Mercurial > repos > astroteam > plot_tools_astro_tool

annotate sky_plot.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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0
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
astroteam
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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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2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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20 ra_col = "c3" # 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 dec_col = "c4" # 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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22 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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23 binsz = 0.02 # 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 window_size_RA = 2.0 # http://odahub.io/ontology#Degree
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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25 window_size_DEC = 2.0 # http://odahub.io/ontology#Degree
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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26
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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27 _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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28
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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29 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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30 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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31 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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32 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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33 else:
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
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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35 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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36 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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37 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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38 ra_col = str(inp_pdic["ra_col"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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39 dec_col = str(inp_pdic["dec_col"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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40 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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41 binsz = float(inp_pdic["binsz"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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42 window_size_RA = float(inp_pdic["window_size_RA"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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43 window_size_DEC = float(inp_pdic["window_size_DEC"])
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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44
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45 import astropy.units as u
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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46 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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47 import numpy as np
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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48 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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49 from astropy.coordinates import SkyCoord
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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50 from gammapy.maps import Map
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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51 from oda_api.data_products import ImageDataProduct, PictureProduct
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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52
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53 separators = {
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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54 "tab": "\t",
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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55 "comma": ",",
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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56 "semicolon": ";",
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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57 "whitespace": "\s+",
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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58 "space": " ",
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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59 }
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 df = None
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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62
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63 if sep == "auto":
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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64 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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65 try:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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66 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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67 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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68 sep = s
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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69 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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70 break
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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71 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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72 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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73 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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74
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75 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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76 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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77
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78 df.columns
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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79
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80 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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81 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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82 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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83 print(colname, c)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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84 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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85 elif colname == c:
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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86 print(colname, c)
2b1759ccaa8b planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit f28a8cb73a7f3053eac92166867a48b3d4af28fd
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87 return df[c].values
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88
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89 assert optional, colname + " column not found"
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90 return None
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91
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92 ra = read_data(df, ra_col)
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93 dec = read_data(df, dec_col)
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94 w = read_data(df, weight_col, optional=True)
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95 if w is None:
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96 w = np.ones_like(ra)
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97
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98 source = SkyCoord(ra=np.mean(ra) * u.deg, dec=np.mean(dec) * u.deg)
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99
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100 map = Map.create(
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101 binsz=binsz,
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102 width=(window_size_RA * u.deg, window_size_DEC * u.deg),
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103 frame="icrs",
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104 axes=[],
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105 skydir=SkyCoord(source),
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106 )
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107
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108 map.fill_by_coord({"lat": dec * u.deg, "lon": ra * u.deg}, weights=w)
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109
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110 map.plot()
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111 plt.savefig("map.png")
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112
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113 map.write("map.fits", overwrite=True)
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114 fits_image = ImageDataProduct.from_fits_file("map.fits")
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115
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116 plot = PictureProduct.from_file("map.png")
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117
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118 plot = plot # http://odahub.io/ontology#ODAPictureProduct
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119 fits_image = fits_image # http://odahub.io/ontology#Image
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120
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121 # output gathering
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122 _galaxy_meta_data = {}
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123 _oda_outs = []
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124 _oda_outs.append(("out_sky_plot_plot", "plot_galaxy.output", plot))
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125 _oda_outs.append(
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126 ("out_sky_plot_fits_image", "fits_image_galaxy.output", fits_image)
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127 )
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128
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129 for _outn, _outfn, _outv in _oda_outs:
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130 _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
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131 if isinstance(_outv, str) and os.path.isfile(_outv):
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132 shutil.move(_outv, _galaxy_outfile_name)
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133 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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134 elif getattr(_outv, "write_fits_file", None):
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135 _outv.write_fits_file(_galaxy_outfile_name)
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136 _galaxy_meta_data[_outn] = {"ext": "fits"}
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137 elif getattr(_outv, "write_file", None):
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138 _outv.write_file(_galaxy_outfile_name)
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139 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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140 else:
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141 with open(_galaxy_outfile_name, "w") as fd:
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142 json.dump(_outv, fd, cls=CustomJSONEncoder)
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143 _galaxy_meta_data[_outn] = {"ext": "json"}
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144
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145 with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
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146 json.dump(_galaxy_meta_data, fd)
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147 print("*** Job finished successfully ***")