Scyjava Refactor #133
Merged
Scyjava Refactor #133
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Does not work yet.
One step toward eliminating the bioformats subpackage.
The python-bioformats read function code has been migrated here now, and updated to use scyjava instead of javabridge. Most code is the same!
These are jpype JArrays now and can be iterated directly
Add a shutdown hook to close the reader, and don't try to close it if it's already closed.
This adds logback-classic and a logback.xml configuration file which sets logging to INFO level, ensuring an slf4j implementation is present and not defaulting to DEBUG level spam.
This is used and was undeclared, previously coming in transitively through python-bioformats.
TODO: are these all accurate?
writer now works on writing single channel images, but wip on multi-channel
add log level and origin to log messages
bethac07
reviewed
Dec 8, 2022
bethac07
reviewed
Dec 8, 2022
bethac07
reviewed
Dec 8, 2022
bethac07
reviewed
Dec 8, 2022
| openBytes_func = self._reader.openBytes | ||
| width, height = self._reader.getSizeX(), self._reader.getSizeY() | ||
|
|
||
| # FIXME instead of np.frombuffer use scyjava.to_python, ideally that wraps memory |
Member
There was a problem hiding this comment.
It seems like we now have a mix of the two, is this note intended to resolve the later ones (and if so, is there a reason not to just do it now, or is the one place where it's now used meant to be the only place and thus can it be resolved?
bethac07
reviewed
Dec 8, 2022
bethac07
reviewed
Dec 8, 2022
bethac07
approved these changes
Dec 8, 2022
Member
bethac07
left a comment
bethac07
left a comment
There was a problem hiding this comment.
I've left a couple small notes here for things I noticed where we may want to clean some stuff or leave better notes for future us, but otherwise, 😍 😍 😍 😍 . Great work everyone!
fix jamboree issue, where Metadata module options disapper upon loading cppipe that made reference to a nonexistent input folder
* split out note by regex rather than pipes * Add back support for older pipelines
* Remove deprecated numpy aliases * Recompile centrosome
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Companion to CellProfiler/CellProfiler#4681