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iCAPs/packages/spm12/@slover/fill_defaults.m
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fill_defaults.m
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function obj = fill_defaults(obj)
% Check and fill fields in object
% FORMAT obj = fill_defaults(obj)
%
% Input
% obj - object to fill
%
% Output
% obj - object filled
%__________________________________________________________________________
% Matthew Brett
% $Id: fill_defaults.m 6623 2015-12-03 18:38:08Z guillaume $
% Some default structures
def_labs = struct('colour',[1 1 1],'size',0.075,'format', '%+3.0f');
def_fig = struct('position', [0 0 1 0.92], 'units', 'normalized', ...
'valign', 'top');
def_area = struct('position', [0 0 1 1], ...
'units', '', ...
'halign', 'center',...
'valign', 'middle');
% Figure. We allow the figure to be dead, if we are going to resurrect
% it later.
dead_f = 0;
if ~isempty(obj.figure)
% Is it dead?
if ~ishandle(obj.figure)
% Do we want to revive it?
if ~obj.resurrectf
error('Figure handle is not a valid figure')
end
dead_f = 1;
obj.refreshf = 1;
elseif ~strcmp(get(obj.figure,'Type'),'figure')
error('Figure handle is not a figure')
end
else
% no figure handle. Try spm figure, then gcf
obj.figure = spm_figure('FindWin', 'Graphics');
if isempty(obj.figure)
obj.figure = gcf;
end
end
% set defaults for SPM figure
if ~dead_f
if strcmp(get(obj.figure, 'Tag'),'Graphics')
% position figure nicely for SPM
obj.area = mars_struct('fillafromb', obj.area, def_fig);
end
end
% orientation; string or 4x4 matrix
if ischar(obj.transform)
orientn = find(strcmpi(obj.transform, {'axial', ...
'coronal', ...
'sagittal'}));
if isempty(orientn)
error('Unexpected orientation %s', obj.transform);
end
ts = [0 0 0 0 0 0 1 1 1;...
0 0 0 pi/2 0 0 1 -1 1;...
0 0 0 pi/2 0 -pi/2 -1 1 1];
obj.transform = spm_matrix(ts(orientn,:));
end
% default slice size, slice matrix depends on orientation
if (isempty(obj.slicedef) || isempty(obj.slices)) ...
&& ~isempty(obj.img)
% take image sizes from first image
V = obj.img(1).vol;
D = V.dim(1:3);
T = obj.transform * V.mat;
vcorners = [1 1 1; D(1) 1 1; 1 D(2) 1; D(1:2) 1; ...
1 1 D(3); D(1) 1 D(3); 1 D(2:3) ; D(1:3)]';
corners = T * [vcorners; ones(1,8)];
SC = sort(corners, 2);
vxsz = sqrt(sum(T(1:3,1:3).^2));
if isempty(obj.slicedef)
obj.slicedef = [SC(1,1) vxsz(1) SC(1,8);SC(2,1) vxsz(2) SC(2,8)];
end
if isempty(obj.slices)
obj.slices = SC(3,1):vxsz(3):SC(3,8);
end
end
% labels
if ischar(obj.labels)
if ~strcmpi(obj.labels, 'none')
error('If labels is string, should be ''none''');
end
else
obj.labels = mars_struct('fillafromb', obj.labels, def_labs);
dist = mean(diff(obj.slices));
prec = ceil(-min(log10(dist), 0));
obj.labels.format = sprintf('%%+3.%1df', prec);
end
% figure area stuff
obj.area = mars_struct('fillafromb', obj.area, def_area);
if isempty(obj.area.units)
if (all(obj.area.position>=0 & obj.area.position<=1))
obj.area.units = 'normalized';
else
obj.area.units = 'pixels';
end
end
% fill various img arguments
% set colour intensities as we go
remcol = 1;
for i = 1:length(obj.img)
if ~mars_struct('isthere', obj.img(i), 'type')
% default is true colour, unless prop is Inf
obj.img(i).type = 'truecolour';
if mars_struct('isthere', obj.img(i), 'prop')
if obj.img(i).prop == Inf
obj.img(i).type = 'split';
obj.img(i).prop = 1;
end
end
end
if ~mars_struct('isthere', obj.img(i), 'hold')
if ~mars_struct('isthere', obj.img(i).vol, 'imgdata')
% normal file vol struct
obj.img(i).hold = 1;
else
% 3d matrix vol struct
obj.img(i).hold = 0;
end
end
if ~mars_struct('isthere', obj.img(i), 'background')
obj.img(i).background = NaN;
end
if ~mars_struct('isthere', obj.img(i), 'prop')
% default is true colour
if strcmpi(obj.img(i).type, 'truecolour')
obj.img(i).prop = remcol/(length(obj.img)-i+1);
remcol = remcol - obj.img(i).prop;
else
obj.img(i).prop = 1;
end
end
if ~mars_struct('isthere', obj.img(i), 'range')
[mx,mn] = pr_volmaxmin(obj.img(i).vol);
obj.img(i).range = [mn mx];
end
if ~mars_struct('isthere', obj.img(i), 'cmap')
if strcmpi(obj.img(i).type, 'split')
if obj.range(1)<obj.range(2)
obj.img(i).cmap = pr_getcmap('hot');
else
obj.img(i).cmap = pr_getcmap('winter');
end
else % true colour
obj.img(i).cmap = gray;
end
else % check cmap is OK
if ischar(obj.img(i).cmap)
obj.img(i).cmap = pr_getcmap(obj.img(i).cmap);
end
end
if ~mars_struct('isthere', obj.img(i), 'outofrange')
% this can be complex, and depends on split/true colour
if strcmpi(obj.img(i).type, 'split')
if xor(obj.img(i).range(1) < obj.img(i).range(2), ...
obj.img(i).range(2) < 0)
obj.img(i).outofrange = {0, size(obj.img(i).cmap,1)};
else
obj.img(i).outofrange={1, 0};
end
else % true colour
obj.img(i).outofrange = {1,size(obj.img(i).cmap,1)};
end
end
for j=1:2
if isempty(obj.img(i).outofrange{j})
obj.img(i).outofrange(j) = {0};
end
end
if ~mars_struct('isthere', obj.img(i), 'nancol')
obj.img(i).nancol = 0;
end
end
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