Closed GenevieveBuckley closed 6 years ago
The fix appears to be:
It works at least, but it's not exactly neatly self-contained.
From the pims bioformats page:
To interface with the java library, we use JPype, which allows fast and easy access to all java functions. JRE or JDK are not required.
This is odd, since we saw very clearly that the app (pims build) did not function before the JDK was installed, but did run afterwards.
Hi @genevievebuckley!
This is very interesting and mildly tragic. Thanks for the detailed updates. Feel free to self-merge if I am unresponsive as I have a busy week ahead!
Incidentally I met @jakirkham earlier today and he too has run into PIMS as a solution to his totally orthogonal problem (finding out the size of a tiff without opening it). Seems like an exceedingly useful library!
The way I understood it, you can get the metadata for all image series by opening just one of those series (the default being series=0).
But it sounds like @jakirkham is querying only the metadata directly? Is that true, or did I misunderstand
Closing this issue, since the decision has been made to go with pims & jpype instead of python-bioformats & javabridge (and the decision merged into master with pull request https://github.com/monashmicroimaging/podocytes/pull/7).
User testing:
Testing the Podo.app mac build from branch process-images, as of this commit - also see pull request https://github.com/monashmicroimaging/podocytes/pull/4
Problems the users ran into:
But after all of that they're stll getting this error message:
Neither user have $JAVA_HOME set to anything.