Mercurial > repos > astroteam > hess_astro_tool

annotate Spectrum_gammapy.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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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
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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
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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 astropy.units as u
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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11 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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12 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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13 from astropy.coordinates import Angle, 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.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 gammapy.data import DataStore
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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16 from gammapy.datasets import (
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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17 Datasets,
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18 FluxPointsDataset,
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19 SpectrumDataset,
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20 SpectrumDatasetOnOff,
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21 )
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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22 from gammapy.makers import (
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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23 ReflectedRegionsBackgroundMaker,
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24 SafeMaskMaker,
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25 SpectrumDatasetMaker,
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26 )
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27
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28 # from gammapy.makers.utils import make_theta_squared_table
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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29 from gammapy.maps import MapAxis, RegionGeom, WcsGeom
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30 from oda_api.data_products import ODAAstropyTable, PictureProduct
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31 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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32 from regions import CircleSkyRegion
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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33
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34 hess_data = "gammapy-datasets/1.1/hess-dl3-dr1/"
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35 if not (os.path.exists(hess_data)):
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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36 get_ipython().system("gammapy download datasets") # noqa: F821
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 data_store = DataStore.from_dir(hess_data)
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 # src_name='Crab' #http://odahub.io/ontology#AstrophysicalObject
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41 # RA = 83.628700 # http://odahub.io/ontology#PointOfInterestRA
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42 # DEC = 22.014700 # http://odahub.io/ontology#PointOfInterestDEC
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43 src_name = "PKS 2155-304"
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44 RA = 329.716938 # http://odahub.io/ontology#PointOfInterestRA
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45 DEC = -30.225588 # http://odahub.io/ontology#PointOfInterestDEC
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46 T1 = "2000-10-09T13:16:00.0" # http://odahub.io/ontology#StartTime
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47 T2 = "2022-10-10T13:16:00.0" # http://odahub.io/ontology#EndTime
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48 Radius = 2.5 # http://odahub.io/ontology#AngleDegrees
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49 R_s = 0.5 # http://odahub.io/ontology#AngleDegrees
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50
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51 Emin = 100.0 # http://odahub.io/ontology#Energy_GeV
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52 Emax = 10000.0 # http://odahub.io/ontology#Energy_GeV
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53 NEbins = 20 # http://odahub.io/ontology#Integer
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54
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55 _galaxy_wd = os.getcwd()
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56
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57 with open("inputs.json", "r") as fd:
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58 inp_dic = json.load(fd)
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59 if "_data_product" in inp_dic.keys():
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60 inp_pdic = inp_dic["_data_product"]
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61 else:
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62 inp_pdic = inp_dic
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63
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64 for vn, vv in inp_pdic.items():
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65 if vn != "_selector":
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66 globals()[vn] = type(globals()[vn])(vv)
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67
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68 T1 = Time(T1, format="isot", scale="utc").mjd
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69 T2 = Time(T2, format="isot", scale="utc").mjd
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70
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71 dates1 = data_store.obs_table["DATE-OBS"]
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72 dates2 = data_store.obs_table["DATE-END"]
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73 times1 = data_store.obs_table["TIME-OBS"]
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74 times2 = data_store.obs_table["TIME-END"]
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75 OBSIDs = data_store.obs_table["OBS_ID"]
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76 Tstart = []
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77 Tstop = []
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78 for i in range(len(dates1)):
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79 Tstart.append(
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80 Time(dates1[i] + "T" + times1[i], format="isot", scale="utc").mjd
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81 )
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82 Tstop.append(
02e4bb4fa10c planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit 2991f65b25d4e6d1b69458603fce917adff40f94
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83 Time(dates2[i] + "T" + times2[i], format="isot", scale="utc").mjd
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84 )
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85
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86 RA_pnts = np.array(data_store.obs_table["RA_PNT"])
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87 DEC_pnts = np.array(data_store.obs_table["DEC_PNT"])
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88
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89 Coords_s = SkyCoord(RA, DEC, unit="degree")
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90 COORDS_pnts = SkyCoord(RA_pnts, DEC_pnts, unit="degree")
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91 seps = COORDS_pnts.separation(Coords_s).deg
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92
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93 mask = np.where((seps < Radius) & (Tstart > T1) & (Tstop < T2))[0]
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94 OBSlist = []
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95 obs_ids = OBSIDs[mask]
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96 if len(obs_ids) == 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 obs_ids
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100
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101 observations = data_store.get_observations(obs_ids)
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102
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103 target_position = Coords_s
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104 on_region_radius = Angle(str(R_s) + " deg")
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105 on_region = CircleSkyRegion(center=target_position, radius=on_region_radius)
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106 skydir = target_position.galactic
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107 geom = WcsGeom.create(
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108 npix=(150, 150), binsz=0.05, skydir=skydir, proj="TAN", frame="icrs"
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109 )
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110
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111 Emin = 100.0 # http://odahub.io/ontology#Energy_GeV
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112 Emax = 10000.0 # http://odahub.io/ontology#Energy_GeV
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113 NEbins = 20 # http://odahub.io/ontology#Integer
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114
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115 energy_axis = MapAxis.from_energy_bounds(
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116 Emin * 1e-3,
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117 Emax * 1e-3,
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118 nbin=NEbins,
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119 per_decade=True,
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120 unit="TeV",
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121 name="energy",
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122 )
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123 energy_axis_true = MapAxis.from_energy_bounds(
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124 0.05, 100, nbin=20, per_decade=True, unit="TeV", name="energy_true"
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125 )
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126
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127 geom = RegionGeom.create(region=on_region, axes=[energy_axis])
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128 dataset_empty = SpectrumDataset.create(
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129 geom=geom, energy_axis_true=energy_axis_true
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130 )
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131
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132 dataset_maker = SpectrumDatasetMaker(
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133 containment_correction=True, selection=["counts", "exposure", "edisp"]
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134 )
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135 bkg_maker = ReflectedRegionsBackgroundMaker()
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136 safe_mask_masker = SafeMaskMaker(methods=["aeff-max"], aeff_percent=10)
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137
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138 datasets = Datasets()
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139
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140 for obs_id, observation in zip(obs_ids, observations):
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141 dataset = dataset_maker.run(
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142 dataset_empty.copy(name=str(obs_id)), observation
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143 )
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144 dataset_on_off = bkg_maker.run(dataset, observation)
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145 # dataset_on_off = safe_mask_masker.run(dataset_on_off, observation)
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146 datasets.append(dataset_on_off)
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147
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148 print(datasets)
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149
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150 from pathlib import Path
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151
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152 path = Path("spectrum_analysis")
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153 path.mkdir(exist_ok=True)
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154
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155 for dataset in datasets:
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156 dataset.write(
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157 filename=path / f"obs_{dataset.name}.fits.gz", overwrite=True
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158 )
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159
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160 datasets = Datasets()
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161
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162 for obs_id in obs_ids:
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163 filename = path / f"obs_{obs_id}.fits.gz"
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164 datasets.append(SpectrumDatasetOnOff.read(filename))
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165
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166 from gammapy.modeling import Fit
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167 from gammapy.modeling.models import ExpCutoffPowerLawSpectralModel, SkyModel
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168
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169 spectral_model = ExpCutoffPowerLawSpectralModel(
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170 amplitude=1e-12 * u.Unit("cm-2 s-1 TeV-1"),
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171 index=2,
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172 lambda_=0.1 * u.Unit("TeV-1"),
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173 reference=1 * u.TeV,
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174 )
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175 model = SkyModel(spectral_model=spectral_model, name="crab")
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176
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177 datasets.models = [model]
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178
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179 fit_joint = Fit()
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180 result_joint = fit_joint.run(datasets=datasets)
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181
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182 # we make a copy here to compare it later
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183 model_best_joint = model.copy()
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184
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185 print(result_joint)
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186
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187 display(result_joint.models.to_parameters_table()) # noqa: F821
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188
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189 e_min, e_max = Emin * 1e-3, Emax * 1e-3
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190 energy_edges = np.geomspace(e_min, e_max, NEbins) * u.TeV
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191
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192 from gammapy.estimators import FluxPointsEstimator
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193
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194 fpe = FluxPointsEstimator(
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195 energy_edges=energy_edges, source="crab", selection_optional="all"
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196 )
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197 flux_points = fpe.run(datasets=datasets)
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198
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199 flux_points_dataset = FluxPointsDataset(
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200 data=flux_points, models=model_best_joint
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201 )
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202 flux_points_dataset.plot_fit()
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203 # plt.show()
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204 plt.savefig("Spectrum.png", format="png", bbox_inches="tight")
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205
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206 res = flux_points.to_table(sed_type="dnde", formatted=True)
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207 np.array(res["dnde"])
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208
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209 bin_image = PictureProduct.from_file("Spectrum.png")
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210 from astropy.table import Table
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211
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212 Emean = np.array(res["e_ref"])
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213 Emin = np.array(res["e_min"])
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214 Emax = np.array(res["e_max"])
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215 flux = Emean**2 * np.array(res["dnde"])
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216 flux_err = Emean**2 * np.array(res["dnde_err"])
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217 data = [Emean, Emin, Emax, flux, flux_err]
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218 names = (
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219 "Emean[TeV]",
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220 "Emin[TeV]",
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221 "Emax[TeV]",
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222 "Flux[TeV/cm2s]",
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223 "Flux_error[TeV/cm2s]",
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224 )
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225 spec = ODAAstropyTable(Table(data, names=names))
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226
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227 picture_png = bin_image # http://odahub.io/ontology#ODAPictureProduct
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228 spectrum_astropy_table = spec # http://odahub.io/ontology#ODAAstropyTable
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229
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230 # output gathering
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231 _galaxy_meta_data = {}
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232 _oda_outs = []
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233 _oda_outs.append(
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234 (
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235 "out_Spectrum_gammapy_picture_png",
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236 "picture_png_galaxy.output",
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237 picture_png,
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238 )
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239 )
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240 _oda_outs.append(
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241 (
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242 "out_Spectrum_gammapy_spectrum_astropy_table",
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243 "spectrum_astropy_table_galaxy.output",
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244 spectrum_astropy_table,
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245 )
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246 )
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247
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248 for _outn, _outfn, _outv in _oda_outs:
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249 _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
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250 if isinstance(_outv, str) and os.path.isfile(_outv):
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251 shutil.move(_outv, _galaxy_outfile_name)
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252 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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253 elif getattr(_outv, "write_fits_file", None):
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254 _outv.write_fits_file(_galaxy_outfile_name)
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255 _galaxy_meta_data[_outn] = {"ext": "fits"}
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256 elif getattr(_outv, "write_file", None):
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257 _outv.write_file(_galaxy_outfile_name)
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258 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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259 else:
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260 with open(_galaxy_outfile_name, "w") as fd:
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261 json.dump(_outv, fd, cls=CustomJSONEncoder)
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262 _galaxy_meta_data[_outn] = {"ext": "json"}
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263
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264 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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265 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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266 print("*** Job finished successfully ***")