MATLAB: Speeding up fread for true 12bit data

12bitbinaryfreadMATLABrawread dataubit12uint16

I'm using fread to load 12bit data files (raw files from a high-speed camera). The relevant part of the code is here:
precision='ubit12=>uint16'; % convert 12bit to 16bit on reading
machinefmt='b';
fseek(mraw_file, 0, 'bof');
vid_segments=fread(mraw_file,inf,precision,machinefmt);
N = [im_width im_height length(frames)];
im=permute(reshape(vid_segments,N),[2 1 3]);
The code is working smoothly, however I've noticed that it is about 10x slower than if I use the same code to read other data stored as 16bit data using:
precision='*uint16';
I'm guessing this is because of how Matlab deals with data that isn't formatted as multiples of 1 byte? Is there any way I can read in the 12bit data files faster, using 8bit or 16bit precision and then converting to 12 bit?
For reference, the data is true 12bit so 2 x 12 bits of data = 3 bytes. It's not padded with zeros or random numbers so that 1 x 12bit of data = 2 bytes (which would simplify things).
Any help would be greatly appreciated!

Best Answer

Read the data as bytes at first:
data = fread(mraw_file, inf, 'uint8=>uint16', machinefmt);
pad  = ceil(length(data) / 3) * 3 - length(data);
data = cat(1, data, zeros(pad, 1, 'uint16));
data = reshape(data, 3, []).';
Then convert the data in the memory:
video = [bitshift(data(:, 1), 4) + bitshift(data(:, 2), -4), ...
         bitshift(rem(data(:, 2), 16), 8) + data(:, 3)];
Is this faster? I'm not sure, if multiplications are faster than bit-shifting in Matlab. Try this:
video = [data(:, 1) * 16 + data(:, 2) / 16, ...
         rem(data(:, 2), 16) *256 + data(:, 3)];
A simple C-mex function would be faster, because it can avoid to create the temporary vectors. Do you have a C compiler installed?
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