Open jo-mueller opened 2 months ago
I think I have a fix on my fork - I'd need somehelp with testing though - how exactly would I be able to test my changes in the underlying Java code in my Python workflow? 🤔
This issue has been mentioned on Image.sc Forum. There might be relevant details there:
https://forum.image.sc/t/ome-zarr-import-to-omero-failure-response-on-import/82067/7
Thank you for opening the issue and investigating a fix. I believe the version of ZarrReader you are using is 0.3.1 so the initial failure would have been here: https://github.com/ome/ZarrReader/blob/v0.3.1/src/loci/formats/in/ZarrReader.java#L704
This would make sense based on the sample file. From that file the OMERO metadata looks like this:
"omero": {
"channels": [
{
"active": true,
"coefficient": 1,
"color": "000000",
"family": "linear",
"inverted": false,
"label": "test",
"window": {
"end": 1.0,
"max": 1.0,
"min": 0.0,
"start": 0.0
}
}
],
"id": 1,
"name": "test",
"rdefs": {
"defaultT": 0,
"defaultZ": 32,
"model": "color"
},
"version": "0.4"
}
@jo-mueller, if you want to open a Pull Request against this repository then we can review and test the fix for a future release. If you wanted to test it locally as part of your own workflow then you would have to build the jar file using mvn clean package
and then replace your existing OMEZarrReader jar file.
Hi @dgault ,
thanks for the hint. I am not super-experienced with Java (actually not at all 😅 ) - I successfully built my fork using maven. Where exactly would the current OMEZarrReader.jar
be stored for me to replace by my own build? I did not find it in the site-packages
directory. That said, I am not even exactly sure which package exactly would invoke the build jar - is that omero-py?
Hi @jo-mueller, sorry for the slow response. The OMEZarrReader.jar
file should be part of the main OMERO server. In the maoin server location you should see a number of .jar files under lib/server
, including formats-api.jar
, formats-bsd.jar
, formats-gpl.jar
etc. This will also be were the OMEZarrReader.jar
file lives.
Hi @dgault ,
I tried myself at fixing this but no success, unfortunately - I think I would have to limit myself to an observer on this issue :/ I'll be happy to test any changes on the project though, if need be.
@jo-mueller could you open a PR with your branch? @dgault is unfortunately leaving the OME team - today is his last day - but we may be able to test your fix. I am seeing a similar error trying to import a Plate with acquisition starttime Int/Long issue. see https://github.com/ome/ZarrReader/issues/55
I have opened a PR which contains the 2 commits from that fork for testing: https://github.com/ome/ZarrReader/pull/95
Hi all,
following up an issue I created over at ezomero, I am having some trouble uploading zarr to our omero server.
I created a test zarr file for trial with this Python code:
and tried the upload through both ezomero as well as the CLI using
You can create the zarr yourself, otherwise, you can also download the test file here.
Full traceback:
Any help is much appreciated and thanks already in advance :)