Mercurial > repos > muon-spectroscopy-computational-project > larch_lcf
annotate larch_lcf.py @ 0:f59731986b61 draft
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
| author | muon-spectroscopy-computational-project |
|---|---|
| date | Tue, 14 Nov 2023 15:35:22 +0000 |
| parents | |
| children | 6c28339b73f7 |
| rev | line source |
|---|---|
|
0
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
1 import json |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
2 import sys |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
3 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
4 from common import read_group |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
5 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
6 from larch.math.lincombo_fitting import get_label, lincombo_fit |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
7 from larch.symboltable import Group |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
8 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
9 import matplotlib |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
10 import matplotlib.pyplot as plt |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
11 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
12 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
13 def plot( |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
14 group_to_fit: Group, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
15 fit_group: Group, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
16 energy_min: float, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
17 energy_max: float, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
18 ): |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
19 formatted_label = "" |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
20 for label, weight in fit_group.weights.items(): |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
21 formatted_label += f"{label}: {weight:.3%}\n" |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
22 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
23 plt.figure() |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
24 plt.plot( |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
25 group_to_fit.energy, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
26 group_to_fit.norm, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
27 label=group_to_fit.filename, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
28 linewidth=4, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
29 color="blue", |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
30 ) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
31 plt.plot( |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
32 fit_group.xdata, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
33 fit_group.ydata, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
34 label=formatted_label[:-1], |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
35 linewidth=2, |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
36 color="orange", |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
37 linestyle="--", |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
38 ) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
39 plt.grid(color="black", linestyle=":", linewidth=1) # show and format grid |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
40 plt.xlim(energy_min, energy_max) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
41 plt.xlabel("Energy (eV)") |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
42 plt.ylabel("normalised x$\mu$(E)") # noqa: W605 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
43 plt.legend() |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
44 plt.savefig("plot.png", format="png") |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
45 plt.close("all") |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
46 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
47 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
48 def set_label(component_group, label): |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
49 if label is not None: |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
50 component_group.filename = label |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
51 else: |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
52 component_group.filename = get_label(component_group) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
53 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
54 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
55 if __name__ == "__main__": |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
56 # larch imports set this to an interactive backend, so need to change it |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
57 matplotlib.use("Agg") |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
58 prj_file = sys.argv[1] |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
59 input_values = json.load(open(sys.argv[2], "r", encoding="utf-8")) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
60 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
61 group_to_fit = read_group(prj_file) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
62 set_label(group_to_fit, input_values["label"]) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
63 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
64 component_groups = [] |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
65 for component in input_values["components"]: |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
66 component_group = read_group(component["component_file"]) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
67 set_label(component_group, component["label"]) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
68 component_groups.append(component_group) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
69 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
70 fit_group = lincombo_fit(group_to_fit, component_groups) |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
71 print(f"Goodness of fit (rfactor): {fit_group.rfactor:.6%}") |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
72 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
73 energy_min = input_values["energy_min"] |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
74 energy_max = input_values["energy_max"] |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
75 if input_values["energy_format"] == "relative": |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
76 e0 = group_to_fit.e0 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
77 if energy_min is not None: |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
78 energy_min += e0 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
79 if energy_max is not None: |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
80 energy_max += e0 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
81 |
|
f59731986b61
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_lcf commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff
changeset
|
82 plot(group_to_fit, fit_group, energy_min, energy_max) |