Function fill_quant_fluor_data_dict

pyxrf/core/quant_analysis.py:498–577

r""" Computes average normalized fluorescence values for element lines that are part of the reference sample and listed in ``quant_fluor_data_dict["element_lines"]`` and present in the ``xrf_map_dict`` and writes the result to ``quant_fluor_data_dict["element_lines"][ ][

(quant_fluor_data_dict, *, xrf_map_dict, scaler_name)

def fill_quant_fluor_data_dict(quant_fluor_data_dict, *, xrf_map_dict, scaler_name):
    r"""
    Computes average normalized fluorescence values for element lines that are part of
    the reference sample and listed in ``quant_fluor_data_dict["element_lines"]`` and
    present in the ``xrf_map_dict`` and writes the result to
    ``quant_fluor_data_dict["element_lines"][<element_line>]["fluorescence"]``.
    Fluorescence is set to None for the element lines that are not present in ``xrf_map_dict``.
    Element lines that are present in ``xrf_map_dict``, but not part of the reference
    standard, are ignored. If `scaler_name` is one of the keys of ``xrf_map_dict``, then
    fluorescence map is normalized by the scaler before average value is computed. If
    ``scaler_name`` is not one of the keys of ``xrf_map_dict`` or set to None, then
    the average fluorescence is computed without normalization.

    Pixels along the edges of the map are very likely to contain outliers, so the edges
    are not used in computation whenever sufficient data is available (if map contains
    more than 2 pixels along a dimension, the first and the last pixels are not used
    for averaging)

    Parameters
    ----------

    quant_fluor_data_dict: dict
        Dictionary with XRF reference sample data. This dictionary is modified by the function.
        The dictionary must satisfy the '_xrf_quant_fluor_schema' schema.

    xrf_map_dict: dict(array)
        The dictionary of 2D ndarrays, which contain XRF maps for element lines and scalers.
        Dictionary keys are the names of the emission lines (e.g. Fe_K, S_K, Au_M etc.)

    scaler_name: str
        Scaler name. In order for the scaler to be applied, the name must match one of the
        keys of `xrf_map_dict&#x27;. If the scaler name is not one of the list keys or set to None,
        then fluorescence is not normalized

    Returns

        No value is returned. The computed fluorescence for the element lines is saved to
        ``quant_fluor_data_dict["element_lines"][<element_line>]["fluorescence"]``

    """

    if not scaler_name:
        logger.warning("No scaler is selected for computing quantitative coefficients. Data is not normalized.")
    elif scaler_name not in xrf_map_dict:
        logger.warning("Scaler '{scaler_name}' is not in XRF map dictionary. Normalization can not be performed.")
        scaler_name = None

    # Clear ALL fluorescence values. Don't touch any other data
    for eline, info in quant_fluor_data_dict["element_lines"].items():
        info["fluorescence"] = None

    # Save the scaler name
    quant_fluor_data_dict["scaler_name"] = scaler_name

    # Compute fluorescence of the emission lines
    eline_list = tuple(quant_fluor_data_dict["element_lines"].keys())
    for eline, map in xrf_map_dict.items():
        if eline in eline_list: