# HG changeset patch
# User muon-spectroscopy-computational-project
# Date 1701867826 0
# Node ID 84c8e04bc1a12e31d709a12cf8fb1842b6701b7f
# Parent 2752b2dd7ad65ab57250906c67702ace6fffd9fe
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
diff -r 2752b2dd7ad6 -r 84c8e04bc1a1 common.py
--- a/common.py Tue Nov 14 15:34:23 2023 +0000
+++ b/common.py Wed Dec 06 13:03:46 2023 +0000
@@ -7,38 +7,145 @@
def get_group(athena_group: AthenaGroup, key: str = None) -> Group:
+ group_keys = list(athena_group._athena_groups.keys())
if key is None:
- group_keys = list(athena_group._athena_groups.keys())
key = group_keys[0]
- return extract_athenagroup(athena_group._athena_groups[key])
+ 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]":
+ # Cannot rely on do_ABC as _larch is None
+ athena_group = read_athena(
+ dat_file,
+ do_preedge=False,
+ do_bkg=False,
+ do_fft=False,
+ )
+ all_groups = {}
+ for key in athena_group._athena_groups.keys():
+ group = get_group(athena_group, key)
+ pre_edge_with_defaults(group=group)
+ xftf_with_defaults(group=group)
+ all_groups[key] = group
+
+ return all_groups
+
+
+def read_group(dat_file: str, key: str = None):
+ # Cannot rely on do_ABC as _larch is None
+ athena_group = read_athena(
+ dat_file,
+ do_preedge=False,
+ do_bkg=False,
+ do_fft=False,
+ )
+ group = get_group(athena_group, key)
+ pre_edge_with_defaults(group=group)
+ xftf_with_defaults(group=group)
+ return group
-def read_group(dat_file: str, key: str = None, xftf_params: dict = None):
- athena_group = read_athena(dat_file)
- group = get_group(athena_group, key)
- bkg_parameters = group.athena_params.bkg
- print(group.athena_params.fft)
- print(group.athena_params.fft.__dict__)
- pre_edge(
- group,
- e0=bkg_parameters.e0,
- pre1=bkg_parameters.pre1,
- pre2=bkg_parameters.pre2,
- norm1=bkg_parameters.nor1,
- norm2=bkg_parameters.nor2,
- nnorm=bkg_parameters.nnorm,
- make_flat=bkg_parameters.flatten,
+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),
+ ("norm1", "nor1", None),
+ ("norm2", "nor2", None),
+ ("nnorm", "nnorm", None),
+ ("make_flat", "flatten", None),
+ ("step", "step", None),
+ # This cannot be read from file as it is not stored by Larch (0.9.71)
+ # ("nvict", "nvict", None),
)
- autobk(group)
- if xftf_params is None:
- xftf(group)
- else:
- print(xftf_params)
- xftf(group, **xftf_params)
- xftf_details = Group()
- setattr(xftf_details, "call_args", xftf_params)
- group.xftf_details = xftf_details
- return group
+ 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":
+ print(
+ "WARNING: `nvict` can be used for pre-edge but is not "
+ "saved to file, so value used will not be accessible in "
+ "future operations using this Athena .prj"
+ )
+ merged_settings[k] = v
+
+ print(f"Pre-edge normalization with {merged_settings}")
+ try:
+ pre_edge(group, **merged_settings)
+ except Warning as e:
+ raise Warning(
+ "Unable to perform pre-edge fitting with:\n\n"
+ f"energy:\n{group.energy}\n\nmu:{group.mu}\n\n"
+ "Consider checking the correct columns have been extracted"
+ ) from e
+ autobk(group, pre_edge_kws=merged_settings)
+
+
+def xftf_with_defaults(group: Group, settings: dict = None):
+ merged_settings = {}
+ try:
+ fft_parameters = group.athena_params.fft
+ except AttributeError as e:
+ print(f"Cannot load group.athena_params.fft from group:\n{e}")
+ fft_parameters = None
+
+ keys = (
+ ("kmin", "kmin", 0),
+ ("kmax", "kmax", 20),
+ ("dk", "dk", 1),
+ ("kweight", "kw", 2),
+ ("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
+
+ print(f"XFTF with {merged_settings}")
+ xftf(group, **merged_settings)
+ xftf_details = Group()
+ setattr(xftf_details, "call_args", merged_settings)
+ group.xftf_details = xftf_details
+
+
+def extract_attribute(
+ merged_settings: dict,
+ key: str,
+ parameters_group: Group,
+ parameters_key: str,
+ default: "str|int" = None,
+):
+ if parameters_group is not None:
+ try:
+ merged_settings[key] = getattr(parameters_group, parameters_key)
+ return
+ except AttributeError:
+ pass
+
+ if default is not None:
+ merged_settings[key] = default
def read_groups(dat_files: "list[str]", key: str = None) -> Iterable[Group]:
diff -r 2752b2dd7ad6 -r 84c8e04bc1a1 larch_artemis.py
--- a/larch_artemis.py Tue Nov 14 15:34:23 2023 +0000
+++ b/larch_artemis.py Wed Dec 06 13:03:46 2023 +0000
@@ -5,20 +5,16 @@
import os
import sys
-from common import get_group
+from common import read_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
@@ -39,14 +35,6 @@
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:
@@ -209,12 +197,10 @@
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)
+ data_group = read_group(prj_file)
print(f"Fitting project from file {data_group.filename}")
diff -r 2752b2dd7ad6 -r 84c8e04bc1a1 larch_artemis.xml
--- a/larch_artemis.xml Tue Nov 14 15:34:23 2023 +0000
+++ b/larch_artemis.xml Wed Dec 06 13:03:46 2023 +0000
@@ -4,7 +4,7 @@
0.9.71
- 0
+ 1
10.1088/1742-6596/430/1/012007
@@ -40,6 +40,7 @@
+
Filtered k-space
-
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 2752b2dd7ad6 -r 84c8e04bc1a1 macros.xml
--- a/macros.xml Tue Nov 14 15:34:23 2023 +0000
+++ b/macros.xml Wed Dec 06 13:03:46 2023 +0000
@@ -1,26 +1,6 @@
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
+
+
+
\ No newline at end of file