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palm_viewsub.m
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palm_viewsub.m
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function fighandle = palm_viewsub(varargin)
% Simple visualisation of subcortical surface results still in Octave/MATLAB.
% The principles are generally similar to those of the tool "dpx2map.m",
% described here:
% https://brainder.org/2013/07/28/displaying-vertexwise-and-facewise-brain-maps/
%
% Usage:
% h = palm_viewsub( ...
% dat_file.csv, ...
% { srf_file1, srf_file2, srf_file3, ... }, ...
% Name, Value, ...)
%
% The first argument is .csv file with one column containing the values for
% each subcortical region. The second is a cell-array with the file names
% for the surfaces, in .srf format, and in the same order as the values
% were entered in the .csv file.
%
% File formats for these inputs are those accepted by PALM.
%
% All subsequent arguments are supplied as pairs "Name,Value", as typical
% in many MATLAB/Octave commands. Accepted Names and descriptions are:
%
% MapName : A MATLAB/Octave colourmap (default: 'viridis').
% DataRange : Interval to be used to define the colourscale [min max].
% If not specified, it uses the min and max of the DPX file.
% ShowRange : Interval to be shown (coloured) [min max]. If not specified,
% it uses the same as datarange.
% Dual : True/False. If true, applies the map to the values of no
% overlap between datarange and showrange. Useful for
% thresholded positive+negative maps. Default is false.
% ColourGap : Colour for values that off the colourscale, including NaN.
% Default is light gray, 25%, i.e. [.75 .75 .75];
% COption : True/False. The behavior varies if 'dual' is true or not.
% - For 'dual' = true:
% If coption is false, don't rescale the extremities of the
% colourmap. Default is true, i.e., produce a higher contrast.
% - For 'dual' = false:
% If coption is false, show the out-of-range values with the
% colour specified by 'colourgap'. Default is true, so the
% out-of-range values are shown with the extremities of the
% colourmap.
% MapSize : Maximum number of colours in the colourmap. Default 2^16.
% Title : Title of the figure (to appear at the top of the colourbar).
% Layout : How to distribute the brain views in the page? The
% following layouts are available:
% - 'Simple' : A simple layout meant to be interactively
% explored using the MATLAB/Octave figure tools.
% - 'Cardinal' : Show 4 views (lateral and medial of left and right
% hemispheres), plus colorbar in the centre.
% - 'Left' : Left hemisphere only (lateral and medial).
% - 'Right' : Right hemisphere only (lateral and medial).
% - 'Strip' : Similar to cardinal but shows all views in a
% single row. Useful for stacking subjects.
% - 'Publication' : A well rounded layout, meant to be (nearly) ready
% for publication. It always includes a colourbar.
% - 'Worsley' : The layout proposed by K. Worsley. Always includes
% a colourbar.
% Background : A 3-element vector of the RGB color of the background.
% Default is [1 1 1] (white).
% CamLight : Boolean indicating whether a light should be placed in the
% same location as the camera.
% Lightning : Lighting mode. Valid options are:
% - 'None'
% - 'Flat'
% - 'Gouraud'
% Material : Material mode. Valid options are:
% - 'Dull'
% - 'Shiny'
% - 'Metal'
% Shading : Shading mode. Valid options are:
% - 'Flat'
% - 'Interp'
% - 'Faceted'
% ColourBar : Boolean indicating whether the colour bar should be shown.
% Note that for the 'publication' and 'worsley' layouts, the
% colour bar is always shown.
%
% Example:
% freesurfer_dir = getenv('FREESURFER_DIR');
% data = 'mydata.csv';
% surfs = { ...
% fullfile(srfdir,'Left-Accumbens-area.srf'),...
% fullfile(srfdir,'Left-Amygdala.srf'),...
% fullfile(srfdir,'Left-Caudate.srf'),...
% fullfile(srfdir,'Left-Hippocampus.srf'),...
% fullfile(srfdir,'Left-Pallidum.srf'),...
% fullfile(srfdir,'Left-Putamen.srf'),...
% fullfile(srfdir,'Left-Thalamus-Proper.srf'),...
% fullfile(srfdir,'Left-VentralDC.srf'),...
% fullfile(srfdir,'Right-Accumbens-area.srf'),...
% fullfile(srfdir,'Right-Amygdala.srf'),...
% fullfile(srfdir,'Right-Caudate.srf'),...
% fullfile(srfdir,'Right-Hippocampus.srf'),...
% fullfile(srfdir,'Right-Pallidum.srf'),...
% fullfile(srfdir,'Right-Putamen.srf'),...
% fullfile(srfdir,'Right-Thalamus-Proper.srf'),...
% fullfile(srfdir,'Right-VentralDC.srf') };
% palm_viewsurf(data,surfs,'layout','top','background',[.5 .5 .5],'colormap','inferno');
%
% _____________________________________
% A. Winkler and K. Kircanski
% National Institutes of Health
% May/2021
% http://brainder.org
% Defaults
opts.mapname = 'viridis';
opts.datarange = []; % clim, datarange
opts.showrange = [];
opts.dual = false;
opts.colourgap = [.75 .75 .75];
opts.coption = true;
opts.mapsize = 2^14;
opts.title = '';
opts.layout = 'superior';
opts.background = [1 1 1];
opts.camlight = true;
opts.lightning = 'gouraud'; % {'none', 'flat', 'gouraud'}
opts.material = 'dull'; % {'shiny', 'dull', 'metal'}
opts.shading = 'interp'; % {'flat', 'interp', 'faceted'}
opts.colourbar = true;
% Parse inputs and check for most common errors.
dat = varargin{1};
srf = varargin{2};
for a = 3:2:nargin
opts.(lower(varargin{a})) = varargin{a + 1};
end
if numel(opts.datarange) ~= 2 && ~ isempty(opts.datarange)
error('The supplied DataRange has to be a two-element vector, or be empty.');
end
if numel(opts.showrange) ~= 2 && ~ isempty(opts.showrange)
error('The supplied ShowRange has to be a two-element vector, or be empty.');
end
if numel(opts.background) ~= 3 || numel(opts.colourgap) ~= 3
error('The supplied ColourGap or Background has to be a two-element vector, or be empty.');
end
if ~ islogical(opts.dual) || ~ islogical(opts.coption)
error('The supplied Dual or COption must be a logical type (i.e., true/false).');
end
if ~ ischar(opts.title)
error('The supplied Title must be a string.');
end
if ~ islogical(opts.camlight)
error('The CamLight option must be a logical type (i.e., true/false).');
end
if ~ any(strcmpi(opts.lightning,{'none','flat','gouraud'}))
error('Unknown Lightning style: %s',opts.lightning);
end
if ~ any(strcmpi(opts.material,{'shiny','dull','metal'}))
error('Unknown Material style: %s',opts.material);
end
if ~ any(strcmpi(opts.shading,{'flat','interp','faceted'}))
error('Unknown Shading style: %s',opts.shading);
end
if ~ islogical(opts.colourbar)
error('The Colourbar option must be a logical type (i.e., true/false).');
end
if strcmpi(opts.layout,'worsley')
opts.mapname = 'spectral';
end
if palm_isoctave && opts.mapsize > 2^14
error('Octave cannot plot more than 2^14 = 32768 colors.');
end
% Ensure we gave the programs needed to read the data
palm_checkprogs;
% Read input files
for s = 1:numel(srf)
srf{s} = palm_miscread(srf{s});
end
dat = palm_miscread(dat);
% Open a new figure window. The handle will be returned.
fighandle = figure;
% Ensure data and colour ranges are well behaved
if isempty(opts.datarange)
iinf = isinf(dat.data);
inan = isnan(dat.data);
iidx = ~(iinf | inan);
opts.datarange = [min(dat.data(iidx)) max(dat.data(iidx))];
end
if isempty(opts.showrange)
opts.showrange = opts.datarange;
end
opts.showrange(1) = max(opts.showrange(1),opts.datarange(1));
opts.showrange(2) = min(opts.showrange(2),opts.datarange(2));
for h = 1:numel(dat)
infneg = isinf(dat.data) & dat.data < 0;
infpos = isinf(dat.data) & dat.data > 0;
dat.data(infneg) = opts.datarange(1);
dat.data(infpos) = opts.datarange(2);
end
% Define the colourmap
if opts.dual
if opts.coption
neg = opts.showrange(1) - opts.datarange(1);
cen = opts.showrange(2) - opts.showrange(1);
pos = opts.datarange(2) - opts.showrange(2);
tot = opts.datarange(2) - opts.datarange(1);
fracs = round([neg cen pos]./tot*opts.mapsize);
maptmp = eval(sprintf('%s(%d)',opts.mapname,fracs(1)+fracs(3)));
map = nan(opts.mapsize,3);
map(1:fracs(1),:) = maptmp(1:fracs(1),:);
map(fracs(1)+1:fracs(1)+fracs(2),:) = repmat(opts.colourgap,[fracs(2) 1]);
map(fracs(1)+fracs(2)+1:sum(fracs),:) = maptmp(fracs(1)+1:fracs(1)+fracs(3),:);
else
map = eval(sprintf('%s(%d)',opts.mapname,opts.mapsize));
idxmin = round((opts.showrange(1) - opts.datarange(1)) / (opts.datarange(2) - opts.datarange(1)) * (opts.mapsize - 1) + 1);
idxmax = round((opts.showrange(2) - opts.datarange(1)) / (opts.datarange(2) - opts.datarange(1)) * (opts.mapsize - 1) + 1);
map(idxmin:idxmax,:) = repmat(opts.colourgap,[idxmax-idxmin+1 1]);
end
else
neg = opts.showrange(1) - opts.datarange(1);
cen = opts.showrange(2) - opts.showrange(1);
pos = opts.datarange(2) - opts.showrange(2);
tot = opts.datarange(2) - opts.datarange(1);
fracs = round([neg cen pos]./tot*opts.mapsize);
maptmp = eval(sprintf('%s(%d)',opts.mapname,fracs(2)));
map = nan(opts.mapsize,3);
map(fracs(1)+1:fracs(1)+fracs(2),:) = maptmp;
if opts.coption
map(1:fracs(1),:) = repmat(maptmp(1,:),[fracs(1) 1]);
map(fracs(1)+fracs(2)+1:sum(fracs),:) = repmat(maptmp(fracs(2),:),[fracs(3) 1]);
else
map(1:fracs(1),:) = repmat(opts.colourgap,[fracs(1) 1]);
map(fracs(1)+fracs(2)+1:sum(fracs),:) = repmat(opts.colourgap,[fracs(3) 1]);
end
end
colormap(map)
% Render using the selected layout
switch opts.layout
case 'superior'
% Top view
ax(1) = axes();
for s = 1:numel(srf)
trisurf(...
srf{s}.data.fac,...
srf{s}.data.vtx(:,1),srf{s}.data.vtx(:,2),srf{s}.data.vtx(:,3),...
dat.data(s)*ones(size(srf{s}.data.vtx,1),1),...
'EdgeColor','None');
hold on
end
hold off
view(0,90);
useopts(opts,fighandle);
% If a colorbar was asked
if opts.colourbar
cb = colorbar('Location','South');
if isempty(opts.title)
set(cb,'Position',[0.41 0.085 0.3 0.03]);
else
set(cb,'Position',[0.41 0.05 0.3 0.03]);
end
end
case 'inferior'
% Bottom view
ax(1) = axes();
for s = 1:numel(srf)
trisurf(...
srf{s}.data.fac,...
srf{s}.data.vtx(:,1),srf{s}.data.vtx(:,2),srf{s}.data.vtx(:,3),...
dat.data(s)*ones(size(srf{s}.data.vtx,1),1),...
'EdgeColor','None');
hold on
end
hold off
view(180,-90);
useopts(opts,fighandle);
% If a colorbar was asked
if opts.colourbar
cb = colorbar('Location','South');
if isempty(opts.title)
set(cb,'Position',[0.32 0.085 0.3 0.03]);
else
set(cb,'Position',[0.32 0.05 0.3 0.03]);
end
end
otherwise
error('Unknown layout style %s.\n',opts.layout)
end
% Deal with the colour limits
for i=1:length(ax)
set(ax(i),'CLim',opts.datarange);
end
% This layout always includes a colourbar
% Deal with the colourbar
if opts.colourbar
set(get(cb,'Title'),'String',opts.title);
end
function useopts(opts,fighandle) % ==================================================
daspect([1 1 1]);
axis tight;
axis vis3d off;
box off
if strcmpi(opts.layout,'worsley')
set(fighandle,'Color',[1 1 1],'InvertHardcopy','Off');
camlight;
lighting ('gouraud');
material ('shiny');
shading ('interp');
else
set(fighandle,'Color',opts.background,'InvertHardcopy','Off');
if opts.camlight
camlight;
end
lighting (opts.lightning);
material (opts.material);
shading (opts.shading);
end