Incorrect NIfTI orientations

[fyrdahl]

The orientations in the NIfTI output currently need to be correctly implemented.

I have attempted to implement this (https://nipy.org/nibabel/dicom/dicom_orientation.html#dicom-affine-formula) in the affine3d function, but the current implementation is not correct.

def affine3d(ds_list):
    """See: https://nipy.org/nibabel/dicom/dicom_orientation.html#dicom-affine-formula"""

    N = len(ds_list)
    if N < 2:
        raise ValueError(
            "ds_list must contain at least two datasets to compute affine matrix"
        )

    # Extract image positions
    positions = np.array([ds.ImagePositionPatient for ds in ds_list])
    T1, T2, T3 = positions[:, 0], positions[:, 1], positions[:, 2]

    # Extract orientation
    orientation = np.array(ds_list[0].ImageOrientationPatient)
    row_x, row_y, row_z = orientation[:3]
    col_x, col_y, col_z = orientation[3:]

    # Calculate slice direction
    slice_x, slice_y, slice_z = np.cross([row_x, row_y, row_z], [col_x, col_y, col_z])

    # Extract pixel spacing
    dr, dc = ds_list[0].PixelSpacing

    # Try to get slice thickness
    try:
        dslice = float(ds_list[0].SliceThickness)
    except AttributeError:
        try:
            dslice = float(ds_list[0][0x0018, 0x0050].value)
        except KeyError:
            dslice = np.linalg.norm(positions[-1] - positions[0]) / (N - 1)

    # Calculate affine matrix
    affine = np.array(
        [
            [row_x * dr, col_x * dc, slice_x * dslice, T1[0]],
            [row_y * dr, col_y * dc, slice_y * dslice, T2[0]],
            [row_z * dr, col_z * dc, slice_z * dslice, T3[0]],
            [0, 0, 0, 1],
        ]
    )

    return affine