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Integrates the training recipe of the 'mitochondria2' model, which so far only existed outside this repository, as a first-class part of the package. - synapse_net/training/mitochondria.py: get_mitochondria_paths for the recursive data discovery and the train/val split (optionally from a split file), and mitochondria_training, which fixes the hyperparameters of the published model. Registered as the CLI synapse_net.run_mitochondria_training. - supervised_training: expose initial_features, mixed_precision, early_stopping and log_image_interval. The defaults keep the previous behaviour for all other callers. - scripts/cooper/training/train_mitochondria_tomo.py plus the split file of the published run, so it can be reproduced file for file. - test/training/__init__.py, without which unittest discovery skipped all of test/training. Discovery goes from 106 to 121 tests with this commit. The recipe was taken from the init of the deployed checkpoint, not from the training script. Verified by training on the real tomograms and comparing the resulting checkpoint against the deployed one: model kwargs, loss, optimizer, scheduler, mixed_precision, early_stopping, log_image_interval and the loader kwargs all agree, and both models have the same state dict and the same 18 InstanceNorm3d layers. Note that the percentile normalization is part of the model: the same preprocessing has to be passed to segment_mitochondria at inference time. Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>
The previous commit added test/training/__init__.py so that unittest discovery would pick
up that folder. That also enabled the eight tests in test/training/test_training_cli.py,
which had never run in CI before and do not pass there: all three CI jobs failed, while
main is green. Windows failed within seconds, which matches the skip that test/test_cli.py
already carries ("CLI does not work on Windows") for the same kind of subprocess test.
Fixing those tests is not this change's job, so restore test/training to the state it was
in and move the new mitochondria tests to test/, where discovery finds them without
enabling anything else. CI now runs 113 tests, the 106 from main plus these 7.
Also skip the CLI test on Windows, following test/test_cli.py.
The tests in test/training/test_training_cli.py are still invisible to CI. That is
pre-existing and worth a separate look.
Co-Authored-By: Claude Opus 5 (1M context) <[email protected]>
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Integrates the training recipe of the 'mitochondria2' model, which so far only existed outside this repository, as a first-class part of the package.
The recipe was taken from the init of the deployed checkpoint, not from the training script. Verified by training on the real tomograms and comparing the resulting checkpoint against the deployed one: model kwargs, loss, optimizer, scheduler, mixed_precision, early_stopping, log_image_interval and the loader kwargs all agree, and both models have the same state dict and the same 18 InstanceNorm3d layers.
Note that the percentile normalization is part of the model: the same preprocessing has to be passed to segment_mitochondria at inference time.