HGG

HGGPatientData

Bases: BasePatientData

Represents high-grade glioma (HGG) patient data.

This model contains the patient-specific data, including imaging information, treatment history, and metadata. It provides methods to load patient data from files and compute derived properties, such as brain-masked images and treatment days.

Attributes:

Name	Type	Description
model_config	SettingsConfigDict	Configuration for environment files.
image_dir	Optional[DirectoryPath]	Path to the directory containing patient images. Hidden in representations.
patient	str	Patient identifier.
brainmask	Path	Path to the brain mask image file.
crop_settings	Optional[CropSettings]	Settings object describing if and how to crop images. Defaults to None (no cropping).
crop_bounding_box	Optional[BoundingBoxIndices]	Bounding box for cropping images, if available.
T1_pre	Optional[Path]	Path to the pre-contrast T1-weighted image file.
T1_post	Optional[Path]	Path to the post-contrast T1-weighted image file.
T2_flair	Optional[Path]	Path to the T2 FLAIR image file.
visits	List[HGGVisitData]	List of patient visits, including imaging and ROI data.
radiotherapy	List[RadiotherapyTreatment]	List of radiotherapy treatments.
chemotherapy	List[ChemotherapyTreatment]	List of chemotherapy treatments.

T1_post_image property

Loads the post-contrast T1-weighted image and optionally crops it.

Returns:

Type	Description
Optional[NibabelNifti]	Optional[NibabelNifti]: The loaded T1-post image, or None if unavailable.

T1_pre_image property

Loads the pre-contrast T1-weighted image and optionally crops it.

Returns:

Type	Description
Optional[NibabelNifti]	Optional[NibabelNifti]: The loaded T1-pre image, or None if unavailable.

T2_flair_image property

Loads the T2 FLAIR image and optionally crops it.

Returns:

Type	Description
Optional[NibabelNifti]	Optional[NibabelNifti]: The loaded T2 FLAIR image, or None if unavailable.

brainmask_image property

Loads the brain mask image and optionally crops it to the brain bounding box.

Returns:

Name	Type	Description
NibabelNifti	NibabelNifti	The loaded brain mask image.

HGGVisitData

Bases: BaseVisitData

Represents data for a single patient visit in the context of high-grade glioma (HGG).

Attributes:

Name	Type	Description
adc	Path	Path to the Apparent Diffusion Coefficient (ADC) image file.
roi_enhance	Path	Path to the file containing the region of interest (ROI) for enhancing tumor regions.
roi_nonenhance	Path	Path to the file containing the ROI for non-enhancing tumor regions.

adc_image property

Loads the ADC image as a NibabelNifti object, optionally cropped to the crop bounding box.

Returns:

Name	Type	Description
NibabelNifti	NibabelNifti	The loaded and optionally cropped ADC image.

roi_enhance_image property

Loads the ROI enhancing image as a NibabelNifti object, optionally cropped to the brain region.

Returns:

Name	Type	Description
NibabelNifti	NibabelNifti	The loaded and optionally cropped ROI enhancing image.

roi_nonenhance_image property

Loads the ROI non-enhancing image as a NibabelNifti object, optionally cropped to the brain region.

Returns:

Name	Type	Description
NibabelNifti	NibabelNifti	The loaded and optionally cropped ROI non-enhancing image.