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Inference in lightning #236
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Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
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* added primitive xy scaling feature to inference * fixed opset mismatches * changes to model + scripts for exporting to onnx * fixed dropout incompatibility, moved logger to utils. * removed inference session from model export script * use builtins to normalize * caching argument not doing anything yet * profiling script * separate augmentation * Revert "separate augmentation" This reverts commit c30ed61. * remove unused import * let zarr auto-detect multi-processing * remove unused import * copy zarr store to memory * allow cache and preload * update profiling script * format * remove preload this is not practical for larger datasets * cleanup * configurable number of log samples * split train and validation dataset at fov level * fix shuffling * fix dropout layers initialization * fix filter hyperparameter check * disable dropout for the head * stronger default augmentation * formalized onnx exporting and moved script to CLI, updated documentation in inference readme * fix merge conflict * isort * combine training CLI with others * Multi-GPU training (#235) * sync log metrics * example of using more GPUs * sync log metrics * example of using more GPUs * revised data format * updated data org * remove profile output this was accidentally tracked * Inference in lightning (#236) * rename lightning cli main script * add docstring * predict stage in data module * write predict result with callback * remove old inference module * rename tests Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> --------- Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> --------- Signed-off-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com> Co-authored-by: Christian Foley <christian.foley@login-01.clusternet> Co-authored-by: Christian Foley <christian.foley@gpu-c-1.clusternet> Co-authored-by: Ziwen Liu <67518483+ziw-liu@users.noreply.github.com>
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Removed the previous inference and implemented it as the predict step in lightning.