Allow SlideData to use existing h5path files #337
Conversation
This file contains 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
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Outdated suggestions cannot be applied.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.
As motivated by #332 and #300, this modifies SlideData to read and update Tiles from an existing h5path file instead of requiring each pipeline run to recreate all tiles from scratch.
This includes #335 as many transforms (e.g.
BoxBlur) require np.uint8 data instead of the default float16 saved to h5path files. I was also working off my load-data-in-workers branch because it had significant performance changes for my use cases. Sorry about the branching messiness, hopefully the changes will be clearer as other branches are merged intodev.This makes breaking changes to the
SlideDataAPI, namely replacinggenerate_tileswithget_tilesand moving the tile parameterization fromrunto theSlideDataconstructor.