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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

The colours of the graphics may be controlled with the calc_colours function. This applies to output of the show_fem and show_slices and other functions that work using the matlab graphics engine.
% Show EIDORS colours $Id: eidors_vars01.m 3273 2012-06-30 18:00:35Z aadler $

imdl= mk_common_model('a2c2',16);
img= mk_image(imdl.fwd_model,0);
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_convert  eidors_vars01a.png '-density 50'


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 2757 2011-07-14 15:56:06Z bgrychtol $

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_convert eidors_vars02a.png '-density 100'


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 2757 2011-07-14 15:56:06Z bgrychtol $

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_convert eidors_vars03a.png '-density 20'

calc_colours('greylev',.2); % grey background level
show_slices(img);
print_convert eidors_vars03b.png '-density 20'

calc_colours('greylev',-.2); %light grey background level
show_slices(img);
print_convert eidors_vars03c.png '-density 20'

calc_colours('greylev',-.001); %white background level (default)
show_slices(img);
print_convert eidors_vars03d.png '-density 20'


calc_colours('backgnd',[0.2,0.1,0.15]);
show_slices(img);
calc_colours('backgnd',[0.5,0.5,0.15]); %default value
print_convert eidors_vars03e.png '-density 20'
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

The default EIDORS behaviour is to auto range the colours, so that the full image range is displayed. This can be changed to set a strict colour limit, or to show a non linear colour break.
% Show EIDORS colours $Id: eidors_vars04.m 2757 2011-07-14 15:56:06Z bgrychtol $

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_convert eidors_vars04a.png '-density 100'


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

Last Modified: $Date: 2017-02-28 13:12:08 -0500 (Tue, 28 Feb 2017) $ by $Author: aadler $