Update Bio-Formats to 6.13.0 #103
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One outstanding question re the JSON dependency. Otherwise, happy to see this merged so that we can evaluate #68 (comment)
build.gradle
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| @@ -39,7 +39,7 @@ dependencies { | |||
| implementation 'com.bc.zarr:jzarr:0.3.5' | |||
| implementation 'info.picocli:picocli:4.2.0' | |||
| implementation 'me.tongfei:progressbar:0.9.0' | |||
| implementation 'ome:formats-bsd:6.12.0' | |||
| implementation 'ome:formats-bsd:6.13.0' | |||
| // be careful here, this is a newer version of org.json:json than formats-gpl uses | |||
| implementation 'org.json:json:20190722' | |||
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Now that this dependency has been upgraded in the Bio-Formats stack, do we want to look into dropping this dependency and consume the transitive one?
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That required switching to formats-gpl, since formats-bsd does not have a dependency on org.json:json. I'm fine with that, but can also revert a187d92 and just bump the org.json:json version if you prefer.
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Thank Melissa, I had missed this aspect of the dependency tree.
Although, it would be certainly fine to use formats-gpl, I think it's probably better to only depend formats-bsd and indeed increment the version of the json dependency to match the one in formats-gpl 6.13.0 (with the latest release addressing CVEs notably).
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Changes look good and all CI tests keep passing.
Functionally tested in the context of #68 as the codec extension proposed in ome/ome-codecs#26 and included in Bio-Formats 6.13.0 should allow to control the JPEG quality.
Running
./raw2ometiff-0.5.0-SNAPSHOT/bin/raw2ometiff CMU-1.zarr CMU-1.ome.tiff
./raw2ometiff-0.5.0-SNAPSHOT/bin/raw2ometiff CMU-1.zarr CMU-1_jpeg.ome.tiff --compression JPEG
./raw2ometiff-0.5.0-SNAPSHOT/bin/raw2ometiff CMU-1.zarr CMU-1_jpeg_20.ome.tiff --compression JPEG --quality 0.2
./raw2ometiff-0.5.0-SNAPSHOT/bin/raw2ometiff CMU-1.zarr CMU-1_jpeg_95.ome.tiff --compression JPEG --quality 0.95
yields
$ ls -alh CMU-1*
-rw-rw-r-- 1 omero omero 1.9G May 17 18:58 CMU-1.ome.tiff
-rw-rw-r-- 1 omero omero 335M May 17 18:59 CMU-1_jpeg.ome.tiff
-rw-rw-r-- 1 omero omero 159M May 18 09:08 CMU-1_jpeg_20.ome.tiff
-rw-rw-r-- 1 omero omero 629M May 18 09:09 CMU-1_jpeg_95.ome.tiff
So the logic works as expected. It is worth noting that
JPEG2000Codec so I suspect as we start enabling more configuration on the codec options we will need to start instantiating the appropriate CodecOptionss subclass.
Immediately happy for this to be included as is in the upcoming 0.5.0 release
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