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

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planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 7f52c8654581d23a2acffc818e0c197cf8e04504
author muon-spectroscopy-computational-project
date Tue, 03 Sep 2024 11:51:45 +0000
parents 35d24102cefd
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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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35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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6 from larch.symboltable import Group
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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8 import matplotlib
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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9 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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11 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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002c18a3e642 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 1cf6d7160497ba58fe16a51f00d088a20934eba6
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14 AXIS_LABELS = {
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35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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15 "energy": "Energy (eV)",
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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16 "distance": "r (ang)",
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17 "sample": "Sample",
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18 "flat": r"x$\mu$(E), flattened",
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19 "dmude": r"d(x$\mu$(E))/dE, normalised",
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20 "chir_mag": r"|$\chi$(r)|",
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21 "e0": "Edge Energy (eV)",
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22 }
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25 def sample_plot(groups: "list[Group]", y_variable: str):
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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26 x = [get_label(group) for group in groups]
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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27 y = [getattr(group, y_variable) for group in groups]
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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28 plt.scatter(x, y)
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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31 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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32 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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34 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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35 data_list = []
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36 y_variable = settings["variable"]["variable"]
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37 plot_path = f"plots/{i}_{y_variable}.png"
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38 plt.figure()
886949a03377 planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 5be486890442dedfb327289d597e1c8110240735
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40 if y_variable == "e0":
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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41 x_variable = "sample"
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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42 sample_plot(groups, y_variable)
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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43 else:
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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44 x_variable = "energy"
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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45 x_min = settings["variable"]["x_limit_min"]
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46 x_max = settings["variable"]["x_limit_max"]
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47 y_min = settings["variable"]["y_limit_min"]
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48 y_max = settings["variable"]["y_limit_max"]
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49 for group in groups:
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50 label = get_label(group)
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51 if y_variable == "chir_mag":
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52 x_variable = "distance"
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53 x = group.r
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54 else:
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55 x = group.energy
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56
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57 y = getattr(group, y_variable)
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58 if x_min is None and x_max is None:
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59 plt.plot(x, y, label=label)
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60 else:
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61 data_list.append({"x": x, "y": y, "label": label})
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62
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63 if x_min is not None or x_max is not None:
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64 for data in data_list:
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65 index_min = None
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66 index_max = None
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67 x = data["x"]
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68 if x_min is not None:
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69 index_min = max(np.searchsorted(x, x_min) - 1, 0)
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70 if x_max is not None:
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71 index_max = min(np.searchsorted(x, x_max) + 1, len(x))
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72 plt.plot(
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73 x[index_min:index_max],
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74 data["y"][index_min:index_max],
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75 label=data["label"],
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76 )
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77
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78 plt.xlim(x_min, x_max)
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79 plt.ylim(y_min, y_max)
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81 save_plot(x_variable, y_variable, plot_path)
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84 def get_label(group: Group) -> str:
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85 params = group.athena_params
35d24102cefd planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8
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86 annotation = getattr(params, "annotation", None)
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87 file = getattr(params, "file", None)
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88 params_id = getattr(params, "id", None)
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89 label = annotation or file or params_id
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90 return label
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91
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92
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93 def save_plot(x_type: str, y_type: str, plot_path: str):
0
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94 plt.grid(color="r", linestyle=":", linewidth=1)
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95 plt.xlabel(AXIS_LABELS[x_type])
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96 plt.ylabel(AXIS_LABELS[y_type])
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97 plt.legend()
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98 plt.savefig(plot_path, format="png")
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99 plt.close("all")
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100
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101
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102 if __name__ == "__main__":
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103 # larch imports set this to an interactive backend, so need to change it
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104 matplotlib.use("Agg")
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105
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106 dat_files = sys.argv[1]
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107 input_values = json.load(open(sys.argv[2], "r", encoding="utf-8"))
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108
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109 main(dat_files.split(","), input_values["plots"])