OMEPyramidWriter logic for bigtiff can fail for image pyramids #858
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petebankhead
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Dec 14, 2021
Fixes for * qupath#857 * qupath#858 This introduces the ability to write some other file formats using OMEPyramidWriter. It also adds the ability to specify --big-tif with the convert-ome command.
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Bug report
Describe the bug
The logic used here to identify whether a bigtiff should be written appears to be incorrect, because it ignored multiple resolutions (and any space required for IFDs etc.).
To Reproduce
Difficult, because it requires an image that is on the borderline of what is acceptable.
But see https://forum.image.sc/t/qupath-out-of-memory-problem-when-creating-training-image/60985/5 for a case where I think that has happened.
Expected behavior
QuPath should always write bigtiff when it needs to. Multiple resolutions should be included in any calculation.
It might be necessary to provide the user with a way to control this.
Desktop (please complete the following information):
Additional context
This can be difficult to discern in advance whenever compression is involved.
The logic used for setting the bigtiff flag automatically in Bio-Formats is in
TiffWriter(but it applies only if the image is uncompressed, and it's not totally clear to me if it uses the multiple resolutions).The text was updated successfully, but these errors were encountered: