DicomRTTool 3.0.3

Services for reading DICOM files, RT structures, and dose files, as well as tools for converting numpy prediction masks back to an RT structure.

DicomRTTool

Published! See the Technical Note and please cite it if you find this work useful.
DOI: https://doi.org/10.1016/j.prro.2021.02.003

Convert DICOM images and RT structures into NIfTI files, NumPy arrays, and SimpleITK image handles — and convert prediction masks back into RT structures.

Installation

pip install DicomRTTool

For the interactive image viewer (requires matplotlib):

pip install "DicomRTTool[viewer]"

Supported Python versions: 3.8, 3.10, 3.12+

Quick Start

from DicomRTTool.ReaderWriter import DicomReaderWriter, ROIAssociationClass

dicom_path = "/path/to/dicom"
reader = DicomReaderWriter(description="Examples", arg_max=True)
reader.walk_through_folders(dicom_path)

# Inspect available ROIs
all_rois = reader.return_rois(print_rois=True)

# Define target ROIs with optional name aliases
contour_names = ["tumor"]
associations = [ROIAssociationClass("tumor", ["tumor_mr", "tumor_ct"])]
reader.set_contour_names_and_associations(
    contour_names=contour_names, associations=associations
)

# Load images and masks
reader.get_images_and_mask()

image_numpy = reader.ArrayDicom          # NumPy image array
mask_numpy = reader.mask                  # NumPy mask array
image_handle = reader.dicom_handle        # SimpleITK Image
mask_handle = reader.annotation_handle    # SimpleITK Image

Reading Extra DICOM Tags

from pydicom.tag import Tag

plan_keys = {"MyNamedRTPlan": Tag((0x300a, 0x002))}
image_keys = {"MyPatientName": "0010|0010"}

reader = DicomReaderWriter(
    description="Examples",
    arg_max=True,
    plan_pydicom_string_keys=plan_keys,
    image_sitk_string_keys=image_keys,
)

What's New in v3.0

• Modern Python packaging — pyproject.toml replaces setup.py
• Type annotations throughout — better IDE support and documentation
• logging module replaces print() — configurable verbosity
• concurrent.futures replaces raw threading.Queue — cleaner parallelism
• dataclasses for all internal data models
• No bare except: — proper exception handling everywhere
• Deprecated pandas.DataFrame.append replaced with pd.concat
• Full backward compatibility — existing import paths still work

License

GPL-3.0-or-later

Citation

If you find this code useful, please reference the publication and the GitHub page.