Migrate to Keras 3.0 with TF backend #373
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…ltiprocessing=False from fit() as it is no longer an input. test_train() passing
…ve from fit() signature (keras3 change)
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Hiya @sfmig - quick question: does your Just intrigued to know whether our seg-fault might have something to do with |
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Hi @willGraham01! |
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No problem, just wanted to check since I noticed all your tests are passing without issue and was wondering if the problems we're facing in #372 were tensorflow related. (In classic Will fashion essentially hoping you might have fixed it for me 😅) But if you already have the hotfix branch pulled in that's cool. Just to warn you too, #369 has had some more updates which have removed the un-neccessary |
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IgorTatarnikov
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* remove pytest-lazy-fixture as dev dependency and skip test (with WG temp fix) * Test Keras is present (#374) * check if Keras present * change TF to Keras in CI * remove comment * change dependencies in pyproject.toml for Keras 3.0 * Migrate to Keras 3.0 with TF backend (#373) * remove pytest-lazy-fixture as dev dependency and skip test (with WG temp fix) * change tensorflow dependency for cellfinder * replace keras imports from tensorflow to just keras imports * add keras import and reorder * add keras and TF 2.16 to pyproject.toml * comment out TF version check for now * change checkpoint filename for compliance with keras 3. remove use_multiprocessing=False from fit() as it is no longer an input. test_train() passing * add multiprocessing parameters to cube generator constructor and remove from fit() signature (keras3 change) * apply temp garbage collector fix * skip troublesome test * skip running tests on CI on windows * remove commented out TF check * clean commented out code. Explicitly pass use_multiprocessing=False (as before) * remove str conversion before model.save * raise test_detection error for sonarcloud happy * skip running tests on windows on CI * remove filename comment and small edits * Replace TF references in comments and warning messages (#378) * change some old references to TF for the import check * change TF cached model to Keras * Cellfinder with Keras 3.0 and jax backend (#379) * replace tensorflow Tensor with keras tensor * add case for TF prep in prep_model_weights * add different backends to pyproject.toml * add backend configuration to cellfinder init file. tests passing with jax locally * define extra dependencies for cellfinder with different backends. run tox with TF backend * run tox using TF and JAX backend * install TF in brainmapper environment before running tests in CI * add backends check to cellfinder init file * clean up comments * fix tf-nightly import check * specify TF backend in include guard check * clarify comment * remove 'backend' from dependencies specifications * Apply suggestions from code review Co-authored-by: Igor Tatarnikov <[email protected]> --------- Co-authored-by: Igor Tatarnikov <[email protected]> * Run cellfinder with JAX in Windows tests in CI (#382) * use jax backend in brainmapper tests in CI * skip TF backend on windows * fix pip install cellfinder for brainmapper CI tests * add keras env variable for brainmapper CLI tests * fix prep_model_weights * It/keras3 pytorch (#396) * replace tensorflow Tensor with keras tensor * add case for TF prep in prep_model_weights * add different backends to pyproject.toml * add backend configuration to cellfinder init file. tests passing with jax locally * define extra dependencies for cellfinder with different backends. run tox with TF backend * run tox using TF and JAX backend * install TF in brainmapper environment before running tests in CI * add backends check to cellfinder init file * clean up comments * fix tf-nightly import check * specify TF backend in include guard check * clarify comment * remove 'backend' from dependencies specifications * Apply suggestions from code review Co-authored-by: Igor Tatarnikov <[email protected]> * PyTorch runs utilizing multiple cores * PyTorch fix with default models * Tests run on every push for now * Run test on torch backend only * Fixed guard test to set torch as KERAS_BACKEND * KERAS_BACKEND env variable set directly in test_include_guard.yaml * Run test on python 3.11 * Remove tf-nightly from __init__ version check * Added 3.11 to legacy tox config * Changed legacy tox config for real this time * Don't set the wrong max_processing value * Torch is now set as the default backend * Tests only run with torch, updated comments * Unpinned torch version * Add codecov token (#403) * add codecov token * generate xml coverage report * add timeout to testing jobs * Allow turning off classification or detection in GUI (#402) * Allow turning off classification or detection in GUI. * Fix test. * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Refactor to fix code analysis errors. * Ensure array is always 2d. * Apply suggestions from code review Co-authored-by: Igor Tatarnikov <[email protected]> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Igor Tatarnikov <[email protected]> * Support single z-stack tif file for input (#397) * Support single z-stack tif file for input. * Fix commit hook. * Apply review suggestions. * Remove modular asv benchmarks (#406) * remove modular asv benchmarks * recover old structure * remove asv-specific lines from gitignore and manifest * prune benchmarks * Adapt CI so it covers both new and old Macs, and installs required additional dependencies on M1 (#408) * naive attempt at adapting to silicon mac CI * run include guard test on Silicon CI * double-check hdf5 is needed * Optimize cell detection (#398) (#407) * Replace coord map values with numba list/tuple for optim. * Switch to fortran layout for faster update of last dim. * Cache kernel. * jit ball filter. * Put z as first axis to speed z rolling (row-major memory). * Unroll recursion (no perf impact either way). * Parallelize cell cluster splitting. * Parallelize walking for full images. * Cleanup docs and pep8 etc. * Add pre-commit fixes. * Fix parallel always being selected and numba function 1st class warning. * Run hook. * Older python needs Union instead of |. * Accept review suggestion. * Address review changes. * num_threads must be an int. --------- Co-authored-by: Matt Einhorn <[email protected]> * [pre-commit.ci] pre-commit autoupdate (#412) updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.4.3](astral-sh/ruff-pre-commit@v0.3.5...v0.4.3) - [github.com/psf/black: 24.3.0 → 24.4.2](psf/black@24.3.0...24.4.2) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Apply suggestions from code review Co-authored-by: sfmig <[email protected]> * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Simplify model download (#414) * Simplify model download * Update model cache * Remove jax and tf tests * Standardise the data types for inputs to all be float32 * Force torch to use CPU on arm based macOS during tests * Added PYTORCH_MPS_HIGH_WATERMARK_RATION env variable * Set env variables in test setup * Try to set the default device to cpu in the test itself * Add device call to Conv3D to force cpu * Revert changes, request one cpu left free * Revers the numb cores, don't use arm based mac runner * Merged main, removed torch flags on cellfinder install for guards and brainmapper * Lowercase Torch * Change cache directory --------- Co-authored-by: sfmig <[email protected]> Co-authored-by: Kimberly Meechan <[email protected]> Co-authored-by: Matt Einhorn <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder <[email protected]> Co-authored-by: Adam Tyson <[email protected]> * Set pooling padding to valid by default on all MaxPooling3D layers * Removed tf error suppression and other tf related functions * Force torch to use cpu device when CELLFINDER_TEST_DEVICE env variable set to cpu * Added nev variable to test step * Use the GITHUB ACTIONS environemntal variable instead * Added docstring for fixture setting device to cpu on arm based mac * Revert changes to no_free_cpus being fixture, and default param * Fixed typo in test_and_deploy.yml * Set multiprocessing to false for the data generators * Update all cache steps to match * Remove reference to TF * Make sure tests can run locally when GITHUB_ACTIONS env variable is missing2 * Removed warning when backend is not configured * Set the label tensor to be float32 to ensure compatibility with mps * Always set KERAS_BACKEND to torch on init * Remove code in __init__ checking for if backend is installed --------- Co-authored-by: sfmig <[email protected]> Co-authored-by: Kimberly Meechan <[email protected]> Co-authored-by: Matt Einhorn <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Alessandro Felder <[email protected]> Co-authored-by: Adam Tyson <[email protected]>
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A PR to migrate cellfinder to Keras 3.0 with tensorflow backend.
Two main changes from Keras 3.0:
model.fit())In
trian_yml.pyfor thetraining_generatorand thevalidation_generator, I explicitly setuse_multiprocessing=Falseeven though it is the default, since this was done explicitly before too (see here).