Method __init__

dosma/cli.py:78–161

The class for command-line handling around :class:`ScanSequence`. The command line interface for :class:`ScanSequence` data is highly structured, particularly in data saving and loading to support easy and accurate command-line compatibility. This class overloads so

(
        self,
        scan_type: type,
        dicom_path,
        load_path,
        ignore_ext: bool = False,
        group_by=None,
        num_workers=0,
        **kwargs,
    )

class CommandLineScanContainer:
    def __init__(
        self,
        scan_type: type,
        dicom_path,
        load_path,
        ignore_ext: bool = False,
        group_by=None,
        num_workers=0,
        **kwargs,
    ):
        """The class for command-line handling around :class:`ScanSequence`.

        The command line interface for :class:`ScanSequence` data is highly structured,
        particularly in data saving and loading to support easy and accurate command-line
        compatibility.

        This class overloads some standard functionality in :class:`ScanSequence`
        (:func:`save`, :func:`load`). When methods are not implemented, this class provides
        access directly to attributes/methods of the underlying scan instantiation.
        For example, if ``scan_type=QDess``, the following will call
        :func:`QDess.generate_t2_map`:

        >>> cli_scan = CommandLineScanContainer(QDess, dicom_path="/path/to/qdess/scan")
        >>> cli_scan.generate_t2_map(...)  # this calls cli_scan.scan.generate_t2_map

        Data is loaded either from the ``dicom_path`` or the ``load_path``. If both are specified,
        the data is loaded from the ``dicom_path``.

        Args:
            scan_type (type): A scan type. Should be subclass of `ScanSequence`.
            dicom_path (str): The dicom path. This value can be ``None``, but must
                be explicitly set.
            load_path (str): The load path. This value can be ``None``, but must be
                explicitly set.
            ignore_ext (bool, optional): If ``True``, ignore extensions when loading
                dicom data. See :func:`DicomReader.load` for details.
            group_by (optional): The value(s) to group dicoms by. See :func:`DicomReader.load`
                for details.
            num_workers (int, optional): Number of works for loading scan.

        Attributes:
            scan_type (type): The scan type to instantiate.
            scan (ScanSequence): The instantiated scan.
            generic_args (Dict[str, Any]): Generic duck typed parameter names and values.
                If parameters with this name are part of the method signature, they will
                automatically be set to the values in this dictionary. Keys include:
                    * "num_workers": Number of cpu workers to use.
                    * "max_workers": Alias for "num_workers" in some functions
                    * "verbose": Verbosity
                    * "show_pbar": Show progress bar.

        Raises:
            NotADirectoryError: If ``dicom_path`` is not a path to a directory.
        """
        self.scan_type = scan_type

        if (dicom_path is not None) and (not os.path.isdir(dicom_path)):
            if load_path is not None: