Evaluate existing segmentation #213
Merged
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
* update torch >2.4.1 * black * ruff
This reverts commit 8c13f49.
ziw-liu
added
enhancement
|
@edyoshikun can I get a review on this? |
ziw-liu
changed the title
edyoshikun
approved these changes
Mar 25, 2025
There was a problem hiding this comment.
Apologies for the super delay on this PR!!
I see this PR also adds the changes to support the iohub 0.2.0!
I was going to request that we do at a FOV inclusion/exclusion, but it looks like you do it in the next PR #218
Thank you!
edyoshikun
added a commit
that referenced
this pull request
Apr 15, 2025
* caching dataloader * caching data module * black * ruff * Bump torch to 2.4.1 (#174) * update torch >2.4.1 * black * ruff * adding timeout to ram_dataloader * bandaid to cached dataloader * fixing the dataloader using torch collate_fn * replacing dictionary with single array * loading prior to epoch 0 * Revert "replacing dictionary with single array" This reverts commit 8c13f49. * using multiprocessing manager * add sharded distributed sampler * add example script for ddp caching * format and lint * addding the custom distrb sampler to hcs_ram.py * adding sampler to val train dataloader * fix divisibility of the last shard * hcs_ram format and lint * data module that only crops and does not collate * wip: execute transforms on the GPU * path for if not ddp * fix randomness in inversion transform * add option to pop the normalization metadata * move gpu transform definition back to data module * add tiled crop transform for validation * add stack channel transform for gpu augmentation * fix typing * collate before sending to gpu * inherit gpu transforms for livecell dataset * update fcmae engine to apply per-dataset augmentations * format and lint hcs_ram * fix abc type hint * update docstring style * disable grad for validation transforms * improve sample image logging in fcmae * fix dataset length when batch size is larger than the dataset * fix docstring * add option to disable normalization metadata * inherit gpu transform for ctmc * remove duplicate method overrride * update docstring for ctmc * allow skipping caching for large datasets * make the fcmae module compatible with image translation * remove prototype implementation * fix import path * Arbitrary prediction time transforms (#209) * fix spelling in docstring and comment * add batched zoom transform for tta * add standalone lightning module for arbitrary TTA * fix composition of different zoom factors * add docstrings * wip: segmentation module * avoid casting * update import path from iohub * make integer array in fixture * labels fixture * test segmentation metrics modules * less strings * test non-empty * select which wells to include in fit #205 --------- Co-authored-by: Eduardo Hirata-Miyasaki <[email protected]>
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.
Add data modules and lightning modules to evaluate segmentation generated outside of VisCy, e.g. with czbiohub-sf/biahub#17.