MIMIC-IV MEDS Extraction ETL
This pipeline extracts the MIMIC-IV dataset (from physionet) into the MEDS format.
Usage:
pip install MIMIC_IV_MEDS
export DATASET_DOWNLOAD_USERNAME=$PHYSIONET_USERNAME
export DATASET_DOWNLOAD_PASSWORD=$PHYSIONET_PASSWORD
MEDS_extract-MIMIC_IV root_output_dir=$ROOT_OUTPUT_DIR
When you run this, the program will:
- Download the needed raw MIMIC files for the currently supported version into
$ROOT_OUTPUT_DIR/raw_input. - Perform initial, pre-MEDS processing on the raw MIMIC files, saving the results in
$ROOT_OUTPUT_DIR/pre_MEDS. - Construct the final MEDS cohort, and save it to
$ROOT_OUTPUT_DIR/MEDS_cohort.
You can also specify the target directories more directly, with
export DATASET_DOWNLOAD_USERNAME=$PHYSIONET_USERNAME
export DATASET_DOWNLOAD_PASSWORD=$PHYSIONET_PASSWORD
MEDS_extract-MIMIC_IV raw_input_dir=$RAW_INPUT_DIR pre_MEDS_dir=$PRE_MEDS_DIR MEDS_cohort_dir=$MEDS_COHORT_DIR
Examples and More Info:
You can run MEDS_extract-MIMIC_IV --help for more information on the arguments and options. You can also run
MEDS_extract-MIMIC_IV root_output_dir=$ROOT_OUTPUT_DIR do_demo=True
to run the entire pipeline over the publicly available, fully open MIMIC-IV demo dataset.
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