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avw_view.m
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avw_view.m
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function [ varargout ] = avw_view(avw,parent,command),
% avw_view - create and navigate ortho views of Analyze 7.5 volume
%
% [ avw ] = avw_view([avw], [parent], [command])
%
% avw - a struct, created by avw_read; if omitted, a gui file locator will
% prompt for a .hdr file.
%
% parent - an optional handle to the gui that calls this gui, useful for
% updating the UserData field of the parent. The avw structure may be
% returned to the parent, if possible.
%
% command - an optional string, such as 'init' or various callback
% commands, 'init' is the default.
%
% The navigation is by sliders, mouse clicks and arrow keys. Right mouse
% clicks on any ortho-view will show a command menu, for simple block
% region of interest (ROI) calculations, image zoom, and save image. The
% ROI calculations are returned into avw.stats.
%
% Fiducial points can be selected, which are returned into 'avw.fiducials'
% in the base workspace. These points are given in several coordinate
% frameworks (voxels, mm, and meters), with values given relative to an
% origin located at the "center" of the MRI volume (see avw_center, which
% returns abs and corner values, abs used here).
%
% The AC location can be selected and the values are returned into 'avw.ac'
% in the base workspace. These points are given in voxels, mm & meters; for
% the latter, the values are given as offsets from the "center" of the MRI
% volume (see avw_center).
%
% +X is left (L), +Y is anterior (A), +Z is superior (S), the default LAS
% orientation of the Analyze 7.5 format. The coordinate system is left
% handed. This is the radiological convention, as opposed to the
% neurological convention (RAS). The latter can be emulated by using the
% 'Flip L/R' button.
%
% Example of loading and viewing the SPM T1 template:
% avw = avw_read('T1')
% avw = avw_view(avw);
%
% Similarly, just 'avw_view' can be typed at the command prompt and you can
% use the gui file locator to select any .hdr file.
%
% See also, avw_read, avw_img_read, avw_hdr_read
%
% $Revision: 1.5 $ $Date: 2007/05/09 00:06:58 $
% Licence: GNU GPL, no express or implied warranties
% History: 06/2002, Darren.Weber_at_flinders.edu.au
% 10/2002, Darren.Weber_at_flinders.edu.au
% added fiducial point determination
% changed plots from surf to imagesc commands
% added handling of datatype for avw.img
% altered daspect to use avw.hdr.dime.pixdim
% altered color scheme
% 01/2003, Darren.Weber_at_flinders.edu.au
% added parent GUI handling
% 10/2003, Darren.Weber_at_radiology.ucsf.edu
% added right click options, including simple block ROI
% functions, zoom and save image
% 11/2003, Darren.Weber_at_radiology.ucsf.edu
% added arrow key navigation
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
if gcbf,
AVWVIEW = get(gcbf,'Userdata');
end
if ~exist('command','var'), command = 'init'; end
command = lower(command);
% Check for specific keys and assign command
if strcmp(command, 'keypress'),
cc = get(AVWVIEW.gui,'CurrentCharacter');
cc = double(cc);
if cc,
switch cc,
case 27, command = 'quit'; % ESC
case 28, command = 'left'; % left
case 29, command = 'right'; % right
case 30, command = 'up'; % up
case 31, command = 'down'; % down
otherwise, return; % all other keys
end
end
end
switch command,
case 'init',
if ~exist('avw','var'),
avw = avw_read;
end
if nargin == 0,
AVWVIEW = init(avw);
elseif isempty(inputname(1)),
AVWVIEW = init(avw);
else
AVWVIEW = init(avw,inputname(1));
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'coordinates',
AVWVIEW = set_coordinates(AVWVIEW);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'crosshairs',
AVWVIEW = set_coordinates(AVWVIEW);
%AVWVIEW = set_crosshairs(AVWVIEW);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'axial_image','coronal_image','sagittal_image'},
switch command,
case 'axial_image',
AVWVIEW.view = 'axi'; axi_update = 0; cor_update = 1; sag_update = 1;
case 'coronal_image',
AVWVIEW.view = 'cor'; axi_update = 1; cor_update = 0; sag_update = 1;
case 'sagittal_image',
AVWVIEW.view = 'sag'; axi_update = 1; cor_update = 1; sag_update = 0;
end
AVWVIEW = get_current_position(AVWVIEW);
if axi_update,
axial_update(AVWVIEW);
end
if cor_update,
coronal_update(AVWVIEW);
end;
if sag_update,
sagittal_update(AVWVIEW);
end;
AVWVIEW = set_coordinates(AVWVIEW);
%AVWVIEW = set_display_values(AVWVIEW);
%AVWVIEW = set_crosshairs(AVWVIEW);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'axial_slider','coronal_slider','sagittal_slider'},
switch command,
case 'axial_slider',
AVWVIEW.view = 'axi';
AVWVIEW = get_slider_position(AVWVIEW);
axial_update(AVWVIEW);
case 'coronal_slider',
AVWVIEW.view = 'cor';
AVWVIEW = get_slider_position(AVWVIEW);
coronal_update(AVWVIEW);
case 'sagittal_slider',
AVWVIEW.view = 'sag';
AVWVIEW = get_slider_position(AVWVIEW);
sagittal_update(AVWVIEW);
end
AVWVIEW = set_coordinates(AVWVIEW);
%AVWVIEW = set_display_values(AVWVIEW);
%AVWVIEW = set_crosshairs(AVWVIEW);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'left','right','up','down'},
AVWVIEW = get_slider_position(AVWVIEW);
% what axes are we in?
if isequal(gca, AVWVIEW.handles.axial_axes),
switch command,
case 'left',
% decrease sagittal slice
if AVWVIEW.slices.sag > 1,
AVWVIEW.slices.sag = AVWVIEW.slices.sag - 1;
end
case 'right',
% increase sagittal slice
if AVWVIEW.slices.sag < AVWVIEW.xdim,
AVWVIEW.slices.sag = AVWVIEW.slices.sag + 1;
end
case 'up',
% increase coronal slice
if AVWVIEW.slices.cor < AVWVIEW.ydim,
AVWVIEW.slices.cor = AVWVIEW.slices.cor + 1;
end
case 'down',
% decrease coronal slice
if AVWVIEW.slices.cor > 1,
AVWVIEW.slices.cor = AVWVIEW.slices.cor - 1;
end
end
switch command,
case {'left','right'}
set(AVWVIEW.handles.sagittal_slider,'Value',AVWVIEW.slices.sag);
Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
set(AVWVIEW.handles.sagittal_sliderN,'String',num2str(AVWVIEW.slices.sag));
set(AVWVIEW.handles.sagittal_sliderN,'Value',AVWVIEW.slices.sag);
case {'up','down'},
set(AVWVIEW.handles.coronal_slider,'Value',AVWVIEW.slices.cor);
Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
set(AVWVIEW.handles.coronal_image,'CData',Scor');
set(AVWVIEW.handles.coronal_sliderN,'String',num2str(AVWVIEW.slices.cor));
set(AVWVIEW.handles.coronal_sliderN,'Value',AVWVIEW.slices.cor);
end
end
if isequal(gca, AVWVIEW.handles.coronal_axes),
switch command,
case 'left',
% decrease sagittal slice
if AVWVIEW.slices.sag > 1,
AVWVIEW.slices.sag = AVWVIEW.slices.sag - 1;
end
case 'right',
% increase sagittal slice
if AVWVIEW.slices.sag < AVWVIEW.xdim,
AVWVIEW.slices.sag = AVWVIEW.slices.sag + 1;
end
case 'up',
% increase axial slice
if AVWVIEW.slices.axi < AVWVIEW.zdim,
AVWVIEW.slices.axi = AVWVIEW.slices.axi + 1;
end
case 'down',
% decrease axial slice
if AVWVIEW.slices.axi > 1,
AVWVIEW.slices.axi = AVWVIEW.slices.axi - 1;
end
end
switch command,
case {'left','right'}
set(AVWVIEW.handles.sagittal_slider,'Value',AVWVIEW.slices.sag);
Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
set(AVWVIEW.handles.sagittal_sliderN,'String',num2str(AVWVIEW.slices.sag));
set(AVWVIEW.handles.sagittal_sliderN,'Value',AVWVIEW.slices.sag);
case {'up','down'},
set(AVWVIEW.handles.axial_slider,'Value',AVWVIEW.slices.axi);
Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
set(AVWVIEW.handles.axial_image,'CData',Saxi');
set(AVWVIEW.handles.axial_sliderN,'String',num2str(AVWVIEW.slices.axi));
set(AVWVIEW.handles.axial_sliderN,'Value',AVWVIEW.slices.axi);
end
end
if isequal(gca, AVWVIEW.handles.sagittal_axes),
switch command,
case 'left',
% decrease sagittal slice
if AVWVIEW.slices.cor > 1,
AVWVIEW.slices.cor = AVWVIEW.slices.cor - 1;
end
case 'right',
% increase sagittal slice
if AVWVIEW.slices.cor < AVWVIEW.ydim,
AVWVIEW.slices.cor = AVWVIEW.slices.cor + 1;
end
case 'up',
% increase axial slice
if AVWVIEW.slices.axi < AVWVIEW.zdim,
AVWVIEW.slices.axi = AVWVIEW.slices.axi + 1;
end
case 'down',
% decrease axial slice
if AVWVIEW.slices.axi > 1,
AVWVIEW.slices.axi = AVWVIEW.slices.axi - 1;
end
end
switch command,
case {'left','right'}
set(AVWVIEW.handles.coronal_slider,'Value',AVWVIEW.slices.cor);
Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
set(AVWVIEW.handles.coronal_image,'CData',Scor');
set(AVWVIEW.handles.coronal_sliderN,'String',num2str(AVWVIEW.slices.cor));
set(AVWVIEW.handles.coronal_sliderN,'Value',AVWVIEW.slices.cor);
case {'up','down'},
set(AVWVIEW.handles.axial_slider,'Value',AVWVIEW.slices.axi);
Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
set(AVWVIEW.handles.axial_image,'CData',Saxi');
set(AVWVIEW.handles.axial_sliderN,'String',num2str(AVWVIEW.slices.axi));
set(AVWVIEW.handles.axial_sliderN,'Value',AVWVIEW.slices.axi);
end
end
AVWVIEW = set_coordinates(AVWVIEW);
%AVWVIEW = set_crosshairs(AVWVIEW);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'roi_9','roi_7','roi_5','roi_3'},
position = [ AVWVIEW.slices.sag, AVWVIEW.slices.cor, AVWVIEW.slices.axi ];
shape.type = 'block';
if findstr(command,'9'), shape.size = [9,9,9]; end
if findstr(command,'7'), shape.size = [7,7,7]; end
if findstr(command,'5'), shape.size = [5,5,5]; end
if findstr(command,'3'), shape.size = [3,3,3]; end
stats.roi = avw_roi(AVWVIEW.avw,position,shape);
AVWVIEW.avw.stats = avw_stats(stats);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'nasion','rpa','lpa','ac'},
% return voxel coordinates into AVWVIEW.imgXYZ
AVWVIEW = slices2metric(AVWVIEW);
if get(AVWVIEW.handles.coord,'value') == 2,
format = '%7.3f %7.3f %7.3f';
imgXYZ = AVWVIEW.imgXYZ.mm;
string = sprintf('%7.3f %7.3f %7.3f',imgXYZ);
elseif get(AVWVIEW.handles.coord,'value') == 3,
format = '%7.3f %7.3f %7.3f';
imgXYZ = AVWVIEW.imgXYZ.meters;
string = sprintf('%7.3f %7.3f %7.3f',imgXYZ);
else
imgXYZ = AVWVIEW.imgXYZ.voxels;
string = sprintf('%7.0f %7.0f %7.0f',imgXYZ);
end;
switch command,
case 'nasion',
set(AVWVIEW.handles.nasion,'String',string);
AVWVIEW.avw.fiducials.nasion.voxels(1,:) = AVWVIEW.imgXYZ.voxels;
AVWVIEW.avw.fiducials.nasion.meters(1,:) = AVWVIEW.imgXYZ.meters;
AVWVIEW.avw.fiducials.nasion.mm(1,:) = AVWVIEW.imgXYZ.mm;
case 'rpa',
set(AVWVIEW.handles.rpa,'String',string);
AVWVIEW.avw.fiducials.rpa.voxels(1,:) = AVWVIEW.imgXYZ.voxels;
AVWVIEW.avw.fiducials.rpa.meters(1,:) = AVWVIEW.imgXYZ.meters;
AVWVIEW.avw.fiducials.rpa.mm(1,:) = AVWVIEW.imgXYZ.mm;
case 'lpa',
set(AVWVIEW.handles.lpa,'String',string);
AVWVIEW.avw.fiducials.lpa.voxels(1,:) = AVWVIEW.imgXYZ.voxels;
AVWVIEW.avw.fiducials.lpa.meters(1,:) = AVWVIEW.imgXYZ.meters;
AVWVIEW.avw.fiducials.lpa.mm(1,:) = AVWVIEW.imgXYZ.mm;
case 'ac',
set(AVWVIEW.handles.ac,'String',string);
AVWVIEW.avw.ac.voxels(1,:) = AVWVIEW.imgXYZ.voxels;
AVWVIEW.avw.ac.meters(1,:) = AVWVIEW.imgXYZ.meters;
AVWVIEW.avw.ac.mm(1,:) = AVWVIEW.imgXYZ.mm;
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'flip',
% flip X dim here...
AVWVIEW.avw.img = flipdim(AVWVIEW.avw.img,1);
if isfield(AVWVIEW.handles,'axial_image'),
Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
set(AVWVIEW.handles.axial_image,'CData',Saxi');
end;
if isfield(AVWVIEW.handles,'coronal_image'),
Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
set(AVWVIEW.handles.coronal_image,'CData',Scor');
end;
if isfield(AVWVIEW.handles,'sagittal_image'),
Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
end;
flipStatus = get(AVWVIEW.handles.flipStatus,'string');
if strmatch(flipStatus,'R>>L (radiological)'),
flipStatus = 'L>>R (neurological)';
else,
flipStatus = 'R>>L (radiological)';
end;
set(AVWVIEW.handles.flipStatus,'string',flipStatus);
AVWVIEW = set_coordinates(AVWVIEW);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case {'brighter','dimmer','setclimit'},
switch command,
case 'brighter',
AVWVIEW.clim = AVWVIEW.clim .* 0.9;
case 'dimmer',
AVWVIEW.clim = AVWVIEW.clim .* 1.1;
case 'setclimit',
clim = get(AVWVIEW.handles.clim,'string');
AVWVIEW.clim(2) = str2num(clim);
end
climString = sprintf('%05.2f',AVWVIEW.clim(2));
set(AVWVIEW.handles.clim,'string',climString);
if isfield(AVWVIEW.handles,'axial_image'),
set(AVWVIEW.handles.axial_axes,'Clim',AVWVIEW.clim);
end;
if isfield(AVWVIEW.handles,'coronal_image'),
set(AVWVIEW.handles.coronal_axes,'Clim',AVWVIEW.clim);
end;
if isfield(AVWVIEW.handles,'sagittal_image'),
set(AVWVIEW.handles.sagittal_axes,'Clim',AVWVIEW.clim);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'contrast'
if isfield(AVWVIEW.handles,'axial_image'),
X = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
AVWVIEW.cmap = contrast(X);
colormap(AVWVIEW.handles.axial_axes,AVWVIEW.cmap);
end;
if isfield(AVWVIEW.handles,'coronal_image'),
X = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
AVWVIEW.cmap = contrast(X);
colormap(AVWVIEW.handles.axial_axes,AVWVIEW.cmap);
end;
if isfield(AVWVIEW.handles,'sagittal_image'),
X = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
AVWVIEW.cmap = contrast(X);
colormap(AVWVIEW.handles.axial_axes,AVWVIEW.cmap);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'setcmap'
cmapIndex = get(AVWVIEW.handles.cmap,'value');
cmapString = get(AVWVIEW.handles.cmap,'string');
AVWVIEW.cmapString = cmapString{cmapIndex};
if isfield(AVWVIEW.handles,'axial_image'),
AVWVIEW.cmap = colormap(AVWVIEW.handles.axial_axes,AVWVIEW.cmapString);
end;
if isfield(AVWVIEW.handles,'coronal_image'),
AVWVIEW.cmap = colormap(AVWVIEW.handles.coronal_axes,AVWVIEW.cmapString);
end;
if isfield(AVWVIEW.handles,'sagittal_image'),
AVWVIEW.cmap = colormap(AVWVIEW.handles.sagittal_axes,AVWVIEW.cmapString);
end;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'histogram',
avw = AVWVIEW.avw;
% would be nice to use bins that reflect
% the bits per pixel, but it seems to take
% forever for a 16 bit image, otherwise
% use this code:
% %check the bits per pixel of avw
% bitpix = avw.hdr.dime.bitpix;
% % set the bins according to the data type
% if bitpix <= 8, bins = 0:255; end
% if bitpix > 8, bins = 0:65535; end
%bins = linspace(0,intensity_max,255);
[bins,intensity_volume] = avw_histogram(avw);
figure('name','intensity histogram');
bar(bins,intensity_volume);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'zoom'
x = AVWVIEW.slices.sag;
y = AVWVIEW.slices.cor;
z = AVWVIEW.slices.axi;
switch AVWVIEW.view,
case 'axi',
slice = rot90(AVWVIEW.avw.img(:,:,z));
case 'cor',
slice = rot90(squeeze(AVWVIEW.avw.img(:,y,:)));
case 'sag',
slice = rot90(squeeze(AVWVIEW.avw.img(x,:,:)));
end
figure;
imagesc(slice,AVWVIEW.clim);
colormap(gray); axis off; zoom on;
daspect(AVWVIEW.daspect);
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'save_image',
[filename, pathname] = uiputfile(...
{ '*.png','PNG Files (*.png)'; ...
'*.jpg','JPG Files (*.jpg)'; ...
'*.ppm;*.pgm;*.pbm','Portable Anymap (*.ppm,*.pgm,*.pbm)'; ...
'*.*', 'All Files (*.*)'}, ...
'IMWrite to file');
if filename,
x = AVWVIEW.slices.sag;
y = AVWVIEW.slices.cor;
z = AVWVIEW.slices.axi;
pixelsPerMM = 1 ./ double(AVWVIEW.avw.hdr.dime.pixdim(2:4));
pixelsPerMeter = pixelsPerMM .* 1000;
switch AVWVIEW.view,
case 'axi',
slice = rot90(AVWVIEW.avw.img(:,:,z));
xresolution = pixelsPerMeter(1);
yresolution = pixelsPerMeter(2);
case 'cor',
slice = rot90(squeeze(AVWVIEW.avw.img(:,y,:)));
xresolution = pixelsPerMeter(1);
yresolution = pixelsPerMeter(3);
case 'sag',
slice = rot90(squeeze(AVWVIEW.avw.img(x,:,:)));
xresolution = pixelsPerMeter(2);
yresolution = pixelsPerMeter(3);
end
% scale the image values to between 0-1 for imwrite
% (initially used max of slice, but actually want to
% use the scaled intensity from the gui).
%maxValue = max(max(slice));
%scaledSlice = slice ./ maxValue;
scaledSlice = slice ./ AVWVIEW.clim(2);
% RGB = ind2rgb(X,map) converts the matrix X and corresponding
% colormap map to RGB (truecolor)
file = [pathname,filename];
fprintf('saving to:...%s\n',file);
%Most of the supported image file formats store uint8 data.
%PNG and TIFF formats additionally support uint16 data. For
%grayscale and RGB images, if the data array is double, the
%assumed dynamic range is [0,1]. The data array is automatically
%scaled by 255 before being written as uint8. If the data array
%is uint8 or uint16, it is written without scaling as uint8 or
%uint16, respectively.
[pathname,filename,ext] = fileparts([pathname,filename]);
switch ext,
case '.png',
%imwrite(uint8(image),colormap,file,format);
%imwrite(slice,colormap(gray),file,format,...
% 'XResolution' A scalar indicating the number of
% pixels/unit in the horizontal direction
%
% 'YResolution' A scalar indicating the number of
% pixels/unit in the vertical direction
%
% 'ResolutionUnit' Either 'unknown' or 'meter'
format = 'png';
imwrite(scaledSlice,file,format,...
'BitDepth',16,'ResolutionUnit','meter',...
'XResolution',xresolution,...
'YResolution',yresolution);
case '.jpg',
format = 'jpg';
imwrite(scaledSlice,file,format);
case {'.ppm','.pgm','.pbm'},
format = ext(2:end);
imwrite(scaledSlice,file,format);
otherwise
fprintf('...cannot write %s image files\n',ext);
end
end
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
case 'quit',
flipStatus = get(AVWVIEW.handles.flipStatus,'string');
if strmatch(flipStatus,'L>>R (neurological)'),
fprintf('...returning avw.img to radiological orientation;\n');
fprintf('...use avw_flip to permanently change the orientation.\n');
AVWVIEW.avw.img = flipdim(AVWVIEW.avw.img,1);
end;
% try to assign back into the input struct
if ~isempty(AVWVIEW.invarname),
fprintf('...returning data to base workspace struct ''%s''\n',AVWVIEW.invarname);
assignin('base',AVWVIEW.invarname,AVWVIEW.avw);
elseif evalin('base','exist(''mri'',''var'')'),
fprintf('...returning data to base workspace struct ''mri''\n');
string = ['AVWVIEW = get(', num2str(AVWVIEW.gui),...
',''Userdata''); mri.data = AVWVIEW.avw; clear AVWVIEW;'];
evalin('base',string);
else
fprintf('...returning data into base workspace struct ''avw''\n');
assignin('base','avw',AVWVIEW.avw);
end
close gcbf;
otherwise,
end
switch command,
case 'quit',
otherwise,
set(AVWVIEW.gui,'UserData',AVWVIEW);
end
if nargout > 0,
varargout{1} = AVWVIEW.avw;
end
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% SUBFUNCTIONS
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function axial_update(AVWVIEW)
if isfield(AVWVIEW.handles,'axial_image'),
Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
set(AVWVIEW.handles.axial_image,'CData',Saxi');
end
if isfield(AVWVIEW.handles,'axial_sliderN'),
set(AVWVIEW.handles.axial_sliderN,'String',num2str(AVWVIEW.slices.axi));
set(AVWVIEW.handles.axial_sliderN,'Value',AVWVIEW.slices.axi);
end
if isfield(AVWVIEW.handles,'axial_slider'),
set(AVWVIEW.handles.axial_slider,'Value',AVWVIEW.slices.axi);
end;
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function coronal_update(AVWVIEW)
if isfield(AVWVIEW.handles,'coronal_image'),
Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
set(AVWVIEW.handles.coronal_image,'CData',Scor');
end
if isfield(AVWVIEW.handles,'coronal_sliderN'),
set(AVWVIEW.handles.coronal_sliderN,'String',num2str(AVWVIEW.slices.cor));
set(AVWVIEW.handles.coronal_sliderN,'Value',AVWVIEW.slices.cor);
end
if isfield(AVWVIEW.handles,'coronal_slider'),
set(AVWVIEW.handles.coronal_slider,'Value',AVWVIEW.slices.cor);
end;
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function sagittal_update(AVWVIEW)
if isfield(AVWVIEW.handles,'sagittal_image'),
Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
end
if isfield(AVWVIEW.handles,'sagittal_sliderN'),
set(AVWVIEW.handles.sagittal_sliderN,'String',num2str(AVWVIEW.slices.sag));
set(AVWVIEW.handles.sagittal_sliderN,'Value',AVWVIEW.slices.sag);
end
if isfield(AVWVIEW.handles,'sagittal_slider'),
set(AVWVIEW.handles.sagittal_slider,'Value',AVWVIEW.slices.sag);
end;
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function AVWVIEW = set_crosshairs(AVWVIEW)
current_axes = gca;
[AVWVIEW, metric] = slices2metric(AVWVIEW);
if isfield(AVWVIEW.handles,'axial_axes'),
axes(AVWVIEW.handles.axial_axes)
axialXline = findobj('Tag','axialXline');
if axialXline,
delete(axialXline);
end
axialYline = findobj('Tag','axialYline');
if axialYline,
delete(axialYline);
end
AVWVIEW.handles.axial_xlim = get(AVWVIEW.handles.axial_axes,'Xlim');
AVWVIEW.handles.axial_ylim = get(AVWVIEW.handles.axial_axes,'Ylim');
AVWVIEW.handles.axial_xline = line('Xdata',[metric.sag metric.sag],'Ydata',AVWVIEW.handles.axial_ylim);
AVWVIEW.handles.axial_yline = line('Ydata',[metric.cor metric.cor],'Xdata',AVWVIEW.handles.axial_xlim);
set(AVWVIEW.handles.axial_xline,'Color','b','EraseMode','xor','Tag','axialXline');
set(AVWVIEW.handles.axial_yline,'Color','b','EraseMode','xor','Tag','axialYline');
if get(AVWVIEW.handles.crosshairs,'value'),
set(AVWVIEW.handles.axial_xline,'visible','on');
set(AVWVIEW.handles.axial_yline,'visible','on');
else
set(AVWVIEW.handles.axial_xline,'visible','off');
set(AVWVIEW.handles.axial_yline,'visible','off');
end
end
if isfield(AVWVIEW.handles,'coronal_axes'),
axes(AVWVIEW.handles.coronal_axes);
coronalXline = findobj('Tag','coronalXline');
if coronalXline,
delete(coronalXline);
end
coronalYline = findobj('Tag','coronalYline');
if coronalYline,
delete(coronalYline);
end
AVWVIEW.handles.coronal_xlim = get(AVWVIEW.handles.coronal_axes,'Xlim');
AVWVIEW.handles.coronal_ylim = get(AVWVIEW.handles.coronal_axes,'Ylim');
AVWVIEW.handles.coronal_xline = line('Xdata',[metric.sag metric.sag],'Ydata',AVWVIEW.handles.coronal_ylim);
AVWVIEW.handles.coronal_yline = line('Ydata',[metric.axi metric.axi],'Xdata',AVWVIEW.handles.coronal_xlim);
set(AVWVIEW.handles.coronal_xline,'Color','b','EraseMode','xor','Tag','coronalXline');
set(AVWVIEW.handles.coronal_yline,'Color','b','EraseMode','xor','Tag','coronalYline');
if get(AVWVIEW.handles.crosshairs,'value'),
set(AVWVIEW.handles.coronal_xline,'visible','on');
set(AVWVIEW.handles.coronal_yline,'visible','on');
else
set(AVWVIEW.handles.coronal_xline,'visible','off');
set(AVWVIEW.handles.coronal_yline,'visible','off');
end
end
if isfield(AVWVIEW.handles,'sagittal_axes'),
axes(AVWVIEW.handles.sagittal_axes);
sagittalXline = findobj('Tag','sagittalXline');
if sagittalXline,
delete(sagittalXline);
end
sagittalYline = findobj('Tag','sagittalYline');
if sagittalYline,
delete(sagittalYline);
end
AVWVIEW.handles.sagittal_xlim = get(AVWVIEW.handles.sagittal_axes,'Xlim');
AVWVIEW.handles.sagittal_ylim = get(AVWVIEW.handles.sagittal_axes,'Ylim');
AVWVIEW.handles.sagittal_xline = line('Xdata',[metric.cor metric.cor],'Ydata',AVWVIEW.handles.sagittal_ylim);
AVWVIEW.handles.sagittal_yline = line('Ydata',[metric.axi metric.axi],'Xdata',AVWVIEW.handles.sagittal_xlim);
set(AVWVIEW.handles.sagittal_xline,'Color','b','EraseMode','xor','Tag','sagittalXline');
set(AVWVIEW.handles.sagittal_yline,'Color','b','EraseMode','xor','Tag','sagittalYline');
if get(AVWVIEW.handles.crosshairs,'value'),
set(AVWVIEW.handles.sagittal_xline,'visible','on');
set(AVWVIEW.handles.sagittal_yline,'visible','on');
else
set(AVWVIEW.handles.sagittal_xline,'visible','off');
set(AVWVIEW.handles.sagittal_yline,'visible','off');
end
end
axes(current_axes);
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function AVWVIEW = set_coordinates(AVWVIEW)
% set the axis coordinates to voxels, mm or meters
s = size(AVWVIEW.avw.img);
if length(s) > 0, xdim = s(1); else xdim = 1; end
if length(s) > 1, ydim = s(2); else ydim = 1; end
if length(s) > 2, zdim = s(3); else zdim = 1; end
% initialise for voxel coordinates
xpixdim = double(AVWVIEW.avw.hdr.dime.pixdim(2));
ypixdim = double(AVWVIEW.avw.hdr.dime.pixdim(3));
zpixdim = double(AVWVIEW.avw.hdr.dime.pixdim(4));
xdata = [0 xdim];
ydata = [0 ydim];
zdata = [0 zdim];
aspect = 1./AVWVIEW.daspect; %AVWVIEW.avw.hdr.dime.pixdim(2:4);
if get(AVWVIEW.handles.coord,'value') == 2, % mm
xdata = xdata .* xpixdim;
ydata = ydata .* ypixdim;
zdata = zdata .* zpixdim;
aspect = [1 1 1];
end
if get(AVWVIEW.handles.coord,'value') == 3, % meters
xpixdim = xpixdim / 1000;
ypixdim = ypixdim / 1000;
zpixdim = zpixdim / 1000;
xdata = xdata .* xpixdim;
ydata = ydata .* ypixdim;
zdata = zdata .* zpixdim;
aspect = [1 1 1];
end
if isfield(AVWVIEW.handles,'axial_image'),
set(AVWVIEW.handles.axial_axes,'Xlim',xdata);
set(AVWVIEW.handles.axial_axes,'Ylim',ydata);
set(AVWVIEW.handles.axial_axes,'Zlim',zdata);
set(AVWVIEW.handles.axial_image,'Xdata',xdata);
set(AVWVIEW.handles.axial_image,'Ydata',ydata);
daspect(AVWVIEW.handles.axial_axes,aspect([1 2 3]));
end;
if isfield(AVWVIEW.handles,'coronal_image'),
set(AVWVIEW.handles.coronal_axes,'Xlim',xdata);
set(AVWVIEW.handles.coronal_axes,'Ylim',zdata);
set(AVWVIEW.handles.coronal_axes,'Zlim',ydata);
set(AVWVIEW.handles.coronal_image,'Xdata',xdata);
set(AVWVIEW.handles.coronal_image,'Ydata',zdata);
daspect(AVWVIEW.handles.coronal_axes,aspect([1 3 2]));
end;
if isfield(AVWVIEW.handles,'sagittal_image'),
set(AVWVIEW.handles.sagittal_axes,'Xlim',ydata);
set(AVWVIEW.handles.sagittal_axes,'Ylim',zdata);
set(AVWVIEW.handles.sagittal_axes,'Zlim',xdata);
set(AVWVIEW.handles.sagittal_image,'Xdata',ydata);
set(AVWVIEW.handles.sagittal_image,'Ydata',zdata);
daspect(AVWVIEW.handles.sagittal_axes,aspect([2 3 1]));
end;
AVWVIEW = set_display_values(AVWVIEW);
AVWVIEW = set_crosshairs(AVWVIEW);
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function AVWVIEW = get_current_position(AVWVIEW),
AVWVIEW = get_slider_position(AVWVIEW);
[AVWVIEW, metric] = slices2metric(AVWVIEW);
switch AVWVIEW.view,
case 'sag',
currentpoint = get(get(AVWVIEW.handles.sagittal_image,'Parent'),'CurrentPoint');
metric.cor = currentpoint(1,1);
metric.axi = currentpoint(1,2);
case 'cor',
currentpoint = get(get(AVWVIEW.handles.coronal_image,'Parent'),'CurrentPoint');
metric.sag = currentpoint(2,1);
metric.axi = currentpoint(2,2);
case 'axi',
currentpoint = get(get(AVWVIEW.handles.axial_image,'Parent'),'CurrentPoint');
metric.sag = currentpoint(2,1);
metric.cor = currentpoint(2,2);
end
AVWVIEW = metric2slices(AVWVIEW,metric);
AVWVIEW = check_slices(AVWVIEW);
return
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
function AVWVIEW = get_slider_position(AVWVIEW),
[AVWVIEW.slices.sag,AVWVIEW.slices.cor,AVWVIEW.slices.axi] = deal(0);
if isfield(AVWVIEW.handles,'sagittal_slider'),
if ishandle(AVWVIEW.handles.sagittal_slider),
AVWVIEW.slices.sag = round(get(AVWVIEW.handles.sagittal_slider,'Value'));
end
end
if AVWVIEW.slices.sag == 0,
if isfield(AVWVIEW.handles,'sagittal_sliderN'),
if ishandle(AVWVIEW.handles.sagittal_sliderN),
AVWVIEW.slices.sag = round(get(AVWVIEW.handles.sagittal_sliderN,'Value'));
end
end
end
if isfield(AVWVIEW.handles,'coronal_slider'),
if ishandle(AVWVIEW.handles.coronal_slider),
AVWVIEW.slices.cor = round(get(AVWVIEW.handles.coronal_slider,'Value'));
end
end
if AVWVIEW.slices.cor == 0,
if isfield(AVWVIEW.handles,'coronal_sliderN'),
if ishandle(AVWVIEW.handles.coronal_sliderN),
AVWVIEW.slices.cor = round(get(AVWVIEW.handles.coronal_sliderN,'Value'));
end
end
end
if isfield(AVWVIEW.handles,'axial_slider'),
if ishandle(AVWVIEW.handles.axial_slider),
AVWVIEW.slices.axi = round(get(AVWVIEW.handles.axial_slider,'Value'));
end
end
if AVWVIEW.slices.axi == 0,
if isfield(AVWVIEW.handles,'axial_sliderN'),
if ishandle(AVWVIEW.handles.axial_sliderN),
AVWVIEW.slices.axi = round(get(AVWVIEW.handles.axial_sliderN,'Value'));
end
end
end
AVWVIEW = check_slices(AVWVIEW);
return