replace all saveubjson by savebj, clarify row-major/column-major conversion

Author: fangq

JNIfTI_specification.md

@@ -436,7 +436,7 @@ is listed below
 |*NIFTI code for ppm*                          |	      |
 |        `NIFTI_UNITS_PPM    40               `|  `"ppm"`     |
 |*NIFTI code for radians per second*           |	      |
-|        `NIFTI_UNITS_RADS   48               `|  `"rad"`     |
+|        `NIFTI_UNITS_RADS   48               `|  `"rad/s"    |
 
 
 #### Intent (NIFTI-1 header: `intent_code`)
@@ -629,9 +629,21 @@ One can also apply data compression to reduce file sizes. In this case
 ```
 
 Please note that all composite data types (marked by "\*" in Table 2)
-can not be stored in the direct form and therefore must be stored using the annotated array format.
-
-All three of the above  forms are valid JSON formats, and thus can be converted to the corresponding 
+can not be stored in the direct form and therefore must be stored using
+the annotated array format.
+
+NIfTI-1/2 stores raw data values in the column-major element order (meaning
+that the left-most index (`dim[1]`) is the fastest index while the right-most index
+is the slowest) while JData `_ArrayData_` construct by default stores data elements
+in the row-major order (i.e. the right-most index is the fastest index). As a result,
+if one has to directly copy the NIfTI data buffer to the `_ArrayData_` element,
+one must add `"_ArrayOrder_" : "c"` or `"_ArrayOrder_" : "col"` before `_ArrayData_`
+or `_ArrayZipData_` entries in the above annotated `NIFTIData` forms.
+Alternatively, if `_ArrayOrder_` is not specified (which suggests "row-major" order),
+one must perform an N-D transpose operation to the NIfTI image data buffer before
+serializing those to `_ArrayData_`.
+
+All three of the above forms are valid JSON formats, and thus can be converted to the corresponding
 BJData formats when a binary JNIfTI file is desired. Using the optimized N-D array 
 header defined in the JData specification, the binary storage of the direct-form 
 array can be efficiently written as

lib/easyh5

@@ -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

lib/matlab/loadjnifti.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

lib/matlab/nii2jnii.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{:});

lib/matlab/savebnii.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: