ngff_zarr.nibabel_image_to_ngff_image

Module Contents

Functions

decompose_affine_with_shear	Decompose affine transformation matrix into translation, scale, shear, and orientation.
extract_spatial_metadata	Extract translation, scale, and orientation from NIfTI spatial metadata.
nibabel_image_to_ngff_image	Convert a nibabel image to an NgffImage, preserving spatial metadata.
extract_omero_metadata_from_nibabel	Extract OMERO windowing metadata from a nibabel image’s cal_min/cal_max headers.

API

ngff_zarr.nibabel_image_to_ngff_image.decompose_affine_with_shear(affine)

Decompose affine transformation matrix into translation, scale, shear, and orientation.

ngff_zarr.nibabel_image_to_ngff_image.extract_spatial_metadata(

img,

) → Tuple[Dict[str, float], Dict[str, float], numpy.ndarray]

Extract translation, scale, and orientation from NIfTI spatial metadata.

ngff_zarr.nibabel_image_to_ngff_image.nibabel_image_to_ngff_image(

nibabel_image,

add_anatomical_orientation: bool = True,

) → ngff_zarr.ngff_image.NgffImage

Convert a nibabel image to an NgffImage, preserving spatial metadata.

This function optimizes memory usage by checking the NIfTI scaling parameters:

• If scl_slope=1.0 and scl_inter=0.0 (identity scaling), uses the raw dataobj to preserve the original data type and minimize memory usage

• If scaling is required, uses get_fdata(dtype=np.float32) to balance memory usage and precision

Args: nibabel_image: A nibabel image object add_anatomical_orientation: Whether to add anatomical orientation metadata. Only added if orientation matrix is identity (no rotation/shear).

Returns: NgffImage with spatial metadata from the NIfTI file

Note: The data is returned as a numpy array (not Dask) to maintain compatibility with the original implementation requirements.

ngff_zarr.nibabel_image_to_ngff_image.extract_omero_metadata_from_nibabel(nibabel_image)

Extract OMERO windowing metadata from a nibabel image’s cal_min/cal_max headers.

Args: nibabel_image: A nibabel image object

Returns: Omero metadata if cal_min and cal_max are available and valid, None otherwise

Note: This function creates OMERO windowing metadata from NIfTI cal_min and cal_max header values when both are not 0.0 and neither is NaN. The windowing applies to all channels in the image.