EIDORS: Electrical Impedance Tomography and Diffuse Optical Tomography Reconstruction Software

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Using new ng_mk_geometric_models interface

Here are some examples of the varity of models which can be generated using the function: ng_mk_geometric_models.

1: Simple 3D cylinder. Radius = 1 with no electrodes

body_geometry.cylinder = struct;
fmdl = ng_mk_geometric_models(body_geometry);

2: Simple 3D cylinder. Radius = 1 with 16 spherical electrodes.

body_geometry.cylinder = struct;
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.sphere.center = [cos(theta(i)) sin(theta(i)) 0.5];
    electrode_geometry{i}.sphere.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

3: Simple 3D cylinder. Radius = 1 with 16 cylindrical electrodes.

body_geometry.cylinder = struct;
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

4: 3D Cylinder with electrodes which stick out of body

body_geometry.cylinder = struct;
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
    electrode_geometry{i}.keep_material_flag = 1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

5: 3D Cylinder with electrodes which stick out of body

body_geometry.cylinder = struct;
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
    electrode_geometry{i}.enter_body_flag = 1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

6: 3D Cylinder with electrodes which stick out of body

body_geometry.cylinder = struct;
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
    electrode_geometry{i}.keep_material_flag = 1;
    electrode_geometry{i}.enter_body_flag = 1;                
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

7: 3D Cylinder and sphere with electrodes

body_geometry.cylinder = struct;
body_geometry.sphere.center = [0 0 1];
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

8: 3D Cylinder and sphere with electrodes

body_geometry.cylinder  = struct;
body_geometry.sphere(1) = struct;  
body_geometry.sphere(2).center = [0 0 1];         
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);   

9: 3D Cylinder with inner cylinder

body_geometry.intersection.cylinder(1) = struct;
body_geometry.intersection.cylinder(2).radius     = 0.5;
body_geometry.intersection.cylinder(2).complement_flag = 1;   
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

10: 3D Cylinder and sphere with inner objects

body_geometry.intersection(1).sphere(1).radius     = 0.5;
body_geometry.intersection(1).sphere(1).center     = [0 0 2];
body_geometry.intersection(1).sphere(1).complement_flag = 1;
body_geometry.intersection(1).sphere(2).center     = [0 0 2];
body_geometry.intersection(2).cylinder(1).top_center = [0 0 2];
body_geometry.intersection(2).cylinder(2).radius     = 0.5;
body_geometry.intersection(2).cylinder(2).top_center = [0 0 2];
body_geometry.intersection(2).cylinder(2).complement_flag = 1;   
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

11: 3D Cylinder and sphere with inner objects

body_geometry.intersection.union(1).sphere.radius = 0.5;
body_geometry.intersection.union(1).sphere.center = [0 0 2];
body_geometry.intersection.union(1).cylinder.radius = 0.5;
body_geometry.intersection.union(1).cylinder.top_center = [0 0 2];
body_geometry.intersection.union(1).complement_flag = 1;
body_geometry.intersection.union(2).sphere.center = [0 0 2];
body_geometry.intersection.union(2).cylinder.top_center = [0 0 2]; 
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

12: 3D Cone with electrodes

body_geometry.cone = struct; 
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [0.85*cos(theta(i)) 0.85*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.65*cos(theta(i)) 0.65*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

13: 3D Cone with electrodes

body_geometry.cone = struct; 
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.sphere.center = [0.75*cos(theta(i)) 0.75*sin(theta(i)) 0.5];
    electrode_geometry{i}.sphere.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

14: 3D Cones and cylinders with electrodes

body_geometry.cone(1).top_center = [0 0 1.5];
body_geometry.cone(1).bottom_center = [0 0 0.5];
body_geometry.cone(2).top_center = [0 0 -1.5];
body_geometry.cone(2).bottom_center = [0 0 -0.5];
body_geometry.cylinder.top_center    = [0, 0, 0.5];
body_geometry.cylinder.bottom_center = [0, 0, -0.5];
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.sphere.center = [0.75*cos(theta(i)) 0.75*sin(theta(i)) 1.0];
    electrode_geometry{i}.sphere.radius = 0.1;
    electrode_geometry{i + n_elect}.sphere.center = [cos(theta(i)) sin(theta(i)) 0];
    electrode_geometry{i + n_elect}.sphere.radius = 0.15;
    electrode_geometry{i + 2*n_elect}.sphere.center = [0.75*cos(theta(i)) 0.75*sin(theta(i)) -1.0];
    electrode_geometry{i + 2*n_elect}.sphere.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

15: 3D Cube

body_geometry.ortho_brick = struct;
fmdl = ng_mk_geometric_models(body_geometry);

16: 3D Cube with holes

body_geometry.intersection.ortho_brick.opposite_corner_a = [0 0 0];
body_geometry.intersection.ortho_brick.opposite_corner_b = [5 5 4];
for i = 1:4; 
    for j = 1:4; 
        body_geometry.intersection.cylinder(i,j).radius = 0.15;
        body_geometry.intersection.cylinder(i,j).top_center = [i, j, 4];
        body_geometry.intersection.cylinder(i,j).bottom_center = [i, j, 2];
        body_geometry.intersection.cylinder(i,j).complement_flag = 1;
    end; 
end;
fmdl = ng_mk_geometric_models(body_geometry);    

17: 3D Cube with holes and electrodes

body_geometry.intersection.ortho_brick.opposite_corner_a = [0 0 0];
body_geometry.intersection.ortho_brick.opposite_corner_a = [0 0 0];
body_geometry.intersection.ortho_brick.opposite_corner_b = [5 5 4];
for i = 1:4; 
    for j = 1:4; 
        body_geometry.intersection.cylinder(i, j).radius = 0.15;
        body_geometry.intersection.cylinder(i, j).top_center    = [i, j, 4];
        body_geometry.intersection.cylinder(i, j).bottom_center = [i, j, 2];
        body_geometry.intersection.cylinder(i, j).complement_flag = 1;
        electrode_geometry{i, j, 1}.cylinder.radius        = 0.2;
        electrode_geometry{i, j, 1}.cylinder.top_center    = [i, j, 3.1];
        electrode_geometry{i, j, 1}.cylinder.bottom_center = [i, j, 2.9];
        electrode_geometry{i, j, 2}.cylinder.radius        = 0.2;
        electrode_geometry{i, j, 2}.cylinder.top_center    = [i, j, 2.2];
        electrode_geometry{i, j, 2}.cylinder.bottom_center = [i, j, 2.0];
    end; 
end;
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

18: 3D Cube with max_edge_length

body_geometry.parallelepiped  = struct;
body_geometry.max_edge_length = 0.15;
fmdl = ng_mk_geometric_models(body_geometry);

19: 3D Parallelepiped

body_geometry.parallelepiped.vertex   = [ 0;  0;  0];
body_geometry.parallelepiped.vector_a = [ 1;  1;  0];
body_geometry.parallelepiped.vector_b = [ 0;  1;  1];
body_geometry.parallelepiped.vector_c = [ 1;  0;  1];
body_geometry.max_edge_length = 0.15;
fmdl = ng_mk_geometric_models(body_geometry);

20: 3D Wedge

body_geometry.intersection.ortho_brick.opposite_corner_a = [-15, -15, 0];
body_geometry.intersection.ortho_brick.opposite_corner_b = [15, 15, 5];
body_geometry.intersection.half_space.point = [0, 0, 5];
body_geometry.intersection.half_space.outward_normal_vector = [-1, -1, 5];

fmdl = ng_mk_geometric_models(body_geometry);

21: ellipsoid

body_geometry.ellipsoid.axis_a = [1 0 0];
body_geometry.ellipsoid.axis_b = [0 2 0];
body_geometry.ellipsoid.axis_c = [0 0 3];
fmdl = ng_mk_geometric_models(body_geometry);   

22: ellipsoid

body_geometry.ellipsoid.axis_a = [1 0 0];
body_geometry.ellipsoid.axis_b = [0 1 1];
body_geometry.ellipsoid.axis_c = [0 -2 2];
fmdl = ng_mk_geometric_models(body_geometry);   

23: cropped cylinder

body_geometry.elliptic_cylinder.top_center = [0, 0, 10];
body_geometry.elliptic_cylinder.bottom_center = [0, 0, 0];           
body_geometry.elliptic_cylinder.axis_a = [1 0 0];
body_geometry.elliptic_cylinder.axis_b = [0 2 0];  
fmdl = ng_mk_geometric_models(body_geometry);

24: cropped cylinder

body_geometry.elliptic_cylinder.top_center = [0, 5, 5];
body_geometry.elliptic_cylinder.bottom_center = [0, 0, 0];           
body_geometry.elliptic_cylinder.axis_a = [1 0 0];
body_geometry.elliptic_cylinder.axis_b = [0 -2 2];  
fmdl = ng_mk_geometric_models(body_geometry);

25: cylinder with hole

body_geometry.body_of_revolution = struct;
body_geometry.max_edge_length = 0.15;
fmdl = ng_mk_geometric_models(body_geometry);

26: cone with hole

body_geometry.body_of_revolution.points   = [1 1; 1 2; 2 1.5; 2 1];
body_geometry.body_of_revolution.segments = [1 2; 2 3; 3 4; 4 1];
body_geometry.max_edge_length = 0.15;
fmdl = ng_mk_geometric_models(body_geometry);

27: torus

n_points = 24;
theta = linspace(0, 2*pi, n_points+1)'; theta(end) = [];
body_geometry.body_of_revolution.points   = 2 + [sin(theta) cos(theta)];
body_geometry.body_of_revolution.segments = [(1:n_points)' [(2:n_points) 1]'];
body_geometry.max_edge_length = 0.15;
fmdl = ng_mk_geometric_models(body_geometry);

28: torus

n_points = 24;
theta = linspace(0, 2*pi, n_points+1)'; theta(end) = [];
body_geometry.body_of_revolution.points   = 2 + [sin(theta) cos(theta)];
body_geometry.body_of_revolution.segments = [(1:2:n_points)' (2:2:n_points)' [(3:2:n_points) 1]'];
body_geometry.max_edge_length = 0.15;
fmdl = ng_mk_geometric_models(body_geometry);

29: Cylinder with electrodes

body_geometry{1}.cylinder(1).radius        = 0.5;
body_geometry{1}.cylinder(1).top_center    = [0 0 0.75];
body_geometry{1}.cylinder(1).bottom_center = [0 0 0.25];
body_geometry{1}.name                      = 'Object';           
body_geometry{2}.cylinder(2).radius        = 1;
body_geometry{2}.name                      = 'Tank';
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.cylinder.top_center    = [1.03*cos(theta(i)) 1.03*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.bottom_center = [0.97*cos(theta(i)) 0.97*sin(theta(i)) 0.5];
    electrode_geometry{i}.cylinder.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

30: Cylinder with ball

body_geometry{1}.sphere.radius     = 0.25;
body_geometry{1}.sphere.center     = [0 0 0.5];
body_geometry{1}.name              = 'Sphere';
body_geometry{2}.cylinder.radius   = 1;
body_geometry{2}.name              = 'Tank';           
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.sphere.center = [cos(theta(i)) sin(theta(i)) 0.5];
    electrode_geometry{i}.sphere.radius = 0.1;
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

31: Cylinder with many ball

n_sphere = 8;
theta = linspace(0, 2*pi, n_sphere+1); theta(end) = [];   
for i = 1:n_sphere
    body_geometry{i}.sphere.radius   = 0.2;
    body_geometry{i}.sphere.center   = [0.65*cos(theta(i)) 0.65*sin(theta(i)) 0.5];  
    body_geometry{i}.max_edge_length = 0.025*(1 + rem(i,2));
    body_geometry{i}.name            = sprintf('Sphere%d', i);  
end        
body_geometry{n_sphere+1}.cylinder.radius = 1;
body_geometry{n_sphere+1}.name            = 'Tank';  
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.sphere.center = [cos(theta(i)) sin(theta(i)) 0.5];
    electrode_geometry{i}.sphere.radius = 0.1;
    electrode_geometry{i}.max_edge_length = 0.025*(1 + rem(i,2));
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

32: Cylinder with point electrodes

body_geometry.cylinder = struct;
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    electrode_geometry{i}.point = [cos(theta(i)) sin(theta(i)) 0.5];
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

33: Cylinder with point and round electrodes

body_geometry.cylinder = struct;
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect
    if (rem(i,2))
        electrode_geometry{i}.point = [cos(theta(i)) sin(theta(i)) 0.5];
        electrode_geometry{i}.name  = sprintf('Point_Electrode%d', ceil(i/2));
    else
        electrode_geometry{i}.sphere.center = [cos(theta(i)) sin(theta(i)) 0.5];
        electrode_geometry{i}.sphere.radius = 0.1;
        electrode_geometry{i}.name          = sprintf('Circular_Electrode%d', floor(i/2));
    end
end
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);

34: Extrusion

body_geometry.body_of_extrusion = struct;
body_geometry.max_edge_length = 0.15;
fmdl = ng_mk_geometric_models(body_geometry);

35: Extrusion

body_geometry.body_of_extrusion.path_points   = [0 0 0; 0.25 0 1; 0.25 0 2; 0.25 0 3; 0 0 4];
body_geometry.body_of_extrusion.path_segments = [1 2; 2 3; 3 4; 4 5];
body_geometry.max_edge_length = 0.15;
fmdl = ng_mk_geometric_models(body_geometry);

36: Extruded torus

n_points = 16;
theta = linspace(0, 2*pi, n_points+1)'; theta(end) = [];
body_geometry.body_of_extrusion.profile_points   = 0.2*(2 + [0.75*sin(theta) cos(theta)]);
body_geometry.body_of_extrusion.profile_segments = [(1:n_points)' [(2:n_points) 1]'];
n_points = 32;
theta = linspace(0, 2*pi, n_points+1)'; theta(end) = [];          
body_geometry.body_of_extrusion.path_points   = 1*(2 + [sin(theta) 1.5*cos(theta) zeros(n_points, 1)]);
body_geometry.body_of_extrusion.path_segments = [(1:n_points)' [(2:n_points) 1]'];
body_geometry.body_of_extrusion.vector_d      = [0; 0; 1];
body_geometry.max_edge_length = 0.15;
fmdl = ng_mk_geometric_models(body_geometry); 

37: Lots of electrodes

body_geometry.ortho_brick.opposite_corner_a = [0 0 0];
body_geometry.ortho_brick.opposite_corner_b = [5 5 4];
body_geometry.max_edge_length = 3;
electrode_geometry{1}.sphere.center = [4,4,0];
electrode_geometry{1}.sphere.radius = [0.3];
electrode_geometry{2}.sphere.center = [4,0,2];
electrode_geometry{2}.sphere.radius = [0.2];
electrode_geometry{3}.ortho_brick.opposite_corner_a = [3,4,-.1];
electrode_geometry{3}.ortho_brick.opposite_corner_b = [2,2,.1];
electrode_geometry{3}.max_edge_length = .1;
electrode_geometry{4}.ortho_brick.opposite_corner_b = [3,5.1,2.5];
electrode_geometry{4}.ortho_brick.opposite_corner_a = [2,4.9,2];

fmdl = ng_mk_geometric_models(body_geometry,electrode_geometry);

38: Inclusion in an object

body_geometry{1}.cylinder.radius = 1.0; % main body 
body_geometry{2}.sphere.radius = 0.2;   % inclusion
body_geometry{2}.sphere.center = [0.2,0.2,0.2];
n_elect = 16;
theta = linspace(0, 2*pi, n_elect+1); theta(end) = [];
for i = 1:n_elect; thi= theta(i);
    electrode_geometry{i}.sphere.center = [cos(thi),sin(thi),0.5];
    electrode_geometry{i}.sphere.radius = 0.1;
end
electrode_geometry{i+1}.sphere.radius = 0.2;
electrode_geometry{i+1}.sphere.center = [0.4,0.2,1.0];
electrode_geometry{i+2}.sphere.radius = 0.2;
electrode_geometry{i+2}.sphere.center = [-0.4,-0.4,0.0];
fmdl = ng_mk_geometric_models(body_geometry, electrode_geometry);
img = mk_image(fmdl,1);
img.elem_data(fmdl.mat_idx{2}) = 1.1;