Homec4science
Diffusion ShoulderDB_ImportSegmentMeasureAnalyze (pezhman_excelExport) Browse

R8218/CT/private/dicom_prep_ImagePixel.m
3761869a7f6dpezhman_excelExport

Last Change
Raw File

dicom_prep_ImagePixel.m
View Options

function metadata = dicom_prep_ImagePixel(metadata, X, map, txfr, useExistingBitDepths, dictionary)
%DICOM_PREP_IMAGEPIXEL Set necessary values for Image Pixel module.
%
% See PS 3.3 Sec C.7.6.3
% Copyright 1993-2014 The MathWorks, Inc.
metadata(1).(dicom_name_lookup('0028', '0002', dictionary)) = size(X, 3);
metadata.(dicom_name_lookup('0028', '0004', dictionary)) = getPhotometricInterp(metadata, X, map, txfr, dictionary);
metadata.(dicom_name_lookup('0028', '0010', dictionary)) = size(X, 1);
metadata.(dicom_name_lookup('0028', '0011', dictionary)) = size(X, 2);
[ba, bs, hb, pr] = getPixelStorage(X, txfr, useExistingBitDepths, metadata, dictionary);
metadata.(dicom_name_lookup('0028', '0100', dictionary)) = ba;
metadata.(dicom_name_lookup('0028', '0101', dictionary)) = bs;
metadata.(dicom_name_lookup('0028', '0102', dictionary)) = hb;
metadata.(dicom_name_lookup('0028', '0103', dictionary)) = pr;
metadata.(dicom_name_lookup('7FE0', '0010', dictionary)) = encodePixelData(metadata, X, map, txfr, dictionary);
% Values that depend on the number of samples present.
if (metadata.(dicom_name_lookup('0028', '0002', dictionary)) > 1)
metadata.(dicom_name_lookup('0028', '0006', dictionary)) = 0; % Interleaved pixels.
else
% Only include min/max pixel value for single-sample (grayscale) images.
switch class(X)
case {'single', 'double', 'logical'}
% The min/max values will have changed during prep.
data = metadata.(dicom_name_lookup('7FE0', '0010', dictionary));
metadata.(dicom_name_lookup('0028', '0106', dictionary)) = min(data(:));
metadata.(dicom_name_lookup('0028', '0107', dictionary)) = max(data(:));
otherwise
metadata.(dicom_name_lookup('0028', '0106', dictionary)) = min(X(:));
metadata.(dicom_name_lookup('0028', '0107', dictionary)) = max(X(:));
end
end
if (~isempty(map))
[rdes, gdes, bdes, rdata, gdata, bdata] = processColormap(X, map);
metadata.(dicom_name_lookup('0028', '1101', dictionary)) = rdes;
metadata.(dicom_name_lookup('0028', '1102', dictionary)) = gdes;
metadata.(dicom_name_lookup('0028', '1103', dictionary)) = bdes;
metadata.(dicom_name_lookup('0028', '1201', dictionary)) = rdata;
metadata.(dicom_name_lookup('0028', '1202', dictionary)) = gdata;
metadata.(dicom_name_lookup('0028', '1203', dictionary)) = bdata;
end
% Technically (0028,0008) isn't part of the Image Pixel module, but it's
% fundamental to several overlapping, optional modules that we don't
% have "prep" functions for yet; and we need to put the right value when
% copying metadata.
if ((isfield(metadata, dicom_name_lookup('0028', '0008', dictionary))) || ...
(size(X,4) > 1))
% Add the attribute if it isn't present and there's more than one frame.
metadata.(dicom_name_lookup('0028', '0008', dictionary)) = size(X, 4);
end
function pInt = getPhotometricInterp(metadata, X, map, txfr, dictionary)
%GETPHOTOMETRICINTERP Get the string code for the image's photometric interp
if (isempty(map))
if (size(X, 3) == 1)
% 0 is black. Grayscale images should always have a value of
% 'MONOCHROME1' or 'MONOCHROME2', regardless of compression. The
% default should be consistent with IPT's interpretation that the
% "minimum is black," which is 'MONOCHROME2'.
pIntFieldname = dicom_name_lookup('0028', '0004', dictionary);
if isfield(metadata, pIntFieldname)
switch (metadata.(pIntFieldname))
case {'MONOCHROME1', 'MONOCHROME2'}
pInt = metadata.(pIntFieldname);
otherwise
pInt = 'MONOCHROME2';
end
else
pInt = 'MONOCHROME2';
end
elseif (size(X, 3) == 3)
switch (txfr)
case {'1.2.840.10008.1.2.4.50'
'1.2.840.10008.1.2.4.51'
'1.2.840.10008.1.2.4.52'
'1.2.840.10008.1.2.4.53'
'1.2.840.10008.1.2.4.54'
'1.2.840.10008.1.2.4.55'
'1.2.840.10008.1.2.4.56'
'1.2.840.10008.1.2.4.57'
'1.2.840.10008.1.2.4.58'
'1.2.840.10008.1.2.4.59'
'1.2.840.10008.1.2.4.60'
'1.2.840.10008.1.2.4.61'
'1.2.840.10008.1.2.4.62'
'1.2.840.10008.1.2.4.63'
'1.2.840.10008.1.2.4.64'
'1.2.840.10008.1.2.4.65'
'1.2.840.10008.1.2.4.66'
'1.2.840.10008.1.2.4.70'
'1.2.840.10008.1.2.4.80'
'1.2.840.10008.1.2.4.81'}
pInt = 'YBR_FULL_422';
case {'1.2.840.10008.1.2.4.90'
'1.2.840.10008.1.2.4.92'}
% See PS 3.5 Sec. 8.2.4
pInt = 'YBR_RCT';
case {'1.2.840.10008.1.2.4.91'
'1.2.840.10008.1.2.4.93'}
% See PS 3.5 Sec. 8.2.4
pInt = 'YBR_ICT';
otherwise
pInt = 'RGB';
end
else
error(message('images:dicom_prep_ImagePixel:photoInterp'))
end
else
if (size(X, 3) == 1)
pInt = 'PALETTE COLOR';
elseif (size(X, 3) == 4)
pInt = 'RGBA';
else
error(message('images:dicom_prep_ImagePixel:photoInterp'))
end
end
function [ba, bs, hb, pr] = getPixelStorage(X, txfr, useExistingBitDepths, metadata, dictionary)
%GETPIXELSTORAGE Get details about the pixel cells.
switch (class(X))
case {'uint8', 'logical'}
ba = 8;
bs = 8;
pr = 0;
case {'int8'}
ba = 8;
bs = 8;
pr = 1;
case {'uint16'}
ba = 16;
bs = 16;
pr = 0;
case {'int16'}
ba = 16;
bs = 16;
pr = 1;
case {'uint32'}
ba = 32;
bs = 32;
pr = 0;
case {'int32'}
ba = 32;
bs = 32;
pr = 1;
case {'double'}
switch (txfr)
case '1.2.840.10008.1.2.4.50'
ba = 8;
bs = 8;
pr = 0;
otherwise
% Customers report that UINT8 data isn't large enough.
ba = 16;
bs = 16;
pr = 0;
end
otherwise
error(message('images:dicom_prep_ImagePixel:bitDepth'))
end
hb = ba - 1;
% Override values if the user requested it and the metadata is there.
computedBitsRequired = ba;
if (useExistingBitDepths)
% BitsAllocated
if isfield(metadata, dicom_name_lookup('0028', '0100', dictionary))
ba = metadata.(dicom_name_lookup('0028', '0100', dictionary));
end
% BitsStored
if isfield(metadata, dicom_name_lookup('0028', '0101', dictionary))
bs = metadata.(dicom_name_lookup('0028', '0101', dictionary));
end
% HighBit
if isfield(metadata, dicom_name_lookup('0028', '0102', dictionary))
hb = metadata.(dicom_name_lookup('0028', '0102', dictionary));
end
end
% Ensure that the metadata values are reasonable. (Technically, there's
% nothing wrong with having a BA or BS value of less than 8 if the data is
% in an 8-bit integer type.)
if (bs > ba)
error(message('images:dicom_prep_ImagePixel:bitsStoredTooBig', ...
dicom_name_lookup('0028', '0101', dictionary), ...
dicom_name_lookup('0028', '0100', dictionary)))
elseif (hb >= ba)
error(message('images:dicom_prep_ImagePixel:highBitTooBig', ...
dicom_name_lookup('0028', '0102', dictionary), ...
dicom_name_lookup('0028', '0100', dictionary)))
elseif ((computedBitsRequired == 32) && (bs <= 16))
error(message('images:dicom_prep_ImagePixel:bitsStoredTooSmall', ...
dicom_name_lookup('0028', '0101', dictionary)))
elseif ((computedBitsRequired == 16) && (bs <= 8))
error(message('images:dicom_prep_ImagePixel:bitsStoredTooSmall', ...
dicom_name_lookup('0028', '0101', dictionary)))
end
function [rdes, gdes, bdes, rdata, gdata, bdata] = processColormap(~, map)
%PROCESSCOLORMAP Turn a MATLAB colormap into a DICOM colormap.
% Always use 16-bits.
% First descriptor: number of rows in the table.
map_rows = size(map, 1);
if (map_rows == (2^16))
map_rows = 0;
end
% Second descriptor: index to start row mapping. Always 0 for MATLAB's use
% of colormaps.
% Third descriptor: bit-depth.
map_bits = 16;
rdes = [map_rows 0 map_bits];
gdes = rdes;
bdes = rdes;
% PS 3.3 Sec. C.7.6.3.1.6 says data must span the full range.
rdata = uint16(map(:, 1) .* (2 ^ map_bits - 1));
gdata = uint16(map(:, 2) .* (2 ^ map_bits - 1));
bdata = uint16(map(:, 3) .* (2 ^ map_bits - 1));
function pixelData = encodePixelData(metadata, X, map, txfr, dictionary)
%ENCODEPIXELCELLS Turn a MATLAB image into DICOM-encoded pixel data.
%
% Rescale logical and double data.
%
switch (txfr)
case {'1.2.840.10008.1.2.4.50'
'1.2.840.10008.1.2.4.51'
'1.2.840.10008.1.2.4.52'
'1.2.840.10008.1.2.4.53'
'1.2.840.10008.1.2.4.54'
'1.2.840.10008.1.2.4.55'
'1.2.840.10008.1.2.4.56'
'1.2.840.10008.1.2.4.57'
'1.2.840.10008.1.2.4.58'
'1.2.840.10008.1.2.4.59'
'1.2.840.10008.1.2.4.60'
'1.2.840.10008.1.2.4.61'
'1.2.840.10008.1.2.4.62'
'1.2.840.10008.1.2.4.63'
'1.2.840.10008.1.2.4.64'
'1.2.840.10008.1.2.4.65'
'1.2.840.10008.1.2.4.66'
'1.2.840.10008.1.2.4.70'
'1.2.840.10008.1.2.4.80'
'1.2.840.10008.1.2.4.81'
'1.2.840.10008.1.2.4.90'
'1.2.840.10008.1.2.4.91'}
% Let IMWRITE handle all of the transformations.
pixelCells = X;
otherwise
% Handle the special syntaxes where endianness changes for pixels.
X = changePixelEndian(X, txfr, metadata, dictionary);
pixelCells = dicom_encode_pixel_cells(X, map, ...
metadata.(dicom_name_lookup('0028', '0100', dictionary)), ...
metadata.(dicom_name_lookup('0028', '0101', dictionary)), ...
metadata.(dicom_name_lookup('0028', '0102', dictionary)));
end
%
% Encode pixels.
%
uid_details = dicom_uid_decode(txfr);
if (uid_details.Compressed)
% Compress the pixel cells and add delimiters.
pixelData = dicom_compress_pixel_cells(pixelCells, txfr, ...
metadata.(dicom_name_lookup('0028','0100', dictionary)), ...
size(X));
pixelData = dicom_encode_attrs(pixelData, txfr, dicom_uid_decode(txfr));
pixelData = pixelData{1}; % Encoding produces a cell array.
else
% Create the (possibly packed) pixel cells.
pixelData = pixelCells;
end
function out = changePixelEndian(in, txfr, metadata, dictionary)
%CHANGEPIXELENDIAN Swap pixel bytes for special transfer syntaxes
uid_details = dicom_uid_decode(txfr);
% After this function, the pixel data should be in the right order so that
% dicom_encode_attr can translate it directly to the output endianness.
% Special syntaxes where (a) the pixel endianness doesn't match the
% endianness of the rest of the metadata or (b) 32-bit data is being
% written on a big-endian machine to a little-endian transfer syntax
% require "pre-work" on the pixels to allow correct encoding later.
in_class = class(in);
if (~isequal(uid_details.Endian, uid_details.PixelEndian))
% Pixel data is stored OB (unswapped) iff bits/sample <= 8, otherwise
% it's stored OW (swapped). When swapping OW data, words are swapped
% not the entire data. So a 32-bit sample with bytes (ABCD) becomes
% (BADC).
if (metadata.(dicom_name_lookup('0028', '0100', dictionary)) <= 16) % BitsAllocated
out = dicom_typecast(in(:), 'uint8', true);
out = dicom_typecast(out, in_class);
else
out = dicom_typecast(in(:), 'uint16', false);
out = dicom_typecast(out, 'uint8', true);
out = dicom_typecast(out, in_class);
end
out = reshape(out, size(in));
else
[~, ~, endian] = computer;
if (isequal(endian, 'B') && ...
isequal(uid_details.PixelEndian, 'ieee-le') && ...
metadata.(dicom_name_lookup('0028', '0100', dictionary)) > 16)
% The pixels need to look like the final little-endian
% representation, which will then be undone and redone.
out = dicom_typecast(in(:), 'uint16', true);
out = dicom_typecast(out, 'uint8', true);
out = dicom_typecast(out, in_class);
out = reshape(out, size(in));
else
out = in;
end
end
c4science · Help