updated camelyon16 configs to save embeddings less frequent #539
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
…7-fix-memory-leak-embeddingswriter
roman807
changed the title
nkaenzig
approved these changes
Jun 18, 2024
roman807
merged commit 0656202
into
360-aggregated-feature-support-wsi-level-tasks
6 checks passed
roman807
added a commit
that referenced
this pull request
Jun 24, 2024
* Add base class for WSIs & `openslide` implementation (#365) * Add WSI dataset classes (#368) * Add baseline `panda` workflow (#373) * add panda config * adjust batch size * addressed comments * addressed comments * addressed comments * Add support for grid sampling to `WsiDataset` (#377) * Replaced cached_property in WsiDataset by LRU cache (#388) * Updated `EmbeddingsWriter` to support multi-embedding file outputs (#384) * Simple baseline sampler for foreground patches (#394) * add foreground kaggle * added random foreground sampler kaggle * refactored sampler * moved get_mask * typo * refactor sampler * refactor sampler * addressed comments * addressed comments * Fixed linting in WSI feature branch (#407) * added openslide-python to all dependencies * Fix input batch class name (#414) * Add lower bound for wsi resolution level during mask generation (#412) * Move sampler logic to `samplers` module and add unit tests (#420) * Add `WsiClassificationDataset` (#429) * Retrieve MPP from WSIs (#432) * add mpp conversion * formatting * addressed comments * addressed comments * addressed comments * formatting * formatting * formatting * updated panda config (#437) * update WSI foreground segmentation algorithm (#456) * Add `PANDA` dataset class (#430) * fixed panda (#463) * Update `EmbeddingsWriter` to store tensors as lists (#465) * add tiffslide backend (#468) * added panda cli unit tests (#470) * move wsi initialization to setup method of `MultiWsiDataset` (#472) * 459 add camelyon16 slide level task (#476) * added panda dataset class * clean up * remove samples with noisy labels * clean up table in dataset readme * added function for stratified splits * added unit tests * cleanup * addressed comments * fixed issue with resource download * validation fix * updated readme * added to mkdocs * added image_dir to exception print * updated root path in yaml config * added panda to datasets overview table in docs * added md5 hash for downloaded resources * update init * added camelyon16 * added camelyon16 * updated camelyon16 class * added tests and config * formatting * formatting * formatting * formatting * added test files * formatting * lint * added target transforms * formatting * fixed dataset * addressed comments * addressed comments * fix test * fix test * fixed test * addressed comments * updated loss * fix annotations * lint --------- Co-authored-by: Nicolas Kaenzig <nkaenzig@gmail.com> * 475 define slide level evaluation protocol (#511) * updated configs * adjust patience * addressed comments * fixed typo * remove prefetch factor * update 360-aggregated-feature before PR to main (#527) * Updated developer guide (#418) * Update `TotalSegmentator2D` dataset to fetch all the slices (#416) * Move metrics to CPU when using single device (#446) * Remove total segmentator classification dataset (#450) * updated eva logo (#454) * updated eva logo * renamed files * Update actions/checkout digest to a5ac7e5 (#458) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Add configuration logger (#466) * Update `README` with paper citation (#474) * update docs (#482) * Update img shields of README (#480) * Fix `torch` and `jsonargparse` versions (#483) * update depedencies * update * bump micro version (#486) * update config links (#487) * Update paper citation format (#489) * Update the vision dataset return types to `tv_tensors` (#478) * Refactor embeddings writer (#461) * fixed phikon configs (#493) * Refactor embeddings datasets (#495) * Add doc tests and minor fixes (#492) * support setting download as env-variable (#514) * updated confis and doc * typo * update datasets * fixed types * src/eva/core/callbacks/writers/embeddings/base.py * formatting * types --------- Co-authored-by: Nicolas Känzig <36882833+nkaenzig@users.noreply.github.com> Co-authored-by: ioangatop <johngatop@gmail.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Updated documentation with new datasets and leaderboard (#531) * updated layout * updated layout * addressed comment * 532 update leaderboard results with slide level tasks (#538) * updated docs * update leaderboard * update docs and links * updated configs (#539) * updated leaderboard (#543) --------- Co-authored-by: Nicolas Känzig <36882833+nkaenzig@users.noreply.github.com> Co-authored-by: Nicolas Kaenzig <nkaenzig@gmail.com> Co-authored-by: ioangatop <johngatop@gmail.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
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.
closes #537
Note: memory still builds up during predict and accumulates across dataloaders/splits. However, ray node does not crash anymore with example camelyon16/phikon