make_nii_sr(varargin)

%  Make nii structure specified by an N-D matrix. Usually, N is 3 for
%  3D matrix [x y z], or 4 for 4D matrix with time series [x y z t].
%  However, NIfTI allows a maximum of 7D matrix. For RGB24 datatype, an
%  extra dimension for RGB should be inserted immediately after [x y z].
%  Optional parameters can also be included, such as: voxel_size,
%  origin, datatype, and description.
%
%  Usage: nii = make_nii(img, [voxel_size], [origin], [datatype], ...
%		[description])
%
%  Where:
%
%	img:		Usually, img is a 3D matrix [x y z], or a 4D
%			matrix with time series [x y z t]. However,
%			NIfTI allows a maximum of 7D matrix. For RGB
%			datatype, an extra dimension for RGB should
%			be inserted immediately after [x y z].
%
%	voxel_size (optional):	Voxel size in millimeter for each
%				dimension. Default is [1 1 1].
%
%	origin (optional):	The AC origin. Default is [0 0 0].
%
%	datatype (optional):	Storage data type. Default is float32 [16]:
%		2 - uint8,  4 - int16,  8 - int32,  16 - float32,
%		32 - complex64,  64 - float64,  128 - RGB24,
%		256 - int8,  512 - uint16,  768 - uint32, 1792 - complex128
%
%	description (optional):	Description of data. Default is ''.
%
%  e.g.:
%     origin = [33 44 13]; datatype = 64;
%     nii = make_nii(img, [], origin, datatype);    % default voxel_size
%
%  NIFTI data format can be found on: http://nifti.nimh.nih.gov
%
%  - Jimmy Shen ([e-mail])
%  - Simon Robinson, changed default type to type of input matrix

function nii = make_nii_sr(varargin)

nii.img = varargin{1};
dims = size(nii.img);
dims = [length(dims) dims ones(1,8)];
dims = dims(1:8);

voxel_size = [0 ones(1,7)];
origin = zeros(1,5);
%srobi
%   datatype = 16;
switch class(nii.img)
    case 'uint8'
        datatype = 2;
    case 'int16'
        datatype = 4;
    case 'int32'
        datatype = 8;
    case 'single'
        datatype = 16;
    case 'double'
        datatype = 64;
    case 'uint8'
        datatype = 128;
    case 'int8'
        datatype = 256;
    case 'uint16'
        datatype = 512;
    case 'uint32'
        datatype = 768;
    case 'double'
        datatype = 1792;
    otherwise
        error('Datatype is not supported by make_nii.');
end
%srobi

descrip = '';

if nargin > 1 & ~isempty(varargin{2})
    voxel_size(2:4) = double(varargin{2});
end

if nargin > 2 & ~isempty(varargin{3})
    origin(1:3) = double(varargin{3});
end

if nargin > 3 & ~isempty(varargin{4})
    datatype = double(varargin{4});
end

if nargin > 4 & ~isempty(varargin{5})
    descrip = varargin{5};
end

if datatype == 128
    if ndims(nii.img) > 8
        error('NIfTI only allows a maximum of 7 Dimension matrix.');
    end

    dims(1) = dims(1)-1;
    dims(5:8) = [dims(6:8) 1];

else
    if ndims(nii.img) > 7
        error('NIfTI only allows a maximum of 7 Dimension matrix.');
    end
end

maxval = round(double(max(nii.img(:))));
minval = round(double(min(nii.img(:))));

nii.hdr = make_header(dims, voxel_size, origin, datatype, ...
    descrip, maxval, minval);

switch nii.hdr.dime.datatype
    case 2
        nii.img = uint8(nii.img);
    case 4
        nii.img = int16(nii.img);
    case 8
        nii.img = int32(nii.img);
    case 16
        nii.img = single(nii.img);
    case 32
        nii.img = single(nii.img);
    case 64
        nii.img = double(nii.img);
    case 128
        nii.img = uint8(nii.img);
    case 256
        nii.img = int8(nii.img);
    case 512
        nii.img = uint16(nii.img);
    case 768
        nii.img = uint32(nii.img);
    case 1792
        nii.img = double(nii.img);
    otherwise
        error('Datatype is not supported by make_nii.');
end

return;					% make_nii


%---------------------------------------------------------------------
function hdr = make_header(dims, voxel_size, origin, datatype, ...
    descrip, maxval, minval)

hdr.hk   = header_key;
hdr.dime = image_dimension(dims, voxel_size, datatype, maxval, minval);
hdr.hist = data_history(origin, descrip);

return;					% make_header


%---------------------------------------------------------------------
function hk = header_key

hk.sizeof_hdr       = 348;			% must be 348!
hk.data_type        = '';
hk.db_name          = '';
hk.extents          = 0;
hk.session_error    = 0;
hk.regular          = 'r';
hk.dim_info         = 0;

return;					% header_key


%---------------------------------------------------------------------
function dime = image_dimension(dims, voxel_size, datatype, maxval, minval)

dime.dim = dims;
dime.intent_p1 = 0;
dime.intent_p2 = 0;
dime.intent_p3 = 0;
dime.intent_code = 0;
dime.datatype = datatype;

switch dime.datatype
    case   2,
        dime.bitpix = 8;  precision = 'uint8';
    case   4,
        dime.bitpix = 16; precision = 'int16';
    case   8,
        dime.bitpix = 32; precision = 'int32';
    case  16,
        dime.bitpix = 32; precision = 'float32';
    case  32,
        dime.bitpix = 64; precision = 'float32';
    case  64,
        dime.bitpix = 64; precision = 'float64';
    case  128,
        dime.bitpix = 24; precision = 'uint8';
    case 256
        dime.bitpix = 8;  precision = 'int8';
    case 512
        dime.bitpix = 16; precision = 'uint16';
    case 768
        dime.bitpix = 32; precision = 'uint32';
    case  1792,
        dime.bitpix = 128; precision = 'float64';
    otherwise
        error('Datatype is not supported by make_nii.');
end

dime.slice_start = 0;
dime.pixdim = voxel_size;
dime.vox_offset = 0;
dime.scl_slope = 0;
dime.scl_inter = 0;
dime.slice_end = 0;
dime.slice_code = 0;
dime.xyzt_units = 0;
dime.cal_max = 0;
dime.cal_min = 0;
dime.slice_duration = 0;
dime.toffset = 0;
dime.glmax = maxval;
dime.glmin = minval;

return;					% image_dimension


%---------------------------------------------------------------------
function hist = data_history(origin, descrip)

hist.descrip = descrip;
hist.aux_file = 'none';
hist.qform_code = 0;
hist.sform_code = 0;
hist.quatern_b = 0;
hist.quatern_c = 0;
hist.quatern_d = 0;
hist.qoffset_x = 0;
hist.qoffset_y = 0;
hist.qoffset_z = 0;
hist.srow_x = zeros(1,4);
hist.srow_y = zeros(1,4);
hist.srow_z = zeros(1,4);
hist.intent_name = '';
hist.magic = '';
hist.originator = origin;

return;					% data_history