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

annotate larch_plot.py @ 0:886949a03377 draft

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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
author muon-spectroscopy-computational-project
date Tue, 14 Nov 2023 15:35:36 +0000
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children 002c18a3e642
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886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
muon-spectroscopy-computational-project
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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
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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
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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8
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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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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12 Y_LABELS = {
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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13 "norm": r"x$\mu$(E), normalised",
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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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
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15 "chir_mag": r"|$\chi$(r)|",
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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16 }
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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19 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
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20 groups = list(read_groups(dat_files))
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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21
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22 for i, settings in enumerate(plot_settings):
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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23 data_list = []
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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24 e0_min = None
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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25 e0_max = None
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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26 variable = settings["variable"]["variable"]
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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27 x_min = settings["variable"]["energy_min"]
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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28 x_max = settings["variable"]["energy_max"]
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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29 plot_path = f"plots/{i}_{variable}.png"
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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30 plt.figure()
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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31
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32 for group in groups:
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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33 label = group.athena_params.annotation or group.athena_params.id
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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34 if variable == "chir_mag":
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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35 x = group.r
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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36 energy_format = None
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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37 else:
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38 x = group.energy
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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39 energy_format = settings["variable"]["energy_format"]
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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40 if energy_format == "relative":
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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41 e0 = group.athena_params.bkg.e0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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42 e0_min = find_relative_limit(e0_min, e0, min)
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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43 e0_max = find_relative_limit(e0_max, e0, max)
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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44
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45 y = getattr(group, variable)
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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46 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
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47 plt.plot(x, y, label=label)
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48 else:
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49 data_list.append({"x": x, "y": y, "label": label})
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50
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51 if variable != "chir_mag" and energy_format == "relative":
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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52 if x_min is not None:
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53 x_min += e0_min
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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54 if x_max is not None:
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55 x_max += e0_max
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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56
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57 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
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58 for data in data_list:
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59 index_min = None
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60 index_max = None
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61 x = data["x"]
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62 if x_min is not None:
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63 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
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64 if x_max is not None:
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65 index_max = min(np.searchsorted(x, x_max) + 1, len(x))
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66 plt.plot(
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67 x[index_min:index_max],
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68 data["y"][index_min:index_max],
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69 label=data["label"],
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70 )
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71
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72 plt.xlim(x_min, x_max)
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73
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74 save_plot(variable, plot_path)
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75
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76
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77 def find_relative_limit(e0_min: "float|None", e0: float, function: callable):
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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78 if e0_min is None:
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79 e0_min = e0
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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80 else:
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81 e0_min = function(e0_min, e0)
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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82 return e0_min
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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83
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84
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85 def save_plot(y_type: str, plot_path: str):
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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86 plt.grid(color="r", linestyle=":", linewidth=1)
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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87 plt.xlabel("Energy (eV)")
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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88 plt.ylabel(Y_LABELS[y_type])
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89 plt.legend()
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90 plt.savefig(plot_path, format="png")
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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91 plt.close("all")
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92
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93
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94 if __name__ == "__main__":
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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95 # 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
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96 matplotlib.use("Agg")
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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97
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98 dat_files = sys.argv[1]
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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99 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
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100
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101 main(dat_files.split(","), input_values["plots"])