generated from erosita/uds
maps
This commit is contained in:
@@ -2,37 +2,74 @@
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from pysas.wrapper import Wrapper as w
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import os, sys
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from os.path import dirname
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import inspect
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import glob
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import arches
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from arches.utils import *
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from arches.config import *
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root_path=dirname(dirname(dirname(inspect.getfile(arches))))
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print("Arches root path: {}".format(root_path))
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sys.exit()
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archive_dir=root_path+'/data/archive'
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events_dir=root_path+'/data/processed'
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products_dir=root_path+'/products'
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root='/data/xmm'
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create_folder(events_dir)
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inargs = ['--version']
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t = w('sasver', inargs)
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t.run()
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obsid='0862470501'
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local_ccf=f'{root}/work/{obsid}/ccf.cif'
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work_dir=f'{root}/work/{obsid}'
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files = glob.glob(archive_dir+'/0862*')
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os.environ['SAS_ODF'] = f'{root}/arc/{obsid}/odf/'
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if not os.path.exists(work_dir):
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os.makedirs(work_dir)
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os.chdir(work_dir)
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if not os.path.exists(local_ccf):
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w('cifbuild', []).run()
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else:
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print("Skip cifbuild, SAS_CCF = {}".format(local_ccf))
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for obsid in files:
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obsid = os.path.basename(obsid)
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os.environ['SAS_CCF'] = local_ccf
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local_ccf=f'{events_dir}/{obsid}/ccf.cif'
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work_dir=f'{events_dir}/{obsid}'
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print(os.environ['SAS_CCF'])
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#inargs = [f'odfid={obsid}',f'workdir={work_dir}']
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#w('startsas', inargs).run()
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os.environ['SAS_ODF'] = f'{archive_dir}/{obsid}/odf'
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create_folder(work_dir)
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os.chdir(work_dir)
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if not os.path.exists(local_ccf):
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w('cifbuild', []).run()
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else:
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print("*** Skip cifbuild, SAS_CCF = {}".format(local_ccf))
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os.environ['SAS_CCF'] = local_ccf
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print("Set SAS_CCF = {}".format(os.environ['SAS_CCF']))
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w('sasver', []).run() # print info
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sasfiles = glob.glob(work_dir+'/*SUM.SAS')
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if(sasfiles):
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print("*** Skip odfingest ***")
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else:
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w('odfingest', []).run()
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sasfiles = glob.glob(work_dir+'/*SUM.SAS') # search files again
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os.environ['SAS_ODF'] = sasfiles[0]
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w('sasver', []).run() # print info
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print(f'{work_dir}/????_{obsid}_EPN_S???_ImagingEvts.ds')
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epfiles = glob.glob(f'{work_dir}/????_{obsid}_EPN_S???_ImagingEvts.ds')
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if not (epfiles):
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print('Running epproc')
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w('epproc', []).run()
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emfiles = glob.glob(f'{work_dir}/????_{obsid}_EMOS?_S???_ImagingEvts.ds')
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if not (emfiles):
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print('Running emproc')
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w('emproc', []).run()
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395
scripts/02_filter_flares.py
Executable file
395
scripts/02_filter_flares.py
Executable file
@@ -0,0 +1,395 @@
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#!/usr/bin/env python
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from pysas.wrapper import Wrapper as w
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import os, sys
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from os.path import dirname
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import inspect
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import glob
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import os.path
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from os import path
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import subprocess
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import numpy as np
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import matplotlib.pyplot as plt
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from astropy.io import fits
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from astropy.table import Table
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from matplotlib.colors import LogNorm
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import pyds9
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import arches
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from arches.utils import *
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from arches.config import *
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root_path=dirname(dirname(dirname(inspect.getfile(arches))))
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print("Arches root path: {}".format(root_path))
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archive_dir=root_path+'/data/archive'
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events_dir=root_path+'/data/processed'
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products_dir=root_path+'/products'
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create_folder(products_dir)
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inargs = ['--version']
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t = w('sasver', inargs)
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t.run()
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files = glob.glob(archive_dir+'/0862*')
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for obsid in files:
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obsid = os.path.basename(obsid)
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print(f'*** ObsID: {obsid} ***')
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local_ccf=f'{events_dir}/{obsid}/ccf.cif'
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work_dir=f'{products_dir}/{obsid}'
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create_folder(work_dir)
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os.chdir(work_dir)
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if not os.path.exists(local_ccf):
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print("*** Not found SAS_CCF = {}".format(local_ccf))
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sys.exit()
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sasfiles = glob.glob(events_dir+f'/{obsid}/*SUM.SAS')
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if not (sasfiles):
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print("*** run 01_init_events.py ***")
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sys.exit()
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os.environ['SAS_ODF'] = sasfiles[0]
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os.environ['SAS_CCF'] = local_ccf
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w('sasver', []).run() # print info
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inargs = [f'workdir={work_dir}']
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w('startsas', inargs).run()
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search_str = f'{events_dir}/{obsid}/????_{obsid}_EPN_S???_ImagingEvts.ds'
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print(search_str)
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epfiles = glob.glob(search_str)
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if not (epfiles):
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print("*** run 01_init_events.py ***")
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#w('epproc', []).run()
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eventfile = epfiles[0]
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print("Checking for EPIC-pn Event Files ..... \n")
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# Check if epproc has already run.
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if os.path.isfile(eventfile):
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print ("File "+eventfile+" exists. \n")
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else:
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print ("File "+eventfile+" does not exist, please check. \n")
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#############################################################
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# For display purposes only define the following event cuts #
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#############################################################
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pn_pattern = 4 # pattern selection
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pn_pi_min = 300. # Low energy range eV
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pn_pi_max = 12000. # High energy range eV
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pn_flag = 0 # FLAG
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plt.figure(figsize=(20,8))
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pl=1
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hdu_list = fits.open(eventfile, memmap=True)
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evt_data = Table(hdu_list[1].data)
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mask = ((evt_data['PATTERN'] <= pn_pattern) &
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(evt_data['FLAG'] == pn_flag) &
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(evt_data['PI'] >= pn_pi_min) &
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(evt_data['PI'] <= pn_pi_max))
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print("Events in event file" + " " + eventfile + ": " + str(len(evt_data)) + "\n")
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print("Events in filtered event file" + " " + eventfile + ": " + str(np.sum(mask)) + "\n")
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print(" Filter: PATTERN <= " + str(pn_pattern) +
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" : " + str(pn_pi_min) + " <= E(eV) <= " + str(pn_pi_max) +
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" : " + " FLAG == " + str(pn_flag)+ "\n")
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xmax=np.amax(evt_data['X'])
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xmin=np.amin(evt_data['X'])
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xmid=(xmax-xmin)/2.+xmin
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ymax=np.amax(evt_data['Y'])
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ymin=np.amin(evt_data['Y'])
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xbin_size=80
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ybin_size=80
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NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
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plt.subplot(1, 2, pl)
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img_zero_mpl = plt.hist2d(evt_data['X'], evt_data['Y'], NBINS, cmap='GnBu', norm=LogNorm())
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cbar = plt.colorbar(ticks=[10.,100.,1000.])
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cbar.ax.set_yticklabels(['10','100','1000'])
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plt.title(obsid)
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plt.xlabel('x')
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plt.ylabel('y')
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pl=pl+1
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# Create Filtered Events image
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xmax=np.amax(evt_data['X'][mask])
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xmin=np.amin(evt_data['X'][mask])
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xmid=(xmax-xmin)/2.+xmin
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ymax=np.amax(evt_data['Y'][mask])
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ymin=np.amin(evt_data['Y'][mask])
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xbin_size=80
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ybin_size=80
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NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
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plt.subplot(1, 2, pl)
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img_zero_mpl = plt.hist2d(evt_data['X'][mask], evt_data['Y'][mask], NBINS, cmap='GnBu', norm=LogNorm())
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cbar = plt.colorbar(ticks=[10.,100.,1000.])
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cbar.ax.set_yticklabels(['10','100','1000'])
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plt.title(obsid)
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plt.xlabel('x')
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plt.ylabel('y')
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txt=("PATTERN <= " + str(pn_pattern) +
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" : " + str(pn_pi_min) + " <= E(eV) <= " + str(pn_pi_max) +
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" : " + " FLAG == " + str(pn_flag))
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plt.text(xmid, ymin+0.1*(ymax-ymin), txt, ha='center')
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pl=pl+1
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hdu_list.close()
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plt.show()
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##################################################################
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# Define a SAS filter expression to derive a background rate cut #
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##################################################################
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pn_pattern = 0 # pattern selection
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pn_pi_min = 10000. # Low energy range eV
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pn_pi_max = 12000. # High energy range eV
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pn_threshold = 0.75 # cts/sec (only used here for display purposes)
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out_LCFile = work_dir+'/EPIC_pn_FlareBKGRate.fit' # Name of the output BKG lightcurve
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# SAS Command
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cmd = "evselect" # SAS task to be executed
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# Arguments of SAS Command
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expression = f'#XMMEA_EP&&(PI>={pn_pi_min}&&PI<={pn_pi_max})&&(PATTERN=={pn_pattern})' # event filter expression
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inargs = [f'table={eventfile}','withrateset=Y',f'rateset={out_LCFile}','maketimecolumn=Y','timebinsize=100','makeratecolumn=Y',f'expression={expression}']
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print(" Filter expression to use: "+expression+" \n")
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print(" SAS command to be executed: "+cmd+", with arguments; \n")
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# Execute SAS task with parameters
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w(cmd, inargs).run()
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# Open event file
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hdu_list = fits.open(eventfile, memmap=True)
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evt_data = Table(hdu_list[1].data)
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prihdu = hdu_list[1].header
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mask = ((evt_data['PATTERN'] <= pn_pattern) &
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(evt_data['FLAG'] == pn_flag) &
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(evt_data['PI'] >= pn_pi_min) &
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(evt_data['PI'] <= pn_pi_max))
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# Read some information from keywords to be used later on
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if ('INSTRUME' in prihdu):
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ins = prihdu['INSTRUME']
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print("Looking into instrument: "+ins+" \n")
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if ('EXPIDSTR' in prihdu):
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expid = prihdu['EXPIDSTR']
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print("Looking at exposure: "+expid+" \n")
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# Check number of event in initial event file
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print("Events in event file" + " " + eventfile + ": " + str(len(evt_data)) + "\n")
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print("Events in filtered event file" + " " + eventfile + ": " + str(np.sum(mask)) + "\n")
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print(" Filter: PATTERN <= " + str(pn_pattern) +
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" : " + str(pn_pi_min) + " <= E(eV) <= " + str(pn_pi_max) +
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" : " + " FLAG == " + str(pn_flag)+ "\n")
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# Create events image and background lightcurve
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plt.figure(figsize=(20,8))
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pl=1
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xmax=np.amax(evt_data['X'][mask])
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xmin=np.amin(evt_data['X'][mask])
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xmid=(xmax-xmin)/2.+xmin
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ymax=np.amax(evt_data['Y'][mask])
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ymin=np.amin(evt_data['Y'][mask])
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xbin_size=80
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ybin_size=80
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NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
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# Plot image
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plt.subplot(1, 2, pl)
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img_zero_mpl = plt.hist2d(evt_data['X'][mask], evt_data['Y'][mask], NBINS, cmap='GnBu', norm=LogNorm())
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cbar = plt.colorbar(ticks=[10.,100.,1000.])
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cbar.ax.set_yticklabels(['10','100','1000'])
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plt.title(obsid)
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plt.xlabel('x')
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plt.ylabel('y')
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plt.text(xmid, ymin+0.1*(ymax-ymin), expression, ha='center')
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pl=pl+1
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plt.subplot(1, 2, pl)
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# Plot BKG lightcurve
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plotLC(plt,pn_threshold,out_LCFile)
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pl=pl+1
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plt.show()
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hdu_list.close()
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############################################
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# Define energy range to filter event file #
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############################################
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pn_pattern = 4 # pattern selection
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pn_pi_min = 200. # Low energy range eV
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pn_pi_max = 10000. # High energy range eV
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pn_threshold = 0.75 # Cut to be applied to filter event file (cts/sec)
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# Define the input and output file names
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in_LCFile = work_dir+'/EPIC_pn_FlareBKGRate.fit' # Name of the input BKG lightcurve
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out_gti_set = work_dir+'/EPIC_pn_gti.fit' # Name of the output file containing GTI intervals
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out_clean_evtFile = work_dir+'/EPIC_pn_gtiFilteredEvts.ds' # Name of the output Event file filtered by GTI
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# SAS Command
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cmd = "tabgtigen"
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# Arguments of SAS Command
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expression = 'RATE<='+str(pn_threshold) # event filter expression
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inargs = [f'table={in_LCFile}',f'gtiset={out_gti_set}',f'expression={expression}']
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print(" Filter expression to use: "+expression+" \n")
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print(" SAS command to be executed: "+cmd+", with arguments; \n")
|
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# Execute SAS task with parameters
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w(cmd, inargs).run()
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# SAS Command
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cmd = "evselect"
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# Arguments of SAS Command
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expression = ('#XMMEA_EP&&FLAG==0&&(PI>='+str(pn_pi_min)+'&&PI<='+str(pn_pi_max)+
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')&&(gti('+str(out_gti_set)+',TIME))')
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inargs = [f'table={eventfile}','withfilteredset=Y',f'filteredset={out_clean_evtFile}',
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'destruct=Y','keepfilteroutput=T',f'expression={expression}']
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print(" Filter expression to use: "+expression+" \n")
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print(" SAS command to be executed: "+cmd+", with arguments; \n")
|
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# Execute SAS task with parameters
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w(cmd, inargs).run()
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plt.figure(figsize=(20,8))
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pl=1
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hdu_list = fits.open(eventfile, memmap=True)
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evt_data = Table(hdu_list[1].data)
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prihdu = hdu_list[1].header
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print("Events in event file" + " " + eventfile + ": " + str(len(evt_data)) + "\n")
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gti_hdu_list = fits.open(out_clean_evtFile, memmap=True)
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gti_evt_data = Table(gti_hdu_list[1].data)
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print("Events in GTI clean event file" + " " + out_clean_evtFile + ": " + str(len(gti_evt_data)) + "\n")
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# Create Events image
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xmax=np.amax(evt_data['X'])
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xmin=np.amin(evt_data['X'])
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xmid=(xmax-xmin)/2.+xmin
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ymax=np.amax(evt_data['Y'])
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ymin=np.amin(evt_data['Y'])
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xbin_size=80
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ybin_size=80
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NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
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plt.subplot(1, 2, pl)
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img_zero_mpl = plt.hist2d(evt_data['X'], evt_data['Y'], NBINS, cmap='GnBu', norm=LogNorm())
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cbar = plt.colorbar(ticks=[10.,100.,1000.])
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cbar.ax.set_yticklabels(['10','100','1000'])
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plt.title(eventfile)
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plt.xlabel('x')
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plt.ylabel('y')
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pl=pl+1
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# Create Clean Events image
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xmax=np.amax(gti_evt_data['X'])
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xmin=np.amin(gti_evt_data['X'])
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xmid=(xmax-xmin)/2.+xmin
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ymax=np.amax(gti_evt_data['Y'])
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ymin=np.amin(gti_evt_data['Y'])
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xbin_size=80
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ybin_size=80
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NBINS = (int((xmax-xmin)/xbin_size),int((ymax-ymin)/ybin_size))
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plt.subplot(1, 2, pl)
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img_zero_mpl = plt.hist2d(gti_evt_data['X'], gti_evt_data['Y'], NBINS, cmap='GnBu', norm=LogNorm())
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cbar = plt.colorbar(ticks=[10.,100.,1000.])
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||||
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()
|
||||
|
||||
Reference in New Issue
Block a user