Module i2pp.core.export_data

Export data to a file using user function.

Functions

def export_data(transformed_data: Any,
elements: list[Element],
discretization: Discretization,
export_format: str,
property_output_file: pathlib.Path,
name_of_output_property: str,
vtk_output_file: pathlib.Path,
pixel_type: PixelValueType) ‑> None

Expand source code

def export_data(
    transformed_data: Any,
    elements: list[Element],
    discretization: Discretization,
    export_format: str,
    property_output_file: Path,
    name_of_output_property: str,
    vtk_output_file: Path,
    pixel_type: PixelValueType,
) -> None:
    """Exports already-transformed data.

    This function handles the export of transformed data to a specified
    format. It performs the following steps:
        - Writes the export string to a file using `Exporter.write_data()`.
        - Depending on the export format, it also exports the data to a VTK
          file. This is not possible if the user function returns a string.

    Arguments:
        transformed_data (Any): The result from the transform_data function.
        elements (List[Element]): List of elements with IDs and data.
        dis (Discretization): The discretization object containing nodes
            and elements.
        export_format (str): The format in which the data will be
            exported (e.g., "json", "txt").
        property_output_file (Path): Path to the output file where the
            exported data will be written.
        name_of_output_property (str): Name of the property to be exported.
        vtk_output_file (Path): Path to the output file for VTK export.
        pixel_type (PixelValueType): Type of pixel values.
    """
    logging.info("Exporting file.")

    # export data
    export_format_enum = ExportFormat(export_format)
    exporter: Exporter = export_format_enum.get_exporter()()
    exported_data = exporter.write_data(
        transformed_data, property_output_file, name_of_output_property
    )

    # if we have a json exporter, we can export to vtk
    if exporter.export_format == ExportFormat.JSON.value:
        logging.info(f"Exporting data to VTK file {vtk_output_file}.")
        export_vtk(
            vtk_output_file,
            elements,
            pixel_type,
            exported_data,
            discretization,
        )

Exports already-transformed data.

This function handles the export of transformed data to a specified format. It performs the following steps: - Writes the export string to a file using Exporter.write_data(). - Depending on the export format, it also exports the data to a VTK file. This is not possible if the user function returns a string.

Arguments

transformed_data (Any): The result from the transform_data function. elements (List[Element]): List of elements with IDs and data. dis (Discretization): The discretization object containing nodes and elements. export_format (str): The format in which the data will be exported (e.g., "json", "txt"). property_output_file (Path): Path to the output file where the exported data will be written. name_of_output_property (str): Name of the property to be exported. vtk_output_file (Path): Path to the output file for VTK export. pixel_type (PixelValueType): Type of pixel values.

def export_vtk(output_file: pathlib.Path,
elements: list[Element],
pixel_type: PixelValueType,
exported_data: dict,
dis: Discretization)

Expand source code

def export_vtk(
    output_file: Path,
    elements: list[Element],
    pixel_type: PixelValueType,
    exported_data: dict,
    dis: Discretization,
):
    """Exports the interpolated physical property data to a VTK file for the
    verification of the i2pp output.

    Arguments:
        output_file (Path): The path to the output vtk file.
        elements (list[Element]): List of elements with IDs and data.
        pixel_type (PixelValueType): Type of pixel values used in the
            discretization.
        exported_data (dict): Data to be exported, typically containing
            interpolated physical properties.
    """
    unstructured_grid, _ = initialize_unstructured_grid(
        elements, pixel_type, dis
    )
    for key, value in exported_data.items():
        names = exported_data[key].dtype.names
        if names is None:
            raise RuntimeError(
                "The exported data must be a structured numpy array "
                "with named fields."
            )
        assert np.array_equal(
            np.array([ele.id for ele in dis.elements]), value[names[0]] - 1
        ), "The keys of the exported data must match the element IDs."
        for name in names[1:]:  # Skip the 'index' field
            if np.issubdtype(value[name].dtype, np.number):
                # only add if the data is transferable to a VTK file
                unstructured_grid.cell_data[f"{key}_{name}"] = value[name]

    # Ensure the output file ends with the correct suffix
    if not output_file.suffix:
        logging.warning(
            "Output file has no suffix. Appending the export format " "suffix."
        )
        output_file = output_file.with_suffix(".vtu")

    unstructured_grid.save(output_file)

Exports the interpolated physical property data to a VTK file for the verification of the i2pp output.

Arguments

output_file (Path): The path to the output vtk file. elements (list[Element]): List of elements with IDs and data. pixel_type (PixelValueType): Type of pixel values used in the discretization. exported_data (dict): Data to be exported, typically containing interpolated physical properties.