Source code for fileformats.medimage.diffusion

import typing

from fileformats.core import extra, validated_property
from fileformats.core.mixin import WithAdjacentFiles
from fileformats.core.typing import TypeAlias
from fileformats.generic import BinaryFile

from .nifti import Nifti1, NiftiGz, NiftiGzX, NiftiX

if typing.TYPE_CHECKING:
    import numpy.typing  # noqa: F401

EncodingArrayType: TypeAlias = (
    typing.Any
)  # In Py<3.9 this is problematic "numpy.typing.NDArray[numpy.floating[typing.Any]]"




class DwiEncoding:


    @extra
    def read_encodings(self) -> EncodingArrayType:
        "Both the gradient direction and weighting combined into a single Nx4 array"
        raise NotImplementedError


    @property
    def encodings_array(self) -> EncodingArrayType:
        return self.read_encodings()

    @property
    def directions(self) -> EncodingArrayType:
        "gradient direction and weighting combined into a single Nx4 array"
        return self.encodings_array[:, :3]

    @property
    def b_values(self) -> EncodingArrayType:
        "the b-value weighting"
        return self.encodings_array[:, 3]





class Bval(BinaryFile):

    ext = ".bval"

    @extra
    def read_array(self) -> EncodingArrayType:
        raise NotImplementedError





class Bvec(WithAdjacentFiles, DwiEncoding, BinaryFile):
    """FSL-style diffusion encoding, in two separate files"""

    ext = ".bvec"

    @validated_property
    def b_values_file(self) -> Bval:
        return Bval(self.select_by_ext(Bval))

    @validated_property
    def num_encodings(self) -> int:
        num_bvals = len(self.b_values_file.read_contents().split())
        x_len, y_len, z_len = [
            len(ln.split()) for ln in self.read_contents().splitlines()
        ]
        if not (x_len == y_len == z_len):
            raise ValueError(
                "The number of entries in each bvec component must match"
                f"x_len={x_len}, y_len={y_len}, z_len={z_len}"
            )
        num_bvecs = x_len
        if num_bvals != num_bvecs:
            raise ValueError(
                f"The number of b-values ({num_bvals}) does not match the number of "
                f"directions {num_bvecs}"
            )
        return num_bvals



# NIfTI file format gzipped with BIDS side car
class WithBvec(WithAdjacentFiles):
    @validated_property
    def encoding(self) -> Bvec:
        return Bvec(self.select_by_ext(Bvec))  # type: ignore[attr-defined]




class NiftiBvec(WithBvec, Nifti1):
    iana_mime = "application/x-nifti2+bvec"





class NiftiGzBvec(WithBvec, NiftiGz):
    iana_mime = "application/x-nifti2+gzip.bvec"





class NiftiXBvec(WithBvec, NiftiX):
    iana_mime = "application/x-nifti2+json.bvec"





class NiftiGzXBvec(WithBvec, NiftiGzX):
    iana_mime = "application/x-nifti2+gzip.json.bvec"