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R8218/CT/private/dicom_decode_pixel_cells.m
1ba0b9dff245Bashardoust_SystCoord

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dicom_decode_pixel_cells.m
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function [pixels, overlays] = dicom_decode_pixel_cells(data, info, ol_bits)
%DICOM_DECODE_PIXEL_CELLS Get pixel values and overlay bits from pixel cells.
% [PIXELS, OVERLAYS] = DICOM_DECODE_PIXEL_CELLS(DATA, INFO, BITS)
% extracts the pixel and overlay data from the pixel cells DATA. INFO
% is the metadata structure for the pixel data array DATA. OL_BITS is
% a vector of bit positions in DATA which contain overlay data, which
% are always single bits.
%
% The PIXELS returned are a vector of integer values without overlay
% data. The values in PIXELS have been shifted to start at the
% least-significant byte for each element, so that they actually
% represent the correct pixel values without further modification.
%
% The OVERLAYS array is an m-by-n-by-1-by-p logical array, where p is
% the number of overlays in the DATA.
% Copyright 1993-2005 The MathWorks, Inc.
%
% Read overlays.
%
if (isempty(ol_bits))
overlays = logical([]);
else
overlays = repmat(false, [info.Rows info.Columns info.NumberOfFrames ...
length(ol_bits)]);
end
level = 0;
for p = 1:length(ol_bits)
level = level + 1;
plane = bitget(data, (ol_bits(p) + 1));
plane = reshape(plane, [size(overlays,1), size(overlays,2), ...
size(overlays,3)]);
plane = permute(plane, [2 1 3]);
overlays(:, :, :, level) = plane;
end
%
% Strip out overlays.
%
% Convert signed data temporarily to unsigned.
if (info.PixelRepresentation == 1)
switch (class(data))
case 'int8'
data = dicom_typecast(data, 'uint8');
case 'int16'
data = dicom_typecast(data, 'uint16');
case 'int32'
data = dicom_typecast(data, 'uint32');
end
end
% Remove higher order overlays.
mask = (2^(info.HighBit + 1) - 1);
data = bitand(data, mask);
% Remove lower order overlays.
bit_offset = (info.HighBit + 1) - info.BitsStored;
data = bitshift(data, -bit_offset);
% Fit the data into an appropriate sized storage unit.
container_size = ceil(info.BitsStored / 8) * 8;
if (info.PixelRepresentation == 1)
sign_bit = info.HighBit - bit_offset + 1;
has_negative = any(bitget(data, sign_bit));
% Move the size bit to the end of the data container (e.g., the 8th
% or 16th bit) and fill old sign bit with 0.
if ((sign_bit ~= container_size) && (has_negative))
mask = bitget(data, sign_bit);
data = bitor(data, bitshift(mask, container_size));
data = bitset(data, sign_bit, 0);
end
end
% Convert signed data back from unsigned.
if (info.PixelRepresentation == 1)
switch (class(data))
case 'uint8'
data = dicom_typecast(data, 'int8');
case 'uint16'
data = dicom_typecast(data, 'int16');
case 'uint32'
data = dicom_typecast(data, 'int32');
end
end
%
% Store pixel bits.
%
switch (container_size)
case 8
if (info.PixelRepresentation == 0)
pixels = uint8(data);
else
pixels = int8(data);
end
case 16
if (info.PixelRepresentation == 0)
pixels = uint16(data);
else
pixels = int16(data);
end
case 32
if (info.PixelRepresentation == 0)
pixels = uint32(data);
else
pixels = int32(data);
end
end
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