TidalPaladin/dicom-structs

DICOM Structs

Library and CLI interface for manipulating DICOM files, primarly focusing on DICOM to Parquet conversion and the preparation of DICOM files for ingestion into a data warehouse. Note, Data Wranger is a great tool for inspecting Parquet files.

Usage

Convert files Parquet

Use dicom-to-parquet to convert DICOM files to parquet. It accepts a directory of DICOM files to convert and an output directory to write the parquet files to. One Parquet file will be created for each DICOM file.

Convert DICOM files to parquet

Usage: dicom-to-parquet [OPTIONS] <SOURCE_DIR> <OUTPUT_DIR>

Arguments:
  <SOURCE_DIR>  Directory of DICOM files to process
  <OUTPUT_DIR>  Directory to write outputs to

Options:
      --header-only  Don't include pixel data in the output
      --hash         Include a hash of the pixel data in the output. Uses xxh3-64 with seed=0.
  -t, --tag <TAGS>   Override a DICOM tag with a constant value
  -s, --snake-case   Convert DICOM tag names to snake case
  -h, --help         Print help
  -V, --version      Print version

Collect and Merge Parquet files

Use collect-parquet to collect individual DICOM parquet files into a single parquet file. It accepts a directory of parquet files to aggregate and an output path to write the aggregated parquet file to.

Aggregate Parquet files into a single file

Usage: collect-parquet <SOURCE_DIR> <OUTPUT_PATH>

Arguments:
  <SOURCE_DIR>   Directory of Parquet files to process
  <OUTPUT_PATH>  Path to write output to

Options:
  -h, --help     Print help
  -V, --version  Print version