Mercurial > repos > astroteam > hess_astro_tool

annotate Image.py @ 0:02e4bb4fa10c draft

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
author astroteam
date Mon, 19 Feb 2024 10:56:44 +0000
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children 593c4b45eda5
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02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
astroteam
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1 #!/usr/bin/env python
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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2 # coding: utf-8
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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3
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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4 # flake8: noqa
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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5
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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6 import json
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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7 import os
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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8 import shutil
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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9
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10 import matplotlib.pyplot as plt
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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11 import numpy as np
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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12 from astropy import wcs
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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13 from astropy.coordinates import SkyCoord
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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14 from astropy.io import fits
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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15 from astropy.time import Time
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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16 from numpy import cos, pi
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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17 from oda_api.data_products import ImageDataProduct, PictureProduct
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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18 from oda_api.json import CustomJSONEncoder
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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19
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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20 if os.path.exists("hess_dl3_dr1.tar.gz") == False:
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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21 get_ipython().system( # noqa: F821
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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22 "wget https://zenodo.org/record/1421099/files/hess_dl3_dr1.tar.gz"
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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23 )
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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24 get_ipython().system("tar -zxvf hess_dl3_dr1.tar.gz") # noqa: F821
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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25
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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26 src_name = "Crab" # http://odahub.io/ontology#AstrophysicalObject
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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27 RA = 83.628700 # http://odahub.io/ontology#PointOfInterestRA
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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28 DEC = 22.014700 # http://odahub.io/ontology#PointOfInterestDEC
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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29 T1 = "2000-10-09T13:16:00.0" # http://odahub.io/ontology#StartTime
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30 T2 = "2022-10-10T13:16:00.0" # http://odahub.io/ontology#EndTime
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31 Radius = 2.5 # http://odahub.io/ontology#AngleDegrees
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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32 pixsize = (
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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33 0.1 # http://odahub.io/ontology#AngleDegrees ; oda:label "Pixel size"
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34 )
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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35 Emin = 100.0 # http://odahub.io/ontology#Energy_GeV
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36 Emax = 10000.0 # http://odahub.io/ontology#Energy_GeV
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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37
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38 _galaxy_wd = os.getcwd()
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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39
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40 with open("inputs.json", "r") as fd:
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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41 inp_dic = json.load(fd)
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42 if "_data_product" in inp_dic.keys():
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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43 inp_pdic = inp_dic["_data_product"]
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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44 else:
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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45 inp_pdic = inp_dic
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46
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47 for vn, vv in inp_pdic.items():
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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48 if vn != "_selector":
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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49 globals()[vn] = type(globals()[vn])(vv)
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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50
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51 T1 = Time(T1, format="isot", scale="utc").mjd
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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52 T2 = Time(T2, format="isot", scale="utc").mjd
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53 message = ""
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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54 RA_pnts = []
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55 DEC_pnts = []
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56 DL3_files = []
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57 OBSIDs = []
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58 Tstart = []
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59 Tstop = []
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60 flist = os.listdir("data")
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61 for f in flist:
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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62 if f[-7:] == "fits.gz":
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63 DL3_files.append(f)
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64 OBSIDs.append(int(f[20:26]))
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65 hdul = fits.open("data/" + f)
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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66 RA_pnts.append(float(hdul[1].header["RA_PNT"]))
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67 DEC_pnts.append(float(hdul[1].header["DEC_PNT"]))
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68 Tstart.append(
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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69 Time(
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70 hdul[1].header["DATE-OBS"] + "T" + hdul[1].header["TIME-OBS"],
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71 format="isot",
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72 scale="utc",
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73 ).mjd
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74 )
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75 Tstop.append(
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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76 Time(
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77 hdul[1].header["DATE-END"] + "T" + hdul[1].header["TIME-END"],
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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78 format="isot",
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79 scale="utc",
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80 ).mjd
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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81 )
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82 hdul.close()
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83
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84 Coords_s = SkyCoord(RA, DEC, unit="degree")
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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85 COORDS_pnts = SkyCoord(RA_pnts, DEC_pnts, unit="degree")
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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86 seps = COORDS_pnts.separation(Coords_s).deg
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87
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88 mask = np.where((seps < Radius) & (Tstart > T1) & (Tstop < T2))[0]
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89 OBSlist = []
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90 for i in mask:
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91 OBSlist.append(DL3_files[i])
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92 if len(OBSlist) == 0:
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93 message = "No data found"
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94 raise RuntimeError("No data found")
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95 message
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96
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97 cdec = cos(DEC * pi / 180.0)
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98 Npix = int(4 * Radius / pixsize) + 1
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99 RA_bins = np.linspace(RA - Radius / cdec, RA + Radius / cdec, Npix + 1)
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100 DEC_bins = np.linspace(DEC - Radius, DEC + Radius, Npix + 1)
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101 image = np.zeros((Npix, Npix))
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102 for f in OBSlist:
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103 hdul = fits.open("data/" + f)
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104 ev = hdul["EVENTS"].data
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105 ev_ra = ev["RA"]
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106 ev_dec = ev["DEC"]
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107 ev_en = ev["ENERGY"]
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108 ev_time = ev["TIME"]
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109 h = np.histogram2d(ev_ra, ev_dec, bins=[RA_bins, DEC_bins])
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110 image += h[0]
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111 hdul.close()
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112
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113 plt.imshow(
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114 np.flip(image, axis=1),
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115 extent=(RA_bins[-1], RA_bins[0], DEC_bins[0], DEC_bins[-1]),
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116 origin="lower",
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117 )
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118 plt.colorbar()
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119
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120 plt.xlabel("RA, degrees")
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121 plt.ylabel("DEC,degrees")
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122 plt.savefig("Image.png", format="png")
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123
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124 # Create a new WCS object. The number of axes must be set
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125 # from the start
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126 w = wcs.WCS(naxis=2)
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127
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128 # Set up an "Airy's zenithal" projection
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129 # Vector properties may be set with Python lists, or Numpy arrays
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130 w.wcs.crpix = [Npix / 2.0, Npix / 2.0]
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131 w.wcs.cdelt = np.array([pixsize / cdec, pixsize])
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132 w.wcs.crval = [RA, DEC]
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133 w.wcs.ctype = ["RA---AIR", "DEC--AIR"]
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134 w.wcs.set_pv([(2, 1, 45.0)])
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135
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136 # Now, write out the WCS object as a FITS header
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137 header = w.to_header()
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138
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139 # header is an astropy.io.fits.Header object. We can use it to create a new
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140 # PrimaryHDU and write it to a file.
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141 hdu = fits.PrimaryHDU(image, header=header)
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142 hdu.writeto("Image.fits", overwrite=True)
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143 hdu = fits.open("Image.fits")
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144 im = hdu[0].data
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145 from astropy.wcs import WCS
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146
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147 wcs = WCS(hdu[0].header)
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148 plt.subplot(projection=wcs)
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149 plt.imshow(im, origin="lower")
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150 plt.grid(color="white", ls="solid")
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151 plt.xlabel("RA")
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152 plt.ylabel("Dec")
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153
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154 bin_image = PictureProduct.from_file("Image.png")
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155 fits_image = ImageDataProduct.from_fits_file("Image.fits")
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156
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157 picture = bin_image # http://odahub.io/ontology#ODAPictureProduct
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158 image = fits_image # http://odahub.io/ontology#Image
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159
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160 # output gathering
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161 _galaxy_meta_data = {}
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162 _oda_outs = []
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163 _oda_outs.append(("out_Image_picture", "picture_galaxy.output", picture))
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164 _oda_outs.append(("out_Image_image", "image_galaxy.output", image))
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165
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166 for _outn, _outfn, _outv in _oda_outs:
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167 _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
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168 if isinstance(_outv, str) and os.path.isfile(_outv):
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169 shutil.move(_outv, _galaxy_outfile_name)
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170 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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171 elif getattr(_outv, "write_fits_file", None):
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172 _outv.write_fits_file(_galaxy_outfile_name)
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173 _galaxy_meta_data[_outn] = {"ext": "fits"}
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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174 elif getattr(_outv, "write_file", None):
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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175 _outv.write_file(_galaxy_outfile_name)
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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176 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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177 else:
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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178 with open(_galaxy_outfile_name, "w") as fd:
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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179 json.dump(_outv, fd, cls=CustomJSONEncoder)
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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180 _galaxy_meta_data[_outn] = {"ext": "json"}
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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181
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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182 with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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183 json.dump(_galaxy_meta_data, fd)
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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184 print("*** Job finished successfully ***")