Trainable implementation of full autoencoder. #4

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cellistigs wants to merge 40 commits intomainfrom

Commits on Mar 4, 2025

started taking some notes on preprocessing.

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added and tested pytorch data module

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Commits on Mar 5, 2025

added source code for a minimal implementation of single session AE.

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added rudimentary tests of function for all components. Can get a baby training loop to train.

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added config params for training of ALM network.

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have a script that should in theory train

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got training script to run in dev mode.

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added configs for debugging and training.

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fixed some attributes in dataloading.

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deleted crop configs

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fixed up tests for data configs.

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added some docstring for bad stub
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fixed merge conflict
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some messaging for the dataloading.

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finishing merge
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updated mean image calc.

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updated dataloading
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fixed argument passing

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issue with editor
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trying to keep all predictions in memory is infeasible. save out training frames.
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tested additional flags on valset
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eval test failing for some reason
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adapted training for high frame count
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added back mean image when predicting
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Commits on Mar 6, 2025

added learning rate monitoring and fixed checkpointing conditions.
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played with learning rate scheduling.
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added chained lr scheduler

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Merge branch 'taiga-dev' of https://github.com/druckmann-lab/VideoAnalysisTools into taiga-dev

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arg order wrong for chainedscheduler

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step scheduler needs to be passed the raw functions, not dict
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Commits on Mar 7, 2025

was scheduling on epochs, not steps!
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added string matching to only create some frames.
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Commits on Mar 19, 2025

started building stub of eval

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make sure we save data path.
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added sequence dataset (used for eval for now)
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the parameter for the trainer set up should be fit, not train
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Commits on Mar 20, 2025

added evaluation script that saves out results per trial
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moved things around so we have a preliminary version of eval loop
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played with changes to training and added caching

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subset of data config variables are useful.

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