2024 Review

[neptunes5thmoon]

Finished reviewing (looked at ben/denoisplit as per mattermost).
01 and 04 need some work I think but for the other ones only minor comments:

Installation

• end up in a different directory after running source setup.sh
• recommended is putting data on our s3 bucket and download from there
• dependencies of denoiSplit not installed

01_CARE

• missing colored boxes for checkpoints, exercises etc. in the exercise notebook
• still got TODOs in there (most importantly: missing scaffolding for some tasks)
• import for augment_batch and normalize is at the very beginning and defined by you. Maybe add a comment that makes clear that it's provided by you and add a cell with ?augment_batch and ?normalize at task 1, similarly for denormalize in task 3
• agree that calculation of means and stds should go in the function
• they already know about data loaders in principle
• the unet should come from here: https://github.com/dlmbl/dlmbl-unet
• IMO importing torch.nn and torch.optim would be better than importing with as nn
• I got NaNs in my loss when my lr was too high
• something with the training is not working for me - validation loss is always the same

02_Noise2Void

• config explanation: I think axes being "YX" warrants more explanation (e.g. they might get 2D but be thrown for a loop by it not being "XY" )
• getting some warnings during training
• Task2: tensorboard is already started
• in export: TypeError: CAREamist.export_to_bmz() got an unexpected keyword argument 'path' (parameter is called path_to_archive)
• Task 5: detail but data is already downloaded, so change text to "loaded in the following cell"

03_COSDD

• put explanation for dimensions before or in the task instead of after
• still has two TODOs (figure and pretrained model)
• in tensorboard metrics: 20 min in text instead of 10 min
• if you can add tensorboard logs for the pretrained models that'd be great
• Bonus
  • import is wrong
  • also still TODO: add pretrained
  • device is not defined

04_DenoiSplit

• sys path extension isn't right
• missing dependency albumentations
• I assume this isn't done? Very light on details of what's happening
• exercise version has answers to questions

05 Noise2Noise

• text: "regression exercises" -> restoration exercises
• Task1: typo vizualize -> visualize