[release] JSNIRF V1 Draft-2

Author: fangq

ChangeLog.txt

@@ -0,0 +1,51 @@
+= Change Log =
+
+Major updates are marked with a "*"
+
+== JSNIRF Spec Draft-2, FangQ <q.fang (a) neu.edu> ==
+
+ 2025-03-23 [1c24550] [ci] fix spellchecking
+ 2025-03-23 [9d01cd1] [spec] update spec abstract, update wordlist
+ 2025-03-23 [7846561] [ci] add spellchecker
+ 2025-03-23*[5074dc3] [bug] add the missing SNIRFData.nirs object, sync SNIRF 1.2
+ 2025-03-23 [b3a0bdf] [lib] update submodule github URLs
+
+== JSNIRF Spec Draft-1, FangQ <q.fang (a) neu.edu> ==
+
+ 2022-03-15 [4eb46e0] update jsnirfy toolbox
+ 2022-02-22 [3430920] Update README.md
+ 2020-05-22 [e906c1f] add sample data, update jsnirfy
+ 2020-05-16 [6e745cf] Update to map the latest SNIRF data fileds
+ 2020-05-04 [ba60b53] Add project banner to README
+ 2019-11-05 [9d9a215] update jsnirf toolbox readme
+ 2019-11-05 [c23ea18] add jsnirfy as matlab parser
+ 2019-11-05 [e2bf825] separate jsnirf toolbox into a separate repo
+ 2019-10-30 [51cc620] add missing TimeUnit
+ 2019-10-30 [e52d47a] use correct MeasurentTime MeasurementDate default value
+ 2019-10-30 [5e30e0f] use the latest option of easyh5
+ 2019-10-01 [10fc8d3] update easyh5 module
+ 2019-10-01 [4b780f6] readd easyh5 submodule
+ 2019-10-01 [1da7860] update easyh5 url
+ 2019-09-28 [2be2603] collapse measurementList according to JSNIRF spec
+ 2019-09-19 [876547c] fix typos
+ 2019-09-19 [808d45e] add Changelog
+ 2019-09-19 [61def95] adding issues link
+ 2019-09-19 [8136520] use brain parts as code names, set default version to 1.0
+ 2019-09-19 [b4d357c] polishing snirf toolbox, handling root object names
+ 2019-09-19 [53966d4] pass variable name from savesnirf to saveh5
+ 2019-09-19 [4744840] jsnirf toolbox v0.4
+ 2019-09-19 [a9ffd3b] initial version of jsnirf toolbox
+ 2019-09-17 [1e93c02] remove tic toc for speed test
+ 2019-09-17 [3559dcb] a compact SNIRF MATLAB parser and converter to JSNIRF JSON file
+ 2019-06-23 [af57f8c] Minor language updates
+ 2019-06-21 [53663d0] Use the name "indexed group"
+ 2019-06-20 [33b3cf1] Correct minor typo
+ 2019-06-18 [55349ab] Add ... for metadatatags
+ 2019-06-18 [d7908c7] More language updates
+ 2019-06-17 [3f299de] Correct the position of formatVersion
+ 2019-06-17 [a354d90] Reformat the mapping table
+ 2019-06-17 [621db3b] Update mapping table, complete the summary section, add more mapping instructions
+ 2019-06-16 [3ebbb83] Fix typo in abstract, add link to SNIRF spec
+ 2019-06-14 [b115b86] Use unicode U+2000 to format space inside table
+ 2019-06-14 [8d34bcc] Update toc
+ 2019-06-14 [a741ce7] initial version

JSNIRF_specification.md

@@ -1,19 +1,19 @@
-JSNIRF: A JSON/binary JSON extension to the SNIRF format
+JSNIRF: A Lightweight JSON/Binary JSON Extension to the SNIRF Format
 ============================================================
 
 - **Copyright**: (C) 2019-2025 Qianqian Fang <q.fang at neu.edu>
 - **License**: Apache License, Version 2.0
-- **Version**: V1 (Draft-2.preview)
+- **Version**: V1 (Draft-2)
 - **URL**: https://neurojson.org/jsnirf/draft2
-- **Status**: Draft-2 is a work-in-progress
+- **Status**: Frozen on March 23, 2025. For future updates, please see the Development URL below
 - **Development**: https://github.com/NeuroJSON/jsnirf
 - **Abstract**:
 
 > This specification defines the JSNIRF standard format. The JSNIRF format
 allows one to store and extend the HDF5 based SNIRF format (.snirf) using
 JavaScript Object Notation (JSON) [RFC4627] and binary JSON serialization
-methods. It loss-lessly maps all SNIRF/HDF5 headers and data structures to
-a human-readable JSON-based wrapper. Use of JSON and JSNIRF formats to store
+methods. It losslessly maps all SNIRF metadata and data structures to a
+lighweight human-readable JSON-based wrapper. Use of JSON and JSNIRF formats to store
 SNIRF data makes it possible to rapidly index, exchange, and query large amount
 of SNIRF datasets and metadata using modern database engines where JSON is used
 as the underlying data exchange format. With the extension of JData annotations,
@@ -78,14 +78,14 @@ easy integration with other neuroanatomical or functional measurements
 that can be potentially stored using [JData-based formats](https://github.com/NeuroJSON/jdata)
 
 Instead of using HDF5, JSNIRF utilizes [JavaScript Object Notation](https://json.org) 
-(JSON) as the text-based storage format and [Binary JData](https://github.com/NeuroJSON/bjdata)
+(JSON) as the text-based storage format and [Binary JData, or BJData](https://github.com/NeuroJSON/bjdata)
 derived based on [Universal Binary JSON (UBJSON)](https://ubjson.org),
 as the binary interface to gain smaller file sizes and faster processing speed. The 
 [JData specification](https://github.com/NeuroJSON/jdata/blob/master/JData_specification.md)
 provides the foundation for serializing complex hierarchical data using
-JSON/UBJSON constructs. This permits us to define language- and library-neutral
+JSON/BJData constructs. This permits us to define language- and library-neutral
 fNIRS data representations using the simple and extensible constructs 
-using the JSON and UBJSON syntax. The use of JSON/UBJSON based JSNIRF data
+using the JSON and BJData syntax. The use of JSON/BJData based JSNIRF data
 files also extends reading and writing SNIRF in environments where the HDF5 format
 is not supported, such as MATLAB older than R2011a and GNU Octave.
 
@@ -94,13 +94,13 @@ is not supported, such as MATLAB older than R2011a and GNU Octave.
 
 In this specification, we define data containers that are capable of storing 
 SNIRF-based fNIRS data structure, and allow one to convert SNIRF files to
-JSON and UBJSON based files for easy sharing, parsing and integration.
+JSON and BJData based files for easy sharing, parsing and integration.
 
 The purpose of this document is to
 
 - define a 1-to-1 mapping between the existing SNIRF data structures
-  to a JSON/UBJSON-based flexible data structure to allow lossless conversion
-  from HDF5 data to JSON/UBJSON data
+  to a JSON/BJData-based flexible data structure to allow lossless conversion
+  from HDF5 data to JSON/BJData data
 - demonstrate a set of flexible mechanisms to extend the capability of the 
   format to accommodate additional physiological, anatomical and multi-modal data
 
@@ -115,11 +115,11 @@ Grammar
 
 All JSNIRF files are JData specification compliant. The same as JData, it has
 both a text format based on JSON serialization and a binary format based on 
-the UBJSON serialization scheme. The two forms can be converted from one
+the BJData serialization scheme. The two forms can be converted from one
 to another.
 
 Briefly, the text-based JSNIRF is a valid JSON file with the extension to 
-support concatenated JSON objects; the binary-format JSNIRF is a valid UBJSON 
+support concatenated JSON objects; the binary-format JSNIRF is a valid BJData 
 file with the extended syntax to support N-D array. Please refer to the JData 
 specification for the definitions.
 
@@ -390,16 +390,16 @@ Summary
 ----------
 
 In summary, this specification defines a 1-to-1 mapping between the HDF5-based SNIRF storage
-format to JSON/UBJSON based JSNIRF format. Any previously generated SNIRF file can be 100% 
-mapped to a JSNIRF document without losing any information. However, JSNIRF adds readability, 
+format to JSON/BJData based JSNIRF format. Any previously generated SNIRF file can be 100% 
+mapped to a JSNIRF document without losing information. However, JSNIRF adds readability, 
 portability with lightweight and widely available parsers. It also allows one to easily 
 combine NIRS measurements with other experimental data stored in JData-compliant 
 formats, such as [JNIfTI](https://github.com/NeuroJSON/jnifti) or [JMesh](https://github.com/NeuroJSON/jmesh), 
 especially in a multi-modal imaging study.
 
-Compared to HDF5, JSON and UBJSON is significantly simpler when encoding and decoding 
+Compared to HDF5, JSON and BJData are significantly simpler when encoding and decoding 
 unstructured data, such as the data structure defined in a SNIRF file. 
-The broad availability of JSON and UBJSON parsers, along with the simple underlying syntax, allows one
+The broad availability of JSON and BJData parsers, along with the simple underlying syntax, allows one
 to easily share, parse and process such data files without imposing extensive programming
 overhead. The flexible data organization and referencing mechanisms offered by the underlying 
 JData specification make it possible to record and share large scale complex neuroimaging 

README.md

@@ -14,7 +14,7 @@ for convenient editing and version control.
 
 The JSNIRF format is built upon the [JData specification](https://github.com/NeuroJSON/jdata/) - 
 a generalized framework to serialize and convert complex scientific data. 
-The JSNIRF specification is compatible with [JData specification Draft 1](https://github.com/NeuroJSON/jdata/commit/f8fc8f1b814e7a4654b7b0092de15eaafa94d3da).
+The JSNIRF specification is compatible with [JData specification Draft 3](https://neurojson.org/jdata/draft3).
 
 ## How to participate
 
@@ -27,7 +27,7 @@ draft of this file specification, including
     question, report a bug, provide a feature request, or simply propose
     general discussions. Please use URLs or keywords to link your discussion 
     to a specific line/section/topic in the document.
-- [Write short comments on Request for Comments (RFC) commits](https://github.com/NeuroJSON/jsnirf/)
+- [Write short comments on Request for Comments (RFC) commits](https://github.com/NeuroJSON/jsnirf/releases/tag/Draft-2)
   - A milestone version of the specification will be associated with an
     RFC (Request for comments) commit (where the entire file is removed
     and re-added so that every line appears in such comment). One can