view Spectrum.py @ 0:02e4bb4fa10c draft

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
parents
children 593c4b45eda5
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#!/usr/bin/env python
# coding: utf-8

# flake8: noqa

import json
import os
import shutil

import matplotlib.pyplot as plt
import numpy as np
from astropy.coordinates import SkyCoord
from astropy.io import fits
from astropy.time import Time
from numpy import log10, sqrt
from oda_api.data_products import ODAAstropyTable, PictureProduct
from oda_api.json import CustomJSONEncoder

if os.path.exists("hess_dl3_dr1.tar.gz") == False:
    get_ipython().system(   # noqa: F821
        "wget https://zenodo.org/record/1421099/files/hess_dl3_dr1.tar.gz"
    )
    get_ipython().system("tar -zxvf hess_dl3_dr1.tar.gz")   # noqa: F821

# src_name='Crab' #http://odahub.io/ontology#AstrophysicalObject
# RA = 83.628700  # http://odahub.io/ontology#PointOfInterestRA
# DEC = 22.014700 # http://odahub.io/ontology#PointOfInterestDEC
src_name = "PKS 2155-304"
RA = 329.716938  # http://odahub.io/ontology#PointOfInterestRA
DEC = -30.225588  # http://odahub.io/ontology#PointOfInterestDEC

T1 = "2000-10-09T13:16:00.0"  # http://odahub.io/ontology#StartTime
T2 = "2022-10-10T13:16:00.0"  # http://odahub.io/ontology#EndTime
Radius = 2.5  # http://odahub.io/ontology#AngleDegrees
R_s = 0.2  # http://odahub.io/ontology#AngleDegrees

Emin = 100.0  # http://odahub.io/ontology#Energy_GeV
Emax = 10000.0  # http://odahub.io/ontology#Energy_GeV
NEbins = 20  # http://odahub.io/ontology#Integer

_galaxy_wd = os.getcwd()

with open("inputs.json", "r") as fd:
    inp_dic = json.load(fd)
if "_data_product" in inp_dic.keys():
    inp_pdic = inp_dic["_data_product"]
else:
    inp_pdic = inp_dic

for vn, vv in inp_pdic.items():
    if vn != "_selector":
        globals()[vn] = type(globals()[vn])(vv)

Emin = Emin / 1e3
Emax = Emax / 1e3
Ebins = np.logspace(log10(Emin), log10(Emax), NEbins + 1)
Ebins
Emin = Ebins[:-1]
Emax = Ebins[1:]
Emean = sqrt(Emin * Emax)
lgEmean = log10(Emean)

T1 = Time(T1, format="isot", scale="utc").mjd
T2 = Time(T2, format="isot", scale="utc").mjd
message = ""
RA_pnts = []
DEC_pnts = []
DL3_files = []
OBSIDs = []
Tstart = []
Tstop = []
flist = os.listdir("data")
for f in flist:
    if f[-7:] == "fits.gz":
        DL3_files.append(f)
        OBSIDs.append(int(f[20:26]))
        hdul = fits.open("data/" + f)
        RA_pnts.append(float(hdul[1].header["RA_PNT"]))
        DEC_pnts.append(float(hdul[1].header["DEC_PNT"]))
        Tstart.append(
            Time(
                hdul[1].header["DATE-OBS"] + "T" + hdul[1].header["TIME-OBS"],
                format="isot",
                scale="utc",
            ).mjd
        )
        Tstop.append(
            Time(
                hdul[1].header["DATE-END"] + "T" + hdul[1].header["TIME-END"],
                format="isot",
                scale="utc",
            ).mjd
        )
        hdul.close()

Coords_s = SkyCoord(RA, DEC, unit="degree")
COORDS_pnts = SkyCoord(RA_pnts, DEC_pnts, unit="degree")
seps = COORDS_pnts.separation(Coords_s).deg

mask = np.where((seps < Radius) & (Tstart > T1) & (Tstop < T2))[0]
OBSlist = []
for i in mask:
    OBSlist.append(DL3_files[i])
if len(OBSlist) == 0:
    message = "No data found"
    raise RuntimeError("No data found")
message

cts_s = np.zeros(NEbins)
cts_b = np.zeros(NEbins)
Expos = np.zeros(NEbins)
for f in OBSlist:
    hdul = fits.open("data/" + f)
    RA_pnt = hdul[1].header["RA_PNT"]
    DEC_pnt = hdul[1].header["DEC_PNT"]
    Texp = hdul[1].header["LIVETIME"]
    dRA = RA - RA_pnt
    dDEC = DEC - DEC_pnt
    RA_b = RA_pnt - dRA
    DEC_b = DEC_pnt - dDEC
    Coords_b = SkyCoord(RA_b, DEC_b, unit="degree")
    Coords_pnt = SkyCoord(RA_pnt, DEC_pnt, unit="degree")
    dist = Coords_pnt.separation(Coords_s).deg

    ev = hdul["EVENTS"].data
    ev_ra = ev["RA"]
    ev_dec = ev["DEC"]
    ev_en = ev["ENERGY"]
    ev_time = ev["TIME"]
    ev_coords = SkyCoord(ev_ra, ev_dec, unit="degree")
    sep_s = ev_coords.separation(Coords_s).deg
    sep_b = ev_coords.separation(Coords_b).deg

    hdu = hdul["AEFF"].data
    EEmin = hdu["ENERG_LO"][0]
    EEmax = hdu["ENERG_HI"][0]
    lgEE = log10(sqrt(EEmin * EEmax))
    lgAA = log10(hdu["EFFAREA"][0] + 1e-10)
    Thmin = hdu["THETA_LO"][0]
    Thmax = hdu["THETA_HI"][0]
    ind = np.argmin((Thmin - dist) ** 2)
    Expos += 10 ** (np.interp(lgEmean, lgEE, lgAA[ind])) * Texp
    mask = sep_s < R_s
    cts_s += np.histogram(ev_en[mask], bins=Ebins)[0]
    mask = sep_b < R_s
    cts_b += np.histogram(ev_en[mask], bins=Ebins)[0]
    hdul.close()

flux = (cts_s - cts_b) / (Emax - Emin) * Emax * Emin / (Expos * 1e4)
flux_err = sqrt(cts_s + cts_b) / (Emax - Emin) * Emax * Emin / (Expos * 1e4)
plt.errorbar(Emean, flux, yerr=flux_err, xerr=[Emean - Emin, Emax - Emean])
plt.xscale("log")
plt.yscale("log")
plt.xlabel("$E$, TeV")
plt.ylabel("$E^2 dN/dE$, erg/(cm$^2$s)")
plt.savefig("Spectrum.png", format="png")

bin_image = PictureProduct.from_file("Spectrum.png")
from astropy.table import Table

data = [Emean, Emin, Emax, flux, flux_err, cts_s, cts_b, Expos * 1e4]
names = (
    "Emean[TeV]",
    "Emin[TeV]",
    "Emax[TeV]",
    "Flux[TeV/cm2s]",
    "Flux_error[TeV/cm2s]",
    "Cts_s",
    "Cts_b",
    "Exposure[cm2s]",
)
spec = ODAAstropyTable(Table(data, names=names))

picture_png = bin_image  # http://odahub.io/ontology#ODAPictureProduct
spectrum_astropy_table = spec  # http://odahub.io/ontology#ODAAstropyTable

# output gathering
_galaxy_meta_data = {}
_oda_outs = []
_oda_outs.append(
    ("out_Spectrum_picture_png", "picture_png_galaxy.output", picture_png)
)
_oda_outs.append(
    (
        "out_Spectrum_spectrum_astropy_table",
        "spectrum_astropy_table_galaxy.output",
        spectrum_astropy_table,
    )
)

for _outn, _outfn, _outv in _oda_outs:
    _galaxy_outfile_name = os.path.join(_galaxy_wd, _outfn)
    if isinstance(_outv, str) and os.path.isfile(_outv):
        shutil.move(_outv, _galaxy_outfile_name)
        _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
    elif getattr(_outv, "write_fits_file", None):
        _outv.write_fits_file(_galaxy_outfile_name)
        _galaxy_meta_data[_outn] = {"ext": "fits"}
    elif getattr(_outv, "write_file", None):
        _outv.write_file(_galaxy_outfile_name)
        _galaxy_meta_data[_outn] = {"ext": "_sniff_"}
    else:
        with open(_galaxy_outfile_name, "w") as fd:
            json.dump(_outv, fd, cls=CustomJSONEncoder)
        _galaxy_meta_data[_outn] = {"ext": "json"}

with open(os.path.join(_galaxy_wd, "galaxy.json"), "w") as fd:
    json.dump(_galaxy_meta_data, fd)
print("*** Job finished successfully ***")