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comparison larch_artemis.py @ 1:84c8e04bc1a1 draft

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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
author muon-spectroscopy-computational-project
date Wed, 06 Dec 2023 13:03:46 +0000
parents 2752b2dd7ad6
children 39ab361e6d59
comparison
equal deleted inserted replaced
0:2752b2dd7ad6 1:84c8e04bc1a1
3 import gc 3 import gc
4 import json 4 import json
5 import os 5 import os
6 import sys 6 import sys
7 7
8 from common import get_group 8 from common import read_group
9 9
10 from larch.fitting import guess, param, param_group 10 from larch.fitting import guess, param, param_group
11 from larch.io import read_athena
12 from larch.symboltable import Group 11 from larch.symboltable import Group
13 from larch.xafs import ( 12 from larch.xafs import (
14 FeffPathGroup, 13 FeffPathGroup,
15 FeffitDataSet, 14 FeffitDataSet,
16 TransformGroup, 15 TransformGroup,
17 autobk,
18 feffit, 16 feffit,
19 feffit_report, 17 feffit_report,
20 pre_edge,
21 xftf,
22 ) 18 )
23 19
24 import matplotlib 20 import matplotlib
25 import matplotlib.pyplot as plt 21 import matplotlib.pyplot as plt
26 22
35 for row in reader: 31 for row in reader:
36 csv_data[int(row[id_field])] = row 32 csv_data[int(row[id_field])] = row
37 except FileNotFoundError: 33 except FileNotFoundError:
38 print("The specified file does not exist") 34 print("The specified file does not exist")
39 return csv_data 35 return csv_data
40
41
42 def calc_with_defaults(xafs_group: Group) -> Group:
43 """Calculate pre_edge and background with default arguments"""
44 pre_edge(xafs_group)
45 autobk(xafs_group)
46 xftf(xafs_group)
47 return xafs_group
48 36
49 37
50 def dict_to_gds(data_dict): 38 def dict_to_gds(data_dict):
51 dgs_group = param_group() 39 dgs_group = param_group()
52 for par_idx in data_dict: 40 for par_idx in data_dict:
207 ) -> Group: 195 ) -> Group:
208 report_path = f"report/fit_report{series_id}.txt" 196 report_path = f"report/fit_report{series_id}.txt"
209 rmr_path = f"rmr/rmr{series_id}.png" 197 rmr_path = f"rmr/rmr{series_id}.png"
210 chikr_path = f"chikr/chikr{series_id}.png" 198 chikr_path = f"chikr/chikr{series_id}.png"
211 199
212 athena_project = read_athena(prj_file)
213 athena_group = get_group(athena_project)
214 # calc_with_defaults will hang indefinitely (>6 hours recorded) if the 200 # calc_with_defaults will hang indefinitely (>6 hours recorded) if the
215 # data contains any NaNs - consider adding an early error here if this is 201 # data contains any NaNs - consider adding an early error here if this is
216 # not fixed in Larch? 202 # not fixed in Larch?
217 data_group = calc_with_defaults(athena_group) 203 data_group = read_group(prj_file)
218 204
219 print(f"Fitting project from file {data_group.filename}") 205 print(f"Fitting project from file {data_group.filename}")
220 206
221 gds = read_gds(gds_file) 207 gds = read_gds(gds_file)
222 selected_paths = read_selected_paths_list(sp_file) 208 selected_paths = read_selected_paths_list(sp_file)