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arrShow.m
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arrShow.m
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% arrShow Image viewer.
% obj = arrShow(imageArray) displays the image in imageArray in an arrayShow GUI
% and returns an instance of the arrShow class. Most properties of the GUI
% (image contrast, cursor position, ROI ...) can also be created and controlled
% by object methods, e.g. obj.createRoi(roiPos); or obj.window.setCW([center, width]);
%
% Hint: don't call the arrShow constructor directly but use the function
% "as" instead. All arrayShow instances are hereby collected in a global
% workspace array "asObjs" which can be used e.g. for batch tasks.
%
% ------------------------------------------------------------------------
% Copyright (C) 2009-2013 Biomedizinische NMR Forschungs GmbH
% http://www.biomednmr.mpg.de
% Author: Tilman Johannes Sumpf <tsumpf@gwdg.de>
%
% Distributed under the Boost Software License, Version 1.0.
% (See accompanying file LICENSE_1_0.txt or copy at
% http://www.boost.org/LICENSE_1_0.txt)
classdef arrShow < handle
properties (Access = public)
data = []; % object containing the data and data operations
selection = []; % asSelectionClass object containing the valueChanger array
complexSelect = []; % cmplxChooser object
statistics = []; % image statistics object
cursor = []; % cursor position object
infotext = []; % info text object
window = []; % image windowing object
roi = []; % region of interest object
imageText = []; % image text object
markers = []; % pixel markers
sendGroup = []; % asSendGroupClass
UserData = []; % this is not used within this class
% and may be set and
% changed for arbitrary purpose
end
properties (Access = protected)
% debug messeges
% msg = @fprintf; % use fprintf for debugging
msg = @nop; % use nop as default
% icons
icons = []; % asIcon class
% main figure
fh = 0; % main figure handle
title = ''; % main figure title
figurePosition = []; % main figure position
userCallback = []; % callback is executed at the end of updFig,
% e.g. when the selected image or
% selected complex part has changed
linkedToWorkspaceArray = false; % is (automatically) set to true if input array is a variable in workspace
% (rather than e.g. a variable in the debugger, or the result of an operation
% as in e.g. "as(a + b)"). If linked to workspace array, this array can be reloaded
% and updated by clicking the according buttons within the arrShow main window.
workspaceArrayName = ''; % name of the input array in workspace (will be set automatically)
arrShowPath = ''; % root path of the arrShowClass
cMapStdPath = ''; % standard path for colormaps
fcmh = struct; % struct of figure context menu handle
fph = 0; % figure panel handle
bph = 0; % bottom panal handle
cph = 0 ; % control panel handle
cpcmh = struct; % control panel context menu handle
mbh = struct; % menu bar handle
tbh = struct; % tool bar handle
trph = 0; % top right panel handle
ih = []; % image handle
% (this is an array of N handles, if we display
% N images)
fp_height = 0; % the figure panel height is usually set to the constant
% variable FP_MAX_HEIGHT.
% However, for small screens it
% might have to be set to a
% smaller value
postProcFun = []; % postprocessing function handle
mouseMovementMode = 0; % behaviour on mouse movements:
% 0 : just update the cursorPositionClass
% 1 : mouse windowing mode
% 2 : dragging mode
mouseReferencePoint = []; % reference point for mouse windowing or dragging
buttonUpCbTime = uint64(0); % Workaround: if a mouse click changes the focus
% of different uiObjects, apparently the mouseUp callback is sometimes called prior the
% mouseDown callback. I guess the reason is, that the up-callback is called more or less
% directly, whereas the down-callback is called after the
% window manager has finished all its focus operations... However:
% The manual check of the callback time is a workaround for simetimes 'jammed'
% dragging operations.
mouse_wheel_zoom_factor = 1.5; % default zoom factor per mouse wheel step
processingCallback = false;
forceComplexRepresentation = true; % use phase overlay in complex mode even if imaginary part
% of the frame is zero at every point
relatives = []; % list of other arrShow objects in current environment
noRelatives = 0; % number of relatives
useGlobalArray= false; % if the "useGlobalArray" toggle
% is set to true, no individual relatives list is populated within this object and
% a global workspace array "asObjs" is used instead.
sendWdwSize = false; % send main figure window size to relatives
titleAsImageText = false; % draw the title as a text within the images
saveInfosAtImageExport = true; % if true, a description text file is created when exporting images (containing dinensions, norm, i.e.)
playAlongDim = false; % this is set to true if the play button has been pressed
framerate = 50; % Standard framerate for the play function.
% Note: the framerate setting
% currently does not consider
% the execution time of updFig and is thus not precise.
% The actual framerate can be assumed to
% be lower.
stdColormap = 'Gray(256)'; % standard colormap
phaseColormap = 'martin_phase(256)'; % standard colormap for phase display
stdCmapMightBeModified = false; % The matlab colormapeditor allows for altering the colormap
phaCmapMightBeModified = false; % even after the actual command 'colormapeditor' has already returned.
% The 'cmapMightBeModified' workaround causes
% arrayShow to retrieve the potentially modified colormap from the
% figure handle during updFig.
end
properties (Constant, GetAccess = private)
% image export presets
RESIZE_AXES_FOR_SCREENSHOTS = false;
% panel positions
TR_PANEL_POS = [5/6, 0, 1/6, 1]; % relative position and size of the complexSelector in the top Panel
STATISTICS_POS = [4/6, 0, 1/6, 1]; % relative position and size of the statistics in the top Panel
INFOTEXT_POS = [2/6, 0, 1/6, 1]; % ...
WINDOWING_POS = [3/6, 0, 1/6, 1];
% sizes
CP_HEIGHT = 2.2; % fixed height for the controlPanel (in centimeters)
BP_HEIGHT = .5; % fixed height for the bottom panel (in centimeters)
FP_MAX_HEIGHT = 18; % desired height for the figurePanel (in centimeters)
% (for small screens, the actual fp_height
% might be smaller)
% marker colors
MARKER_COL_PHA = 'white'; % default marker color for phase representations
MARKER_COL_REAL= 'yellow'; % default marker color for real valued images
end
properties (Access = private);
updFigCount = 0; % counter for updateFig calls for
% debugging and speed improvements
processingError = false; % if an error in the data is detected during
% updFig, the function can be restarted
% with new values and this flag set to
% true. The flag is a quick and dirty workaround
% to avoid endless loops if an error
% persists in a second updFig call
end
properties (Constant, GetAccess = public)
% arrShow version
VERSION = 0.35;
end
%#ok<*FPARK>
% Deactivate the warning telling me that I should use textscan instead
% of strread... I like strread. I'll change it if I feel like having
% too much time...
methods (Access = public)
function obj = arrShow(arr, varargin)
% evaluate varagin
CW = [];
userFigurePosition = [];
selectionOffset = [];
selectedImageStr = '';
pixMarkers = [];
imageTextVal = [];
initComplexSelect = [];
infoText = '';
renderUi = true;
viewMode = 'default'; % could be quiver (vector plot) as well
if nargin > 1
if length(varargin) ==1
obj.title = varargin{1};
if strcmp(obj.title,inputname(1))
obj.workspaceArrayName = inputname(1);
obj.linkedToWorkspaceArray = true;
end
end
for i = 1 : floor(length(varargin)/2)
option = varargin{i*2-1};
option_value = varargin{i*2};
switch lower(option)
case {'title','tit'}
obj.title = option_value;
case 'info'
infoText = option_value;
case {'imagetext', 'imgtxt'}
imageTextVal = option_value;
case {'windowing','window','wdw'}
CW = option_value;
case {'select','sel'}
selectedImageStr = option_value;
case {'complexselect','cplxselect','cplx','complex','cplxsel'}
initComplexSelect = option_value;
case {'colormap', 'stdcolormap'}
obj.stdColormap = option_value;
case 'phasecolormap'
obj.phaseColormap = option_value;
case {'position','pos'}
userFigurePosition = option_value;
case 'inputname'
if isempty(obj.title)
obj.title = option_value;
end
if ~isempty(option_value)
obj.workspaceArrayName = option_value;
obj.linkedToWorkspaceArray = true;
end
case {'callback','cb'}
obj.userCallback = option_value;
case 'useglobalarray'
obj.useGlobalArray = option_value;
case {'renderui','render'} % this option has been introduced
% to initialize an arrShow object without
% drawing the actual ui elements. This is
% currently used to create temporary object
% copies which are saveable in matlab >= 2014b
renderUi = option_value;
case {'offset','offs'} % offset to the asSelection class
selectionOffset = option_value;
case {'markers','marker','mark'} % pixel markers
pixMarkers = option_value;
case {'viewmode','view','mode'} % view mode can be 'default' or 'quiver' (or equivalent: 'vector')
viewMode = option_value;
otherwise
error('arrShow:varargin','unknown option [%s]!\n',option);
end;
end;
clear('option','option_value');
clear('varargin');
% If we don't explicitly delete it here,
% the varargin is stored within the
% object, wasting memory
end
% assure that all support function paths are registered
arrShow.checkPath();
% initialize the asData object (which also performs some
% initial data validity tests)
obj.data = asDataClass(arr, @obj.updFig);
si = size(obj.data.dat);
% store standard paths
obj.arrShowPath = fileparts(mfilename('fullpath'));
obj.cMapStdPath = [obj.arrShowPath, filesep, 'customColormaps'];
iconPath = [obj.arrShowPath, filesep, 'icons'];
% load icons
obj.icons = asIconClass.getInstance(iconPath);
% create main figure
fpos = obj.deriveFigurePos();
obj.fh = figure('Units','centimeters',...
'Resize','on',... % it's tempting to set this to off during initialization. However, this can cause problems with certain linux window managers
'Position',fpos,...
'KeyPressFcn',@(src,evnt)obj.keyPressCb(evnt),...
'CloseRequestFcn',@(src,evnt)obj.closeReq(src),...
'WindowButtonMotionFcn',@(src, evnt)obj.mouseMovementCb,...
'WindowButtonDownFcn',@obj.buttonDownCb,...
'WindowButtonUpFcn',@(src,evnt)obj.buttonUpCb(src),...
'WindowScrollWheelFcn',@obj.scollWheelCb,...
'MenuBar','none',...
'toolbar','none',...
'Visible','off',...
'Tag','arrShowFig',...
'IntegerHandle','on');
set(obj.fh,'UserData',obj) % link this object to main figure
% set title
if ~isempty(obj.title)
set(obj.fh,'Name',obj.title);
end
% change figure icon :-)
warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
jframe=get(obj.fh,'javaframe');
jIcon=javax.swing.ImageIcon(fullfile(iconPath,'figure.png'));
jframe.setFigureIcon(jIcon);
clear jframe jIcon
% init menu- and toolbar
obj.initMenuBar();
obj.initToolBar();
% shortcuts to some dimensions
fphe = obj.fp_height; % figure panel height
cphe = obj.CP_HEIGHT; % control panel (top panel) height
bphe = obj.BP_HEIGHT; % bottom panel height
% control panel
obj.cph = uipanel(obj.fh,'Units','centimeters',...
'Position',[0, fphe + bphe, fpos(3), cphe],...
'Interruptible','off',...
'BorderType','none',...
'BusyAction','cancel',...
'Tag','asControlPanel');
set(obj.cph,'Units','normalized');
% bottom panel
obj.bph = uipanel(obj.fh,'Units','centimeters',...
'Position',[0, 0, fpos(3), bphe],...
'Interruptible','off',...
'BusyAction','cancel' ,...
'BorderType','none',...
'Tag','asBottomPanel');
set(obj.bph,'Units','normalized');
% figure panel
obj.fph = uipanel(obj.fh,'Units','centimeters',...
'Position',[0, bphe, fpos(3), fphe],...
'Interruptible','off',...
'BorderType','beveledin',...
'BusyAction','cancel',...
'Tag','asFigurePanel');
set(obj.fph,'Units','normalized');
% image statistics object (min, max, l2 ...)
obj.statistics = asStatisticsClass(obj.cph, obj.STATISTICS_POS);
% image windowing object (the center and width slider i.e. contrast
% and brightness)
obj.window = asWindowingClass(...
obj.cph,...
obj.WINDOWING_POS,...
@obj.updFig,...
@obj.applyToRelatives,...
@()obj.getColormap('phase',true),...
obj.icons);
% info textbox object
obj.infotext = asInfoTextClass(obj.cph, obj.INFOTEXT_POS);
% top right panel
obj.trph = uipanel('visible','on','Units','normalized',...
'Position',obj.TR_PANEL_POS,'Parent',obj.cph,...
'Tag','trPanel');
% complex part selector (the dropdown menu on the top right of
% the arrayShow window)
obj.complexSelect = asCmplxChooserClass(...
obj.trph,...
@obj.updFig,...
@obj.applyToRelatives,...
obj.icons.send);
dataIsreal = isreal(obj.data.dat);
if dataIsreal
% disable the imag and phase button in the complexSelect
% object
obj.complexSelect.lockImagAndPhase;
% select real part per default
if isempty(initComplexSelect)
initComplexSelect = 'Re';
end
end
if ~isempty(initComplexSelect)
obj.complexSelect.setSelection(initComplexSelect, true);
end
% send group class
obj.sendGroup = asSendGroupClass(obj.trph);
% init the figure context menu (first entries are created
% within the asCursorPosClass)
obj.fcmh.base = uicontextmenu;
% cursor position object
obj.cursor = asCursorPosClass(...
obj.fh,...
obj.bph,...
obj.fcmh,...
obj.mbh,...
obj.icons,...
~dataIsreal,...
@obj.applyToRelatives,...
@obj.getCurrentAxesHandle,...
obj);
% valueChanger array (the +/- buttons on the top left of the
% arrayShow window)
initStrings = cell(length(si),1);
initStrings{1} = ':';
initStrings{2} = ':';
for i = 3 : length(si)
initStrings{i} = '1';
end
obj.selection = asSelectionClass(obj.cph, si,...
'figureUpdateCallback',@obj.updFig,...
'apply2allCb',@obj.applyToRelatives,...
'InitStrings',initStrings,...
'dataObject',obj.data,...
'offsets', selectionOffset,...
'sendIcon',obj.icons.send);
obj.data.linkToSelectionClassObject(obj.selection);
% init the control panel context menu and create additional
% entries in the previously created figure context menu...
obj.initContextMenus(infoText);
clear('infoText');
set(obj.fh,'HandleVisibility','off');
% ...we don't want other matlab routines to print stuff on our
% main figure
if ~isempty(selectedImageStr)
obj.selection.setValue(selectedImageStr,true,true,true);
end
% pixel markers
obj.markers = asMarkerClass(obj.selection, pixMarkers, obj.mbh.markers, @obj.applyToRelatives);
% if specific figure position is given, resize the gui
if ~isempty(userFigurePosition)
obj.setFigurePosition(userFigurePosition);
obj.fpResize(true); % manually call resize function
end
% find relatives
if ~obj.useGlobalArray
obj.refreshRelativesList();
% since this object is not yet in the cloud, add it manually to
% the list
obj.relatives = [obj.relatives,obj];
obj.noRelatives = obj.noRelatives + 1;
% (this assures that the send2all function does
% include this object, if the "includeSelf"-toggle is switched
% on)
end
% check, if we want to use a vector plot
if any(strcmp(viewMode,{'quiver','vector'}))
set(obj.mbh.quiver,'Checked','on');
end
% all gui components should be ready by now, so start
% updateFigure to find the selected array part and convert it
% to an image object in the axes region
if obj.updFigCount == 0 && renderUi
% for new figures, updFig sometimes seems to be triggered
% when setting the figure resize function...
% I haven't figured why and when exactly that happens.
% However, to speedup the start time, we don't call updFig again in
% this case.
obj.updFig;
end
% apply the initial window (center and width setting), if we
% got one as a constructor input argument
if ~isempty(CW)
obj.window.setCW(CW);
end
% select proper valueChanger object (VCO)
if length(si) > 2
obj.selection.selectVco(3);
end
% write the imagetext
if ~isempty(imageTextVal)
% deal with special case of a one-dimensional image
% text cell array and a 3 dimensional image array
if iscell(imageTextVal) && isvector(imageTextVal)
if length(size(obj.data.dat)) == 3
imageTextVal = reshape(imageTextVal,[1,1,length(imageTextVal)]);
end
end
obj.createImageText(imageTextVal);
if renderUi
obj.updFig
end
end
if ~renderUi
return;
end
% save figure position in the object property (pixel units) and activate
% figure resize function
set(obj.fh,'Visible', 'on');
drawnow; % apparently it's a good idea to draw the figure before
% activating the resize callback. Otherwise, the
% callback is sometimes triggered for no obvious
% reasons.
set(obj.fh,'Units', 'pixel',...
'ResizeFcn',@(src, evnt)obj.fpResize);
obj.figurePosition = get(obj.fh,'Position');
% put focus on complexSelector
% (this was written to put the focus away from the selection
% class at initialization of arrShow objects. As a result, key
% press calbacks can be evaluated without initial mouseclick on
% the figure window. Unfortunately, this command also seems to
% notably increases the startup time :-/ )
obj.complexSelect.focus;
end
function reloadWorkspaceArray(obj)
if obj.linkedToWorkspaceArray
% try to get the workspace array
try
WA = evalin('base',obj.workspaceArrayName);
catch err
if strcmp(err.identifier,'MATLAB:UndefinedFunction')
WA = [];
else
rethrow(err);
end
end
if isempty(WA)
fprintf('workspace variable ''%s'' seems not to be valid anymore\n',obj.workspaceArrayName);
else
obj.data.overwriteImageArray(WA);
end
else
disp('asObject is not linked to a workspace array');
end
end
function updateWorkspaceArray(obj)
if obj.linkedToWorkspaceArray
assignin('base',obj.workspaceArrayName,obj.data.dat);
end
end
function overwriteImageArray(obj, arr)
obj.data.overwriteImageArray(arr);
end
function refreshRelativesList(obj)
if obj.useGlobalArray
global asObjs %#ok<TLEV>
asObjs = arrShow.findAllObjects();
evalin('base','global asObjs');
else
obj.relatives = arrShow.findAllObjects();
obj.noRelatives = length(obj.relatives);
end
% if according options are set, send object properties to
% relatives
if obj.sendWdwSize
obj.sendFigureSize();
end
% obj.sendColormap(false);
if obj.complexSelect.sendToggleState
if obj.selection.sendToggleState
obj.applyToRelatives('complexSelect.setSelection',false,obj.complexSelect.getSelection(),true);
else
obj.applyToRelatives('complexSelect.setSelection',false,obj.complexSelect.getSelection(),false);
end
end
if obj.selection.sendToggleState
obj.selection.send;
end
if obj.window.sendAbsWindow
obj.window.sendAbsWindowToRelatives()
else
if obj.window.sendRelWindow
obj.window.sendRelWindowToRelatives();
end
end
if obj.roiExists()
if obj.roi.getSendPositionToggle();
obj.roi.callSendPositionCallback;
end
end
end
function wipeRelativesList(obj)
% obj.relatives = [];
% obj.noRelatives = 0;
% fprintf('deleted all relatives from list\n');
obj.msg('wipe call');
end
function sendColormap(obj, mapType)
% mapType can be either
% current, standard or phase
if nargin < 2
mapType = 'current';
end
obj.applyToRelatives('setColormap',false,obj.getColormap(mapType),mapType);
end
function sendAll(obj, bool)
% toggle send all (sendable) settings to the relatives
if nargin < 2
bool = true;
end
obj.selection.toggleSend(bool);
obj.window.toggleSendRelWindow(bool);
obj.window.toggleSendAbsWindow(bool);
obj.complexSelect.toggleSend2all(bool);
obj.cursor.toggleSend(bool);
% also send non toggleable options
if bool
obj.sendColormap();
obj.sendZoom();
end
end
function printCurrentImage(obj)
% this is a workaround to print an image without the uipanels
% create a help figure without menues
helpFigure = figure('MenuBar','none',...
'ToolBar','none');
colormap(obj.getColormap);
% copy current axes to the help figure
ah = obj.getCurrentAxesHandle;
helpAxes = copyobj(ah,helpFigure);
set(helpAxes,'Units','normalized','position',[0,0,1,1])
% delete cursor rectangle in helpFigure
rect = findobj(helpFigure,'type','rectangle');
delete(rect);
% print helpFigure
ph = printpreview(helpFigure);
% wait until print dialog is closed
while(ishandle(ph))
pause(0.1);
end
% ...and close the help figure
if ishandle(helpFigure)
close(helpFigure);
end
end
function batchExportDimension(obj, dim, filename, createMovie, framerate,...
screenshot, includePanels, includeCursor, scrshotPauseTime, movieType)
% export all 2D frames of dimension dim to either bitmap files
% or an avi file
% create bitmap series by default (rather than a movie file)
if nargin < 4 ||isempty(createMovie)
createMovie = false;
end
if nargin < 6 || isempty(screenshot)
screenshot = false;
end
if nargin < 7 || isempty(includePanels)
includePanels = false;
end
if nargin < 8 || isempty(includeCursor)
includeCursor = false;
end
if nargin < 9 || isempty(scrshotPauseTime)
scrshotPauseTime = 0;
end
if nargin < 10 || isempty(movieType)
movieType = 'Uncompressed AVI';
end
% use the image title as filename by default
if nargin < 3 || isempty(filename)
filename = obj.title;
if isempty(filename)
disp('Need a figure title to create a filename');
return;
end
end
% remove special characters from the filename
filename = arrShow.removeSpecialCharsFromString(filename);
% get data dimensions
dims = obj.selection.getDimensions;
noDims = length(dims);
% if no export dimension is give, open an input dialog
if nargin < 2 || isempty(dim)
dim = mydlg('Enter dimension','Enter dimension for batch export',num2str(noDims));
dim = str2double(dim);
if isnan(dim)
return
end
end
% check validity of the given export dimension
if noDims < dim
disp('invalid dimension number given');
return;
end
% if we want to create a movie file, initialize the VideoWriter
% object
if createMovie
vwObj = VideoWriter(filename, movieType);
if nargin < 5 || isempty(framerate)
framerate = mydlg('Enter framerate','Enter framerate for the movie','30');
framerate = str2double(framerate);
if isnan(framerate)
return
end
end
vwObj.FrameRate = framerate;
vwObj.open();
% check if we need to crop the frames: .avi-files require that
% the dimensions be divisible by four. Therefore, in
% exportCurrentImage, we make sure that they are. Since that
% function is called quite often and would therefore lead to
% warning spam, we issue the warning here
% instead of where we actually do the cropping.
exportSize = size(get(findobj( ...
obj.getCurrentAxesHandle(),'type','image'),'Cdata'));
rem = [mod(exportSize(1), 4) mod(exportSize(2), 4)];
if any(rem)
warning('arrShow:writeMovie',['image dimension not divisible by four, ',...
'which is required for .avi-export. Cropping image to be divisible by four...']);
end
end
% select the export dimension
obj.selection.selectVco(dim)
% store the current selection
origValue = obj.selection.getCurrentVcValue;
% loop through all frames in the export dimension
obj.selection.setCurrentVcValue(1);
for i = 1 : dims(dim);
if createMovie
obj.exportCurrentImage(vwObj,...
screenshot, includePanels, includeCursor, scrshotPauseTime);
else
obj.exportCurrentImage([filename,'_',num2str(i, '%05.5d'),'.png'],...
screenshot, includePanels, includeCursor, scrshotPauseTime);
end
obj.selection.increaseCurrentVc;
end
% reset selection
obj.selection.setCurrentVcValue(origValue);
% close videoWriter
if createMovie
vwObj.close();
end
disp('Done batchexport.');
end
function createMovie(obj, dim, framerate, movieType)
% shortcut to batchExportDimension with enabled movie export
if nargin < 4
movieType = 'Uncompressed AVI';
end
if nargin < 3
framerate = [];
end
if nargin < 2
dim = [];
end
obj.batchExportDimension(dim, [], true, framerate, ...
[],[],[],[],movieType);
end
function img = getScreenshot(obj, includePanels, includeCursor, scrshotPauseTime)
% use the matlab getframe routines to capture the current image
% with all its child-objects.
warning('arrShow:exportCurrentImage','output image might not have the exact original image''s resolution');
if nargin < 4
scrshotPauseTime = 0;
if nargin < 3
includeCursor = false;
if nargin < 2
includePanels = false;
end
end
end
ah = obj.getCurrentAxesHandle();
imh = findobj(ah,'type','image');
img = get(imh,'Cdata');
origUnits = get(ah,'units');
set(ah,'units','pixel');
origPos = get(ah,'position');
% show cursor rectangle?
if ~includeCursor
ud = get(ah,'UserData');
if ~isempty(ud) && isfield(ud,'rect') && ~isempty(ud.rect)
delete(ud.rect);
ud.rect = [];
set(ah,'UserData',ud);
end
end
if obj.RESIZE_AXES_FOR_SCREENSHOTS
si = size(img) -1;
set(ah,'position',[origPos(1:2),si(1:2)]);
end
% assure that current window is on top of all others
if scrshotPauseTime
figure(obj.fh);
drawnow;
pause(scrshotPauseTime);
end
if includePanels
img = getframe(obj.fh);
else
img = getframe(ah);
end
set(ah,'position',origPos);
set(ah,'units',origUnits);
end
function exportCurrentImage(obj, filenameOrVideoWriterObj, screenshot, includePanels, includeCursor, scrshotPauseTime)
% export data (original image or a screenshot containing
% arrayShow controls etc.) to either a bitmap file of a
% videoWriter object.
%
% filename can be either a string or a VideoWriter object.
if nargin < 6
scrshotPauseTime = 0;
if nargin < 5
includeCursor = false;
if nargin < 4
includePanels = false;
if nargin < 3
screenshot = false;
if nargin < 2
filenameOrVideoWriterObj = '';
end
end
end
end
end
if isempty(filenameOrVideoWriterObj)
% generate filename from title
filenameOrVideoWriterObj = arrShow.removeSpecialCharsFromString(obj.title);
[file,path] = uiputfile({'*.png';'*.bmp'},'Save image as', filenameOrVideoWriterObj);
if isnumeric(file)
return;
end
filenameOrVideoWriterObj = strcat(path, file);
if isempty(filenameOrVideoWriterObj)
warning('arrShow:exportCurrentImage','image export aborted, no filename given');
return;
end
if exist(filenameOrVideoWriterObj,'file');
fprintf('Fig. %d: overwriting existing file: %s\n',obj.getFigureNumber, filenameOrVideoWriterObj);
end
end
% define the method to write single frames
writeVideo = isa(filenameOrVideoWriterObj,'VideoWriter');
if writeVideo
vwObj = filenameOrVideoWriterObj;
writeFrame = @(dat, tmp1, tmp2)vwObj.writeVideo(dat);
else
writeFrame = @imwrite;
end
%img = obj.getSelectedImages();
ah = obj.getCurrentAxesHandle();
imh = findobj(ah,'type','image');
img = get(imh,'Cdata');
% .avi files need to have dimensions divisible by four
% so if we write to a movie, we should make sure that this is
% fulfilled. Therefore, we crop the image here to make sure
% that its size is divisible by four.
if writeVideo
rem = [mod(size(img, 1), 4) mod(size(img, 2), 4)];
if any(rem)
tmpstr = repmat({':'}, 1, ndims(img));
for currDim = 1:2
r = rem(currDim);
switch r
case 1
% Just leave out the last value
tmpstr{currDim} = 1:size(img,currDim)-1;
case 2
% Leave out first and last
tmpstr{currDim} = 2:size(img,currDim)-1;
case 3
% First and last two
tmpstr{currDim} = 2:size(img,currDim)-2;
end
end
% Crop image using the subscript vector
img = img(tmpstr{:});
end
end
if screenshot || includePanels
% use the matlab getframe routines to capture the current image
% with all its child-objects.
img = obj.getScreenshot(includePanels, includeCursor, scrshotPauseTime);
% write image to file
writeFrame(img.cdata,filenameOrVideoWriterObj);
else
if size(img,3) == 3
% cdata is already in RGB format, so just write it
% to file
[~, ~, extension] = fileparts(filenameOrVideoWriterObj);
if strcmp(extension, '.png')
%NaN values are rendered transparent
% get NaN positions
NaNpos = isnan(img);
% if one component is NaN, set it to transparent
NaNpos = double(~prod(NaNpos,3));
writeFrame(img,filenameOrVideoWriterObj,...
'alpha', NaNpos);
else
writeFrame(img,filenameOrVideoWriterObj);
end
else
% cdata represents intensity values while the
% visible representation is windowed and color coded
% using the colormap and CLim property of the axes object.
% In order to properly save the image we need to
% mimic the windowing of the axes object.
% get range limitations and center/width values
Clim = obj.window.getCLim();
CW = obj.window.getCW();