TopoStats Modules

For decoding and loading .topostats (HDF5 format) AFM file format into Python Nympy arrays.

load_topostats(file_path)

Extract image and pixel to nm scaling from the .topostats (HDF5 format) file.

Parameters:

Name Type Description Default
file_path Path or str

Path to the .topostats file.

 required

Returns:

Type Description
tuple(ndarray, float)

A tuple containing the image, its pixel to nm scaling factor and the data dictionary containing all the extra image data and metadata in dictionary format.

Raises:

Type Description
OSError

If the file is not found.

Examples:

>>> image, pixel_to_nm_scaling = load_topostats("path/to/topostats_file.topostats")
Source code in AFMReader/topostats.py 
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def load_topostats(file_path: Path | str) -> tuple:
    """
    Extract image and pixel to nm scaling from the .topostats (HDF5 format) file.

    Parameters
    ----------
    file_path : Path or str
        Path to the .topostats file.

    Returns
    -------
    tuple(np.ndarray, float)
        A tuple containing the image, its pixel to nm scaling factor and the data dictionary
        containing all the extra image data and metadata in dictionary format.

    Raises
    ------
    OSError
        If the file is not found.

    Examples
    --------
    >>> image, pixel_to_nm_scaling = load_topostats("path/to/topostats_file.topostats")
    """
    logger.info(f"Loading image from : {file_path}")
    file_path = Path(file_path)
    filename = file_path.stem
    try:
        with h5py.File(file_path, "r") as f:
            data = unpack_hdf5(open_hdf5_file=f, group_path="/")

            file_version = data["topostats_file_version"]
            logger.info(f"[{filename}] TopoStats file version : {file_version}")
            image = data["image"]
            pixel_to_nm_scaling = data["pixel_to_nm_scaling"]

    except OSError as e:
        if "Unable to open file" in str(e):
            logger.error(f"[{filename}] File not found : {file_path}")
        raise e

    return (image, pixel_to_nm_scaling, data)