[doc] update documentation for v0.9

Author: fangq

AUTHORS.txt

@@ -1,6 +1,6 @@
-JSNIRF Toolbox is written by Qianqian Fang as part of the NeuroJData/OpenJData project.
+JSNIRFY Toolbox is written by Qianqian Fang as part of the NeuroJSON project.
 
-Qianqian is currently an Assistant Professor in the 
+Qianqian is currently an Associate Professor in the
 Department of Bioengineering at Northeastern University.
 
 Address: Dept. of Bioengineering
@@ -9,5 +9,4 @@ Address: Dept. of Bioengineering
 URL: http://fanglab.org
 Email: <q.fang at neu.edu>
 
-OpenJData Website : http://openjdata.org
-
+NeuroJSON Website : https://neurojson.org

ChangeLog.txt

@@ -2,7 +2,7 @@
 
 Major updates are marked with a "*"
 
-== JSNIRFY Toolbox v0.5 (Amygdala), FangQ <q.fang (a) neu.edu> ==
+== JSNIRFY Toolbox v0.9 (Amygdala - final), FangQ <q.fang (a) neu.edu> ==
 
  2025-03-15 [672e388] [bug] support pre-R2016b matlab, although output snirf is not compliant
  2025-03-14 [f0caf85]*[bug] saving detectorLabels and sourceLabels as strings, fNIRS/snirf-samples#13

LICENSE_GPLv3.txt

@@ -1,8 +1,8 @@
 ===============================================================================
-=                      Monte Carlo eXtreme (MCX) -- CUDA                      =
+=    JSNIRFY - A compact MATLAB/Octave toolbox to read/write SNIRF files      =
 ===============================================================================
 
-Copyright (c) 2010-2019  Qianqian Fang <q.fang at neu.edu>
+Copyright (c) 2019-2025  Qianqian Fang <q.fang at neu.edu>
 
 -------------------------------------------------------------------------------
 

README.md

@@ -1,9 +1,9 @@
-# JSNIRF Toolbox - A portable MATLAB toolbox for parsing SNIRF (HDF5) and JSNIRF (JSON) files
+# JSNIRFY - A MATLAB/Octave toolbox for parsing SNIRF (HDF5) and JSNIRF (JSON) files
 
-* Copyright (C) 2019,2025  Qianqian Fang <q.fang at neu.edu>
+* Copyright (C) 2019-2025  Qianqian Fang <q.fang at neu.edu>
 * License: GNU General Public License version 3 (GPL v3) or Apache License 2.0, see License*.txt
-* Version: 0.5 (code name: Amygdala)
-* Compatibility: MATLAB R2010b or newer, R2016b or newer saves SNIRF-1.1 compliant files
+* Version: 0.9 (code name: Amygdala - final)
+* Compatibility: MATLAB R2010b or newer, R2016b or newer to save SNIRF-1.1 compliant files, or Octave 5.0 and newer
 * URL: https://github.com/NeuroJSON/jsnirfy
 
 ## Overview
@@ -12,7 +12,7 @@ JSNIRF is a portable format for storage, interchange and processing data generat
 from functional near-infrared spectroscopy, or fNIRS - an emerging functional neuroimaging 
 technique. Built upon the JData and SNIRF specifications, a JSNIRF file has both a 
 text-based interface using the JavaScript Object Notation (JSON) [RFC4627] format 
-and a binary interface using the Universal Binary JSON (UBJSON, http://ubjson.org) derived 
+and a binary interface using the University Binary JSON (UBJSON, https://ubjson.org) derived 
 Binary JData ([BJData](https://github.com/NeuroJSON/bjdata)) serialization format.
 It contains a compatibility layer to provide a 1-to-1 mapping to the existing 
 HDF5 based SNIRF files. A JSNIRF file can be directly parsed by most existing 
@@ -22,17 +22,19 @@ enabled by JData data serialization framework.
 
 This toolbox also provides a fast/complete reader/writer for the HDF5-based SNIRF
 files (along with any HDF5 data) via the EasyH5 toolbox 
-(http://github.com/NeuroJSON/easyh5). The toolbox can read/write SNIRF v1.0 data
-files specified by the SNIRF specification http://github.com/fNIRS/snirf .
+(https://github.com/NeuroJSON/easyh5). The toolbox can read/write SNIRF v1.0 data
+files specified by the SNIRF specification https://github.com/fNIRS/snirf .
 
 This toolbox is selectively dependent on the below toolboxes
 - To read/write SNIRF/HDF5 files, one must install the EasyH5 toolbox at 
-  http://github.com/NeuroJSON/easyh5 ; this is only supported on MATLAB, not Octave.
+  https://github.com/NeuroJSON/easyh5
+- To read/write SNIRF/HDF5 files in GNU Octave, one must install the oct-hdf5 using
+  `pkg install https://github.com/fangq/oct-hdf5/archive/refs/heads/main.zip`
 - To create/read/write JSNIRF files, one must install the JSONLab toolbox
-  http://github.com/NeuroJSON/jsonlab ; this is supported on both MATLAB and Octave.
+  https://github.com/NeuroJSON/jsonlab; this is supported on both MATLAB and Octave.
 - To read/write JSNIRF files with internal data compression, one must install 
-  the JSONLab toolbox http://github.com/NeuroJSON/jsonlab as well as ZMat toolbox
-  http://github.com/NeuroJSON/zmat ; this is supported on both MATLAB and Octave.
+  the JSONLab toolbox https://github.com/NeuroJSON/jsonlab as well as ZMat toolbox
+  https://github.com/NeuroJSON/zmat ; this is supported on both MATLAB and Octave.
 
 ## Why JSNIRF?
 
@@ -59,7 +61,7 @@ JSNIRF file is a plain JSON file, and has various advantages
 
 The binary JSNIRF format uses a binary JSON format (BJData) which is also
 - quasi-human readable despite it is binary
-- free parsers available for [MATLAB](http://github.com/NeuroJSON/jsonlab),
+- free parsers available for [MATLAB](https://github.com/NeuroJSON/jsonlab),
   [Python](https://pypi.org/project/bjdata/), [C++](https://github.com/NeuroJSON/json),
   and [C](https://github.com/NeuroJSON/ubj)
 - easy to write your own parser because of the simplicity
@@ -145,20 +147,20 @@ is converted to the below JSON/JSNIRF data structure
 
 ## Installation
 
-The JSNIRF toolbox can be installed using a single command
+The JSNIRFY toolbox can be installed using a single command
 ```
-    addpath('/path/to/jsnirf');
+  addpath('/path/to/jsnirf');
 ```
 where the `/path/to/jsnirf` should be replaced by the unzipped folder
 of the toolbox (i.e. the folder containing `savejsnirf.m/loadjsnirf.m`).
 
 In order for this toolbox to work, one must install the below dependencies
 - the `saveh5/loadh5` functions are provided by the EasyH5 toolbox at 
-  http://github.com/NeuroJSON/easyh5
+  https://github.com/NeuroJSON/easyh5
 - the `savejson` and `savebj` functions are provided by the JSONLab 
-  toolbox at http://github.com/NeuroJSON/jsonlab 
+  toolbox at https://github.com/NeuroJSON/jsonlab 
 - if data compression is specified by `'compression','zlib'` param/value 
-  pairs, ZMat toolbox will be needed, http://github.com/NeuroJSON/zmat
+  pairs, ZMat toolbox will be needed, https://github.com/NeuroJSON/zmat
 
 
 ## Usage
@@ -193,7 +195,7 @@ Example:
 
 Please submit your bug reports, feature requests and questions to the Github Issues page at
 
-https://github.com/NeuroJSON/jsnirf/issues
+https://github.com/NeuroJSON/jsnirfy/issues
 
 Please feel free to fork our software, making changes, and submit your revision back
-to us via "Pull Requests". JSNIRF toolbox is open-source and we welcome your contributions!
+to us via "Pull Requests". JSNIRFY toolbox is open-source and we welcome your contributions!

aos2soa.m

@@ -20,7 +20,7 @@
 %
 %    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
 %
-%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
+%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirfy for details
 %
 
 if (nargin < 1 || ~isstruct(starray))

jsnirfcreate.m

@@ -7,7 +7,7 @@
 %
 %    Create an empty JSNIRF data structure defined in the JSNIRF
 %    specification: https://github.com/NeuroJSON/jsnirf or a SNIRF data structure
-%    based on https://github.com/fNIRS/snirf
+%    based on the SNIRF specification at https://github.com/fNIRS/snirf
 %
 %    author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -27,7 +27,7 @@
 %
 %    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
 %
-%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
+%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirfy for details
 %
 
 % define empty SNIRF data structure with all required fields

loadjsnirf.m

@@ -6,7 +6,7 @@
 %
 %    Load a text (.jnirs or .json) or binary (.bnirs) based JSNIRF
 %    file defined in the JSNIRF specification:
-%    https://github.com/NeuroJSON/jsnirf or a .snirf/.h5 SNIRF data defined in
+%    https://github.com/NeuroJSON/jsnirfy or a .snirf/.h5 SNIRF data defined in
 %    the SNIRF specification https://github.com/fNIRS/snirf
 %
 %    author: Qianqian Fang (q.fang <at> neu.edu)
@@ -32,7 +32,7 @@
 %
 %    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
 %
-%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
+%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirfy for details
 %
 
 if (nargin < 1)

loadsnirf.m

@@ -6,7 +6,7 @@
 %
 %    Load an HDF5 based SNIRF file, and optionally convert it to a JSON
 %    file based on the JSNIRF specification:
-%    https://github.com/NeuroJSON/jsnirf
+%    https://github.com/NeuroJSON/jsnirfy
 %
 %    author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -29,7 +29,7 @@
 %
 %    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
 %
-%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
+%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirfy for details
 %
 
 if (nargin == 0 || ~ischar(fname))

savejsnirf.m

@@ -39,7 +39,7 @@
 %
 %    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
 %
-%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
+%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirfy for details
 %
 
 if (nargin < 2)

savesnirf.m

@@ -6,7 +6,7 @@ function savesnirf(data, outfile, varargin)
 %
 %    Load an HDF5 based SNIRF file, and optionally convert it to a JSON
 %    file based on the JSNIRF specification:
-%    https://github.com/NeuroJSON/jsnirf
+%    https://github.com/NeuroJSON/jsnirfy
 %
 %    author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -24,7 +24,7 @@ function savesnirf(data, outfile, varargin)
 %
 %    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
 %
-%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
+%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirfy for details
 %
 
 if (nargin < 2 || ~ischar(outfile))

snirfcreate.m

@@ -26,7 +26,7 @@
 %
 %    this file is part of JSNIRFY toolbox: https://github.com/NeuroJSON/jsnirfy
 %
-%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
+%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirfy for details
 %
 
 if (nargin == 1)

snirfdecode.m

@@ -27,7 +27,7 @@
 %
 %    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
 %
-%    License: Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
+%    License: Apache 2.0, see https://github.com/NeuroJSON/jsnirfy for details
 %
 
 if (nargin < 1)

soa2aos.m

@@ -19,7 +19,7 @@
 %
 %    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
 %
-%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
+%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirfy for details
 %
 
 if (nargin < 1 || ~isstruct(starray))