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--- a +++ b/Cobiveco/@cobiveco/cobiveco.m @@ -0,0 +1,267 @@ +% Consistent Biventricular Coordinates +% +% Usage: +% c = cobiveco(config); +% c.computeAll; +% result = c.result; +% +% Input: +% - config: configuration struct with the following fields: +% config.inPrefix: prefix for input files, e.g. 'inputDir/namePrefix'; +% a tetrahedral mesh has to be provided as VTU (inPrefix + '.vtu'); +% boundary surfaces can either be providing as individual PLY files: +% inPrefix + '_base.ply', '_epi.ply', '_endo_lv.ply', '_endo_rv.ply' +% or as one VTP file (inPrefix + '.vtp') containing point data 'class' with the following values: +% 1: base, 2: epi, 3: endo_lv, 4: endo_rv +% config.outPrefix: prefix for output files, e.g. 'outputDir/' (trailing slash for directories!) +% config.exportLevel: integer defining what should be exported as files: +% 0: nothing +% 1: only the final result and the rotation matrix (default) +% 2: + intermediate PDE-solutions, all volume meshes and mmg command line outputs +% 3: + septal curves, heart axes, apicobasal streamlines and an axes-aligned version of the final result +% config.verbose: whether to print status messages (optional, default: true) +% config.mappingTol: tolerance for mapping of boundary surfaces, unit: mean edge length (optional, default: 0.5) +% config.tol: tolerance for iterative solvers (optional, default: 1e-8) +% config.maxit: maximum number of iterations for iterative solvers (optional, default: 3000) +% config.truncSeptSur: percentages of triangles to truncate from the septal surface on the anterior and posterior side, respectively; +% affects the left-right axis and the position of the apex point (optional, default: [20 10]) +% config.abExtrapSmooth: smoothness for extrapolation of apicobasal coord from contour lines to mesh nodes +% (RMS deviation from the contour line values in percent), useful range: 0.1...1 (optional, default: 0.25) +% config.mmgSizingParam: a vector [hausd hmin hmax] defining sizing parameters for mmg (optional), unit: mean edge length +% hausd: maximal Hausdorff distance for approximation of boundaries (default: 0.1) +% hmin: minimal edge size (default: 0.9) +% hmax: maximal edge size (default: 1.1) +% +% Outputs: +% - c.result: VTK struct with the following point data fields: +% c.result.pointData.tv: transventricular coordinate +% c.result.pointData.tm: transmural coordinate +% c.result.pointData.ab: apicobasal coordinate +% c.result.pointData.rt: rotational coordinate +% c.result.pointData.rtSin: rotational sine coordinate +% c.result.pointData.rtCos: rotational cosine coordinate +% - c.R: rotation matrix for alignment of heart axes with x,y,z +% - c.cfg: complete configuration struct with all parameters +% +% Dependencies: +% - MMG3D by INP/Inria/U Bordeaux +% https://github.com/MmgTools/mmg +% Tested version: Release 5.4.3, 26 Feb 2020 +% - gptoolbox by Alec Jacobson +% https://github.com/alecjacobson/gptoolbox +% Tested version: Commit bee2edb, 20 Aug 2020 +% - vtkToolbox by Steffen Schuler +% https://github.com/KIT-IBT/vtkToolbox +% Run dependencies/install.sh to install them from source +% +% Written in 2020 by Steffen Schuler +% Institute of Biomedical Engineering, KIT +% www.ibt.kit.edu + +classdef cobiveco < handle + + properties (SetAccess = private) + + % Configuration parameters + % (default values) + cfg = struct( ... + 'inPrefix', '', ... + 'outPrefix', '', ... + 'exportLevel', 1, ... + 'verbose', true, ... + 'mappingTol', 0.5, ... + 'tol', 1e-8, ... + 'maxit', 3000, ... + 'truncSeptSur', [20 10], ... + 'abExtrapSmooth', 0.25, ... + 'mmgSizingParam', [0.1 0.9 1.1], ... + 'rvepi', false ... + ); + + % Mesh 0 (original mesh) + m0 = struct( ... + 'vol', [], ... + 'sur', [], ... + 'surToVol', [], ... + 'meanEdgLen', [], ... + 'L', [], ... + 'tv', [], ... + 'tm', [], ... + 'tmRVEpi', [], ... + 'rtSin', [], ... + 'rtCos', [], ... + 'rt', [], ... + 'ab', [], ... + 'debug', [] ... + ); + + % Mesh 1 (isovalue discretization at boundary between LV and RV) + m1 = struct( ... + 'vol', [], ... + 'sur', [], ... + 'surToVol', [], ... + 'meanEdgLen', [], ... + 'L', [], ... + 'G', [], ... + 'massMat', [], ... + 'M', [], ... + 'tm', [], ... + 'tmRVEpi', [], ... + 'ridgeLaplace', [], ... + 'debug', [] ... + ); + + % Mesh 2 (isovalue discretization at ridge) + m2 = struct( ... + 'vol', [], ... + 'sur', [], ... + 'surToVol', [], ... + 'L', [], ... + 'G', [], ... + 'M', [], ... + 'abLaplace', [], ... + 'rtSin', [], ... + 'rtCos', [], ... + 'rt', [], ... + 'debug', [] ... + ); + + % VTK struct with final coordinates as pointData + result + + % Rotation matrix aligning heart axes with x,y,z + R + + end + + properties (Access = private) + + septCurveAnt + septCurvePost + + % used to keep track of what has already been computed + available = struct( ... + 'mesh0', false, ... + 'transventricular', false, ... + 'mesh1', false, ... + 'transmural', false, ... + 'heartAxesAndApex', false, ... + 'mesh2', false, ... + 'rotational', false, ... + 'apicobasal', false ... + ); + + end + + methods + + function o = cobiveco(config) + % c = cobiveco(config) + + % overwrite default parameters, if provided by the user + fns = fieldnames(config); + for i = 1:numel(fns) + fn = fns{i}; + if ~isfield(o.cfg,fn) + error('Unknown parameter ''%s'' found in config.', fn); + end + o.cfg.(fn) = config.(fn); + end + + % check mandatory parameters + if ~isfield(config,'inPrefix') + error('Mandatory parameter ''inPrefix'' missing in config.'); + end + if o.cfg.exportLevel > 0 + if isempty(o.cfg.outPrefix) + error('Mandatory parameter ''outPrefix'' missing in config or empty.'); + end + outPath = fileparts(o.cfg.outPrefix); + if ~isempty(outPath) && ~exist(outPath, 'dir') + mkdir(outPath); + end + testfile = sprintf('%stest', o.cfg.outPrefix); + [fid,errmsg] = fopen(testfile, 'w'); + if fid==-1 + error('Invalid parameter outPrefix. Could not create ''%s'' (%s).', testfile, errmsg); + else + fclose(fid); + delete(testfile); + end + end + + % start timer + tic; + + % set up paths + mpath = fileparts(mfilename('fullpath')); + addpath(['../functions']); +% if ~exist([mpath '/../dependencies/mmg/build/bin/mmg3d_O3'], 'file') +% error('Dependency ''mmg'' not found. Run dependencies/install_cobiveco.sh to install.'); +% end + if ~exist('cotmatrix.m', 'file') + if ~exist(['../dependencies/gptoolbox'], 'dir') + error('Dependency ''gptoolbox'' not found. Run dependencies/install_cobiveco.sh to install.'); + end + addpath(['../dependencies/gptoolbox/matrix']); + addpath(['../dependencies/gptoolbox/mesh']); + end + if ~exist('vtkRead.m', 'file') + if ~exist(['../dependencies/vtkToolbox'], 'dir') + error('Dependency ''vtkToolbox'' not found. Run dependencies/install_cobiveco.sh to install.'); + end + addpath(['../dependencies/vtkToolbox/MATLAB']); + end + end + + function computeAll(o) + % Compute all coordinates + + t = toc; + o.prepareMesh0; + o.computeTransventricular; + o.prepareMesh1; + if o.cfg.rvepi + o.computeTransmuralRVEpi; + else + o.computeTransmural; + end + o.computeHeartAxesAndApex; + o.prepareMesh2; + o.computeRotational; + o.computeApicobasal; + o.exportResult; + o.printStatus('Total elapsed time:'); + o.printStatus(sprintf('%.1f seconds\n', toc-t), true); + end + + % declare methods defined in separate files + prepareMesh0(o) + computeTransventricular(o) + prepareMesh1(o) + computeTransmural(o) + computeTransmrualRVEpi(o) + computeHeartAxesAndApex(o) + prepareMesh2(o) + computeRotational(o) + computeApicobasal(o) + exportResult(o) + + end + + methods (Access = private) + + function printStatus(o, msg, noPadding) + if o.cfg.verbose + if nargin > 2 && noPadding + fprintf('%s', msg); + else + pad = repmat(' ', 1, 41-numel(msg)); + fprintf('%s%s', msg, pad); + end + end + end + + end + +end