Inconsistent output of logger message in NNunet train stage

[iffthomas]

Describe the bug logger output during training can deviate when using custom made splits.

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To Reproduce Steps to reproduce the behavior:

• have already a splits_final.json file in the correct format
• run training it with nnUNetTrainerv2 train
• if it doesn't give out the correct logger input rerun Expected behavior 2023-11-16 09:58:49.044835: unpacking dataset... 2023-11-16 09:59:21.353696: unpacking done... 2023-11-16 09:59:21.355801: do_dummy_2d_data_aug: False 2023-11-16 09:59:21.365563: Creating new 5-fold cross-validation split... 2023-11-16 09:59:21.369237: Desired fold for training: 0 2023-11-16 09:59:21.369696: This split has 156 training and 40 validation cases. 2023-11-16 09:59:21.460418: Unable to plot network architecture: 2023-11-16 09:59:21.460952: No module named 'hiddenlayer' 2023-11-16 09:59:21.480445:
  2023-11-16 09:59:21.480848: Epoch 0 2023-11-16 09:59:21.481394: Current learning rate: 0.01

this behavior happened after just rerunning it after I canceled the job 2023-11-16 10:08:15.432898: unpacking dataset... 2023-11-16 10:08:16.039125: unpacking done... 2023-11-16 10:08:16.041371: do_dummy_2d_data_aug: False 2023-11-16 10:08:16.043030: Using splits from existing split file: ./data/nnUNet_preprocessed/Dataset006_SPIDER/splits_final.json 2023-11-16 10:08:16.044067: The split file contains 5 splits. 2023-11-16 10:08:16.044394: Desired fold for training: 0 2023-11-16 10:08:16.044732: This split has 156 training and 40 validation cases. 2023-11-16 10:08:16.106095: Unable to plot network architecture: 2023-11-16 10:08:16.106503: No module named 'hiddenlayer' 2023-11-16 10:08:16.120372:
2023-11-16 10:08:16.120819: Epoch 0 2023-11-16 10:08:16.121274: Current learning rate: 0.01

Important note : the splits that get created are still the same i guess, I have slightly imbalanced splits and the number is still the same which would be an indication that just the logger message is faulty.

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Environment (please complete the following information):

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• CUDA/cuDNN version
• GPU models and configuration

Additional context Add any other context about the problem here.

[KumoLiu]

Hi @iffthomas, I didn't get the point what inconsistent logger info do you refer to?

[iffthomas]

Hi @KumoLiu The logger message highlighted in bold is different while not changeing the splits.json file or changing any command for the same dataset.

If I run only train for the first time after I've ran plan_and_preprocess with the splits.json file i get this message in the logger: 2023-11-16 09:59:21.365563: Creating new 5-fold cross-validation split...

While this is wrong I cancel the job and resubmit it so: i get this message in the logger: 2023-11-16 10:08:16.043030: Using splits from existing split file: ./data/nnUNet_preprocessed/Dataset006_SPIDER/splits_final.json

[KumoLiu]

Hi @iffthomas, I think that's expected unless you remove the "splits_final.json" otherwise it may use the splits from the existing split file. Find more information here. https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/manual_data_splits.md

[iffthomas]

Hi KumoLiu,

I see where the problem is: the splits from ma nnUNetraw folder and nnUNetpreprocessed aren't the same. the reason for this is that my splits don't get transfered when doing plan_and_preprocess from the raw folder to the preprocessed folder

I will have a look wheter it's possible for nnUnet to transfer this file during the plan_and_preprocess phase

[KumoLiu]

Convert to discussion for now, feel free to create another one if meet any issues. Thanks!