initial commit

2026-09-17 19:39:08 +09:00 · 2026-08-07 15:56:42 +09:00
commit 91ad25aca9
1012 changed files with 159314 additions and 0 deletions
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+ function [im_out,range]=imagesc_tomo( varargin )    
+    % Function [im_out]=imagesc_tomo( varargin )
+    % Parameters: 
+    %   data - 3D array to be shown 
+    %   colormap - name of standard matlab colormap, default = bone 
+    %   clim - range of the colorbar, default is [] (auto range)
+    %   axis - cell of strings with axis parameters, eg. {'image', 'off'}
+
+    import math.sp_quantile
+    import plotting.imagesc3D
+    
+
+    par = inputParser;
+    par.addOptional('data', [])
+    par.addParameter('colormap',  'bone' )
+    par.addParameter('clim',  [] , @isnumeric )
+    par.addParameter('axis',  {'image', 'off'}, @iscell)
+    par.addParameter('colorbar',false, @islogical)
+
+    par.parse(varargin{:})
+    r = par.Results;
+    data = r.data;
+    
+    if ismatrix(data) 
+       imagesc3D(data);
+       return
+    end
+        
+    Npix = size(data);
+    cntr = ceil(Npix/2);
+        
+    if isa(data, 'gpuArray')
+        data = gather(data); % download data from GPU 
+    end
+    
+    if isempty(r.clim)
+        range = sp_quantile(data, [1e-3, 1-1e-3], max(1, ceil(sqrt(numel(data))/1e3)));
+    else
+        range = r.clim;
+    end
+    %disp('range:')
+    %disp(range)
+    
+    colormap(r.colormap)
+           
+    args = {'show_play_button', false, 'show_edit_box', false };
+    
+    ax(1) = subplot(2,3,1);
+    imagesc3D(rot90(permute(data, [2,3,1]),1), 'init_frame', cntr(1), 'slider_position',slider_pos(ax(1)),  args{:}); 
+    axis(r.axis{:});
+    if isreal(data) && range(1) < range(2); caxis(range); end
+    if r.colorbar; colorbar; end
+    title('Centralslice xz');
+    ax(2) = subplot(2,3,2);
+    imagesc3D(rot90(permute(data, [1,3,2]),1), 'init_frame', cntr(2),'slider_position',slider_pos(ax(2)), args{:});
+    axis(r.axis{:});
+    if isreal(data) && range(1) < range(2); caxis(range); end
+    if r.colorbar; colorbar; end
+    title('Centralslice yz');
+    ax(3) = subplot(2,3,3);
+    imagesc3D(data, 'init_frame', cntr(3),'slider_position',slider_pos(ax(3)), args{:});
+    axis(r.axis{:});
+    if isreal(data) && range(1) < range(2); caxis(range); end
+    if r.colorbar; colorbar; end
+    title('Centralslice xy');
+    ax(4) = subplot(2,3,4);
+    imagesc3D(rot90(squeeze(sum(data,1)),1));
+    axis(r.axis{:});
+    title('Projection xz');
+    if r.colorbar; colorbar; end
+    ax(5) = subplot(2,3,5);
+    imagesc3D(rot90(squeeze(sum(data,2)),1));
+    axis(r.axis{:});
+    title('Projection yz');
+    if r.colorbar; colorbar; end
+    ax(6) = subplot(2,3,6);
+    imagesc3D(squeeze(sum(data,3)));
+    axis(r.axis{:});
+    title('Projection xy');
+    if r.colorbar; colorbar; end
+    
+    % link together axis from the projections and the slices 
+    linkaxes(ax([1,4]), 'xy')       
+    linkaxes(ax([2,5]), 'xy')
+    linkaxes(ax([3,6]), 'xy')
+    
+    if nargout > 0
+       im_out = ax; 
+    end
+
+end
+
+function slider_default = slider_pos(ax)
+    pos = ax.Position;
+    slider_default = [pos(1)+pos(3)/2-0.095 pos(2)-0.045 0.2 0.04];
+end
+
+