comparison common.py @ 3:6bb927e155fc draft

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8

2:85284c3e1354

from larch.symboltable import Group
from larch.xafs import autobk, pre_edge, xftf


def get_group(athena_group: AthenaGroup, key: str = None) -> Group:
    group_keys = list(athena_group._athena_groups.keys())
    if key is None:
        key = group_keys[0]
    else:
        key = key.replace("-", "_")

    try:
        return extract_athenagroup(athena_group._athena_groups[key])
    except KeyError as e:
        raise KeyError(f"{key} not in {group_keys}") from e


def read_all_groups(dat_file: str, key: str = None) -> "dict[str, Group]":

        do_preedge=False,
        do_bkg=False,
        do_fft=False,
    )
    all_groups = {}
    for key in athena_group._athena_groups.keys():
        print(f"\nExtracting group {key}")
        group = get_group(athena_group, key)
        pre_edge_with_defaults(group=group)
        xftf_with_defaults(group=group)
        all_groups[key] = group

    pre_edge_with_defaults(group=group)
    xftf_with_defaults(group=group)
    return group


def pre_edge_with_defaults(group: Group, settings: dict = None):
    merged_settings = {}
    try:
        bkg_parameters = group.athena_params.bkg
    except AttributeError as e:
        print(f"Cannot load group.athena_params.bkg from group:\n{e}")
        bkg_parameters = None

    keys = (
        ("e0", "e0", None),
        ("pre1", "pre1", None),
        ("pre2", "pre2", None),

        ("step", "step", None),
        ("nvict", "nvict", None),
    )
    for key, parameters_key, default in keys:
        extract_attribute(
            merged_settings, key, bkg_parameters, parameters_key, default
        )

    if settings:
        for k, v in settings.items():
            if k == "nvict":

        ("kweight", "kweight", 2),
        ("window", "kwindow", "kaiser"),
    )
    for key, parameters_key, default in keys:
        extract_attribute(
            merged_settings, key, fft_parameters, parameters_key, default
        )

    if settings:
        for k, v in settings.items():
            merged_settings[k] = v

3:6bb927e155fc

from larch.symboltable import Group
from larch.xafs import autobk, pre_edge, xftf


def get_group(athena_group: AthenaGroup, key: str = None) -> Group:
    group_keys = list(athena_group.keys())
    if key is None:
        key = group_keys[0]
    else:
        key = key.replace("-", "_")

    try:
        return extract_athenagroup(athena_group.groups[key])
    except KeyError as e:
        raise KeyError(f"{key} not in {group_keys}") from e


def read_all_groups(dat_file: str, key: str = None) -> "dict[str, Group]":

        do_preedge=False,
        do_bkg=False,
        do_fft=False,
    )
    all_groups = {}
    for key in athena_group.keys():
        print(f"\nExtracting group {key}")
        group = get_group(athena_group, key)
        pre_edge_with_defaults(group=group)
        xftf_with_defaults(group=group)
        all_groups[key] = group

    pre_edge_with_defaults(group=group)
    xftf_with_defaults(group=group)
    return group


def pre_edge_with_defaults(
    group: Group, settings: dict = None, ref_channel: str = None
):
    merged_settings = {}
    if ref_channel is not None:
        print(f"Performing pre-edge with reference channel {ref_channel}")
        ref = getattr(group, ref_channel.lower())
        group.e0 = None
        pre_edge(energy=group.energy, mu=ref, group=group)
        bkg_parameters = group.pre_edge_details
    else:
        try:
            bkg_parameters = group.athena_params.bkg
        except AttributeError as e:
            print(f"Cannot load group.athena_params.bkg from group:\n{e}")
            bkg_parameters = None

    keys = (
        ("e0", "e0", None),
        ("pre1", "pre1", None),
        ("pre2", "pre2", None),

        ("step", "step", None),
        ("nvict", "nvict", None),
    )
    for key, parameters_key, default in keys:
        extract_attribute(
            merged_settings=merged_settings,
            key=key,
            parameters_group=bkg_parameters,
            parameters_key=parameters_key,
            default=default,
        )

    if settings:
        for k, v in settings.items():
            if k == "nvict":

        ("kweight", "kweight", 2),
        ("window", "kwindow", "kaiser"),
    )
    for key, parameters_key, default in keys:
        extract_attribute(
            merged_settings=merged_settings,
            key=key,
            parameters_group=fft_parameters,
            parameters_key=parameters_key,
            default=default,
        )

    if settings:
        for k, v in settings.items():
            merged_settings[k] = v