Mercurial > repos > astroteam > hess_astro_tool

annotate Lightcurve.py @ 1:593c4b45eda5 draft default tip

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2f23ec010eab8d33d2760f061286756e17015af7
author astroteam
date Thu, 18 Apr 2024 09:26:15 +0000
parents 02e4bb4fa10c
children
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02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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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
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4 # flake8: noqa
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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
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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 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
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17 from oda_api.json import CustomJSONEncoder
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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
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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
1
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24 from oda_api.api import ProgressReporter
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26 pr = ProgressReporter()
593c4b45eda5 planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2f23ec010eab8d33d2760f061286756e17015af7
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27 pr.report_progress(stage="Progress", progress=5.0)
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02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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29 src_name = "Crab" # http://odahub.io/ontology#AstrophysicalObject
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30 RA = 83.628700 # http://odahub.io/ontology#PointOfInterestRA
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31 DEC = 22.014700 # http://odahub.io/ontology#PointOfInterestDEC
1
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32 T1 = "2004-11-20T13:16:00.0" # http://odahub.io/ontology#StartTime
593c4b45eda5 planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2f23ec010eab8d33d2760f061286756e17015af7
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33 T2 = "2004-12-20T13:16:00.0" # http://odahub.io/ontology#EndTime
0
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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
1
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36 Emin = 1 # http://odahub.io/ontology#Energy_TeV
593c4b45eda5 planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2f23ec010eab8d33d2760f061286756e17015af7
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37 Emax = 100.0 # http://odahub.io/ontology#Energy_TeV
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38 NTbins = 30 # http://odahub.io/ontology#Integer
0
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39
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40 _galaxy_wd = os.getcwd()
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41
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42 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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43 inp_dic = json.load(fd)
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44 if "_data_product" in inp_dic.keys():
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45 inp_pdic = inp_dic["_data_product"]
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46 else:
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47 inp_pdic = inp_dic
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48
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49 for vn, vv in inp_pdic.items():
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50 if vn != "_selector":
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51 globals()[vn] = type(globals()[vn])(vv)
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52
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53 T1 = Time(T1, format="isot", scale="utc").mjd
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54 T2 = Time(T2, format="isot", scale="utc").mjd
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55 message = ""
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56 RA_pnts = []
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57 DEC_pnts = []
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58 DL3_files = []
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59 OBSIDs = []
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60 Tstart = []
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61 Tstop = []
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62 flist = os.listdir("data")
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63 for f in flist:
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64 if f[-7:] == "fits.gz":
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65 DL3_files.append(f)
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66 OBSIDs.append(int(f[20:26]))
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67 hdul = fits.open("data/" + f)
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68 RA_pnts.append(float(hdul[1].header["RA_PNT"]))
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69 DEC_pnts.append(float(hdul[1].header["DEC_PNT"]))
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70 Tstart.append(
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71 Time(
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72 hdul[1].header["DATE-OBS"] + "T" + hdul[1].header["TIME-OBS"],
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73 format="isot",
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74 scale="utc",
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75 ).mjd
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76 )
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77 Tstop.append(
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78 Time(
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79 hdul[1].header["DATE-END"] + "T" + hdul[1].header["TIME-END"],
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80 format="isot",
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81 scale="utc",
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82 ).mjd
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83 )
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84 hdul.close()
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85
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86 Coords_s = SkyCoord(RA, DEC, unit="degree")
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87 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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88 seps = COORDS_pnts.separation(Coords_s).deg
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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89
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90 mask = np.where((seps < Radius) & (Tstart > T1) & (Tstop < T2))[0]
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91 OBSlist = []
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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92 Tbegs = []
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93 for i in mask:
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94 OBSlist.append(DL3_files[i])
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95 Tbegs.append(Tstart[i])
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96 if len(OBSlist) == 0:
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97 message = "No data found"
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98 raise RuntimeError("No data found")
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99 message
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100
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101 Tbins = np.linspace(T1, T2, NTbins + 1)
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102 Tmin = Tbins[:-1]
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103 Tmax = Tbins[1:]
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104 Tmean = (Tmin + Tmax) / 2.0
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105 Tbins
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106
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107 flux = np.zeros(NTbins)
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108 flux_err = np.zeros(NTbins)
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109 flux_b = np.zeros(NTbins)
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110 flux_b_err = np.zeros(NTbins)
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111 Expos = np.zeros(NTbins)
1
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112 src_cts = np.zeros(NTbins)
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113 bkg_cts = np.zeros(NTbins)
0
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114 for count, f in enumerate(OBSlist):
1
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115 pr.report_progress(
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116 stage="Progress", progress=5.0 + 95 * count / len(OBSlist)
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117 )
0
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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118 hdul = fits.open("data/" + f)
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119 RA_pnt = hdul[1].header["RA_PNT"]
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120 DEC_pnt = hdul[1].header["DEC_PNT"]
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121 Texp = hdul[1].header["LIVETIME"]
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122 Trun_start = hdul[1].header["TSTART"]
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123 dRA = RA - RA_pnt
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124 dDEC = DEC - DEC_pnt
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125 RA_b = RA_pnt - dRA
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126 DEC_b = DEC_pnt - dDEC
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127 Coords_b = SkyCoord(RA_b, DEC_b, unit="degree")
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128 Coords_pnt = SkyCoord(RA_pnt, DEC_pnt, unit="degree")
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129 dist = Coords_pnt.separation(Coords_s).deg
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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130
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131 ev = hdul["EVENTS"].data
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132 ev_ra = ev["RA"]
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133 ev_dec = ev["DEC"]
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134 ev_en = ev["ENERGY"]
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135 ev_time = (ev["TIME"] - Trun_start) / 86400.0 + Tbegs[count]
1
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136 Nevents = len(ev)
0
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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137 print(ev_time[0])
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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138 ev_coords = SkyCoord(ev_ra, ev_dec, unit="degree")
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139 sep_s = ev_coords.separation(Coords_s).deg
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140 sep_b = ev_coords.separation(Coords_b).deg
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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141
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142 hdu = hdul["AEFF"].data
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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143 EEmin = hdu["ENERG_LO"][0]
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144 EEmax = hdu["ENERG_HI"][0]
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145 EE = sqrt(EEmin * EEmax)
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146 EEbins = np.concatenate((EEmin, [EEmax[-1]]))
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147 AA = hdu["EFFAREA"][0] + 1e-10
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148 Thmin = hdu["THETA_LO"][0]
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149 Thmax = hdu["THETA_HI"][0]
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150 ind = np.argmin((Thmin - dist) ** 2)
1
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151 mask = EE < Emin
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152 ind_en = len(EE[mask])
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153 Expos += np.histogram(
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154 ev_time,
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diff changeset
155 weights=AA[ind, ind_en] * Texp * 1e4 * np.ones(Nevents) / Nevents,
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156 bins=Tbins,
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157 )[0]
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158 mask = np.where((sep_s < R_s) & (ev_en > Emin) & (ev_en < Emax))
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159 src_cts += np.histogram(ev_time[mask], bins=Tbins)[0]
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160 mask = np.where((sep_b < R_s) & (ev_en > Emin) & (ev_en < Emax))
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161 bkg_cts += np.histogram(ev_time[mask], bins=Tbins)[0]
0
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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162 hdul.close()
1
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163 print(src_cts)
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164 print(bkg_cts)
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165 print(Expos)
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166 src = src_cts - bkg_cts
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167 src_err = sqrt(src_cts + bkg_cts)
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168 flux = src / (Expos + 1)
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169 flux_err = src_err / (Expos + 1)
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170 flux_b = bkg_cts / (Expos + 1)
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171 flux_b_err = sqrt(bkg_cts) / (Expos + 1)
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172 # flux_err+=np.sum(src_err/AA,axis=1)
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173 # flux_b+=np.sum(cts2/AA,axis=1)
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174 # flux_b_err+=np.sum(sqrt(cts2)/AA,axis=1)
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175 print(flux)
0
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176
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177 if message == "":
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178 plt.errorbar(
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179 Tmean,
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180 flux,
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181 yerr=flux_err,
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182 xerr=[Tmean - Tmin, Tmax - Tmean],
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183 linestyle="none",
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184 label="source",
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185 )
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186 plt.errorbar(
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187 Tmean,
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188 flux_b,
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189 yerr=flux_b_err,
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190 xerr=[Tmean - Tmin, Tmax - Tmean],
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191 linestyle="none",
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192 label="background",
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193 )
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194 plt.xlabel("Time, MJD")
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195 plt.ylabel("Flux, cts/cm$^2$s")
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196 plt.yscale("log")
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197 ymin = min(min(flux - flux_err), min(flux_b - flux_b_err))
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198 ymax = max(max(flux + flux_err), max(flux_b + flux_b_err))
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199 plt.ylim(ymin / 2.0, 2 * ymax)
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200 plt.legend(loc="lower left")
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201 plt.savefig("Lightcurve.png", format="png")
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202
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203 if message == "":
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204 bin_image = PictureProduct.from_file("Lightcurve.png")
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205 from astropy.table import Table
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206
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207 data = [Tmean, Tmin, Tmax, flux, flux_err, flux_b, flux_b_err]
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208 names = (
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209 "Tmean[MJD]",
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210 "Tmin[MJD]",
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211 "Tmax[MJD]",
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212 "Flux[counts/cm2s]",
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213 "Flux_error[counts/cm2s]",
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214 "Background[counts/cm2s]",
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215 "Background_error[counts/cm2s]",
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216 )
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217 lc = ODAAstropyTable(Table(data, names=names))
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218
1
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219 png = bin_image # http://odahub.io/ontology#ODAPictureProduct
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220 table = lc # http://odahub.io/ontology#ODAAstropyTable
0
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221
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222 # output gathering
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223 _galaxy_meta_data = {}
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224 _oda_outs = []
1
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225 _oda_outs.append(("out_Lightcurve_png", "png_galaxy.output", png))
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226 _oda_outs.append(("out_Lightcurve_table", "table_galaxy.output", table))
0
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227
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228 for _outn, _outfn, _outv in _oda_outs:
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229 _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
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230 if isinstance(_outv, str) and os.path.isfile(_outv):
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231 shutil.move(_outv, _galaxy_outfile_name)
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232 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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233 elif getattr(_outv, "write_fits_file", None):
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234 _outv.write_fits_file(_galaxy_outfile_name)
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235 _galaxy_meta_data[_outn] = {"ext": "fits"}
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236 elif getattr(_outv, "write_file", None):
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237 _outv.write_file(_galaxy_outfile_name)
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238 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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239 else:
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240 with open(_galaxy_outfile_name, "w") as fd:
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241 json.dump(_outv, fd, cls=CustomJSONEncoder)
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242 _galaxy_meta_data[_outn] = {"ext": "json"}
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243
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244 with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
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245 json.dump(_galaxy_meta_data, fd)
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246 print("*** Job finished successfully ***")