[release] update all units for v0.8 release

Author: fangq

DESCRIPTION

@@ -1,7 +1,7 @@
-Name: jnifti
-Version: 0.6.1
-Date: 2020-15-06
-Title: fast NIfTI-1/2 reader and NIfTI-to-JNIfTI converter for MATLAB/Octave
+Name: jnifty
+Version: 0.8.0
+Date: 2025-23-03
+Title: Fast NIfTI-1/2 reader/writer and NIfTI-to-JNIfTI converter for MATLAB/Octave
 Author: Qianqian Fang <fangqq@gmail.com>
 Maintainer: Qianqian Fang <fangqq@gmail.com>
 Description: JNIfTI Toolbox is a fully functional NIfTI-1/2 reader/writer that supports both
@@ -10,7 +10,7 @@ Description: JNIfTI Toolbox is a fully functional NIfTI-1/2 reader/writer that s
  files (.hdr/.img and .hdr.gz/.img.gz). 
  More importantly, this is a toolbox that converts NIfTI data to its JSON-based
  replacement, JNIfTI (.jnii for text-based and .bnii for binary-based), defined
- by the JNIfTI specification (http://github.com/NeuroJSON/jnifti). JNIfTI is a
+ by the JNIfTI specification (https://github.com/NeuroJSON/jnifty). JNIfTI is a
  much more flexible, human-readable and extensible file format compared to the
  more rigid and opaque NIfTI format, making the data much easier to manipulate
  and share.

INDEX

@@ -1,18 +1,19 @@
-jnifti >> JNIfTI
-JNIfTI
- jnifticreate
- loadjnifti
- loadnifti
- memmapstream
- nifticreate
- niftiread
- niftiinfo
- niftiwrite
- nii2jnii
- jnii2nii
- niicodemap
- niiformat
- savebnii
- savejnifti
- savejnii
- savenifti
+jnifty >> JNIFTY
+JNIFTY
+ gzipdecode.m
+ gzipencode.m
+ jnifticreate.m
+ jnii2nii.m
+ loadjnifti.m
+ loadnifti.m
+ memmapstream.m
+ nifticreate.m
+ nii2jnii.m
+ niicodemap.m
+ niiformat.m
+ niiheader2jnii.m
+ octavezmat.m
+ savebnii.m
+ savejnifti.m
+ savejnii.m
+ savenifti.m

LICENSE_GPLv3.txt

@@ -1,8 +1,8 @@
 ===============================================================================
-=                      Monte Carlo eXtreme (MCX) -- CUDA                      =
+=  JNIfTI -- Fast and portable NIfTI-1/2 reader/writer for MATLAB and Octave  =
 ===============================================================================
 
-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 +1,15 @@
-# JNIfTI Toolbox - Fast and portable NIfTI-1/2 reader and NIfTI-to-JNIfTI converter
+![image](https://neurojson.org/wiki/upload/neurojson_banner_long.png)
 
-* Copyright (C) 2019-2024  Qianqian Fang <q.fang at neu.edu>
+# JNIfTI Toolbox - Fast and portable NIfTI-1/2 reader/writer for MATLAB and Octave
+
+* 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: 0.6 (Epica)
-* URL: http://github.com/NeuroJSON/jnifti
+* Version: 0.8 (Tree of Life)
+* URL: https://github.com/NeuroJSON/jnifty
+* Compatibility: MATLAB R2008a or newer, or Octave 4.0 and newer
+* JNIfTI Specification Version: V1 Draft-2 (https://neurojson.org/jnifti/draft2)
+* Acknowledgement: This project is supported by US National Institute of Health (NIH)
+  grant [U24-NS124027 (NeuroJSON)](https://reporter.nih.gov/project-details/10308329)
 
 ## Overview
 
@@ -14,7 +20,7 @@ files (`.hdr/.img` and `.hdr.gz/.img.gz`).
 
 More importantly, this is a toolbox that converts NIfTI data to its JSON-based
 replacement, JNIfTI (`.jnii` for text-based and `.bnii` for binary-based), defined
-by the JNIfTI specification (http://github.com/NeuroJSON/jnifti). JNIfTI is a 
+by the JNIfTI specification (https://github.com/NeuroJSON/jnift). JNIfTI is a 
 much more flexible, human-readable and extensible file format compared to the
 more rigid and opaque NIfTI format, making the data much easier to manipulate
 and share.
@@ -24,25 +30,20 @@ and share.
 The JNIfTI toolbox includes a stand-alone NIfTI-1/2 parser that works on both
 MATLAB and GNU Octave without needing additional components. To just reading and
 writing the un-compressed NIfTI and Analyze7.5 files (.nii, .hdr/.img), one 
-only needs to run `addpath('/path/to/jnifti')`. For MATLAB, JNIfTI toolbox
+only needs to run `addpath('/path/to/jnifty')`. For MATLAB, JNIfTI toolbox
 utilizes `memmapfile`-based disk-reading, making it very fast. For Octave, 
 `memmapfile` is currently not implemented, so, a full reading is required.
 
 The JNIfTI toolbox is also capable of reading/writing gzip-compressed NIfTI and 
 Analyze7.5 files (`.nii.gz, .hdr.gz, .img.gz`). This feature is supported in MATLAB
 directly without needing another toolbox (MATLAB must be in the JVM-enabled mode).
 
-To process gzip-compressed NIfTI/Analyze files in Octave and MATLAB with `-nojvm`,
-one need to install the open-source JSONLab and ZMat toolboxes, both supporting
-MATLAB and Octave. They can be downloaded at
-
-* JSONLab: http://github.com/NeuroJSON/jsonlab
-* ZMat: http://github.com/NeuroJSON/zmat
-
 To save NIfTI-1/2 data as JNIfTI files, one needs to install JSONLab. The JNIfTI
 data format supports internal compression (as oppose to external compression such
-as `*.gz` files). To create or read compressed JNIfTI files in Octave, one must 
-install the ZMat toolbox, as listed above.
+as `*.gz` files).
+
+To create or read compressed NIfTI/JNIfTI files in Octave, one may install the
+ZMat toolbox (https://github.com/NeuroJSON/zmat), although it is optional.
 
 ## Usage
 
@@ -63,29 +64,29 @@ Example:
 ### `savenifti` - To write an image as NIfTI-1/2 (.nii or .nii.gz) file
 Example:
 ```
-  savenifti(img,'test.nii.gz');         % save an array img to a compressed nifti file
+  savenifti(img, 'test.nii.gz');        % save an array img to a compressed nifti file
   savenifti(img, 'test.nii', 'nifti2'); % save an array img to a nifti-2 file file
   savenifti(img, 'test.nii', header);   % save an array img with an existing header
 ```
 ### `loadjnifti` - To read a JNIfTI (.jnii or .bnii) file
 Example:
 ```
-  jnii=nii2jnii('test.nii.gz');
-  savejnifti(jnii, 'magic10.bnii','Compression','gzip');
-  newjnii=loadjnifti('magic10.bnii');
+  jnii = nii2jnii('test.nii.gz');
+  savejnifti(jnii, 'magic10.bnii', 'Compression', 'gzip');
+  newjnii = loadjnifti('magic10.bnii');
 ```
 ### `savejnifti` - To write a JNIfTI structure into a file (.jnii or .bnii)
 Example:
 ```
-  jnii=jnifticreate(uint8(magic(10)),'Name','10x10 magic matrix');
+  jnii = jnifticreate(uint8(magic(10)), 'Name', '10x10 magic matrix');
   savejnifti(jnii, 'magic10.jnii');
-  savejnifti(jnii, 'magic10_debug.bnii','Compression','gzip');
+  savejnifti(jnii, 'magic10_debug.bnii', 'Compression', 'gzip');
 ```
 ### `jnii2nii` - To convert a JNIfTI file or data structure to a NIfTI-1/2 file
 Example:
 ```
-  nii=jnii2nii('test.jnii');             % read a .jnii file as an nii structure
-  nii=jnii2nii('test.bnii');             % read a .bnii file as an nii structure
+  nii = jnii2nii('test.jnii');             % read a .jnii file as an nii structure
+  nii = jnii2nii('test.bnii');             % read a .bnii file as an nii structure
   jnii2nii('test.jnii', 'newdata.nii.gz'); % read a text-JNIfTI file to an .nii.gz file
-  jnii2nii('test.bnii', 'newdata.nii'); % read a text-JNIfTI file to an .nii file
+  jnii2nii('test.bnii', 'newdata.nii');    % read a text-JNIfTI file to an .nii file
 ```

gzipdecode.m

@@ -6,7 +6,7 @@
 %
 % 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/NeuroJSON/zmat)
+% toolbox (https://github.com/NeuroJSON/zmat)
 %
 % Copyright (c) 2012, Kota Yamaguchi
 % URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
@@ -36,15 +36,19 @@
 if (nargin == 0)
     error('you must provide at least 1 input');
 end
-if (exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3)
+
+nozmat = getvarfrom({'caller', 'base'}, 'NO_ZMAT');
+
+if ((exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3) && (isempty(nozmat) || nozmat == 0))
     if (nargin > 1)
         [varargout{1:nargout}] = zmat(varargin{1}, varargin{2:end});
     else
         [varargout{1:nargout}] = zmat(varargin{1}, 0, 'gzip', varargin{2:end});
     end
     return
 elseif (isoctavemesh)
-    error('You must install the ZMat toolbox (http://github.com/NeuroJSON/zmat) to use this function in Octave');
+    [varargout{1:nargout}] = octavezmat(varargin{1}, 0, 'gzip');
+    return
 end
 error(javachk('jvm'));
 

gzipencode.m

@@ -7,7 +7,7 @@
 % 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/NeuroJSON/zmat)
+% toolbox (https://github.com/NeuroJSON/zmat)
 %
 % Copyright (c) 2012, Kota Yamaguchi
 % URL: https://www.mathworks.com/matlabcentral/fileexchange/39526-byte-encoding-utilities
@@ -35,20 +35,28 @@
     error('you must provide at least 1 input');
 end
 
-if (exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3)
+nozmat = getvarfrom({'caller', 'base'}, 'NO_ZMAT');
+
+if ((exist('zmat', 'file') == 2 || exist('zmat', 'file') == 3) && (isempty(nozmat) || nozmat == 0))
     [varargout{1:nargout}] = zmat(varargin{1}, 1, 'gzip');
     return
 elseif (isoctavemesh)
-    error('You must install the ZMat toolbox (http://github.com/NeuroJSON/zmat) to use this function in Octave');
+    [varargout{1:nargout}] = octavezmat(varargin{1}, 1, 'gzip');
+    return
 end
 
 error(javachk('jvm'));
 
-if (ischar(varargin{1}))
-    varargin{1} = uint8(varargin{1});
+input = varargin{1}(:)';
+if (ischar(input))
+    input = uint8(input);
+elseif (isa(input, 'string'))
+    input = uint8(char(input));
+else
+    input = typecast(input, 'uint8');
 end
 
-input = typecast(varargin{1}(:)', 'uint8');
+input = typecast(input, 'uint8');
 
 buffer = java.io.ByteArrayOutputStream();
 gzip = java.util.zip.GZIPOutputStream(buffer);

jnifticreate.m

@@ -12,17 +12,17 @@
 %    input:
 %        img: set the jnii.NIFTIData section
 %        'header_i': the header subfield name defined in the JNIfTI
-%                    specification, see https://github.com/NeuroJSON/jnifti
+%                    specification, see https://github.com/NeuroJSON/jnifty
 %        value_i: set the value for the specified JNIfTI header field
 %
 %    output:
 %        jnii: without any input, jnii gives the default jnii header
 %              if img is given, jnii also includes the NIFTIData field
 %
 %
-%    this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifti
+%    this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifty
 %
-%    License: Apache 2.0, see https://github.com/NeuroJSON/jnifti for details
+%    License: Apache 2.0, see https://github.com/NeuroJSON/jnifty for details
 %
 
 jnii = struct(encodevarname('_DataInfo_'), struct(), 'NIFTIHeader', struct(), 'NIFTIData', []);
@@ -59,9 +59,9 @@
 % jnii.NIFTIHeader.A75GlobalMax=  255;
 % jnii.NIFTIHeader.A75GlobalMin=   0;
 jnii.NIFTIHeader.Description =    '';
-% jnii.NIFTIHeader.AuxFile=        '';
-jnii.NIFTIHeader.QForm =          0;
-jnii.NIFTIHeader.SForm =          1;
+% jnii.NIFTIHeader.AuxFile=       '';
+jnii.NIFTIHeader.QForm =          '';
+jnii.NIFTIHeader.SForm =          'scanner_anat';
 jnii.NIFTIHeader.Quatern.b =      0;
 jnii.NIFTIHeader.Quatern.c =      0;
 jnii.NIFTIHeader.Quatern.d =      0;
@@ -77,8 +77,8 @@
 
 datainfo.JNIFTIVersion = '0.5';
 datainfo.Comment = 'Created by JNIFTY Toolbox (https://github.com/NeuroJSON/jnifty)';
-datainfo.AnnotationFormat = 'https://github.com/NeuroJSON/jnifti/blob/master/JNIfTI_specification.md';
-datainfo.SerialFormat = 'http://json.org';
+datainfo.AnnotationFormat = 'https://neurojson.org/jnifti/draft2';
+datainfo.SerialFormat = 'https://json.org';
 datainfo.Parser = struct('Python', [], ...
                          'MATLAB', [], ...
                          'JavaScript', 'https://github.com/NeuroJSON/jsdata', ...

jnii2nii.m

@@ -45,12 +45,12 @@
 %    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/NeuroJSON/zmat) and
-%          JSONLab Toolbox (http://github.com/NeuroJSON/jsonlab);
+%          one must install the ZMat Toolbox (https://github.com/NeuroJSON/zmat) and
+%          JSONLab Toolbox (https://github.com/NeuroJSON/jsonlab);
 %
-%    this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifti
+%    this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifty
 %
-%    License: Apache 2.0, see https://github.com/NeuroJSON/jnifti for details
+%    License: Apache 2.0, see https://github.com/NeuroJSON/jnifty for details
 %
 
 if (nargin <= 0)
@@ -96,11 +96,11 @@
 nii.hdr.intent_p2   = bytematch(jnii.NIFTIHeader, 'Param2', nii.hdr.intent_p2);
 nii.hdr.intent_p3   = bytematch(jnii.NIFTIHeader, 'Param3', nii.hdr.intent_p3);
 
-if (ischar(jnii.NIFTIHeader.Intent))
+if (isfield(jnii.NIFTIHeader, 'Intent') && ischar(jnii.NIFTIHeader.Intent))
     jnii.NIFTIHeader.Intent = niicodemap('intent', jnii.NIFTIHeader.Intent);
 end
 nii.hdr.intent_code = bytematch(jnii.NIFTIHeader, 'Intent', nii.hdr.intent_code);
-if (ischar(jnii.NIFTIHeader.DataType))
+if (isfield(jnii.NIFTIHeader, 'DataType') && ischar(jnii.NIFTIHeader.DataType))
     jnii.NIFTIHeader.DataType = niicodemap('datatype', jnii.NIFTIHeader.DataType);
 end
 
@@ -114,14 +114,14 @@
 nii.hdr.scl_inter   = bytematch(jnii.NIFTIHeader, 'ScaleOffset', nii.hdr.scl_inter);
 nii.hdr.slice_end   = bytematch(jnii.NIFTIHeader, 'LastSliceID', nii.hdr.slice_end);
 
-if (ischar(jnii.NIFTIHeader.SliceType))
+if (isfield(jnii.NIFTIHeader, 'SliceType') && ischar(jnii.NIFTIHeader.SliceType))
     jnii.NIFTIHeader.SliceType = niicodemap('slicetype', jnii.NIFTIHeader.SliceType);
 end
 nii.hdr.slice_code  = bytematch(jnii.NIFTIHeader, 'SliceType', nii.hdr.slice_code);
-if (ischar(jnii.NIFTIHeader.Unit.L))
+if (isfield(jnii.NIFTIHeader, 'Unit') && isfield(jnii.NIFTIHeader.Unit, 'L') && ischar(jnii.NIFTIHeader.Unit.L))
     jnii.NIFTIHeader.Unit.L = niicodemap('unit', jnii.NIFTIHeader.Unit.L);
 end
-if (ischar(jnii.NIFTIHeader.Unit.T))
+if (isfield(jnii.NIFTIHeader, 'Unit') && isfield(jnii.NIFTIHeader.Unit, 'T') && ischar(jnii.NIFTIHeader.Unit.T))
     jnii.NIFTIHeader.Unit.T = niicodemap('unit', jnii.NIFTIHeader.Unit.T);
 end
 
@@ -140,6 +140,13 @@
 nii.hdr.descrip = bytematch(jnii.NIFTIHeader, 'Description', nii.hdr.descrip);
 nii.hdr.aux_file    = bytematch(jnii.NIFTIHeader, 'AuxFile', nii.hdr.aux_file);
 
+if (isfield(jnii.NIFTIHeader, 'QForm') && ischar(jnii.NIFTIHeader.QForm))
+    jnii.NIFTIHeader.QForm = niicodemap('qform_code', jnii.NIFTIHeader.QForm);
+end
+if (isfield(jnii.NIFTIHeader, 'SForm') && ischar(jnii.NIFTIHeader.SForm))
+    jnii.NIFTIHeader.SForm = niicodemap('sform_code', jnii.NIFTIHeader.SForm);
+end
+
 nii.hdr.qform_code  = bytematch(jnii.NIFTIHeader, 'QForm', nii.hdr.qform_code);
 nii.hdr.sform_code  = bytematch(jnii.NIFTIHeader, 'SForm', nii.hdr.sform_code);
 nii.hdr.quatern_b   = bytematch(jnii.NIFTIHeader, 'Quatern.b', nii.hdr.quatern_b);
@@ -181,7 +188,6 @@
 
 function dat = bytematch(jobj, key, orig)
 dtype = class(orig);
-dat = orig;
 if (isfield(jobj, key))
     dat = cast(jobj.(key), dtype);
 else

loadjnifti.m

@@ -5,7 +5,7 @@
 %    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/NeuroJSON/jnifti
+%    format defined in JNIfTI specification: https://github.com/NeuroJSON/jnifty
 %
 %    author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -33,17 +33,17 @@
 %        savejnifti(jnii, 'magic10.jnii')
 %        newjnii=loadjnifti('magic10.jnii');
 %
-%    this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifti
+%    this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifty
 %
-%    License: Apache 2.0, see https://github.com/NeuroJSON/jnifti for details
+%    License: Apache 2.0, see https://github.com/NeuroJSON/jnifty for details
 %
 
 if (nargin < 1)
     error('you must provide data and output file name');
 end
 
 if (~exist('savejson', 'file'))
-    error('you must first install JSONLab from http://github.com/NeuroJSON/jsonlab/');
+    error('you must first install JSONLab from https://github.com/NeuroJSON/jsonlab/');
 end
 
 if (regexp(filename, '\.nii$'))