[io] update embedded IO toolboxes: jsonlab, jnifty, jsnirfy, easyh5

Author: fangq

gzipdecode.m

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

gzipencode.m

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

jdatadecode.m

@@ -477,12 +477,29 @@
         end
         if (~isempty(ref.path))
             uripath = [ref.proto ref.path];
-            [newdata, fname] = jdlink(uripath);
-            if (exist(fname, 'file'))
-                opt.maxlinklevel = opt.maxlinklevel - 1;
-                if (~isempty(ref.jsonpath))
-                    newdata = jsonpath(newdata, ref.jsonpath);
-                end
+            [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);
             end
         end
     end

jdataencode.m

@@ -107,7 +107,7 @@
     newitem = mat2jd(item, varargin{:});
 elseif (ischar(item) || isa(item, 'string'))
     newitem = mat2jd(item, varargin{:});
-elseif (isa(item, 'containers.Map') || isa(item, 'dictionary'))
+elseif (isa(item, 'containers.Map'))
     newitem = map2jd(item, varargin{:});
 elseif (isa(item, 'categorical'))
     newitem = cell2jd(cellstr(item), varargin{:});
@@ -166,21 +166,13 @@
         end
     end
 else   % keep as a map and only encode its values
-    if (isa(item, 'dictionary'))
-        newitem = dictionary();
-    elseif (strcmp(item.KeyType, 'char'))
+    if (strcmp(item.KeyType, 'char'))
         newitem = containers.Map();
     else
         newitem = containers.Map('KeyType', item.KeyType, 'ValueType', 'any');
     end
-    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
+    for i = 1:length(names)
+        newitem(names{i}) = obj2jd(item(names{i}), varargin{:});
     end
 end