Comp2Comp-main/comp2comp/utils/orientation.py

import nibabel as nib

from comp2comp.inference_class_base import InferenceClass


class ToCanonical(InferenceClass):
    """Convert spine segmentation to canonical orientation."""

    def __init__(self):
        super().__init__()

    def __call__(self, inference_pipeline):
        """
        First dim goes from L to R.
        Second dim goes from P to A.
        Third dim goes from I to S.
        """
        canonical_segmentation = nib.as_closest_canonical(
            inference_pipeline.segmentation
        )
        canonical_medical_volume = nib.as_closest_canonical(
            inference_pipeline.medical_volume
        )

        inference_pipeline.segmentation = canonical_segmentation
        inference_pipeline.medical_volume = canonical_medical_volume
        inference_pipeline.pixel_spacing_list = (
            canonical_medical_volume.header.get_zooms()
        )
        return {}