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I'm currently using DPP to transform RAW files to TIFF (16 bits) files, and I have encountered some issues with some MATLAB routines I use to analyze the files. Tracing the problem, I noticed that the generated .tif files have '2' images; being 1 the actual image, and the other being a very compressed image. See attached images.

Actual image

highly compressed second image

The problem with this is that some of my MATLAB routines automatically assume that there is one image in the file, and hence they crash or do not operate with these particular files.

I have not encountered the issue with, e.g., the 'Photos' app, which is able to open the .cr2 files and exports them into tiff files. Sadly they are only 8 bits TIFF files, and I need 16 bits TIFF files.

Is there a way to solve this problem? I mean, to be able to export them into 16 bits TIFF files with only one image.

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This is completely valid for a TIFF image. There is in fact no limit to the number of subfiles a TIFF may contain You should either update your routines to support this, or use an intermediate program to rewrite them in a way your code expects.

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Answering to myself in view of the not-sufficiently-good answers, I have found that apple's scriptable image processing system (sips) is able to transform RAW to .TIFF images with only one subfile (the actual image). In particular, I have used the methodology described here:

Can I convert raw files to TIFFs via the command line using Apple's converting engine?

With this, there is no need to update the routines. I hope this serves people with similar problems.

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    As long as you don't mind giving up the demosaicing algorithms in DPP. Although 16-bit, the TIFF files will not contain all of the information found in the raw files. White and black points will be "baked in", as will white balance (although at 16-bits, to a lesser degree than with an 8-bit TIFF or JPEG). – Michael C Dec 4 '15 at 1:25
  • @MichaelClark Do you have any better solution? I'm currently using this for Digital Image Correlation analysis, and I'm very inexperienced in this area, so I'm currently exploring. All I know is that JPG files are too noisy, and 16-bit TIFF files are not. – Francisco Dec 9 '15 at 2:16
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Here is discussed the same issue. And multipage TIFF is standard, not error. So you should check why your MATLAB libraries do not support multipage tiff or use instruments to remove second page or make matlab libraries work only with first page

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