Mercurial > repos > astroteam > crbeam_astro_tool

annotate Generate_events.py @ 0:f40d05521dca draft default tip

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planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
author astroteam
date Fri, 25 Apr 2025 19:33:20 +0000
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f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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1 #!/usr/bin/env python
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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2 # coding: utf-8
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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3
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4 #!/usr/bin/env python
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5
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6 # This script is generated with nb2galaxy
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7
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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8 # flake8: noqa
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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9
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10 import json
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11 import os
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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12 import shutil
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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13
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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14 from oda_api.json import CustomJSONEncoder
f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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16 # oda:usesResource oda:CRBeamS3 .
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17 # oda:CRBeamS3 a oda:S3 .
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18 # oda:CRBeamS3 oda:resourceBindingEnvVarName "S3_CREDENTIALS" .
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f40d05521dca planemo upload for repository https://github.com/esg-epfl-apc/tools-astro/tree/main/tools commit de01e3c02a26cd6353a6b9b6f8d1be44de8ccd54
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20 src_name = "1ES 1215+303" # http://odahub.io/ontology#AstrophysicalObject
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22 z_start = 0.13 # http://odahub.io/ontology#Float
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23 Npart = 10000 # http://odahub.io/ontology#Integer ; oda:lower_limit 1 ; oda:upper_limit 100000
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24 particle_type = "gamma" # http://odahub.io/ontology#String ; oda:allowed_value "gamma","electron","proton"
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25 Emax = 50 # http://odahub.io/ontology#Energy_TeV
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26 Emin = 0.01 # http://odahub.io/ontology#Energy_TeV
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27 EminSource = 0.01 # http://odahub.io/ontology#Energy_TeV
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28 Gamma = 2.0 # http://odahub.io/ontology#Float
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29 EGMF_fG = 100 # http://odahub.io/ontology#Float
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30 lmaxEGMF_Mpc = 5 # http://odahub.io/ontology#Float
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31 jet_half_size = 180.0 # http://odahub.io/ontology#AngleDegrees
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32 jet_direction = 0.0 # http://odahub.io/ontology#AngleDegrees
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33 psf = 180.0 # http://odahub.io/ontology#AngleDegrees
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34 window_size_RA = 4.0 # http://odahub.io/ontology#AngleDegrees
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35 window_size_DEC = 4.0 # http://odahub.io/ontology#AngleDegrees
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36 EBL = "Franceschini 2017" # http://odahub.io/ontology#String ; oda:allowed_value "Franceschini 2017","Stecker 2016 lower limit","Stecker 2016 upper limit","Inoue 2012 Baseline","Inoue 2012 lower limit","Inoue 2012 upper limit"
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37
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38 _galaxy_wd = os.getcwd()
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39
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40 with open("inputs.json", "r") as fd:
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41 inp_dic = json.load(fd)
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42 if "C_data_product_" in inp_dic.keys():
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43 inp_pdic = inp_dic["C_data_product_"]
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44 else:
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45 inp_pdic = inp_dic
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46 src_name = str(inp_pdic["src_name"])
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47 z_start = float(inp_pdic["z_start"])
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48 Npart = int(inp_pdic["Npart"])
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49 particle_type = str(inp_pdic["particle_type"])
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50 Emax = float(inp_pdic["Emax"])
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51 Emin = float(inp_pdic["Emin"])
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52 EminSource = float(inp_pdic["EminSource"])
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53 Gamma = float(inp_pdic["Gamma"])
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54 EGMF_fG = float(inp_pdic["EGMF_fG"])
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55 lmaxEGMF_Mpc = float(inp_pdic["lmaxEGMF_Mpc"])
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56 jet_half_size = float(inp_pdic["jet_half_size"])
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57 jet_direction = float(inp_pdic["jet_direction"])
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58 psf = float(inp_pdic["psf"])
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59 window_size_RA = float(inp_pdic["window_size_RA"])
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60 window_size_DEC = float(inp_pdic["window_size_DEC"])
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61 EBL = str(inp_pdic["EBL"])
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62
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63 import os
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64
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65 from astropy.coordinates import SkyCoord
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66 from astropy.table import Table
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67 from oda_api.api import ProgressReporter
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68 from oda_api.data_products import ODAAstropyTable
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69 from utils import find_redshift
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70
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71 if z_start <= 0:
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72 z_start = find_redshift(src_name)
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73
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74 source = SkyCoord.from_name(src_name, frame="icrs", parse=False, cache=True)
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75
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76 pr = ProgressReporter()
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77 pr.report_progress(
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78 stage="Initialization",
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79 progress=0,
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80 substage="spectra",
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81 subprogress=30,
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82 message="some message",
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83 )
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84
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85 import light_curve as lc
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86 import numpy as np
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87 from crbeam import CRbeam
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88
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89 EGMF = EGMF_fG * 1e-15
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90
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91 # internal units are eV
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92 Emax *= 1e12
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93 Emin *= 1e12
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94 EminSource *= 1e12
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95
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96 background = {
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97 "Franceschini 2017": 12,
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98 "Stecker 2016 lower limit": 10,
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99 "Stecker 2016 upper limit": 11,
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100 "Inoue 2012 Baseline": 3,
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101 "Inoue 2012 lower limit": 4,
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102 "Inoue 2012 upper limit": 5,
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103 }[EBL]
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104
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105 prog = CRbeam(
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106 z=z_start,
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107 nparticles=Npart,
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108 primary=particle_type,
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109 emax=Emax,
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110 emin=Emin,
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111 emin_source=EminSource,
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112 EGMF=EGMF,
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113 lmaxEGMF=lmaxEGMF_Mpc,
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114 background=background,
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115 )
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116 cmd = prog.command
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117 cmd
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118
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119 # Here is one way to call CRbeam without global cache
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120 # prog.run(force_overwrite=False)
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121 # Here we call CRbeam with global cache
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122 # prog.run_cached(overwrite_local_cache=True)
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123 # to clear s3 cache run the following command
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124 # prog.remove_cache()
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125
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126 # To report the progress we will split running CRbeam into 10 parts
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127 n_steps = 10
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128 # Initialize multistep simulation
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129 data_exists = not prog.start_multistage_run(
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130 overwrite_local_cache=True, n_steps=n_steps
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131 )
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132 proceed = not data_exists
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133
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134 if proceed:
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135 for step in range(n_steps):
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136 pr.report_progress(
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137 stage="Running Simulation", progress=100 * step // n_steps
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138 )
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139 proceed = prog.simulation_step()
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140 # todo: report progress using rest API
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141 pr.report_progress(stage="Running Simulation", progress=100)
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142
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143 assert not proceed, "must be completed before this cell"
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144 if not data_exists:
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145 prog.end_multistep_run()
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146
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147 def adjust_weights(mc_file, power):
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148 # converting weights to mimic required injection spectrum power
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149 header = ""
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150 with open(mc_file, "rt") as lines:
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151 for line in lines:
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152 if len(line) > 0 and line[0] == "#":
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153 header += line[1:].strip() + "\n"
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154 else:
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155 break
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156 weight_col = 2
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157 E_src_col = 12
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158 data = np.loadtxt(mc_file)
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159 weight = data[:, weight_col - 1]
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160 E_src = data[:, E_src_col - 1]
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161 orig_power = (
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162 prog.power_law
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163 ) # CRBeam is always called with fixed power=1 to optimize cache usage
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164 weight *= np.power(E_src / Emax, -(power - orig_power))
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165 output_file = f"{mc_file}_p{power}"
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166 np.savetxt(output_file, data, header=header.strip(), fmt="%.6g")
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167 return output_file
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168
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169 # this code will not execute program since files already exist on server
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170 # prog.run(force_overwrite=False)
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171
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172 # one can upload cache explicitely by call
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173 # prog.upload_cache()
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174
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175 pr.report_progress(stage="Building Plots and Tables", progress=0)
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176
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177 print(prog.output_path)
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178 get_ipython().system("ls {prog.output_path}") # noqa: F821
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179
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180 mc_file = prog.output_path + "/photon"
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181
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182 if Emax != EminSource:
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183 mc_file = adjust_weights(mc_file, Gamma)
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184
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185 # rotating the beam
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186
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187 if EGMF > 0:
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188 from mc_rotate import mc_rotate
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189
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190 mc_rotated_file = mc_rotate(
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191 mc_file, jet_half_size, jet_direction, psf_deg=psf
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192 )
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193 else:
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194 mc_rotated_file = mc_file
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195 mc_rotated_file
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196
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197 # reading the source distance in Mpc from the data file
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198 T_Mpc = lc.get_distance_Mpc(mc_file)
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199 T_Mpc
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200
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201 from oda_api.data_products import ODAAstropyTable
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202
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203 d = np.genfromtxt(mc_rotated_file, skip_header=3)
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204 # E/eV,weight,Theta,Phi,dT_raw/T dT_calc/T,z_cascade_production,N_interactions,z_src,E_src/eV,z_prod
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205 names = (
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206 "E/eV",
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207 "weight",
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208 "Theta",
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209 "Phi",
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210 "dT_raw/T",
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211 "dT_calc/T",
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212 "z_cascade_production",
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213 "N_interactions",
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214 "z_src",
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215 "E_src/eV",
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216 "z_prod",
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217 )
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218 res = ODAAstropyTable(Table(d, names=names))
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219
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220 pr.report_progress(stage="Building Plots and Tables", progress=100)
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221
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222 Event_file = res # http://odahub.io/ontology#ODAAstropyTable
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223
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224 # output gathering
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225 _galaxy_meta_data = {}
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226 _oda_outs = []
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227 _oda_outs.append(
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228 ("out_Generate_events_Event_file", "Event_file_galaxy.output", Event_file)
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229 )
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230
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231 for _outn, _outfn, _outv in _oda_outs:
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232 _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
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233 if isinstance(_outv, str) and os.path.isfile(_outv):
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234 shutil.move(_outv, _galaxy_outfile_name)
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235 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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236 elif getattr(_outv, "write_fits_file", None):
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237 _outv.write_fits_file(_galaxy_outfile_name)
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238 _galaxy_meta_data[_outn] = {"ext": "fits"}
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239 elif getattr(_outv, "write_file", None):
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240 _outv.write_file(_galaxy_outfile_name)
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241 _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
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242 else:
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243 with open(_galaxy_outfile_name, "w") as fd:
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244 json.dump(_outv, fd, cls=CustomJSONEncoder)
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245 _galaxy_meta_data[_outn] = {"ext": "json"}
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246
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247 with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
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248 json.dump(_galaxy_meta_data, fd)
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249 print("*** Job finished successfully ***")