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Describe the bug OMEPyramidWriter was created to write OME-TIFF images. However, it is possible to pass it a path with any extension - in which case it may write an ome.tif masquerading as something else.
To Reproduce
Steps to reproduce the behavior:
Open a 'small' image, e.g. CMU-1-Small-Region.svs
Run a script like the one below to try to write a JPEG 2000 image
Use tiff info to confirm that the .jp2 image written is actually a TIFF
Refuse to write the image if it doesn't end with ome.tif
Add ome.tif as a file extension if it is originally anything else
Actually support writing in different file formats, if allowed by Bio-Formats
The third seems more desirable - particularly as Bio-Formats 6.8.0 introduces support for writing DICOM whole slide images, which may be very useful in the future.
Desktop (please complete the following information):
OS: All
QuPath Version 0.3.0
Additional context
I have explored some small changes that come closer to supporting different file formats, although there can be some gotchas - for example, if other formats don't support multiple resolutions or tiling, or require the reader to be initialised in a specific way.
It is likely that QuPath's OMEPyramidWriter.CompressionType may become inadequate; certainly it isn't desirable to always require a compression type for formats where it isn't customisable.
The text was updated successfully, but these errors were encountered:
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.
Bug report
Describe the bug
OMEPyramidWriter
was created to write OME-TIFF images. However, it is possible to pass it a path with any extension - in which case it may write an ome.tif masquerading as something else.To Reproduce
Steps to reproduce the behavior:
tiff info
to confirm that the .jp2 image written is actually a TIFFExpected behavior
There are three main options:
The third seems more desirable - particularly as Bio-Formats 6.8.0 introduces support for writing DICOM whole slide images, which may be very useful in the future.
Desktop (please complete the following information):
Additional context
I have explored some small changes that come closer to supporting different file formats, although there can be some gotchas - for example, if other formats don't support multiple resolutions or tiling, or require the reader to be initialised in a specific way.
It is likely that QuPath's
OMEPyramidWriter.CompressionType
may become inadequate; certainly it isn't desirable to always require a compression type for formats where it isn't customisable.The text was updated successfully, but these errors were encountered: