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nii_viewer.m
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function varargout = nii_viewer(fname, varargin)
% Basic tool to visualize NIfTI images.
%
% NII_VIEWER('/data/subj2/fileName.nii.gz')
% NII_VIEWER('background.nii', 'overlay.nii')
% NII_VIEWER('background.nii', {'overlay1.nii' 'overlay2.nii'})
%
% If no input is provided, the viewer will load included MNI_2mm brain as
% background NIfTI. Although the preferred format is NIfTI, NII_VIEWER accepts
% any files that can be converted into NIfTI by dicm2nii, including NIfTI,
% dicom, PAR/REC, etc. In case of CIfTI file, it will show both the volume and
% surface view if GIfTI is available.
%
% Here are some features and usage.
%
% The basic use is to open a NIfTI file to view. When a NIfTI (background) is
% open, the display always uses the image plane close to xyz axes (voxel space)
% even for oblique acquisition. The possible confusion arises if the acquisition
% was tilted with a large angle, and then the orientation labels will be less
% accurate. The benefit is that no interpolation is needed for the background
% image, and there is no need to switch coordinate system when images with
% different systems are overlaid. The display is always in correct scale at
% three vies even with non-isotropic voxels. The displayed IJK always correspond
% to left -> right, posterior -> anterior and inferior -> superior directions,
% while the NIfTI data may not be saved in this order or along these directions.
% The I-index is increasing from left to right even when the display is flipped
% as radiological convention (right on left side).
%
% Navigation in 4D can be by mouse click, dialing IJK and volume numbers, or
% using keys (arrow keys and [ ] for 3D, and < > for volume).
%
% After the viewer is open, one can drag-and-drop a NIfTI file into the viewer
% to open as background, or drop a NIfTI with Control key down to add it as
% overlay.
%
% By default, the viewer shows full view of the background image data. The
% zoom-in always applies to three views together, and enlarges around the
% location of the crosshair. To zoom around a different location, set the
% crosshair to the interested location, and apply zoom again either by View ->
% Zoom in, or pressing Ctrl (Cmd) and +/-. View -> Set crosshair at -> center of
% view (or pressing key C) can set the crosshair to the center of display for
% all three views.
%
% Overlays are always mapped onto the coordinate of background image, so
% interpolation (nearest/linear/cubic/spline) is usually involved. The overlay
% makes sense only when it has the same coordinate system as the background
% image, while the resolution and dimension can be different. The viewer tries
% to match any of sform and qform between the images. If there is no match, a
% warning message will show up.
%
% A special overlay feature "Add aligned overlay" can be used to check the
% effect of registration, or overlay an image to a different coordinate system
% without creating a transformed file. It will ask for two files. The first is
% the overlay NIfTI file, and the second is either a transformation matrix file
% which aligns the overlay to the background image, or a warp file which
% transforms the overlay into the background reference.
%
% Here is an example to check FSL alignment. From a .feat/reg folder, Open
% "highres" as background image. "Add overlay" for "example_func". If there is
% head movement between the highres and the functional scans, the overlap will
% be off. Now "Add aligned overlay" for "example_func", and use
% example_func2highres.mat as the matrix. The two dataset should overlap well if
% the alignment matrix is accurate.
%
% Here is another example to overlay to a different coordinate system for FSL
% result. Open .feat/reg/standard.nii.gz as background. If an image like
% .feat/stats/zstat1.nii.gz is added as an overlay, a warning message will say
% inconsistent coordinate system since the zstat image is in Scanner Anat. The
% correct way is to "Add aligned overlay" for zstat1, and either use
% .feat/reg/example_func2standard.mat for linear transformation or better use
% .feat/reg/example_func2standard_warp.nii.gz if available for alignment.
%
% When the mouse pointer is moved onto a voxel, the x/y/z coordinates and voxel
% value will show on the panel. If there is an overlay, the overlay voxel value
% will also show up, unless its display is off. When the pointer moves onto the
% panel or out of an image, the information for the voxel at crosshair will be
% displayed. The display format is as following with val of the top image
% displayed first:
% (x,y,z): val_1 val_2 val_3 ...
%
% Note that although the x/y/z coordinates are shared by background and overlay
% images, IJK indices are always for background image (name shown on title bar).
%
% The mouse-over display can be turned on/off from Help -> Preferences ...
%
% If there is a .txt label file in the same folder as the NIfTI file, like for
% AAL, the labels will be shown instead of voxel value. The txt file should have
% a voxel value and ROI label pair per line, like
% 1 Precentral_L
% 2 Precentral_R
% 3 ...
%
% Image display can be smoothed in 3D (default is off). The smooth is slow when
% the image dimension is large, even when the current implementation of smooth
% does not consider voxel size.
%
% Background image and overlays are listed at the top-left of the panel. All
% parameters of the bottom row of the panel are for the highlighted image. This
% feature is indicated by the highlighted frame the parameters. Each NIfTI file
% has its own set of parameters (display min and max value, LUT, alpha, whether
% to smooth, interpolation method, and volume number) to control its display.
% Moving the mouse onto a parameter will show the meaning of the parameter.
%
% The lastly added overlay is on the top of display and top of the file list.
% This also applies in case there is surface figure for CIfTI files. The
% background and overlay order can be changed by the two small arrows next to
% the list, or from Overlay -> Move selected image ...
%
% Each NIfTI display can be turned on/off by clicking the small checkbox at the
% left side of the file (or pressing spacebar for the selected NIfTI). This
% provides a way to turn on/off an overlay to view the overlap. Most operations
% are applied to the selected NIfTI in the list, such as Show NIfTI hdr/ext
% under Window menu, Move/Close overlay under Overlay menu, and most operations
% under File menu.
%
% A NIfTI mask can be applied to the selected image. Ideally, the mask should be
% binary, and the image corresponding to the non-zero part of the mask will be
% displayed. If non-binary mask is detected, a threshold to binarize will be
% asked. If the effect is not satisfied with the threshold, one can apply the
% mask with a different threshold without re-loading image. The way to remove a
% mask is to Remove, then Add overlay again. In case one likes to modulate the
% selected image with another NIfTI image (multiply two images), File -> Apply
% modulation will do it. If the mask image is not within 0 and 1, the lower and
% upper bound will be asked to normalize the range to [0 1]. A practical use of
% modulation is to use dti_FA map as weight for dti_V1 RGB image.
%
% For multi-volume data, one can change the Volume Number (the parameter at
% rightmost of the panel) to check the head motion. Click in the number dialer
% or press < or > key, to simulate movie play. It is better to open the 4D data
% as background, since it may be slower to map it to the background image.
%
% Popular LUT options are implemented. Custom LUT can be added by Overlay ->
% Load LUT for selected overlay. The custom LUT file can be in text format (each
% line represents an RGB triplet, while the first line corresponds to the value
% 0 in the image data), or binary format (uint8 for all red, then green then
% blue). The color coding can be shown by View -> Show colorbar. There are
% several special LUTs. The "two-sided" allows to show both positive and
% negative data in one view. For example, if the display range is 3 to 10 for a
% t-map, positive T above 3 will be coded as red-yellow, and T below -3 will be
% coded as blue-green. This means the absolute display range values are used.
%
% One of the special LUT is "lines". This is for normalized vector display,
% e.g. for diffusion vector. The viewer will refuse the LUT selection if
% the data is not normalized vector. Under this LUT, all other parameters
% for the display are ignored. The color of the "lines" is the max color of
% previous LUT. For example, if one likes to show blue vector lines, choose
% LUT "blue" first, then change it to "lines".
%
% In case of complex image, most LUTs will display only the magnitude of the
% data, except the following three phase LUTs, where the magnitude is used as
% mask. Here is how the 3 phase LUTs encodes phase from 0 to 360 degree:
% phase: red-yellow monotonically,
% phase3: red-yellow-green-yellow-red circularly, and
% phase6: red-yellow-green/violet-blue-cyan, with sharp change at 180 degree.
% These LUTs are useful to visualize activation of periodic stimulus, such as
% those by expanding/shrinking ring or rotating wedge for retinotopy. To use
% this feature, one can save an complex NIfTI storing the Fourier component at
% the stimulus frequency.
%
% Note that, for RGB NIfTI, the viewer always displays the data as color
% regardless of the LUT option. The display min and max value also have no
% effect on RGB image. There is a special LUT, RGB, which is designed to display
% non-RGB NIfTI data as RGB, e.g. FSL-style 3-volome data.
%
% The viewer figure can be copied into clipboard (not available for Linux) or
% saved as variety of image format. For high quality picture, one can increase
% the output resolution by Help -> Preferences -> Resolution. Higher resolution
% will take longer time to copy or save, and result in larger file. If needed,
% one can change to white background for picture output. With white background,
% the threshold for the background image needs to be carefully selected to avoid
% strange effect with some background images. For this reason, white background
% is intended only for picture output.
%
% The selected NIfTI can also be saved as different format from File -> Save
% NIfTI as. For example, a file can be saved as a different resolution. With a
% transformation matrix, a file can also be saved into a different template. The
% latter is needed for FSLview since it won't allow overlay with different
% resolution or dimension at least till version 5.0.8.
%
% See also NII_TOOL DICM2NII NII_XFORM
%% By Xiangrui Li (xiangrui.li at gmail.com)
% History(yymmdd):
% 151021 Almost ready to publish.
% 151104 Include drag&drop by Maarten van der Seijs.
% 151105 Bug fix for Show NIfTI hdr/ext.
% 151106 Use p.interp to avoid unnecessary interp for overlay;
% Use check mark for colorbar/crosshair/background menu items.
% 151111 Take care of slope/inter of img; mask applies to DTI lines.
% 151114 Avoid see-thu for white background.
% 151119 Make smooth faster by using only 3 slices; Allow flip L/R.
% 151120 Implement key navigation and zoom in/out.
% 151121 Implement erode for white background; Add 'Show NIfTI essentials'.
% 151122 Bug fix for background img with sform=0.
% 151123 Show coordinate system in fig title; show masked/aligned in file list;
% Bug fix for alpha (0/1 only); Bug fix for background image R change.
% 151125 Avoid recursion for white background (failed under Linux).
% 151128 Change checkbox to radiobutton: looks better;
% Fix the bug in reorient dim(perm), introduced in last revision.
% 151129 Correct Center crosshair (was off by 0.5); Use evt.Key & add A/C/X/F1.
% 151201 Keep fig location & pref when 'open' & dnd: more user friendly.
% 151202 java robot trick allows to add overlay by Ctrl-dnd.
% 151207 Implement 'Add modulation'.
% 151208 Add xyz display for each view.
% 151217 Callback uses subfunc directly, and include fh as input.
% 151222 Show ROI labels (eg AAL) if .txt file with same name exists.
% 151224 Implement more matlab LUTs and custom LUT.
% 151230 Use listbox for files; Add stack buttons; file order reversed.
% 160102 Store p.R0 if need interp; No coordinate change for background.
% 160104 set_cdata: avoid indexing for single vol img: may be much faster!
% jscroll_handle from findjobj.m to set vertical scoll bar as needed.
% 160107 Rename XYZ label to IJK, implement "Set crosshair at XYZ".
% 160108 Fix the case of 2-form_code for background and addMask.
% 160109 Allow to turn off mouse-over display from Preferences;
% Implement Help -> Check update for easy update;
% Use Matlab built-in pref method for all files in the package.
% 160111 Use image ButtonDownFcn; Mouse down&move now is same as mouse move.
% 160112 Change back to line for crosshair: quiver is slow;
% Bug fix for white backgrnd & saveas backgrnd due to list order reverse.
% 160113 Implement time course for a cube.
% 160114 Figure visible avoids weird hanging problem for some matlab versions.
% 160119 Allow adding multiple overlays with cellstr as 2nd input.
% 160131 set_file: bug fix for cb(j); dnd: restore mouse location.
% 160208 Allow moving background image in stack.
% 160209 RGBA data supported; Background image can use lut "lines".
% 160218 "lines": Fix non-isovoxel display; Same-dim background not required.
% 160402 nii_xform_mat: make up R for possible Analyze file.
% 160506 phase LUT to map complex img: useful for retinotopy.
% 160509 Have 3 phase LUTs; Implement 'Open in new window'.
% 160512 KeyPressFcn bug fix: use the smallest axis dim when zoom in.
% 160517 KeyPressFcn: avoid double-dlg by Ctrl-A; phase6: bug fix for blue b3.
% 160531 use handle() for fh & others: allow dot convention for early matlab.
% 160601 Add cog and to image center, re-organize 'Set crosshair at' menu.
% 160602 bug fix for 'closeAll' files.String(ib); COG uses abs and excludes NaN.
% 160605 Add 'RGB' LUT to force RGB display: DTI_V1 or fsl style RGB file.
% 160608 javaDropFcn: 2 more method for ctlDn; bug fix for fh.xxx in Resize.
% 160620 Use JIDE CheckBoxList; Simplify KeyFcn by not focusing on active items.
% 160627 javaDropFcn: robot-click drop loc to avoid problem with vnc display.
% 160701 Implement hist for current volume; hs.value show top overlay first.
% 160703 bug fix for 'Add aligned' complex img: set p.phase after re-orient.
% 160710 Implement 'Create ROI file'; Time coure is for sphere, not cube.
% 160713 javaDropFnc for Linux: Robot key press replaces mouse click;
% Implement 'Set crosshair at' 'Smoothed maximum'.
% 160715 lut2img: bug fix for custom LUT; custom LUT uses rg [0 255]; add gap=0.
% 160721 Implement 'Set crosshair at' & 'a point with value of'.
% 160730 Allow to load single volume for large dataset.
% 161003 Add aligned overlay: accept FSL warp file as transformation.
% 161010 Implement 'Save volume as'; xyzr2roi: use valid q/sform.
% 161018 Take care of issue converting long file name to var name.
% 161103 Fix qform-only overlay, too long fig title, overlay w/o valid formCode.
% 161108 Implement "Crop below crosshair" to remove excessive neck tissue.
% 161115 Use .mat file for early spm Analyze file.
% 161216 Show more useful 4x4 R for both s/q form in nii essentials.
% 170109 bug fix: add .phase for background nifti.
% 170130 get_range: use nii as input, so always take care of slope/inter.
% 170210 Use flip for flipdim if available (in multiple files).
% 170212 Can open nifti-convertible files; Add Save NIfTI as -> a copy.
% 170421 java_dnd() changed as func, ControlDown OS independent by ACTION_LINK.
% 170515 Use area to normalize histogram.
% 171031 Implement layout. axes replace subplot to avoid overlap problem.
% 171129 bug fix save_nii_as(): undo img scale for no_save_nii.
% 171214 Try to convert back to volume in case of CIfTI (need anatomical gii).
% 171226 Store all info into sag img handle (fix it while it aint broke :)
% 171228 Surface view for gii (include HCP gii template).
% 171229 combine into one overlay for surface view.
% 180103 Allow inflated surface while mapping to correct location in volume.
% 180108 set_file back to nii_viewer_cb for cii_view_cb convenience.
% 180128 Preference stays for current window, and applies to new window only.
% 180228 'Add overlay' check nii struct in base workspace first.
% 180309 Implement 'Standard deviation' like for 'time course'.
% 180522 set_xyz: bug fix for display val >2^15.
% Later update history can be found at github.
%%
if nargin==2 && ischar(fname) && strcmp(fname, 'func_handle')
varargout{1} = str2func(varargin{1});
return;
elseif nargin>1 && ischar(fname) && strcmp(fname, 'LocalFunc')
[varargout{1:nargout}] = feval(varargin{:});
return;
end
if nargin<1 || isempty(fname) % open the included standard_2mm
fname = fullfile(fileparts(mfilename('fullpath')), 'example_data.mat');
fname = load(fname, 'nii'); fname = fname.nii;
end
nii = get_nii(fname);
[p, hs.form_code, rg, dim] = read_nii(nii); % re-oriented
p.Ri = inv(p.R);
nVol = size(p.nii.img, 4);
hs.bg.R = p.R;
hs.bg.Ri = p.Ri;
hs.bg.hdr = p.hdr0;
if ~isreal(p.nii.img)
p.phase = angle(p.nii.img); % -pi to pi
p.phase = mod(p.phase/(2*pi), 1); % 0~1
p.nii.img = abs(p.nii.img); % real now
end
hs.dim = single(dim); % single saves memory for ndgrid
hs.pixdim = p.pixdim;
hs.gap = min(hs.pixdim) ./ hs.pixdim * 3; % in unit of smallest pixdim
p.lb = rg(1); p.ub = rg(2);
p = dispPara(p);
[pName, niiName, ext] = fileparts(p.nii.hdr.file_name);
if strcmpi(ext, '.gz'), [~, niiName] = fileparts(niiName); end
if nargin>1 && any(ishandle(varargin{1})) % called by Open or dnd
fh = varargin{1};
hsN = guidata(fh);
pf = hsN.pref.UserData; % use the current pref for unless new figure
fn = get(fh, 'Number');
close(fh);
else
pf = getpref('nii_viewer_para');
if isempty(pf) || ~isfield(pf, 'layout') % check lastly-added field
pf = struct('openPath', pwd, 'addPath', pwd, 'interp', 'linear', ...
'extraV', NaN, 'dpi', '0', 'rightOnLeft', false, ...
'mouseOver', true, 'layout', 2);
setpref('nii_viewer_para', fieldnames(pf), struct2cell(pf));
end
a = handle(findall(0, 'Type', 'figure', 'Tag', 'nii_viewer'));
if isempty(a)
fn = 'ni' * 256.^(1:2)'; % start with a big number for figure
elseif numel(a) == 1
fn = get(a, 'Number') + 1; % this needs handle() to work
if isempty(fn), fn = 'ni' * 256.^(1:2)'; end
else
fn = max(cell2mat(get(a, 'Number'))) + 1;
end
end
[siz, axPos, figPos] = plot_pos(dim.*hs.pixdim, pf.layout);
fh = figure(fn);
if nargout, varargout{1} = fh; end
hs.fig = handle(fh); % have to use numeric for uipanel for older matlab
figNam = p.nii.hdr.file_name;
if numel(figNam)>40, figNam = [figNam(1:40) '...']; end
figNam = ['nii_viewer - ' figNam ' (' formcode2str(hs.form_code(1)) ')'];
set(fh, 'Toolbar', 'none', 'Menubar', 'none', ... % 'Renderer', 'opengl', ...
'NumberTitle', 'off', 'Tag', 'nii_viewer', 'DockControls', 'off', ...
'Position', [figPos siz+[2 66]], 'Name', figNam);
cb = @(cmd) {@nii_viewer_cb cmd hs.fig}; % callback shortcut
xyz = [0 0 0]; % start cursor location
c = round(p.Ri * [xyz 1]'); c = c(1:3)' + 1; %
ind = c<=1 | c>=dim;
c(ind) = round(dim(ind)/2);
% c = round(dim/2); % start cursor at the center of images
xyz = round(p.R * [c-1 1]'); % take care of rounding error
%% control panel
pos = getpixelposition(fh); pos = [1 pos(4)-64 pos(3) 64];
hs.panel = uipanel(fh, 'Units', 'pixels', 'Position', pos, 'BorderType', 'none');
hs.focus = uicontrol(hs.panel, 'Style', 'text'); % dummy uicontrol for focus
% file list by JIDE CheckBoxList: check/selection independent
mdl = handle(javax.swing.DefaultListModel, 'CallbackProperties'); % dynamic item
mdl.add(0, niiName);
mdl.IntervalAddedCallback = cb('width');
mdl.IntervalRemovedCallback = cb('width');
mdl.ContentsChangedCallback = cb('width'); % add '(mask)' etc
h = handle(com.jidesoft.swing.CheckBoxList(mdl), 'CallbackProperties');
h.setFont(java.awt.Font('Tahoma', 0, 11));
% h.ClickInCheckBoxOnly = true; % it's default
h.setSelectionMode(0); % single selection
h.setSelectedIndex(0); % 1st highlighted
h.addCheckBoxListSelectedIndex(0); % check it
h.ValueChangedCallback = cb('file'); % selection change
h.MouseReleasedCallback = @(~,~)uicontrol(hs.focus); % move focus away
% h.Focusable = false;
h.setToolTipText(['<html>Select image to show/modify its display ' ...
'parameters.<br>Click checkbox to turn on/off image']);
jScroll = com.mathworks.mwswing.MJScrollPane(h); %#ok<*JAPIMATHWORKS>
width = h.getPreferredScrollableViewportSize.getWidth;
width = max(60, min(width+20, pos(3)-408)); % 20 pixels for vertical scrollbar
warning('off', 'MATLAB:ui:javacomponent:FunctionToBeRemoved');
[~, hs.scroll] = javacomponent(jScroll, [2 4 width 60], hs.panel); %#ok<*JAVCM>
hCB = handle(h.getCheckBoxListSelectionModel, 'CallbackProperties');
hCB.ValueChangedCallback = cb('toggle'); % check/uncheck
hs.files = javaObjectEDT(h); % trick to avoid java error by Yair
% panel for controls except hs.files
pos = [width 1 pos(3)-width pos(4)];
ph = uipanel(hs.panel, 'Units', 'pixels', 'Position', pos, 'BorderType', 'none');
clr = get(ph, 'BackgroundColor');
hs.params = ph;
feature('DefaultCharacterSet', 'UTF-8'); % for old matlab to show triangles
hs.overlay(1) = uicontrol(ph, 'Style', 'pushbutton', 'FontSize', 7, ...
'Callback', cb('stack'), 'Enable', 'off', 'SelectionHighlight', 'off', ...
'String', char(9660), 'Position', [1 37 16 15], 'Tag', 'down', ...
'TooltipString', 'Move selected image one level down');
hs.overlay(2) = copyobj(hs.overlay(1), ph);
set(hs.overlay(2), 'Callback', cb('stack'), ...
'String', char(9650), 'Position', [1 50 16 15], 'Tag', 'up', ...
'TooltipString', 'Move selected image one level up');
hs.value = uicontrol(ph, 'Style', 'text', 'Position', [208 40 pos(3)-208 20], ...
'BackgroundColor', clr, 'FontSize', 8+(~ispc && ~ismac), ...
'TooltipString', '(x,y,z): top ... bottom');
% IJK java spinners
labls = 'IJK';
str = {'Left to Right' 'Posterior to Anterior' 'Inferior to Superior'};
pos = [42 44 22]; posTxt = [40 10 20];
for i = 1:3
loc = [(i-1)*64+34 pos];
txt = sprintf('%s, 1:%g', str{i}, dim(i));
hs.ijk(i) = java_spinner(loc, [c(i) 1 dim(i) 1], ph, cb('ijk'), '#', txt);
uicontrol(ph, 'Style', 'text', 'String', labls(i), 'BackgroundColor', clr, ...
'Position', [loc(1)-11 posTxt], 'TooltipString', txt, 'FontWeight', 'bold');
end
% Controls for each file
h = hs.files.SelectionBackground; fClr = [h.getRed h.getGreen h.getBlue]/255;
uicontrol(ph, 'Style', 'frame', 'Position', [1 5 412 32], 'ForegroundColor', fClr);
hs.lb = java_spinner([7 10 48 22], [p.lb -inf inf p.lb_step], ph, ...
cb('lb'), '#.##', 'min value (threshold)');
hs.ub = java_spinner([59 10 56 22], [p.ub -inf inf p.ub_step], ph, ...
cb('ub'), '#.##', 'max value (clipped)');
hs.lutStr = {'grayscale' 'red' 'green' 'blue' 'violet' 'yellow' 'cyan' ...
'red-yellow' 'blue-green' 'two-sided' '<html><font color="red">lines' ...
'parula' 'jet' 'hsv' 'hot' 'cool' 'spring' 'summer' 'autumn' 'winter' ...
'bone' 'copper' 'pink' 'prism' 'flag' 'phase' 'phase3' 'phase6' 'RGB' 'custom'};
hs.lut = uicontrol(ph, 'Style', 'popup', 'Position', [113 10 74 22], ...
'String', hs.lutStr, 'BackgroundColor', 'w', 'Callback', cb('lut'), ...
'Value', p.lut, 'TooltipString', 'Lookup table options for non-RGB data');
if p.lut==numel(hs.lutStr), set(hs.lut, 'Enable', 'off'); end
hs.alpha = java_spinner([187 10 44 22], [1 0 1 0.1], ph, cb('alpha'), '#.#', ...
'Alpha: 0 transparent, 1 opaque');
hs.smooth = uicontrol(ph, 'Style', 'checkbox', 'Value', p.smooth, ...
'Position', [231 10 60 22], 'String', 'smooth', 'BackgroundColor', clr, ...
'Callback', cb('smooth'), 'TooltipString', 'Smooth image in 3D');
hs.interp = uicontrol(ph, 'Style', 'popup', 'Position', [291 10 68 22], ...
'String', {'nearest' 'linear' 'cubic' 'spline'}, 'Value', p.interp, ...
'Callback', cb('interp'), 'Enable', 'off', 'BackgroundColor', 'w', ...
'TooltipString', 'Interpolation method for overlay');
hs.volume = java_spinner([361 10 44 22], [1 1 nVol 1], ph, cb('volume'), '#', ...
['Volume number, 1:' num2str(nVol)]);
hs.volume.setEnabled(nVol>1);
%% Three views: sag, cor, tra
% this panel makes resize easy: axes relative to panel
hs.frame = uipanel(fh, 'Units', 'pixels', 'Position', [2 2 siz], ...
'BorderType', 'none', 'BackgroundColor', 'k');
for i = 1:3
j = 1:3; j(j==i) = [];
hs.ax(i) = axes('Position', axPos(i,:), 'Parent', hs.frame);
hs.hsI(i) = handle(image(zeros(dim(j([2 1])), 'single')));
set(hs.ax(i), 'DataAspectRatio', [1./hs.pixdim(j) 1]);
hold(hs.ax(i), 'on');
x = [c(j(1))+[-1 1 0 0]*hs.gap(j(1)); 0 dim(j(1))+1 c(j(1))*[1 1]];
y = [c(j(2))+[0 0 -1 1]*hs.gap(j(2)); c(j(2))*[1 1] 0 dim(j(2))+1];
hs.cross(i,:) = line(x, y);
hs.xyz(i) = text(0.02, 0.96, num2str(xyz(i)), 'Parent', hs.ax(i), ...
'Units', 'normalized', 'FontSize', 12);
end
set(hs.hsI, 'ButtonDownFcn', cb('mousedown'));
p.hsI = hs.hsI; % background img
p.hsI(1).UserData = p; % store everything in sag img UserData
labls='ASLSLP';
pos = [0.95 0.5; 0.47 0.96; 0 0.5; 0.47 0.96; 0 0.5; 0.47 0.05];
for i = 1:numel(labls)
hs.ras(i) = text(pos(i,1), pos(i,2), labls(i), 'Units', 'normalized', ...
'Parent', hs.ax(ceil(i/2)), 'FontSize', 12, 'FontWeight', 'bold');
end
% early matlab's colormap works only for axis, so ax(4) is needed.
hs.ax(4) = axes('Position', axPos(4,:), 'Parent', hs.frame);
try
hs.colorbar = colorbar(hs.ax(4), 'YTicks', [0 0.5 1], 'Color', [1 1 1], ...
'Location', 'West', 'PickableParts', 'none', 'Visible', 'off');
catch % for early matlab
colorbar('peer', hs.ax(4), 'Location', 'West', 'Units', 'Normalized');
hs.colorbar = findobj(fh, 'Tag', 'Colorbar');
set(hs.colorbar, 'Visible', 'off', 'HitTest', 'off', 'EdgeColor', [1 1 1]);
end
% image() reverses YDir. Turn off ax and ticks
set(hs.ax, 'YDir', 'normal', 'Visible', 'off');
set([hs.ras hs.cross(:)' hs.xyz], 'Color', 'b', 'UIContextMenu', '');
try set([hs.ras hs.cross(:)' hs.xyz], 'PickableParts', 'none'); % new matlab
catch, set([hs.ras hs.cross(:)' hs.xyz], 'HitTest', 'off'); % old ones
end
%% menus
h = uimenu(fh, 'Label', '&File');
uimenu(h, 'Label', 'Open', 'Accelerator', 'O', 'UserData', pName, 'Callback', cb('open'));
uimenu(h, 'Label', 'Open in new window', 'Callback', cb('open'));
uimenu(h, 'Label', 'Apply mask', 'Callback', @addMask);
uimenu(h, 'Label', 'Apply modulation', 'Callback', @addMask);
h_savefig = uimenu(h, 'Label', 'Save figure as');
h_saveas = uimenu(h, 'Label', 'Save NIfTI as');
uimenu(h, 'Label', 'Save volume as ...', 'Callback', cb('saveVolume'));
uimenu(h, 'Label', 'Export as movie ...', 'Callback', cb('MP4'));
uimenu(h, 'Label', 'Crop below crosshair', 'Callback', cb('cropNeck'));
uimenu(h, 'Label', 'Create ROI file ...', 'Callback', cb('ROI'));
uimenu(h, 'Label', 'Close window', 'Accelerator', 'W', 'Callback', 'close gcf');
uimenu(h_saveas, 'Label', 'SPM 3D NIfTI (one file/pair per volume)', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'NIfTI standard RGB (for AFNI, later mricron)', ...
'Callback', @save_nii_as, 'Separator', 'on');
uimenu(h_saveas, 'Label', 'FSL style RGB (RGB saved in dim 4)', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'Old mricron style RGB (RGB saved in dim 3)', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'a copy', 'Callback', @save_nii_as, 'Separator', 'on');
uimenu(h_saveas, 'Label', 'file with a new resolution', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'file matching background', 'Callback', @save_nii_as);
uimenu(h_saveas, 'Label', 'file in aligned template space', 'Callback', @save_nii_as);
fmt = {'png' 'jpg' 'tif' 'bmp' 'pdf' 'eps'};
if ispc, fmt = [fmt 'emf']; end
for i = 1:numel(fmt)
uimenu(h_savefig, 'Label', fmt{i}, 'Callback', cb('save'));
end
if ispc || ismac
h = uimenu(fh, 'Label', '&Edit');
uimenu(h, 'Label', 'Copy figure', 'Callback', cb('copy'));
end
h_over = uimenu(fh, 'Label', '&Overlay');
uimenu(h_over, 'Label', 'Add overlay', 'Accelerator', 'A', 'Callback', cb('add'));
uimenu(h_over, 'Label', 'Add aligned overlay', 'Callback', cb('add'));
h = uimenu(h_over, 'Label', 'Move selected image', 'Enable', 'off');
uimenu(h, 'Label', 'to top', 'Callback', cb('stack'), 'Tag', 'top');
uimenu(h, 'Label', 'to bottom', 'Callback', cb('stack'), 'Tag', 'bottom');
uimenu(h, 'Label', 'one level up', 'Callback', cb('stack'), 'Tag', 'up');
uimenu(h, 'Label', 'one level down', 'Callback', cb('stack'), 'Tag', 'down');
hs.overlay(3) = h;
hs.overlay(5) = uimenu(h_over, 'Label', 'Remove overlay', 'Accelerator', 'R', ...
'Callback', cb('close'), 'Enable', 'off');
hs.overlay(4) = uimenu(h_over, 'Label', 'Remove overlays', ...
'Callback', cb('closeAll'), 'Enable', 'off');
uimenu(h_over, 'Label', 'Load LUT for current overlay', 'Callback', cb('custom'));
h_view = uimenu(fh, 'Label', '&View');
h = uimenu(h_view, 'Label', 'Zoom in by');
for i = [1 1.2 1.5 2 3 4 5 8 10 20]
uimenu(h, 'Label', num2str(i), 'Callback', cb('zoom'));
end
h = uimenu(h_view, 'Label', 'Layout', 'UserData', pf.layout);
uimenu(h, 'Label', 'one-row', 'Callback', cb('layout'), 'Tag', '1');
uimenu(h, 'Label', 'two-row sag on right', 'Callback', cb('layout'), 'Tag', '2');
uimenu(h, 'Label', 'two-row sag on left', 'Callback', cb('layout'), 'Tag', '3');
uimenu(h_view, 'Label', 'White background', 'Callback', cb('background'));
hLR = uimenu(h_view, 'Label', 'Right on left side', 'Callback', cb('flipLR'));
uimenu(h_view, 'Label', 'Show colorbar', 'Callback', cb('colorbar'));
uimenu(h_view, 'Label', 'Show crosshair', 'Separator', 'on', ...
'Checked', 'on', 'Callback', cb('cross'));
h = uimenu(h_view, 'Label', 'Set crosshair at');
uimenu(h, 'Label', 'center of view', 'Callback', cb('viewCenter'));
uimenu(h, 'Label', 'center of image', 'Callback', cb('center'));
uimenu(h, 'Label', 'COG of image', 'Callback', cb('cog'));
uimenu(h, 'Label', 'Smoothed maximum', 'Callback', cb('maximum'));
uimenu(h, 'Label', 'a point [x y z] ...', 'Callback', cb('toXYZ'));
uimenu(h, 'Label', 'a point with value of ...', 'Callback', cb('toValue'));
uimenu(h_view, 'Label', 'Crosshair color', 'Callback', cb('color'));
h = uimenu(h_view, 'Label', 'Crosshair gap');
for i = [0 1 2 3 4 5 6 8 10 20 40]
str = num2str(i); if i==6, str = [str ' (default)']; end %#ok
uimenu(h, 'Label', str, 'Callback', cb('gap'));
end
h = uimenu(h_view, 'Label', 'Crosshair thickness');
uimenu(h, 'Label', '0.5 (default)', 'Callback', cb('thickness'));
for i = [0.75 1 2 4 8]
uimenu(h, 'Label', num2str(i), 'Callback', cb('thickness'));
end
h = uimenu(fh, 'Label', '&Window');
uimenu(h, 'Label', 'Show NIfTI essentials', 'Callback', cb('essential'));
uimenu(h, 'Label', 'Show NIfTI hdr', 'Callback', cb('hdr'));
uimenu(h, 'Label', 'Show NIfTI ext', 'Callback', cb('ext'));
uimenu(h, 'Label', 'DICOM to NIfTI converter', 'Callback', 'dicm2nii', 'Separator', 'on');
th = uimenu(h, 'Label', 'Time course ...', 'Callback', cb('tc'), 'Separator', 'on');
setappdata(th, 'radius', 6);
th = uimenu(h, 'Label', 'Standard deviation ...', 'Callback', cb('tc'));
setappdata(th, 'radius', 6);
uimenu(h, 'Label', 'Histogram', 'Callback', cb('hist'));
h = uimenu(fh, 'Label', '&Help');
hs.pref = uimenu(h, 'Label', 'Preferences', 'UserData', pf, 'Callback', @pref_dialog);
uimenu(h, 'Label', 'Key shortcut', 'Callback', cb('keyHelp'));
uimenu(h, 'Label', 'Show help text', 'Callback', 'doc nii_viewer');
checkUpdate = dicm2nii('', 'checkUpdate', 'func_handle');
uimenu(h, 'Label', 'Check update', 'Callback', @(~,~)checkUpdate('nii_viewer'));
uimenu(h, 'Label', 'About', 'Callback', cb('about'));
%% finalize gui
if isnumeric(fh) % for older matlab
fh = handle(fh);
schema.prop(fh, 'Number', 'mxArray'); fh.Number = fn;
hs.lut = handle(hs.lut);
hs.frame = handle(hs.frame);
hs.value = handle(hs.value);
hs.panel = handle(hs.panel);
hs.params = handle(hs.params);
hs.scroll = handle(hs.scroll);
hs.pref = handle(hs.pref);
end
guidata(fh, hs); % store handles and data
%% java_dnd based on dndcontrol at matlabcentral/fileexchange/53511
try % panel has JavaFrame in later matlab
warning('off', 'MATLAB:ui:javaframe:PropertyToBeRemoved');
jFrame = handle(hs.frame.JavaFrame.getGUIDEView, 'CallbackProperties');
catch
warning('off', 'MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
jFrame = fh.JavaFrame.getAxisComponent; %#ok<*JAVFM>
end
try java_dnd(jFrame, cb('drop')); catch me, disp(me.message); end
% iconPNG = fullfile(fileparts(mfilename('fullpath')), 'nii_viewer.png');
% fh.JavaFrame.setFigureIcon(javax.swing.ImageIcon(iconPNG)); % windows only
set(fh, 'ResizeFcn', cb('resize'), ... % 'SizeChangedFcn' for later matlab
'WindowKeyPressFcn', @KeyPressFcn, 'CloseRequestFcn', cb('closeFig'), ...
'PaperPositionMode', 'auto', 'InvertHardcopy', 'off', 'HandleVisibility', 'Callback');
nii_viewer_cb(fh, [], 'resize', fh); % avoid some weird problem
if pf.mouseOver, set(fh, 'WindowButtonMotionFcn', cb('mousemove')); end
if pf.rightOnLeft, nii_viewer_cb(hLR, [], 'flipLR', fh); end
set_cdata(hs);
set_xyz(hs);
if nargin>1
if ischar(varargin{1}) || isstruct(varargin{1})
addOverlay(varargin{1}, fh);
elseif iscell(varargin{1})
for i=1:numel(varargin{1}), addOverlay(varargin{1}{i}, fh); end
end
end
if hs.form_code(1)<1
warndlg(['There is no valid form code in NIfTI. The orientation ' ...
'labeling is likely meaningless.']);
end
if isfield(p.nii, 'cii'), cii_view(hs); end
%% Get info from sag img UserData
function p = get_para(hs, iFile)
if nargin<2, iFile = hs.files.getSelectedIndex + 1; end
hsI = findobj(hs.ax(1), 'Type', 'image', '-or', 'Type', 'quiver');
p = get(hsI(iFile), 'UserData');
%% callbacks
function nii_viewer_cb(h, evt, cmd, fh)
hs = guidata(fh);
switch cmd
case 'ijk' % IJK spinner
ix = find(h == hs.ijk);
set_cdata(hs, ix);
set_cross(hs, ix);
xyz = set_xyz(hs);
for i = 1:3, set(hs.xyz(i), 'String', xyz(i)); end % need 3 if oblique
case 'mousedown' % image clicked
% if ~strcmp(get(fh, 'SelectionType'), 'normal'), return; end
ax = gca;
c = get(ax, 'CurrentPoint');
c = round(c(1, 1:2));
i = 1:3;
i(ax==hs.ax(1:3)) = [];
hs.ijk(i(1)).setValue(c(1));
hs.ijk(i(2)).setValue(c(2));
case {'lb' 'ub' 'lut' 'alpha' 'smooth' 'interp' 'volume'}
if ~strcmp(cmd, 'volume'), uicontrol(hs.focus); end % move away focus
p = get_para(hs);
val = get(h, 'Value');
if strcmp(cmd, 'smooth')
if val==1 && numel(p.nii.img(:,:,:,1))<2
set(h, 'Value', 0); return;
end
elseif strcmp(cmd, 'lut')
err = false;
if val == 11 % error check for vector lines
if p.lut~=11, hs.lut.UserData = p.lut; end % remember old lut
err = true;
if size(p.nii.img,4)~=3
errordlg('Not valid vector data: dim4 is not 3');
else
a = sum(p.nii.img.^2, 4); a = a(a(:)>1e-4);
if any(abs(a-1)>0.1)
errordlg('Not valid vector data: squared sum is not 1');
else, err = false; % passed all checks
end
end
elseif any(val == 26:28) % error check for phase img
err = ~isfield(p, 'phase');
if err, warndlg('Seleced image is not complex data.'); end
elseif val == 29 % RGB
err = size(p.nii.img,4)~=3;
if err, errordlg('RGB LUT requries 3-volume data.'); end
elseif val == numel(hs.lutStr)
err = true;
errordlg('Custom LUT is used be NIfTI itself');
end
if err, hs.lut.Value = p.lut; return; end % undo selection
end
p.hsI(1).UserData.(cmd) = val;
if any(strcmp(cmd, {'lut' 'lb' 'ub' 'volume'})), set_colorbar(hs); end
if strcmp(cmd, 'volume'), set_xyz(hs); end
set_cdata(hs);
case 'resize'
if isempty(hs), return; end
htP = hs.panel.Position(4); % get old height in pixels
posF = getpixelposition(fh); % asked size by user
hs.panel.Position(2:3) = posF([4 3]) - [htP 2]; % control panel
hs.frame.Position(3:4) = posF(3:4) - [2 htP]; % image panel
nii_viewer_cb([], [], 'width', fh);
case 'toggle' % turn on/off NIfTI
i = h.getAnchorSelectionIndex+1;
if i<1, return; end
checked = hs.files.getCheckBoxListSelectedIndices+1;
p = get_para(hs, i);
if p.show == any(checked==i), return; end % no change
p.show = ~p.show;
p.hsI(1).UserData = p;
states = {'off' 'on'};
try %#ok<*TRYNC>
set(p.hsI, 'Visible', states{p.show+1});
if p.show, set_cdata(hs); end
set_xyz(hs);
end
case 'mousemove'
% if ~strcmp(get(fh, 'SelectionType'), 'normal'), return; end
c = cell2mat(get(hs.ax(1:3), 'CurrentPoint'));
c = c([1 3 5], 1:2); % 3x2
x = cell2mat(get(hs.ax(1:3), 'XLim'));
y = cell2mat(get(hs.ax(1:3), 'YLim'));
I = cell2mat(get(hs.ijk, 'Value'))';
if c(1,1)>x(1,1) && c(1,1)<x(1,2) && c(1,2)>y(1,1) && c(1,2)<y(1,2)%sag
I = [I(1) c(1,:)];
elseif c(2,1)>x(2,1) && c(2,1)<x(2,2) && c(2,2)>y(2,1) && c(2,2)<y(2,2)%cor
I = [c(2,1) I(2) c(2,2)];
elseif c(3,1)>x(3,1) && c(3,1)<x(3,2) && c(3,2)>y(3,1) && c(3,2)<y(3,2)%tra
I = [c(3,:) I(3)];
end
set_xyz(hs, I);
case 'open' % open on current fig or new fig
pName = hs.pref.UserData.openPath;
[fname, pName] = uigetfile([pName '/*.nii; *.hdr;*.nii.gz; *.hdr.gz'], ...
'Select a NIfTI to view', 'MultiSelect', 'on');
if isnumeric(fname), return; end
fname = strcat([pName '/'], fname);
if strcmp(get(h, 'Label'), 'Open in new window'), nii_viewer(fname);
else, nii_viewer(fname, fh);
end
return;
case 'add' % add overlay
vars = evalin('base', 'who');
is_nii = @(v)evalin('base', ...
sprintf('isstruct(%s) && all(isfield(%s,{''hdr'',''img''}))', v, v));
for i = numel(vars):-1:1, if ~is_nii(vars{i}), vars(i) = []; end; end
if ~isempty(vars)
a = listdlg('SelectionMode', 'single', 'ListString', vars, ...
'ListSize', [300 100], 'CancelString', 'File dialog', ...
'Name', 'Select a NIfTI in the list or click File dialog');
if ~isempty(a), fname = evalin('base', vars{a}); end
end
pName = hs.pref.UserData.addPath;
label = get(h, 'Label');
if strcmp(label, 'Add aligned overlay')
if ~exist('fname', 'var')
[fname, pName] = uigetfile([pName '/*.nii; *.hdr;*.nii.gz;' ...
'*.hdr.gz'], 'Select overlay NIfTI');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
end
[mtx, pName] = uigetfile([pName '/*.mat;*_warp.nii;*_warp.nii.gz'], ...
'Select FSL mat file or warp file transforming the nii to background');
if ~ischar(mtx), return; end
mtx = fullfile(pName, mtx);
addOverlay(fname, fh, mtx);
else
if ~exist('fname', 'var')
[fname, pName] = uigetfile([pName '/*.nii; *.hdr;*.nii.gz;' ...
'*.hdr.gz'], 'Select overlay NIfTI', 'MultiSelect', 'on');
if ~ischar(fname) && ~iscell(fname), return; end
fname = get_nii(strcat([pName filesep], fname));
end
addOverlay(fname, fh);
end
setpref('nii_viewer_para', 'addPath', pName);
case 'closeAll' % close all overlays
for j = hs.files.getModel.size:-1:1
p = get_para(hs, j);
if p.hsI(1) == hs.hsI(1), continue; end
delete(p.hsI); % remove image
hs.files.getModel.remove(j-1);
end
hs.files.setSelectedIndex(0);
set_xyz(hs);
case 'close' % close selected overlay
jf = hs.files.getSelectedIndex+1;
p = get_para(hs, jf);
if p.hsI(1) == hs.hsI(1), return; end % no touch to background
delete(p.hsI); % 3 view
hs.files.getModel.remove(jf-1);
hs.files.setSelectedIndex(max(0, jf-2));
set_xyz(hs);
case {'hdr' 'ext' 'essential'} % show hdr ext or essential
jf = hs.files.getSelectedIndex+1;
p = get_para(hs, jf);
if strcmp(cmd, 'hdr')
hdr = p.hdr0;
elseif strcmp(cmd, 'ext')
if ~isfield(p.nii, 'ext')
errordlg('No extension for the selected NIfTI');
return;
end
hdr = {};
for i = 1:numel(p.nii.ext)
if ~isfield(p.nii.ext(i), 'edata_decoded'), continue; end
hdr{end+1} = p.nii.ext(i).edata_decoded; %#ok
end
if isempty(hdr)
errordlg('No known extension for the selected NIfTI');
return;
elseif numel(hdr) == 1, hdr = hdr{1};
end
elseif strcmp(cmd, 'essential')
hdr = nii_essential(p);
end
nam = hs.files.getModel.get(jf-1);
if ~isstrprop(nam(1), 'alpha'), nam = ['x' nam]; end % like genvarname
nam(~isstrprop(nam, 'alphanum')) = '_'; % make it valid for var name
nam = [nam '_' cmd];
nam = strrep(nam, '__', '_');
n = numel(nam); nm = namelengthmax;
if n>nm, nam(nm-4:n-4) = ''; end
assignin('base', nam, hdr);
evalin('base', ['openvar ' nam]);
case 'cross' % show/hide crosshairs and RAS labels
if strcmp(get(h, 'Checked'), 'on')
set(h, 'Checked', 'off');
set([hs.cross(:)' hs.ras hs.xyz], 'Visible', 'off');
else
set(h, 'Checked', 'on');
set([hs.cross(:)' hs.ras hs.xyz], 'Visible', 'on');
end
case 'color' % crosshair color
c = uisetcolor(get(hs.ras(1), 'Color'), 'Pick crosshair color');
if numel(c) ~= 3, return; end
set([hs.cross(:)' hs.ras hs.xyz], 'Color', c);
case 'thickness' % crosshair thickness
c = strtok(get(h, 'Label'));
set(hs.cross(:)', 'LineWidth', str2double(c));
case 'gap' % crosshair gap
c = str2double(strtok(get(h, 'Label')));
hs.gap = min(hs.pixdim) ./ hs.pixdim * c / 2;
guidata(fh, hs);
set_cross(hs, 1:3);
case 'copy' % copy figure into clipboard
fh1 = ancestor(h, 'figure');
if strncmp(get(fh1, 'Name'), 'nii_viewer', 10)
set(hs.panel, 'Visible', 'off');
clnObj = onCleanup(@() set(hs.panel, 'Visible', 'on'));
end
print(fh1, '-dbitmap', '-noui', ['-r' hs.pref.UserData.dpi]);
% print('-dmeta', '-painters');
case 'save' % save figure as picture
ext = get(h, 'Label');
fmt = ext;
if strcmp(ext, 'jpg'), fmt = 'jpeg';
elseif strcmp(ext, 'tif'), fmt = 'tiff';
elseif strcmp(ext, 'eps'), fmt = 'epsc';
elseif strcmp(ext, 'emf'), fmt = 'meta';
end
[fname, pName] = uiputfile(['*.' ext], 'Input file name to save figure');
if ~ischar(fname), return; end
fname = fullfile(pName, fname);
if any(strcmp(ext, {'eps' 'pdf' 'emf'})), render = '-painters';
else, render = '-opengl';
end
fh1 = ancestor(h, 'figure');
if strncmp(get(fh1, 'Name'), 'nii_viewer', 10)
set(hs.panel, 'Visible', 'off');
clnObj = onCleanup(@() set(hs.panel, 'Visible', 'on'));
end
print(fh1, fname, render, '-noui', ['-d' fmt], ['-r' hs.pref.UserData.dpi], '-cmyk');
case 'colorbar' % colorbar on/off
if strcmpi(get(hs.colorbar, 'Visible'), 'on')
set(hs.colorbar, 'Visible', 'off');
set(h, 'Checked', 'off');
else
set(hs.colorbar, 'Visible', 'on');
set(h, 'Checked', 'on');
set_colorbar(hs);
end
case 'about'
getVersion = dicm2nii('', 'getVersion', 'func_handle');
str = sprintf(['nii_viewer.m by Xiangrui Li\n\n' ...
'Last updated on %s\n\n', ...
'Feedback to: [email protected]\n'], getVersion());
helpdlg(str, 'About nii_viewer')
case 'stack'
uicontrol(hs.focus); % move focus out of buttons
jf = hs.files.getSelectedIndex+1;
p = get_para(hs, jf);
n = hs.files.getModel.size;
switch get(h, 'Tag') % for both uimenu and pushbutton
case 'up' % one level up
if jf==1, return; end
for j = 1:3, uistack(p.hsI(j)); end
ind = [1:jf-2 jf jf-1 jf+1:n]; jf = jf-1;
case 'down' % one level down
if jf==n, return; end
for j = 1:3, uistack(p.hsI(j), 'down'); end
ind = [1:jf-1 jf+1 jf jf+2:n]; jf = jf+1;
case 'top'
if jf==1, return; end
for j = 1:3, uistack(p.hsI(j), 'up', jf-1); end
ind = [jf 1:jf-1 jf+1:n]; jf = 1;
case 'bottom'
if jf==n, return; end
for j = 1:3, uistack(p.hsI(j), 'down', n-jf); end
ind = [1:jf-1 jf+1:n jf]; jf = n;
otherwise
error('Unknown stack level: %s', get(h, 'Tag'));
end
str = cell(hs.files.getModel.toArray);
str = str(ind);
for j = 1:n, hs.files.getModel.set(j-1, str{j}); end
chk = false(1,n);
chk(hs.files.getCheckBoxListSelectedIndices+1) = true;
chk = find(chk(ind)) - 1;
if ~isempty(chk), hs.files.setCheckBoxListSelectedIndices(chk); end
hs.files.setSelectedIndex(jf-1);
set_xyz(hs);
case 'zoom'
m = str2double(get(h, 'Label'));
a = min(hs.dim) / m;
if a<1, m = min(hs.dim); end
set_zoom(m, hs);
case 'background'
if strcmp(get(h, 'Checked'), 'on')
set(h, 'Checked', 'off');
hs.frame.BackgroundColor = [0 0 0];
set(hs.colorbar, 'EdgeColor', [1 1 1]);
else
set(h, 'Checked', 'on');
hs.frame.BackgroundColor = [1 1 1];
set(hs.colorbar, 'EdgeColor', [0 0 0]);
end
set_cdata(hs);
case 'flipLR'
hs.pref.UserData.rightOnLeft = strcmp(get(h, 'Checked'), 'on');
if hs.pref.UserData.rightOnLeft
set(h, 'Checked', 'off');
set(hs.ax([2 3]), 'XDir', 'normal');
set(hs.ras([3 5]), 'String', 'L');
else
set(h, 'Checked', 'on');
set(hs.ax([2 3]), 'XDir', 'reverse');
set(hs.ras([3 5]), 'String', 'R');
end
case 'layout'
layout = str2double(get(h, 'Tag'));
parent = get(h, 'Parent');
if get(parent, 'UserData') == layout, return; end
set(parent, 'UserData', layout);
htP = hs.panel.Position(4);
[siz, axPos, figPos] = plot_pos(hs.dim.*hs.pixdim, layout);
hs.fig.Position = [figPos siz+[2 htP+2]];
hs.frame.Position(3:4) = siz;
hs.panel.Position(2:3) = [hs.fig.Position(4)-htP siz(1)+2];
for i = 1:4, set(hs.ax(i), 'Position', axPos(i,:)); end
case 'keyHelp'
str = sprintf([ ...
'Key press available when focus is not in a number dialer:\n\n' ...
'Left or Right arrow key: Move crosshair left or right.\n\n' ...
'Up or Down arrow key: Move crosshair superior or inferior.\n\n' ...
'[ or ] key: Move crosshair posterior or anterior.\n\n' ...
'< or > key: Decrease or increase volume number.\n\n' ...
'Ctrl + or - key: Zoom in or out by 10%% around crosshair.\n\n' ...
'A: Toggle on/off crosshair.\n\n' ...
'C: Crosshair to view center.\n\n' ...
'Space: Toggle on/off selected image.\n\n' ...
'F1: Show help text.\n']);
helpdlg(str, 'Key Shortcut');
case 'center' % image center
p = get_para(hs);
dim = p.nii.hdr.dim(2:4);
c = round(hs.bg.Ri * (p.R * [dim/2-1 1]')) + 1;
for i = 1:3, hs.ijk(i).setValue(c(i)); end
case 'viewCenter'
c(1) = mean(get(hs.ax(2), 'XLim'));