loadbj.m

function [data, mmap] = loadbj(fname, varargin)
%
% data=loadbj(fname,opt)
%    or
% [data, mmap]=loadbj(fname,'param1',value1,'param2',value2,...)
%
% Parse a Binary JData (BJData v1 Draft-2, defined in https://github.com/NeuroJSON/bjdata)
% file or memory buffer and convert into a MATLAB data structure
%
% By default, this function parses BJD-compliant output. The BJD
% specification is largely similar to UBJSON, with additional data types
% including uint16(u), uint32(m), uint64(M) and half-precision float (h).
% Starting from BJD Draft-2 (JSONLab 3.0 beta or later), all integer and
% floating-point numbers are parsed in Little-Endian as opposed to
% Big-Endian form as in BJD Draft-1/UBJSON Draft-12 (JSONLab 2.0 or older)
%
% authors:Qianqian Fang (q.fang <at> neu.edu)
% initially created on 2013/08/01
%
% input:
%      fname: input file name, if fname contains "{}" or "[]", fname
%             will be interpreted as a BJData/UBJSON string
%      opt: a struct to store parsing options, opt can be replaced by
%           a list of ('param',value) pairs - the param string is equivalent
%           to a field in opt. opt can have the following
%           fields (first in [.|.] is the default)
%
%           SimplifyCell [1|0]: if set to 1, loadbj will call cell2mat
%                         for each element of the JSON data, and group
%                         arrays based on the cell2mat rules.
%           Endian ['L'|'B']: specify the endianness of the numbers
%                         in the BJData/UBJSON input data. Default: 'L'.
%
%                         Starting from JSONLab 2.9, BJData by default uses
%                         [L] Little-Endian for both integers and floating
%                         point numbers. This is a major departure from the
%                         UBJSON specification, where 'B' - Big-Endian -
%                         format is used for integer fields. UBJSON does
%                         not specifically define Endianness for
%                         floating-point numbers, resulting in mixed
%                         implementations. JSONLab 2.0-2.1 used 'B' for
%                         integers and floating-points; JSONLab 1.x uses
%                         'B' for integers and native-endianness for
%                         floating-point numbers.
%           NameIsString [0|1]: for UBJSON Specification Draft 8 or
%                         earlier versions (JSONLab 1.0 final or earlier),
%                         the "name" tag is treated as a string. To load
%                         these UBJSON data, you need to manually set this
%                         flag to 1.
%           UseMap [0|1]: if set to 1, loadbj uses a containers.Map to
%                         store map objects; otherwise use a struct object
%           ObjectID [0|integer or list]: if set to a positive number,
%                         it returns the specified JSON object by index
%                         in a multi-JSON document; if set to a vector,
%                         it returns a list of specified objects.
%           FormatVersion [2|float]: set the JSONLab format 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 1.9 or earlier.
%           MmapOnly [0|1]: if set to 1, this function only returns mmap
%           MMapInclude 'str1' or  {'str1','str2',..}: if provided, the
%                         returned mmap will be filtered by only keeping
%                         entries containing any one of the string patterns
%                         provided in a cell
%           MMapExclude 'str1' or  {'str1','str2',..}: if provided, the
%                         returned mmap will be filtered by removing
%                         entries containing any one of the string patterns
%                         provided in a cell
%
% output:
%      dat: a cell array, where {...} blocks are converted into cell arrays,
%           and [...] are converted to arrays
%      mmap: (optional) a cell array in the form of
%           {{jsonpath1,[start,length]}, {jsonpath2,[start,length]}, ...}
%           where jsonpath_i is a string in the form of JSONPath, and
%           start is an integer referring to the offset from the beginning
%           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 returned 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);
%      dat=loadbj(ubjdata)
%      dat=loadbj(['examples' filesep 'example1.bjd'])
%      dat=loadbj(['examples' filesep 'example1.bjd'],'SimplifyCell',0)
%
% 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)
%

opt = varargin2struct(varargin{:});

if (length(fname) < 4096 && exist(fname, 'file'))
    fid = fopen(fname, 'rb');
    string = fread(fid, jsonopt('MaxBuffer', inf, opt), 'uint8=>char')';
    fclose(fid);
elseif (all(fname < 128) && ~isempty(regexpi(fname, '^\s*(http|https|ftp|file)://')))
    if (exist('webread'))
        string = char(webread(fname, weboptions('ContentType', 'binary')))';
    else
        string = urlread(fname);
    end
elseif (~isempty(fname) && any(fname(1) == '[{SCHiUIulmLMhdDTFZN'))
    string = fname;
else
    error('input file does not exist or buffer is invalid');
end

pos = 1;
inputlen = length(string);
inputstr = string;

opt.simplifycell = jsonopt('SimplifyCell', 1, opt);
opt.simplifycellarray = jsonopt('SimplifyCellArray', 0, opt);
opt.usemap = jsonopt('UseMap', 0, opt);
opt.nameisstring = jsonopt('NameIsString', 0, opt);
mmaponly = jsonopt('MmapOnly', 0, opt);

[os, maxelem, systemendian] = computer;
opt.flipendian_ = (systemendian ~= upper(jsonopt('Endian', 'L', opt)));

objid = jsonopt('ObjectID', 0, opt);
maxobjid = max(objid);
if (maxobjid == 0)
    maxobjid = inf;
end

opt.jsonpath_ = '$';
if (nargout > 1 || mmaponly)
    mmap = {};
end
jsoncount = 1;
while pos <= inputlen
    [cc, pos] = next_char(inputstr, pos);
    switch (cc)
        case '{'
            if (nargout > 1 || mmaponly)
                mmap{end + 1} = {opt.jsonpath_, pos};
                [data{jsoncount}, pos, newmmap] = parse_object(inputstr, pos, opt);
                if (pos < 0)
                    opt.usemap = 1;
                    [data{jsoncount}, pos, newmmap] = parse_object(inputstr, -pos, opt);
                end
                mmap{end}{2} = [mmap{end}{2}, pos - mmap{end}{2}];
                mmap = [mmap(:); newmmap(:)];
            else
                [data{jsoncount}, pos] = parse_object(inputstr, pos, opt);
                if (pos < 0)
                    opt.usemap = 1;
                    [data{jsoncount}, pos] = parse_object(inputstr, -pos, opt);
                end
            end
        case '['
            if (nargout > 1 || mmaponly)
                mmap{end + 1} = {opt.jsonpath_, pos};
                [data{jsoncount}, pos, newmmap] = parse_array(inputstr, pos, opt);
                mmap{end}{2} = [mmap{end}{2}, pos - mmap{end}{2}];
                mmap = [mmap(:); newmmap(:)];
            else
                [data{jsoncount}, pos] = parse_array(inputstr, pos, opt);
            end
        case {'S', 'C', 'H', 'i', 'U', 'I', 'u', 'l', 'm', 'L', 'M', 'h', 'd', 'D', 'T', 'F', 'Z', 'N'}
            [data{jsoncount}, pos] = parse_value(inputstr, pos, [], opt);
        otherwise
            error_pos('Root level structure must start with a valid marker "{[SCHiUIulmLMhdDTFZN"', inputstr, pos);
    end
    if (jsoncount >= maxobjid)
        break
    end
    opt.jsonpath_ = sprintf('$%d', jsoncount);
    jsoncount = jsoncount + 1;
end % while

if (length(objid) > 1 || min(objid) > 1)
    data = data(objid(objid <= length(data)));
end

jsoncount = length(data);
if (jsoncount == 1 && iscell(data))
    data = data{1};
end
if (nargout > 1 || mmaponly)
    mmap = mmap';
    mmap = filterjsonmmap(mmap, jsonopt('MMapExclude', {}, opt), 0);
    mmap = filterjsonmmap(mmap, jsonopt('MMapInclude', {}, opt), 1);
end
if (jsonopt('JDataDecode', 1, varargin{:}) == 1)
    try
        data = jdatadecode(data, 'Base64', 0, 'Recursive', 1, varargin{:});
    catch ME
        warning(['Failed to decode embedded JData annotations, '...
                 'return raw JSON data\n\njdatadecode error: %s\n%s\nCall stack:\n%s\n'], ...
                ME.identifier, ME.message, char(savejson('', ME.stack)));
    end
end
if (mmaponly)
    data = mmap;
end

%% -------------------------------------------------------------------------
%% helper functions
%% -------------------------------------------------------------------------

function [data, adv] = parse_block(inputstr, pos, type, count, varargin)
if (count >= 0 && ~isempty(type) && isempty(strfind('iUIulmLMdDh', type)))
    adv = 0;
    switch (type)
        case {'S', 'H', '{', '['}
            data = cell(1, count);
            adv = pos;
            for i = 1:count
                [data{i}, pos] = parse_value(inputstr, pos, type, varargin{:});
            end
            adv = pos - adv;
        case 'C'
            data = inputstr(pos:pos + count);
            adv = count;
        case {'T', 'F', 'N'}
            error_pos(sprintf('For security reasons, optimized type %c is disabled at position %%d', type), inputstr, pos);
        otherwise
            error_pos(sprintf('Unsupported optimized type %c at position %%d', type), inputstr, pos);
    end
    return
end
[cid, len] = elem_info(inputstr, pos, type);
datastr = inputstr(pos:pos + len * count - 1);
newdata = uint8(datastr);
if (varargin{1}.flipendian_)
    newdata = swapbytes(typecast(newdata, cid));
end
data = typecast(newdata, cid);
adv = double(len * count);
%% -------------------------------------------------------------------------

function [object, pos, mmap] = parse_array(inputstr,  pos, varargin) % JSON array is written in row-major order
if (nargout > 2)
    mmap = {};
    origpath = varargin{1}.jsonpath_;
end
pos = parse_char(inputstr, pos, '[');
object = cell(0, 1);
dim = [];
type = '';
count = -1;
[cc, pos] = next_char(inputstr, pos);
if (cc == '$')
    type = inputstr(pos + 1);
    pos = pos + 2;
end
[cc, pos] = next_char(inputstr, pos);
if (cc == '#')
    pos = pos + 1;
    [cc, pos] = next_char(inputstr, pos);
    if (cc == '[')
        if (isfield(varargin{1}, 'noembedding_') && varargin{1}.noembedding_ == 1)
            error_pos('ND array size specifier does not support embedding', inputstr, pos);
        end
        varargin{1}.noembedding_ = 1;
        [dim, pos] = parse_array(inputstr, pos, varargin{:});
        count = prod(double(dim));
        varargin{1}.noembedding_ = 0;
    else
        [val, pos] = parse_number(inputstr, pos, varargin{:});
        count = double(val);
    end
end
if (~isempty(type))
    if (count >= 0)
        [object, adv] = parse_block(inputstr, pos, type, count, varargin{:});
        if (~isempty(dim) && length(dim) > 1)
            object = permute(reshape(object, fliplr(dim(:)')), length(dim):-1:1);
        end
        pos = pos + adv;
        return
    else
        endpos = match_bracket(inputstr, pos);
        [cid, len] = elem_info(inputstr, pos, type);
        count = (endpos - pos) / len;
        [object, adv] = parse_block(inputstr, pos, type, count, varargin{:});
        pos = pos + adv;
        pos = parse_char(inputstr, pos, ']');
        return
    end
end
[cc, pos] = next_char(inputstr, pos);
if cc ~= ']'
    while 1
        if (nargout > 2)
            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}];
            mmap = [mmap(:); newmmap(:)];
        else
            [val, pos] = parse_value(inputstr, pos, [], varargin{:});
        end
        object{end + 1} = val;
        [cc, pos] = next_char(inputstr, pos);
        if cc == ']'
            break
        end
    end
end
if (varargin{1}.simplifycell)
    if (iscell(object) && ~isempty(object) && isnumeric(object{1}))
        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)
                    catdim = size(object{1});
                    catdim = ndims(object{1}) - (catdim(end) == 1) + 1;
                    object = cat(catdim, object{:});
                    object = permute(object, ndims(object):-1:1);
                else
                    object = cell2mat(object')';
                end
                if (iscell(oldobj) && isstruct(object) && numel(object) > 1 && varargin{1}.simplifycellarray == 0)
                    object = oldobj;
                end
            catch
            end
        end
    end
    if (~iscell(object) && size(object, 1) > 1 && ndims(object) == 2)
        object = object';
    end
end
if (count == -1)
    pos = parse_char(inputstr, pos, ']');
end

%% -------------------------------------------------------------------------

function pos = parse_char(inputstr, pos, c)
if pos > length(inputstr) || inputstr(pos) ~= c
    error_pos(sprintf('Expected %c at position %%d', c), inputstr, pos);
else
    pos = pos + 1;
end

%% -------------------------------------------------------------------------

function [c, pos] = next_char(inputstr, pos)
if pos > length(inputstr)
    c = [];
else
    c = inputstr(pos);
    while (c == 'N')
        pos = pos + 1;
        c = inputstr(pos);
    end
end

%% -------------------------------------------------------------------------
function [str, pos] = parse_name(inputstr, pos, varargin)
[val, pos] = parse_number(inputstr, pos, varargin{:});
bytelen = double(val);
if (length(inputstr) >= pos + bytelen - 1)
    str = inputstr(pos:pos + bytelen - 1);
    pos = pos + bytelen;
else
    error_pos('End of file while expecting end of name', inputstr, pos);
end

%% -------------------------------------------------------------------------

function [str, pos] = parseStr(inputstr, pos, type, varargin)
if (isempty(type))
    type = inputstr(pos);
    if type ~= 'S' && type ~= 'C' && type ~= 'H'
        error_pos('String starting with S expected at position %d', inputstr, pos);
    else
        pos = pos + 1;
    end
end

if (type == 'C')
    str = inputstr(pos);
    pos = pos + 1;
    return
end
[val, pos] = parse_number(inputstr, pos, varargin{:});
bytelen = double(val);
if (length(inputstr) >= pos + bytelen - 1)
    str = inputstr(pos:pos + bytelen - 1);
    pos = pos + bytelen;
else
    error_pos('End of file while expecting end of inputstr', inputstr, pos);
end

%% -------------------------------------------------------------------------

function [num, pos] = parse_number(inputstr, pos, varargin)
id = strfind('iUIulmLMhdD', inputstr(pos));
if (isempty(id))
    error_pos('expecting a number at position %d', inputstr, pos);
end
type = {'int8', 'uint8', 'int16', 'uint16', 'int32', 'uint32', 'int64', 'uint64', 'half', 'single', 'double'};
bytelen = [1, 1, 2, 2, 4, 4, 8, 8, 2, 4, 8];
if (~exist('half', 'builtin'))
    type{9} = 'uint16';
end
datastr = inputstr(pos + 1:pos + bytelen(id));
newdata = uint8(datastr);
if (varargin{1}.flipendian_)
    newdata = swapbytes(typecast(newdata, type{id}));
end
num = typecast(newdata, type{id});
pos = pos + bytelen(id) + 1;

%% -------------------------------------------------------------------------

function varargout = parse_value(inputstr, pos, type, varargin)
if (length(type) == 1)
    cc = type;
    varargout{2} = pos;
else
    [cc, varargout{2}] = next_char(inputstr, pos);
end
if (nargout > 2)
    varargout{3} = {};
end
switch (cc)
    case {'S', 'C', 'H'}
        [varargout{1:2}] = parseStr(inputstr, varargout{2}, type, varargin{:});
        return
    case '['
        [varargout{1:nargout}] = parse_array(inputstr, varargout{2}, varargin{:});
        return
    case '{'
        [varargout{1:nargout}] = parse_object(inputstr, varargout{2}, varargin{:});
        if (varargout{2} < 0)
            varargin{1}.usemap = 1;
            [varargout{1:nargout}] = parse_object(inputstr, -varargout{2}, varargin{:});
        end
        return
    case {'i', 'U', 'I', 'u', 'l', 'm', 'L', 'M', 'h', 'd', 'D'}
        [varargout{1:2}] = parse_number(inputstr, varargout{2}, varargin{:});
        return
    case 'T'
        varargout{1} = true;
        varargout{2} = varargout{2} + 1;
        return
    case 'F'
        varargout{1} = false;
        varargout{2} = varargout{2} + 1;
        return
    case {'Z', 'N'}
        varargout{1} = [];
        varargout{2} = varargout{2} + 1;
        return
end
error_pos('Value expected at position %d', inputstr, varargout{2});
%% -------------------------------------------------------------------------

function pos = error_pos(msg, inputstr, pos)
poShow = max(min([pos - 15 pos - 1 pos pos + 20], length(inputstr)), 1);
if poShow(3) == poShow(2)
    poShow(3:4) = poShow(2) + [0 -1];  % display nothing after
end
msg = [sprintf(msg, pos) ': ' ...
       inputstr(poShow(1):poShow(2)) '<error>' inputstr(poShow(3):poShow(4))];
error('JSONLAB:BJData:InvalidFormat', msg);

%% -------------------------------------------------------------------------
function [object, pos, mmap] = parse_object(inputstr, pos, varargin)
oldpos = pos;
if (nargout > 2)
    mmap = {};
    origpath = varargin{1}.jsonpath_;
end
pos = parse_char(inputstr, pos, '{');
usemap = varargin{1}.usemap;
if (usemap)
    object = containers.Map();
else
    object = [];
end
count = -1;
[cc, pos] = next_char(inputstr, pos);
if (cc == '$')
    pos = pos + 2;
end
[cc, pos] = next_char(inputstr, pos);
if (cc == '#')
    pos = pos + 1;
    [val, pos] = parse_number(inputstr, pos, varargin{:});
    count = double(val);
end
[cc, pos] = next_char(inputstr, pos);
if cc ~= '}'
    num = 0;
    while 1
        if (varargin{1}.nameisstring)
            [str, pos] = parseStr(inputstr, pos, [], varargin{:});
        else
            [str, pos] = parse_name(inputstr, pos, varargin{:});
        end
        if (length(str) > 63)
            pos = -oldpos;
            object = [];
            return
        end
        if isempty(str)
            str = 'x0x0_'; % empty name is valid in BJData/UBJSON, decodevarname('x0x0_') restores '\0'
        end
        if (nargout > 2)
            varargin{1}.jsonpath_ = [origpath, '.', str];
            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}];
            mmap = [mmap(:); newmmap(:)];
        else
            [val, pos] = parse_value(inputstr, pos, [], varargin{:});
        end
        num = num + 1;
        if (usemap)
            object(str) = val;
        else
            str = encodevarname(str, varargin{:});
            if (length(str) > 63)
                pos = -oldpos;
                object = [];
                return
            end
            object.(str) = val;
        end
        [cc, pos] = next_char(inputstr, pos);
        if (count >= 0 && num >= count) || cc == '}'
            break
        end
    end
end
if (count == -1)
    pos = parse_char(inputstr, pos, '}');
end

%% -------------------------------------------------------------------------
function [cid, len] = elem_info(inputstr, pos, type)
id = strfind('iUIulmLMhdD', type);
type = {'int8', 'uint8', 'int16', 'uint16', 'int32', 'uint32', 'int64', 'uint64', 'half', 'single', 'double'};
bytelen = [1, 1, 2, 2, 4, 4, 8, 8, 2, 4, 8];
if (~exist('half', 'builtin'))
    type{9} = 'uint16';
end
if (id > 0)
    cid = type{id};
    len = bytelen(id);
else
    error_pos('unsupported type at position %d', inputstr, pos);
end