/
jdatadecode.m
512 lines (497 loc) · 21.9 KB
/
jdatadecode.m
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function newdata=jdatadecode(data,varargin)
%
% newdata=jdatadecode(data,opt,...)
%
% Convert all JData object (in the form of a struct array) into an array
% (accepts JData objects loaded from either loadjson/loadubjson or
% jsondecode for MATLAB R2016b or later)
%
% This function implements the JData Specification Draft 3 (Jun. 2020)
% see http://github.com/NeuroJSON/jdata for details
%
% authors:Qianqian Fang (q.fang <at> neu.edu)
%
% input:
% data: a struct array. If data contains JData keywords in the first
% level children, these fields are parsed and regrouped into a
% data object (arrays, trees, graphs etc) based on JData
% specification. The JData keywords are
% "_ArrayType_", "_ArraySize_", "_ArrayData_"
% "_ArrayIsSparse_", "_ArrayIsComplex_",
% "_ArrayZipType_", "_ArrayZipSize", "_ArrayZipData_"
% opt: (optional) a list of 'Param',value pairs for additional options
% The supported options include
% Recursive: [1|0] if set to 1, will apply the conversion to
% every child; 0 to disable
% Base64: [0|1] if set to 1, _ArrayZipData_ is assumed to
% be encoded with base64 format and need to be
% decoded first. This is needed for JSON but not
% UBJSON data
% Prefix: ['x0x5F'|'x'] for JData files loaded via loadjson/loadubjson, the
% default JData keyword prefix is 'x0x5F'; if the
% json file is loaded using matlab2018's
% jsondecode(), the prefix is 'x'; this function
% attempts to automatically determine the prefix;
% for octave, the default value is an empty string ''.
% FullArrayShape: [0|1] if set to 1, converting _ArrayShape_
% objects to full matrices, otherwise, stay sparse
% MaxLinkLevel: [0|int] When expanding _DataLink_ pointers,
% this sets the maximum level of recursion
% FormatVersion: [2|float]: set the JSONLab output version;
% since v2.0, JSONLab uses JData specification Draft 1
% for output format, it is incompatible with all
% previous releases; if old output is desired,
% please set FormatVersion to 1
%
% output:
% newdata: the converted data if the input data does contain a JData
% structure; otherwise, the same as the input.
%
% examples:
% obj={[],{'test'},true,struct('sparse',sparse(2,3),'magic',uint8(magic(5)))}
% jdata=jdatadecode(jdataencode(obj))
% isequaln(obj,jdata)
%
% 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)
%
newdata=data;
opt=struct;
if(nargin==2)
opt=varargin{1};
elseif(nargin>2)
opt=varargin2struct(varargin{:});
end
opt.fullarrayshape=jsonopt('FullArrayShape',0,opt);
opt.maxlinklevel=jsonopt('MaxLinkLevel',0,opt);
%% process non-structure inputs
if(~isstruct(data))
if(iscell(data))
newdata=cellfun(@(x) jdatadecode(x,opt),data,'UniformOutput',false);
elseif(isa(data,'containers.Map'))
newdata=containers.Map('KeyType',data.KeyType,'ValueType','any');
names=data.keys;
for i=1:length(names)
newdata(names{i})=jdatadecode(data(names{i}),opt);
end
end
return;
end
%% assume the input is a struct below
fn=fieldnames(data);
len=length(data);
needbase64=jsonopt('Base64',0,opt);
format=jsonopt('FormatVersion',2,opt);
if(isoctavemesh)
prefix=jsonopt('Prefix','',opt);
else
prefix=jsonopt('Prefix','x0x5F',opt);
end
if(~isfield(data,N_('_ArrayType_')) && isfield(data,'x_ArrayType_'))
prefix='x';
opt.prefix='x';
end
%% recursively process subfields
if(jsonopt('Recursive',1,opt)==1)
for i=1:length(fn) % depth-first
for j=1:len
if(isstruct(data(j).(fn{i})) || isa(data(j).(fn{i}),'containers.Map'))
newdata(j).(fn{i})=jdatadecode(data(j).(fn{i}),opt);
elseif(iscell(data(j).(fn{i})))
newdata(j).(fn{i})=cellfun(@(x) jdatadecode(x,opt),newdata(j).(fn{i}),'UniformOutput',false);
end
end
end
end
%% handle array data
if(isfield(data,N_('_ArrayType_')) && (isfield(data,N_('_ArrayData_')) || isfield(data,N_('_ArrayZipData_'))))
newdata=cell(len,1);
for j=1:len
if(isfield(data,N_('_ArrayZipSize_')) && isfield(data,N_('_ArrayZipData_')))
zipmethod='zip';
if(isstruct(data(j).(N_('_ArrayZipSize_'))))
data(j).(N_('_ArrayZipSize_'))=jdatadecode(data(j).(N_('_ArrayZipSize_')),opt);
end
dims=data(j).(N_('_ArrayZipSize_'))(:)';
if(length(dims)==1)
dims=[1 dims];
end
if(isfield(data,N_('_ArrayZipType_')))
zipmethod=data(j).(N_('_ArrayZipType_'));
end
if(ismember(zipmethod,{'zlib','gzip','lzma','lzip','lz4','lz4hc','base64'}) || ~isempty(regexp(zipmethod,'^blosc2', 'once')))
decodeparam={};
if(~isempty(regexp(zipmethod,'^blosc2', 'once')))
decompfun=@blosc2decode;
decodeparam={zipmethod};
else
decompfun=str2func([zipmethod 'decode']);
end
arraytype=data(j).(N_('_ArrayType_'));
chartype=0;
if(strcmp(arraytype,'char') || strcmp(arraytype,'logical'))
chartype=1;
arraytype='uint8';
end
if(needbase64 && strcmp(zipmethod,'base64')==0)
ndata=reshape(typecast(decompfun(base64decode(data(j).(N_('_ArrayZipData_'))),decodeparam{:}),arraytype),dims);
else
ndata=reshape(typecast(decompfun(data(j).(N_('_ArrayZipData_')),decodeparam{:}),arraytype),dims);
end
if(chartype)
ndata=char(ndata);
end
else
error('compression method is not supported');
end
else
if(isstruct(data(j).(N_('_ArrayData_'))))
data(j).(N_('_ArrayData_'))=jdatadecode(data(j).(N_('_ArrayData_')),opt);
end
if(isstruct(data(j).(N_('_ArrayData_'))) && isfield(data(j).(N_('_ArrayData_')),N_('_ArrayType_')))
data(j).(N_('_ArrayData_'))=jdatadecode(data(j).(N_('_ArrayData_')),varargin{:});
end
if(iscell(data(j).(N_('_ArrayData_'))))
data(j).(N_('_ArrayData_'))=cell2mat(cellfun(@(x) double(x(:)),data(j).(N_('_ArrayData_')),'uniformoutput',0)).';
end
ndata=cast(data(j).(N_('_ArrayData_')),char(data(j).(N_('_ArrayType_'))));
end
if(isfield(data,N_('_ArrayZipSize_')))
if(isstruct(data(j).(N_('_ArrayZipSize_'))))
data(j).(N_('_ArrayZipSize_'))=jdatadecode(data(j).(N_('_ArrayZipSize_')),opt);
end
dims=data(j).(N_('_ArrayZipSize_'))(:)';
if(iscell(dims))
dims=cell2mat(dims);
end
if(length(dims)==1)
dims=[1 dims];
end
ndata=reshape(ndata(:),fliplr(dims));
ndata=permute(ndata,ndims(ndata):-1:1);
end
iscpx=0;
if(isfield(data,N_('_ArrayIsComplex_')) && isstruct(data(j).(N_('_ArrayIsComplex_'))) )
data(j).(N_('_ArrayIsComplex_'))=jdatadecode(data(j).(N_('_ArrayIsComplex_')),opt);
end
if(isfield(data,N_('_ArrayIsComplex_')) && data(j).(N_('_ArrayIsComplex_')) )
iscpx=1;
end
iscol=0;
if(isfield(data,N_('_ArrayOrder_')))
arrayorder=data(j).(N_('_ArrayOrder_'));
if(~isempty(arrayorder) && (arrayorder(1)=='c' || arrayorder(1)=='C'))
iscol=1;
end
end
if(isfield(data,N_('_ArrayIsSparse_')) && isstruct(data(j).(N_('_ArrayIsSparse_'))) )
data(j).(N_('_ArrayIsSparse_'))=jdatadecode(data(j).(N_('_ArrayIsSparse_')),opt);
end
if(isfield(data,N_('_ArrayIsSparse_')) && data(j).(N_('_ArrayIsSparse_')))
if(isfield(data,N_('_ArraySize_')))
if(isstruct(data(j).(N_('_ArraySize_'))))
data(j).(N_('_ArraySize_'))=jdatadecode(data(j).(N_('_ArraySize_')),opt);
end
dim=data(j).(N_('_ArraySize_'))(:)';
if(iscell(dim))
dim=cell2mat(dim);
end
dim=double(dim);
if(length(dim)==1)
dim=[1 dim];
end
if(iscpx)
ndata(end-1,:)=complex(ndata(end-1,:),ndata(end,:));
end
if isempty(ndata)
% All-zeros sparse
ndata=sparse(dim(1),prod(dim(2:end)));
elseif dim(1)==1
% Sparse row vector
ndata=sparse(1,ndata(1,:),ndata(2,:),dim(1),prod(dim(2:end)));
elseif dim(2)==1
% Sparse column vector
ndata=sparse(ndata(1,:),1,ndata(2,:),dim(1),prod(dim(2:end)));
else
% Generic sparse array.
ndata=sparse(ndata(1,:),ndata(2,:),ndata(3,:),dim(1),prod(dim(2:end)));
end
else
if(iscpx && size(ndata,2)==4)
ndata(3,:)=complex(ndata(3,:),ndata(4,:));
end
ndata=sparse(ndata(1,:),ndata(2,:),ndata(3,:));
end
elseif(isfield(data,N_('_ArrayShape_')))
if(isstruct(data(j).(N_('_ArrayShape_'))))
data(j).(N_('_ArrayShape_'))=jdatadecode(data(j).(N_('_ArrayShape_')),opt);
end
if(iscpx)
if(size(ndata,1)==2)
dim=size(ndata);
dim(end+1)=1;
arraydata=reshape(complex(ndata(1,:),ndata(2,:)),dim(2:end));
else
error('The first dimension must be 2 for complex-valued arrays');
end
else
arraydata=data.(N_('_ArrayData_'));
end
shapeid=data.(N_('_ArrayShape_'));
if(isfield(data,N_('_ArrayZipSize_')))
datasize=data.(N_('_ArrayZipSize_'));
if(iscell(datasize))
datasize=cell2mat(datasize);
end
datasize=double(datasize);
if(iscpx)
datasize=datasize(2:end);
end
else
datasize=size(arraydata);
end
if(isstruct(data(j).(N_('_ArraySize_'))))
data(j).(N_('_ArraySize_'))=jdatadecode(data(j).(N_('_ArraySize_')),opt);
end
arraysize=data.(N_('_ArraySize_'));
if(iscell(arraysize))
arraysize=cell2mat(arraysize);
end
arraysize=double(arraysize);
if(ischar(shapeid))
shapeid={shapeid};
end
arraydata=double(arraydata).';
if(strcmpi(shapeid{1},'diag'))
ndata=spdiags(arraydata(:),0,arraysize(1),arraysize(2));
elseif(strcmpi(shapeid{1},'upper') || strcmpi(shapeid{1},'uppersymm'))
ndata=zeros(arraysize);
ndata(triu(true(size(ndata)))')=arraydata(:);
if(strcmpi(shapeid{1},'uppersymm'))
ndata(triu(true(size(ndata))))=arraydata(:);
end
ndata=ndata.';
elseif(strcmpi(shapeid{1},'lower') || strcmpi(shapeid{1},'lowersymm'))
ndata=zeros(arraysize);
ndata(tril(true(size(ndata)))')=arraydata(:);
if(strcmpi(shapeid{1},'lowersymm'))
ndata(tril(true(size(ndata))))=arraydata(:);
end
ndata=ndata.';
elseif(strcmpi(shapeid{1},'upperband') || strcmpi(shapeid{1},'uppersymmband'))
if(length(shapeid)>1 && isvector(arraydata))
datasize=double([shapeid{2}+1, prod(datasize)/(shapeid{2}+1)]);
end
ndata=spdiags(reshape(arraydata,min(arraysize),datasize(1)),-datasize(1)+1:0,arraysize(2),arraysize(1)).';
if(strcmpi(shapeid{1},'uppersymmband'))
diagonal=diag(ndata);
ndata=ndata+ndata.';
ndata(1:arraysize(1)+1:end)=diagonal;
end
elseif(strcmpi(shapeid{1},'lowerband') || strcmpi(shapeid{1},'lowersymmband'))
if(length(shapeid)>1 && isvector(arraydata))
datasize=double([shapeid{2}+1, prod(datasize)/(shapeid{2}+1)]);
end
ndata=spdiags(reshape(arraydata,min(arraysize),datasize(1)),0:datasize(1)-1,arraysize(2),arraysize(1)).';
if(strcmpi(shapeid{1},'lowersymmband'))
diagonal=diag(ndata);
ndata=ndata+ndata.';
ndata(1:arraysize(1)+1:end)=diagonal;
end
elseif(strcmpi(shapeid{1},'band'))
if(length(shapeid)>1 && isvector(arraydata))
datasize=double([shapeid{2}+shapeid{3}+1, prod(datasize)/(shapeid{2}+shapeid{3}+1)]);
end
ndata=spdiags(reshape(arraydata,min(arraysize),datasize(1)),double(shapeid{2}):-1:-double(shapeid{3}),arraysize(1),arraysize(2));
elseif(strcmpi(shapeid{1},'toeplitz'))
arraydata=reshape(arraydata,flipud(datasize(:))');
ndata=toeplitz(arraydata(1:arraysize(1),2),arraydata(1:arraysize(2),1));
end
if(opt.fullarrayshape && issparse(ndata))
ndata=cast(full(ndata),data(j).(N_('_ArrayType_')));
end
elseif(isfield(data,N_('_ArraySize_')))
if(isstruct(data(j).(N_('_ArraySize_'))))
data(j).(N_('_ArraySize_'))=jdatadecode(data(j).(N_('_ArraySize_')),opt);
end
if(iscpx)
ndata=complex(ndata(1,:),ndata(2,:));
end
if(format>1.9 && iscol==0)
data(j).(N_('_ArraySize_'))=data(j).(N_('_ArraySize_'))(end:-1:1);
end
dims=data(j).(N_('_ArraySize_'))(:)';
if(iscell(dims))
dims=cell2mat(dims);
end
if(length(dims)==1)
dims=[1 dims];
end
ndata=reshape(ndata(:),dims(:)');
if(format>1.9 && iscol==0)
ndata=permute(ndata,ndims(ndata):-1:1);
end
end
newdata{j}=ndata;
end
if(len==1)
newdata=newdata{1};
end
end
%% handle table data
if(isfield(data,N_('_TableRecords_')))
newdata=cell(len,1);
for j=1:len
ndata=data(j).(N_('_TableRecords_'));
if(iscell(ndata))
if(iscell(ndata{1}))
rownum=length(ndata);
colnum=length(ndata{1});
nd=cell(rownum, colnum);
for i1=1:rownum
for i2=1:colnum
nd{i1,i2}=ndata{i1}{i2};
end
end
newdata{j}=cell2table(nd);
else
newdata{j}=cell2table(ndata);
end
else
newdata{j}=array2table(ndata);
end
if(isfield(data(j),N_('_TableRows_'))&& ~isempty(data(j).(N_('_TableRows_'))))
newdata{j}.Properties.RowNames=data(j).(N_('_TableRows_'))(:);
end
if(isfield(data(j),N_('_TableCols_')) && ~isempty(data(j).(N_('_TableCols_'))))
newdata{j}.Properties.VariableNames=data(j).(N_('_TableCols_'));
end
end
if(len==1)
newdata=newdata{1};
end
end
%% handle map data
if(isfield(data,N_('_MapData_')))
newdata=cell(len,1);
for j=1:len
key=cell(1,length(data(j).(N_('_MapData_'))));
val=cell(size(key));
for k=1:length(data(j).(N_('_MapData_')))
key{k}=data(j).(N_('_MapData_')){k}{1};
val{k}=jdatadecode(data(j).(N_('_MapData_')){k}{2},opt);
end
ndata=containers.Map(key,val);
newdata{j}=ndata;
end
if(len==1)
newdata=newdata{1};
end
end
%% handle graph data
if(isfield(data,N_('_GraphNodes_')) && exist('graph','file') && exist('digraph','file'))
newdata=cell(len,1);
isdirected=1;
for j=1:len
nodedata=data(j).(N_('_GraphNodes_'));
if(isstruct(nodedata))
nodetable=struct2table(nodedata);
elseif(isa(nodedata,'containers.Map'))
nodetable=[keys(nodedata);values(nodedata)];
if(strcmp(nodedata.KeyType,'char'))
nodetable=table(nodetable(1,:)',nodetable(2,:)','VariableNames',{'Name','Data'});
else
nodetable=table(nodetable(2,:)','VariableNames',{'Data'});
end
else
nodetable=table;
end
if(isfield(data,N_('_GraphEdges_')))
edgedata=data(j).(N_('_GraphEdges_'));
elseif(isfield(data,N_('_GraphEdges0_')))
edgedata=data(j).(N_('_GraphEdges0_'));
isdirected=0;
elseif(isfield(data,N_('_GraphMatrix_')))
edgedata=jdatadecode(data(j).(N_('_GraphMatrix_')),varargin{:});
end
if(exist('edgedata','var'))
if(iscell(edgedata))
endnodes=edgedata(:,1:2);
endnodes=reshape([endnodes{:}],size(edgedata,1),2);
weight=cell2mat(edgedata(:,3:end));
edgetable=table(endnodes,[weight.Weight]','VariableNames',{'EndNodes','Weight'});
if(isdirected)
newdata{j}=digraph(edgetable,nodetable);
else
newdata{j}=graph(edgetable,nodetable);
end
elseif(ndims(edgedata)==2 && isstruct(nodetable))
newdata{j}=digraph(edgedata,fieldnames(nodetable));
end
end
end
if(len==1)
newdata=newdata{1};
end
end
%% handle bytestream and arbitrary matlab objects
if(isfield(data,N_('_ByteStream_')) && isfield(data,N_('_DataInfo_')))
newdata=cell(len,1);
for j=1:len
if(isfield(data(j).(N_('_DataInfo_')),'MATLABObjectClass'))
if(needbase64)
newdata{j}=getArrayFromByteStream(base64decode(data(j).(N_('_ByteStream_'))));
else
newdata{j}=getArrayFromByteStream(data(j).(N_('_ByteStream_')));
end
end
end
if(len==1)
newdata=newdata{1};
end
end
%% handle data link
if(opt.maxlinklevel>0 && isfield(data,N_('_DataLink_')))
if(ischar(data.(N_('_DataLink_'))))
datalink=data.(N_('_DataLink_'));
if(regexp(datalink,'\:\$'))
ref=regexp(datalink, '^(?<proto>[a-zA-Z]+://)*(?<path>.+)(?<delim>\:)()*(?<jsonpath>(?<=:)\$\d*\.*.*)*', 'names');
else
ref=regexp(datalink, '^(?<proto>[a-zA-Z]+://)*(?<path>.+)(?<delim>\:)*(?<jsonpath>(?<=:)\$\d*\..*)*', 'names');
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);
end
end
end
end
%% subfunctions
function escaped=N_(str)
escaped=[prefix str];
end
end