annotate larch_plot.py @ 4:35d24102cefd draft

planemo upload for repository https://github.com/MaterialsGalaxy/larch-tools/tree/main/larch_plot commit 3fe6078868efd0fcea0fb5eea8dcd4b152d9c0a8

import json
import sys

from common import read_groups

from larch.symboltable import Group

import matplotlib
import matplotlib.pyplot as plt

import numpy as np


AXIS_LABELS = {
    "energy": "Energy (eV)",
    "distance": "r (ang)",
    "sample": "Sample",
    "flat": r"x$\mu$(E), flattened",
    "dmude": r"d(x$\mu$(E))/dE, normalised",
    "chir_mag": r"|$\chi$(r)|",
    "e0": "Edge Energy (eV)",
}


def sample_plot(groups: "list[Group]", y_variable: str):
    x = [get_label(group) for group in groups]
    y = [getattr(group, y_variable) for group in groups]
    plt.scatter(x, y)


def main(dat_files: "list[str]", plot_settings: "list[dict]"):
    groups = list(read_groups(dat_files))

    for i, settings in enumerate(plot_settings):
        data_list = []
        y_variable = settings["variable"]["variable"]
        plot_path = f"plots/{i}_{y_variable}.png"
        plt.figure()

        if y_variable == "e0":
            x_variable = "sample"
            sample_plot(groups, y_variable)
        else:
            x_variable = "energy"
            x_min = settings["variable"]["x_limit_min"]
            x_max = settings["variable"]["x_limit_max"]
            y_min = settings["variable"]["y_limit_min"]
            y_max = settings["variable"]["y_limit_max"]
            for group in groups:
                label = get_label(group)
                if y_variable == "chir_mag":
                    x_variable = "distance"
                    x = group.r
                else:
                    x = group.energy

                y = getattr(group, y_variable)
                if x_min is None and x_max is None:
                    plt.plot(x, y, label=label)
                else:
                    data_list.append({"x": x, "y": y, "label": label})

            if x_min is not None or x_max is not None:
                for data in data_list:
                    index_min = None
                    index_max = None
                    x = data["x"]
                    if x_min is not None:
                        index_min = max(np.searchsorted(x, x_min) - 1, 0)
                    if x_max is not None:
                        index_max = min(np.searchsorted(x, x_max) + 1, len(x))
                    plt.plot(
                        x[index_min:index_max],
                        data["y"][index_min:index_max],
                        label=data["label"],
                    )

            plt.xlim(x_min, x_max)
            plt.ylim(y_min, y_max)

        save_plot(x_variable, y_variable, plot_path)


def get_label(group: Group) -> str:
    params = group.athena_params
    annotation = getattr(params, "annotation", None)
    file = getattr(params, "file", None)
    params_id = getattr(params, "id", None)
    label = annotation or file or params_id
    return label


def save_plot(x_type: str, y_type: str, plot_path: str):
    plt.grid(color="r", linestyle=":", linewidth=1)
    plt.xlabel(AXIS_LABELS[x_type])
    plt.ylabel(AXIS_LABELS[y_type])
    plt.legend()
    plt.savefig(plot_path, format="png")
    plt.close("all")


if __name__ == "__main__":
    # larch imports set this to an interactive backend, so need to change it
    matplotlib.use("Agg")

    dat_files = sys.argv[1]
    input_values = json.load(open(sys.argv[2], "r", encoding="utf-8"))

    main(dat_files.split(","), input_values["plots"])