Mercurial > repos > astroteam > plot_tools_astro_tool

annotate spectrum.py @ 0:2b1759ccaa8b draft default tip

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
author astroteam
date Fri, 25 Apr 2025 21:48:27 +0000
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2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
astroteam
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diff changeset
1 #!/usr/bin/env python
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
astroteam
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2 # coding: utf-8
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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3
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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4 #!/usr/bin/env python
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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5
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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6 # This script is generated with nb2galaxy
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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7
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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8 # flake8: noqa
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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9
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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10 import json
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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11 import os
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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12 import shutil
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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13
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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14 from oda_api.json import CustomJSONEncoder
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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15
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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16 fn = "data.tsv" # oda:POSIXPath
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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17 skiprows = 0 # http://odahub.io/ontology#Integer
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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18 sep = "whitespace" # http://odahub.io/ontology#String ; oda:allowed_value "auto", "comma", "tab", "whitespace", "semicolon"
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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19 column = "c1" # http://odahub.io/ontology#String
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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20 weight_col = "" # http://odahub.io/ontology#String
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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21 binning = "logarithmic" # http://odahub.io/ontology#String ; oda:allowed_value "linear","logarithmic"
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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22 minval = 0 # http://odahub.io/ontology#Float
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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23 maxval = 0 # http://odahub.io/ontology#Float
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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24 nbins = 15 # http://odahub.io/ontology#Integer
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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25 xlabel = "Energy, [eV]" # http://odahub.io/ontology#String
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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26 ylabel = "Flux E^2, [eV]" # http://odahub.io/ontology#String
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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27 spec_power = 2.0 # http://odahub.io/ontology#Float
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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28
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29 _galaxy_wd = os.getcwd()
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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30
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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31 with open("inputs.json", "r") as fd:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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32 inp_dic = json.load(fd)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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33 if "C_data_product_" in inp_dic.keys():
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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34 inp_pdic = inp_dic["C_data_product_"]
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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35 else:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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36 inp_pdic = inp_dic
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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37 fn = str(inp_pdic["fn"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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38 skiprows = int(inp_pdic["skiprows"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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39 sep = str(inp_pdic["sep"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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40 column = str(inp_pdic["column"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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41 weight_col = str(inp_pdic["weight_col"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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42 binning = str(inp_pdic["binning"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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43 minval = float(inp_pdic["minval"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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44 maxval = float(inp_pdic["maxval"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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45 nbins = int(inp_pdic["nbins"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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46 xlabel = str(inp_pdic["xlabel"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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47 ylabel = str(inp_pdic["ylabel"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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48 spec_power = float(inp_pdic["spec_power"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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49
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50 import matplotlib.pyplot as plt
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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51 import numpy as np
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52 import pandas as pd
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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53
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54 separators = {
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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55 "tab": "\t",
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56 "comma": ",",
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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57 "semicolon": ";",
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58 "whitespace": "\s+",
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59 "space": " ",
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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60 }
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61
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62 df = None
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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63
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64 if sep == "auto":
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65 for name, s in separators.items():
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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66 try:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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67 df = pd.read_csv(fn, sep=s, index_col=False, skiprows=skiprows)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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68 if len(df.columns) > 2:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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69 sep = s
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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70 print("Detected separator: ", name)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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71 break
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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72 except Exception as e:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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73 print("Separator ", s, " failed", e)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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74 assert sep != "auto", "Failed to find valid separator"
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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75
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76 if df is None:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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77 df = pd.read_csv(fn, sep=separators[sep], index_col=False)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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78
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79 df.columns
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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80
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81 def read_data(df, colname, optional=False):
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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82 for i, c in enumerate(df.columns):
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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83 if colname == f"c{i+1}":
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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84 print(colname, c)
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85 return df[c].values
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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86 elif colname == c:
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parents:
diff changeset
87 print(colname, c)
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parents:
diff changeset
88 return df[c].values
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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89
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astroteam
parents:
diff changeset
90 assert optional, colname + " column not found"
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
astroteam
parents:
diff changeset
91 return None
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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92
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93 values = read_data(df, column)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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94 weights = read_data(df, weight_col, optional=True)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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95 if weights is None:
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96 weights = np.ones_like(values)
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97
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98 values, weights
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99
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100 from numpy import log10
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101
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102 if minval == 0:
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103 minval = np.min(values)
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104
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105 if maxval == 0:
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106 maxval = np.max(values)
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107
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108 if binning == "linear":
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109 bins = np.linspace(minval, maxval, nbins + 1)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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110 else:
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111 bins = np.logspace(log10(minval), log10(maxval), nbins + 1)
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112 bins
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113
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114 bin_val, _ = np.histogram(values, weights=weights, bins=bins)
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115 len(bin_val), len(bins)
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116 bin_width = bins[1:] - bins[:-1]
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117 flux = bin_val / bin_width
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118 if binning == "linear":
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119 spec_point = 0.5 * (bins[1:] + bins[:-1])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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120 else:
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121 spec_point = np.sqrt(bins[1:] * bins[:-1])
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122
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123 plt.figure()
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124 h = plt.plot(spec_point, flux * spec_point**spec_power)
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125
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126 if binning == "logarithmic":
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127 plt.xscale("log")
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128 plt.yscale("log")
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129
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130 plt.xlabel(xlabel)
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131 plt.ylabel(ylabel)
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132 plt.savefig("spectrum.png", format="png", dpi=150)
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133
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134 from astropy.table import Table
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135 from oda_api.data_products import ODAAstropyTable, PictureProduct
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136
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137 names = ("bins_min", "bins_max", "flux")
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138
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diff changeset
139 res = ODAAstropyTable(Table([bins[:-1], bins[1:], flux], names=names))
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140
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diff changeset
141 plot = PictureProduct.from_file("spectrum.png")
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142
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143 histogram_data = res # http://odahub.io/ontology#ODAAstropyTable
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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144 histogram_picture = plot # http://odahub.io/ontology#ODAPictureProduct
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145
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146 # output gathering
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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147 _galaxy_meta_data = {}
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148 _oda_outs = []
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parents:
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149 _oda_outs.append(
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150 (
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151 "out_spectrum_histogram_data",
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152 "histogram_data_galaxy.output",
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153 histogram_data,
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154 )
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155 )
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156 _oda_outs.append(
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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157 (
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158 "out_spectrum_histogram_picture",
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159 "histogram_picture_galaxy.output",
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160 histogram_picture,
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161 )
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162 )
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163
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164 for _outn, _outfn, _outv in _oda_outs:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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165 _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
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166 if isinstance(_outv, str) and os.path.isfile(_outv):
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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167 shutil.move(_outv, _galaxy_outfile_name)
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168 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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169 elif getattr(_outv, "write_fits_file", None):
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170 _outv.write_fits_file(_galaxy_outfile_name)
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171 _galaxy_meta_data[_outn] = {"ext": "fits"}
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172 elif getattr(_outv, "write_file", None):
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173 _outv.write_file(_galaxy_outfile_name)
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174 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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175 else:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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176 with open(_galaxy_outfile_name, "w") as fd:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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177 json.dump(_outv, fd, cls=CustomJSONEncoder)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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178 _galaxy_meta_data[_outn] = {"ext": "json"}
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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179
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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180 with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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181 json.dump(_galaxy_meta_data, fd)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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182 print("*** Job finished successfully ***")