sync with the version in jnifti repo

Author: fangq

README.md

@@ -1,19 +1,19 @@
 # JNIfTI Toolbox - Fast and portable NIfTI-1/2 reader and NIfTI-to-JNIfTI converter
 
-* Copyright (C) 2019  Qianqian Fang <q.fang at neu.edu>
+* Copyright (C) 2019-2020  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 (Ascendence)
+* Version: 0.6 (Epica)
 * URL: http://github.com/fangq/jnifti
 
 ## Overview
 
 This is a fully functional NIfTI-1/2 reader/writer that supports both 
 MATLAB and GNU Octave, and is capable of reading/writing both non-compressed 
-and compressed NIfTI files (.nii, .nii.gz) as well as two-part Analyze7.5/NIfTI
-files (.hdr/.img and .hdr.gz/.img.gz).
+and compressed NIfTI files (`.nii, .nii.gz`) as well as two-part Analyze7.5/NIfTI
+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
+replacement, JNIfTI (`.jnii` for text-based and `.bnii` for binary-based), defined
 by the JNIfTI specification (http://github.com/fangq/jnifti). 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
@@ -29,7 +29,7 @@ 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
+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`,
@@ -41,7 +41,7 @@ MATLAB and Octave. They can be downloaded at
 
 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 
+as `*.gz` files). To create or read compressed JNIfTI files in Octave, one must 
 install the ZMat toolbox, as listed above.
 
 ## Usage
@@ -81,3 +81,11 @@ Example:
   savejnifti(jnii, 'magic10.jnii');
   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
+  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
+```

loadjnifti.m

@@ -15,7 +15,7 @@
 %                *.jnii for text JNIfTI file
 %                *.nii  for NIFTI-1/2 files
 %        options: (optional) if loading from a .bnii file, please see the options for
-%               loadubjson.m (part of JSONLab); if loading from a .jnii, please see the 
+%               loadbj.m (part of JSONLab); if loading from a .jnii, please see the 
 %               supported options for loadjson.m (part of JSONLab).
 %
 %    output:
@@ -51,7 +51,7 @@
 elseif(regexp(filename,'\.jnii$'))
     jnii=loadjson(filename,varargin{:});
 elseif(regexp(filename,'\.bnii$'))
-    jnii=loadubjson(filename,varargin{:});
+    jnii=loadbj(filename,varargin{:});
 else
     error('file suffix must be .jnii for text JNIfTI, .bnii for binary JNIfTI or .nii for NIFTI-1/2 files');
 end

nii2jnii.m

@@ -25,7 +25,7 @@
 %               file name - *.jnii for text-based JNIfTI, or *.bnii for the 
 %               binary version
 %        options: (optional) if saving to a .bnii file, please see the options for
-%               saveubjson.m (part of JSONLab); if saving to .jnii, please see the 
+%               savebj.m (part of JSONLab); if saving to .jnii, please see the 
 %               supported options for savejson.m (part of JSONLab).
 %
 %    output:
@@ -338,7 +338,7 @@
     if(regexp(format,'\.jnii$'))
         savejson('',nii,'FileName',format,varargin{:});
     elseif(regexp(format,'\.bnii$'))
-        saveubjson('',nii,'FileName',format,varargin{:});
+        savebj('',nii,'FileName',format,varargin{:});
     else
         error('file suffix must be .jnii for text JNIfTI or .bnii for binary JNIfTI');
     end

savebnii.m

@@ -20,7 +20,7 @@ function savebnii(jnii, filename, varargin)
 %                jnii.NIFTIExtension - a cell array contaiing the extension data buffers
 %        filename: the output file name to the binary-JNIfTI file (.bnii)
 %        options: (optional) if saving to .bnii, please see the 
-%               supported options for saveubjson.m (part of JSONLab).
+%               supported options for savebj.m (part of JSONLab).
 %
 %    example:
 %        jnii=jnifticreate(uint8(magic(10)),'Name','10x10 magic matrix');
@@ -36,8 +36,8 @@ function savebnii(jnii, filename, varargin)
     error('you must provide data and output file name');
 end
 
-if(~exist('saveubjson','file'))
+if(~exist('savebj','file'))
     error('you must first install JSONLab from http://github.com/fangq/jsonlab/');
 end
 
-saveubjson('',jnii,'FileName',filename,varargin{:});
+savebj('',jnii,'FileName',filename,varargin{:});

savejnifti.m

@@ -22,7 +22,7 @@ function savejnifti(jnii, filename, varargin)
 %                *.bnii for binary JNIfTI file
 %                *.jnii for text JNIfTI file
 %        options: (optional) if saving to a .bnii file, please see the options for
-%               saveubjson.m (part of JSONLab); if saving to .jnii, please see the 
+%               savebj.m (part of JSONLab); if saving to .jnii, please see the 
 %               supported options for savejson.m (part of JSONLab).
 %
 %    example: