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sd_display.m
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sd_display.m
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function [settings, p, h_figure] = sd_display(layers, settings)
% SD_DISPLAY Displays one or more layers of a series of NIfTI image slices
%
% DESCRIPTION
% Displays layered brain maps
%
% SYNTAX
% [settings, p] = SD_DISPLAY(layers, settings);
%
% layers - Nx1 struct, specifying the N layers to be displayed (for
% details, type 'help sd_config_layers')
% settings - 1x1 struct, specifying the figure and display settings
% (for details, type 'help sd_config_settings')
%
% p - panel object (for details, type 'help panel')
% h_figure - figure handle
%
% EXAMPLES
% Display the single subject T1-weighted scan in SPM's canonical directory
% layers = sd_config_layers('init',{'truecolor'});
% settings = sd_config_settings('init');
% layers(1).color.file = fullfile(spm('Dir'),'canonical','single_subj_T1.nii');
% layers(1).color.map = gray(256);
% sd_display(layers,settings);
%
% .........................................................................
% Bram Zandbelt ([email protected]), Radboud University
% Make sure required toolboxes are on path
assert(~isempty(spm('Dir')),'<a href="http://www.fil.ion.ucl.ac.uk/spm/">SPM</a> cannot be found; make sure it is on MATLAB''s search path.')
assert(exist('panel.m','file') > 0,'<a href="https://www.mathworks.com/matlabcentral/fileexchange/20003-panel">Panel</a> cannot be found; make sure it is on MATLAB''s search path')
% Fill in defaults for empty fields in settings and layers
% -------------------------------------------------------------------------
layers = sd_config_layers('fill-defaults',layers);
settings = sd_config_settings('fill-defaults',settings);
% Gather information from image(s)
% -------------------------------------------------------------------------
settings = sd_get_image_specs(layers, settings);
transform = settings.slice.transform;
x = settings.slice.x;
y = settings.slice.y;
zmm = settings.slice.zmm;
vdims = settings.slice.vdims;
nvox = prod(vdims(1:2));
% Set up figure
% -------------------------------------------------------------------------
[h_figure, ...
p, ...
settings] = sd_config_figure(layers, settings);
% Display slices
% -------------------------------------------------------------------------
figure(h_figure);
if ~isempty(settings.fig_specs.title)
title(settings.fig_specs.title);
axis off
end
for i_slice = 1:settings.fig_specs.n.slice
xyzmm = [x(:)';y(:)';ones(1,nvox)*zmm(i_slice);ones(1,nvox)];
% Select axis/panel
p(1, i_slice).select();
axis image; axis off;
p(1, i_slice).hold('on')
for i_layer = 1:numel(layers)
% Color-coding
% =================================================================
% Get slice data
Y_c = sd_get_slice(layers(i_layer).color.header, ...
xyzmm, ...
transform, ...
vdims, ...
layers(i_layer).color.hold);
% Convert to RGB
switch lower(layers(i_layer).type)
case {'truecolor', 'blob', 'dual', 'cluster'}
Y_rgb = sd_slice_to_rgb(Y_c,layers(i_layer),settings);
end
% Opacity settings
switch lower(layers(i_layer).type)
case {'truecolor','blob','cluster'}
Y_alpha = ones(size(Y_c)) .* layers(i_layer).color.opacity;
case 'contour'
end
% Opacity-coding
% =================================================================
switch lower(layers(i_layer).type)
case 'dual'
% Get slice data
Y_o = sd_get_slice(layers(i_layer).opacity.header, ...
xyzmm, ...
transform, ...
vdims, ...
layers(i_layer).opacity.hold);
% Convert to alpha map
Y_alpha = sd_slice_to_alpha(Y_o,layers(i_layer));
end
% Masking
% =================================================================
if ~isempty(layers(i_layer).mask.file)
Y_m = sd_get_slice(layers(i_layer).mask.header, ...
xyzmm, ...
transform, ...
vdims, ...
layers(i_layer).color.hold);
else
switch lower(layers(i_layer).type)
case 'cluster'
Y_m = ones(size(Y_c));
Y_m(Y_c == 0) = 0;
otherwise
Y_m = ones(size(Y_c));
end
end
% Display layer
% =================================================================
switch lower(layers(i_layer).type)
case {'truecolor', 'blob', 'dual','cluster'}
h_image = image(Y_rgb);
set(h_image,'alphaData',Y_alpha .* Y_m);
case 'contour'
contour_color = layers(i_layer).color.map;
if strncmp(spm_type(layers(i_layer).color.header.dt),'int',3)
[~, h_contour] = contour(Y_c,1);
else
% TODO: implement contour level(s) for float data
[~, h_contour] = contour(Y_c,1);
end
set(h_contour,'LineColor',contour_color)
set(h_contour,'LineStyle',layers(i_layer).color.line_style);
set(h_contour,'LineWidth',layers(i_layer).color.line_width);
end
% Display slice labels
if settings.slice.show_labels
text(.025,.025,sprintf('%d mm',round(settings.slice.zmm(i_slice),2)), ...
'Color','w', ...
'HorizontalAlignment','left', ...
'VerticalAlignment','bottom', ...
'Units','normalized', ...
'FontUnits','normalized', ...
'FontSize',0.075);
end
% Display orientation on last slice (L/R,
if i_slice == settings.fig_specs.n.slice
if settings.slice.show_orientation
switch lower(settings.slice.orientation)
case {'axial','coronal'}
text(.025,.975,'L', ...
'Color','w', ...
'HorizontalAlignment','left', ...
'VerticalAlignment','top', ...
'Units','normalized', ...
'FontUnits','normalized', ...
'FontSize',0.1);
text(.975,.975,'R', ...
'Color','w', ...
'HorizontalAlignment','right', ...
'VerticalAlignment','top', ...
'Units','normalized', ...
'FontUnits','normalized', ...
'FontSize',0.1);
case 'sagittal'
text(.025,.975,'A', ...
'Color','w', ...
'HorizontalAlignment','left', ...
'VerticalAlignment','top', ...
'Units','normalized', ...
'FontUnits','normalized', ...
'FontSize',0.1);
text(.975,.975,'P', ...
'Color','w', ...
'HorizontalAlignment','r', ...
'VerticalAlignment','top', ...
'Units','normalized', ...
'FontUnits','normalized', ...
'FontSize',0.1);
end
end
end
end
end
% Display color bars
% =========================================================================
for i_colorbar = 1:settings.fig_specs.n.colorbar
i_layer = settings.fig_specs.i.colorbar(i_colorbar);
[i_row,i_col] = ind2sub([settings.fig_specs.n.colorbar_row, ...
settings.fig_specs.n.colorbar_column], ...
i_colorbar);
p(2,i_row,i_col).select();
switch lower(layers(i_layer).type)
case {'blob','cluster'}
% Transform vectors coding for color and opacity into 2D matrix
color_vector = linspace(layers(i_layer).color.range(1), ...
layers(i_layer).color.range(2), ...
size(layers(i_layer).color.map,1));
alpha_vector = linspace(1,1, ...
256);
% Transform into a 2D matrix
[color_mat,~] = meshgrid(color_vector,alpha_vector);
% Plot the colorbar
imagesc(color_vector,alpha_vector,color_mat);
colormap(gca, layers(i_layer).color.map);
axis tight
h_xlabel = xlabel(layers(i_layer).color.label);
set(h_xlabel,'interpreter','tex')
if numel(unique(layers(i_layer).color.range)) == 1
set(gca, 'Box', 'off', ...
'XTick',[], ...
'YTick',[]);
else
set(gca, 'Box', 'off', ...
'XLim',layers(i_layer).color.range, ...
'YTick',[]);
end
case 'dual'
% Transform vectors coding for color and opacity into 2D matrix
color_vector = linspace(layers(i_layer).color.range(1), ...
layers(i_layer).color.range(2), ...
size(layers(i_layer).color.map,1));
alpha_vector = linspace(layers(i_layer).opacity.range(1), ...
layers(i_layer).opacity.range(2), ...
256);
% Transform into a 2D matrix
[color_mat,alpha_mat] = meshgrid(color_vector,alpha_vector);
% Plot the colorbar
imagesc(color_vector,alpha_vector,color_mat);
colormap(gca, layers(i_layer).color.map);
alpha(alpha_mat);
alpha('scaled');
axis tight
h_xlabel = xlabel(layers(i_layer).color.label);
h_ylabel = ylabel(layers(i_layer).opacity.label);
set([h_xlabel, h_ylabel],'interpreter','tex')
set(gca, 'Box', 'off', ...
'XLim',layers(i_layer).color.range, ...
'YLim',layers(i_layer).opacity.range, ...
'YTick',layers(i_layer).opacity.range, ...
'YTickLabel',{layers(i_layer).opacity.range(1),sprintf('>%.1f',layers(i_layer).opacity.range(2))});
end
end