Description of unit_test

UNIT_TEST_CMP: compare matrices in eidors output unit_test_cmp(txt,a,b,tol) if tol = -negative it is an expected fail if tol = -inf then expented fail with no tolerance if a==b print ok, otherwise print fail To run unit tests and keep statistics unit_test_cmp UNIT_TEST_FCN fun_name

CROSS-REFERENCE INFORMATION

eidors_msg EIDORS_MSG eidors progress and status messages

eidors_debug EIDORS_DEBUG Global managment of debug flags

unit_test_cmp UNIT_TEST_CMP: compare matrices in eidors output

freq_filt FREQ_FILT: frequency filter data

left_divide [V] = LEFT_DIVIDE(E,I,tol,pp,V);

calc_noise_params params = GREIT_noise_params(imdl, homg_voltage, sig_voltage)

np_fwd_solve NP_FWD_SOLVE: data= np_fwd_solve( fwd_model, img)

distmat DISTMAT Distance matrix for a set of points

calc_colours [colours,scl_data]= calc_colours(img, set_value, do_colourbar)

calc_slices calc_slices (img, levels, clim ) show slices at levels of an

img_point_mapper IMG_POINT_MAPPER - image values at points

level_model_slice LEVEL_MODEL_SLICE - level 3D points for slicing at z=0

mdl_slice_mapper MDL_SLICE_MAPPER: map pixels to FEM elements or nodes

eidors_readdata EIDORS readdata - read data files from various EIT equipment

eidors_saveimg EIDORS saveimg - save reconstructed image files in formats

sigmatome2_filter SIGMATOME2_FILTER: Hardware filter and stim_patterns for Sigmatome II device

calc_mesh_quality CALC_MESH_QUALITY Various measures of mesh quality.

crop_model CROP_MODEL: Crop away parts of a fem model

dm_2d_circ_pt_elecs DM_2D_CIRC_PT_ELECS: Create circle mesh (or radius 1) refined with electrodes

gmsh_mk_2d_model GMSH_MK_2D_MODEL create a 2D mesh with GMSH

gmsh_mk_fwd_model GMSH_MK_FWD_MODEL: create a fwd_model object from a Gmsh file

gmsh_read_mesh [srf,vtx,fc,bc,simp,edg,mat_ind,phys_names,entities] = gmsh_read_mesh(filename)

gmsh_write_mesh gmsh_read_mesh(mdl, [data,] outfile)

join_models JOIN_MODELS: Join two fmdl structures to create one

mat_idx_to_electrode MAT_IDX_TO_ELECTRODE: create electrodes from mat_idx values

fourier_fit FOURIER_FIT: use fourier series to interpolate onto a boundary

ng_mk_fwd_model NG_MK_FWD_MODEL: create a fwd_model object from a netgen vol file

ng_mk_geometric_models NG_MK_GEOMETRIC_MODELS: create geometric mesh models using Netgen. Body

ng_read_opt NG_READ_OPT Read Netgen's ng.opt

ng_write_opt NG_WRITE_OPT Write an ng.opt file in current directory

order_loop ORDER_LOOP Order a list of points on a loop

GREIT3D_distribution GREIT3D_distribution: create target distributions for 3D GREIT

add_noise ADD_NOISE: Add a given SNR to EIDORS data

analytic_2d_circle V = analytic_2d_circle(J, [s_h, s_i, b, a, angl])

calc_elem_current calc_elem_current: calculate current vector in each FEM element

calc_model_reduction calc_model_reduction: calculate the fields for a reduced model

convhulln_clean CONVHULLN_CLEAN: run convhulln and catch errors

elec_rearrange ELEC_REARRANGE: rearrange electrodes for given pattern

elem_dim ELEM_DIM: dimension of elements in space (are elements in 2D or 3D space)

elem_select ELEM_SELECT: select element fractions inside a function

fix_model FIX_MODEL: Add useful fields to a model

get_elem_volume GET_ELEM_VOLUME: VOL = get_elem_volume(fwd_model, map_node )

interp_mesh INTERP_MESH: calculate interpolation points onto mdl elements

linear_reorder [fwd_model] = linear_reorder(fwd_model,ccw)

mdl_dim MDL_DIM: dimension of model space (are nodes in 2D or 3D space)

merge_meshes MERGE_MESHES - merges two meshes based on common nodes

mk_GREIT_model MK_GREIT_MODEL: make EIDORS inverse models using the GREIT approach

mk_analytic_c2f MK_ANALYTIC_C2F: create a mapping matrix from coarse to fine FEM

mk_approx_c2f MK_APPROX_C2F: create a mapping matrix from coarse to fine FEM

mk_c2f_circ_mapping MK_C2F_CIRC_MAPPING: create a mapping matrix from circles/spheres to FEM

mk_circ_tank MK_CIRC_TANK: make a cylindrical tank FEM geometry in 2D or 3D

mk_common_model MK_COMMON_MODEL: make common EIT models

mk_geophysics_model imdl = mk_geophysics_model(str, ne, [option])

mk_grid_c2f MK_GRID_C2F - calculate a coarse2fine mapping for grid coarse models.

mk_image MK_IMAGE: create eidors image object

mk_stim_patterns MK_STIM_PATTERNS: create an EIDORS stimulation pattern structure

mk_tet_c2f MK_TET_C2F - calculate a coarse2fine mapping for two tet-based models.

mk_tri2tet_c2f MK_TRI2TET_C2F - coarse2fine mapping between tri-based and tet-based models

mk_tri_c2f MK_TRI_C2F - calculate a coarse2fine mapping for triangle-based models.

mono2stim MONO2SIM transform monopolar stimulation into another stim pattern

num_elecs NUM_ELECS: number of electrodes attached to model

num_elems NUM_ELEMS: number of elemnts in a (fwd or inv model or image)

num_nodes NUM_NODES: number of elemnts in a (fwd or inv model or image)

point_in_tet POINT_IN_TET test for points contained in elements

uniquetol C = uniquetol(A,TOL): unique values in A using tolerance TOL.

reciprocity_idx RECIPROCITY_IDX: find indices of stim, meas pairs that are recirocal

remove_unused_nodes REMOVE_UNUSED_NODES: identify and remove unused nodes in model

simulate_movement SIMULATE_MOVEMENT simulate small conductivity perturbations

solve_RM_2Dslice SOLVE_RM_2DSLICE: cut slices out of a 3D model

stim_meas_list STIM_MEAS_LIST: mk stimulation pattern from list of electrodes

stim_pattern_geophys STIM_PATTERN_GEOPHYS: Create Geophysical Stimulation Patterns

tet_to_inequal [A,b]=tet_to_inequal(v)

uniquetol C = uniquetol(A,TOL): unique values in A using tolerance TOL.

calc_R_prior R = calc_R_prior( inv_model, varargin )

calc_RtR_prior RtR = calc_RtR_prior( inv_model )

calc_jacobian_bkgnd CALC_JACOBIAN_BKGND: calculate background image around

calc_transferimpedance CALC_TRANSFERIMPEDANCE: Calculates transfer impedance matrix

fem_1st_to_higher_order FEM_1ST_TO_HIGH_ORDER: Modify the FEM for high order FEM called as

find_boundary [srf, idx] = find_boundary(simp);

fwd_model_parameters FWD_MODEL_PARAMETERS: data= fwd_solve_1st_order( fwd_model, image)

fwd_solve_1st_order FWD_SOLVE_1ST_ORDER: data= fwd_solve_1st_order( img)

fwd_solve_2p5d_1st_order FWD_SOLVE_2P5D_1ST_ORDER: data= fwd_solve_2p5d_1st_order( img)

fwd_solve_apparent_resistivity fwd_solve_apparent_resistivity: fwd_solve output as apparent resistivity

fwd_solve_halfspace FWD_SOLVE_HALFSPACE: data = fwd_solve_halfspace(img)

fwd_solve_higher_order Solve for voltages (nodes/electrodes) for a forward model.

jacobian_adjoint JACOBIAN_ADJOINT: J= jacobian_adjoint( img )

jacobian_adjoint_2p5d_1st_order JACOBIAN_ADJOINT_2P5D: J= jacobian_adjoint_2p5d_1st_order( img )

jacobian_adjoint_higher_order Find the Jacobian associated with an image (and forward model)

jacobian_movement JACOBIAN_MOVEMENT Computes the Jacobian matrix for conductivity and

jacobian_movement_2p5d_1st_order JACOBIAN_MOVEMENT_2P5D: J = jacobian_movement_2p5d_1st_order( img )

jacobian_perturb JACOBIAN_PERTURB: J= jacobian_perturb( fwd_model, img)

system_mat_1st_order SYSTEM_MAT_1ST_ORDER: SS= system_mat_1st_order( fwd_model, img)

system_mat_2p5d_1st_order SYSTEM_MAT_2P5D_1ST_ORDER: 2.5D system matrix

system_mat_2p5d_fields SYSTEM_MAT_2P5D_FIELDS: fields (elem to nodes) fraction of system mat

system_mat_fields SYSTEM_MAT_FIELDS: fields (elem to nodes) fraction of system mat

system_mat_higher_order Assemble the total stiffness matrix : s_mat.E=At;

system_mat_instrument SYSTEM_MAT_INSTRUMENT:

update_system_mat_fields UPDATE_SYSTEM_MAT_FIELDS: fields (elem to nodes) fraction of system mat

fwd_solve FWD_SOLVE: calculate data from a fwd_model object and an image

get_img_data GET_IMG_DATA: get parameter data from eidors image object

inv_solve INV_SOLVE: calculate imag from an inv_model and data

GREIT_desired_img_FEMmesh GREIT_DESIRED_IMG_FEMmesh GREIT onto a FEM mesh

calc_TSVD_RM CALC_TSVD_RM: Calculated truncated Jacobian SVD reconstruction matrix

calc_noise_figure CALC_NOISE_FIGURE: calculate the noise amplification (NF) of an algorithm

inv_solve_cg function img= inv_solve_cg( inv_model, data1);

inv_solve_core INV_SOLVE_CORE Solver using a generic iterative algorithm

inv_solve_gn function img= inv_solve_gn( inv_model, data1);

meas_icov_rm_elecs MEAS_ICOV_RM_ELECS: remove electrodes from consideration

prior_covar PRIOR_COVAR image prior with distance-based interelement covar

prior_gaussian_HPF PRIOR_GAUSSIAN_HPF calculate image prior

prior_laplace PRIOR_LAPLACE calculate image prior

prior_laplace_old PRIOR_LAPLACE calculate image prior

test_2d_resistor Create 2D model of a cylindrical resistor

test_3d_resistor Create 3D model of a Rectangular resistor

eidors_cache EIDORS_CACHE Control eidors caching

eidors_default EIDORS_DEFAULT Default function handler.

unit_test_cmp UNIT_TEST_CMP: compare matrices in eidors output

vectorize_inverse vectorize_inverse: fast computation of 3x3 and 4x4 inverses

SOURCE CODE

0001 function res = unit_test_cmp(txt,a,b,tol)
0002 % UNIT_TEST_CMP: compare matrices in eidors output
0003 % unit_test_cmp(txt,a,b,tol)
0004 % if tol = -negative it is an expected fail
0005 % if tol = -inf then expented fail with no tolerance
0006 % if a==b print ok, otherwise print fail
0007 %
0008 % To run unit tests and keep statistics
0009 %   unit_test_cmp UNIT_TEST_FCN fun_name
0010 
0011 % License GPL v2 or v3: $Id: unit_test_cmp.m 6501 2022-12-30 14:22:04Z aadler $
0012 
0013 persistent ntotal;
0014 persistent test_start_time;
0015 persistent npass;
0016 if strcmp(txt,'RESET_COUNTER');
0017     ntotal=0; npass=0; test_start_time=cputime(); return;
0018 end
0019 if strcmp(txt,'SHOW_COUNTER');
0020   if ntotal == 0;
0021      eidors_msg('%s: pass %d/%d (t=%6.2fs)',a, ...
0022          npass, ntotal, cputime() - test_start_time, 0 );
0023   else
0024      eidors_msg('%s: pass %d/%d = %5.1f%% (t=%6.2fs)', a, ...
0025          npass, ntotal, 100*npass/ntotal, ...
0026          cputime() - test_start_time, 0 );
0027   end
0028   return;
0029 end
0030 if strcmp(txt,'UNIT_TEST_FCN');
0031   unit_test_cmp('RESET_COUNTER');
0032   feval(a,'UNIT_TEST');
0033   unit_test_cmp( 'SHOW_COUNTER',a);
0034   return
0035 end
0036 
0037 
0038 if strcmp(txt,'UNIT_TEST'); do_unit_test; return; end
0039 
0040 
0041 if nargin < 4; tol = 0; end
0042 if tol<0;
0043    expect_fail = 1;
0044    if tol==-inf; tol= 0; end
0045 else
0046    expect_fail= 0;
0047 end
0048 tolstr='';
0049 
0050    fprintf('TEST: %20s = ',txt);
0051    ok='Fail';
0052    if (isnumeric(a) || islogical(a)) && ...
0053       (isnumeric(b) || islogical(b))
0054       sza = size(a); szb= size(b);
0055       eqsz= isequal( size(a), size(b));
0056       sza1 = all(sza==1); szb1 = all(szb==1);
0057       if ~eqsz && ~sza1 && ~szb1
0058          ok='Fail (size change)';
0059       elseif any(isnan(a(:)) ~= isnan(b(:)))
0060              ok='Fail (NaNs change)';
0061       else
0062          rel_err = full(max(abs(double(a(:))-double(b(:)))));
0063          if rel_err <= tol;
0064             ok='OK';
0065          end
0066 
0067          if abs(rel_err)>0
0068             tolstr= sprintf('(%1.3f x tol)', rel_err/tol); 
0069          end
0070       end
0071    else
0072       if strcmp(eidors_var_id(a), eidors_var_id(b)); ok='OK';end
0073    end
0074 
0075    if expect_fail
0076       ok = 'OK (fail as expected)';
0077    end
0078 
0079    fprintf('%4s %s\n', ok, tolstr);
0080    if strcmp(ok(1:2),'OK');
0081       npass= npass+1;
0082    else
0083       if eidors_debug('query','unit_test_cmp:fail')
0084           keyboard % uncomment to debug
0085       end
0086    end
0087    ntotal= ntotal+1;
0088    
0089    if nargout>0
0090        res = strcmp(ok(1:2),'OK');
0091    end
0092 
0093 function do_unit_test
0094    unit_test_cmp('Expect OK'  ,3,3);
0095 
0096    unit_test_cmp('Expect Fail',1,1.01, -inf);
0097    unit_test_cmp('Expect OK'  ,1,.99,.02);
0098    unit_test_cmp('Expect Fail',1,.99,-.002);
0099 
0100    a= rand(10); b = a;
0101    unit_test_cmp('Expect OK'  ,a,b);
0102    unit_test_cmp('Expect Fail',a,b+.001, -inf);
0103    unit_test_cmp('Expect OK  ',a,b+.001, .002);
0104 
0105    a(1,1) = NaN; b=a;
0106    unit_test_cmp('Expect OK'  ,a,b);
0107    unit_test_cmp('Expect Fail',a,b+.001, -inf);
0108    unit_test_cmp('Expect OK  ',a,b+.001, .002);
0109 
0110    unit_test_cmp('Expect Fail',a,'boo', -inf);
0111    unit_test_cmp('Expect OK','boo','boo');
0112 
0113    t.a= a; s.a=b;
0114    unit_test_cmp('Expect OK'  ,t,s);
0115    s2.b= b; 
0116    unit_test_cmp('Expect Fail'  ,t,s2, -inf);
0117 
0118    unit_test_cmp('Expect Fail', ones(3,3), ones(3,3,3), -inf);
0119    unit_test_cmp('Expect Fail', ones(3,1), ones(1,3), -inf);
0120    unit_test_cmp('Expect OK'  ,3,[3,3,3,3]);
0121    unit_test_cmp('Expect OK'  ,3,[3,3,3,3]);

unit_test_cmp

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE