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TIFF: correctly account for fakeBigTiff when reading IFD entries #1205

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merged 1 commit into from Jul 14, 2014

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melissalinkert
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Fixes https://trac.openmicroscopy.org.uk/ome/ticket/12367. Easiest way to test is probably to import the files from data_repo/from_skyking/hamamatsu/kristian into OMERO, and verify that import is successful and there is nothing obviously wrong with the resulting images. Checking these files in ImageJ or Matlab is going to be much trickier given their size.

@bramalingam
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Works as expected with Insight. Good to merge.

Trying with ImageJ and Matlab gave the same error,
Java exception occurred:
java.lang.IllegalArgumentException: Array size too large: 135168 x 96000 x 1
at loci.common.DataTools.safeMultiply32(DataTools.java:854)
at loci.common.DataTools.allocate(DataTools.java:828)
at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:153)

This is definitely not a heap space error, @melissalinkert : what does it mean when it says Array size too large.

@melissalinkert
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That exception occurs when attempting to open more than 2147483648 bytes (2GB) of image data at a time. It is a limitation of Java that arrays cannot contain more than 2147483648 elements, so to open large images like this in Matlab or ImageJ you will need to open the image as a set of tiles (Crop on import in ImageJ; change the x, y, width, and height arguments when calling openBytes in Matlab).

melissalinkert added a commit that referenced this pull request Jul 14, 2014
TIFF: correctly account for ```fakeBigTiff``` when reading IFD entries
@melissalinkert melissalinkert merged commit 4829951 into ome:develop Jul 14, 2014
@melissalinkert
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--rebased-to #1214

@sbesson sbesson added this to the 5.1.0-m1 milestone Oct 14, 2014
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3 participants