savejmesh.m

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