Class ITKReader

monai/data/image_reader.py:169–389

Load medical images based on ITK library. All the supported image formats can be found at: https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/IO The loaded data array will be in C order, for example, a 3D image NumPy array index order will be `CDWH`. Args:

@require_pkg(pkg_name="itk")
class ITKReader(ImageReader):
    """
    Load medical images based on ITK library.
    All the supported image formats can be found at:
    https://github.com/InsightSoftwareConsortium/ITK/tree/master/Modules/IO
    The loaded data array will be in C order, for example, a 3D image NumPy
    array index order will be `CDWH`.

    Args:
        channel_dim: the channel dimension of the input image, default is None.
            This is used to set original_channel_dim in the metadata, EnsureChannelFirstD reads this field.
            If None, `original_channel_dim` will be either `no_channel` or `-1`.

                - Nifti file is usually "channel last", so there is no need to specify this argument.
                - PNG file usually has `GetNumberOfComponentsPerPixel()==3`, so there is no need to specify this argument.

        series_name: the name of the DICOM series if there are multiple ones.
            used when loading DICOM series.
        reverse_indexing: whether to use a reversed spatial indexing convention for the returned data array.
            If ``False``, the spatial indexing convention is reversed to be compatible with ITK;
            otherwise, the spatial indexing follows the numpy convention. Default is ``False``.
            This option does not affect the metadata.
        series_meta: whether to load the metadata of the DICOM series (using the metadata from the first slice).
            This flag is checked only when loading DICOM series. Default is ``False``.
        affine_lps_to_ras: whether to convert the affine matrix from "LPS" to "RAS". Defaults to ``True``.
            Set to ``True`` to be consistent with ``NibabelReader``, otherwise the affine matrix remains in the ITK convention.
        kwargs: additional args for `itk.imread` API. more details about available args:
            https://github.com/InsightSoftwareConsortium/ITK/blob/master/Wrapping/Generators/Python/itk/support/extras.py

    """

    def __init__(
        self,
        channel_dim: str | int | None = None,
        series_name: str = "",
        reverse_indexing: bool = False,
        series_meta: bool = False,
        affine_lps_to_ras: bool = True,
        **kwargs,
    ):
        super().__init__()
        self.kwargs = kwargs
        self.channel_dim = float("nan") if channel_dim == "no_channel" else channel_dim
        self.series_name = series_name
        self.reverse_indexing = reverse_indexing
        self.series_meta = series_meta
        self.affine_lps_to_ras = affine_lps_to_ras

    def verify_suffix(self, filename: Sequence[PathLike] | PathLike) -> bool:
        """
        Verify whether the specified file or files format is supported by ITK reader.

        Args:
            filename: file name or a list of file names to read.
                if a list of files, verify all the suffixes.

        """
        return has_itk