sync jsonlab and jnifty to the latest versions

Author: fangq

Content.txt

@@ -2931,7 +2931,7 @@
  initially created on 2013/08/17
 
  Format specifications:
-    Binary JData (BJData):https://github.com/fangq/bjdata
+    Binary JData (BJData):https://github.com/NeuroJSON/bjdata
     UBJSON:               https://github.com/ubjson/universal-binary-json
     MessagePack:          https://github.com/msgpack/msgpack
 
@@ -3074,7 +3074,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
  including uint16(u), uint32(m), uint64(M) and half-precision float (h)
 
  Format specifications:
-    Binary JData (BJD):   https://github.com/fangq/bjdata
+    Binary JData (BJD):   https://github.com/NeuroJSON/bjdata
     UBJSON:               https://github.com/ubjson/universal-binary-json
     MessagePack:          https://github.com/msgpack/msgpack
 
@@ -3430,7 +3430,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
 
  savejmesh(node,face,elem,fname,opt)
 
- export a mesh to the JMesh format defined in http://github.com/fangq/jmesh
+ export a mesh to the JMesh format defined in http://github.com/NeuroJSON/jmesh
 
 
  input:
@@ -3469,7 +3469,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
     jnii=loadjnifti(inputfile, 'Param1',value1, 'Param2',value2,...)
 
     Load a standard NIFTI-1/2 file or text or binary JNIfTI file with
-    format defined in JNIfTI specification: https://github.com/fangq/jnifti
+    format defined in JNIfTI specification: https://github.com/NeuroJSON/jnifti
 
 
     input:
@@ -3504,7 +3504,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
     savejnifti(jnii, outputfile, 'Param1',value1, 'Param2',value2,...)
 
     Save an in-memory JNIfTI structure into a JNIfTI file with format
-    defined in JNIfTI specification: https://github.com/fangq/jnifti
+    defined in JNIfTI specification: https://github.com/NeuroJSON/jnifti
 
 
     input:
@@ -3559,7 +3559,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
         img: this is a numerical array to be stored in the NIfTI file
         filename: output file name, can have a suffix of '.nii' or '.nii.gz'
                  if a .gz suffix is used, this function needs the JSONLab 
-                 (http://gitlab.com/fangq/jsonlab) and ZMat (http://gitlab.com/fangq/zmat)
+                 (http://gitlab.com/fangq/jsonlab) and ZMat (http://gitlab.com/NeuroJSON/zmat)
                  to perform the compression.
         rawhdr (optional): a struct, as a pre-created/loaded NIfTI header data structure
                 if rawhdr is 'nifti1' or 'nifti2', this function calls 
@@ -3767,7 +3767,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
       fname: (optional) output file name; if not given, save to 'jamdata.jamm'
            if fname has a '.json' or '.jdt' suffix, a text-based
            JSON/JData file will be created (slow); if the suffix is '.jamm' or
-           '.jdb', a Binary JData (https://github.com/fangq/bjdata/) file will be created.
+           '.jdb', a Binary JData (https://github.com/NeuroJSON/bjdata/) file will be created.
       opt: (optional) 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 
@@ -3868,7 +3868,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
     input:
         img: set the jnii.NIFTIData section
         'header_i': the header subfield name defined in the JNIfTI
-                    specification, see https://github.com/fangq/jnifti
+                    specification, see https://github.com/NeuroJSON/jnifti
         value_i: set the value for the specified JNIfTI header field
 
     output:
@@ -3903,7 +3903,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
 
     A fast and portable NIFTI-1/2 and Analyze7.5 file parser and converter
     to the text and binary JNIfTI formats defined in JNIfTI specification:
-    https://github.com/fangq/jnifti  
+    https://github.com/NeuroJSON/jnifti  
 
     This function is compatible with both MATLAB and GNU Octave. 
     It accepts .nii, .nii.gz, .hdr/.img and .hdr.gz/.img.gz input files
@@ -3952,7 +3952,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
           No external dependency if reading .nii/.hdr/.img files;
 
           To load gzipped input files (.nii.gz/.hdr.gz/.img.gz), one must
-          install the ZMat Toolbox (http://github.com/fangq/zmat) and
+          install the ZMat Toolbox (http://github.com/NeuroJSON/zmat) and
           JSONLab Toolbox (http://github.com/fangq/jsonlab);
 
           To save files into the text/binary JNIfTI formatted files, one
@@ -4007,7 +4007,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
     dependency:
 
           To load a JNIfTI file with compression or niifile ends with (.nii.gz/.hdr.gz/.img.gz),
-          one must install the ZMat Toolbox (http://github.com/fangq/zmat) and
+          one must install the ZMat Toolbox (http://github.com/NeuroJSON/zmat) and
           JSONLab Toolbox (http://github.com/fangq/jsonlab);
 
 
@@ -4074,7 +4074,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
     savebnii(jniidata, bniifile, 'Param1',value1, 'Param2',value2,...)
 
     Save an in-memory JNIfTI structure into a binary-JNIfTI file with format
-    defined in JNIfTI specification: https://github.com/fangq/jnifti
+    defined in JNIfTI specification: https://github.com/NeuroJSON/jnifti
 
 
     input:
@@ -4103,7 +4103,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
     savejnii(jniidata, jniifile, 'Param1',value1, 'Param2',value2,...)
 
     Save an in-memory JNIfTI structure into a text-JNIfTI file with format
-    defined in JNIfTI specification: https://github.com/fangq/jnifti
+    defined in JNIfTI specification: https://github.com/NeuroJSON/jnifti
 
 
     input:
@@ -4135,7 +4135,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
  Compress a string or numerical array using the ZLIB-compression
 
  This function depends on JVM in MATLAB or, can optionally use the ZMat 
- toolbox (http://github.com/fangq/zmat)
+ toolbox (http://github.com/NeuroJSON/zmat)
 
  Copyright (c) 2012, Kota Yamaguchi
  URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
@@ -4164,7 +4164,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
 
  Decompressing a ZLIB-compressed byte-stream to recover the original data
  This function depends on JVM in MATLAB or, can optionally use the ZMat 
- toolbox (http://github.com/fangq/zmat)
+ toolbox (http://github.com/NeuroJSON/zmat)
 
  Copyright (c) 2012, Kota Yamaguchi
  URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
@@ -4197,7 +4197,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
  Compress a string or numerical array using the GZIP-compression
 
  This function depends on JVM in MATLAB or, can optionally use the ZMat 
- toolbox (http://github.com/fangq/zmat)
+ toolbox (http://github.com/NeuroJSON/zmat)
 
  Copyright (c) 2012, Kota Yamaguchi
  URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
@@ -4226,7 +4226,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
 
  Decompressing a GZIP-compressed byte-stream to recover the original data
  This function depends on JVM in MATLAB or, can optionally use the ZMat 
- toolbox (http://github.com/fangq/zmat)
+ toolbox (http://github.com/NeuroJSON/zmat)
 
  Copyright (c) 2012, Kota Yamaguchi
  URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
@@ -4258,7 +4258,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
 
  Compress a string or a numerical array using LZMA-compression
 
- This function depends on the ZMat toolbox (http://github.com/fangq/zmat)
+ This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
 
 
  input:
@@ -4283,7 +4283,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
  output = lzmadecode(input,info)
 
  Decompressing an LZMA-compressed byte-stream to recover the original data
- This function depends on the ZMat toolbox (http://github.com/fangq/zmat)
+ This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
 
 
  input:
@@ -4312,7 +4312,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
 
  Compress a string or a numerical array using LZip-compression
 
- This function depends on the ZMat toolbox (http://github.com/fangq/zmat)
+ This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
 
 
  input:
@@ -4337,7 +4337,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
  output = lzipdecode(input,info)
 
  Decompressing an Lzip-compressed byte-stream to recover the original data
- This function depends on the ZMat toolbox (http://github.com/fangq/zmat)
+ This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
 
 
  input:
@@ -4366,7 +4366,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
 
  Compress a string or a numerical array using LZ4-compression
 
- This function depends on the ZMat toolbox (http://github.com/fangq/zmat)
+ This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
 
 
  input:
@@ -4391,7 +4391,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
  output = lz4decode(input,info)
 
  Decompressing an LZ4-compressed byte-stream to recover the original data
- This function depends on the ZMat toolbox (http://github.com/fangq/zmat)
+ This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
 
 
  input:
@@ -4420,7 +4420,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
 
  Compress a string or a numerical array using LZ4HC-compression
 
- This function depends on the ZMat toolbox (http://github.com/fangq/zmat)
+ This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
 
 
  input:
@@ -4445,7 +4445,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
  output = lz4hcdecode(input,info)
 
  Decompressing an LZ4HC-compressed byte-stream to recover the original data
- This function depends on the ZMat toolbox (http://github.com/fangq/zmat)
+ This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
 
 
  input:
@@ -4472,7 +4472,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
 
  Decoding a Base64-encoded byte-stream to recover the original data
  This function depends on JVM in MATLAB or, can optionally use the ZMat 
- toolbox (http://github.com/fangq/zmat)
+ toolbox (http://github.com/NeuroJSON/zmat)
 
  Copyright (c) 2012, Kota Yamaguchi
  URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
@@ -4499,7 +4499,7 @@ LOADMSGPACK parses a msgpack byte buffer into Matlab data structures
  Encoding a binary vector or array using Base64
 
  This function depends on JVM in MATLAB or, can optionally use the ZMat 
- toolbox (http://github.com/fangq/zmat)
+ toolbox (http://github.com/NeuroJSON/zmat)
 
  Copyright (c) 2012, Kota Yamaguchi
  URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities

README.md

@@ -65,12 +65,12 @@ are even more popular than Iso2Mesh itself. For example:
  encoder and decoder [(Editor Pick-of-the-week, Popular File 2018)](https://www.mathworks.com/matlabcentral/fileexchange/33381-jsonlab-a-toolbox-to-encode-decode-json-files)
 - Brain2Mesh (http://mcx.space/brain2mesh): a fully automated
  high-quality brain mesh generation toolbox built on Iso2Mesh
-- JNIfTI (http://github.com/fangq/jnifti): a fast and portable 
+- JNIfTI (http://github.com/NeuroJSON/jnifti): a fast and portable 
  NIfTI-1/2 reader/writer and next-gen NIfTI file format
 - Metch (http://iso2mesh.sf.net/metch): a 3D mesh registration toolbox
 - JData specification (http://openjdata.org): a highly portable
  easy-to-use scientific data annotation method and specification
-- ZMat (http://github.com/fangq/zmat): a data compression library 
+- ZMat (http://github.com/NeuroJSON/zmat): a data compression library 
  and MATLAB/Octave toolbox
 
 Currently, Iso2Mesh and its submodules are broadly distributed 

README.txt

@@ -61,12 +61,12 @@ are even more popular than Iso2Mesh itself. For example:
  encoder and decoder ([https://www.mathworks.com/matlabcentral/fileexchange/33381-jsonlab-a-toolbox-to-encode-decode-json-files Editor Pick-of-the-week, Popular Files 2018])
 * Brain2Mesh (http://mcx.space/brain2mesh): a fully automated \
  high-quality brain mesh generation toolbox built on Iso2Mesh
-* JNIfTI (http://github.com/fangq/jnifti): a fast and portable \
+* JNIfTI (http://github.com/NeuroJSON/jnifti): a fast and portable \
  NIfTI-1/2 reader/writer and next-gen NIfTI file format
 * Metch (http://iso2mesh.sf.net/metch): a 3D mesh registration toolbox
 * JData specification (http://openjdata.org): a highly portable \
  easy-to-use scientific data annotation method and specification
-* ZMat (http://github.com/fangq/zmat): a data compression library \
+* ZMat (http://github.com/NeuroJSON/zmat): a data compression library \
  and MATLAB/Octave toolbox
 
 Currently, Iso2Mesh and its submodules are broadly distributed 

base64decode.m

@@ -4,7 +4,7 @@
 %
 % Decoding a Base64-encoded byte-stream to recover the original data
 % This function depends on JVM in MATLAB or, can optionally use the ZMat 
-% toolbox (http://github.com/fangq/zmat)
+% toolbox (http://github.com/NeuroJSON/zmat)
 %
 % Copyright (c) 2012, Kota Yamaguchi
 % URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
@@ -34,7 +34,7 @@
     output=zmat(varargin{1},0,'base64');
     return;
 elseif(isoctavemesh)
-    error('You must install the ZMat toolbox (http://github.com/fangq/zmat) to use this function in Octave');
+    error('You must install the ZMat toolbox (http://github.com/NeuroJSON/zmat) to use this function in Octave');
 end
 
 error(javachk('jvm'));

base64encode.m

@@ -5,7 +5,7 @@
 % Encoding a binary vector or array using Base64
 %
 % This function depends on JVM in MATLAB or, can optionally use the ZMat 
-% toolbox (http://github.com/fangq/zmat)
+% toolbox (http://github.com/NeuroJSON/zmat)
 %
 % Copyright (c) 2012, Kota Yamaguchi
 % URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities

blosc2decode.m

@@ -0,0 +1,50 @@
+function varargout = blosc2decode(varargin)
+%
+% output = blosc2decode(input,codec)
+% output = blosc2decode(input)
+%    or
+% output = blosc2decode(input,info)
+%
+% Decompressing an blosc2-compressed byte-stream to recover the original data
+% This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
+%
+% authors:Qianqian Fang (q.fang <at> neu.edu)
+%
+% input:
+%      input: a string, int8/uint8 vector or numerical array to store blosc2-compressed data
+%      codec: if the 2nd input is a string, it is treated as a compression method that
+%           blosc2 supports, it can be one of:
+%            'blosc2blosclz', 'blosc2lz4', 'blosc2lz4hc', 'blosc2zlib' and 'blosc2zstd'
+%           if no codec is specified, 'blosc2blosclz' method is assumed
+%      info (optional): a struct produced by the zmat/blosc2encode function during
+%            compression; if not given, the inputs/outputs will be treated as a
+%            1-D vector
+%
+% output:
+%      output: the decompressed byte stream stored in a uint8 vector; if info is
+%            given, output will restore the original data's type and dimensions
+%
+% examples:
+%      [bytes, info]=blosc2encode(eye(10));
+%      orig=blosc2decode(bytes,info);
+%
+% 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)
+%
+
+if (nargin == 0)
+    error('you must provide at least 1 input');
+end
+if (exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3)
+    if (nargin >= 2 && ischar(varargin{2}))
+        [varargout{1:nargout}] = zmat(varargin{1}, 0, varargin{2:end});
+    elseif (nargin > 1)
+        [varargout{1:nargout}] = zmat(varargin{1}, varargin{2:end});
+    else
+        [varargout{1:nargout}] = zmat(varargin{1}, 0, 'blosc2blosclz', varargin{2:end});
+    end
+else
+    error('you must install ZMat toolbox to use this feature: http://github.com/NeuroJSON/zmat');
+end

blosc2encode.m

@@ -0,0 +1,43 @@
+function varargout = blosc2encode(varargin)
+%
+% output = blosc2encode(input)
+%    or
+% [output, info] = blosc2encode(input)
+%
+% Compress a string or a numerical array using LZ4-compression
+%
+% This function depends on the ZMat toolbox (http://github.com/NeuroJSON/zmat)
+%
+% authors:Qianqian Fang (q.fang <at> neu.edu)
+%
+% input:
+%      input: the original data, can be a string, a numerical vector or array
+%
+% output:
+%      output: the compressed byte stream stored in a uint8 vector
+%      info: (optional) a struct storing the metadata of the input, see "help zmat" for details
+%
+% examples:
+%      [bytes, info]=blosc2encode(eye(10));
+%      orig=blosc2decode(bytes,info);
+%
+% 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)
+%
+
+if (nargin == 0)
+    error('you must provide at least 1 input');
+end
+
+if (exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3)
+    if (nargin > 1 && ischar(varargin{2}))
+        [varargout{1:nargout}] = zmat(varargin{1}, 1, varargin{2:end});
+    else
+        [varargout{1:nargout}] = zmat(varargin{1}, 1, 'blosc2blosclz', varargin{2:end});
+    end
+    return
+else
+    error('you must install ZMat toolbox to use this feature: http://github.com/NeuroJSON/zmat');
+end