PetPvc#

class petpal.preproc.partial_volume_corrections.PetPvc#

Handles operations for PET partial volume correction using a Docker container.

This class manages the setup and execution of processes using the PETPVC package, accessible via PETPVC on GitHub and a Docker image hosted on DockerHub. It manages image retrieval, input/output setup, and command execution.

Variables:

client (docker.DockerClient) – A Docker client connected to the local system.
image_name (str) – The Docker image name to use for PETPVC processes.

Examples

Initialize the PETPVC handler and run a correction process:

from petpvc_module import PetPvc
petpvc_handler = PetPvc()
petpvc_handler.run_petpvc(
    pet_4d_filepath="/path/to/input/pet_image.nii",
    output_filepath="/path/to/output/corrected_pet_image.nii",
    pvc_method="RBV",
    psf_dimensions=(6.0, 6.0, 6.0),
    mask_filepath="/path/to/input/brain_mask.nii",
    verbose=True)

Initializes the PetPvc instance and ensures the required Docker image is available.

run_petpvc(pet_4d_filepath: str, output_filepath: str, pvc_method: str, psf_dimensions: Tuple[float, float, float] | float, mask_filepath: str = None, verbose: bool = False, debug: bool = False) → None#

Executes the PETPVC correction process within a Docker container.

Parameters:

pet_4d_filepath (str) – The file path to the input 4D PET image.
output_filepath (str) – The file path where the output image should be saved.
pvc_method (str) – The partial volume correction method to apply.
psf_dimensions (Union[Tuple[float, float, float], float]) – The full-width half-max (FWHM) in mm along x, y, z axes.
mask_filepath (str, optional) – The file path to the mask image. Defaults to None.
verbose (bool, optional) – If True, prints the output from the Docker container. Defaults to False.
debug (bool, optional) – If True, adds the –debug flag to the command for detailed logs. Defaults to False.

Prints:: Outputs from the Docker container if verbose is True.

Raises:

docker.errors.ImageNotFound – If the Docker image is not available.
docker.errors.APIError – If the Docker client encounters an API error.

_pull_image_if_not_exists() → None#: Checks if the Docker image is locally available and pulls it if not.

PetPvc#

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