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This commit is contained in:
Roman Krivonos
2025-04-22 19:33:01 +03:00
parent 2ccfff694b
commit a665b052ec
4 changed files with 487 additions and 3584 deletions
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108
arches/arches/config.py
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@@ -1,109 +1,3 @@
from pathlib import Path
work_dir = Path('/path/to/some/logical/parent/dir')
"""
Координаты сентрального кадра, к которому будут
приводиться изображения всех списков событий
"""
ra_cen=34.5342131
de_cen=-4.7956710
"""
Словарь камер со списком наблюдений каждой камеры.
Номера камер должны быть отсортированы
"""
keylist_tm={'1':['tm1_obs_1',],
'5':['tm5_obs_1','tm5_obs_2',],
'6':['tm6_obs_1','tm6_obs_2_badpix','tm6_obs_3_badpix',
'tm6_park_1','tm6_park_2','tm6_park_3','tm6_park_4',
'tm6_scan_1','tm6_scan_2','tm6_scan_3','tm6_scan_4'],
'7':['tm7_obs_1','tm7_obs_2',]}
"""
Примерные центры изображений каждого наблюдения.
Требуется для астрокоррекции. Будет расчитываться матрица сдвигов и поворотов,
так вот, повороты будут проводиться вокруг данных координат.
"""
wcslist={'tm1_obs_1':[34.7279760,-5.0680267],
'tm5_obs_1':[34.7351248,-4.4407314],
'tm5_obs_2':[34.8748997,-4.4871658],
'tm7_obs_1':[35.0015120,-4.7602124],
'tm7_obs_2':[34.9810029,-4.5915912],
'tm6_obs_1':[34.4227062,-4.7207170],
'tm6_obs_2_badpix':[34.7272339,-4.4294153],
'tm6_obs_3_badpix':[34.8750291,-4.4708468],
'tm6_park_1':[35.0544951,-4.0613619],
'tm6_park_2':[35.0558675,-4.0683084],
'tm6_park_3':[35.0565263,-4.0583538],
'tm6_park_4':[35.0602986,-4.0622220],
'tm6_scan_1':[34.5405596,-4.8088748],
'tm6_scan_2':[34.5405596,-4.8088748],
'tm6_scan_3':[34.5405596,-4.8088748],
'tm6_scan_4':[34.5405596,-4.8088748]}
""" like in the paper (Table 1) """
obslist={'tm1_obs_1':'N01',
'tm5_obs_1':'N02',
'tm5_obs_2':'N03',
'tm7_obs_1':'N15',
'tm7_obs_2':'N16',
'tm6_obs_1':'N12',
'tm6_obs_2_badpix':'N13',
'tm6_obs_3_badpix':'N14',
'tm6_park_1':'N04',
'tm6_park_2':'N06',
'tm6_park_3':'N08',
'tm6_park_4':'N10',
'tm6_scan_1':'N05',
'tm6_scan_2':'N07',
'tm6_scan_3':'N09',
'tm6_scan_4':'N11'}
""" Это просто индекс диапазона для выходных файлов. """
eband=[ "0", "1", "2", "3", "4", "5", "6", "7", "8"]
""" Диапазоны энергий. """
emin_ev=[ 300, 300, 600, 2300, 200, 300, 5000, 500, 1000]
emax_ev=[2300, 600, 2300, 5000, 10000,8000, 8000, 1000, 2000]
emin_kev=[0.3, 0.3, 0.6, 2.3, 0.2, 0.3, 5.0, 0.5, 1.0]
emax_kev=[2.3, 0.6, 2.3, 5.0, 10.0, 8.0, 8.0, 1.0, 2.0]
#ecf = [ 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]
# something is wrong here
#ecf = [9.7817E+11, 3.2982E+12, 1.3903E+12, 2.3322E+12, 5.2022E+11, 5.8453E+11, 3.8468E+12]
"""
*** en0 ecf 9.7817E+11 +/- 2.4606E+10 2.52% N=17
*** en1 ecf 3.2982E+12 +/- 8.2963E+10 2.52% N=17
*** en2 ecf 1.3903E+12 +/- 3.5036E+10 2.52% N=17
*** en3 ecf 2.3322E+12 +/- 5.8717E+10 2.52% N=17
*** en4 ecf 5.2022E+11 +/- 1.3110E+10 2.52% N=17
*** en5 ecf 5.8453E+11 +/- 1.4743E+10 2.52% N=17
"""
# finally use Pavel's file ../data/ECF/ecf_tbabspow_g2nh0.02.pkl
"""
for e in [(0.3, 2.3), (0.3, 0.6), (0.6, 2.3), (2.3, 5.0), (5.0, 8.0)]:
print(f'{ecf[e]:g}')
"""
ecf = [1.0911e+12, # (0.3, 2.3)
1.07252e+12, # (0.3, 0.6)
1.08963e+12, # (0.6, 2.3)
1.14674e+11, # (2.3, 5.0)
1.0,
1.0,
2.77581e+10, # (5.0, 8.0)
1354632916123.6191, # (0.5, 1.0) 4XMM-DR12 EP2 band
1014764099304.4968] # (1.0, 2.0) 4XMM-DR12 EP3 band
outfile_post='.fits'
"""
Pavel Medvedev:
0.3-2.3: 9.135819435325375e-13
0.3-0.6: 9.160477830652834e-13
0.6-2.3: 9.201664167869427e-13
2.3-5.0: 8.721504826794627e-12
"""
good_pn=['0862470801','0862470601']

3495
arches/arches/utils.py
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73
scripts/01_init_events.py
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@@ -2,37 +2,74 @@
from pysas.wrapper import Wrapper as w
import os, sys
from os.path import dirname
import inspect
import glob
import arches
from arches.utils import *
from arches.config import *
root_path=dirname(dirname(dirname(inspect.getfile(arches))))
print("Arches root path: {}".format(root_path))
sys.exit()
archive_dir=root_path+'/data/archive'
events_dir=root_path+'/data/processed'
products_dir=root_path+'/products'
root='/data/xmm'
create_folder(events_dir)
inargs = ['--version']
t = w('sasver', inargs)
t.run()
obsid='0862470501'
local_ccf=f'{root}/work/{obsid}/ccf.cif'
work_dir=f'{root}/work/{obsid}'
files = glob.glob(archive_dir+'/0862*')
os.environ['SAS_ODF'] = f'{root}/arc/{obsid}/odf/'
if not os.path.exists(work_dir):
os.makedirs(work_dir)
os.chdir(work_dir)
if not os.path.exists(local_ccf):
w('cifbuild', []).run()
else:
print("Skip cifbuild, SAS_CCF = {}".format(local_ccf))
for obsid in files:
obsid = os.path.basename(obsid)
os.environ['SAS_CCF'] = local_ccf
local_ccf=f'{events_dir}/{obsid}/ccf.cif'
work_dir=f'{events_dir}/{obsid}'
print(os.environ['SAS_CCF'])
#inargs = [f'odfid={obsid}',f'workdir={work_dir}']
#w('startsas', inargs).run()
os.environ['SAS_ODF'] = f'{archive_dir}/{obsid}/odf'
create_folder(work_dir)
os.chdir(work_dir)
if not os.path.exists(local_ccf):
w('cifbuild', []).run()
else:
print("*** Skip cifbuild, SAS_CCF = {}".format(local_ccf))
os.environ['SAS_CCF'] = local_ccf
print("Set SAS_CCF = {}".format(os.environ['SAS_CCF']))
w('sasver', []).run() # print info
sasfiles = glob.glob(work_dir+'/*SUM.SAS')
if(sasfiles):
print("*** Skip odfingest ***")
else:
w('odfingest', []).run()
sasfiles = glob.glob(work_dir+'/*SUM.SAS') # search files again
os.environ['SAS_ODF'] = sasfiles[0]
w('sasver', []).run() # print info
print(f'{work_dir}/????_{obsid}_EPN_S???_ImagingEvts.ds')
epfiles = glob.glob(f'{work_dir}/????_{obsid}_EPN_S???_ImagingEvts.ds')
if not (epfiles):
print('Running epproc')
w('epproc', []).run()
emfiles = glob.glob(f'{work_dir}/????_{obsid}_EMOS?_S???_ImagingEvts.ds')
if not (emfiles):
print('Running emproc')
w('emproc', []).run()

395
scripts/02_filter_flares.py Executable file
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#!/usr/bin/env python
from pysas.wrapper import Wrapper as w
import os, sys
from os.path import dirname
import inspect
import glob
import os.path
from os import path
import subprocess
import numpy as np
import matplotlib.pyplot as plt
from astropy.io import fits
from astropy.table import Table
from matplotlib.colors import LogNorm
import pyds9
import arches
from arches.utils import *
from arches.config import *
root_path=dirname(dirname(dirname(inspect.getfile(arches))))
print("Arches root path: {}".format(root_path))
archive_dir=root_path+'/data/archive'
events_dir=root_path+'/data/processed'
products_dir=root_path+'/products'
create_folder(products_dir)
inargs = ['--version']
t = w('sasver', inargs)
t.run()
files = glob.glob(archive_dir+'/0862*')
for obsid in files:
obsid = os.path.basename(obsid)
print(f'*** ObsID: {obsid} ***')
local_ccf=f'{events_dir}/{obsid}/ccf.cif'
work_dir=f'{products_dir}/{obsid}'
create_folder(work_dir)
os.chdir(work_dir)
if not os.path.exists(local_ccf):
print("*** Not found SAS_CCF = {}".format(local_ccf))
sys.exit()
sasfiles = glob.glob(events_dir+f'/{obsid}/*SUM.SAS')
if not (sasfiles):
print("*** run 01_init_events.py ***")
sys.exit()
os.environ['SAS_ODF'] = sasfiles[0]
os.environ['SAS_CCF'] = local_ccf
w('sasver', []).run() # print info
inargs = [f'workdir={work_dir}']
w('startsas', inargs).run()
search_str = f'{events_dir}/{obsid}/????_{obsid}_EPN_S???_ImagingEvts.ds'
print(search_str)
epfiles = glob.glob(search_str)
if not (epfiles):
print("*** run 01_init_events.py ***")
#w('epproc', []).run()
eventfile = epfiles[0]
print("Checking for EPIC-pn Event Files ..... \n")
# Check if epproc has already run.
if os.path.isfile(eventfile):
print ("File "+eventfile+" exists. \n")
else:
print ("File "+eventfile+" does not exist, please check. \n")
#############################################################
# For display purposes only define the following event cuts #
#############################################################
pn_pattern = 4 # pattern selection
pn_pi_min = 300. # Low energy range eV
pn_pi_max = 12000. # High energy range eV
pn_flag = 0 # FLAG
plt.figure(figsize=(20,8))
pl=1
hdu_list = fits.open(eventfile, memmap=True)
evt_data = Table(hdu_list[1].data)
mask = ((evt_data['PATTERN'] <= pn_pattern) &
(evt_data['FLAG'] == pn_flag) &
(evt_data['PI'] >= pn_pi_min) &
(evt_data['PI'] <= pn_pi_max))
print("Events in event file" + " " + eventfile + ": " + str(len(evt_data)) + "\n")
print("Events in filtered event file" + " " + eventfile + ": " + str(np.sum(mask)) + "\n")
print(" Filter: PATTERN <= " + str(pn_pattern) +
" : " + str(pn_pi_min) + " <= E(eV) <= " + str(pn_pi_max) +
" : " + " FLAG == " + str(pn_flag)+ "\n")
xmax=np.amax(evt_data['X'])
xmin=np.amin(evt_data['X'])
xmid=(xmax-xmin)/2.+xmin
ymax=np.amax(evt_data['Y'])
ymin=np.amin(evt_data['Y'])
xbin_size=80
ybin_size=80
NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
plt.subplot(1, 2, pl)
img_zero_mpl = plt.hist2d(evt_data['X'], evt_data['Y'], NBINS, cmap='GnBu', norm=LogNorm())
cbar = plt.colorbar(ticks=[10.,100.,1000.])
cbar.ax.set_yticklabels(['10','100','1000'])
plt.title(obsid)
plt.xlabel('x')
plt.ylabel('y')
pl=pl+1
# Create Filtered Events image
xmax=np.amax(evt_data['X'][mask])
xmin=np.amin(evt_data['X'][mask])
xmid=(xmax-xmin)/2.+xmin
ymax=np.amax(evt_data['Y'][mask])
ymin=np.amin(evt_data['Y'][mask])
xbin_size=80
ybin_size=80
NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
plt.subplot(1, 2, pl)
img_zero_mpl = plt.hist2d(evt_data['X'][mask], evt_data['Y'][mask], NBINS, cmap='GnBu', norm=LogNorm())
cbar = plt.colorbar(ticks=[10.,100.,1000.])
cbar.ax.set_yticklabels(['10','100','1000'])
plt.title(obsid)
plt.xlabel('x')
plt.ylabel('y')
txt=("PATTERN <= " + str(pn_pattern) +
" : " + str(pn_pi_min) + " <= E(eV) <= " + str(pn_pi_max) +
" : " + " FLAG == " + str(pn_flag))
plt.text(xmid, ymin+0.1*(ymax-ymin), txt, ha='center')
pl=pl+1
hdu_list.close()
plt.show()
##################################################################
# Define a SAS filter expression to derive a background rate cut #
##################################################################
pn_pattern = 0 # pattern selection
pn_pi_min = 10000. # Low energy range eV
pn_pi_max = 12000. # High energy range eV
pn_threshold = 0.75 # cts/sec (only used here for display purposes)
out_LCFile = work_dir+'/EPIC_pn_FlareBKGRate.fit' # Name of the output BKG lightcurve
# SAS Command
cmd = "evselect" # SAS task to be executed
# Arguments of SAS Command
expression = f'#XMMEA_EP&&(PI>={pn_pi_min}&&PI<={pn_pi_max})&&(PATTERN=={pn_pattern})' # event filter expression
inargs = [f'table={eventfile}','withrateset=Y',f'rateset={out_LCFile}','maketimecolumn=Y','timebinsize=100','makeratecolumn=Y',f'expression={expression}']
print(" Filter expression to use: "+expression+" \n")
print(" SAS command to be executed: "+cmd+", with arguments; \n")
# Execute SAS task with parameters
w(cmd, inargs).run()
# Open event file
hdu_list = fits.open(eventfile, memmap=True)
evt_data = Table(hdu_list[1].data)
prihdu = hdu_list[1].header
mask = ((evt_data['PATTERN'] <= pn_pattern) &
(evt_data['FLAG'] == pn_flag) &
(evt_data['PI'] >= pn_pi_min) &
(evt_data['PI'] <= pn_pi_max))
# Read some information from keywords to be used later on
if ('INSTRUME' in prihdu):
ins = prihdu['INSTRUME']
print("Looking into instrument: "+ins+" \n")
if ('EXPIDSTR' in prihdu):
expid = prihdu['EXPIDSTR']
print("Looking at exposure: "+expid+" \n")
# Check number of event in initial event file
print("Events in event file" + " " + eventfile + ": " + str(len(evt_data)) + "\n")
print("Events in filtered event file" + " " + eventfile + ": " + str(np.sum(mask)) + "\n")
print(" Filter: PATTERN <= " + str(pn_pattern) +
" : " + str(pn_pi_min) + " <= E(eV) <= " + str(pn_pi_max) +
" : " + " FLAG == " + str(pn_flag)+ "\n")
# Create events image and background lightcurve
plt.figure(figsize=(20,8))
pl=1
xmax=np.amax(evt_data['X'][mask])
xmin=np.amin(evt_data['X'][mask])
xmid=(xmax-xmin)/2.+xmin
ymax=np.amax(evt_data['Y'][mask])
ymin=np.amin(evt_data['Y'][mask])
xbin_size=80
ybin_size=80
NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
# Plot image
plt.subplot(1, 2, pl)
img_zero_mpl = plt.hist2d(evt_data['X'][mask], evt_data['Y'][mask], NBINS, cmap='GnBu', norm=LogNorm())
cbar = plt.colorbar(ticks=[10.,100.,1000.])
cbar.ax.set_yticklabels(['10','100','1000'])
plt.title(obsid)
plt.xlabel('x')
plt.ylabel('y')
plt.text(xmid, ymin+0.1*(ymax-ymin), expression, ha='center')
pl=pl+1
plt.subplot(1, 2, pl)
# Plot BKG lightcurve
plotLC(plt,pn_threshold,out_LCFile)
pl=pl+1
plt.show()
hdu_list.close()
############################################
# Define energy range to filter event file #
############################################
pn_pattern = 4 # pattern selection
pn_pi_min = 200. # Low energy range eV
pn_pi_max = 10000. # High energy range eV
pn_threshold = 0.75 # Cut to be applied to filter event file (cts/sec)
# Define the input and output file names
in_LCFile = work_dir+'/EPIC_pn_FlareBKGRate.fit' # Name of the input BKG lightcurve
out_gti_set = work_dir+'/EPIC_pn_gti.fit' # Name of the output file containing GTI intervals
out_clean_evtFile = work_dir+'/EPIC_pn_gtiFilteredEvts.ds' # Name of the output Event file filtered by GTI
# SAS Command
cmd = "tabgtigen"
# Arguments of SAS Command
expression = 'RATE<='+str(pn_threshold) # event filter expression
inargs = [f'table={in_LCFile}',f'gtiset={out_gti_set}',f'expression={expression}']
print(" Filter expression to use: "+expression+" \n")
print(" SAS command to be executed: "+cmd+", with arguments; \n")
# Execute SAS task with parameters
w(cmd, inargs).run()
# SAS Command
cmd = "evselect"
# Arguments of SAS Command
expression = ('#XMMEA_EP&&FLAG==0&&(PI>='+str(pn_pi_min)+'&&PI<='+str(pn_pi_max)+
')&&(gti('+str(out_gti_set)+',TIME))')
inargs = [f'table={eventfile}','withfilteredset=Y',f'filteredset={out_clean_evtFile}',
'destruct=Y','keepfilteroutput=T',f'expression={expression}']
print(" Filter expression to use: "+expression+" \n")
print(" SAS command to be executed: "+cmd+", with arguments; \n")
# Execute SAS task with parameters
w(cmd, inargs).run()
plt.figure(figsize=(20,8))
pl=1
hdu_list = fits.open(eventfile, memmap=True)
evt_data = Table(hdu_list[1].data)
prihdu = hdu_list[1].header
print("Events in event file" + " " + eventfile + ": " + str(len(evt_data)) + "\n")
gti_hdu_list = fits.open(out_clean_evtFile, memmap=True)
gti_evt_data = Table(gti_hdu_list[1].data)
print("Events in GTI clean event file" + " " + out_clean_evtFile + ": " + str(len(gti_evt_data)) + "\n")
# Create Events image
xmax=np.amax(evt_data['X'])
xmin=np.amin(evt_data['X'])
xmid=(xmax-xmin)/2.+xmin
ymax=np.amax(evt_data['Y'])
ymin=np.amin(evt_data['Y'])
xbin_size=80
ybin_size=80
NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
plt.subplot(1, 2, pl)
img_zero_mpl = plt.hist2d(evt_data['X'], evt_data['Y'], NBINS, cmap='GnBu', norm=LogNorm())
cbar = plt.colorbar(ticks=[10.,100.,1000.])
cbar.ax.set_yticklabels(['10','100','1000'])
plt.title(eventfile)
plt.xlabel('x')
plt.ylabel('y')
pl=pl+1
# Create Clean Events image
xmax=np.amax(gti_evt_data['X'])
xmin=np.amin(gti_evt_data['X'])
xmid=(xmax-xmin)/2.+xmin
ymax=np.amax(gti_evt_data['Y'])
ymin=np.amin(gti_evt_data['Y'])
xbin_size=80
ybin_size=80
NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
plt.subplot(1, 2, pl)
img_zero_mpl = plt.hist2d(gti_evt_data['X'], gti_evt_data['Y'], NBINS, cmap='GnBu', norm=LogNorm())
cbar = plt.colorbar(ticks=[10.,100.,1000.])
cbar.ax.set_yticklabels(['10','100','1000'])
plt.title(out_clean_evtFile)
plt.xlabel('x')
plt.ylabel('y')
plt.text(xmid, ymin-0.1*(ymax-ymin), expression, ha='center')
pl=pl+1
gti_hdu_list.close()
hdu_list.close()
plt.show()
###############################################################################
# Define some parameters to produce the image and the name of the output file #
###############################################################################
xbin=80 # xbin size
ybin=80 # ybin size
xcoord='X' # coordinate system
ycoord='Y' # coordinate system
out_IMFile = work_dir+'/EPIC_PN_Image.fit' # Name of the output Image file
# SAS Command
cmd = "evselect" # SAS task to be executed
# Arguments of SAS Command
inargs = [f'table={out_clean_evtFile}','imagebinning=binSize',f'imageset={out_IMFile}','withimageset=yes',f'xcolumn={xcoord}',f'ycolumn={ycoord}',f'ximagebinsize={xbin}',f'yimagebinsize={ybin}']
print(" SAS command to be executed: "+cmd+", with arguments; \n")
# Execute the SAS task with the parameters to produce an image
w(cmd, inargs).run()
# Visualize the image with ds9
d = pyds9.DS9()
d.set("file "+out_IMFile)
d.set('cmap bb')
d.set('scale log')
continue
emfiles = glob.glob(f'{work_dir}/????_{obsid}_EMOS?_S???_ImagingEvts.ds')
if not (emfiles):
print('Running emproc')
w('emproc', []).run()