Environment Setup

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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_SOURCE=/PATH/TO/RAW/DATASETS
  • 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 preprocessed data. Preprocessing scripts must save processed data here. Data is stored as tensors: pretraining data as [C, H, W, D], segmentation data as [C+1, H, W, D] (label is always the last channel), and classification/regression data as a list [tensor, label]. The 2D equivalents omit the D dimension.
  • 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 where preprocessing scripts save formatted but unpreprocessed labels. Formatting (e.g. remapping label values) should be applied; preprocessing (e.g. resampling to a target spacing) should not. These unmodified labels are used when computing final test metrics.
  • ASPARAGUS_SOURCE points to the directory containing raw, unprocessed datasets. Preprocessing scripts use this variable to locate source data via get_source_path() from asparagus_preprocessing.paths, keeping scripts portable across users and environments.

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.
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