ImageIO

class petpal.utils.image_io.ImageIO(verbose: bool = True)

ImageIO to handle reading and writing imaging data and metadata.

Provides several tools designed for reading and writing data within the Python environment.

Key methods include:

• save_nii(): Saves a loaded NIfTI file to a file path.

• extract_image_from_nii_as_numpy(): Extracts imaging data from a NIfTI file as a numpy array.

• extract_header_from_nii(): Extracts header information from a NIfTI file as a dictionary.

• extract_np_to_nibabel(): Wraps imaging information in numpy into an Nibabel image.

Variables:

verbose (bool) – Set to True to output processing information.

Initializes ImageIO and sets verbose.

Parameters:

verbose (bool) – Set to True to print debugging info to shell. Defaults to True.

save_nii(image: nibabel.nifti1.Nifti1Image, out_file: str)

Wrapper to save nifti to file.

Parameters:

• image (nibabel.nifti1.Nifti1Image) – Nibabel-type image to write to file.

• out_file (str) – File path to which image will be written.

extract_image_from_nii_as_numpy(image: nibabel.nifti1.Nifti1Image) → numpy.ndarray

Convenient wrapper to extract data from a .nii or .nii.gz file as a numpy array.

Parameters:

image (nibabel.nifti1.Nifti1Image) – Nibabel-type image to write to file.

Returns:

The data contained in the .nii or .nii.gz file as a numpy array.

extract_header_from_nii(image: nibabel.nifti1.Nifti1Image) → nibabel.filebasedimages.FileBasedHeader

Convenient wrapper to extract header information from a .nii or .nii.gz file as a nibabel file-based header.

Parameters:

image (nibabel.nifti1.Nifti1Image) – Nibabel-type image to write to file.

Returns:

image_header (FileBasedHeader) – The nifti header.

extract_np_to_nibabel(image_array: numpy.ndarray, header: nibabel.filebasedimages.FileBasedHeader, affine: numpy.ndarray) → nibabel.nifti1.Nifti1Image

Wrapper to convert an image array into nibabel object.

Parameters:

• image_array (np.ndarray) – Array containing image data.

• header (FileBasedHeader) – Header information to include.

• affine (np.ndarray) – Affine information we need to keep when rewriting image.

Returns:

image_nibabel (nibabel.nifti1.Nifti1Image) – Image stored in nifti-like nibabel format.

static affine_parse(image_affine: numpy.ndarray) → tuple

Parse the components of an image affine to return origin, spacing, direction.

Parameters:

image_affine (np.ndarray) – A 4x4 affine matrix defining spacing, origin, and direction of an image.

extract_np_to_ants(image_array: numpy.ndarray, affine: numpy.ndarray) → ants.ANTsImage

Wrapper to convert an image array into ants object. Note header info is lost as ANTs does not carry this metadata.

Parameters:

• image_array (np.ndarray) – Array containing image data.

• affine (np.ndarray) – Affine information we need to keep when rewriting image.

Returns:

image_ants (ants.ANTsImage) – Image stored in nifti-like nibabel format.