflip,...
'ClickedCallback',{@l_RotateFlip,'custom'},...
'TooltipString','Rotate/Flip Custom',...
'enable','off',...
'separator','off');
% View 3D
H.UITOGGLE_VIEW3D = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.view3d,...
'ClickedCallback',{@l_ChangeView,0},...
'TooltipString','View 3D',...
'enable','off',...
'state','off',...
'separator','on');
H.UITOGGLE_VIEWX = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.viewx,...
'ClickedCallback',{@l_ChangeView,1},...
'TooltipString','View X direction',...
'enable','off',...
'state','off',...
'separator','off');
H.UITOGGLE_VIEWY = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.viewy,...
'ClickedCallback',{@l_ChangeView,2},...
'TooltipString','View Y direction',...
'enable','off',...
'state','off',...
'separator','off');
H.UITOGGLE_VIEWZ = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.viewz,...
'ClickedCallback',{@l_ChangeView,3},...
'TooltipString','View Z direction',...
'enable','off',...
'state','off',...
'separator','off');
% Mouse uitoggletools
H.UITOGGLE_ARROW = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.arrow,...
'ClickedCallback',...
['set(get(gcbo,''userdata''),''state'',''off''),' ...
'set(gcbo,''state'',''on'')'],...
'TooltipString','Mouse: Normal',...
'enable','off',...
'state','on',...
'separator','on');
H.UITOGGLE_PAN = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.pan,...
'ClickedCallback',...
['set(get(gcbo,''userdata''),''state'',''off''),' ...
'set(gcbo,''state'',''on'')'],...
'TooltipString','Mouse: Pan image',...
'enable','off',...
'state','off',...
'separator','off');
% ROI buttons
H.UITOGGLE_DRAWROI = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.freedraw,...
'ClickedCallback',...
['set(get(gcbo,''userdata''),''state'',''off''),' ...
'set(gcbo,''state'',''on'')'],...
'TooltipString','Mouse: Draw ROI',...
'enable','off',...
'state','off',...
'separator','off');
H.UITOGGLE_ERASEROI = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.eraser,...
'ClickedCallback',...
['set(get(gcbo,''userdata''),''state'',''off''),' ...
'set(gcbo,''state'',''on'')'],...
'TooltipString','Mouse: Erase ROI',...
'enable','off',...
'state','off',...
'separator','off');
H.UITOGGLE_FILLROI = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.bucketfill,...
'ClickedCallback',...
['set(get(gcbo,''userdata''),''state'',''off''),' ...
'set(gcbo,''state'',''on'')'],...
'TooltipString','Mouse: Fill ROI',...
'enable','off',...
'state','off',...
'separator','off');
H.UITOGGLE_MOVEROI = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.move,...
'ClickedCallback',...
['set(get(gcbo,''userdata''),''state'',''off''),' ...
'set(gcbo,''state'',''on'')'],...
'TooltipString','Mouse: Move ROI in slice',...
'enable','off',...
'state','off',...
'separator','off');
H.UITOGGLE_MOVEROI3D = uitoggletool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.move3d,...
'ClickedCallback',...
['set(get(gcbo,''userdata''),''state'',''off''),' ...
'set(gcbo,''state'',''on'')'],...
'TooltipString','Mouse: Move ROI in volume',...
'enable','off',...
'state','off',...
'separator','off');
% Show ROI statistics
H.UIPUSH_STATS_ROI = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.statistics,...
'ClickedCallback',@l_RoiViewStats,...
'TooltipString','View ROI statistics',...
'enable','off',...
'separator','on');
H.UIPUSH_NEWROI = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.add_small,...
'ClickedCallback',@l_RoiAdd,...
'TooltipString','New ROI',...
'enable','off',...
'separator','on');
H.UIPUSH_COPYROI = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.copy_small,...
'ClickedCallback',@l_RoiCopy,...
'TooltipString','Copy ROI to slices/volumes',...
'enable','off',...
'separator','off');
% $$$ H.UIPUSH_DELETEROI = uipushtool('parent',H.UITOOLBAR,...
% $$$ 'CData',btn_cdata.cdata.delete_small,...
% $$$ 'ClickedCallback',{@l_RoiFunctions,'delete'},...
% $$$ 'TooltipString','Delete selected ROI(s)',...
% $$$ 'enable','off',...
% $$$ 'separator','off');
% $$$
% $$$ H.UIPUSH_DELETEALLROI = uipushtool('parent',H.UITOOLBAR,...
% $$$ 'CData',btn_cdata.cdata.deleteall_small,...
% $$$ 'ClickedCallback',{@l_RoiFunctions,'delete_all'},...
% $$$ 'TooltipString','Delete ALL ROI(s)',...
% $$$ 'enable','off',...
% $$$ 'separator','off');
H.UIPUSH_UNDOROI = uipushtool('parent',H.UITOOLBAR,...
'CData',btn_cdata.cdata.undo_small,...
'ClickedCallback',@l_RoiUndo,...
'TooltipString','Undo last ROI action',...
'enable','off',...
'separator','off');
set([H.UITOGGLE_ARROW,H.UITOGGLE_PAN,...
H.UITOGGLE_DRAWROI,H.UITOGGLE_ERASEROI,H.UITOGGLE_MOVEROI,...
H.UITOGGLE_MOVEROI3D,H.UITOGGLE_FILLROI],...
'userdata',[H.UITOGGLE_ARROW,H.UITOGGLE_PAN,...
H.UITOGGLE_DRAWROI,H.UITOGGLE_ERASEROI,H.UITOGGLE_MOVEROI,...
H.UITOGGLE_MOVEROI3D,H.UITOGGLE_FILLROI])
fig_pos = get(H.FIG,'position');
H.ORIG_FIG_POS = fig_pos;
%% Draw uicontrol frame behind the uicontrols
% to make them draw faster in opengl mode
H.SIDEBAR_FRAME=uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[0 0 232 fig_pos(4)+2],...
'backgroundcolor',GD.col.frame,...
'style','frame',...
'visible','on');
%% Draw sidebar -------------------------------
% H.SIDEBAR=uipanel('parent',H.FIG,...
% 'units','pixel',...
% 'position',[0 0 232 fig_pos(4)+1],...
% 'backgroundcolor',GD.col.frame);
%% Draw image sliders
%tmp=get(H.SIDEBAR,'position');
tmp=get(H.SIDEBAR_FRAME,'position');
% Draw frame to hide the opening in the corner
H.IMSLIDER_FRAME = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3)+1 0 fig_pos(3)-tmp(1)-tmp(3) 17],...
'style','frame',...
'backgroundcolor',GD.col.mainfig,...
'visible','off');
% x-slider
H.IMSLIDER(1) = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3) 0 fig_pos(3)-tmp(1)-tmp(3)-17 17],...
'style','slider',...
'min',0,...
'max',1,...
'visible','off');%'callback',@l_AxesPositions);%@l_ImSliderCB);
% y-slider
H.IMSLIDER(2) = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[fig_pos(3)-17 17 17 fig_pos(4)-17+1],...
'style','slider',...
'min',-1,...
'max',0,...
'visible','off');%'callback',@l_AxesPositions);%@l_ImSliderCB);
% If JavaFigures are enabled, set image sliders to work while moving
if ~Dat.HG2graphics
if Dat.MatlabVersion>7.03
SliderListener1 = handle.listener(H.IMSLIDER(1),...
'ActionEvent',...
@l_AxesPositions);%@l_ImSliderCB);
SliderListener2 = handle.listener(H.IMSLIDER(2),...
'ActionEvent',...
@l_AxesPositions);%@l_ImSliderCB);
setappdata(H.IMSLIDER_FRAME,'ImSliderListener',...
[SliderListener1,...
SliderListener2])
else
if feature('javafigures')
SliderListener1 = handle.listener(H.IMSLIDER(1),...
'ActionEvent',...
@l_AxesPositions);%@l_ImSliderCB);
SliderListener2 = handle.listener(H.IMSLIDER(2),...
'ActionEvent',...
@l_AxesPositions);%@l_ImSliderCB);
setappdata(H.IMSLIDER_FRAME,'ImSliderListener',...
[SliderListener1,...
SliderListener2])
else
set(H.IMSLIDER,'callback',@l_AxesPositions)
end
end
else
SliderListener1 = addlistener(H.IMSLIDER(1),...
'ContinuousValueChange',@l_AxesPositions);
SliderListener2 = addlistener(H.IMSLIDER(2),...
'ContinuousValueChange',@l_AxesPositions);
setappdata(H.IMSLIDER_FRAME,'ImSliderListener',[SliderListener1,...
SliderListener2])
end
%% Slice viewing tools uipanel
% H.SLICE_TOOLS=uipanel('parent',H.FIG,...H.SIDEBAR,...
% 'units','pixel',...
% 'position',[round(0.01*232) round(0.79*fig_pos(4)) ...
% round(0.98*232)-2 round(0.18*fig_pos(4))],...
% 'title','Slice viewing tools',...
% 'fontsize',8,...
% 'backgroundcolor',GD.col.frame,...%'highlightcolor',[0.5 0.5 0.5],...%'shadowcolor',[0 0 0],...
% 'fontweight','bold',...
% 'bordertype','etchedin');
fig_pos=get(H.FIG,'position');
H.SLICE_TOOLS=uicontrol('parent',H.FIG,...
'style','frame',...
'units','pixel',...
'position',[5 fig_pos(4)-105-2 ...
232-10 105],...%135
'backgroundcolor',GD.col.frame);
% Slice Tools text
tmp=get(H.SLICE_TOOLS,'position');
H.SLICE_TOOLS_TX = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+5 tmp(2)+tmp(4)-20 150 15],...
'style','text',...
'horizontalalign','left',...
'fontweight','bold',...
'backgroundcolor',GD.col.frame,...
'string','Image Coordinates');
% Volume popup
tmp = get(H.SLICE_TOOLS,'position');
% $$$ H.VOL_POPUP = uicontrol('parent',H.FIG,...
% $$$ 'units','pixel',...%'normal',...
% $$$ 'position',[85 ...
% $$$ 80+tmp(2) ...
% $$$ 45 ...
% $$$ 34],...%[0.37 0.8 0.2 0.15],...
% $$$ 'style','popup',...
% $$$ 'backgroundcolor','w',...
% $$$ 'string',{'1'},...
% $$$ 'callback','');
% $$$
% $$$ % Volume text
% $$$ h1 = uicontrol('parent',H.FIG,...
% $$$ 'units','pixel',...
% $$$ 'position',[tmp(1)+5 tmp(2)+95 72 15],...
% $$$ 'style','text',...
% $$$ 'horizontalalign','left',...
% $$$ 'backgroundcolor',GD.col.frame,...
% $$$ 'string','Select volume');
% Slice slider
H.SL_SLIDER = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+5 tmp(2)+60 215 20],...
'style','slider',...
'backgroundcolor',GD.col.slider);
% If JavaFigures are enabled, set slider to work while moving
if ~Dat.HG2graphics
if Dat.MatlabVersion>7.03
SliderListener = handle.listener(H.SL_SLIDER,...
'ActionEvent',...
{@l_ChangeSlice,'slider'});
setappdata(H.SL_SLIDER,'SliderListener',SliderListener)
else
if feature('javafigures')
SliderListener = handle.listener(H.SL_SLIDER,...
'ActionEvent',...
{@l_ChangeSlice,'slider'});
setappdata(H.SL_SLIDER,'SliderListener',SliderListener)
else
set(H.SL_SLIDER,'callback',{@l_ChangeSlice,'slider'})
end
end
else
SliderListener = addlistener(H.SL_SLIDER,...
'ContinuousValueChange',@l_ChangeSlice);
setappdata(H.SL_SLIDER,'SliderListener',SliderListener)
end
% X --------------------------
H.X_BTN = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+5 tmp(2)+35 30 22],...
'style','togglebutton',...
'fontweight','bold',...
'string','X:',...
'value',1,...
'callback',{@l_ChangeSliderOrient,1});
tmp=get(H.X_BTN,'pos');
H.X_EDIT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[5+tmp(3)+5 tmp(2) 35 tmp(4)],...
'style','edit',...
'backgroundcolor','w',...
'string','1',...
'callback',{@l_ChangeSlice,'editbox'});
% Y -----------------------------
tmp_gap = 8;
tmp=get(H.X_EDIT,'pos');
H.Y_BTN = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3)+tmp_gap tmp(2) 30 tmp(4)],...
'style','togglebutton',...
'string','Y:',...
'fontweight','normal',...
'value',0,...
'callback',{@l_ChangeSliderOrient,2});
tmp=get(H.Y_BTN,'pos');
H.Y_EDIT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3) tmp(2) 35 tmp(4)],...
'style','edit',...
'backgroundcolor','w',...
'string','1',...
'callback',{@l_ChangeSlice,'editbox'});
% Z -----------------------------
tmp=get(H.Y_EDIT,'pos');
H.Z_BTN = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3)+tmp_gap tmp(2) 30 tmp(4)],...
'style','togglebutton',...
'fontweight','normal',...
'string','Z:',...
'value',0,...
'callback',{@l_ChangeSliderOrient,3});
tmp=get(H.Z_BTN,'pos');
H.Z_EDIT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3) tmp(2) 35 tmp(4)],...
'style','edit',...
'backgroundcolor','w',...
'string','1',...
'callback',{@l_ChangeSlice,'editbox'});
% V ------------------------------
tmp=get(H.Z_BTN,'pos');
H.V_BTN = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1) tmp(2)-tmp(4)-tmp_gap 30 tmp(4)],...
'style','togglebutton',...
'fontweight','normal',...
'string','V:',...
'value',0,...
'callback',{@l_ChangeSliderOrient,4},...
'enable','off');
tmp=get(H.V_BTN,'pos');
H.V_EDIT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3) tmp(2) 35 tmp(4)],...
'style','edit',...
'backgroundcolor','w',...
'string','1',...
'callback',{@l_ChangeVolume,'editbox'},...
'enable','off');
% Crossbars
tmp=get(H.SLICE_TOOLS,'pos');
% H.SHOW_CROSSBARS = uicontrol('parent',H.FIG,...
% 'units','pixel',...
% 'position',[tmp(1)+5 tmp(2)+25 130 20],...
% 'style','checkbox',...
% 'fontweight','normal',...
% 'string','Show Crossbars',...
% 'backgroundcolor',GD.col.frame,...
% 'value',0,...
% 'callback',@l_ShowHideCrossbars);
H.VOXEL_VALUE_TX = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+5 tmp(2)+20 130 13],...
'style','text',...
'fontweight','normal',...
'string','Current pixel value:',...
'horizontalalign','left',...
'backgroundcolor',GD.col.frame);
H.VOXEL_VALUE = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+5 tmp(2)+5 130 13],...
'style','text',...
'fontweight','normal',...
'string','-',...
'horizontalalign','left',...
'backgroundcolor',GD.col.frame);
tmp=get(H.SLICE_TOOLS,'position');
fig_pos = get(H.FIG,'position');
%% Window/Level tools frame
H.WINDOWLEVEL_TOOLS=uicontrol('parent',H.FIG,...
'style','frame',...
'units','pixel',...
'position',[tmp(1) tmp(2)-5-220 ...
tmp(3) 220],...
'backgroundcolor',GD.col.frame);
% Window/Level text
tmp=get(H.WINDOWLEVEL_TOOLS,'position');
H.WINDOWLEVEL_TOOLS_TX = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+5 tmp(2)+tmp(4)-18 150 13],...
'style','text',...
'horizontalalign','left',...
'fontweight','bold',...
'backgroundcolor',GD.col.frame,...
'string','Window/Level');
% Window slider ------------------------------
tmp=get(H.WINDOWLEVEL_TOOLS,'position');
H.WINDOW_SLIDER = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+5 tmp(2)+165 173 18],...
'style','slider',...
'min',0,...
'max',100,...
'value',100,...
'sliderstep',[0.01 0.1],...
'backgroundcolor',GD.col.slider);
tmp=get(H.WINDOW_SLIDER,'position');
% Window Edit box
H.WINDOW_EDIT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3)+3 tmp(2) 37 tmp(4)],...
'style','edit',...
'backgroundcolor','w',...
'string','',...
'callback',@l_SetWindowLevel);
% Window text
h1 = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1) tmp(2)+tmp(4)+2 150 12],...
'style','text',...
'horizontalalign','left',...
'backgroundcolor',GD.col.frame,...
'string','Window (0% - 100%)');
% Level slider ---------------------------------
tmp=get(H.WINDOW_SLIDER,'position');
tmp_gap=20;
H.LEVEL_SLIDER = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1) tmp(2)-tmp(4)-tmp_gap tmp(3) tmp(4)],...
'style','slider',...
'min',0,...
'max',100,...
'value',50,...
'sliderstep',[0.01 0.1],...
'backgroundcolor',GD.col.slider);
tmp=get(H.LEVEL_SLIDER,'position');
% Level Edit box
H.LEVEL_EDIT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3)+3 tmp(2) 37 tmp(4)],...
'style','edit',...
'backgroundcolor','w',...
'string','',...
'callback',@l_SetWindowLevel);
% Level text
h1 = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1) tmp(2)+tmp(4)+2 170 12],...
'style','text',...
'horizontalalign','left',...
'backgroundcolor',GD.col.frame,...
'string','Level (0% - 100%)');
if ~Dat.HG2graphics
if Dat.MatlabVersion>7.03
WindowSliderListener = handle.listener(H.WINDOW_SLIDER,...
'ActionEvent',@l_SetWindowLevel);
LevelSliderListener = handle.listener(H.LEVEL_SLIDER,...
'ActionEvent',@l_SetWindowLevel);
setappdata(H.WINDOW_SLIDER,'HandleListeners',...
[WindowSliderListener,LevelSliderListener])
else
if feature('javafigures')
WindowSliderListener = handle.listener(H.WINDOW_SLIDER,...
'ActionEvent',@l_SetWindowLevel);
LevelSliderListener = handle.listener(H.LEVEL_SLIDER,...
'ActionEvent',@l_SetWindowLevel);
setappdata(H.WINDOW_SLIDER,'HandleListeners',...
[WindowSliderListener,LevelSliderListener])
else
set(H.WINDOW_SLIDER,'callback',@l_SetWindowLevel)
set(H.LEVEL_SLIDER,'callback',@l_SetWindowLevel)
end
end
else
WindowSliderListener = addlistener(H.WINDOW_SLIDER,...
'ContinuousValueChange',@l_SetWindowLevel);
LevelSliderListener = addlistener(H.LEVEL_SLIDER,...
'ContinuousValueChange',@l_SetWindowLevel);
setappdata(H.WINDOW_SLIDER,'HandleListeners',...
[WindowSliderListener,LevelSliderListener])
end
tmp=get(H.LEVEL_SLIDER,'position');
% Clim Min text
H.CLIMRANGETEXT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',...
[10 tmp(2)-25 50 15],...
'string','Range:',...
'horizontalalign','left',...
'style','text',...
'backgroundcolor',GD.col.frame);
tmp=get(H.CLIMRANGETEXT,'position');
H.CLIMMINEDIT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',...
[tmp(1)+tmp(3)+5 tmp(2) 60 18],...
'string','',...
'style','edit',...
'backgroundcolor','w',...
'callback',@l_ChangeClim);
tmp=get(H.CLIMMINEDIT,'position');
% % Clim Max text
H.CLIMMAXTEXT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',...
[tmp(1)+tmp(3)+5 tmp(2) 25 15],...
'string','-',...
'horizontalalign','center',...
'style','text',...
'backgroundcolor',GD.col.frame);
% tmp=get(H.CLIMMAXTEXT,'position');
% Max (Clim(2))
H.CLIMMAXEDIT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',...
[tmp(1)+tmp(3)+35 tmp(2) 60 18],...
'string','',...
'style','edit',...
'backgroundcolor','w',...
'callback',@l_ChangeClim);
tmp=get(H.CLIMMINEDIT,'position');
% Clim range behavior text
H.CLIMRANGEBEHTEXT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',...
[10 tmp(2)-25 200 15],...
'string','Range in image stack:',...
'horizontalalign','left',...
'style','text',...
'backgroundcolor',GD.col.frame);
tmp=get(H.CLIMMINEDIT,'position');
% Clim range popup
H.CLIMRANGE_POPUP = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',...
[10 tmp(2)-45 210 20],...
'string',{'Range fixed (all images)',...
'Range fixed (image)','Range image min-max','Range auto-balanced W/L'},...
'horizontalalign','left',...
'style','popup',...
'enable','on',...
'value',1,...
'callback',@l_ChangeClimRange,...
'backgroundcolor','w');
% Window/level autobalance
tmp=get(H.CLIMRANGE_POPUP,'position');
H.WINDOWLEVEL_AUTO = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',...
[tmp(1) tmp(2)-tmp(4)-30 35 35],...
'string','',...
'CData',btn_cdata.cdata.contrast,...
'tooltip','Window/level auto-balance',...
'style','pushbutton',...
'callback',@l_SetAutoWindowLevel);
tmp=get(H.WINDOWLEVEL_AUTO,'position');
H.CONTRAST_INVERT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',...
[tmp(1)+tmp(3)+5 tmp(2) 35 35],...
'string','',...
'CData',btn_cdata.cdata.invertcontrast,...
'style','togglebutton',...
'tooltip','Invert contrast',...
'callback',@l_ColormapInvert);
tmp=get(H.CONTRAST_INVERT,'position');
% Colormap popup
H.COLMAP_POPUP = uicontrol('parent',H.FIG,...
'style','popup',...
'units','pixel',...
'position',[tmp(1)+tmp(3)+5 tmp(2) 130 25],...
'string',{'Gray','Jet','HSV','Cool','Hot','Spring',...
'Summer','Autumn','Winter','Bone','Copper','Pink','Custom'},...
'enable','on',...
'value',1,...
'backgroundcolor','w',...
'callback',{@l_ChangeColormap,[]});
tmp=get(H.COLMAP_POPUP,'position');
h1=uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1) tmp(2)+tmp(4)+2 80 12],...
'style','text',...
'horizontalalign','left',...
'backgroundcolor',GD.col.frame,...
'string','Colormap');
%% Analyze tools ------------------------
tmp = get(H.WINDOWLEVEL_TOOLS,'position');
H.ANALYZE_TOOLS = uicontrol('parent',H.FIG,...H.SIDEBAR,...
'style','frame',...
'units','pixel',...
'position',[tmp(1) tmp(2)-318-5 tmp(3) 318],...%[tmp(1) tmp(2)-348-5+40 tmp(3) 308],...
'backgroundcolor',GD.col.frame);
% Tab-group for uitabs
% $$$ H.ANALYZE_TABGROUP = uitabgroup('parent',H.ANALYZE_TOOLS,...
% $$$ 'units','normalized',...
% $$$ 'position',[0 0 1 1],...
% $$$ 'backgroundcolor',GD.col.frame);
% H.ANALYZE_TABGROUP = uipanel('parent',H.ANALYZE_TOOLS,...
% 'units','normalized',...
% 'position',[0 0 1 1],...
% 'backgroundcolor',GD.col.frame);
% Create uitabs
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% $$$ H.ROI_UITAB = uitab('parent',H.ANALYZE_TABGROUP,...
% $$$ 'title','ROI tools');
% H.ROI_ANALYSIS = uicontrol('parent',H.FIG,...H.ROI_UITAB,...
% 'units','normal',...
% 'position',[0 0 1 1],...
% 'backgroundcolor',GD.col.frame,...
% 'bordertype','etchedin');
tmp = get(H.ANALYZE_TOOLS,'position');
h1 = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[10 tmp(2)+tmp(4)-20 200 14],...%[10 332-40 200 14],...
'style','text',...
'string','ROI Analysis',...
'horizontalalign','left',...
'fontweight','bold',...
'backgroundcolor',GD.col.frame);
% Radiobutton group for ROI buttons
tmp=get(h1,'position');
H.ROITOOLS_FRAME=uicontrol('parent',H.FIG,...
'style','frame',...
'units','pixel',...
'position',[tmp(1) tmp(2)-55 212 50]);%[10 259-40 212 70]);
tmp=get(H.ROITOOLS_FRAME,'position');
% ROI buttons
tmp=get(H.ROITOOLS_FRAME,'position');
H.ROIBTN_NEW = uicontrol('parent',H.FIG,...
'style','pushbutton',...
'units','pixel',...
'position',[14 tmp(2)+5 40 40],...
'string','',...
'CData',btn_cdata.cdata.add,...
'callback',@l_RoiAdd,...
'tooltip','Create a new ROI');
tmp=get(H.ROIBTN_NEW,'position');
tmp_gap=1;
H.ROIBTN_COPY = uicontrol('parent',H.FIG,...
'style','pushbutton',...
'units','pixel',...
'position',[tmp(1)+tmp(3)+tmp_gap tmp(2:4)],...
'string','',...
'CData',btn_cdata.cdata.copy,...
'callback',@l_RoiCopy,...
'enable','off',...
'tooltip','Copy ROI to slices/volumes');
tmp=get(H.ROIBTN_COPY,'position');
H.ROIBTN_DEL = uicontrol('parent',H.FIG,...
'style','pushbutton',...
'units','pixel',...
'position',[tmp(1)+tmp(3)+tmp_gap tmp(2:4)],...
'string','',...
'enable','off',...
'CData',btn_cdata.cdata.delete,...
'callback',{@l_RoiDelete,'selected'},...
'tooltip','Delete selected ROI(s)');
tmp=get(H.ROIBTN_DEL,'position');
H.ROIBTN_DELALL = uicontrol('parent',H.FIG,...
'style','pushbutton',...
'units','pixel',...
'position',[tmp(1)+tmp(3)+tmp_gap tmp(2:4)],...
'string','',...
'enable','off',...
'CData',btn_cdata.cdata.deleteall,...
'callback',{@l_RoiDelete,'all'},...
'tooltip','Delete ALL ROIs');
tmp=get(H.ROIBTN_DELALL,'position');
H.ROIBTN_UNDO = uicontrol('parent',H.FIG,...
'style','pushbutton',...
'units','pixel',...
'position',[tmp(1)+tmp(3)+tmp_gap tmp(2:4)],...
'string','',...
'fontweight','bold',...
'enable','off',...
'CData',btn_cdata.cdata.undo,...
'tooltip','Undo last draw action',...
'callback',@l_RoiUndo);
tmp=get(H.ROITOOLS_FRAME,'position');
H.ROIBTN_LOAD = uicontrol('parent',H.FIG,...
'style','pushbutton',...
'units','pixel',...
'position',[tmp(1) tmp(2)-70 40 40],...
'string','',...
'fontweight','bold',...
'enable','on',...
'CData',btn_cdata.cdata.load,...
'tooltip','Load ROI(s)',...
'callback',{@l_RoiLoad,'interactive'});
tmp=get(H.ROIBTN_LOAD,'position');
H.ROIBTN_SAVE = uicontrol('parent',H.FIG,...
'style','pushbutton',...
'units','pixel',...
'position',[tmp(1) tmp(2)-tmp(4)-5 tmp(3:4)],...
'string','',...
'fontweight','bold',...
'enable','off',...
'CData',btn_cdata.cdata.save2,...
'tooltip','Save ROI(s)',...
'callback',@l_RoiSave);
tmp=get(H.ROIBTN_SAVE,'position');
H.ROIBTN_STATS = uicontrol('parent',H.FIG,...
'style','pushbutton',...
'units','pixel',...
'position',[tmp(1) tmp(2)-tmp(4)-5 tmp(3:4)],...
'string','',...
'fontweight','bold',...
'enable','off',...
'CData',btn_cdata.cdata.statistics_large,...
'tooltip','View ROI statistics',...
'callback',@l_RoiViewStats);
tmp=get(H.ROIBTN_LOAD,'position');
% ROI selection listbox
%uicm=uicontextmenu;
%uimenu(uicm,'Label','Add')
%uimenu(uicm,'Label','testi2')
H.ROIVIEW_LBOX = uicontrol('parent',H.FIG,...
'style','listbox',...
'units','pixel',...
'position',[tmp(1)+tmp(3)+5 tmp(2)-85+40 165 85],...
'string','',...
'min',0,...
'max',2,...
'value',[],...
'backgroundcolor','w',...
'fontweight','bold',...
'string','',...
'callback',@l_RoiView);
tmp=get(H.ROIVIEW_LBOX,'position');
h1=uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1) tmp(2)+tmp(4)+2 86 14],...
'style','text',...
'string','View ROI(s)',...
'horizontalalign','left',...
'fontweight','normal',...
'backgroundcolor',GD.col.frame);
h1=uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1) tmp(2)-21 150 14],...
'style','text',...
'string','Edit/Current ROI',...
'horizontalalign','left',...
'fontweight','normal',...
'backgroundcolor',GD.col.frame);
tmp=get(h1,'position');
H.ROI_EDIT = uicontrol('parent',H.FIG,...
'style','popup',...
'units','pixel',...
'position',[tmp(1) tmp(2)-24 165 24],...
'string',{''},...
'enable','off',...
'backgroundcolor','w',...
'callback',@l_UpdateRoiInfoText);
tmp=get(H.ROI_EDIT,'position');
h1 = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[10 tmp(2)-35 133 14],...
'style','text',...
'string','ROI Transparency',...
'horizontalalign','left',...
'fontweight','normal',...
'backgroundcolor',GD.col.frame);
tmp=get(h1,'position');
H.ROI_TRANSP_SLIDER = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[10 tmp(2)-18 170 18],...
'style','slider',...
'min',0,...
'max',1,...
'value',0.5,...
'sliderstep',[0.1 0.3],...
'backgroundcolor',GD.col.slider);
if ~Dat.HG2graphics
RoiTransparencyListener = handle.listener(H.ROI_TRANSP_SLIDER,...
'ActionEvent',...
{@l_SetRoiTransparency, ...
'slider'});
set(H.ROI_TRANSP_SLIDER,'userdata',RoiTransparencyListener)
else
RoiTransparencyListener=addlistener(H.ROI_TRANSP_SLIDER,...
'ContinuousValueChange',@l_SetRoiTransparency);
set(H.ROI_TRANSP_SLIDER,'userdata',RoiTransparencyListener)
end
tmp=get(H.ROI_TRANSP_SLIDER,'position');
h1 = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[10 tmp(2)-14 88 14],...
'style','text',...
'string','Transparent',...
'horizontalalign','left',...
'fontweight','normal',...
'fontsize',8,...
'backgroundcolor',GD.col.frame);
h1 = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3)-88 tmp(2)-14 88 14],...
'style','text',...
'string','Opaque',...
'horizontalalign','right',...
'fontweight','normal',...
'fontsize',8,...
'backgroundcolor',GD.col.frame);
H.ROI_TRANSP_EDIT = uicontrol('parent',H.FIG,...
'units','pixel',...
'position',[tmp(1)+tmp(3)+3 tmp(2) 38 tmp(4)],...
'style','edit',...
'backgroundcolor','w',...
'string','0.5',...
'callback',{@l_SetRoiTransparency,'edit'},...
'userdata',0.5);
%% Draw invisible uipanel for axes
%tmp=get(H.SIDEBAR,'position');
tmp=get(H.SIDEBAR_FRAME,'position');
% $$$ H.AXES_UIPANEL = uipanel('parent',H.FIG,...
% $$$ 'units','pixel',...
% $$$ 'position',[tmp(1)+tmp(3) ...
% $$$ 0 fig_pos(3)-(tmp(1)+tmp(3)) fig_pos(4)],...
% $$$ 'backgroundcolor',GD.col.mainfig,...
% $$$ 'bordertype','none',...
% $$$ 'tag','ax_uipanel');
%% Draw image axes
gap=10*dxx;
%pos=get(H.SIDEBAR,'position');
pos=get(H.SIDEBAR_FRAME,'position');
% Calculate axis positions
%ax_pos=l_AxesPositions([],[],0,[256,256;256,256;256,256]);
ax_pos = ones(3,4);
H.IMAX1=axes('Parent',H.FIG,...
'units','pixel',...
'Position', ...
ax_pos(1,:),'Ylim',[0 1], ...
'xlim',[0 1],...
'ydir','reverse',...%'Yticklabel',{},... 'Xticklabel',{},...
'Box','on', ...
'xgrid','on',...
'ygrid','on',...
'Fontsize',GD.ax_fs,...
'visible','off');
H.IMOVERLAYAX(1)=axes('Parent',H.FIG,...
'units','pixel',...
'Position', ...
ax_pos(1,:),'Ylim',[0 1], ...
'xlim',[0 1],...
'ydir','reverse',...
'Box','on', ...
'xgrid','off',...
'ygrid','off',...
'Fontsize',GD.ax_fs,...
'visible','off',...
'hittest','off');
H.IMAX2=axes('Parent',H.FIG,...
'units','pixel',...
'Position', ...
ax_pos(2,:),'Ylim',[0 1], ...
'xlim',[0 1],...
'ydir','reverse',...%'Yticklabel',{},... 'Xticklabel',{},...
'Box','on', ...
'Fontsize',GD.ax_fs,...
'visible','off');
H.IMOVERLAYAX(2)=axes('Parent',H.FIG,...
'units','pixel',...
'Position', ...
ax_pos(2,:),'Ylim',[0 1], ...
'xlim',[0 1],...
'ydir','reverse',...
'Box','on', ...
'xgrid','off',...
'ygrid','off',...
'Fontsize',GD.ax_fs,...
'visible','off',...
'hittest','off');
H.IMAX3=axes('Parent',H.FIG,...
'units','pixel',...
'Position', ...
ax_pos(3,:),'Ylim',[0 1], ...
'xlim',[0 1],...
'ydir','reverse',...%'Yticklabel',{},... 'Xticklabel',{},...
'Box','on', ...
'Fontsize',GD.ax_fs,...
'visible','off');
H.IMOVERLAYAX(3)=axes('Parent',H.FIG,...
'units','pixel',...
'Position', ...
ax_pos(3,:),'Ylim',[0 1], ...
'xlim',[0 1],...
'ydir','reverse',...
'Box','on', ...
'xgrid','off',...
'ygrid','off',...
'Fontsize',GD.ax_fs,...
'visible','off',...
'hittest','off');
H.COLORBAR_AX = axes('Parent',H.FIG,...
'units','pixel',...
'Position', ...
[1 1 1 1],'Ylim',[0 1], ...
'xlim',[0 1],...
'yaxislocation','right',...
'ydir','reverse',...%'Yticklabel',{},... 'Xticklabel',{},...
'Box','on', ...%'fontunits','normal',...'Fontsize',0.023,...
'fontsize',8,...
'visible','on');
H.COLORBAR_IM = [];
H.IMROI=[];
H.ROIAX=[];
H.IMOVERLAY=[];
% Info text
H.INFOTEXT = text('parent',H.IMAX1,...
'units','normalized',...
'position',[0.01 0.99],...
'verticalalign','top',...
'horizontalalign','left',...
'string',{'File: ','Slice: ','Image size: ','Zoom: '},...
'visible','off',...
'color','w',...
'interpreter','none',...
'fontsize',9,...
'fontname','fixedwidth',...
'backgroundcolor','none');
if ~Dat.HG2graphics
set(H.INFOTEXT,'erasemode','normal')
end
if isunix
set(H.INFOTEXT,'fontname','bitstream vera sans mono')
end
H.ROIINFOTEXT = text('parent',H.IMAX1,...
'units','normalized',...
'position',[0.01 0.01],...
'verticalalign','bottom',...
'horizontalalign','left',...
'color','w',...
'string',...
{'Current ROI:',...
'Mean:',...
'STD:',...
'Sum:',...
'Min:',...
'Max:',...
'Pixel Count:'},...
'visible','off',...
'interpreter','none',...
'fontsize',9,...
'fontname','fixedwidth',...
'backgroundcolor','none');
if ~Dat.HG2graphics
set(H.ROIINFOTEXT,'erasemode','normal')
end
if isunix
set(H.ROIINFOTEXT,'fontname','bitstream vera sans mono')
end
% Set axes to the bottom of the uistack
fig_childs = get(H.FIG,'children');
ind=ismember(double(fig_childs),double([H.IMAX1,H.IMAX2,H.IMAX3])');
fig_childs(end+1:end+3)=fig_childs(ind);
fig_childs(ind)=[];
set(H.FIG,'children',fig_childs)
% Set KeyPressFcn for uicontrol objects
h=findobj(H.FIG,'type','uicontrol');
set(h,'KeyPressFcn',@l_KeyPressFcn);
set(h(strcmpi(get(h,'style'),'edit')),'KeyPressFcn','')
%% Draw frame
H.BLANK_FRAME = uicontrol('Parent',H.FIG,'Units','normalized', ...
'Backgroundcol',[0.5 0.5 0.5], ...
'Tag','BLANK_FRAME', ...
'Position',[0 0 1 1],'Style','frame',...
'visible','on');
% Get uicontrol original positions for ResizeFcn -------------
uich=findobj(H.FIG,'type','uicontrol');
uich(find(uich==H.IMSLIDER_FRAME))=[];
uich(find(uich==H.SIDEBAR_FRAME))=[];
uich(find(uich==H.IMSLIDER(1)))=[];
uich(find(uich==H.IMSLIDER(2)))=[];
uich(find(uich==H.BLANK_FRAME))=[];
tmp=get(uich,'position');
H.UICH_ORIG_POS = reshape([tmp{:}],4,length(tmp))';
% Get handles to uicontrols that need to be enabled after initialising
H.UICH_ENABLED=uich(strcmp(get(uich,'enable'),'on'));
H.UICH_ENABLED(end+1)=view_h;
H.UICH_ENABLED(end+1)=edit_h;
H.UICH_ENABLED(end+1)=roi_tools_h;
H.UICH_ENABLED(end+1)=closefile_h;
%H.UICH_ENABLED(end+1)=H.viewprocpar_h;
H.UICH_ENABLED(end+1)=H.UIOVERLAY;
H.UICH_ENABLED(end+1)=H.UIPUSH_SAVE;
%H.UICH_ENABLED(end+1)=H.UIPUSH_PRINT;
H.UICH_ENABLED(end+1)=H.FILEMENU_SAVE_IMAGE;
H.UICH_ENABLED(end+1)=H.FILEMENU_SAVERES;
H.UICH_ENABLED(end+1)=H.UIPUSH_IMSTACK;
H.UICH_ENABLED(end+1)=H.UIPUSH_ROTATE;
H.UICH_ENABLED(end+1)=H.UITOGGLE_VIEW3D;
H.UICH_ENABLED(end+1)=H.UITOGGLE_VIEWX;
H.UICH_ENABLED(end+1)=H.UITOGGLE_VIEWY;
H.UICH_ENABLED(end+1)=H.UITOGGLE_VIEWZ;
H.UICH_ENABLED(end+1)=H.UITOGGLE_GRID;
H.UICH_ENABLED(end+1)=H.UIPLUGINS;
H.UICH_ENABLED(end+1)=H.UITOGGLE_INFO;
H.UICH_ENABLED(end+1)=H.UIPUSH_NEWROI;
H.UICH_ENABLED(end+1)=H.ROIBTN_LOAD;
H.UICH_ENABLED(end+1)=H.FILEMENU_EXPORT;
H.UICH_ENABLED(end+1)=H.UITOGGLE_COLORBAR;
H.UICH_ENABLED(end+1)=H.UITOGGLE_CROSSHAIRS;
H.UICH_ENABLED(end+1)=H.UNFOLD_DATA;
% Get handles to the uicontrols that need to enabled when ROIs are
% defined
H.UICH_ROIENABLED = [H.UIROITOOLS_SAVE,...
H.UIROITOOLS_SAVETEMPLATE,...
H.UIROITOOLS_COPY,...
H.UIROITOOLS_COMP,...
H.UIROITOOLS_FLIP,...
H.UIROISTATS,...
H.UITOGGLE_DRAWROI,...
H.UITOGGLE_ERASEROI,...
H.UITOGGLE_FILLROI,...
H.UITOGGLE_MOVEROI,...
H.UITOGGLE_MOVEROI3D,...
H.UIPUSH_COPYROI,...
H.ROIBTN_COPY,...
H.ROIBTN_DEL,...
H.ROIBTN_DELALL,...
H.ROIBTN_SAVE,...
H.ROIBTN_STATS,...
H.ROI_EDIT,...
H.UIROISHOWEDGES,...
H.UIROIRENAME,...
H.UIROISETCOLOR,...
H.UIPUSH_STATS_ROI];
% Set enable off for all the uicontrols, when there is no data
set(uich,'enable','off')
end % function H=l_draw_gui()
%%%%%%%%%%%%%%%%%%%%%%
%%
%% Open file(s)
%%
%%%%%%%%%%%%%%%%%%%%%%
function l_OpenFile(h,evd,opt,FileName)
try
% Ask if ROI(s) should be saved
cancel=l_CheckRoiSaved;
if cancel
return
end
if exist('FileName','var')
PromptFiles = false;
else
PromptFiles = true;
end
%Dat.LoadRoiAtStartUp = false;
if PromptFiles
% Default filepath
try
filepath=getpref('Aedes','GetDataFileDir');
catch
filepath='';
end
[filefilt,dataformats] = aedes_getfilefilter;
% Ask for a file
if strcmpi(opt,'single')
[f_name, f_path, f_index] = uigetfile( ...
filefilt, ...
'Select data file',filepath);
if ( all(f_name==0) | all(f_path==0) ) % Cancel is pressed
return
end
% There is a bug in uigetfile in OSX version of Matlab and the
% fid-directory may be returned instead of the fid-file.
if ismac
if length(f_name)>3 && strcmpi(f_name(end-3:end),'.fid')
f_path = [fullfile(f_path,f_name),filesep];
f_name = 'fid';
end
end
else
[f_name, f_path, f_index] = aedes_juigetfiles( ...
filefilt, ...
'Select data file(s)',filepath);
if ~iscell(f_name) && ~iscell(f_path)
if ( all(f_name==0) | all(f_path==0) ) % Cancel is pressed
return
end
end
end
% Put strings in a cell array so we don't have to check it all the
% time...
if ~iscell(f_name)
f_path = {f_path};
f_name = {f_name};
end
% Set current directory to preferences
setpref('Aedes','GetDataFileDir',f_path{1})
else
if strcmpi(opt,'single')
[f_path,f_name,f_ext]=fileparts(FileName);
if isempty(f_path)
f_path = {[pwd,filesep]};
else
if ispc && length(f_path)<3
f_path = {[pwd,filesep,f_path,filesep]};
elseif isunix && f_path(1)~=filesep
f_path = {[pwd,filesep,f_path,filesep]};
else
f_path = {[f_path,filesep]};
end
end
f_name = {[f_name,f_ext]};
% f_index = 0;
% dataformat = '';
% Check that the file exists...
if exist([f_path{1},f_name{1}],'file')~=2
showError = true;
% If the file cannot be found, it might be a VNMR file with only
% folder reference...
if strcmpi(f_ext,'.fid')
if exist([f_path{1},f_name{1},filesep,'fid'],'file')~=2
showError = true;
else
showError = false;
f_path = {[f_path{1},f_name{1},filesep]};
f_name = {'fid'};
end
end
if showError
h=errordlg({'Could not find file',...
['"',f_path{1},f_name{1},'"'],...
'','Check that the file has not been removed and can be accessed.'},...
'Cannot not find file', ...
'modal');
uiwait(h);
return
end
end
else
f_name = {};
f_path = {};
%f_index = 0;
%% Extract file and path names to separate cell arrays
for ii=1:length(FileName)
[fp,fn,fe]=fileparts(FileName{ii});
f_path{ii} = [fp,filesep];
f_name{ii} = [fn,fe];
end
%dataformat = '';
end
end
% Close file if necessary
if ~isempty(DATA)
l_CloseFile([],[]);
end
%% Read the data from other data files
if strcmpi(opt,'single') || length(f_name)==1
try
DATA=aedes_data_read([f_path{1},f_name{1}]);
catch
h=errordlg({['Could not read file "',[f_path{1},f_name{1}],'"'],'',lasterr},...
'Error reading file', ...
'modal');
uiwait(h);
return
end
% Set to Recent Files menu
l_BuildRecentFilesMenu([],[],[],[f_path{1},f_name{1}]);
else
DATA={};
count=0;
SkippedFiles={};
SkippedInd = [];
[h,txh]=aedes_calc_wait({['Reading file 1/',...
num2str(length(f_name))],'""'});
for ii=1:length(f_name)
set(txh,'String',...
sprintf('%s\n%s',['Reading file ' num2str(ii) '/' num2str(length(f_name))],...
['"',f_path{ii},f_name{ii},'"']))
drawnow
try
tmp=aedes_data_read([f_path{ii},f_name{ii}],'wbar','off');
% Determine from the first file if we are reading one slice data into
% "mixed" cell arrayed format or 3D volumes into a 4D file
if ii==1
if ndims(tmp.FTDATA)==3
% Read 3D data into 4D array
Read2Mixed = false;
% Reserve space for data
DATA = tmp;
DATA.FTDATA = zeros(size(tmp.FTDATA,1),...
size(tmp.FTDATA,2),size(tmp.FTDATA,3),...
length(f_name),class(tmp.FTDATA));
DATA.FTDATA(:,:,:,1)=tmp.FTDATA;
elseif ndims(tmp.FTDATA)==2
% Read 2D slices into mixed cell array...
Read2Mixed = true;
DATA = {tmp};
else
% Throw error...
Read2Mixed = false;
error('Reading of multiple 4D files is not supported.')
end
end
if ~Read2Mixed
if isequal(size(DATA.FTDATA(:,:,:,1)),size(tmp.FTDATA))
DATA.FTDATA(:,:,:,ii) = tmp.FTDATA;
else
count=count+1;
SkippedFiles{count} = [f_path{ii},f_name{ii}];
disp(['Aedes: Warning: Data size in file "',f_path{ii},...
f_name{ii},'" does not match with the first data file! Skipping file...'])
end
elseif Read2Mixed
DATA{ii}=tmp;
if length(size(tmp.FTDATA))>2
count=count+1;
SkippedInd(end+1) = ii;
SkippedFiles{count} = [f_path{ii},f_name{ii}];
DATA{ii}=[];
disp(['Aedes: Warning: File "',f_path{ii},...
f_name{ii},'" contains multiple slices! Skipping file...'])
end
end
catch
if ii==1
h=errordlg({'Could not read file',...
['"',f_path{ii},f_name{ii},'"'],...
'','Returned error:',lasterr},...
'Could not read file','modal');
DATA = [];
break
elseif Read2Mixed
count=count+1;
SkippedFiles{count} = [f_path{ii},f_name{ii}];
DATA{ii}=[];
disp(['Aedes: Warning: Could not read file "',...
f_path{ii},f_name{ii},'". Skipping file...'])
else
% Throw the actual error and break
h=errordlg({'Could not read file',...
['"',f_path{ii},f_name{ii},'"'],...
'','Returned error:',lasterr},...
'Could not read file','modal');
DATA = [];
break
end
end
end
delete(h)
% Ensure that there are no empty values in DATA
if iscell(DATA)
empty_val=cellfun('isempty',DATA);
if all(empty_val)
DATA=[];
else
DATA(empty_val)=[];
end
end
% If the data consists of multiple 2D files that are all of the same
% size, ask if the user wants to view them as 3D data.
if Read2Mixed
nFiles = length(DATA);
X = zeros(1,nFiles);
Y = zeros(1,nFiles);
for ii = 1:nFiles
X(ii)=size(DATA{ii}.FTDATA,1);
Y(ii)=size(DATA{ii}.FTDATA,2);
end
if all(X==X(1)) && all(Y==Y(1))
resp = questdlg('Do you want to view data as a 3D data set or a 2D image stack?',...
'View data 3D or 2D?','View as 3D data','View as 2D image stack','View as 2D image stack');
if isempty(resp)
viewAs3D = false;
elseif strcmpi(resp,'View as 3D data')
viewAs3D = true;
else
viewAs3D = false;
end
if viewAs3D
tmp = DATA{1};
tmp.FTDATA = zeros(X(1),Y(1),nFiles,class(DATA{1}.FTDATA));
for ii = 1:nFiles
tmp.FTDATA(:,:,ii) = DATA{ii}.FTDATA;
DATA{ii}.FTDATA=[];
end
DATA=[];
DATA=tmp;
end
end
end
% Remove skipped volumes
if ~Read2Mixed && ~isempty(SkippedInd)
DATA.FTDATA(:,:,:,SkippedInd) = [];
end
% Warn about skipped files
if count~=0
if isempty(DATA)
h=errordlg(['All files were skipped either due to errors ',...
'or because they contained multiple slices.'],...
'Could not read files','modal');
return
else
h=warndlg({['The following file(s) were ',...
'skipped either due to errors or ',...
'because they contained multiple slices:'],'',SkippedFiles{:}},...
'Some Files Were Skipped','modal');
uiwait(h)
end
end
end
if isempty(DATA)
% Canceled
return
end
if isstruct(DATA)
DATA = {DATA};
end
%% Load ROI also if they can be found in the DATA structure
if isfield(DATA{1},'ROI')
ROI = DATA{1}.ROI;
DATA{1}=rmfield(DATA{1},'ROI');
end
%% If the DATA was loaded from MAT-File, it might also contain rotation
%% and flipping and clim information
if isfield(DATA{1},'DataRotation') && isfield(DATA{1},'DataFlip')
Dat.DataRotation = DATA{1}.DataRotation;
Dat.DataFlip = DATA{1}.DataFlip;
DATA{1}=rmfield(DATA{1},'DataRotation');
DATA{1}=rmfield(DATA{1},'DataFlip');
end
if isfield(DATA{1},'RotateFlip3d')
Dat.RotateFlip3d = DATA{1}.RotateFlip3d;
DATA{1}=rmfield(DATA{1},'RotateFlip3d');
end
% Check if data file contain only kspace information
if length(DATA)==1 && isfield(DATA{1},'KSPACE') && ...
(isempty(DATA{1}.FTDATA) & ~isempty(DATA{1}.KSPACE) )
drawnow;
resp=questdlg(['The inputted DATA structure contains only k-space',...
' information. Do you want to view real, imaginary, or absolute',...
' part of the complex k-space?'],...
'Complex data inputted',...
'Real','Imaginary','Absolute','Absolute');
if strcmpi(resp,'Real')
DATA{1}.FTDATA = real(DATA{1}.KSPACE);
elseif strcmpi(resp,'Imaginary')
DATA{1}.FTDATA = imag(DATA{1}.KSPACE);
elseif strcmpi(resp,'Absolute')
DATA{1}.FTDATA = abs(DATA{1}.KSPACE);
else
DATA=[];
return
end
end
% Initialize GUI
l_Initialize([],[]);
if isfield(DATA{1},'SliceClim')
Dat.SliceClim = DATA{1}.SliceClim;
DATA{1}=rmfield(DATA{1},'SliceClim');
set(H.CLIMRANGE_POPUP,'value',2)
l_ChangeClimRange([],[])
end
%% If the ROI-structure has been given in file load time, refresh ROIs
if ~isempty(ROI)
l_RoiLoad([],[],'')
end
catch
aedes_errordump(lasterror);
end
end % function l_OpenFile(h,
%%%%%%%%%%%%%%%%%%%%%%%%%
%%
%% Save Image Data
%%
%%%%%%%%%%%%%%%%%%%%%%%%%
function l_SaveImageData(h,evd)
try
%% Get default save path
try
filepath=getpref('Aedes','PutDataFileDir');
catch
filepath='';
end
%% Save 3D data
if length(DATA)==1
%% Get default save file name
try
if isfield(DATA{Dat.DataInd},'DataFormat') && ...
strcmpi(DATA{Dat.DataInd}.DataFormat,'vnmr')
[fp,fn,fe]=fileparts([DATA{Dat.DataInd}.HDR.fpath,DATA{Dat.DataInd}.HDR.fname]);
[fp,fn,fe]=fileparts(fp);
else
[fp,fn,fe]=fileparts([DATA{Dat.DataInd}.HDR.fpath,DATA{Dat.DataInd}.HDR.fname]);
end
catch
fp=[pwd,filesep];
fn='';
fe='';
end
%% Get saved file name and type
[fname, fpath, findex] = uiputfile( ...
{'*.nii;*.NII','NIfTI-files (*.nii)'; ...
'*.hdr;*.HDR','Analyze 7.5 files (*.hdr)';...
'*.mat:*.MAT','Matlab MAT-File (*.mat)';...
'*.mri;*.MRI','MRI-files (*.mri)'}, ...
'Save Image Data as', [filepath,fn]);
if ( all(fname==0) | all(fpath==0) ) % Cancel is pressed
return
end
%% Set fpath to preferences
setpref('Aedes','PutDataFileDir',fpath);
% Write NIfTI-files -------------------------
if findex==1
%% Prompt save type
resp=questdlg('Save slices in separate NIfTI-files or in a single file?',...
'Separate files or single file?',...
'Separate files','Single file','Cancel',...
'Separate files');
if isempty(resp) || strcmpi(resp,'Cancel')
return
elseif strcmpi(resp,'Separate files')
singleFile = false;
else
singleFile = true;
end
fext = '.nii';
fileType = 'NIfTI';
elseif findex==2 % Write Analyze 7.5 file(s) ----------------
%% Prompt save type
resp=questdlg('Save slices in separate Analyze75-files or in a single file?',...
'Separate files or single file?',...
'Separate files','Single file','Cancel',...
'Separate files');
if isempty(resp) || strcmpi(resp,'Cancel')
return
elseif strcmpi(resp,'Separate files')
singleFile = false;
else
singleFile = true;
end
fext = '.hdr';
fileType = 'Analyze 7.5';
elseif findex==3 % Save data in MATLAB MAT-File ------------------
[fp,fn,fe]=fileparts([fpath,fname]);
try
SliceClim = Dat.SliceClim;
if strcmpi(fe,'.mat')
save([fpath,fname],'DATA','SliceClim','-mat')
else
save([fp,filesep,fn,'.mat'],'DATA','SliceClim','-mat')
end
catch
errordlg({'Could not save MAT-file. The following error was returned:',...
'',lasterr},'Error saving MAT-file!','modal')
end
return
else % Save data in MRI-files -------------------
singleFile = false;
%% Warn about MRI-files
resp=questdlg({['WARNING! Exporting data to MRI-format is not advisable. ' ...
'The data will be scaled and rounded to 12-bit before ' ...
'writing into the MRI-file, and scaling errors of ' ...
'various severities will occur!'],'',...
'Are you sure you want to continue?'},'WARNING!',...
'Yes','No','No');
if isempty(resp) || strcmpi(resp,'No')
return
end
fileType = 'MRI';
fext = '.mri';
end
% Determine file prefix
[fp,fn,fe]=fileparts([fpath,fname]);
if strcmpi(fe,fext)
fprefix = fn;
else
fprefix = [fn,fe];
end
done=false;
%% Write separate files
if ~singleFile
% Create file names
filenames={};
for ii=1:Dat.ImageDim(3)
filenames{ii}=sprintf('%s%03d%s',[fprefix,'_'],ii,fext);
end
nFiles = length(filenames);
% Check if files exist
ind=aedes_check_file_exist(filenames,fpath);
if any(ind)
% Warn if some files are about to be overwritten
overwrited_files = {filenames{ind}};
% Limit the file list to 20 files
if length(overwrited_files)>20
overwrited_files = {overwrited_files{1:20}};
overwrited_files{end+1}='...';
end
resp=questdlg({['The following files already exist in the output directory' ...
' "',fpath,'"'],'','(NOTE: max. 20 files shown here)','',...
overwrited_files{:},'',...
'Do you want to overwrite these files?'},...
'Overwrite Existing Files?','Overwrite','Abort','Abort');
if isempty(resp) || strcmpi(resp,'Abort')
return
end
end
if strcmpi(fileType,'MRI')
done=true;
h=aedes_wbar(0,sprintf('Saving slice 1/%d in MRI format...',nFiles));
for ii=1:nFiles
aedes_wbar(ii/nFiles,h,sprintf('Saving slice %d/%d in MRI format...',ii, ...
nFiles))
try
aedes_smiswrite(DATA{Dat.DataInd}.FTDATA(:,:,ii),...
[fpath,filenames{ii}])
catch
done=false;
break
end
end
elseif strcmpi(fileType,'NIfTI')
h=aedes_wbar(0,sprintf('Saving slice 1/%d in NIfTI format...',nFiles));
for ii=1:nFiles
aedes_wbar(ii/nFiles,h,sprintf('Saving slice %d/%d in NIfTI format...',ii, ...
nFiles))
[done,msg]=aedes_write_nifti(DATA{Dat.DataInd}.FTDATA(:,:,ii),...
[fpath,filenames{ii}],'DataType','single',...
'FileType',2,'Clim',Dat.SliceClim(Dat.DataInd,:));
end
elseif strcmpi(fileType,'Analyze 7.5')
h=aedes_wbar(0,sprintf('Saving slice 1/%d in Analyze 7.5 format...',nFiles));
for ii=1:nFiles
aedes_wbar(ii/nFiles,h,sprintf('Saving slice %d/%d in Analyze 7.5 format...',ii, ...
nFiles))
[done,msg]=aedes_write_nifti(DATA{Dat.DataInd}.FTDATA(:,:,ii),...
[fpath,filenames{ii}],'DataType','single',...
'FileType',0,'Clim',Dat.SliceClim(Dat.DataInd,:));
end
end
else
if strcmpi(fileType,'NIfTI')
[h,txh]=aedes_calc_wait('Saving image data in NIfTI format...');
[done,msg]=aedes_write_nifti(DATA{Dat.DataInd}.FTDATA,...
[fpath,fname],'filetype',2,...
'Clim',Dat.SliceClim(Dat.DataInd,:));
elseif strcmpi(fileType,'Analyze 7.5')
[h,txh]=aedes_calc_wait('Saving image data in Analyze 7.5 format...');
[done,msg]=aedes_write_nifti(DATA{Dat.DataInd}.FTDATA,...
[fpath,fname],'filetype',0,...
'Clim',Dat.SliceClim(Dat.DataInd,:));
end
end
delete(h)
%% Show warning if something went wrong
if ~done
h=errordlg(msg,'Error while saving image data','modal')
uiwait(h);
return
end
%% Save Slice Data
else
%% Get default save file name
if strcmpi(DATA{Dat.DataInd}.DataFormat,'vnmr')
[fp,fn,fe]=fileparts([DATA{Dat.DataInd}.HDR.fpath,DATA{Dat.DataInd}.HDR.fname]);
[fp,fn,fe]=fileparts(fp);
else
[fp,fn,fe]=fileparts([DATA{Dat.DataInd}.HDR.fpath,DATA{Dat.DataInd}.HDR.fname]);
end
%% Get saved file name and type
[fname, fpath, findex] = uiputfile( ...
{'*.mat:*.MAT','Matlab MAT-File (*.mat)';...
'*.nii;*.NII','NIfTI-files (*.nii)'; ...
'*.hdr;*.HDR','Analyze 7.5 files (*.hdr)'}, ...
'Save Image Data as', [filepath,fn]);
if ( all(fname==0) | all(fpath==0) ) % Cancel is pressed
return
end
%% Set fpath to preferences
setpref('Aedes','PutDataFileDir',fpath);
if findex==1 %% Save data in MAT-file
% Determine file prefix
[fp,fn,fe]=fileparts([fpath,fname]);
if strcmpi(fe,'.mat')
fprefix = fn;
else
fprefix = [fn,fe];
end
%% Save data in Matlab MAT-file
try
DataRotation = Dat.DataRotation;
DataFlip = Dat.DataFlip;
SliceClim = Dat.SliceClim;
save([fpath,fprefix,'.mat'],'DATA','DataRotation','DataFlip',...
'SliceClim','-mat')
catch
hh=errodlg({'Error occurred while saving DATA to file',...
[fpath,fprefix,'.mat']},'Error.','modal');
return
end
elseif any(findex==[2 3])
if findex==2
fext = '.nii';
fileType = 2;
else
fext = '.hdr';
fileType = 0;
end
if findex==2 && Dat.DataL>1
%% Ask if NIfTI files are saved in separate files or the whole
%% volume into a single file
resp=questdlg('Save slices in separate NIfTI-files or in a single file?',...
'Separate files or single file?',...
'Separate files','Single file','Cancel',...
'Separate files');
if isempty(resp) || strcmpi(resp,'Cancel')
return
elseif strcmpi(resp,'Separate files')
singleFile = false;
else
singleFile = true;
end
else
% Try to write Analyze75 files allways into a single volume file
singleFile = true;
end
% Determine file prefix
[fp,fn,fe]=fileparts([fpath,fname]);
if strcmpi(fe,fext)
fprefix = fn;
else
fprefix = [fn,fe];
end
if singleFile
%% Check if all slices are the same size. Otherwise it is not
%% possible to save all the slices in one file
if all(Dat.ImageDim(:,1)/Dat.ImageDim(1,1)) && ...
all(Dat.ImageDim(:,2)/Dat.ImageDim(1,2))
[calc_h,txh]=aedes_calc_wait({'Writing image data to file',
[fpath,fprefix,fext]});
% Generate a new data matrix. This can in extreme cases inflict
% "out of memory" error.
data_mtx = zeros(Dat.ImageDim(1,1),Dat.ImageDim(1,2),Dat.DataL,...
'single');
for ii=1:Dat.DataL
data_mtx(:,:,ii)=DATA{ii}.FTDATA;
end
% Write data to NIfTI/Analyze75-file
[done,msg]=aedes_write_nifti(data_mtx,[fpath,fprefix,fext],...
'FileType',fileType,'DataType', ...
'single');
clear('data_mtx')
if ~done
delete(calc_h)
hh=errordlg({'An error occurred while writing file',...
[fpath,fprefix,fext]},'Error Writing File',...
'modal');
return
end
delete(calc_h)
else
hh=errordlg(['Cannot write slices into a single file, because all ' ...
'the slices are not of the same size.'],...
'Cannot Write Single File','modal');
return
end
else
%% Write all slices into separate NIfTI-files
% Create file names
filenames={};
for ii=1:Dat.DataL
filenames{ii}=sprintf('%s%03d%s',[fprefix,'_'],ii,fext);
end
nFiles = length(filenames);
% Check if files exist
ind=aedes_check_file_exist(filenames,fpath);
if any(ind)
% Warn if some files are about to be overwritten
overwrited_files = {filenames{ind}};
% Limit the file list to 20 files
if length(overwrited_files)>20
overwrited_files = {overwrited_files{1:20}};
overwrited_files{end+1}='...';
end
resp=questdlg({['The following files already exist in the output directory' ...
' "',fpath,'"'],'','(NOTE: max. 20 files shown here)','',...
overwrited_files{:},'',...
'Do you want to overwrite these files?'},...
'Overwrite Existing Files?','Overwrite','Abort','Abort');
if isempty(resp) || strcmpi(resp,'Abort')
return
end
end
h=aedes_wbar(0,sprintf('Saving slice 1/%d in NIfTI format...',nFiles));
for ii=1:nFiles
aedes_wbar(ii/nFiles,h,sprintf('Saving slice %d/%d in NIfTI format...',ii, ...
nFiles))
[done,msg]=aedes_write_nifti(DATA{ii}.FTDATA,...
[fpath,filenames{ii}],'DataType','single',...
'FileType',2,...
'Clim',Dat.SliceClim(ii,:));
if ~done
delete(h)
hh=errordlg({'An error occurred while writing file',...
[fpath,filenames{ii}]},'Error Writing File', ...
'modal');
return
end
end
delete(h)
end
end
end
catch
aedes_errordump(lasterror);
end
end % function l_SaveImageData(h,
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Check if ROI(s) are saved
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function cancel=l_CheckRoiSaved()
% Warn if ROIs are not saved
if ~isempty(ROI) && ~Dat.RoiSaved
resp=questdlg({'Modified ROI(s) exist.',...
'Do you want save ROI(s) before closing file?'},...
'Save ROI(s) before closing file?','Yes','No','Cancel','Yes');
if strcmpi(resp,'Yes')
l_RoiSave([],[])
cancel = false;
return
elseif isempty(resp) || strcmpi(resp,'Cancel')
cancel = true;
return
else
cancel = false;
end
else
cancel = false;
end
figure(H.FIG)
end % function cancel=l_CheckRoiSaved()
%%%%%%%%%%%%%%%%%%%%%%%%
%%
%% Close File(s)
%%
%%%%%%%%%%%%%%%%%%%%%%%%
function l_CloseFile(h,evd,opt)
try
if nargin>2 && strcmpi(opt,'PreserveData')
PreserveData = true;
else
PreserveData = false;
end
% Warn if ROIs are not saved
if ~isempty(h) && ishandle(h) && ~PreserveData
cancel=l_CheckRoiSaved;
if cancel
return
end
end
% Reset uicontrol focus
%uicontrol(H.SL_SLIDER);
% Remember HG2 status
hg2_status = Dat.HG2graphics;
% Delete Voxel Time Series Figure if open
try
close(H.TSFIG)
end
set(H.UIVIEW_TIMESERIES,'checked','off')
%% Remove callback for Mouse scroll wheel
if Dat.MatlabVersion>=7.05
set(H.FIG,'WindowScrollWheelFcn','')
end
% Delete all ROIs and related images and axes
if ~PreserveData
clear ROI DATA Dat
ROI = [];
else
clear Dat
end
try
delete(H.IMROI)
end
try
delete(H.ROIAX)
end
H.ROIAX=[];
H.IMROI=[];
if isfield(H,'IM')
set(H.IM,'CData',[])
end
% Set mouse for changing window/level
set(get(H.UITOGGLE_ARROW,'userdata'),'state','off')
set(H.UITOGGLE_ARROW,'state','on')
% Clear ROI undo buffer and disable ROI uicontrols
l_RoiUndoBuffer('clear')
set(H.ROIVIEW_LBOX,'value',[],'string','')
set([H.ROIBTN_DEL,H.ROIBTN_DELALL,...
H.ROIBTN_UNDO,H.UIPUSH_UNDOROI,H.ROIBTN_COPY],'enable','off')
set(H.ROI_EDIT,'value',1,'string',{''},'enable','off')
% Delete crossbars
try
delete(H.CROSSBAR_LN)
end
H.CROSSBAR_LN=[];
%set(H.SHOW_CROSSBARS,'value',0)
% Reset image sliders
set(H.IMSLIDER,'visible','off','value',0)
set(H.IMSLIDER_FRAME,'visible','off')
% Reset uitoolbar buttons
set([H.UIPUSH_ZOOMIN,H.UIPUSH_ZOOMOUT,H.UITOGGLE_ZOOMNORM],'enable','off')
set([H.UITOGGLE_VIEW3D,H.UITOGGLE_VIEWY,H.UITOGGLE_VIEWZ,H.UITOGGLE_CROSSHAIRS],'state','off')
set([H.UITOGGLE_ARROW,H.UITOGGLE_PAN,...
H.UITOGGLE_DRAWROI,H.UITOGGLE_ERASEROI,H.UITOGGLE_MOVEROI,...
H.UITOGGLE_MOVEROI3D,H.UITOGGLE_GRID,H.UITOGGLE_CROSSHAIRS],...
'enable','off')
set([H.UIPUSH_NEWROI,H.UIPUSH_UNDOROI],...
'enable','off')
set(H.UICH_ROIENABLED,'enable','off')
set(H.UIMENU_ROTATEFLIP,'enable','off')
set(H.UIEDIT_IMSTACK,'enable','off')
% Delete overlay control window
if isfield(H,'OVERLAY_CONTROL_FIG') && ~isempty(H.OVERLAY_CONTROL_FIG) ...
&& ishandle(H.OVERLAY_CONTROL_FIG)
delete(H.OVERLAY_CONTROL_FIG)
H.OVERLAY_CONTROL_FIG = [];
end
% Disable overlay uimenus
set([H.UIOVERLAY_CONTROLS,...
H.UIOVERLAY_SAVE,...
H.UIOVERLAY_DELETE],'enable','off')
% Reset volume button and editbox
set([H.V_BTN,H.V_EDIT],'enable','off')
set(H.V_EDIT,'string','1')
% Delete overlays if loaded
if isfield(H,'IMOVERLAY') && ~isempty(H.IMOVERLAY)
try
delete(H.IMOVERLAY)
catch
end
H.IMOVERLAY=[];
end
% Delete colorbar image and intensity line
try
delete(H.COLORBAR_IM)
end
try
delete(H.COLORBAR_LN)
end
try
delete(H.COLORBAR_TX)
end
H.COLORBAR_IM=[];
H.COLORBAR_LN=[];
H.COLORBAR_TX=[];
% Delete data images
try
delete(H.IM)
end
% Clear data from memory
if ~PreserveData
DATA = [];
end
% disable uicontrols
set(H.UICH_ENABLED,'enable','off')
% Reset figure window title
set(H.FIG,'Name','Aedes 1.0')
% Update Voxel Value text
set(H.VOXEL_VALUE,'string','-')
%% Place blank frame in front of gui
set(H.BLANK_FRAME,'visible','on')
%drawnow
% Clear internal variables
Dat = [];
Dat.HG2graphics = hg2_status;
catch
aedes_errordump(lasterror);
end
end % function l_CloseFile(h,
%%%%%%%%%%%%%%%%%%%%%%%
%%
%% Initialize GUI
%%
%%%%%%%%%%%%%%%%%%%%%%%
function l_Initialize(h,evd)
try
%% Initialize "Mixed" type (i.e. slice per file) data -------------------
if length(DATA)>1 || ( length(DATA)==1 & any(ndims(DATA{1}.FTDATA)==[1 2]))
Dat.isDataMixed = true;
Dat.DataL = length(DATA);
Dat.RealAxSize = cell(1,Dat.DataL);
for ii=1:Dat.DataL
Dat.ImageDim(ii,:) = [size(DATA{ii}.FTDATA) 1 1];
Dat.RealAxSize{ii} = [Dat.ImageDim(ii,2),Dat.ImageDim(ii,1);...
Dat.ImageDim(ii,3),Dat.ImageDim(ii,1);...
Dat.ImageDim(ii,3),Dat.ImageDim(ii,2)];
end
Dat.DataInd = 1;
if ~isfield(Dat,'DataRotation') || ~isfield(Dat,'DataFlip')
Dat.DataRotation = zeros(1,Dat.DataL);
Dat.DataFlip = zeros(1,Dat.DataL);
end
Dat.RotateFlip3d = {};
else %% Initialize normal 3D- or 4D data --------------
Dat.isDataMixed = false;
Dat.ImageDim = size(DATA{1}.FTDATA);
if length(Dat.ImageDim)<4
le=length(Dat.ImageDim);
Dat.ImageDim = [Dat.ImageDim ones(1,4-le)];
end
Dat.DataL = 1;
Dat.DataInd = 1;
if ~isfield(Dat,'DataRotation') || ~isfield(Dat,'DataFlip')
Dat.DataRotation = [];
Dat.DataFlip = [];
end
if ~isfield(Dat,'RotateFlip3d')
Dat.RotateFlip3d = {};
end
Dat.RealAxSize{Dat.DataInd} = [Dat.ImageDim(Dat.DataInd,2),Dat.ImageDim(Dat.DataInd,1);...
Dat.ImageDim(Dat.DataInd,3),Dat.ImageDim(Dat.DataInd,1);...
Dat.ImageDim(Dat.DataInd,3),Dat.ImageDim(Dat.DataInd,2)];
end
% % Detect if HG2 graphics are used
% if isa(H.FIG,'matlab.ui.Figure')
% Dat.HG2graphics = true;
% else
% Dat.HG2graphics = false;
% set(H.FIG,'DoubleBuffer','on')
% end
% Save data file headers -------------------------------
for ii=1:Dat.DataL
Dat.HDR{ii} = DATA{ii}.HDR;
end
% Initialize volumes and slices ------------------------
Dat.Vols = Dat.ImageDim(Dat.DataInd,4);
Dat.Rcvrs = size(DATA{1}.FTDATA,5);
Dat.CurrentVol = 1;
Dat.Slices = [1 1 1];
% Initialize Clim --------------------------------------
Dat.ScaleMin=[];
Dat.ScaleMax=[];
Dat.OrigClim=[];
for ii=1:Dat.DataL
Dat.ScaleMin(ii) = double(min(min(min(DATA{ii}.FTDATA(:,:,:,Dat.CurrentVol)))));
Dat.ScaleMax(ii) = double(max(max(max(DATA{ii}.FTDATA(:,:,:,Dat.CurrentVol)))));
Dat.OrigClim(ii,:) = [Dat.ScaleMin(ii) Dat.ScaleMax(ii)];
if diff(Dat.OrigClim(ii,:))==0
Dat.OrigClim(ii,:) = [0 1];
end
end
% Detect Matlab version
[Dat.MatlabVersion,Dat.isImageProc] = aedes_getmatlabversion;
% If any of the currently opened files is Analyze or NIfTI type, the
% cal_max and cal_min fields are checked and adjusted accordingly
Dat.Clim = Dat.OrigClim(1,:);
if ~isfield(Dat,'SliceClim')
Dat.SliceClim = Dat.OrigClim;
for ii=1:Dat.DataL
if isfield(DATA{ii},'DataFormat') && ...
any(strcmpi(DATA{ii}.DataFormat,{'analyze75','nifti(1)', ...
'nifti(2)'}))
try
cal_min=DATA{ii}.HDR.FileHeader.dime.cal_min;
cal_max=DATA{ii}.HDR.FileHeader.dime.cal_max;
if cal_min~=0
Dat.SliceClim(ii,1)=cal_min;
end
if cal_max~=0
Dat.SliceClim(ii,2)=cal_max;
end
catch
continue
end
end
end
end
% Get default Clim behavior from preferences -------------
% try
% Dat.LockClim = getpref('Aedes','LockClim');
% if Dat.LockClim==0
% val=3;
% elseif Dat.LockClim==1
% val=1;
% elseif Dat.LockClim==2
% val=2;
% else
% val=4;
% end
% catch
Dat.LockClim = 0; % 0 = clim unlocked
% 1 = clim locked global
% 2 = clim locked slice
% 3 = clim unlocked and auto-balanced
val = 3;
% end
% Set Clim values ----------------------------------
set(H.CLIMMAXEDIT,'string',num2str(Dat.Clim(2)),...
'userdata',Dat.Clim(2))
set(H.CLIMMINEDIT,'string',num2str(Dat.Clim(1)),...
'userdata',Dat.Clim(1))
set(H.CLIMRANGE_POPUP,'value',val)
% Default gap between axes --------------------
Dat.AxGap=4;
% Default view direction --------------------
Dat.AxView=0;
% Initialize colorbar -----------------------
Dat.ColMap = [];
Dat.ColMapInverted=false;
try
Dat.ShowColorbar = getpref('Aedes','ShowColorbar');
if Dat.ShowColorbar
set(H.UITOGGLE_COLORBAR,'state','on')
end
catch
Dat.ShowColorbar = false;
set(H.UITOGGLE_COLORBAR,'state','off')
end
% Try to determine field of view (FOV) ----------------------------
if isfield(DATA{Dat.DataInd},'PROCPAR') && isfield(DATA{Dat.DataInd}.PROCPAR,'lro') && ...
isfield(DATA{Dat.DataInd}.PROCPAR,'lpe')
Dat.FOV = [DATA{Dat.DataInd}.PROCPAR.lpe DATA{Dat.DataInd}.PROCPAR.lro];
else
Dat.FOV = [];
end
% Get default Zoom levels from preferences -----------------------------
Dat.OldZoom = [];
Dat.ZoomStep = 0.2;
try
Dat.ZoomLevel = getpref('Aedes','ZoomLevel');
if Dat.ZoomLevel==0
Dat.AxSize = 0;
set(H.UITOGGLE_ZOOMNORM,'enable','on',...
'state','on')
else
%Dat.AxSize = Dat.RealAxSize*zoom_level;
end
catch
% Default axes sizes
Dat.ZoomLevel=1;
setpref('Aedes','ZoomLevel',1)
end
% Initialize axes ---------------------------------------------
tmp=get(H.SIDEBAR_FRAME,'position');
l_AxesPositions([],[],Dat.AxView,Dat.ZoomLevel);
set(H.IMAX1,'xlim',[0.5 Dat.ImageDim(Dat.DataInd,2)+0.5],...
'ylim',[0.5 Dat.ImageDim(Dat.DataInd,1)+0.49],...
'visible','off',...
'clim',Dat.Clim)
set(H.IMOVERLAYAX(1),'xlim',[0.5 Dat.ImageDim(Dat.DataInd,2)+0.5],...
'ylim',[0.5 Dat.ImageDim(Dat.DataInd,1)+0.49]);
set(H.IMAX2,'xlim',[0.5 Dat.ImageDim(Dat.DataInd,3)+0.5],...
'ylim',[0.5 Dat.ImageDim(Dat.DataInd,1)+0.49],...
'visible','off',...
'clim',Dat.Clim)
set(H.IMOVERLAYAX(2),'xlim',[0.5 Dat.ImageDim(Dat.DataInd,3)+0.5],...
'ylim',[0.5 Dat.ImageDim(Dat.DataInd,1)+0.49]);
set(H.IMAX3,'xlim',[0.5 Dat.ImageDim(Dat.DataInd,3)+0.5],...
'ylim',[0.5 Dat.ImageDim(Dat.DataInd,2)+0.49],...
'visible','off',...
'clim',Dat.Clim)
set(H.IMOVERLAYAX(3),'xlim',[0.5 Dat.ImageDim(Dat.DataInd,3)+0.5],...
'ylim',[0.5 Dat.ImageDim(Dat.DataInd,2)+0.49])
% Get default View direction from preferences ------------------------------
try
Dat.AxView = getpref('Aedes','AxView');
if Dat.AxView==0
set(H.UITOGGLE_VIEW3D,'state','on')
elseif Dat.AxView==1
set(H.UITOGGLE_VIEWX,'state','on')
elseif Dat.AxView==2
set(H.UITOGGLE_VIEWY,'state','on')
else
set(H.UITOGGLE_VIEWZ,'state','on')
end
catch
Dat.AxView = 0;
setpref('Aedes','AxView',Dat.AxView)
set(H.UITOGGLE_VIEW3D,'state','on')
end
if Dat.ImageDim(Dat.DataInd,3)==1
Dat.AxView=3;
set(H.UITOGGLE_VIEWZ,'state','on')
end
% Get grid info from preferences ---------------------------
try
Dat.ShowGrid = getpref('Aedes','ShowGrid');
catch
Dat.ShowGrid = false;
end
if Dat.ShowGrid
set(H.UIVIEW_GRID,'checked','off')
set(H.UITOGGLE_GRID,'state','off',...
'enable','on')
l_ViewAxesUnits([],[],'pixel')
else
set(H.UIVIEW_GRID,'checked','on')
set(H.UITOGGLE_GRID,'state','on',...
'enable','on')
l_ViewAxesUnits([],[],'pixel')
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Initialize toolbar buttons
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Initialize Zoom buttons ----------------------------
if Dat.ZoomLevel==0.5
set(H.UIPUSH_ZOOMIN,'enable','on')
elseif Dat.ZoomLevel==10
set(H.UIPUSH_ZOOMOUT,'enable','on')
else
set([H.UIPUSH_ZOOMIN,H.UIPUSH_ZOOMOUT],'enable','on')
end
set(H.UITOGGLE_ZOOMNORM,'enable','on')
%Dat.ZoomLevel = zoom_level;
% Initialize mouse function buttons --------------------------
set([H.UITOGGLE_ARROW,H.UITOGGLE_PAN],'enable','on')
% Initialize ROI toolbar button -----------------------------
set(H.UIPUSH_NEWROI,'enable','on')
% Set colormap ---------------------------------------
try
ColMap_str=getpref('Aedes','ColorMap');
catch
ColMap_str='gray';
Dat.ColMap=gray(256);
setpref('Aedes','ColorMap',ColMap_str);
end
if strcmpi(ColMap_str,'Custom')
try
Dat.ColMap = getpref('Aedes','CustomColorMap');
if ~isequal(size(Dat.ColMap),[256 3]) || ...
~isnumeric(Dat.ColMap)
ColMap_str='gray';
Dat.ColMap=gray(256);
setpref('Aedes','ColorMap',ColMap_str);
h=errordlg(['Error initializing custom colormap!',...
' Reverting to GRAY.'],...
'Error!','modal');
end
catch
ColMap_str='gray';
Dat.ColMap=gray(256);
setpref('Aedes','ColorMap',ColMap_str);
h=errordlg(['Error initializing custom colormap!',...
' Reverting to GRAY.'],...
'Error!','modal');
end
end
% Set colorbar image -----------------------------
if Dat.ShowColorbar
vis = 'on';
else
vis = 'off';
end
H.COLORBAR_IM = image('parent',H.COLORBAR_AX,...
'cdatamapping','scaled',...
'cdata',gray(256),...
'visible',vis);
set(H.COLORBAR_AX,'xlim',[0.5 3.5],...
'ylim',[0.5 256+0.5],...
'ydir','normal',...
'layer','top',...
'xtick',[])
l_ChangeColorbarLimits([],[])
% Set default Window, Level, and Gamma.
% Store current valid value in the userdata...
Dat.Window = 100;
Dat.Level = 50;
set(H.WINDOW_EDIT,'string',num2str(Dat.Window),...
'userdata',Dat.Window)
set(H.LEVEL_EDIT,'string',num2str(Dat.Level),...
'userdata',Dat.Level)
% Set initial slices ---------------------------------
if ~Dat.isDataMixed && isfield(DATA{1},'DataFormat') && ...
strncmpi(DATA{1}.DataFormat,'NIfTI',5)
if DATA{1}.HDR.FileHeader.hist.qform_code>0
q_b = DATA{1}.HDR.FileHeader.hist.quatern_b;
q_c = DATA{1}.HDR.FileHeader.hist.quatern_c;
q_d = DATA{1}.HDR.FileHeader.hist.quatern_d;
q_a = sqrt(1.0-(q_b*q_b+q_c*q_c+q_d*q_d));
R = [q_a*q_a+q_b*q_b-q_c*q_c-q_d*q_d,2*q_b*q_c-2*q_a*q_d,2*q_b*q_d+2*q_a*q_c;...
2*q_b*q_c+2*q_a*q_d,q_a*q_a+q_c*q_c-q_b*q_b-q_d*q_d,2*q_c*q_d-2*q_a*q_b; ...
2*q_b*q_d-2*q_a*q_c,2*q_c*q_d+2*q_a*q_b,q_a*q_a+q_d*q_d-q_c*q_c-q_b*q_b];
qfac = DATA{1}.HDR.FileHeader.dime.pixdim(1);
qoffset = [DATA{1}.HDR.FileHeader.hist.qoffset_x;...
DATA{1}.HDR.FileHeader.hist.qoffset_y;...
DATA{1}.HDR.FileHeader.hist.qoffset_z];
end
else
set(H.X_EDIT,'string',num2str(Dat.Slices(1)))
set(H.Y_EDIT,'string',num2str(Dat.Slices(2)))
set(H.Z_EDIT,'string',num2str(Dat.Slices(3)))
end
% Initialize volumes
if Dat.Vols>1
set([H.V_BTN,H.V_EDIT],'enable','on')
set(H.V_EDIT,'string','1');
set(H.FLIP3D_V,'enable','on');
else
set([H.V_BTN,H.V_EDIT],'enable','off')
set(H.V_EDIT,'string','1');
set(H.V_BTN,'fontweig','normal');
set(H.FLIP3D_V,'enable','off');
end
% Set defaults for ROIs
Dat.RoiColors = [255 0 0;...
0 255 0;...
0 0 255;...
255 255 0;...
255 0 255;...
0 255 255;...
255 128 0;...
128 255 0;...
0 128 255;...
128 0 255;...
255 0 128;...
0 255 128;...
64 128 255;...
128 64 255;...
255 64 128;...
255 128 64;...
128 255 64;...
64 255 128;...
255 128 128;...
128 255 128;...
128 128 255;...
255 255 128;...
255 128 255;...
128 255 255;...
255 64 64;...
64 255 64;...
64 64 255;...
255 255 64;...
255 64 255;...
64 255 255;...
255 64 0;...
64 255 0;...
64 0 255;...
0 64 255;...
0 255 64;...
255 0 64];
Dat.RoiView = [];
Dat.RoiUndo=[];
Dat.RoiSaved=1;
Dat.ShowRoiEdges = false;
Dat.CopiedROI = [];
% Set ROI transparency --------------------------
try
Dat.RoiTransp=getpref('Aedes','RoiTransp');
catch
Dat.RoiTransp=0.5;
end
set(H.ROI_TRANSP_SLIDER,'value',Dat.RoiTransp)
set(H.ROI_TRANSP_EDIT,'string',Dat.RoiTransp,...
'userdata',Dat.RoiTransp)
% Initialize Info Texts
try
ShowInfoTexts = getpref('Aedes','ShowInfoTexts');
catch
ShowInfoTexts = true;
end
if ShowInfoTexts
set(H.UITOGGLE_INFO,'state','on')
set([H.INFOTEXT,H.ROIINFOTEXT],...
'visible','on')
else
set(H.UITOGGLE_INFO,'state','off')
set([H.INFOTEXT,H.ROIINFOTEXT],...
'visible','off')
end
% Initialize Time Series view
Dat.ShowTimeSeries = false;
% Initialize Info Text Background
try
ShowInfoBackGround = getpref('Aedes','ShowInfoTextBackGround');
catch
ShowInfoBackGround = false;
end
if ShowInfoBackGround
set([H.INFOTEXT,H.ROIINFOTEXT],...
'backgroundcolor','w')
if ~Dat.HG2graphics
set([H.INFOTEXT,H.ROIINFOTEXT],...
'erasemode','normal')
end
set(H.UIVIEW_INFOTXTBACKGROUND,'checked','on')
else
set([H.INFOTEXT,H.ROIINFOTEXT],...
'backgroundcolor','none')
if ~Dat.HG2graphics
set([H.INFOTEXT,H.ROIINFOTEXT],...
'erasemode','normal')
end
set(H.UIVIEW_INFOTXTBACKGROUND,'checked','off')
end
% Initialize variables for imagemask
Dat.ImageOverlay = [];
Dat.ImageOverlayOrig = [];
Dat.isImageOverlayLoaded = false;
% Set figure resize function
set(H.FIG,'resizefcn',@l_ResizeFcn)
% Display data and initialize
l_DisplayData([],[],[1 2 3],1)
% Draw crassbars
l_ShowHideCrossbars;
% Set default zoom level
l_Zoom([],[],Dat.ZoomLevel)
% Set default colormap
l_ChangeColormap([],[],ColMap_str)
% Set default view direction
l_ChangeView([],[],Dat.AxView)
% Refresh Clim values
l_RefreshClim([],[]);
% Enable uicontrols
set(H.UICH_ENABLED,'enable','on')
% Disable "View VNMR Procpar" for non-VNMR data
%if ~isfield(DATA{1},'PROCPAR') || isempty(DATA{1}.PROCPAR)
% set(H.viewprocpar_h,'enable','off')
%end