SAS

scripts/04_sas_spectrum_mos.py

@@ -0,0 +1,176 @@
+#!/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 re
+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/sas'
+ds9reg_dir=root_path+'/data/ds9reg'
+
+if len(sys.argv) > 1:
+    print(f"The first command-line argument is: {sys.argv[1]}")
+    imos=sys.argv[1]
+else:
+    print("No command-line arguments provided. Use MOS1.")
+    imos=1
+
+create_folder(products_dir)
+
+inargs = ['--version']
+t = w('sasver', inargs)
+t.run()
+
+files = glob.glob(archive_dir+'/*')
+
+for obsid in files:
+    obsid = os.path.basename(obsid)
+    if(obsid in skip):
+        continue
+
+    work_dir = init_work_dir(obsid, products_dir=products_dir)
+
+    os.chdir(work_dir)
+
+    eventfile=f'{products_dir}/{obsid}/EPIC_MOS{imos}_gtiFilteredEvts.ds'
+    if(os.path.isfile(eventfile)==False):
+        print("*** run 02_sas_flares_mos.py ***")
+        sys.exit()
+
+    # EPIC_pn_gtiFilteredEvts.ds
+    search_str = f'{products_dir}/{obsid}/EPIC_MOS{imos}_Image_{obsid}.fit'
+    print(search_str)
+    emfiles = glob.glob(search_str)
+    if not (emfiles):
+        print("*** run 02_sas_flares_mos.py ***")
+        sys.exit()
+        
+    out_IMFile   = emfiles[0]
+
+    # Visualize the image with ds9
+    src_fn=f'{ds9reg_dir}/{obsid}/src.reg'
+    bkg_fn=f'{ds9reg_dir}/{obsid}/bkg.reg'
+    x_source,y_source,r_source,x_bkg,y_bkg,r_bkg,r2_bkg = get_ds9_regions(out_IMFile, src_fn, bkg_fn)
+
+    #########################################
+    # Extract the source region light curve #
+    #########################################
+    
+    # Define some parameters for filtering the event file and define the light curve binning
+
+    q_flag       = "#XMMEA_EM" # Quality flag for EPIC pn
+    n_pattern    = 12           # Pattern selection
+    mos_pi_min    = 200.        # Low energy range eV
+    mos_pi_max    = 10000.      # High energy range eV
+    lc_bin       = 100         # Light curve bin in secs
+
+    # Define the output ligthcurve file name
+    in_LCSRCFile = work_dir+f'/EPIC_MOS{imos}_source_lightcurve.lc'   # Name of the output source light curve
+
+    # Arguments of SAS Command
+    expression = f'{q_flag}&&(PATTERN<={n_pattern})&&((X,Y) IN circle({x_source},{y_source},{r_source}))&&(PI in [{mos_pi_min}:{mos_pi_max}])'
+    inargs     = [f'table={eventfile}','energycolumn=PI','withrateset=yes',f'rateset={in_LCSRCFile}',
+                  f'timebinsize={lc_bin}','maketimecolumn=yes','makeratecolumn=yes',f'expression={expression}']
+    
+    print("   Filter expression to use: "+expression+" \n")
+    # Execute the SAS task with the parameters to produce the source region light curve
+    w("evselect", inargs).run()
+
+    # Inspect light curve
+    #plt.figure(figsize=(20,8))  # Size of figure
+    #plotLC(plt,mos_threshold[imos-1],in_LCSRCFile) # Plot source region light curve
+    #plt.legend()
+    #plt.show()
+    
+    ######################################
+    # Extract the source region spectrum #
+    ######################################
+
+    # Define some parameters for filtering the event file
+    q_flag       = "#XMMEA_EM" # Quality flag for EPIC pn
+    n_pattern    = 12           # Pattern selection
+
+    # Define the output ligthcurve file name
+    in_SPSRCFile = work_dir+f'/EPIC_MOS{imos}_source_spectrum.fits'   # Name of the output source spectrum
+
+    # Arguments of SAS Command
+    expression = f'{q_flag}&&(PATTERN<={n_pattern})&&((X,Y) IN circle({x_source},{y_source},{r_source}))'  # event filter expression
+    inargs     = [f'table={eventfile}','withspectrumset=yes',f'spectrumset={in_SPSRCFile}',
+                  'energycolumn=PI','spectralbinsize=5','withspecranges=yes','specchannelmin=0',
+                  'specchannelmax=11999',f'expression={expression}']
+
+    print("   Filter expression to use: "+expression+" \n")
+    w("evselect", inargs).run()
+
+    # Extract the background region spectrum with the same criteria
+
+    # Define the output ligthcurve file name    
+    in_SPBKGFile = work_dir+f'/EPIC_MOS{imos}_background_spectrum.fits'   # Name of the output background spectrum
+
+    # Arguments of SAS Command
+    if(r2_bkg==None):
+        expression = f'{q_flag}&&(PATTERN<={n_pattern})&&((X,Y) IN circle({x_bkg},{y_bkg},{r_bkg}))'
+    else:
+        expression = f'{q_flag}&&(PATTERN<={n_pattern})&&((X,Y) IN annulus({x_bkg},{y_bkg},{r_bkg},{r2_bkg}))'
+
+    inargs     = [f'table={eventfile}','withspectrumset=yes',f'spectrumset={in_SPBKGFile}',
+                  'energycolumn=PI','spectralbinsize=5','withspecranges=yes','specchannelmin=0',
+                  'specchannelmax=11999',f'expression={expression}']
+
+    print("   Filter expression to use: "+expression+" \n")
+    w("evselect", inargs).run()
+
+    w("backscale", [f'spectrumset={in_SPSRCFile}',f'badpixlocation={eventfile}']).run()
+    w("backscale", [f'spectrumset={in_SPBKGFile}',f'badpixlocation={eventfile}']).run()
+
+    # https://www.cosmos.esa.int/web/xmm-newton/sas-thread-epic-merging
+    MAXENERGY=12
+    NBINS=1190
+    in_RESPFile = work_dir+f'/EPIC_MOS{imos}.rmf'   # Name of the output redistribution
+    w("rmfgen", [f'spectrumset={in_SPSRCFile}',f'rmfset={in_RESPFile}',
+                 'withenergybins=yes', 'energymin=0.1',
+                 f'energymax={MAXENERGY}', f'nenergybins={NBINS}',]).run()
+
+    in_ARFFile = work_dir+f'/EPIC_MOS{imos}.arf'   # Name of the output ancillary
+
+    print("   Checking for Response File ..... \n")
+    # Check if RESP file is available.
+    if os.path.isfile(in_RESPFile):
+        print ("File "+in_RESPFile+" exists. \n")
+    else:
+        print ("File "+in_RESPFile+" does not exist, please check. \n")
+        sys.exit()
+
+    # Arguments of SAS Command
+    inargs     = [f'spectrumset={in_SPSRCFile}',f'arfset={in_ARFFile}',
+                  'withrmfset=yes',f'rmfset={in_RESPFile}',f'badpixlocation={eventfile}','detmaptype=psf']
+    w("arfgen", inargs).run()
+
+    # rebin the spectra and link associated files
+    in_GRPFile = work_dir+f'/EPIC_MOS{imos}_spectrum_grp.fits'   # Name of the output specgruop
+    inargs     = [f'spectrumset={in_SPSRCFile}','mincounts=30','oversample=3',
+                  f'rmfset={in_RESPFile}',f'arfset={in_ARFFile}',
+                  f'backgndset={in_SPBKGFile}',f'groupedset={in_GRPFile}']
+    w("specgroup", inargs).run()