Description of eidors

DESCRIPTION

EIDORS_MSG: eidors progress and status messages

 USAGE: eidors_msg('mission accomplished; time to relax', 1)
   prints 'EIDORS:[ mission accomplished; time to relax ]'
       if log_level <=1
   less important messages have higher levels

 other parameters will be sent to print; example
 eidors_msg('did %d of %s at %f', 2, 'stuff', sqrt(2), 1)
   prints 'EIDORS:[ did 2 of stuff at 1.414214 ]'

 if the message starts with '@@@' then the character
   is replaced with the calling function name

 USAGE: eidors_msg( 'log_level', 1)
   sets the loglevel to 1
 USAGE: eidors_msg( 'log_level')
   return the current log_level

 meanings of levels
   0 => keep quiet (no messages should be level=0)
   1 => important messages
   2 => most messages
   3 => detailed information

 Messages at log_level are displayed

CROSS-REFERENCE INFORMATION

eidors_msg EIDORS_MSG: eidors progress and status messages

eidors_obj EIDORS_OBJ: 'constructor' to create a eidors structure

eval_GREIT_fig_merit EVAL_GREIT_FIG_MERIT: calculate GREIT figures of merit for images

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

ab_tv_lagged_diff AB_TV_LAGGED_DIFF Lagged Diffusivity Inverse Solver

calc_noise_params params = GREIT_noise_params(imdl, homg_voltage, sig_voltage)

edge_refined_elem_mapper EDGE_REFINED_ELEM_MAPPER: map elements from coarse to dense model

edge_refined_node_mapper EDGE_REFINED_NODE_MAPPER:

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

np_calc_image_prior NP_CALC_IMAGE_PRIOR calculate image prior

np_calc_system_mat NP_CALC_SYSTEM_MAT: s_mat= np_calc_system_mat( fwd_model, img)

np_fwd_parameters NP_FWD_PARAMETERS: data= np_fwd_solve( fwd_model )

np_inv_solve NP_INV_SOLVE inverse solver for Nick Polydorides EIDORS3D code

eidors_msg EIDORS_MSG: eidors progress and status messages

eidors_startup Script to start EIDORS

demo_real [inhomg_img, demo_img] = demo_real;

moving_tank_objs MOVING_TANK_OBJS: create movies of objects moving in tanks

resistor_model DEMO to show really simple application of EIDORS framework

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

crop_model CROP_MODEL: Crop away parts of a fem model

image_levels IMAGE_LEVELS(img, levels, clim ) show slices at levels of an image

mdl_slice_mapper MDL_SLICE_MAPPER: map pixels to FEM elements or nodes

mdl_slice_mesher MDL_SLICE_MESHER A slice of a 3D FEM as a 2D FEM

print_convert PRINT_CONVERT: print figures and trim them

show_fem SHOW_FEM: show the EIDORS3D finite element model

show_slices out_img = show_slices (img, levels ) show slices at levels of an

eidors_readdata EIDORS readdata - read data files from various EIT equipment

distmeshnd DISTMESHND N-D Mesh Generator using Distance Functions.

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

call_netgen CALL_NETGEN: call netgen to create a vol_file from a geo_file

ng_mk_cyl_models NG_MAKE_CYL_MODELS: create cylindrical models using netgen

ng_mk_gen_models NG_MAKE_ELLIP_MODELS: create elliptical models using netgen

ng_read_mesh [srf,vtx,fc,bc,simp,edg,mat_ind] = ng_read_mesh(filename)

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

mdl_normalize MDL_NORMALIZE Check or set the normalize_measurements flag on a model.

mk_GREIT_model MK_GREIT_MODEL: make EIDORS inverse models using the GREIT approach

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

mk_coarse_fine_mapping MK_COARSE_FINE_MAPPING: create a mapping matrix from coarse to fine FEM

mk_library_model MK_LIBRARY_MODEL - FEM models based on library shapes

physics_data_mapper PHYSICS_DATA_MAPPER maps img.physics data to elem or node data

place_elec_on_surf PLACE_ELEC_ON_SURF Place electrodes on the surface of a model

select_imdl SELECT_IMDL: select pre-packaged inverse model features

shape_library SHAPE_LIBRARY Common shapes for models

simulate_2d_movement SIMULATE_2D_MOVEMENT simulate rotational movement in 2D

simulate_3d_movement SIMULATE_3D_MOVEMENT simulate rotational movement in 3D

calc_JiRtRJt [JiRtRJt,iRtRJt] = calc_JiRtRJt( inv_model, varargin )

calc_R_prior R = calc_R_prior( inv_model, varargin )

calc_RtR_prior RtR = calc_RtR_prior( inv_model )

calc_hyperparameter CALC_HYPERPARAMETER: calculate hyperparameter value

calc_jacobian CALC_JACOBIAN: calculate jacobian from an inv_model

calc_jacobian_bkgnd CALC_JACOBIAN_BKGND: calculate background image around

calc_meas_icov meas_icov = calc_meas_icov( inv_model )

calc_system_mat CALC_SYSTEM_MAT: calculate FEM system matrix from fwd_model and image

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)

jacobian_movement JACOBIAN_MOVEMENT Computes the Jacobian matrix for conductivity and

system_mat_fields 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

inv_solve INV_SOLVE: calculate imag from an inv_model and data

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

choose_noise_figure CHOOSE_NOISE_FIGURE: choose hyperparameter based on NF calculation

inv_solve_TV_irls INV_SOLVE_TV_IRLS Iteratively Reweighted Least Squares inverse solver

inv_solve_abs_GN INV_SOLVE_ABS_GN Absolute solver using Gauss Newton approximation

inv_solve_backproj INV_SOLVE_BACKPROJ inverse solver using backprojection

inv_solve_diff_GN_one_step INV_SOLVE_DIFF_GN_ONE_STEP inverse solver using approach of Adler&Guardo 1996

inv_solve_diff_kalman INV_SOLVE_DIFF_KALMAN inverse solver for difference EIT

inv_solve_time_prior INV_SOLVE_TIME_PRIOR inverse solver to account for time differences

inv_solve_trunc_iterative INV_SOLVE_TRUNC_ITERATIVE using Morozov truncated iteration

nodal_solve NODAL_SOLVE inverse solver using approach of Adler&Guardo 1996

primaldual_tvrecon_lsearch [rs,x]=primaldual_tvrecon_lsearch(inv_mdl, vmeas, ...

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

calc_jacobian_test Verify Jacobian Calculation by small derivative from forward problem

demo_real_test Perform tests based on the demo_real function

demo_real_test2 Perform tests based on the demo_real function with new structs

demo_real_test3 Perform tests based on the demo_real function with new structs

tutorials_test TUTORIAL_TEST: Run all tutorials

eidors_cache EIDORS_CACHE Control eidors caching

SOURCE CODE

0001 function log_level= eidors_msg( message, varargin )
0002 %EIDORS_MSG: eidors progress and status messages
0003 %
0004 % USAGE: eidors_msg('mission accomplished; time to relax', 1)
0005 %   prints 'EIDORS:[ mission accomplished; time to relax ]'
0006 %       if log_level <=1
0007 %   less important messages have higher levels
0008 %
0009 % other parameters will be sent to print; example
0010 % eidors_msg('did %d of %s at %f', 2, 'stuff', sqrt(2), 1)
0011 %   prints 'EIDORS:[ did 2 of stuff at 1.414214 ]'
0012 %
0013 % if the message starts with '@@@' then the character
0014 %   is replaced with the calling function name
0015 %
0016 % USAGE: eidors_msg( 'log_level', 1)
0017 %   sets the loglevel to 1
0018 % USAGE: eidors_msg( 'log_level')
0019 %   return the current log_level
0020 %
0021 % meanings of levels
0022 %   0 => keep quiet (no messages should be level=0)
0023 %   1 => important messages
0024 %   2 => most messages
0025 %   3 => detailed information
0026 %
0027 % Messages at log_level are displayed
0028 
0029 % (C) 2005 Andy Adler. License: GPL version 2 or version 3
0030 % $Id: eidors_msg.m 3361 2012-07-01 21:53:37Z bgrychtol $
0031 
0032 if isstr(message) && strcmp(message,'UNIT_TEST'); do_unit_test; return; end
0033 
0034 global eidors_objects
0035 
0036 if nargin==1
0037    args= {};
0038    level= 2;
0039 else
0040    level= varargin{ nargin-1 };
0041    args= varargin( 1:nargin-2 );
0042 end
0043 
0044 [log_level] = get_levels;
0045 
0046 for i= 1:length(args)
0047    if isa( args{i}, 'function_handle')
0048       args{i} = func2str(args{i});
0049    end
0050 end
0051 
0052 % It makes sense to print to stderr (fid=2), but matlab>7 prints this in red
0053 ver= eidors_obj('interpreter_version');
0054 if ver.ver>=7; fid= 1;
0055 else ;         fid= 2; end
0056 
0057 
0058 %try, lms= eidors_objects.last_message_size;
0059 %  if lms>0; fprintf(fid,'%c', 8*ones(lms,1)); end
0060 %end
0061 
0062 % deal with variables
0063 if ~ischar(message)
0064    var = inputname(1);
0065    message = [var ' = ' num2str(message)];
0066 end
0067 
0068 
0069 % Need to do twice to interpret text in message
0070 % message= sprintf(message, args{:} );
0071 if length(message)>1 % single characters are just for progress
0072    if length(message)>=3 && strcmp(message(1:3),'@@@');
0073       if length(message)==3; msg_extra = '';
0074       else                   msg_extra = [':', message(4:end)];
0075       end
0076       dbs = dbstack;
0077       message = sprintf('%s/%s%s', dbs(2).file, ...
0078             dbs(2).name, msg_extra);
0079    end
0080    string= [sprintf('%c',' ' * ones(1,level-1)), ...
0081             'EIDORS:[',message,']\n'];
0082        
0083 elseif strcmp( message, 'log_level');
0084    log_level= eidors_objects.log_level;
0085 else
0086    string= message;
0087 end
0088 
0089 if strcmp(message,'log_level')
0090    eidors_objects.log_level= level;
0091 elseif level <= log_level
0092    fprintf(fid, string, args{:});
0093    if exist('OCTAVE_VERSION'); fflush(fid); end
0094    eidors_objects.last_message_size= 0;
0095 end
0096 
0097 
0098 function [log_level] = get_levels;
0099    global eidors_objects
0100    try
0101       log_level= eidors_objects.log_level;
0102    catch
0103       log_level= 2; % default;
0104       eidors_objects.log_level= log_level;
0105    end
0106 
0107 function do_unit_test
0108    ll= eidors_msg('log_level');
0109    eidors_msg('log_level',5);
0110    eidors_msg('l1',1); eidors_msg('l2',2); eidors_msg('l3',3); eidors_msg('l4',4);
0111 
0112    eidors_msg('log_level',1);
0113    eidors_msg('l1',1); eidors_msg('l2',2); eidors_msg('l3',3); eidors_msg('l4',4);
0114 
0115 
0116    eidors_msg('@@@',1);
0117    eidors_msg('@@@ a message',1);
0118    eidors_msg('a @@@ message',1);
0119    extra_caller;
0120 
0121    eidors_msg('log_level',ll);
0122 
0123 function extra_caller
0124    eidors_msg('@@@ a message from extra_caller',1);
0125

eidors_msg

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE