[doc] update version to 0.5, add external dependencies as submodule

Author: fangq

.gitmodules

@@ -0,0 +1,9 @@
+[submodule "external/easyh5"]
+	path = external/easyh5
+	url = https://github.com/NeuroJSON/easyh5.git
+[submodule "external/jsonlab"]
+	path = external/jsonlab
+	url = https://github.com/NeuroJSON/jsonlab.git
+[submodule "external/zmat"]
+	path = external/zmat
+	url = https://github.com/NeuroJSON/zmat.git

ChangeLog.txt

@@ -2,7 +2,30 @@
 
 Major updates are marked with a "*"
 
-== JSNIRF Toolbox v0.4 (Amygdala - alpha), FangQ <q.fang (a) neu.edu> ==
+== JSNIRFY Toolbox v0.5 (Amygdala), 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
+ 2025-02-23 [70e6e84] Fix saving cell2mat
+ 2024-10-02 [555c12d] [doc] update upstream repository to NeuroJSON
+ 2024-09-15 [0bc960d]*[format] complete reformat code using miss_hit
+ 2024-09-15 [e5e3fb5] [snirf] allow saving empty 1d vector as timeseries
+ 2024-07-09 [391137b] [snirf] fix probe.sourceLabels with timeseries(string({})), fNIRS/snirf-samples#8
+ 2024-07-08 [a0adfd9]*[feature] use timeseries datatype for true 1d vector, NeuroJSON/easyh5#16, fNIRS/snirf-samples#12
+ 2024-07-07 [966220d]*[bug] store snirf 1D vector fields with ndim=1, NeuroJSON/easyh5#16, fNIRS/snirf-samples#12
+ 2023-02-20 [e196ebd]*force measurementList to be array-of-struct for snirf v1
+ 2023-02-12 [95db007] make variablelengthstring default for snirf, NeuroJSON/jsnirfy#1
+ 2022-03-15 [4e7de16] fix typos, update github repo URLs
+ 2022-03-15 [a648417] rename all ubjson functions to bjdata functions, fix root-obj name typo
+ 2020-05-22 [4140f15] forcing index 1 in indexed group names in savesnirf, see fNIRS/snirf_homer3#4
+ 2020-05-16 [c46eb32] update snirf header to conform to the latest snirf spec
+ 2019-11-05 [3bef8df] add section why JSNIRF
+ 2019-10-30 [6dde565] add missing TimeUnit
+ 2019-10-30 [0b95152] use correct MeasurentTime MeasurementDate default value
+ 2019-10-30 [c99ba31] use the latest option of easyh5
+ 2019-09-28 [1e64227] collapse measurementList according to JSNIRF spec
+
+== JSNIRFY Toolbox v0.4 (Amygdala - alpha), FangQ <q.fang (a) neu.edu> ==
 
  2019-09-19 [61def95] adding issues link in README
  2019-09-19 [b4d357c] polishing snirf toolbox, handling root object names

README.md

@@ -1,9 +1,10 @@
 # JSNIRF Toolbox - A portable MATLAB toolbox for parsing SNIRF (HDF5) and JSNIRF (JSON) files
 
-* Copyright (C) 2019  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: 0.4 (code name: Amygdala - alpha)
-* URL: https://github.com/NeuroJSON/jsnirf/tree/master/lib/matlab
+* Version: 0.5 (code name: Amygdala)
+* Compatibility: MATLAB R2010b or newer, R2016b or newer saves SNIRF-1.1 compliant files
+* URL: https://github.com/NeuroJSON/jsnirfy
 
 ## Overview
 
@@ -20,18 +21,18 @@ storage, grouping, compression, integration with heterogeneous scientific data
 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 EazyH5 toolbox 
-(http://github.com/fangq/eazyh5). The toolbox can read/write SNIRF v1.0 data
+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 .
 
 This toolbox is selectively dependent on the below toolboxes
-- To read/write SNIRF/HDF5 files, one must install the EazyH5 toolbox at 
-  http://github.com/fangq/eazyh5 ; this is only supported on MATLAB, not Octave.
+- 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.
 - 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.
 - 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/fangq/zmat ; this is supported on both MATLAB and Octave.
+  http://github.com/NeuroJSON/zmat ; this is supported on both MATLAB and Octave.
 
 ## Why JSNIRF?
 
@@ -152,12 +153,12 @@ 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 EazyH5 toolbox at 
-  http://github.com/fangq/eazyh5
+- the `saveh5/loadh5` functions are provided by the EasyH5 toolbox at 
+  http://github.com/NeuroJSON/easyh5
 - the `savejson` and `savebj` functions are provided by the JSONLab 
   toolbox at http://github.com/NeuroJSON/jsonlab 
 - if data compression is specified by `'compression','zlib'` param/value 
-  pairs, ZMat toolbox will be needed, http://github.com/fangq/zmat
+  pairs, ZMat toolbox will be needed, http://github.com/NeuroJSON/zmat
 
 
 ## Usage
@@ -168,7 +169,7 @@ Example:
   data=snirfcreate;              % create an empty SNIRF data structure
   data=snirfcreate('data',realdata,'aux',realauxdata); % setting the default values to user data
   data=jsnirfcreate('format','snirf');                 % specify 'snirf' or 'jsnirf' using 'format' option
-  jsn=snirfdecode(loadh5('mydata.snirf'));             % load raw HDF5 data and convert to a JSNIRF struct
+  jsn=snirfdecode(loadh5('mydata.snirf', 'stringarray', 1)); % load raw HDF5 data and convert to a JSNIRF struct
 ```
 ### `loadsnirf/loadjsnirf` - Loading SNIRF/JSNIRF files as in-memory MATLAB data structures
 Example:

external/easyh5

@@ -17,8 +17,8 @@
 %        data: a MATLAB structure with the grouped data fields
 %
 %    dependency:
-%        - the loadh5/regrouph5 functions are provided by the eazyh5
-%          toolbox at http://github.com/fangq/eazyh5
+%        - the loadh5/regrouph5 functions are provided by the EasyH5
+%          toolbox at http://github.com/NeuroJSON/easyh5
 %        - the varargin2struct and jsonopt functions are provided by the JSONLab
 %          toolbox at http://github.com/NeuroJSON/jsonlab
 %        - if data compression is specified by 'compression','zlib' param/value

external/jsonlab

@@ -29,8 +29,8 @@
 %          toolbox at http://github.com/NeuroJSON/jsonlab
 %        - if data compression is specified by 'compression','zlib' param/value
 %          pairs, ZMat toolbox will be needed, http://github.com/fangq/zmat
-%        - the saveh5 function is provided by the eazyh5 toolbox at
-%          http://github.com/fangq/eazyh5
+%        - the saveh5 function is provided by the EasyH5 toolbox at
+%          http://github.com/NeuroJSON/easyh5
 %
 %    example:
 %        jnirs=jsnirfcreate('aux',struct('name','pO2','dataTimeSeries',1:10,'time',1:10));

external/zmat

@@ -24,7 +24,7 @@
 %    example:
 %        snf=snirfcreate('data',mydata,'aux',myauxdata,'comment','test');
 %
-%    this file is part of JSNIRF specification: https://github.com/fangq/snirf
+%    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
 %

loadsnirf.m

@@ -22,7 +22,7 @@
 %              enclosed inside a 'SNIRFData' subfield or cell array.
 %
 %    example:
-%        rawdata=loadh5('mydata.snirf');
+%        rawdata=loadh5('mydata.snirf', 'stringarray', 1);
 %        data=snirfdecode(rawdata);
 %
 %    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf