fastest way to read single tiff images
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I am working with relatively large data sets of single (4 MP, 8-bit) tiff images. Each set contains somewhere in the vicinity of 5000 images (i.e. 20 GB per set). Working with such sets can be very time consuming. For example, simply calculating the time average of a 4000-image set takes over 40 minutes (2441 seconds, to be exact) according to the profiler. Of this, about 85% of the time comes from imread. Is there a way, either by optimizing the use of imread or by using a low-level function, that I can reduce the read out time of the files? I am using imread as follows:
img = imread(filename, 'tif');
Thanks for any help.
Image Analyst on 10 Sep 2014
Copy the images to s solid state drive, or even faster, a RAMdisk, before you begin processing. Look at the charts on this page: http://blog.laptopmag.com/faster-than-an-ssd-how-to-turn-extra-memory-into-a-ram-disk
Sean de Wolski on 10 Sep 2014
Consider using blockproc with the 'UseParallel' option enabled (if you have Parallel Computing Toolbox).
This will do the analysis on pieces of your image chunks at a time, and with parallel enabled will work on the pieces in parallel. You're in luck that tiff images are ideal for this process since the strips can be read in independently.
Stefano on 14 Sep 2014
either low level tiff: http://www.matlabtips.com/how-to-load-tiff-stacks-fast-really-fast/ or if it is uncompressed, fread or memory mapping, the latter seems faster than fread, e.g. m = memmapfile(fname,'Offset',250,'Format','uint16','Writable', false); a2=reshape(swapbytes(m.Data),size2,size1)';
Dylan Muir on 27 Jan 2015