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

annotate larch_plot.py @ 1:002c18a3e642 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
author muon-spectroscopy-computational-project
date Wed, 06 Dec 2023 13:04:06 +0000
parents 886949a03377
children 59d0d15a40ef
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
1 import json
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
2 import sys
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
3
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
4 from common import read_groups
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
5
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
6 import matplotlib
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
7 import matplotlib.pyplot as plt
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
8
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
9 import numpy as np
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
10
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
11
1
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
12 AXIS_LABELS = {
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
13 "norm": r"x$\mu$(E), normalised",
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
14 "dmude": r"d(x$\mu$(E))/dE, normalised",
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
15 "chir_mag": r"|$\chi$(r)|",
1
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
16 "energy": "Energy (eV)",
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
17 "distance": "r (ang)",
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
18 }
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
19
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
20
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
21 def main(dat_files: "list[str]", plot_settings: "list[dict]"):
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
22 groups = list(read_groups(dat_files))
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
23
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
24 for i, settings in enumerate(plot_settings):
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
25 data_list = []
1
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
26 x_variable = "energy"
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
27 y_variable = settings["variable"]["variable"]
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
28 x_min = settings["variable"]["x_limit_min"]
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
29 x_max = settings["variable"]["x_limit_max"]
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
30 y_min = settings["variable"]["y_limit_min"]
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
31 y_max = settings["variable"]["y_limit_max"]
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
32 plot_path = f"plots/{i}_{y_variable}.png"
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
33 plt.figure()
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
34
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
35 for group in groups:
1
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
36 params = group.athena_params
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
37 label = params.annotation or params.file or params.id
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
38 if y_variable == "chir_mag":
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
39 x_variable = "distance"
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
40 x = group.r
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
41 else:
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
42 x = group.energy
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
43
1
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
44 y = getattr(group, y_variable)
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
45 if x_min is None and x_max is None:
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
46 plt.plot(x, y, label=label)
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
47 else:
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
48 data_list.append({"x": x, "y": y, "label": label})
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
49
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
50 if x_min is not None or x_max is not None:
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
51 for data in data_list:
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
52 index_min = None
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
53 index_max = None
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
54 x = data["x"]
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
55 if x_min is not None:
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
56 index_min = max(np.searchsorted(x, x_min) - 1, 0)
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
57 if x_max is not None:
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
58 index_max = min(np.searchsorted(x, x_max) + 1, len(x))
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
59 plt.plot(
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
60 x[index_min:index_max],
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
61 data["y"][index_min:index_max],
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
62 label=data["label"],
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
63 )
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
64
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
65 plt.xlim(x_min, x_max)
1
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
66 plt.ylim(y_min, y_max)
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
67
1
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
68 save_plot(x_variable, y_variable, plot_path)
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
69
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
70
1
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
71 def save_plot(x_type: str, y_type: str, plot_path: str):
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
72 plt.grid(color="r", linestyle=":", linewidth=1)
1
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
73 plt.xlabel(AXIS_LABELS[x_type])
002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
muon-spectroscopy-computational-project
parents: 0
diff changeset
74 plt.ylabel(AXIS_LABELS[y_type])
0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
75 plt.legend()
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
76 plt.savefig(plot_path, format="png")
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
77 plt.close("all")
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
78
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
79
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
80 if __name__ == "__main__":
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
81 # larch imports set this to an interactive backend, so need to change it
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
82 matplotlib.use("Agg")
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
83
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
84 dat_files = sys.argv[1]
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
85 input_values = json.load(open(sys.argv[2], "r", encoding="utf-8"))
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
86
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
87 main(dat_files.split(","), input_values["plots"])