[jnifty] update to the latest jnifty v0.8, add saveh5 from easyh5

Author: fangq

DESCRIPTION

@@ -1,6 +1,6 @@
 Name: jsonlab
-Version: 2.9.8
-Date: 2024-25-03
+Version: 3.0.0
+Date: 2025-23-03
 Title: A JSON/UBJSON/MessagePack encoder/decoder for MATLAB/Octave
 Author: Qianqian Fang <[email protected]>
 Maintainer: Qianqian Fang <[email protected]>

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

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

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$'))

loadnifti.m

@@ -13,9 +13,9 @@
 %    This function is an alias to nii2jnii
 %
 %
-%    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
 %
 
 [varargout{1:nargout}] = nii2jnii(varargin{:});

memmapstream.m

@@ -37,9 +37,9 @@
 %              'uint8', [1,2], 'school'};
 %        data=memmapstream(bytestream,format);
 %
-%    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 < 2)

nii2jnii.m

@@ -7,7 +7,7 @@
 %
 %    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/NeuroJSON/jnifti
+%    https://github.com/NeuroJSON/jnifty
 %
 %    This function is compatible with both MATLAB and GNU Octave.
 %    It accepts .nii, .nii.gz, .hdr/.img and .hdr.gz/.img.gz input files
@@ -51,23 +51,24 @@
 %              magic: must be 'ni1\0' or 'n+1\0'
 %
 %              For the detailed nii header, please see
-%              https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h
+%              https://nifti.nimh.nih.gov/nifti-1/
 %
 %    dependency:
 %          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/NeuroJSON/zmat) and
-%          JSONLab Toolbox (http://github.com/NeuroJSON/jsonlab);
+%          To load gzipped input files (.nii.gz/.hdr.gz/.img.gz), one may
+%          install the ZMat Toolbox (https://github.com/NeuroJSON/zmat) and
+%          JSONLab Toolbox (https://github.com/NeuroJSON/jsonlab), although
+%          it is optional.
 %
 %          To save files into the text/binary JNIfTI formatted files, one
-%          need to install JSONLab (http://github.com/NeuroJSON/jsonlab).
+%          need to install JSONLab (https://github.com/NeuroJSON/jsonlab).
 %
 %    this file was initially developed for the MCX project: https://github.com/fangq/mcx/blob/master/utils/mcxloadnii.m
 %
-%    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
 %
 
 hdrfile = filename;
@@ -95,7 +96,7 @@
 
     if (regexp(hdrfile, '\.[Gg][Zz]$'))
         if (~exist('gzipdecode', 'file'))
-            error('To process zipped files, you must install gzipdecode.m from the JSONLab toolbox: http://github.com/NeuroJSON/jsonlab');
+            error('To process zipped files, you must install gzipdecode.m from the JSONLab toolbox: https://github.com/NeuroJSON/jsonlab');
         end
         gzdata = gzipdecode(input);
     else
@@ -294,7 +295,7 @@
 
 if (nargout == 0 && strcmp(format, 'nii') == 0 && strcmp(format, 'jnii') == 0)
     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(format, '\.jnii$'))
         savejson('', nii, 'FileName', format, varargin{:});

niicodemap.m

@@ -9,8 +9,8 @@
 %
 %    input:
 %        name: a header name as a string, currently support the below nii
-%              headers: 'intent_code', 'slice_code', 'datatype', 'qform',
-%              'sform' and 'xyzt_units' and their corresponding JNIfTI
+%              headers: 'intent_code', 'slice_code', 'datatype', 'qform_code',
+%              'sform_code' and 'xyzt_units' and their corresponding JNIfTI
 %              headers:
 %              'Intent','SliceType','DataType','QForm','SForm','Unit'
 %        value:the current header value, if it is a code, newval will
@@ -30,9 +30,9 @@
 %
 %    this file was initially developed for the MCX project: https://github.com/fangq/mcx/blob/master/utils/mcxloadnii.m
 %
-%    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
 %
 
 % code to name look-up-table
@@ -42,14 +42,18 @@
     return
 end
 
-lut.intent_code = containers.Map([0, 2:24 1001:1011 2001:2005], ...
+lut.intent_code = containers.Map([0, 2:24 1001:1011 2001:2005 2006:2009 2016:2018], ...
                                  {'', 'corr', 'ttest', 'ftest', 'zscore', 'chi2', 'beta', ...
                                   'binomial', 'gamma', 'poisson', 'normal', 'ncftest', ...
                                   'ncchi2', 'logistic', 'laplace', 'uniform', 'ncttest', ...
                                   'weibull', 'chi', 'invgauss', 'extval', 'pvalue', ...
                                   'logpvalue', 'log10pvalue', 'estimate', 'label', 'neuronames', ...
                                   'matrix', 'symmatrix', 'dispvec', 'vector', 'point', 'triangle', ...
-                                  'quaternion', 'unitless', 'tseries', 'elem', 'rgb', 'rgba', 'shape'});
+                                  'quaternion', 'unitless', 'tseries', 'elem', 'rgb', 'rgba', 'shape', ...
+                                  'fsl_fnirt_displacement_field', 'fsl_cubic_spline_coefficients', ...
+                                  'fsl_dct_coefficients', 'fsl_quadratic_spline_coefficients', ...
+                                  'fsl_topup_cubic_spline_coefficients', 'fsl_topup_quadratic_spline_coefficients', ...
+                                  'fsl_topup_field'});
 
 lut.slice_code = containers.Map(0:6, {'', 'seq+', 'seq-', 'alt+', 'alt-', 'alt2+', 'alt-'});
 
@@ -61,10 +65,10 @@
 lut.xyzt_units = containers.Map([0:3 8 16 24 32 40 48], ...
                                 {'', 'm', 'mm', 'um', 's', 'ms', 'us', 'hz', 'ppm', 'rad'});
 
-lut.qform = containers.Map(0:4, {'', 'scanner', 'aligned', 'talairach', 'mni'});
+lut.qform_code = containers.Map(0:5, {'', 'scanner_anat', 'aligned_anat', 'talairach', 'mni_152', 'template_other'});
 
 lut.unit = lut.xyzt_units;
-lut.sform = lut.qform;
+lut.sform_code = lut.qform_code;
 lut.slicetype = lut.slice_code;
 lut.intent = lut.intent_code;
 
@@ -74,9 +78,9 @@
 tul.slice_code = containers.Map(values(lut.slice_code), keys(lut.slice_code));
 tul.datatype = containers.Map(values(lut.datatype), keys(lut.datatype));
 tul.xyzt_units = containers.Map(values(lut.xyzt_units), keys(lut.xyzt_units));
-tul.qform = containers.Map(values(lut.qform), keys(lut.qform));
+tul.qform_code = containers.Map(values(lut.qform_code), keys(lut.qform_code));
 
-tul.sform = tul.qform;
+tul.sform_code = tul.qform_code;
 tul.slicetype = tul.slice_code;
 tul.intent = tul.intent_code;
 tul.unit = tul.xyzt_units;

niiformat.m

@@ -22,9 +22,9 @@
 %             column 2: an integer vector denoting the size of the data
 %             column 3: a string denoting the fieldname in the output struct
 %
-%    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
 %
 
 header.nifti1 = {                            ...

niiheader2jnii.m

@@ -42,8 +42,8 @@
 end
 nii.NIFTIHeader.Description =    deblank(char(nii0.hdr.descrip));
 nii.NIFTIHeader.AuxFile =        deblank(char(nii0.hdr.aux_file));
-nii.NIFTIHeader.QForm =          nii0.hdr.qform_code;
-nii.NIFTIHeader.SForm =          nii0.hdr.sform_code;
+nii.NIFTIHeader.QForm =          niicodemap('qform_code', nii0.hdr.qform_code);
+nii.NIFTIHeader.SForm =          niicodemap('sform_code', nii0.hdr.sform_code);
 nii.NIFTIHeader.Quatern.b =      nii0.hdr.quatern_b;
 nii.NIFTIHeader.Quatern.c =      nii0.hdr.quatern_c;
 nii.NIFTIHeader.Quatern.d =      nii0.hdr.quatern_d;

octavezmat.m

@@ -6,7 +6,7 @@
 % unzipdata = octavezmat(zipdata, info)
 %
 % Compress or decompress zlib and gzip memory buffers using zip/unzip/gzip/gunzip on Octave
-% in case ZMat toolbox (http://github.com/NeuroJSON/zmat) was not installed (ZMat is much faster)
+% in case ZMat toolbox (https://github.com/NeuroJSON/zmat) was not installed (ZMat is much faster)
 %
 % Author: Qianqian Fang (q.fang <at> neu.edu)
 %
@@ -59,7 +59,7 @@
 nowarning = getvarfrom({'caller', 'base'}, 'NO_ZMAT');
 
 if (isempty(nowarning) || nowarning == 0)
-    warning('You are recommended to install ZMat (http://github.com/NeuroJSON/zmat) get much faster speed in Octave');
+    warning('You are recommended to install ZMat (https://github.com/NeuroJSON/zmat) get much faster speed in Octave');
 end
 
 if (nargin < 1)
@@ -102,16 +102,26 @@
     tmpfile = [fname suff.(zipmethod)];
 end
 
-fd = fopen(tmpfile, 'wb');
+writeflag = 'wb';
+
+if (iscompress && strcmp(zipmethod, 'gzip'))
+    writeflag = [writeflag, 'z'];
+end
+
+fd = fopen(tmpfile, writeflag);
 if (~fd)
     error('unable to create temporary file');
 end
 
 fwrite(fd, typecast(data(:), 'uint8'), 'uint8');
 fclose(fd);
 
-if (iscompress)
-    outputfile = [fname suff.(zipmethod)];
+if (strcmp(zipmethod, 'gzip'))
+    outputfile = tmpfile;
+else
+    if (iscompress)
+        outputfile = [fname suff.(zipmethod)];
+    end
 end
 
 if (~iscompress)
@@ -122,22 +132,24 @@
         else
             outputfile = outputfile{1};
         end
-    elseif (strcmp(zipmethod, 'gzip'))
-        gunzip(tmpfile);
     end
 else
     if (strcmp(zipmethod, 'zlib'))
         zip(outputfile, tmpfile);
-    elseif (strcmp(zipmethod, 'gzip'))
-        gzip(tmpfile);
     end
 end
 
-if (exist(tmpfile, 'file'))
+if (strcmp(zipmethod, 'zlib') && exist(tmpfile, 'file'))
     delete(tmpfile);
 end
 
-fd = fopen(outputfile, 'rb');
+readflag = 'rb';
+
+if (~iscompress && strcmp(zipmethod, 'gzip'))
+    readflag = [readflag, 'z'];
+end
+
+fd = fopen(outputfile, readflag);
 if (~fd)
     error('failed to unzip buffer');
 end