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sd_config_layers.m
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sd_config_layers.m
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function layers = sd_config_layers(todo,varargin)
% SD_CONFIG_LAYERS Initializes empty layer variable or fills one with defaults
%
% DESCRIPTION
% This function initializes or completes the layer variable that is used
% by the sd_display function to visualize (layers of) NIfTI images. For
% each layer, it specifies relevant information, such as file name, color
% map, opacity level, and label.
%
% SYNTAX
% * Initialize an empty layers variable:
% layers = SD_CONFIG_LAYERS('init',layer_types)
%
% layer_type - 1xN cell array of charater vectors that can take any of
% the following values:
% - 'truecolor', for unthresholded maps (e.g. anatomical)
% - 'blob', for thresholded maps
% - 'dual', for dual-coded maps (Allen et al., 2012)
% - 'contour', for contour maps
% - 'cluster', for masks/cluster maps
%
% layers - Nx1 struct array, with fields depending on the values in
% layer_type:
%
% * Fill an existing layers variable with defaults:
% layers = SD_CONFIG_LAYERS('fill-defaults',layers)
%
% EXAMPLES
% Initialize an empty layers variable for displaying a dual-coded image on
% top of a truecolor image.
%
% layer_types = {'truecolor','dual'};
% layers = SD_CONFIG_LAYERS('init',layer_types);
%
% Fill an existing layers variable with default
% layers = SD_CONFIG_LAYERS('fill-defaults',layers);
%
% .........................................................................
% Bram Zandbelt (bramzandbelt@gmail.com), 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')
switch lower(todo)
case 'init'
layer_type = varargin{1};
% Check inputs
% =================================================================
if ~iscellstr(layer_type)
error('Input must be an array of strings. Type ''help sd_config_layers''.')
end
valid_layers = ismember(lower(layer_type), ...
{'truecolor','blob','dual','contour','cluster'});
valid_layer_array = layer_type(valid_layers);
n_layer = sum(valid_layers);
if n_layer < numel(layer_type)
invalid_ids = sprintf('%d, ',find(~valid_layers));
warning('%d layers (%s) were incorrectly specified and will be ignored', ...
n_layer, ...
invalid_ids(1:end-2));
end
switch lower(valid_layer_array{1})
case 'contour'
error('First layer cannot be a contour image. Type ''help sd_config_layers''.')
end
% Initialize empty structure arrays
% =================================================================
color_struct = struct('file','', ...
'header',[], ...
'hold',[], ...
'map', [], ...
'range', [], ...
'opacity', [], ...
'label', '');
color_struct_dual = struct('file','', ...
'header',[], ...
'hold',[], ...
'map', [], ...
'range', [], ...
'label', '');
color_struct_contour = struct('file','', ...
'header',[], ...
'hold',[], ...
'map', [], ...
'range', [], ...
'opacity', [], ...
'line_width',[], ...
'line_style','', ...
'label', '');
opacity_struct = struct('file', '', ...
'header',[], ...
'hold',[], ...
'range', [], ...
'label','');
mask_struct = struct('file','', ...
'header',[], ...
'hold',[], ...
'label','');
% Assemble layer-specific structure arrays
truecolor_struct = struct('type','truecolor', ...
'color', color_struct, ...
'mask', mask_struct);
blob_struct = struct('type','blob', ...
'color', color_struct, ...
'mask', mask_struct);
dual_struct = struct('type','dual', ...
'color', color_struct_dual, ...
'opacity', opacity_struct, ...
'mask', mask_struct);
contour_struct = struct('type','contour', ...
'color', color_struct_contour, ...
'mask', mask_struct);
cluster_struct = struct('type','cluster', ...
'color', color_struct, ...
'mask', mask_struct);
% Assemble structs in layer variable
% =================================================================
layers(n_layer,1) = struct();
for i_layer = 1:n_layer
switch lower(valid_layer_array{i_layer})
case 'truecolor'
template_struct = truecolor_struct;
case 'blob'
template_struct = blob_struct;
case 'dual'
template_struct = dual_struct;
case 'contour'
template_struct = contour_struct;
case 'cluster'
template_struct = cluster_struct;
end
for fn = fieldnames(template_struct)'
layers(i_layer).(fn{1}) = template_struct.(fn{1});
end
end
case 'fill-defaults'
layers = varargin{1};
empty_layer_types = cellfun('isempty',{layers.type});
if any(empty_layer_types)
error('Layer type not specified for layer %d.', find(empty_layer_types))
end
for i_layer = 1:numel(layers)
% Color struct
% =====================================================
% File
% -----------------------------------------------------
if isempty(layers(i_layer).color.file)
layers(i_layer).color.file = get_image_file(i_layer, ...
lower(layers(i_layer).type), ...
'color-coding');
end
% Header
% -----------------------------------------------------
if isempty(layers(i_layer).color.header)
layers(i_layer).color.header = spm_vol(layers(i_layer).color.file);
end
% Hold
% -----------------------------------------------------
if isempty(layers(i_layer).color.hold)
layers(i_layer).color.hold = 0;
end
% Color map
% -----------------------------------------------------
if isempty(layers(i_layer).color.map)
switch lower(layers(i_layer).type)
case {'truecolor','blob','dual','cluster'}
if i_layer == 1
layers(i_layer).color.map = gray(256);
elseif i_layer > 1
layers(i_layer).color.map = parula(256);
end
case 'contour'
layers(i_layer).color.map = [0 0 0];
end
end
% Range
% -----------------------------------------------------
if isempty(layers(i_layer).color.range)
[color_max, color_min] = slover('volmaxmin', layers(i_layer).color.header);
% Make map symmetrical
if color_min < 0
abs_color_max = max(abs([color_max, color_min]));
layers(i_layer).color.range = [-abs_color_max, abs_color_max];
else
layers(i_layer).color.range = [color_min, color_max];
end
end
switch lower(layers(i_layer).type)
case {'truecolor','blob','contour','cluster'}
% Opacity
% -----------------------------------------------------
if isempty(layers(i_layer).color.opacity)
layers(i_layer).color.opacity = 1;
end
end
switch lower(layers(i_layer).type)
case 'contour'
if isempty(layers(i_layer).color.line_width)
layers(i_layer).color.line_width = 1;
end
if isempty(layers(i_layer).color.line_style)
layers(i_layer).color.line_style = '-';
end
end
% Label
% -----------------------------------------------------
% Label can be empty, in which case no colorbar is
% plotted
if isempty(layers(i_layer).color.label)
end
% Opacity struct
% =====================================================
switch lower(layers(i_layer).type)
case 'dual'
% File
% -----------------------------------------------------
if isempty(layers(i_layer).opacity.file)
layers(i_layer).color.file = get_image_file(i_layer, ...
lower(layers(i_layer).type), ...
'opacity-coding');
end
% Header
% -----------------------------------------------------
if isempty(layers(i_layer).opacity.header)
layers(i_layer).opacity.header = spm_vol(layers(i_layer).opacity.file);
end
% Hold
% -----------------------------------------------------
if isempty(layers(i_layer).opacity.hold)
layers(i_layer).opacity.hold = 0;
end
% Range
% -----------------------------------------------------
% Assume opacity-coding uses absolute numbers and map
% ranges from 0 to absolute max.
if isempty(layers(i_layer).opacity.range)
[opacity_max, opacity_min] = slover('volmaxmin', layers(i_layer).color.header);
abs_opacity_max = max(abs([opacity_max, opacity_min]));
layers(i_layer).opacity.range = [0, abs_opacity_max];
end
% Label
% -----------------------------------------------------
% Label can be empty, in which case no colorbar is
% plotted
if isempty(layers(i_layer).opacity.label)
end
end
% Mask struct
% =====================================================
% File
% -----------------------------------------------------
% Mask can be empty
if isempty(layers(i_layer).mask.file)
end
% Header
% -----------------------------------------------------
if isempty(layers(i_layer).mask.header)
if ~isempty(layers(i_layer).mask.file)
layers(i_layer).mask.header = spm_vol(layers(i_layer).mask.file);
end
end
% Hold
% -----------------------------------------------------
if isempty(layers(i_layer).color.hold)
layers(i_layer).mask.hold = 0;
end
% Label
% -----------------------------------------------------
% Label can be empty
if isempty(layers(i_layer).mask.label)
end
end
otherwise
error('First element must be ''init'' or ''fill-defaults''. Type ''help sd_config_layers''.')
end
function image_file = get_image_file(i_layer,layer_type,coding_type)
image_file = spm_select(1, ...
'image', ...
sprintf('Select layer %d (%s) %s image',i_layer, layer_type, coding_type));