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environment_variables.md

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Environment Variables

All environment variables should be put in a .env file in the project root which will be loaded automatically. Alternatively they can be set manually using export VAR=VALUE at the start of each session.

Required Environment Variables:

ASPARAGUS_CONFIGS=/PATH/TO/CONFIG/DIR
ASPARAGUS_DATA=/PATH/TO/ASPARAGUS/DATA
ASPARAGUS_MODELS=/PATH/TO/ASPARAGUS/MODELS
ASPARAGUS_RESULTS=/PATH/TO/ASPARAGUS/RESULTS
ASPARAGUS_RAW_LABELS=/PATH/TO/ASPARAGUS/RAW_LABELS
  • ASPARAGUS_CONFIGS points to the directory containing the default configs found in asparagus/configs. This variable is used in the training and inference scripts.
  • ASPARAGUS_DATA points to the directory containing the task converted data and is used to locate data and metadata for the Task. Task Conversion scripts must save processed data here.
  • ASPARAGUS_MODELS points to the directory containing model checkpoints, test outputs (results only), logs and metadata.
  • ASPARAGUS_RESULTS points to the directory containing predict outputs (output files and results).
  • ASPARAGUS_RAW_LABELS points to the directory containing raw labels. Preprocessing scripts must save FORMATTED but NOT PROCESSED labels here. This is used to get results on native labels. I.e. formatting such as changing all LabelX instances to become LabelY SHOULD be done on the RAW labels but preprocessing such as resampling to a specific resolution/spacing SHOULD NOT be done on the RAW labels. For additional explanation see: Asparagus Preprocessing.

Optional Environment Variables

(supports multiple colon-separated (":") paths):

ASPARAGUS_PRETRAIN_CONFIGS=/PATH1/TO/ADDITIONAL/PRETRAIN/CONFIG/DIR:PATH2/TO/ADDITIONAL/PRETRAIN/CONFIG/DIR:PATH3...
ASPARAGUS_TRAIN_CONFIGS=/PATH1/TO/ADDITIONAL/TRAIN/CONFIG/DIR:PATH2/TO/ADDITIONAL/TRAIN/CONFIG/DIR:PATH3...
ASPARAGUS_FINETUNE_CONFIGS=/PATH1/TO/ADDITIONAL/FINETUNE/CONFIG/DIR:PATH2/TO/ADDITIONAL/FINETUNECONFIG/DIR:PATH3...
  • ASPARAGUS_PRETRAIN_CONFIGS points to all directories containing pretraining configs. When asp_pretrain --config-name MyFancyPretrainConfigis called all the given ASPARAGUS_PRETRAIN_CONFIGS directories are scanned for MyFancyPretrainConfig.yaml.
  • ASPARAGUS_TRAIN_CONFIGS points to all directories containing training from scratch configs. When asp_train_[cls,reg,seg] --config-name MyLovelyTrainConfigis called all the given ASPARAGUS_PRETRAIN_CONFIGS directories are scanned for MyLovelyTrainingConfig.yaml.
  • ASPARAGUS_FINETUNE_CONFIGS points to all directories containing finetuning configs. When asp_finetune_[cls,reg,seg] --config-name MyAwesomeFinetuneConfigis called all the given ASPARAGUS_PRETRAIN_CONFIGS directories are scanned for MyAwesomeFinetuneConfig.yaml.