fastest way to read single tiff images

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Humberto
Humberto on 10 Sep 2014
Answered: Dylan Muir on 27 Jan 2015
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.
Humberto

Answers (4)

Image Analyst
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
  3 Comments
Joseph Cheng
Joseph Cheng on 11 Sep 2014
Well from your profiler results the time of read is 85% of your processing time. so if we run the numbers for a single image processing it takes 0.48 seconds which 0.41sec is the opening (73 milli seconds processing). so yeah the reading from the disk is not "slow" however you're doing this 5000 times. and to cut the time you wouldn't get much by processing faster reducing the 6 min (15% processing portion). lets be conservative and say read time is 2x for a SSD then you're reducing the 34 min by about 15 min.

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Sean de Wolski
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.
doc blockproc

Stefano
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
Dylan Muir on 27 Jan 2015

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