Mercurial > repos > astroteam > hess_astro_tool

annotate Spectrum.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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diff changeset
1 #!/usr/bin/env python
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
astroteam
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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
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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.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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13 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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14 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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15 from numpy import log10, sqrt
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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16 from oda_api.data_products import ODAAstropyTable, PictureProduct
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.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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18
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19 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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20 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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21 "wget https://zenodo.org/record/1421099/files/hess_dl3_dr1.tar.gz"
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22 )
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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23 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 # 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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26 # RA = 83.628700 # http://odahub.io/ontology#PointOfInterestRA
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27 # 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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28 src_name = "PKS 2155-304"
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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29 RA = 329.716938 # http://odahub.io/ontology#PointOfInterestRA
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30 DEC = -30.225588 # 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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31
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32 T1 = "2000-10-09T13:16:00.0" # http://odahub.io/ontology#StartTime
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33 T2 = "2022-10-10T13:16:00.0" # http://odahub.io/ontology#EndTime
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34 Radius = 2.5 # http://odahub.io/ontology#AngleDegrees
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35 R_s = 0.2 # http://odahub.io/ontology#AngleDegrees
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36
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37 Emin = 100.0 # http://odahub.io/ontology#Energy_GeV
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38 Emax = 10000.0 # http://odahub.io/ontology#Energy_GeV
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39 NEbins = 20 # http://odahub.io/ontology#Integer
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40
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41 _galaxy_wd = os.getcwd()
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42
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43 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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44 inp_dic = json.load(fd)
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45 if "_data_product" in inp_dic.keys():
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46 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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47 else:
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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48 inp_pdic = inp_dic
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49
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50 for vn, vv in inp_pdic.items():
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51 if vn != "_selector":
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52 globals()[vn] = type(globals()[vn])(vv)
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53
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54 Emin = Emin / 1e3
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55 Emax = Emax / 1e3
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56 Ebins = np.logspace(log10(Emin), log10(Emax), NEbins + 1)
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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57 Ebins
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58 Emin = Ebins[:-1]
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59 Emax = Ebins[1:]
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60 Emean = sqrt(Emin * Emax)
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61 lgEmean = log10(Emean)
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62
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63 T1 = Time(T1, format="isot", scale="utc").mjd
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64 T2 = Time(T2, format="isot", scale="utc").mjd
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65 message = ""
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66 RA_pnts = []
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67 DEC_pnts = []
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68 DL3_files = []
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69 OBSIDs = []
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70 Tstart = []
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71 Tstop = []
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72 flist = os.listdir("data")
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73 for f in flist:
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74 if f[-7:] == "fits.gz":
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75 DL3_files.append(f)
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76 OBSIDs.append(int(f[20:26]))
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77 hdul = fits.open("data/" + f)
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78 RA_pnts.append(float(hdul[1].header["RA_PNT"]))
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79 DEC_pnts.append(float(hdul[1].header["DEC_PNT"]))
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80 Tstart.append(
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81 Time(
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82 hdul[1].header["DATE-OBS"] + "T" + hdul[1].header["TIME-OBS"],
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83 format="isot",
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84 scale="utc",
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85 ).mjd
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86 )
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87 Tstop.append(
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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88 Time(
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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89 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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90 format="isot",
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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91 scale="utc",
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92 ).mjd
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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93 )
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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94 hdul.close()
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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95
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96 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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97 COORDS_pnts = SkyCoord(RA_pnts, DEC_pnts, unit="degree")
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98 seps = COORDS_pnts.separation(Coords_s).deg
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99
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100 mask = np.where((seps < Radius) & (Tstart > T1) & (Tstop < T2))[0]
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101 OBSlist = []
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102 for i in mask:
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103 OBSlist.append(DL3_files[i])
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104 if len(OBSlist) == 0:
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105 message = "No data found"
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106 raise RuntimeError("No data found")
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107 message
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108
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109 cts_s = np.zeros(NEbins)
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110 cts_b = np.zeros(NEbins)
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111 Expos = np.zeros(NEbins)
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112 for f in OBSlist:
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113 hdul = fits.open("data/" + f)
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114 RA_pnt = hdul[1].header["RA_PNT"]
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115 DEC_pnt = hdul[1].header["DEC_PNT"]
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116 Texp = hdul[1].header["LIVETIME"]
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117 dRA = RA - RA_pnt
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118 dDEC = DEC - DEC_pnt
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119 RA_b = RA_pnt - dRA
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120 DEC_b = DEC_pnt - dDEC
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121 Coords_b = SkyCoord(RA_b, DEC_b, unit="degree")
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122 Coords_pnt = SkyCoord(RA_pnt, DEC_pnt, unit="degree")
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123 dist = Coords_pnt.separation(Coords_s).deg
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124
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125 ev = hdul["EVENTS"].data
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126 ev_ra = ev["RA"]
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127 ev_dec = ev["DEC"]
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128 ev_en = ev["ENERGY"]
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129 ev_time = ev["TIME"]
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130 ev_coords = SkyCoord(ev_ra, ev_dec, unit="degree")
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131 sep_s = ev_coords.separation(Coords_s).deg
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132 sep_b = ev_coords.separation(Coords_b).deg
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133
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134 hdu = hdul["AEFF"].data
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135 EEmin = hdu["ENERG_LO"][0]
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136 EEmax = hdu["ENERG_HI"][0]
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137 lgEE = log10(sqrt(EEmin * EEmax))
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138 lgAA = log10(hdu["EFFAREA"][0] + 1e-10)
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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139 Thmin = hdu["THETA_LO"][0]
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140 Thmax = hdu["THETA_HI"][0]
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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141 ind = np.argmin((Thmin - dist) ** 2)
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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142 Expos += 10 ** (np.interp(lgEmean, lgEE, lgAA[ind])) * Texp
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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143 mask = sep_s < R_s
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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144 cts_s += np.histogram(ev_en[mask], bins=Ebins)[0]
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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145 mask = sep_b < R_s
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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146 cts_b += np.histogram(ev_en[mask], bins=Ebins)[0]
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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147 hdul.close()
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148
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149 flux = (cts_s - cts_b) / (Emax - Emin) * Emax * Emin / (Expos * 1e4)
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150 flux_err = sqrt(cts_s + cts_b) / (Emax - Emin) * Emax * Emin / (Expos * 1e4)
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151 plt.errorbar(Emean, flux, yerr=flux_err, xerr=[Emean - Emin, Emax - Emean])
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152 plt.xscale("log")
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153 plt.yscale("log")
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154 plt.xlabel("$E$, TeV")
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155 plt.ylabel("$E^2 dN/dE$, erg/(cm$^2$s)")
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156 plt.savefig("Spectrum.png", format="png")
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157
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158 bin_image = PictureProduct.from_file("Spectrum.png")
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159 from astropy.table import Table
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160
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161 data = [Emean, Emin, Emax, flux, flux_err, cts_s, cts_b, Expos * 1e4]
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162 names = (
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163 "Emean[TeV]",
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164 "Emin[TeV]",
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165 "Emax[TeV]",
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166 "Flux[TeV/cm2s]",
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167 "Flux_error[TeV/cm2s]",
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168 "Cts_s",
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169 "Cts_b",
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170 "Exposure[cm2s]",
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171 )
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172 spec = ODAAstropyTable(Table(data, names=names))
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173
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174 picture_png = bin_image # http://odahub.io/ontology#ODAPictureProduct
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175 spectrum_astropy_table = spec # http://odahub.io/ontology#ODAAstropyTable
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176
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177 # output gathering
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178 _galaxy_meta_data = {}
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179 _oda_outs = []
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180 _oda_outs.append(
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181 ("out_Spectrum_picture_png", "picture_png_galaxy.output", picture_png)
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182 )
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183 _oda_outs.append(
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184 (
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185 "out_Spectrum_spectrum_astropy_table",
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186 "spectrum_astropy_table_galaxy.output",
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187 spectrum_astropy_table,
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188 )
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189 )
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190
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191 for _outn, _outfn, _outv in _oda_outs:
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192 _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
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193 if isinstance(_outv, str) and os.path.isfile(_outv):
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194 shutil.move(_outv, _galaxy_outfile_name)
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195 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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196 elif getattr(_outv, "write_fits_file", None):
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197 _outv.write_fits_file(_galaxy_outfile_name)
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198 _galaxy_meta_data[_outn] = {"ext": "fits"}
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199 elif getattr(_outv, "write_file", None):
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200 _outv.write_file(_galaxy_outfile_name)
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201 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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202 else:
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203 with open(_galaxy_outfile_name, "w") as fd:
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204 json.dump(_outv, fd, cls=CustomJSONEncoder)
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205 _galaxy_meta_data[_outn] = {"ext": "json"}
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206
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207 with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
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208 json.dump(_galaxy_meta_data, fd)
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209 print("*** Job finished successfully ***")