sync jnifty and jsonlab to the latest github version

Author: fangq

barydualmesh.m

@@ -25,6 +25,15 @@
 %
 
 [enodes,eidx]=highordertet(node,elem);               % compute edge-centers
+
+if(size(elem,2)==3)
+    fnodes=meshcentroid(node,elem);                  % compute face-centers
+    fidx=1:
+    newnode=[enodes;fnodes];
+    newidx=[eidx, fidx+size(enodes,1), (1:size(elem,1))'+(size(enodes,1)+size(fnodes,1))];
+    return;
+end
+
 [fnodes,fidx]=elemfacecenter(node,elem);             % compute face-centers
 c0=meshcentroid(node,elem(:,1:min(size(elem,2),4))); % compute elem-centers
 

decodevarname.m

@@ -25,9 +25,9 @@
 %        decodevarname('a_')   % returns a_ as it is a valid variable name
 %        decodevarname('x0xE58F98__0xE9878F_')  % returns '变量' 
 %
-%    this file is part of EasyH5 Toolbox: https://github.com/fangq/easyh5
+%    this file is part of EasyH5 Toolbox: https://github.com/NeuroJSON/easyh5
 %
-%    License: GPLv3 or 3-clause BSD license, see https://github.com/fangq/easyh5 for details
+%    License: GPLv3 or 3-clause BSD license, see https://github.com/NeuroJSON/easyh5 for details
 %
 
 newname=name;

encodevarname.m

@@ -32,9 +32,9 @@
 %        encodevarname('a_')   % returns a_ as it is a valid variable name
 %        encodevarname('变量')  % returns 'x0xE58F98__0xE9878F_' 
 %
-%    this file is part of EasyH5 Toolbox: https://github.com/fangq/easyh5
+%    this file is part of EasyH5 Toolbox: https://github.com/NeuroJSON/easyh5
 %
-%    License: GPLv3 or 3-clause BSD license, see https://github.com/fangq/easyh5 for details
+%    License: GPLv3 or 3-clause BSD license, see https://github.com/NeuroJSON/easyh5 for details
 %
 
     if(~isvarname(str(1)))

filterjsonmmap.m

@@ -23,7 +23,7 @@
 %      str='{"arr":[[1,2],"a",{"c":2}],"obj":{"k":"test"}}';
 %      [dat, mmap]=loadjson(str);
 %      savejson('',mmap)
-%      newmmap=filterjsonmmap(mmap,{'arr.[1]', 'obj.k'});
+%      newmmap=filterjsonmmap(mmap,{'arr[1]', 'obj.k'});
 %      savejson('',newmmap)
 %
 % license:

getfromjsonpath.m

@@ -14,7 +14,7 @@
 %        obj: if the specified element exist, obj returns the result
 %
 %    example:
-%        getfromjsonpath(struct('a',[1,2,3]), '$.a.[1]')      % returns 2
+%        getfromjsonpath(struct('a',[1,2,3]), '$.a[1]')      % returns 2
 %
 % license:
 %     BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details 
@@ -23,6 +23,7 @@
 %
 
 obj=root;
+jsonpath=regexprep(jsonpath,'([^.])(\[\d+\])','$1.$2');
 [pat,paths]=regexp(jsonpath,'\.*([^\s\.]+)\.*','match','tokens');
 if(~isempty(pat) && ~isempty(paths))
 for i=1:length(paths)

highordertet.m

@@ -31,7 +31,7 @@
 if(order>=3 || order<=1)
     error('currently this function only supports order=2');
 end
-[edges,idx,newelem]=uniqedges(elem(:,1:4));
+[edges,idx,newelem]=uniqedges(elem(:,1:min(size(elem,2),4)));
 newnode=node(edges',1:3);
 newnode=reshape(newnode',[3,2,size(edges,1)]);
 newnode=squeeze(mean(permute(newnode,[3 2 1]),2));

jdatadecode.m

@@ -7,7 +7,7 @@
 % jsondecode for MATLAB R2016b or later)
 %
 % This function implements the JData Specification Draft 3 (Jun. 2020)
-% see http://github.com/fangq/jdata for details
+% see http://github.com/NeuroJSON/jdata for details
 %
 % authors:Qianqian Fang (q.fang <at> neu.edu)
 %

jdataencode.m

@@ -6,13 +6,13 @@
 % jdata=jdataencode(data, 'Param1',value1, 'Param2',value2,...)
 %
 % Annotate a MATLAB struct or cell array into a JData-compliant data
-% structure as defined in the JData spec: http://github.com/fangq/jdata.
+% structure as defined in the JData spec: http://github.com/NeuroJSON/jdata.
 % This encoded form servers as an intermediate format that allows unambiguous
 % storage, exchange of complex data structures and easy-to-serialize by
 % json encoders such as savejson and jsonencode (MATLAB R2016b or newer)
 %
 % This function implements the JData Specification Draft 3 (Jun. 2020)
-% see http://github.com/fangq/jdata for details
+% see http://github.com/NeuroJSON/jdata for details
 %
 % author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -139,12 +139,14 @@
        newitem=cell2mat(newitem);
     catch
     end
-else       % a single struct
+elseif(num==1) % a single struct
     names=fieldnames(item);
     newitem=struct;
     for i=1:length(names)
         newitem.(names{i})=obj2jd(item.(names{i}),varargin{:});
     end
+else
+    newitem=item;
 end
 
 %%-------------------------------------------------------------------------

jdatahash.m

@@ -0,0 +1,51 @@
+function key = jdatahash(data, algorithm, varargin)
+%
+%    key = jdatahash(data)
+%        or
+%    key = jdatahash(data, algorithm)
+%    key = jdatahash(data, algorithm, 'param1', value1, ...)
+%
+%    computing the hash key for a string or a numeric array (data elements
+%    are serialized in the row-major order first)
+%
+%    author: Qianqian Fang (q.fang <at> neu.edu)
+%
+%    input:
+%        data: a string or a numeric array
+%        algorithm: a string denoting the data hashing algorithm (case
+%              insensitive); default is 'sha-256'; supported options include
+%
+%        for both MATLAB/Octave: 'sha-256' (default), 'sha-1' ,'sha-384', 'sha-512', 'md2', 'md5'
+%        Octave-only: 'md4'
+%
+%    examples:
+%        sha256key = jdatahash('neurojson')
+%        md5key = jdatahash('reusable data', 'md5')
+%
+%    license:
+%        BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details
+%
+% -- this function is part of JSONLab toolbox (http://iso2mesh.sf.net/cgi-bin/index.cgi?jsonlab)
+%
+
+if(nargin < 2)
+    algorithm = 'sha-256';
+end
+
+if (ischar(data))
+    data = uint8(data);
+end
+
+opt=varargin2struct(varargin{:});
+
+if(jsonopt('rowmajor', 1, opt))
+    data = permute(data, ndims(data):-1:1);
+end
+
+if(isoctavemesh && exist('hash'))
+    algorithm(algorithm=='-')=[];
+    key = hash(algorithm, char(typecast(data(:).', 'uint8')));
+else
+    md = java.security.MessageDigest.getInstance(algorithm);
+    key = sprintf('%2.2x', typecast(md.digest(typecast(data(:), 'uint8')), 'uint8')');
+end

jload.m

@@ -77,7 +77,11 @@
     end
     header=jsondecode(jsonstr(1:pos+1));
 else
-    header=loadfun(filename,'ObjectID',1, varargin{:});
+    try
+        header=loadfun(filename,'ObjectID',1, 'MaxBuffer', 65536, varargin{:});
+    catch
+        header=loadfun(filename,'ObjectID',1, varargin{:});
+    end
 end
 
 allvar=fieldnames(header.WorkspaceHeader);

jsonget.m

@@ -24,8 +24,8 @@
 %      str='[[1,2],"a",{"c":2}]{"k":"test"}';
 %      [dat, mmap]=loadjson(str);
 %      savejson('',dat,'filename','mydata.json','compact',1);
-%      json=jsonget(str,mmap,'$.[0]','$.[2].c')
-%      json=jsonget('mydata.json',mmap,'$.[0]','$.[2].c')
+%      json=jsonget(str,mmap,'$[0]','$[2].c')
+%      json=jsonget('mydata.json',mmap,'$[0]','$[2].c')
 %
 % license:
 %     BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details 
@@ -63,7 +63,7 @@
 
 if(isstruct(fname) || iscell(fname) || isa(fname,'table') || isa(fname,'containers.Map'))
     for i=1:length(keylist)
-        json{end+1}=getobjfrompath(fname,keylist{i});
+        json{end+1}=getfromjsonpath(fname,keylist{i});
     end
     if(length(json)==1)
         json=json{1};

jsonset.m

@@ -31,11 +31,11 @@
 %      % display mmap entries
 %       savejson('',mmap)
 %      % replace value using mmap
-%       json=jsonset(str,mmap,'$.arr.[2].c','5')
+%       json=jsonset(str,mmap,'$.arr[2].c','5')
 %      % save same json string to file (must set savebinary 1)
 %       savejson('',d,'filename','file.json','compact',1,'savebinary',1);
 %      % fast write to file
-%       json=jsonset('file.json',mmap,'$.arr.[2].c','5')
+%       json=jsonset('file.json',mmap,'$.arr[2].c','5')
 %
 % license:
 %     BSD or GPL version 3, see LICENSE_{BSD,GPLv3}.txt files for details 

loadbj.m

@@ -78,6 +78,10 @@
 %           of the stream, and length is the JSON object string length.
 %           For more details, please see the help section of loadjson.m
 %
+%           The format of the mmap table retruned from this function
+%           follows the JSON-Mmap Specification Draft 1 [3] defined by the
+%           NeuroJSON project, see https://neurojson.org/jsonmmap/draft1/
+%
 % examples:
 %      obj=struct('string','value','array',[1 2 3]);
 %      ubjdata=savebj('obj',obj);
@@ -91,9 +95,11 @@
 % -- this function is part of JSONLab toolbox (http://iso2mesh.sf.net/cgi-bin/index.cgi?jsonlab)
 %
 
+    opt=varargin2struct(varargin{:});
+
     if(length(fname)<4096 && exist(fname,'file'))
        fid = fopen(fname,'rb');
-       string = fread(fid,inf,'uint8=>char')';
+       string = fread(fid,jsonopt('MaxBuffer',inf,opt),'uint8=>char')';
        fclose(fid);
     elseif(regexp(fname, '^\s*[\[\{SCHiUIulmLMhdDTFZN]'))
        string=fname;
@@ -105,7 +111,6 @@
     inputlen = length(string);
     inputstr = string;
 
-    opt=varargin2struct(varargin{:});
     opt.simplifycell=jsonopt('SimplifyCell',1,opt);
     opt.simplifycellarray=jsonopt('SimplifyCellArray',0,opt);
     opt.usemap=jsonopt('UseMap',0,opt);
@@ -276,7 +281,7 @@
     if cc ~= ']'
          while 1
             if(nargout>2)
-                varargin{1}.jsonpath_=[origpath '.' sprintf('[%d]',length(object))];
+                varargin{1}.jsonpath_=[origpath sprintf('[%d]',length(object))];
                 mmap{end+1}={varargin{1}.jsonpath_, pos};
                 [val, pos, newmmap] = parse_value(inputstr, pos, [], varargin{:});
                 mmap{end}{2}=[mmap{end}{2}, pos-mmap{end}{2}];

loadjd.m

@@ -12,15 +12,15 @@
 %
 %    input:
 %        inputfile: the input hierarchical container data file, supporting:
-%                *.json,.jnii,.jdt,.jmsh,.jnirs: JSON/JData based data files, see http://neurojson.org/jdata/draft2
-%                *.bjd,.bnii,.jdb,.bmsh,.bnirs: binary JData (BJData) files, see http://neurojson.org/bjdata/draft2
+%                *.json,.jnii,.jdt,.jmsh,.jnirs,.jbids: JSON/JData based data files, see https://neurojson.org/jdata/draft2
+%                *.bjd,.bnii,.jdb,.bmsh,.bnirs: binary JData (BJData) files, see https://neurojson.org/bjdata/draft2
 %                *.ubj: UBJSON-encoded files, see http://ubjson.org
 %                *.msgpack: MessagePack-encoded files, see http://msgpack.org
 %                *.h5,.hdf5,.snirf: HDF5 files, see https://www.hdfgroup.org/
 %        options: (optional) for JSON/JData files, these are optional 'param',value pairs
 %                supported by loadjson.m; for BJData/UBJSON/MessagePack files, these are
 %                options supported by loadbj.m; for HDF5 files, these are options
-%                supported by loadh5.m (part of EasyH5 toolbox, http://github.com/fangq/easyh5/)
+%                supported by loadh5.m (part of EasyH5 toolbox, http://github.com/NeuroJSON/easyh5/)
 %
 %    output:
 %        data: a structure (array) or cell (array) storing the hierarchical data
@@ -43,19 +43,19 @@
     error('you must provide file name');
 end
 
-if(regexpi(filename,'\.json$|\.jnii$\.jdt$\.jdat$|\.jmsh$|\.jnirs$'))
+if(regexpi(filename,'\.json$|\.jnii$|\.jdt$|\.jdat$|\.jmsh$|\.jnirs|\.jbids$'))
     [varargout{1:nargout}]=loadjson(filename,varargin{:});
-elseif(regexpi(filename,'\.bjd$|\.bnii$\.jdb$\.jbat$|\.bmsh$|\.bnirs$'))
+elseif(regexpi(filename,'\.bjd$|\.bnii$|\.jdb$|\.jbat$|\.bmsh$|\.bnirs$'))
     [varargout{1:nargout}]=loadbj(filename,varargin{:});
 elseif(regexpi(filename,'\.ubj$'))
     [varargout{1:nargout}]=loadubjson(filename,varargin{:});
 elseif(regexpi(filename,'\.msgpack$'))
     [varargout{1:nargout}]=loadmsgpack(filename,varargin{:});
 elseif(regexpi(filename,'\.h5$|\.hdf5$|\.snirf$'))
     if(~exist('loadh5','file'))
-        error('you must first install EasyH5 from http://github.com/fangq/easyh5/');
+        error('you must first install EasyH5 from http://github.com/NeuroJSON/easyh5/');
     end
     [varargout{1:nargout}]=loadh5(filename,varargin{:});
 else
-    error('file suffix must be one of .json,.jnii,.jdt,.jmsh,.jnirs,.bjd,.bnii,.jdb,.bmsh,.bnirs,.ubj,.msgpack,.h5,.hdf5,.snirf');
+    error('file suffix must be one of .json,.jnii,.jdt,.jmsh,.jnirs,.jbids,.bjd,.bnii,.jdb,.bmsh,.bnirs,.ubj,.msgpack,.h5,.hdf5,.snirf');
 end

loadjson.m

@@ -8,7 +8,7 @@
 % matlab data structure with optional memory-map (mmap) table
 %
 % authors:Qianqian Fang (q.fang <at> neu.edu)
-% created on 2011/09/09, including previous works from 
+% created on 2011/09/09, including previous works from
 %
 %         Nedialko Krouchev: http://www.mathworks.com/matlabcentral/fileexchange/25713
 %            created on 2009/11/02
@@ -81,15 +81,19 @@
 %      dat: a cell array, where {...} blocks are converted into cell arrays,
 %           and [...] are converted to arrays
 %      mmap: (optional) a cell array as memory-mapping table in the form of
-%             {{jsonpath1,[start,length,<whitespace>]},
-%              {jsonpath2,[start,length,<whitespace>]}, ...}
+%             {{jsonpath1,[start,length,<whitespace_pre>]},
+%              {jsonpath2,[start,length,<whitespace_pre>]}, ...}
 %           where jsonpath_i is a string in the JSONPath [1,2] format, and
 %           "start" is an integer referring to the offset from the begining
 %           of the stream, and "length" is the JSON object string length.
-%           An optional 3rd integer "whitespace" may appear to record the
-%           preceding whitespace length in case expansion of the data
+%           An optional 3rd integer "whitespace_pre" may appear to record
+%           the preceding whitespace length in case expansion of the data
 %           record is needed when using the mmap.
 %
+%           The format of the mmap table retruned from this function
+%           follows the JSON-Mmap Specification Draft 1 [3] defined by the
+%           NeuroJSON project, see https://neurojson.org/jsonmmap/draft1/
+%
 %           Memory-mapping table (mmap) is useful when fast reading/writing
 %           specific data records inside a large JSON file without needing
 %           to load/parse/overwrite the entire file.
@@ -101,10 +105,10 @@
 %           In the mmap jsonpath key, a '$' denotes the root object, a '.'
 %           denotes a child of the preceding element; '.key' points to the
 %           value segment of the child named "key" of the preceding
-%           object; '.[i]' denotes the (i+1)th member of the preceding
+%           object; '[i]' denotes the (i+1)th member of the preceding
 %           element, which must be an array. For example, a key
 %
-%           $.obj1.obj2.[0].obj3
+%           $.obj1.obj2[0].obj3
 %
 %           defines the memory-map of the "value" section in the below
 %           hierarchy:
@@ -134,6 +138,7 @@
 %
 %           [1] https://goessner.net/articles/JsonPath/
 %           [2] http://jsonpath.herokuapp.com/
+%           [3] https://neurojson.org/jsonmmap/draft1/
 %
 % examples:
 %      dat=loadjson('{"obj":{"string":"value","array":[1,2,3]}}')
@@ -335,7 +340,7 @@
                                     pos=endpos;
                                     pos=parse_char(inputstr, pos, ']');
                                     if(pbar>0)
-                                        waitbar(pos/length(inStr),pbar,'loading ...');
+                                        waitbar(pos/length(inputstr),pbar,'loading ...');
                                     end
                                     return;
                                 end
@@ -363,7 +368,7 @@
             while 1
                 varargin{1}.arraydepth_=arraydepth+1;
                 if(nargout>3)
-                    varargin{1}.jsonpath_=[origpath '.' sprintf('[%d]',length(object))];
+                    varargin{1}.jsonpath_=[origpath sprintf('[%d]',length(object))];
                     mmap{end+1}={varargin{1}.jsonpath_, [pos, 0, w2]};
                     [val, pos, index_esc, newmmap] = parse_value(inputstr, pos, esc, index_esc,varargin{:});
                     mmap{end}{2}(2)=pos-mmap{end}{2}(1);
@@ -382,8 +387,8 @@
     end
 
     if(varargin{1}.simplifycell)
-      if(iscell(object) && ~isempty(object) && (isnumeric(object{1}) || isstruct(object{1})) )
-          if(all(cellfun(@(e) isequal(size(object{1}), size(e)) , object(2:end))))
+      if(iscell(object) && ~isempty(object) && (all(cellfun(@isnumeric, object)) || all(cellfun(@isstruct, object))))
+          if(all(cellfun(@(e) isequal(size(object{1}), size(e)), object(2:end))))
               try
                   oldobj=object;
                   if(iscell(object) && length(object)>1 && ndims(object{1})>=2)
@@ -392,7 +397,7 @@
                       object=cat(catdim,object{:});
                       object=permute(object,ndims(object):-1:1);
                   else
-                      object=cell2mat(object')';
+                      object=cell2mat(object.').';
                   end
                   if(iscell(oldobj) && isstruct(object) && numel(object)>1 && varargin{1}.simplifycellarray==0)
                       object=oldobj;
@@ -402,7 +407,7 @@
           end
       end
       if(~iscell(object) && size(object,1)>1 && ndims(object)==2)
-            object=object';
+            object=object.';
       end
     end
     pos=parse_char(inputstr, pos, ']');