EIDORS: Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software

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EIDORS data structures and Variables

What version am I running?

>> eidors_obj('eidors_version')
ans =
3.2

Controlling Output Images

% Show EIDORS colours $Id: eidors_vars01.m 1535 2008-07-26 15:36:27Z aadler $

imdl= mk_common_model('a2c2',16);
img= eidors_obj('image','small demo','fwd_model',imdl.fwd_model, ...
                'elem_data', zeros(1,64) );
img.elem_data(1:2)=[1,1];
img.elem_data([14,16])=[-1,-1];
img.elem_data([27,30])=.5*[1,1];
show_fem(img);

print -r50 -dpng eidors_vars01a.png

Figure: Simple EIDORS image with three contrasts to show the effect of changing the colour mapping parameters

The Calc Colours function can modify these values:

calc_colours( 'param', value );
The following parameters are accepted

• 'greylev' (DEFAULT -.01): the colour of the ref_level.
  Negative values indicate black (inversed colour). For almost white, greylev=.01; Black=> greylev=-.01
• 'sat_adj' (DEFAULT .9): max G,B when R=1
• 'window_range' (DEFAULT .9); window colour range Colour slope outside range is 1/3 of centre slope
• 'backgnd' ( DEFAULT [.5,.5,.15] ): image border colour
• 'ref_level' (DEFAULT 'auto') conductivity of centre of colour mapping. 'auto' tries to estimate a good level.
• 'mapped_colour' (DEFAULT 127) number of colourmap entries using mapped_colour allows matlab to print vector graphics to eps
• 'npoints' (DEFAULT 64) number of points accross the image

Image Output Resolution

% Show EIDORS colours $Id: eidors_vars02.m 1535 2008-07-26 15:36:27Z aadler $

subplot(131)
calc_colours('npoints',32);
show_slices(img);

subplot(132)
calc_colours('npoints',128);
show_slices(img);

subplot(133)
calc_colours('npoints',64);
show_slices(img); %default value
print -r100 -dpng eidors_vars02a.png

Figure: Effect of changing the npoints parameter. From left: 1) npoints=32 2) npoints=128 3) npoints=64 (default)

Image Reference Colours

% Show EIDORS colours $Id: eidors_vars03.m 1535 2008-07-26 15:36:27Z aadler $

clf;
% Set square figure and make figure fill the axis
axes('position',[0 0 1 1]);
pp= get(gcf,'paperposition');
set(gcf,'paperposition',[pp(1:3),pp(3)]);

calc_colours('greylev',.001); % black background level
show_slices(img);
print -r20 -dpng eidors_vars03a.png

calc_colours('greylev',.2); % grey background level
show_slices(img);
print -r20 -dpng eidors_vars03b.png

calc_colours('greylev',-.2); %light grey background level
show_slices(img);
print -r20 -dpng eidors_vars03c.png

calc_colours('greylev',-.001); %white background level (default)
show_slices(img);
print -r20 -dpng eidors_vars03d.png


calc_colours('backgnd',[0.2,0.1,0.15]);
show_slices(img);
calc_colours('backgnd',[0.5,0.5,0.15]); %default value
print -r20 -dpng eidors_vars03e.png
set(gcf,'paperposition',pp(1:4));

Figure: Effect of changing the greylev parameter. From left: 1) greylev=0.001 2) greylev=0.2 3) greylev=-0.2 4) greylev=-0.001 (default) 5) Changing backgnd

Colour Mapping in the image

% Show EIDORS colours $Id: eidors_vars04.m 1535 2008-07-26 15:36:27Z aadler $

idx= [51:52, 56:-1:53, 57:60, 64:-1:61, 49,50]; % clockwise index elements 
img.elem_data(idx)= linspace(-2,2,16);
subplot(131)
calc_colours('clim',1.3); % Limit colours to 1,3
show_slices(img);

subplot(132)
calc_colours('clim',[]); % default
show_slices(img);

subplot(133)
img.calc_colours.clim= .3;
show_slices(img);
print -r100 -dpng eidors_vars04a.png

Figure: Effect of changing the greylev parameter. From left: 1) clim=1.3 2) clim=[] (autorange) 3) clim=0.3