Description of fwd

DESCRIPTION

 FWD_SOLVE: calculate data from a fwd_model object and an image
 
 fwd_solve can be called as
    data= fwd_solve( img)
 or (deprecated)
    data= fwd_solve( fwd_model, img)

 in each case it will call the fwd_model.solve
                        or img.fwd_model.solve method

 For reconstructions on dual meshes, the interpolation matrix
    is defined as fwd_model.coarse2fine. If required, this takes
    coarse2fine * x_coarse = x_fine

 data      is a measurement data structure
 fwd_model is a fwd_model structure
 img       is an img structure

 Options: (not available on all solvers)
    img.fwd_solve.get_all_meas = 1 (data.volt = all FEM nodes, but not CEM)
    img.fwd_solve.get_all_nodes= 1 (data.volt = all nodes, including CEM)
    img.fwd_solve.get_elec_curr= 1 (data.elec_curr = current on electrodes)

 Parameters:
    fwd_model.background = constant conductivity offset added to elem_data
    fwd_model.coarse2fine = linear mapping between img.elem_data and model parameters
    img.params_mapping = function mapping img.elem_data to model parameters

CROSS-REFERENCE INFORMATION

eidors_obj EIDORS_OBJ: maintains EIDORS internals

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

eidors_cache EIDORS_CACHE Control eidors caching

eidors_default EIDORS_DEFAULT Default function handler.

ab_tv_diff_solve AB_TV_DIFF_SOLVE inverse solver for Andrea Borsic's

calc_noise_params params = GREIT_noise_params(imdl, homg_voltage, sig_voltage)

manchester_tomography Example to show reconstructions from

np_calc_jacobian NP_CALC_JACOBIAN: J= np_calc_jacobian( fwd_model, img)

np_fwd_solve NP_FWD_SOLVE: data= np_fwd_solve( fwd_model, img)

np_inv_solve NP_INV_SOLVE inverse solver for Nick Polydorides EIDORS3D code

cheating_2d code to simulate inverse crimes in EIT

compare_2d_algs Compare different 2D reconstructions

compare_3d_algs Compare different 3D reconstructions

demo_2d_simdata Example of using EIDORS to simulate 2D data and to

demo_3d_simdata How to make simulation data using EIDORS3D

demo_real [inhomg_img, demo_img] = demo_real;

eidors2d_demo1 EidorsDemo1 Demonstrates the use of 2D EIT Package with linear basis

ex_fwd2d_high_order ensure dev/m_crabb/forward_problem is on the path

ex_fwd3d_high_order Make common model, and make an image

resistor_model DEMO to show really simple application of EIDORS framework

mdl_slice_mapper MDL_SLICE_MAPPER: map pixels to FEM elements or nodes

show_3d_slices show_3d_slices(img, z_cuts, x_cuts, y_cuts, any_cuts)

show_current SHOW_CURRENT: show current or other quantity defined

show_pseudosection SHOW_PSEUDOSECTION: show a pseudo-section image of data

sigmatome2_filter SIGMATOME2_FILTER: Hardware filter and stim_patterns for Sigmatome II device

mat_idx_to_electrode MAT_IDX_TO_ELECTRODE: create electrodes from mat_idx values

GREIT3D_distribution GREIT3D_distribution: create target distributions for 3D GREIT

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

mk_GREIT_model MK_GREIT_MODEL: make EIDORS inverse models using the GREIT approach

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

mk_grid_model MK_GRID_MODEL: Create reconstruction model on pixelated grid

simulate_2d_movement SIMULATE_2D_MOVEMENT simulate rotational movement in 2D

simulate_3d_movement SIMULATE_3D_MOVEMENT simulate rotational movement in 3D

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

test_GREIT_model

calc_meas_icov meas_icov = calc_meas_icov( inv_model )

calc_all_node_voltages CALC_ALL_NODE_VOLTAGES - calculate voltage on all nodes

calc_transferimpedance CALC_TRANSFERIMPEDANCE: Calculates transfer impedance matrix

eit_spice function spice = eit_spice(img, [name])

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_apparent_resistivity jacobian_apparent_resistivity: Jacobian output as apparent resistivity

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_movement_halfspace JACOBIAN_MOVEMENT_PERTURB: J= jacobian_movement_perturb( img )

jacobian_movement_perturb JACOBIAN_MOVEMENT_PERTURB: J= jacobian_movement_perturb( 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_fields SYSTEM_MAT_FIELDS: fields (elem to nodes) fraction of system mat

GREIT_desired_img_FEMmesh GREIT_DESIRED_IMG_FEMmesh GREIT onto a FEM mesh

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

calc_solution_error CALC_SOLUTION_ERROR Calculate residuals for a solution

inv_solve_TSVD INV_SOLVE_TSVD: inverse solver based on truncatated SVD

inv_solve_TV_pdipm INV_SOLVE_TV_PDIPM inverse solver for Andrea Borsic's

inv_solve_abs_GN_constrain Do Gauss Netwon Method with barrier to ensure positvity of the con

inv_solve_abs_GN_prior INV_SOLVE_ABS_GN_PRIOR inverse solver (WITH DIFFERENT PRIOR AT ITERATION!!!!!)

inv_solve_abs_annealingMetropolis_params INV_SOLVE_ABS_ANNEALINGSIMPLEX_PARAMS absolute solver using the simplex annealing method.

inv_solve_abs_annealingSimplex_params INV_SOLVE_ABS_ANNEALINGSIMPLEX_PARAMS absolute solver using the simplex annealing method.

inv_solve_abs_pdipm INV_SOLVE_ABS_PDIPM inverse solver for absolute data using Primal/Dual interior point method

inv_solve_cg function img= inv_solve_cg( inv_model, data1);

inv_solve_conj_grad INV_SOLVE_CONJ_GRAD inverse solver based on the CG

inv_solve_core INV_SOLVE_CORE Solver using a generic iterative algorithm

inv_solve_gn function img= inv_solve_gn( inv_model, data1);

line_optimize LINE_OPTIMIZE Cheap line optimizer

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

calc_data_prior_test Verify dataprior:

calc_jacobian_test Verify Jacobian Calculation by small derivative from forward problem

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

perturb_jacobian_test Perturbation Jacobians

test_2d_resistor Create 2D model of a cylindrical resistor

test_3d_resistor Create 3D model of a Rectangular resistor

test_colour_direction Test colour mapping

test_performance TEST_PERFORMANCE: test of difference reconstruction algorithms

test_performance_img TEST_PERFORMANCE: test of difference reconstruction algorithms

SOURCE CODE

0001 function data = fwd_solve(fwd_model, img)
0002 % FWD_SOLVE: calculate data from a fwd_model object and an image
0003 %
0004 % fwd_solve can be called as
0005 %    data= fwd_solve( img)
0006 % or (deprecated)
0007 %    data= fwd_solve( fwd_model, img)
0008 %
0009 % in each case it will call the fwd_model.solve
0010 %                        or img.fwd_model.solve method
0011 %
0012 % For reconstructions on dual meshes, the interpolation matrix
0013 %    is defined as fwd_model.coarse2fine. If required, this takes
0014 %    coarse2fine * x_coarse = x_fine
0015 %
0016 % data      is a measurement data structure
0017 % fwd_model is a fwd_model structure
0018 % img       is an img structure
0019 %
0020 % Options: (not available on all solvers)
0021 %    img.fwd_solve.get_all_meas = 1 (data.volt = all FEM nodes, but not CEM)
0022 %    img.fwd_solve.get_all_nodes= 1 (data.volt = all nodes, including CEM)
0023 %    img.fwd_solve.get_elec_curr= 1 (data.elec_curr = current on electrodes)
0024 %
0025 % Parameters:
0026 %    fwd_model.background = constant conductivity offset added to elem_data
0027 %    fwd_model.coarse2fine = linear mapping between img.elem_data and model parameters
0028 %    img.params_mapping = function mapping img.elem_data to model parameters
0029 %
0030 
0031 % (C) 2005 Andy Adler. License: GPL version 2 or version 3
0032 % $Id: fwd_solve.m 5699 2018-03-07 15:52:44Z alistair_boyle $
0033 
0034 if nargin == 1
0035    img= fwd_model;
0036 else
0037    warning('EIDORS:DeprecatedInterface', ...
0038       ['Calling FWD_SOLVE with two arguments is deprecated and will cause' ...
0039        ' an error in a future version. First argument ignored.']);
0040 end
0041 ws = warning('query','EIDORS:DeprecatedInterface');
0042 warning off EIDORS:DeprecatedInterface
0043 
0044 fwd_model= img.fwd_model;
0045 
0046 
0047 fwd_model= prepare_model( fwd_model );
0048 
0049 % TODO: This should be handled by the data_mapper
0050 if isfield(img,'params_mapping')
0051 %     fwd_model data is provided using a mapping function
0052     mapping_function= img.params_mapping.function;
0053     img= feval(mapping_function,img);
0054 end
0055 if isfield(fwd_model,'coarse2fine') && isfield(img,'elem_data')
0056    c2f= fwd_model.coarse2fine;
0057    if size(img.elem_data,1)==size(c2f,2)
0058 %     fwd_model data is provided on coarse mesh
0059       img.elem_data = c2f * img.elem_data; 
0060 
0061       if isfield(fwd_model,'background')
0062           img.elem_data = img.elem_data + fwd_model.background; 
0063       end
0064    end
0065 end
0066 
0067 if ~isfield(fwd_model, 'electrode')
0068    error('EIDORS: attempting to solve on model without electrodes');
0069 end
0070 if ~isfield(fwd_model, 'stimulation')
0071    error('EIDORS: attempting to solve on model without stimulation patterns');
0072 end
0073 
0074 solver = fwd_model.solve;
0075 if ischar(solver)
0076     solver = str2func(solver);
0077 end
0078 
0079 copt.fstr = 'fwd_solve';
0080 n_frames = size(img.elem_data,2);
0081 for frame = 1:n_frames;
0082    imgn = img; imgn.elem_data = imgn.elem_data(:,frame,:,:);
0083    copt.cache_obj = imgn;
0084    copt.boost_priority = -2; % fmdl evaluations are low priority
0085    tmp = eidors_cache(solver, {imgn}, copt);
0086    data(frame) = eidors_obj('data',tmp);  % create data object
0087 end
0088 
0089 if isa(fwd_model.solve,'function_handle')
0090     solver = func2str(fwd_model.solve);
0091 else
0092     solver = fwd_model.solve;
0093 end
0094 if strcmp(solver,'eidors_default');
0095     solver = eidors_default('get','fwd_solve');
0096 end
0097 if isfield(fwd_model,'measured_quantity') && ~isfield(data,'measured_quantity')
0098    warning('EIDORS:MeasurementQuantityObliviousSolver',...
0099       ['The solver %s did not handle the requested measurement quantity properly.\n'...
0100        'The results may be incorrect. Please check the code to verify.'], ...
0101        solver);
0102 elseif isfield(fwd_model,'measured_quantity') ... 
0103         && isfield(data,'measured_quantity') ...
0104         && ~strcmp(fwd_model.measured_quantity, data.measured_quantity)
0105    error('EIDORS:MeasurementQuantityDisagreement',...
0106        'The solver %s return measurements as %s, while %s was expected.',...
0107        solver, data.measured_quantity, fwd_model.measured_quantity);
0108 end
0109     
0110 warning on EIDORS:DeprecatedInterface
0111 
0112 
0113 function mdl = prepare_model( mdl )
0114 mdl = mdl_normalize(mdl,mdl_normalize(mdl));
0115 if ~isfield(mdl,'elems');
0116     return;
0117 end
0118 
0119 mdl.elems  = double(mdl.elems);
0120 mdl.n_elem = size(mdl.elems,1);
0121 mdl.n_node = size(mdl.nodes,1);
0122 if isfield(mdl,'electrode');
0123     mdl.n_elec = length(mdl.electrode);
0124 else
0125     mdl.n_elec = 0;
0126 end

fwd_solve

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE