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R8218/CT/private/dicom_encode_attrs.m
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dicom_encode_attrs.m
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function data_streams = dicom_encode_attrs(attrs, txfr_syntax, uid_details)
%DICOM_ENCODE_ATTRS Encode a collection of attributes to a data stream.
% STREAMS = DICOM_ENCODE_ATTRS(ATTRS, TXFR) encode the attributes in
% the structure ATTRS according to the transfer syntax TXFR. The
% result is a cell array containing vectors of UINT8 values, which
% represent the values to be written to the output device. Each cell
% contains the encoded data stream for all of the attributes which
% share a common group number.
%
% Note: It is assumed that the attribute's data is already in the
% corresponding data type for the VR (e.g., if the VR is UL, the data
% is already UINT32).
%
% See also DICOM_ADD_ATTR, DICOM_ENCODE_PIXEL_CELLS.
% Copyright 1993-2010 The MathWorks, Inc.
%
% Determine whether data will need to be byte swapped.
%
[swap_file, swap_meta, swap_pixel] = determine_swap(txfr_syntax, uid_details);
PIXEL_GROUP = sscanf('7fe0', '%x');
PIXEL_ELEMENT = sscanf('0010', '%x');
%
% Process the attributes.
%
total_attrs = length(attrs);
current_attr = 1;
current_stream = 1;
data_streams = {};
while (current_attr <= total_attrs)
current_group = attrs(current_attr).Group;
stream = uint8([]);
% Process each attribute of the group.
while (attrs(current_attr).Group == current_group)
% Get the current attribute.
attr = attrs(current_attr);
% Create the UINT8 output stream.
if (attr.Element == 0)
% Skip group lengths.
encoded_attr = uint8([]);
elseif (current_group == 2)
encoded_attr = create_encoded_attr(attr, uid_details, swap_file);
elseif ((attr.Group == PIXEL_GROUP) && ...
(attr.Element == PIXEL_ELEMENT))
encoded_attr = create_encoded_attr(attr, uid_details, swap_pixel);
% GE format has different endianness within the PixelData
% attribute. Fix it.
if (isequal(txfr_syntax, '1.2.840.113619.5.2'))
encoded_attr = fix_pixel_attr(encoded_attr);
end
else
encoded_attr = create_encoded_attr(attr, uid_details, swap_meta);
end
% Add to the output stream.
stream = [stream encoded_attr]; %#ok<AGROW>
current_attr = current_attr + 1;
% Don't index past the end of the attrs array.
if (current_attr > total_attrs)
break
end
end
% Prepend group length attribute.
if (current_group == 2)
len_attr.Group = current_group;
len_attr.Element = 0;
len_attr.VR = 'UL';
len_attr.Data = uint32(length(stream));
encoded_attr = create_encoded_attr(len_attr, uid_details, swap_file);
stream = [encoded_attr stream];
end
% Store the stream.
data_streams{current_stream} = stream;
current_stream = current_stream + 1;
end
function segment = create_encoded_attr(attr, uid_details, swap)
% If it's a sequence, recursively enocde the items and attributes.
if (isstruct(attr.Data))
fnames = fieldnames(attr.Data);
if ((isequal(attr.VR, 'PN')) || ...
(~isempty(strfind(lower(fnames{1}), 'name'))))
attr.Data = dicom_encode_pn(attr.Data);
else
attr.Data = encode_structure(attr.Data, uid_details, swap);
end
end
% Determine size of data.
switch (class(attr.Data))
case {'uint8', 'int8', 'char'}
data_size = 1;
case {'uint16', 'int16'}
data_size = 2;
case {'uint32', 'int32', 'single'}
data_size = 4;
case {'double'}
data_size = 8;
end
% Group and Element
segment = dicom_typecast(uint16(attr.Group), 'uint8', swap);
segment = [segment dicom_typecast(uint16(attr.Element), 'uint8', swap)];
% VR and Length
if ((isequal(uid_details.VR, 'Implicit')) && (attr.Group > 2))
% VR does not appear in the file.
len = uint32(data_size * length(attr.Data));
else
% VR.
segment = [segment uint8(attr.VR)];
% Determine length.
switch (attr.VR)
case {'OB', 'OW', 'SQ'}
segment = [segment uint8([0 0])]; % Padding.
len = uint32(data_size * length(attr.Data));
case {'UN'}
if (attr.Group == 65534) % 0xfffe
% Items/delimiters don't have VR or two-byte padding.
segment((end - 1):end) = [];
else
segment = [segment uint8([0 0])]; % Padding.
end
len = uint32(data_size * length(attr.Data));
case {'UT'}
% Syntactically this is read the same as OB/OW/etc., but it
% cannot have undefined length.
segment = [segment uint8([0 0])]; % Padding.
len = uint32(data_size * length(attr.Data));
case {'AE','AS','AT','CS','DA','DS','DT','FD','FL','IS', ...
'LO','LT', 'PN','SH','SL','SS','ST','TM','UI','UL','US'}
len = uint16(data_size * length(attr.Data));
otherwise
% PS 3.5-1999 Sec. 6.2 indicates that all unknown VRs can be
% interpretted as being the same as OB, OW, SQ, or UN. The
% size of data is not known but, the reading structure is.
segment = [segment uint8([0 0])]; % Padding.
len = uint32(data_size * length(attr.Data));
end
% Special case for length of encapsulated (7FE0,0010).
if (((attr.Group == 32736) && (attr.Element == 16)) && ...
(uid_details.Compressed == 1))
% Undefined length.
len = dicom_undefined_length();
end
end
% If the data length is odd, then we will have to pad it. Add one to the
% length of the attribute.
if ((len ~= dicom_undefined_length()) && (rem(len, 2) ~= 0))
len = len + 1;
end
% Add the length and data to the segment.
segment = [segment dicom_typecast(len, 'uint8', swap)];
if (ischar(attr.Data))
segment = [segment uint8(attr.Data(:)')];
else
tmp = dicom_typecast(attr.Data, 'uint8', swap);
segment = [segment tmp(:)'];
end
% Pad the data (if necessary) by adding a null byte.
if (rem(numel(segment), 2) ~= 0)
segment(end + 1) = 0; %#ok<AGROW>
end
function [tf_file, tf_meta, tf_pixel] = determine_swap(txfr_syntax, uid_details)
[a, b, endian] = computer;
switch (endian)
case 'B'
if (isequal(txfr_syntax, '1.2.840.113619.5.2'))
tf_file = 1;
tf_meta = 1;
tf_pixel = 0;
elseif (isequal(uid_details.Endian, 'ieee-be'))
tf_file = 1;
tf_meta = 0;
tf_pixel = 0;
else
tf_file = 1;
tf_meta = 1;
tf_pixel = 1;
end
case 'L'
if (isequal(txfr_syntax, '1.2.840.113619.5.2'))
tf_file = 0;
tf_meta = 0;
tf_pixel = 1;
elseif (isequal(uid_details.Endian, 'ieee-le'))
tf_file = 0;
tf_meta = 0;
tf_pixel = 0;
else
tf_file = 0;
tf_meta = 1;
tf_pixel = 1;
end
end
function data = fix_pixel_attr(data)
% GE's special transfer syntax has different endianness within the
% attribute. Swap the bytes for the tag and length. Leave the rest
% alone.
%
% Swapping always needs to be done regardless of the endianness of the
% processor. It undoes a prior, unwanted swap of the tag and length.
tag = data(1:4);
tag = dicom_typecast(dicom_typecast(tag, 'uint16'), 'uint8', 1);
len = data(5:8);
len = dicom_typecast(dicom_typecast(len, 'uint32'), 'uint8', 1);
data(1:4) = tag;
data(5:8) = len;
function encoded_data = encode_structure(struct_data, uid_details, swap)
%ENCODE_STRUCTURE Turn a structure of data into a byte stream.
% If it's a sequence, the structure will contain fields named 'Item_n'.
% To encode the sequence:
% (1) Add an item tag.
% (2) Encode the attributes within the item.
encoded_data = uint8([]);
for p = 1:numel(struct_data)
tmp = dicom_encode_attrs(struct_data(p), uid_details.Value, uid_details);
encoded_data = [encoded_data ...
tmp{1}];
end
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