[sync] update jsonlab to the latest

Author: fangq

base64decode.m

@@ -34,7 +34,11 @@
     output = zmat(varargin{1}, 0, 'base64');
     return
 elseif (isoctavemesh)
-    error('You must install the ZMat toolbox (http://github.com/NeuroJSON/zmat) to use this function in Octave');
+    try
+        output = matlab.net.base64decode(varargin{1});
+    catch
+        error('You must install the ZMat toolbox (http://github.com/NeuroJSON/zmat) to use this function in Octave');
+    end
 end
 
 error(javachk('jvm'));

gzipdecode.m

@@ -36,15 +36,19 @@
 if (nargin == 0)
     error('you must provide at least 1 input');
 end
-if (exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3)
+
+nozmat = getvarfrom({'caller', 'base'}, 'NO_ZMAT');
+
+if ((exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3) && (isempty(nozmat) || nozmat == 0))
     if (nargin > 1)
         [varargout{1:nargout}] = zmat(varargin{1}, varargin{2:end});
     else
         [varargout{1:nargout}] = zmat(varargin{1}, 0, 'gzip', varargin{2:end});
     end
     return
 elseif (isoctavemesh)
-    error('You must install the ZMat toolbox (http://github.com/NeuroJSON/zmat) to use this function in Octave');
+    [varargout{1:nargout}] = octavezmat(varargin{1}, 0, 'gzip');
+    return
 end
 error(javachk('jvm'));
 

gzipencode.m

@@ -35,20 +35,28 @@
     error('you must provide at least 1 input');
 end
 
-if (exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3)
+nozmat = getvarfrom({'caller', 'base'}, 'NO_ZMAT');
+
+if ((exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3) && (isempty(nozmat) || nozmat == 0))
     [varargout{1:nargout}] = zmat(varargin{1}, 1, 'gzip');
     return
 elseif (isoctavemesh)
-    error('You must install the ZMat toolbox (http://github.com/NeuroJSON/zmat) to use this function in Octave');
+    [varargout{1:nargout}] = octavezmat(varargin{1}, 1, 'gzip');
+    return
 end
 
 error(javachk('jvm'));
 
-if (ischar(varargin{1}))
-    varargin{1} = uint8(varargin{1});
+input = varargin{1}(:)';
+if (ischar(input))
+    input = uint8(input);
+elseif (isa(input, 'string'))
+    input = uint8(char(input));
+else
+    input = typecast(input, 'uint8');
 end
 
-input = typecast(varargin{1}(:)', 'uint8');
+input = typecast(input, 'uint8');
 
 buffer = java.io.ByteArrayOutputStream();
 gzip = java.util.zip.GZIPOutputStream(buffer);

jdatadecode.m

@@ -111,7 +111,7 @@
 end
 
 %% handle array data
-if (isfield(data, N_('_ArrayType_')) && (isfield(data, N_('_ArrayData_')) || isfield(data, N_('_ArrayZipData_'))))
+if (isfield(data, N_('_ArrayType_')) && (isfield(data, N_('_ArrayData_')) || (isfield(data, N_('_ArrayZipData_')) && ~isstruct(data.(N_('_ArrayZipData_'))))))
     newdata = cell(len, 1);
     for j = 1:len
         if (isfield(data, N_('_ArrayZipSize_')) && isfield(data, N_('_ArrayZipData_')))
@@ -477,29 +477,12 @@
         end
         if (~isempty(ref.path))
             uripath = [ref.proto ref.path];
-            [fpath, fname, fext] = fileparts(uripath);
-            opt.maxlinklevel = opt.maxlinklevel - 1;
-            switch (lower(fext))
-                case {'.json', '.jnii', '.jdt', '.jdat', '.jmsh', '.jnirs'}
-                    newdata = loadjson(uripath, opt);
-                case {'.bjd', '.bnii', '.jdb', '.jbat', '.bmsh', '.bnirs', '.pmat'}
-                    newdata = loadbj(uripath, opt, 'Base64', 0);
-                case {'.ubj'}
-                    newdata = loadubjson(uripath, opt, 'Base64', 0);
-                case {'.msgpack'}
-                    newdata = loadmsgpack(uripath, opt, 'Base64', 0);
-                case {'.h5', '.hdf5', '.snirf'}  % this requires EasyH5 toolbox
-                    newdata = loadh5(uripath, opt);
-                otherwise
-                    % _DataLink_ url does not specify type, assuming JSON format
-                    if (regexpi(datalink, '^\s*(http|https|ftp|file)://'))
-                        newdata = loadjson(uripath, opt);
-                    else
-                        warning('_DataLink_ url is not supported');
-                    end
-            end
-            if (~isempty(ref.jsonpath))
-                newdata = getfromjsonpath(newdata, ref.jsonpath);
+            [newdata, fname] = jdlink(uripath);
+            if (exist(fname, 'file'))
+                opt.maxlinklevel = opt.maxlinklevel - 1;
+                if (~isempty(ref.jsonpath))
+                    newdata = jsonpath(newdata, ref.jsonpath);
+                end
             end
         end
     end

jdataencode.m

@@ -101,13 +101,15 @@
 
 if (iscell(item))
     newitem = cell2jd(item, varargin{:});
+elseif (isa(item, 'jdict'))
+    newitem = obj2jd(item(), varargin{:});
 elseif (isstruct(item))
     newitem = struct2jd(item, varargin{:});
-elseif (isnumeric(item) || islogical(item))
+elseif (isnumeric(item) || islogical(item) || isa(item, 'timeseries'))
     newitem = mat2jd(item, varargin{:});
 elseif (ischar(item) || isa(item, 'string'))
     newitem = mat2jd(item, varargin{:});
-elseif (isa(item, 'containers.Map'))
+elseif (isa(item, 'containers.Map') || isa(item, 'dictionary'))
     newitem = map2jd(item, varargin{:});
 elseif (isa(item, 'categorical'))
     newitem = cell2jd(cellstr(item), varargin{:});
@@ -166,13 +168,21 @@
         end
     end
 else   % keep as a map and only encode its values
-    if (strcmp(item.KeyType, 'char'))
+    if (isa(item, 'dictionary'))
+        newitem = dictionary();
+    elseif (strcmp(item.KeyType, 'char'))
         newitem = containers.Map();
     else
         newitem = containers.Map('KeyType', item.KeyType, 'ValueType', 'any');
     end
-    for i = 1:length(names)
-        newitem(names{i}) = obj2jd(item(names{i}), varargin{:});
+    if (isa(item, 'dictionary'))
+        for i = 1:length(names)
+            newitem(names(i)) = obj2jd(item(names(i)), varargin{:});
+        end
+    else
+        for i = 1:length(names)
+            newitem(names{i}) = obj2jd(item(names{i}), varargin{:});
+        end
     end
 end
 
@@ -185,6 +195,18 @@
 zipmethod = varargin{1}.compression;
 minsize = varargin{1}.compressarraysize;
 
+if (isa(item, 'timeseries'))
+    if (item.TimeInfo.isUniform && item.TimeInfo.Increment == 1)
+        if (ndims(item.Data) == 3 && size(item.Data, 1) == 1 && size(item.Data, 2) == 1)
+            item = permute(item.Data, [2 3 1]);
+        else
+            item = squeeze(item.Data);
+        end
+    else
+        item = [item.Time squeeze(item.Data)];
+    end
+end
+
 % 2d numerical (real/complex/sparse) arrays with _ArrayShape_ encoding enabled
 if (varargin{1}.usearrayshape && ndims(item) == 2 && ~isvector(item))
     encoded = 1;
@@ -394,12 +416,15 @@
 
 %% -------------------------------------------------------------------------
 function newitem = any2jd(item, varargin)
-
-N = @(x) N_(x, varargin{:});
-newitem.(N('_DataInfo_')) = struct('MATLABObjectClass', class(item), 'MATLABObjectSize', size(item));
-newitem.(N('_ByteStream_')) = getByteStreamFromArray(item);  % use undocumented matlab function
-if (varargin{1}.base64)
-    newitem.(N('_ByteStream_')) = char(base64encode(newitem.(N('_ByteStream_'))));
+try
+    N = @(x) N_(x, varargin{:});
+    newitem.(N('_DataInfo_')) = struct('MATLABObjectClass', class(item), 'MATLABObjectSize', size(item));
+    newitem.(N('_ByteStream_')) = getByteStreamFromArray(item);  % use undocumented matlab function
+    if (varargin{1}.base64)
+        newitem.(N('_ByteStream_')) = char(base64encode(newitem.(N('_ByteStream_'))));
+    end
+catch
+    error('any2jd: failed to convert object of type %s', class(item));
 end
 
 %% -------------------------------------------------------------------------

loadbidstsv.m

@@ -46,7 +46,7 @@
         fid = fid((endpos + 1):end);
     end
 else
-    fid = fopen(tsvfile, 'rb');
+    fid = fopen(tsvfile, 'rt');
     header = fgetl(fid);
     header = regexprep(header, '\s*$', '');
 end

loadbj.m

@@ -107,7 +107,7 @@
     else
         string = urlread(fname);
     end
-elseif (~isempty(fname) && any(fname(1) == '[{SCHiUIulmLMhdDTFZN'))
+elseif (~isempty(fname) && any(fname(1) == '[{SCBHiUIulmLMhdDTFZN'))
     string = fname;
 else
     error('input file does not exist or buffer is invalid');
@@ -166,10 +166,10 @@
             else
                 [data{jsoncount}, pos] = parse_array(inputstr, pos, opt);
             end
-        case {'S', 'C', 'H', 'i', 'U', 'I', 'u', 'l', 'm', 'L', 'M', 'h', 'd', 'D', 'T', 'F', 'Z', 'N'}
+        case {'S', 'C', 'B', 'H', 'i', 'U', 'I', 'u', 'l', 'm', 'L', 'M', 'h', 'd', 'D', 'T', 'F', 'Z', 'N'}
             [data{jsoncount}, pos] = parse_value(inputstr, pos, [], opt);
         otherwise
-            error_pos('Root level structure must start with a valid marker "{[SCHiUIulmLMhdDTFZN"', inputstr, pos);
+            error_pos('Root level structure must start with a valid marker "{[SCBHiUIulmLMhdDTFZN"', inputstr, pos);
     end
     if (jsoncount >= maxobjid)
         break
@@ -219,8 +219,8 @@
                 [data{i}, pos] = parse_value(inputstr, pos, type, varargin{:});
             end
             adv = pos - adv;
-        case 'C'
-            data = inputstr(pos:pos + count);
+        case {'C', 'B'}
+            data = inputstr(pos:pos + count - 1);
             adv = count;
         case {'T', 'F', 'N'}
             error_pos(sprintf('For security reasons, optimized type %c is disabled at position %%d', type), inputstr, pos);
@@ -247,6 +247,7 @@
 pos = parse_char(inputstr, pos, '[');
 object = cell(0, 1);
 dim = [];
+iscolumn = 0;
 type = '';
 count = -1;
 [cc, pos] = next_char(inputstr, pos);
@@ -263,6 +264,9 @@
             error_pos('ND array size specifier does not support embedding', inputstr, pos);
         end
         varargin{1}.noembedding_ = 1;
+        if (pos + 1 < length(inputstr) && inputstr(pos + 1) == '[')
+            iscolumn = 1;
+        end
         [dim, pos] = parse_array(inputstr, pos, varargin{:});
         count = prod(double(dim));
         varargin{1}.noembedding_ = 0;
@@ -274,8 +278,12 @@
 if (~isempty(type))
     if (count >= 0)
         [object, adv] = parse_block(inputstr, pos, type, count, varargin{:});
-        if (~isempty(dim))
-            object = permute(reshape(object, fliplr(dim(:)')), length(dim):-1:1);
+        if (~isempty(dim) && length(dim) > 1)
+            if (iscolumn == 0)
+                object = permute(reshape(object, fliplr(dim(:)')), length(dim):-1:1);
+            else
+                object = reshape(object, dim);
+            end
         end
         pos = pos + adv;
         return
@@ -302,9 +310,13 @@
             [val, pos] = parse_value(inputstr, pos, [], varargin{:});
         end
         object{end + 1} = val;
-        [cc, pos] = next_char(inputstr, pos);
-        if cc == ']'
+        if count > 0 && length(object) >= count
             break
+        else
+            [cc, pos] = next_char(inputstr, pos);
+            if cc == ']' || (count > 0 && length(object) >= count)
+                break
+            end
         end
     end
 end
@@ -374,14 +386,14 @@
 function [str, pos] = parseStr(inputstr, pos, type, varargin)
 if (isempty(type))
     type = inputstr(pos);
-    if type ~= 'S' && type ~= 'C' && type ~= 'H'
+    if type ~= 'S' && type ~= 'C' && type ~= 'B' && type ~= 'H'
         error_pos('String starting with S expected at position %d', inputstr, pos);
     else
         pos = pos + 1;
     end
 end
 
-if (type == 'C')
+if (type == 'C' || type == 'B')
     str = inputstr(pos);
     pos = pos + 1;
     return
@@ -428,7 +440,7 @@
     varargout{3} = {};
 end
 switch (cc)
-    case {'S', 'C', 'H'}
+    case {'S', 'C', 'B', 'H'}
         [varargout{1:2}] = parseStr(inputstr, varargout{2}, type, varargin{:});
         return
     case '['
@@ -484,8 +496,10 @@
     object = [];
 end
 count = -1;
+type = [];
 [cc, pos] = next_char(inputstr, pos);
 if (cc == '$')
+    type = inputstr(pos + 1);
     pos = pos + 2;
 end
 [cc, pos] = next_char(inputstr, pos);
@@ -518,7 +532,7 @@
             mmap{end}{2} = [mmap{end}{2}, pos - mmap{end}{2}];
             mmap = [mmap(:); newmmap(:)];
         else
-            [val, pos] = parse_value(inputstr, pos, [], varargin{:});
+            [val, pos] = parse_value(inputstr, pos, type, varargin{:});
         end
         num = num + 1;
         if (usemap)
@@ -533,7 +547,7 @@
             object.(str) = val;
         end
         [cc, pos] = next_char(inputstr, pos);
-        if (count >= 0 && num >= count) || cc == '}'
+        if ((count >= 0 && num >= count) || (~isempty(cc) && cc == '}'))
             break
         end
     end

savebj.m

@@ -870,9 +870,14 @@
 %% -------------------------------------------------------------------------
 function val = S_(str, varargin)
 ismsgpack = varargin{1}.messagepack;
+isdebug = varargin{1}.debug;
 Smarker = varargin{1}.SM_;
 if (length(str) == 1)
-    val = [Smarker(1) str];
+    if (isdebug)
+        val = [Smarker(1) sprintf('<%d>', str)];
+    else
+        val = [Smarker(1) str];
+    end
 else
     if (ismsgpack)
         val = [Imsgpk_(length(str), 218, 160, varargin{:}) str];

savejson.m

@@ -289,7 +289,7 @@
 %% -------------------------------------------------------------------------
 function txt = obj2json(name, item, level, varargin)
 
-if (iscell(item) || isa(item, 'string'))
+if (iscell(item) || (isa(item, 'string') && numel(item) > 1))
     txt = cell2json(name, item, level, varargin{:});
 elseif (isa(item, 'jdict'))
     txt = obj2json(name, item, level, varargin{:});