larch_athena: larch_athena.py annotate

annotate larch_athena.py @ 3:82e9dd980916 draft

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f

author	muon-spectroscopy-computational-project
date	Fri, 22 Mar 2024 14:23:27 +0000
parents	a1e26990131c
children	a0d3b0fe0fa3

rev	line source
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	1 import gc
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	2 import json
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	3 import os
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	4 import re
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	5 import sys
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	6
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	7 from common import (
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	8 pre_edge_with_defaults,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	9 read_all_groups,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	10 read_group,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	11 xftf_with_defaults,
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	12 )
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	13
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	14 from larch.io import (
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	15 create_athena,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	16 h5group,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	17 merge_groups,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	18 read_ascii,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	19 set_array_labels,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	20 )
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	21 from larch.symboltable import Group
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	22 from larch.xafs import rebin_xafs
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	23
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	24 import matplotlib
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	25 import matplotlib.pyplot as plt
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	26
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	27 import numpy as np
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	28
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	29
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	30 class Reader:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	31 def __init__(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	32 self,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	33 energy_column: str,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	34 mu_column: str,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	35 data_format: str,
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	36 extract_group: "dict[str, str]" = None,
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	37 ):
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	38 self.energy_column = energy_column
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	39 self.mu_column = mu_column
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	40 self.data_format = data_format
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	41 self.extract_group = extract_group
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	42
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	43 def load_data(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	44 self,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	45 dat_file: str,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	46 merge_inputs: bool,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	47 is_zipped: bool,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	48 ) -> "dict[str, Group]":
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	49 if merge_inputs:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	50 out_group = self.merge_files(
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	51 dat_files=dat_file,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	52 is_zipped=is_zipped,
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	53 )
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	54 return {"out": out_group}
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	55 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	56 return self.load_single_file(
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	57 filepath=dat_file,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	58 is_zipped=is_zipped,
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	59 )
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	60
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	61 def merge_files(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	62 self,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	63 dat_files: str,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	64 is_zipped: bool,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	65 ) -> Group:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	66 if is_zipped:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	67 all_groups = list(self.load_zipped_files().values())
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	68 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	69 all_groups = []
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	70 for filepath in dat_files.split(","):
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	71 for group in self.load_single_file(filepath).values():
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	72 all_groups.append(group)
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	73
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	74 merged_group = merge_groups(all_groups, xarray="energy", yarray="mu")
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	75 pre_edge_with_defaults(merged_group)
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	76 return merged_group
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	77
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	78 def load_single_file(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	79 self,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	80 filepath: str,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	81 is_zipped: bool = False,
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	82 ) -> dict:
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	83 if is_zipped:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	84 return self.load_zipped_files()
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	85
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	86 print(f"Attempting to read from {filepath}")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	87 if self.data_format == "athena":
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	88 if self.extract_group["extract_group"] == "single":
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	89 group = read_group(filepath, self.extract_group["group_name"])
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	90 return {"out": group}
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	91 elif self.extract_group["extract_group"] == "multiple":
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	92 groups = {}
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	93 for repeat in self.extract_group["multiple"]:
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	94 name = repeat["group_name"]
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	95 print(f"\nExtracting group {name}")
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	96 groups[name] = read_group(filepath, name)
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	97 return groups
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	98 else:
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	99 return read_all_groups(filepath)
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	100
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	101 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	102 # Try ascii anyway
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	103 try:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	104 group = self.load_ascii(filepath)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	105 if not group.array_labels:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	106 # In later versions of larch, won't get a type error it
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	107 # will just fail to load any data
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	108 group = self.load_h5(filepath)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	109 except (UnicodeDecodeError, TypeError):
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	110 # Indicates this isn't plaintext, try h5
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	111 group = self.load_h5(filepath)
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	112 pre_edge_with_defaults(group)
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	113 xftf_with_defaults(group)
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	114 return {"out": group}
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	115
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	116 def load_ascii(self, dat_file):
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	117 with open(dat_file) as f:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	118 labels = None
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	119 last_line = None
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	120 line = f.readline()
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	121 while line:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	122 if not line.startswith("#"):
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	123 if last_line is not None and last_line.find("\t") > 0:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	124 labels = []
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	125 for label in last_line.split("\t"):
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	126 labels.append(label.strip())
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	127 break
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	128
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	129 last_line = line
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	130 line = f.readline()
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	131
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	132 xas_data = read_ascii(filename=dat_file, labels=labels)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	133 xas_data = self.rename_cols(xas_data)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	134 return xas_data
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	135
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	136 def load_h5(self, dat_file):
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	137 h5_group = h5group(fname=dat_file, mode="r")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	138 energy = h5_group.entry1.instrument.qexafs_energy.qexafs_energy
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	139 mu = h5_group.entry1.instrument.qexafs_counterTimer01.lnI0It
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	140 xafs_group = Group(data=np.array([energy[:], mu[:]]))
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	141 set_array_labels(xafs_group, ["energy", "mu"])
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	142 return xafs_group
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	143
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	144 def load_zipped_files(self) -> "dict[str, Group]":
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	145 def sorting_key(filename: str) -> str:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	146 return re.findall(r"\d+", filename)[-1]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	147
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	148 all_paths = list(os.walk("dat_files"))
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	149 all_paths.sort(key=lambda x: x[0])
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	150 file_total = sum([len(f) for _, _, f in all_paths])
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	151 print(f"{file_total} files found")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	152 keyed_data = {}
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	153 for dirpath, _, filenames in all_paths:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	154 try:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	155 filenames.sort(key=sorting_key)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	156 except IndexError as e:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	157 print(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	158 "WARNING: Unable to sort files numerically, "
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	159 f"defaulting to sorting alphabetically:\n{e}"
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	160 )
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	161 filenames.sort()
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	162
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	163 for filename in filenames:
2 a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	164 if len(all_paths) > 1:
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	165 key = f"{dirpath}_{filename}"
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	166 else:
a1e26990131c planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 0f66842e802430e887d1c6cb7be1cc5436408fd2 muon-spectroscopy-computational-project parents: 1 diff changeset	167 key = filename
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	168 filepath = os.path.join(dirpath, filename)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	169 xas_data = self.load_single_file(filepath)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	170 keyed_data[key] = xas_data["out"]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	171
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	172 return keyed_data
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	173
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	174 def rename_cols(self, xafs_group: Group) -> Group:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	175 labels = [label.lower() for label in xafs_group.array_labels]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	176 print(f"Read columns: {labels}")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	177
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	178 if "energy" in labels:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	179 print("'energy' present in column headers")
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	180 elif self.energy_column:
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	181 if self.energy_column.lower() in labels:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	182 labels[labels.index(self.energy_column.lower())] = "energy"
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	183 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	184 raise ValueError(f"{self.energy_column} not found in {labels}")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	185 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	186 for i, label in enumerate(labels):
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	187 if label in ("col1", "ef") or label.endswith("energy"):
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	188 labels[i] = "energy"
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	189 break
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	190
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	191 if "mu" in labels:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	192 print("'mu' present in column headers")
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	193 elif self.mu_column:
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	194 if self.mu_column.lower() in labels:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	195 labels[labels.index(self.mu_column.lower())] = "mu"
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	196 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	197 raise ValueError(f"{self.mu_column} not found in {labels}")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	198 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	199 for i, label in enumerate(labels):
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	200 if label in ["col2", "xmu", "lni0it", "ffi0", "ff/i1"]:
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	201 labels[i] = "mu"
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	202 break
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	203
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	204 if labels != xafs_group.array_labels:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	205 print(f"Renaming columns to: {labels}")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	206 return set_array_labels(xafs_group, labels)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	207 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	208 return xafs_group
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	209
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	210
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	211 def calibrate_energy(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	212 xafs_group: Group,
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	213 calibration_e0: float = None,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	214 energy_min: float = None,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	215 energy_max: float = None,
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	216 ):
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	217 if calibration_e0 is not None:
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	218 print(f"Recalibrating edge from {xafs_group.e0} to {calibration_e0}")
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	219 xafs_group.energy = xafs_group.energy + calibration_e0 - xafs_group.e0
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	220 xafs_group.e0 = calibration_e0
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	221
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	222 if not (energy_min or energy_max):
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	223 return xafs_group
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	224
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	225 if energy_min is not None:
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	226 index_min = np.searchsorted(xafs_group.energy, energy_min)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	227 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	228 index_min = 0
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	229
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	230 if energy_max is not None:
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	231 index_max = np.searchsorted(xafs_group.energy, energy_max)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	232 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	233 index_max = len(xafs_group.energy)
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	234
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	235 print(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	236 f"Cropping energy range from {energy_min} to {energy_max}, "
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	237 f"index {index_min} to {index_max}"
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	238 )
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	239 try:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	240 xafs_group.dmude = xafs_group.dmude[index_min:index_max]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	241 xafs_group.pre_edge = xafs_group.pre_edge[index_min:index_max]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	242 xafs_group.post_edge = xafs_group.post_edge[index_min:index_max]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	243 xafs_group.flat = xafs_group.flat[index_min:index_max]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	244 except AttributeError:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	245 pass
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	246
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	247 xafs_group.energy = xafs_group.energy[index_min:index_max]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	248 xafs_group.mu = xafs_group.mu[index_min:index_max]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	249
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	250 # Sanity check
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	251 if len(xafs_group.energy) == 0:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	252 raise ValueError("Energy cropping led to an empty array")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	253
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	254 return xafs_group
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	255
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	256
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	257 def main(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	258 xas_data: Group,
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	259 do_calibrate: bool,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	260 calibrate_settings: dict,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	261 do_rebin: bool,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	262 do_pre_edge: bool,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	263 pre_edge_settings: dict,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	264 do_xftf: bool,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	265 xftf_settings: dict,
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	266 plot_graph: list,
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	267 annotation: str,
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	268 path_key: str = "out",
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	269 ):
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	270 if do_calibrate:
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	271 print(f"Calibrating energy with {calibrate_settings}")
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	272 xas_data = calibrate_energy(xas_data, **calibrate_settings)
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	273 # After re-calibrating, will need to redo pre-edge with new range
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	274 do_pre_edge = True
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	275
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	276 if do_rebin:
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	277 print("Re-binning data")
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	278 rebin_xafs(
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	279 energy=xas_data.energy,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	280 mu=xas_data.mu,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	281 group=xas_data,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	282 **pre_edge_settings,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	283 )
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	284 xas_data = xas_data.rebinned
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	285 # After re-bin, will need to redo pre-edge
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	286 do_pre_edge = True
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	287
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	288 if do_pre_edge:
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	289 pre_edge_with_defaults(xas_data, pre_edge_settings)
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	290
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	291 if do_xftf:
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	292 xftf_with_defaults(xas_data, xftf_settings)
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	293
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	294 if plot_graph:
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	295 plot_graphs(
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	296 plot_path=f"plot/{path_key}.png",
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	297 xas_data=xas_data,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	298 plot_keys=plot_graph,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	299 )
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	300
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	301 xas_project = create_athena(f"prj/{path_key}.prj")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	302 xas_project.add_group(xas_data)
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	303 if annotation:
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	304 group = next(iter(xas_project.groups.values()))
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	305 group.args["annotation"] = annotation
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	306 xas_project.save()
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	307
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	308 # Ensure that we do not run out of memory when running on large zips
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	309 gc.collect()
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	310
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	311
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	312 def plot_graphs(
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	313 plot_path: str,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	314 xas_data: Group,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	315 plot_keys: list,
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	316 ) -> None:
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	317 nrows = len(plot_keys)
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	318 index = 1
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	319 plt.figure(figsize=(6.4, nrows * 4.8))
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	320 if "edge" in plot_keys:
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	321 plt.subplot(nrows, 1, index)
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	322 plt.plot(xas_data.energy, xas_data.pre_edge, "g", label="pre-edge")
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	323 plt.plot(xas_data.energy, xas_data.post_edge, "r", label="post-edge")
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	324 plt.plot(xas_data.energy, xas_data.mu, "b", label="fit data")
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	325 plt.grid(color="r", linestyle=":", linewidth=1)
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	326 plt.xlabel("Energy (eV)")
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	327 plt.ylabel("x$\mu$(E)") # noqa: W605
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	328 plt.title("Pre-edge and post_edge fitting to $\mu$") # noqa: W605
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	329 plt.legend()
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	330 index += 1
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	331
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	332 if "flat" in plot_keys:
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	333 plt.subplot(nrows, 1, index)
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	334 plt.plot(xas_data.energy, xas_data.flat)
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	335 plt.grid(color="r", linestyle=":", linewidth=1)
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	336 plt.xlabel("Energy (eV)")
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	337 plt.ylabel("Flattened x$\mu$(E)") # noqa: W605
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	338 index += 1
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	339
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	340 if "dmude" in plot_keys:
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	341 plt.subplot(nrows, 1, index)
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	342 plt.plot(xas_data.energy, xas_data.dmude)
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	343 plt.grid(color="r", linestyle=":", linewidth=1)
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	344 plt.xlabel("Energy (eV)")
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	345 plt.ylabel("Derivative normalised to x$\mu$(E)") # noqa: W605
82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	346 index += 1
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	347
3 82e9dd980916 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit d4c7e090dc5c94395d7e1574845ac2c76f2e4f5f muon-spectroscopy-computational-project parents: 2 diff changeset	348 plt.tight_layout(rect=(0, 0, 0.88, 1))
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	349 plt.savefig(plot_path, format="png")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	350 plt.close("all")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	351
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	352
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	353 if __name__ == "__main__":
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	354 # larch imports set this to an interactive backend, so need to change it
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	355 matplotlib.use("Agg")
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	356
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	357 dat_file = sys.argv[1]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	358 input_values = json.load(open(sys.argv[2], "r", encoding="utf-8"))
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	359 merge_inputs = input_values["merge_inputs"]["merge_inputs"]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	360 data_format = input_values["merge_inputs"]["format"]["format"]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	361 if "is_zipped" in input_values["merge_inputs"]["format"]:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	362 is_zipped = bool(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	363 input_values["merge_inputs"]["format"]["is_zipped"]["is_zipped"]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	364 )
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	365 else:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	366 is_zipped = False
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	367
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	368 extract_group = None
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	369 if "extract_group" in input_values["merge_inputs"]["format"]:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	370 extract_group = input_values["merge_inputs"]["format"]["extract_group"]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	371
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	372 energy_column = None
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	373 mu_column = None
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	374 if "energy_column" in input_values["merge_inputs"]["format"]:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	375 energy_column = input_values["merge_inputs"]["format"]["energy_column"]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	376 if "mu_column" in input_values["merge_inputs"]["format"]:
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	377 mu_column = input_values["merge_inputs"]["format"]["mu_column"]
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	378
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	379 reader = Reader(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	380 energy_column=energy_column,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	381 mu_column=mu_column,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	382 data_format=data_format,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	383 extract_group=extract_group,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	384 )
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	385 keyed_data = reader.load_data(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	386 dat_file=dat_file,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	387 merge_inputs=merge_inputs,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	388 is_zipped=is_zipped,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	389 )
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	390
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	391 calibrate_items = input_values["processing"]["calibrate"].items()
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	392 calibrate_settings = {k: v for k, v in calibrate_items if v is not None}
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	393 do_calibrate = calibrate_settings.pop("calibrate") == "true"
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	394
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	395 do_rebin = input_values["processing"].pop("rebin")
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	396
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	397 pre_edge_items = input_values["processing"]["pre_edge"].items()
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	398 pre_edge_settings = {k: v for k, v in pre_edge_items if v is not None}
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	399 do_pre_edge = pre_edge_settings.pop("pre_edge") == "true"
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	400
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	401 xftf_items = input_values["processing"]["xftf"].items()
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	402 xftf_settings = {k: v for k, v in xftf_items if v is not None}
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	403 do_xftf = xftf_settings.pop("xftf") == "true"
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	404
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	405 plot_graph = input_values["plot_graph"]
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	406 annotation = input_values["annotation"]
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	407
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	408 for key, group in keyed_data.items():
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	409 main(
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	410 group,
1 2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	411 do_calibrate=do_calibrate,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	412 calibrate_settings=calibrate_settings,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	413 do_rebin=do_rebin,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	414 do_pre_edge=do_pre_edge,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	415 pre_edge_settings=pre_edge_settings,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	416 do_xftf=do_xftf,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	417 xftf_settings=xftf_settings,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	418 plot_graph=plot_graph,
2b3115342fef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 1cf6d7160497ba58fe16a51f00d088a20934eba6 muon-spectroscopy-computational-project parents: 0 diff changeset	419 annotation=annotation,
0 ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	420 path_key=key,
ae2f265ecf8e planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_athena commit 5be486890442dedfb327289d597e1c8110240735 muon-spectroscopy-computational-project parents: diff changeset	421 )

Mercurial > repos > muon-spectroscopy-computational-project > larch_athena

annotate larch_athena.py @ 3:82e9dd980916 draft