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Import and export tasks

Import task

plantseg.tasks.io_tasks.import_image_task(input_path: Path, semantic_type: str, stack_layout: str, image_name: str | None = None, key: str | None = None, m_slicing: str | None = None) -> PlantSegImage

Task wrapper creating a PlantSegImage object from an image file.

Parameters:

  • input_path (Path) –

    path to the image file

  • semantic_type (str) –

    semantic type of the image (raw, segmentation, prediction)

  • stack_layout (str) –

    stack layout of the image (3D, 2D, 2D_time)

  • image_name (str, default: None ) –

    name of the image, if None the name will be the same as the file name

  • key (str | None, default: None ) –

    key for the image (used only for h5 and zarr formats)

  • m_slicing (str | None, default: None ) –

    m_slicing of the image (None, time, z, y, x)

Source code in plantseg/tasks/io_tasks.py 
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@task_tracker(
    is_root=True,
    list_inputs={
        "input_path": RunTimeInputSchema(
            description="Path to a file, or a directory containing files (all files will be imported) or list of paths.",
            required=True,
            is_input_file=True,
        ),
    },
)
def import_image_task(
    input_path: Path,
    semantic_type: str,
    stack_layout: str,
    image_name: str | None = None,
    key: str | None = None,
    m_slicing: str | None = None,
) -> PlantSegImage:
    """
    Task wrapper creating a PlantSegImage object from an image file.

    Args:
        input_path (Path): path to the image file
        semantic_type (str): semantic type of the image (raw, segmentation, prediction)
        stack_layout (str): stack layout of the image (3D, 2D, 2D_time)
        image_name (str): name of the image, if None the name will be the same as the file name
        key (str | None): key for the image (used only for h5 and zarr formats)
        m_slicing (str | None): m_slicing of the image (None, time, z, y, x)
    """

    if image_name is None:
        image_name = input_path.stem

    return import_image(
        path=input_path,
        key=key,
        image_name=image_name,
        semantic_type=semantic_type,
        stack_layout=stack_layout,
        m_slicing=m_slicing,
    )

Export task

plantseg.tasks.io_tasks.export_image_task(image: PlantSegImage, export_directory: Path, name_pattern: str = '{file_name}_export', key: str | None = None, scale_to_origin: bool = True, export_format: str = 'tiff', data_type: str = 'uint16') -> None

Task wrapper for saving an PlantSegImage object to disk.

Parameters:

  • image (PlantSegImage) –

    input image to be saved to disk

  • export_directory (Path) –

    output directory path where the image will be saved

  • name_pattern (str, default: '{file_name}_export' ) –

    output file name pattern, can contain the {image_name} or {file_name} tokens to be replaced in the final file name.

  • key (str | None, default: None ) –

    key for the image (used only for h5 and zarr formats).

  • scale_to_origin (bool, default: True ) –

    scale the voxel size to the original one

  • export_format (str, default: 'tiff' ) –

    file format (tiff, h5, zarr)

  • data_type (str, default: 'uint16' ) –

    data type to save the image.

Source code in plantseg/tasks/io_tasks.py 
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@task_tracker(
    is_leaf=True,
    list_inputs={
        "export_directory": RunTimeInputSchema(
            description="Output directory path where the image will be saved",
            required=True,
        ),
        "name_pattern": RunTimeInputSchema(
            description=(
                "Output file name pattern. Use placeholder {image_name} for "
                "the napari layer name or {file_name} for the input file name"
            ),
            required=False,
        ),
    },
)
def export_image_task(
    image: PlantSegImage,
    export_directory: Path,
    name_pattern: str = "{file_name}_export",
    key: str | None = None,
    scale_to_origin: bool = True,
    export_format: str = "tiff",
    data_type: str = "uint16",
) -> None:
    """
    Task wrapper for saving an PlantSegImage object to disk.

    Args:
        image (PlantSegImage): input image to be saved to disk
        export_directory (Path): output directory path where the image will be saved
        name_pattern (str): output file name pattern, can contain the {image_name} or {file_name} tokens
            to be replaced in the final file name.
        key (str | None): key for the image (used only for h5 and zarr formats).
        scale_to_origin (bool): scale the voxel size to the original one
        export_format (str): file format (tiff, h5, zarr)
        data_type (str): data type to save the image.
    """
    save_image(
        image=image,
        export_directory=export_directory,
        name_pattern=name_pattern,
        key=key,
        scale_to_origin=scale_to_origin,
        export_format=export_format,
        data_type=data_type,
    )
    return None