Mercurial > repos > muon-spectroscopy-computational-project > larch_artemis
annotate common.py @ 0:2752b2dd7ad6 draft
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
| author | muon-spectroscopy-computational-project |
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| date | Tue, 14 Nov 2023 15:34:23 +0000 |
| parents | |
| children | 84c8e04bc1a1 |
| rev | line source |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
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changeset
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1 from typing import Iterable |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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2 |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
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3 from larch.io import extract_athenagroup, read_athena |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
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changeset
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4 from larch.io.athena_project import AthenaGroup |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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5 from larch.symboltable import Group |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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6 from larch.xafs import autobk, pre_edge, xftf |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
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7 |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
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8 |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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9 def get_group(athena_group: AthenaGroup, key: str = None) -> Group: |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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10 if key is None: |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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11 group_keys = list(athena_group._athena_groups.keys()) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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12 key = group_keys[0] |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
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13 return extract_athenagroup(athena_group._athena_groups[key]) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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14 |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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15 |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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16 def read_group(dat_file: str, key: str = None, xftf_params: dict = None): |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
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17 athena_group = read_athena(dat_file) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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18 group = get_group(athena_group, key) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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19 bkg_parameters = group.athena_params.bkg |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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20 print(group.athena_params.fft) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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21 print(group.athena_params.fft.__dict__) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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22 pre_edge( |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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23 group, |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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24 e0=bkg_parameters.e0, |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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25 pre1=bkg_parameters.pre1, |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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26 pre2=bkg_parameters.pre2, |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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27 norm1=bkg_parameters.nor1, |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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28 norm2=bkg_parameters.nor2, |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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29 nnorm=bkg_parameters.nnorm, |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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30 make_flat=bkg_parameters.flatten, |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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31 ) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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32 autobk(group) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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33 if xftf_params is None: |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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34 xftf(group) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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35 else: |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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36 print(xftf_params) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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37 xftf(group, **xftf_params) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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38 xftf_details = Group() |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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39 setattr(xftf_details, "call_args", xftf_params) |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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40 group.xftf_details = xftf_details |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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41 return group |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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42 |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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43 |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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44 def read_groups(dat_files: "list[str]", key: str = None) -> Iterable[Group]: |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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45 for dat_file in dat_files: |
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2752b2dd7ad6
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_artemis commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
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46 yield read_group(dat_file=dat_file, key=key) |