EIDORS: Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software

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EIDORS display functions and control of colours

Colour Mapping in the image

Specify clim=1.5 for all subsequent display

calc_colours('clim',1.5);
show_slices( img )
% future images still use clim=1.5

Specify clim=1.5 for only this image

img.calc_colours.clim= 1.5;
show_slices( img )
% only 'img' uses clim=1.5

Create a demo image

% Show EIDORS colours $Id: eidors_colours01.m 3273 2012-06-30 18:00:35Z aadler $

% Create sample image
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];
idx= [51:52, 56:-1:53, 57:60, 64:-1:61, 49,50]; % clockwise index elements 
img.elem_data(idx)= linspace(-2,2,16);

img.elem_data = img.elem_data + 10;

Change colour mapping parameters: greylev

% Show EIDORS colours $Id: eidors_colours02.m 4855 2015-04-02 15:34:44Z aadler $
clf; subplot(221); clf;
img1= img;
img1.calc_colours.cb_shrink_move = [0.5,0.8,-.10];

clf; subplot(221);
show_fem(img1,1);
axis equal; axis off; axis tight; 
print_convert eidors_colours02a.png '-density 75'

clf; subplot(221);
img1.calc_colours.greylev= -0.35;
show_fem(img1,1);
axis equal; axis off; axis tight; 
print_convert eidors_colours02b.png '-density 75'

clf; subplot(221);
img1.calc_colours.greylev= 0.35;
show_fem(img1,1);
axis equal; axis off; axis tight; 
print_convert eidors_colours02c.png '-density 75'

Figure: greylev values of (from left to right) 1) -.001 default, 2) -.35, 3) +.35,

Change colour mapping parameters: clim

% Show EIDORS colours $Id: eidors_colours03.m 4855 2015-04-02 15:34:44Z aadler $
clf; subplot(221); img1= img;
img1.calc_colours.cb_shrink_move = [0.5,0.8,-.10];

clf; subplot(221)
show_fem(img1,1);
axis equal; axis off; axis tight;
print_convert eidors_colours03a.png '-density 75'

clf; subplot(221)
img1.calc_colours.clim= 1;
show_fem(img1,1);
axis equal; axis off; axis tight;
print_convert eidors_colours03b.png '-density 75'

clf; subplot(221)
img1.calc_colours.clim= 0.3;
show_fem(img1,1);
axis equal; axis off; axis tight;
print_convert eidors_colours03c.png '-density 75'

Figure: clim values of (from left to right) 1) [] default, 2) 1.0, 3) 0.3,

Change colour mapping parameters: sat_adj

% Show EIDORS colours $Id: eidors_colours04.m 4855 2015-04-02 15:34:44Z aadler $
clf; subplot(221); img1= img;
img1.calc_colours.cb_shrink_move = [0.5,0.8,-.10];

clf; subplot(221);
show_fem(img1,1);
axis equal; axis off; axis tight;
print_convert eidors_colours04a.png '-density 75'

clf; subplot(221);
img1.calc_colours.sat_adj= 0.99;
show_fem(img1,1);
axis equal; axis off; axis tight;
print_convert eidors_colours04b.png '-density 75'

clf; subplot(221);
img1.calc_colours.sat_adj= 0.8;
show_fem(img1,1);
axis equal; axis off; axis tight;
print_convert eidors_colours04c.png '-density 75'

Figure: sat_adj values of (from left to right) 1) 0.9 default, 2) 0.90, 3) 0.8,

Change colour mapping parameters: window_range

% Show EIDORS colours $Id: eidors_colours05.m 4855 2015-04-02 15:34:44Z aadler $
clf; subplot(221); img1= img;
img1.calc_colours.cb_shrink_move = [0.5,0.8,-.10];

clf; subplot(221);
show_fem(img1,1);
axis equal; axis off; axis tight;
print_convert eidors_colours05a.png '-density 75'

clf; subplot(221);
img1.calc_colours.window_range= 0.90;
show_fem(img1,1);
axis equal; axis off; axis tight;
print_convert eidors_colours05b.png '-density 75'

clf; subplot(221);
img1.calc_colours.window_range= 0.20;
show_fem(img1,1);
axis equal; axis off; axis tight;
print_convert eidors_colours05c.png '-density 75'

Figure: window_range values of (from left to right) 1) 0.7 default, 2) 0.9, 3) 0.2,

Colours and lung images

% Show lung images $Id: eidors_colours06.m 4855 2015-04-02 15:34:44Z aadler $
load montreal_data_1995
imdl = mk_common_model('c2t2',16);
imdl.fwd_model = mdl_normalize(imdl.fwd_model,1);
imdl.RtR_prior= @prior_gaussian_HPF;
imdl.hyperparameter.value = 0.45;
img = inv_solve(imdl, zc_resp(:,1), zc_resp(:,20));

img.calc_colours.ref_level= 0;
img.calc_colours.cb_shrink_move = [0.5,0.8,-.10];

clf; subplot(221);
show_fem(img,[1,1]);
axis equal; axis off; axis tight;

subplot(222);
img.calc_colours.ref_level =  0.1;
show_fem(img,[1,1]);
axis equal; axis off; axis tight;

print_convert eidors_colours06.png '-density 75'

Figure: Lung images with the zero level centred (left) and set to an off centre value − 0.1 (right)

% Show lung images $Id: eidors_colours07.m 4858 2015-04-02 15:34:51Z aadler $
img = inv_solve(imdl, zc_resp(:,1), zc_resp(:,20));
img.calc_colours.ref_level= 0;
img.calc_colours.cb_shrink_move = [0.5,0.8,-.10];

clf; subplot(221);
img.calc_colours.greylev = 0.01;
show_fem(img,[1,1]);
axis equal; axis off; axis tight;
print_convert eidors_colours07a.png '-density 75'

clf; subplot(221);
img.calc_colours.greylev =  0.3;
show_fem(img,[1,1]);
axis equal; axis off; axis tight;
print_convert eidors_colours07b.png '-density 75'

clf; subplot(221);
img.calc_colours.greylev = -0.01;
show_fem(img,[1,1]);
axis equal; axis off; axis tight;
print_convert eidors_colours07c.png '-density 75'

clf; subplot(221);
img.calc_colours.cmap_type = 'draeger';
show_fem(img,[1,1]);
axis equal; axis off; axis tight;
print_convert eidors_colours07d.png '-density 75'

Figure: Lung images with various colour maps. From left to right: centre-black, centre-grey, centre-white, and the Amato/Dräger Colourmap. set to an off centre value − 0.1 (right)