README.txt

===============================================================================
=                                 JSONLab                                     =
=           An open-source MATLAB/Octave JSON encoder and decoder             =
===============================================================================

*Copyright (C) 2011-2015  Qianqian Fang <fangq at nmr.mgh.harvard.edu>
*License: BSD License, see License_BSD.txt for details
*Version: 1.0 (Optimus - Final)

-------------------------------------------------------------------------------

Table of Content:

I.  Introduction
II. Installation
III.Using JSONLab
IV. Known Issues and TODOs
V.  Contribution and feedback

-------------------------------------------------------------------------------

I.  Introduction

JSON ([http://www.json.org/ JavaScript Object Notation]) is a highly portable, 
human-readable and "[http://en.wikipedia.org/wiki/JSON fat-free]" text format 
to represent complex and hierarchical data. It is as powerful as 
[http://en.wikipedia.org/wiki/XML XML], but less verbose. JSON format is widely 
used for data-exchange in applications, and is essential for the wild success 
of [http://en.wikipedia.org/wiki/Ajax_(programming) Ajax] and 
[http://en.wikipedia.org/wiki/Web_2.0 Web2.0]. 

UBJSON (Universal Binary JSON) is a binary JSON format, specifically 
optimized for compact file size and better performance while keeping
the semantics as simple as the text-based JSON format. Using the UBJSON
format allows to wrap complex binary data in a flexible and extensible
structure, making it possible to process complex and large dataset 
without accuracy loss due to text conversions.

We envision that both JSON and its binary version will serve as part of 
the mainstream data-exchange formats for scientific research in the future. 
It will provide the flexibility and generality achieved by other popular 
general-purpose file specifications, such as
[http://www.hdfgroup.org/HDF5/whatishdf5.html HDF5], with significantly 
reduced complexity and enhanced performance.

JSONLab is a free and open-source implementation of a JSON/UBJSON encoder 
and a decoder in the native MATLAB language. It can be used to convert a MATLAB 
data structure (array, struct, cell, struct array and cell array) into 
JSON/UBJSON formatted strings, or to decode a JSON/UBJSON file into MATLAB 
data structure. JSONLab supports both MATLAB and  
[http://www.gnu.org/software/octave/ GNU Octave] (a free MATLAB clone).

-------------------------------------------------------------------------------

II. Installation

The installation of JSONLab is no different than any other simple
MATLAB toolbox. You only need to download/unzip the JSONLab package
to a folder, and add the folder's path to MATLAB/Octave's path list
by using the following command:

    addpath('/path/to/jsonlab');

If you want to add this path permanently, you need to type "pathtool", 
browse to the jsonlab root folder and add to the list, then click "Save".
Then, run "rehash" in MATLAB, and type "which loadjson", if you see an 
output, that means JSONLab is installed for MATLAB/Octave.

-------------------------------------------------------------------------------

III.Using JSONLab

JSONLab provides two functions, loadjson.m -- a MATLAB->JSON decoder, 
and savejson.m -- a MATLAB->JSON encoder, for the text-based JSON, and 
two equivallent functions -- loadubjson and saveubjson for the binary 
JSON. The detailed help info for the four functions can be found below:

=== loadjson.m ===
<pre>
  data=loadjson(fname,opt)
     or
  data=loadjson(fname,'param1',value1,'param2',value2,...)
 
  parse a JSON (JavaScript Object Notation) file or string
 
  authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
  created on 2011/09/09, including previous works from 
 
          Nedialko Krouchev: http://www.mathworks.com/matlabcentral/fileexchange/25713
             created on 2009/11/02
          François Glineur: http://www.mathworks.com/matlabcentral/fileexchange/23393
             created on  2009/03/22
          Joel Feenstra:
          http://www.mathworks.com/matlabcentral/fileexchange/20565
             created on 2008/07/03
 
  $Id: loadjson.m 452 2014-11-22 16:43:33Z fangq $
 
  input:
       fname: input file name, if fname contains "{}" or "[]", fname
              will be interpreted as a JSON string
       opt: a struct to store parsing options, opt can be replaced by 
            a list of ('param',value) pairs - the param string is equivallent
            to a field in opt. opt can have the following 
            fields (first in [.|.] is the default)
 
            opt.SimplifyCell [0|1]: if set to 1, loadjson will call cell2mat
                          for each element of the JSON data, and group 
                          arrays based on the cell2mat rules.
            opt.FastArrayParser [1|0 or integer]: if set to 1, use a
                          speed-optimized array parser when loading an 
                          array object. The fast array parser may 
                          collapse block arrays into a single large
                          array similar to rules defined in cell2mat; 0 to 
                          use a legacy parser; if set to a larger-than-1
                          value, this option will specify the minimum
                          dimension to enable the fast array parser. For
                          example, if the input is a 3D array, setting
                          FastArrayParser to 1 will return a 3D array;
                          setting to 2 will return a cell array of 2D
                          arrays; setting to 3 will return to a 2D cell
                          array of 1D vectors; setting to 4 will return a
                          3D cell array.
            opt.ShowProgress [0|1]: if set to 1, loadjson displays a progress bar.
 
  output:
       dat: a cell array, where {...} blocks are converted into cell arrays,
            and [...] are converted to arrays
 
  examples:
       dat=loadjson('{"obj":{"string":"value","array":[1,2,3]}}')
       dat=loadjson(['examples' filesep 'example1.json'])
       dat=loadjson(['examples' filesep 'example1.json'],'SimplifyCell',1)
</pre>

=== savejson.m ===

<pre>
  json=savejson(rootname,obj,filename)
     or
  json=savejson(rootname,obj,opt)
  json=savejson(rootname,obj,'param1',value1,'param2',value2,...)
 
  convert a MATLAB object (cell, struct or array) into a JSON (JavaScript
  Object Notation) string
 
  author: Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
  created on 2011/09/09
 
  $Id: savejson.m 458 2014-12-19 22:17:17Z fangq $
 
  input:
       rootname: the name of the root-object, when set to '', the root name
         is ignored, however, when opt.ForceRootName is set to 1 (see below),
         the MATLAB variable name will be used as the root name.
       obj: a MATLAB object (array, cell, cell array, struct, struct array).
       filename: a string for the file name to save the output JSON data.
       opt: a struct for additional options, ignore to use default values.
         opt can have the following fields (first in [.|.] is the default)
 
         opt.FileName [''|string]: a file name to save the output JSON data
         opt.FloatFormat ['%.10g'|string]: format to show each numeric element
                          of a 1D/2D array;
         opt.ArrayIndent [1|0]: if 1, output explicit data array with
                          precedent indentation; if 0, no indentation
         opt.ArrayToStruct[0|1]: when set to 0, savejson outputs 1D/2D
                          array in JSON array format; if sets to 1, an
                          array will be shown as a struct with fields
                          "_ArrayType_", "_ArraySize_" and "_ArrayData_"; for
                          sparse arrays, the non-zero elements will be
                          saved to _ArrayData_ field in triplet-format i.e.
                          (ix,iy,val) and "_ArrayIsSparse_" will be added
                          with a value of 1; for a complex array, the 
                          _ArrayData_ array will include two columns 
                          (4 for sparse) to record the real and imaginary 
                          parts, and also "_ArrayIsComplex_":1 is added. 
         opt.ParseLogical [0|1]: if this is set to 1, logical array elem
                          will use true/false rather than 1/0.
         opt.NoRowBracket [1|0]: if this is set to 1, arrays with a single
                          numerical element will be shown without a square
                          bracket, unless it is the root object; if 0, square
                          brackets are forced for any numerical arrays.
         opt.ForceRootName [0|1]: when set to 1 and rootname is empty, savejson
                          will use the name of the passed obj variable as the 
                          root object name; if obj is an expression and 
                          does not have a name, 'root' will be used; if this 
                          is set to 0 and rootname is empty, the root level 
                          will be merged down to the lower level.
         opt.Inf ['"$1_Inf_"'|string]: a customized regular expression pattern
                          to represent +/-Inf. The matched pattern is '([-+]*)Inf'
                          and $1 represents the sign. For those who want to use
                          1e999 to represent Inf, they can set opt.Inf to '$11e999'
         opt.NaN ['"_NaN_"'|string]: a customized regular expression pattern
                          to represent NaN
         opt.JSONP [''|string]: to generate a JSONP output (JSON with padding),
                          for example, if opt.JSONP='foo', the JSON data is
                          wrapped inside a function call as 'foo(...);'
         opt.UnpackHex [1|0]: conver the 0x[hex code] output by loadjson 
                          back to the string form
         opt.SaveBinary [0|1]: 1 - save the JSON file in binary mode; 0 - text mode.
         opt.Compact [0|1]: 1- out compact JSON format (remove all newlines and tabs)
 
         opt can be replaced by a list of ('param',value) pairs. The param 
         string is equivallent to a field in opt and is case sensitive.
  output:
       json: a string in the JSON format (see http://json.org)
 
  examples:
       jsonmesh=struct('MeshNode',[0 0 0;1 0 0;0 1 0;1 1 0;0 0 1;1 0 1;0 1 1;1 1 1],... 
                'MeshTetra',[1 2 4 8;1 3 4 8;1 2 6 8;1 5 6 8;1 5 7 8;1 3 7 8],...
                'MeshTri',[1 2 4;1 2 6;1 3 4;1 3 7;1 5 6;1 5 7;...
                           2 8 4;2 8 6;3 8 4;3 8 7;5 8 6;5 8 7],...
                'MeshCreator','FangQ','MeshTitle','T6 Cube',...
                'SpecialData',[nan, inf, -inf]);
       savejson('jmesh',jsonmesh)
       savejson('',jsonmesh,'ArrayIndent',0,'FloatFormat','\t%.5g')
 </pre>

=== loadubjson.m ===

<pre>
  data=loadubjson(fname,opt)
     or
  data=loadubjson(fname,'param1',value1,'param2',value2,...)
 
  parse a JSON (JavaScript Object Notation) file or string
 
  authors:Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
  created on 2013/08/01
 
  $Id: loadubjson.m 436 2014-08-05 20:51:40Z fangq $
 
  input:
       fname: input file name, if fname contains "{}" or "[]", fname
              will be interpreted as a UBJSON string
       opt: a struct to store parsing options, opt can be replaced by 
            a list of ('param',value) pairs - the param string is equivallent
            to a field in opt. opt can have the following 
            fields (first in [.|.] is the default)
 
            opt.SimplifyCell [0|1]: if set to 1, loadubjson will call cell2mat
                          for each element of the JSON data, and group 
                          arrays based on the cell2mat rules.
            opt.IntEndian [B|L]: specify the endianness of the integer fields
                          in the UBJSON input data. B - Big-Endian format for 
                          integers (as required in the UBJSON specification); 
                          L - input integer fields are in Little-Endian order.
 
  output:
       dat: a cell array, where {...} blocks are converted into cell arrays,
            and [...] are converted to arrays
 
  examples:
       obj=struct('string','value','array',[1 2 3]);
       ubjdata=saveubjson('obj',obj);
       dat=loadubjson(ubjdata)
       dat=loadubjson(['examples' filesep 'example1.ubj'])
       dat=loadubjson(['examples' filesep 'example1.ubj'],'SimplifyCell',1)
</pre>

=== saveubjson.m ===

<pre>
  json=saveubjson(rootname,obj,filename)
     or
  json=saveubjson(rootname,obj,opt)
  json=saveubjson(rootname,obj,'param1',value1,'param2',value2,...)
 
  convert a MATLAB object (cell, struct or array) into a Universal 
  Binary JSON (UBJSON) binary string
 
  author: Qianqian Fang (fangq<at> nmr.mgh.harvard.edu)
  created on 2013/08/17
 
  $Id: saveubjson.m 440 2014-09-17 19:59:45Z fangq $
 
  input:
       rootname: the name of the root-object, when set to '', the root name
         is ignored, however, when opt.ForceRootName is set to 1 (see below),
         the MATLAB variable name will be used as the root name.
       obj: a MATLAB object (array, cell, cell array, struct, struct array)
       filename: a string for the file name to save the output UBJSON data
       opt: a struct for additional options, ignore to use default values.
         opt can have the following fields (first in [.|.] is the default)
 
         opt.FileName [''|string]: a file name to save the output JSON data
         opt.ArrayToStruct[0|1]: when set to 0, saveubjson outputs 1D/2D
                          array in JSON array format; if sets to 1, an
                          array will be shown as a struct with fields
                          "_ArrayType_", "_ArraySize_" and "_ArrayData_"; for
                          sparse arrays, the non-zero elements will be
                          saved to _ArrayData_ field in triplet-format i.e.
                          (ix,iy,val) and "_ArrayIsSparse_" will be added
                          with a value of 1; for a complex array, the 
                          _ArrayData_ array will include two columns 
                          (4 for sparse) to record the real and imaginary 
                          parts, and also "_ArrayIsComplex_":1 is added. 
         opt.ParseLogical [1|0]: if this is set to 1, logical array elem
                          will use true/false rather than 1/0.
         opt.NoRowBracket [1|0]: if this is set to 1, arrays with a single
                          numerical element will be shown without a square
                          bracket, unless it is the root object; if 0, square
                          brackets are forced for any numerical arrays.
         opt.ForceRootName [0|1]: when set to 1 and rootname is empty, saveubjson
                          will use the name of the passed obj variable as the 
                          root object name; if obj is an expression and 
                          does not have a name, 'root' will be used; if this 
                          is set to 0 and rootname is empty, the root level 
                          will be merged down to the lower level.
         opt.JSONP [''|string]: to generate a JSONP output (JSON with padding),
                          for example, if opt.JSON='foo', the JSON data is
                          wrapped inside a function call as 'foo(...);'
         opt.UnpackHex [1|0]: conver the 0x[hex code] output by loadjson 
                          back to the string form
 
         opt can be replaced by a list of ('param',value) pairs. The param 
         string is equivallent to a field in opt and is case sensitive.
  output:
       json: a binary string in the UBJSON format (see http://ubjson.org)
 
  examples:
       jsonmesh=struct('MeshNode',[0 0 0;1 0 0;0 1 0;1 1 0;0 0 1;1 0 1;0 1 1;1 1 1],... 
                'MeshTetra',[1 2 4 8;1 3 4 8;1 2 6 8;1 5 6 8;1 5 7 8;1 3 7 8],...
                'MeshTri',[1 2 4;1 2 6;1 3 4;1 3 7;1 5 6;1 5 7;...
                           2 8 4;2 8 6;3 8 4;3 8 7;5 8 6;5 8 7],...
                'MeshCreator','FangQ','MeshTitle','T6 Cube',...
                'SpecialData',[nan, inf, -inf]);
       saveubjson('jsonmesh',jsonmesh)
       saveubjson('jsonmesh',jsonmesh,'meshdata.ubj')
</pre>


=== examples ===

Under the "examples" folder, you can find several scripts to demonstrate the
basic utilities of JSONLab. Running the "demo_jsonlab_basic.m" script, you 
will see the conversions from MATLAB data structure to JSON text and backward.
In "jsonlab_selftest.m", we load complex JSON files downloaded from the Internet
and validate the loadjson/savejson functions for regression testing purposes.
Similarly, a "demo_ubjson_basic.m" script is provided to test the saveubjson
and loadubjson pairs for various matlab data structures.

Please run these examples and understand how JSONLab works before you use
it to process your data.

-------------------------------------------------------------------------------

IV. Known Issues and TODOs

JSONLab has several known limitations. We are striving to make it more general
and robust. Hopefully in a few future releases, the limitations become less.

Here are the known issues:

# 3D or higher dimensional cell/struct-arrays will be converted to 2D arrays;
# When processing names containing multi-byte characters, Octave and MATLAB \
can give different field-names; you can use feature('DefaultCharacterSet','latin1') \
in MATLAB to get consistant results
# savejson can not handle class and dataset.
# saveubjson converts a logical array into a uint8 ([U]) array
# an unofficial N-D array count syntax is implemented in saveubjson. We are \
actively communicating with the UBJSON spec maintainer to investigate the \
possibility of making it upstream
# loadubjson can not parse all UBJSON Specification (Draft 9) compliant \
files, however, it can parse all UBJSON files produced by saveubjson.

-------------------------------------------------------------------------------

V. Contribution and feedback

JSONLab is an open-source project. This means you can not only use it and modify
it as you wish, but also you can contribute your changes back to JSONLab so
that everyone else can enjoy the improvement. For anyone who want to contribute,
please download JSONLab source code from it's subversion repository by using the
following command:

 svn checkout svn://svn.code.sf.net/p/iso2mesh/code/trunk/jsonlab jsonlab

You can make changes to the files as needed. Once you are satisfied with your
changes, and ready to share it with others, please cd the root directory of 
JSONLab, and type

 svn diff > yourname_featurename.patch

You then email the .patch file to JSONLab's maintainer, Qianqian Fang, at
the email address shown in the beginning of this file. Qianqian will review 
the changes and commit it to the subversion if they are satisfactory.

We appreciate any suggestions and feedbacks from you. Please use iso2mesh's
mailing list to report any questions you may have with JSONLab:

http://groups.google.com/group/iso2mesh-users?hl=en&pli=1

(Subscription to the mailing list is needed in order to post messages).