| # Site configuration for auto_detect_breast_mri. | |
| # | |
| # cp config.example.yaml config.yaml # config*.yaml is gitignored, this example is not | |
| # export AIMRI_CONFIG=/absolute/path/to/config.yaml | |
| # | |
| # Every value is optional: command line arguments always take precedence, so a fully specified | |
| # command line needs no config file at all. Keep the real file out of the repository -- it is the | |
| # one place where paths of your own machine or cluster are allowed to appear. | |
| # --- paths ------------------------------------------------------------------------------------- | |
| # Root folder of the NIfTI data, i.e. the folder holding one subfolder per examination. | |
| # See README.md ("Data contract") for the two supported folder layouts. | |
| data_root: /path/to/nifti_root | |
| # Metadata export (.csv or .xlsx) with one row per examination and the label columns configured | |
| # under `columns:` below. | |
| metadata_file: /path/to/metadata.csv | |
| # Folder holding the cross validation split files, i.e. the parent of fold0/, fold1/, ... | |
| # Expected file names are documented in README.md ("Split files"). | |
| split_root: /path/to/split_files | |
| # Where runs write checkpoints, ROC plots, heatmaps, prediction tables and pickled results. | |
| output_root: /path/to/outputs | |
| # Where already trained checkpoints are read from. Defaults to output_root when unset. | |
| model_root: /path/to/checkpoints | |
| # --- weights & biases -------------------------------------------------------------------------- | |
| # Project and (optional) team the runs are logged to. Set wandb_mode to 'offline' to keep runs | |
| # local, or 'disabled' to turn logging off entirely -- useful when running on data that must not | |
| # leave the machine, since run names and captions can contain case identifiers. | |
| wandb_project: my-breast-mri-project | |
| wandb_entity: my-team | |
| wandb_mode: online | |
| # --- CSV column names -------------------------------------------------------------------------- | |
| # Names of the columns in your metadata export and split files. Override what differs in your data. Values in the side | |
| # column are matched case insensitively. Unset keys fall back to the defaults in | |
| # auto_detect_breast_mri/config.py (DEFAULT_COLUMNS), which are the original UKA export's names. | |
| # | |
| # tools/make_synthetic_dataset.py reads this block to name the columns of the CSVs it writes and | |
| # copies it into the config it generates, so a renamed column only has to be changed here. | |
| columns: | |
| examination_id: exam_id # one MRI examination, in the split CSVs | |
| metadata_examination_id: exam_id # the same ID in the metadata export | |
| patient_id: pat_id # patient; splits are grouped by this so that no | |
| # patient appears in two folds | |
| side: side # breast side in the split CSVs | |
| metadata_side: side # breast side in the metadata export | |
| criterion: Malign # training label, one row per breast | |
| criterion_left: Malign_Left # per-side label in the wide metadata export | |
| criterion_right: Malign_Right | |
| side_left: left # the two values found in the side column | |
| side_right: right | |
| indication_left: Indication_Left # per-side indication code in the metadata export | |
| indication_right: Indication_Right | |
| birads_left: BIRADS_Left # per-side BI-RADS category | |
| birads_right: BIRADS_Right | |
| biopsy_left: "" # per-side prior biopsy status; leave empty if absent | |
| biopsy_right: "" # (the error analysis then skips its biopsy tables) | |