comparison larch_artemis.py @ 1:84c8e04bc1a1 draft

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 1cf6d7160497ba58fe16a51f00d088a20934eba6

0:2752b2dd7ad6

import gc
import json
import os
import sys

from common import get_group

from larch.fitting import guess, param, param_group
from larch.io import read_athena
from larch.symboltable import Group
from larch.xafs import (
    FeffPathGroup,
    FeffitDataSet,
    TransformGroup,
    autobk,
    feffit,
    feffit_report,
    pre_edge,
    xftf,
)

import matplotlib
import matplotlib.pyplot as plt

            for row in reader:
                csv_data[int(row[id_field])] = row
    except FileNotFoundError:
        print("The specified file does not exist")
    return csv_data


def calc_with_defaults(xafs_group: Group) -> Group:
    """Calculate pre_edge and background with default arguments"""
    pre_edge(xafs_group)
    autobk(xafs_group)
    xftf(xafs_group)
    return xafs_group


def dict_to_gds(data_dict):
    dgs_group = param_group()
    for par_idx in data_dict:

) -> Group:
    report_path = f"report/fit_report{series_id}.txt"
    rmr_path = f"rmr/rmr{series_id}.png"
    chikr_path = f"chikr/chikr{series_id}.png"

    athena_project = read_athena(prj_file)
    athena_group = get_group(athena_project)
    # calc_with_defaults will hang indefinitely (>6 hours recorded) if the
    # data contains any NaNs - consider adding an early error here if this is
    # not fixed in Larch?
    data_group = calc_with_defaults(athena_group)

    print(f"Fitting project from file {data_group.filename}")

    gds = read_gds(gds_file)
    selected_paths = read_selected_paths_list(sp_file)

1:84c8e04bc1a1

import gc
import json
import os
import sys

from common import read_group

from larch.fitting import guess, param, param_group
from larch.symboltable import Group
from larch.xafs import (
    FeffPathGroup,
    FeffitDataSet,
    TransformGroup,
    feffit,
    feffit_report,
)

import matplotlib
import matplotlib.pyplot as plt

            for row in reader:
                csv_data[int(row[id_field])] = row
    except FileNotFoundError:
        print("The specified file does not exist")
    return csv_data


def dict_to_gds(data_dict):
    dgs_group = param_group()
    for par_idx in data_dict:

) -> Group:
    report_path = f"report/fit_report{series_id}.txt"
    rmr_path = f"rmr/rmr{series_id}.png"
    chikr_path = f"chikr/chikr{series_id}.png"

    # calc_with_defaults will hang indefinitely (>6 hours recorded) if the
    # data contains any NaNs - consider adding an early error here if this is
    # not fixed in Larch?
    data_group = read_group(prj_file)

    print(f"Fitting project from file {data_group.filename}")

    gds = read_gds(gds_file)
    selected_paths = read_selected_paths_list(sp_file)