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function savejmesh(node, face, elem, fname, varargin)
%
% savejmesh(node,face,elem,fname,opt)
%
% export a mesh to the JMesh format defined in http://github.com/NeuroJSON/jmesh
%
% author: Qianqian Fang, <q.fang at neu.edu>
% date: 2011/10/06
%
% input:
% node: node list, dimension (nn,3)
% face: can be empty, surface face element list, dimension (be,3)
% elem: can be empty, tetrahedral element list, dimension (ne,4)
% fname: output file name; if file name has a suffix .bmsh,
% the mesh data will be saved in the binary jmesh format; otherwise,
% the file will be saved as a text-based jmesh (which is a plain
% JSON file)
% opt: additional parameters in the form of 'parameter',value pairs
% valid parameters include:
% 'Dimension': 2 - a 2D mesh, 3 - a 3D mesh
% 'Author': a string to set the author of the mesh
% 'MeshTitle': a string to set the title of the mesh
% 'MeshTag': a value as the tag of the mesh data
% 'Comment': a string as the additional note for the mesh data
% 'MeshTag': a value as the tag of the mesh data
% 'Flexible': 0 (default)- use dimension-specific data containers
% (MeshVertex3, MeshTet4 ...). 1 - use flexible mesh data
% containers (MeshNode, MeshSurf, MeshElem)
% 'Header': 1 - include _DataInfo_ header, 0 - do not include
%
% please type 'help savejson' and 'help savebj' to see additional
% supported options
%
% examples:
%
% [no,fc,el]=meshabox([0 0 0],[60,30,40],3,10);
% savejmesh(no,fc,[],'box_surf.jmsh','dimension',3);
% savejmesh(no,fc,el,'box_zlib.jmsh','compression','zlib');
% savejmesh(no,fc,el,'box.bmsh','dimension',3);
% savejmesh(no,fc,el,'box_zlib.bmsh','dimension',3,'compression','zlib');
% savejmesh(no,[],el,'box_elem.jmsh','flexible',1) %sue MeshNode/MeshSurf/MeshElem
% mesh=loadbj('box.bmsh')
%
% -- this function is part of iso2mesh toolbox (http://iso2mesh.sf.net)
%
if (nargin == 2)
fname = face;
face = [];
elem = [];
end
if (nargin == 3)
fname = elem;
elem = [];
end
if (length(varargin) == 1 && ischar(varargin{1}))
opt = struct('FileName', varargin{1});
else
opt = varargin2struct(varargin{:});
end
meshdim = jsonopt('Dimension', size(node, 2), opt);
if (jsonopt('Header', 1, opt) == 1) % use metadata header
mesh.(encodevarname('_DataInfo_')) = struct();
metadata.JMeshVersion = 0.5;
metadata.Dimension = meshdim;
metadata.CreationTime = datestr(now);
metadata.Comment = ['Created by Iso2Mesh ' iso2meshver '(http://iso2mesh.sf.net)'];
metadata.AnnotationFormat = 'https://github.com/NeuroJSON/jmesh/blob/master/JMesh_specification.md';
metadata.SerialFormat = 'http://json.org';
metadata.Parser = struct('Python', [], ...
'MATLAB', 'https://github.com/NeuroJSON/jsonlab', ...
'JavaScript', [], ...
'CPP', 'https://github.com/NeuroJSON/json', ...
'C', []);
metadata.Parser.Python = {'https://pypi.org/project/jdata', 'https://pypi.org/project/bjdata'};
metadata.Parser.JavaScript = {'https://github.com/NeuroJSON/jsdata', 'https://github.com/NeuroJSON/js-bjdata'};
metadata.Parser.C = {'https://github.com/DaveGamble/cJSON', 'https://github.com/NeuroJSON/ubj'};
end
if (jsonopt('Flexible', 0, opt) == 1) % a user-defined mesh
mesh.MeshNode = node;
if (~isempty(face))
mesh.MeshSurf = face;
end
if (~isempty(elem))
mesh.MeshElem = elem;
end
elseif (meshdim == 3) % a 3D mesh
nd = size(node);
if (nd(2) < 3)
error('expecting 3 or more columns in node');
end
mesh.MeshVertex3 = node(:, 1:3);
if (nd(2) > 3)
mesh.MeshVertex3 = struct('Data', mesh.MeshVertex3, 'Properties', struct('Value', node(:, 4:end)));
end
if (~isempty(face))
nd = size(face);
if (nd(2) < 3)
error('expecting 3 or more columns in face');
end
mesh.MeshTri3 = face(:, 1:3);
if (nd(2) > 3)
mesh.MeshTri3 = struct('Data', mesh.MeshTri3, 'Properties', struct('Value', face(:, 4:end)));
end
end
if (~isempty(elem))
nd = size(elem);
if (nd(2) < 4)
error('expecting 4 or more columns in elem');
end
mesh.MeshTet4 = elem(:, 1:4);
if (nd(2) > 4)
mesh.MeshTet4 = struct('Data', mesh.MeshTet4, 'Properties', struct('Value', elem(:, 5:end)));
end
end
elseif (meshdim == 2) % a 2D mesh
nd = size(node);
if (nd(2) < 2)
error('expecting 2 or more columns in node');
end
mesh.MeshVertex2 = node(:, 1:2);
if (nd(2) > 2)
mesh.MeshVertex2 = struct('Data', mesh.MeshVertex2, 'Properties', struct('Value', node(:, 3:end)));
end
if (~isempty(face))
nd = size(face);
if (nd(2) < 3)
error('expecting 3 or more columns in face');
end
mesh.MeshTri3 = face(:, 1:3);
if (nd(2) > 3)
mesh.MeshTri3 = struct('Data', mesh.MeshTri3, 'Properties', struct('Value', face(:, 4:end)));
end
end
if (~isempty(elem))
warning('elem is redundant in a 2D mesh, skip');
end
else
error('the specified Dimension is not supported, please remove to save data to a general format');
end
author = jsonopt('Author', '', opt);
if (~isempty(author))
metadata.Author = author;
end
title = jsonopt('MeshTitle', '', opt);
if (~isempty(title))
metadata.MeshTitle = title;
end
tag = jsonopt('MeshTag', [], opt);
if (~isempty(tag))
metadata.MeshTag = tag;
end
comm = jsonopt('Comment', '', opt);
if (~isempty(comm))
metadata.Comment = comm;
end
if (exist('metadata', 'var')) % use metadata
mesh.(encodevarname('_DataInfo_')) = metadata;
end
if (~isempty(regexp(fname, '\.bmsh$', 'once')) || ~isempty(regexp(fname, '\.bmesh$', 'once')))
savebj('', mesh, 'FileName', fname, varargin{:});
else
savejson('', mesh, 'FileName', fname, varargin{:});
end
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