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

annotate larch_plot.py @ 2:59d0d15a40ef draft

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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 0f66842e802430e887d1c6cb7be1cc5436408fd2
author muon-spectroscopy-computational-project
date Mon, 04 Mar 2024 11:43:46 +0000
parents 002c18a3e642
children 5b993aff09e3
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886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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1 import json
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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2 import sys
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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4 from common import read_groups
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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6 import matplotlib
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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7 import matplotlib.pyplot as plt
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9 import numpy as np
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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11
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12 AXIS_LABELS = {
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13 "norm": r"x$\mu$(E), normalised",
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14 "dmude": r"d(x$\mu$(E))/dE, normalised",
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15 "chir_mag": r"|$\chi$(r)|",
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16 "energy": "Energy (eV)",
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17 "distance": "r (ang)",
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18 }
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21 def main(dat_files: "list[str]", plot_settings: "list[dict]"):
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22 groups = list(read_groups(dat_files))
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24 for i, settings in enumerate(plot_settings):
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25 data_list = []
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26 x_variable = "energy"
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27 y_variable = settings["variable"]["variable"]
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28 x_min = settings["variable"]["x_limit_min"]
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29 x_max = settings["variable"]["x_limit_max"]
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30 y_min = settings["variable"]["y_limit_min"]
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31 y_max = settings["variable"]["y_limit_max"]
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32 plot_path = f"plots/{i}_{y_variable}.png"
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33 plt.figure()
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35 for group in groups:
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36 params = group.athena_params
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37 annotation = getattr(params, "annotation", None)
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38 file = getattr(params, "file", None)
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39 params_id = getattr(params, "id", None)
59d0d15a40ef planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 0f66842e802430e887d1c6cb7be1cc5436408fd2
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40 label = annotation or file or params_id
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41 if y_variable == "chir_mag":
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42 x_variable = "distance"
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43 x = group.r
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44 else:
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45 x = group.energy
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46
1
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47 y = getattr(group, y_variable)
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48 if x_min is None and x_max is None:
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49 plt.plot(x, y, label=label)
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50 else:
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51 data_list.append({"x": x, "y": y, "label": label})
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52
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53 if x_min is not None or x_max is not None:
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54 for data in data_list:
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55 index_min = None
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56 index_max = None
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57 x = data["x"]
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58 if x_min is not None:
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59 index_min = max(np.searchsorted(x, x_min) - 1, 0)
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60 if x_max is not None:
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61 index_max = min(np.searchsorted(x, x_max) + 1, len(x))
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62 plt.plot(
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63 x[index_min:index_max],
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64 data["y"][index_min:index_max],
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65 label=data["label"],
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66 )
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67
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68 plt.xlim(x_min, x_max)
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69 plt.ylim(y_min, y_max)
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70
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71 save_plot(x_variable, y_variable, plot_path)
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73
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74 def save_plot(x_type: str, y_type: str, plot_path: str):
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75 plt.grid(color="r", linestyle=":", linewidth=1)
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76 plt.xlabel(AXIS_LABELS[x_type])
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77 plt.ylabel(AXIS_LABELS[y_type])
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78 plt.legend()
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79 plt.savefig(plot_path, format="png")
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80 plt.close("all")
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81
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82
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83 if __name__ == "__main__":
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84 # larch imports set this to an interactive backend, so need to change it
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85 matplotlib.use("Agg")
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86
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87 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
88 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
89
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
parents:
diff changeset
90 main(dat_files.split(","), input_values["plots"])