esas

.gitignore

@@ -16,7 +16,7 @@ lib64/
 parts/
 sdist/
 var/
-products/
+products*/
 data/archive
 data/processed
 wheels/

arches/arches/config.py

@@ -5,9 +5,10 @@ good=['0862470801','0862470701','0862470601']
 """ The angular size of an XMM DETXY physical coordinate system is 0.05 arcseconds """
 det_pix_as=0.05
 
-arches_ra=266.4604208
+""" Arches core R=15 arcsec """
-arches_dec=-28.8244444
+arches_ra=266.4595833
-arches_Rmax_as=40
+arches_dec=-28.8219444
+arches_Rmax_as=15
 
 pn_threshold = 0.2
 mos_threshold=[0.2,0.3]

arches/arches/utils.py

@@ -33,6 +33,24 @@ import shutil
 
 from arches.config import *
 
+def test_exe(program):
+    """ Tests if executable exists in PATH """
+    import os
+    def is_exe(fpath):
+        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+    fpath, fname = os.path.split(program)
+    if fpath:
+        if is_exe(program):
+            return program
+    else:
+        for path in os.environ["PATH"].split(os.pathsep):
+            exe_file = os.path.join(path, program)
+            if is_exe(exe_file):
+                return exe_file
+
+    print("\n*** Command {} not found ***\n".format(program))
+    sys.exit()
 
 def create_folder(folder):
     if not (os.path.exists(folder)):
@@ -157,7 +175,7 @@ def get_det_coords(ra,dec,image,key):
                 dety=float(dy)
     return detx,dety
 
-def run_mosspectra(key,ccds,check=False):
+def run_mosspectra(key,ccds,check=True):
 
     eventfile = f'{key}-allevc.fits'
     
@@ -182,10 +200,11 @@ def run_mosspectra(key,ccds,check=False):
                   'ximagemax=19500','yimagemax=19500', 'ximagemin=-19499', 'yimagemin=-19499',]
         w('evselect', inargs).run()
     
-        d = pyds9.DS9()
+        #d = pyds9.DS9()
-        d.set("file "+unfilt_image)
+        #d.set("file "+unfilt_image)
-        d.set('cmap bb')
+        #d.set('cmap bb')
-        d.set('scale log')
+        #d.set('scale log')
+        #return
     
     
     inargs = [f'eventfile={eventfile}',
@@ -204,7 +223,7 @@ def run_mosspectra(key,ccds,check=False):
 
     w('mosspectra', inargs).run()
 
-def run_pnspectra(key,quads,check=False):
+def run_pnspectra(key,quads,check=True):
     eventfile = f'{key}-allevc.fits'
 
     (detx,dety)=get_det_coords(arches_ra,arches_dec,f'{key}-fovimt.fits',key)
@@ -228,10 +247,11 @@ def run_pnspectra(key,quads,check=False):
                   'ximagemax=19500','yimagemax=19500', 'ximagemin=-19499', 'yimagemin=-19499',]
         w('evselect', inargs).run()
     
-        d = pyds9.DS9()
+        #d = pyds9.DS9()
-        d.set("file "+unfilt_image)
+        #d.set("file "+unfilt_image)
-        d.set('cmap bb')
+        #d.set('cmap bb')
-        d.set('scale log')
+        #d.set('scale log')
+        #return
     
     inargs = [f'eventfile={key}-allevc.fits',
               'withsrcrem=yes',
@@ -268,3 +288,37 @@ def run_pnback(key,quads):
               f'quads="{quads}"',]
 
     w('pnback', inargs).run()
+
+def group_spectrum(key=None, group_min=25, oot=False):
+    if not (key):
+        print("Provide key= parameter, e.g. mos1S001")
+        return
+    
+    test_exe('grppha')
+    specfile=f'{key}-fovt.pi' if not (oot) else f'{key}-fovtootsub.pi'
+    backfile=f'{key}-bkg.pi'
+    respfile=f'{key}.rmf'
+    ancrfile=f'{key}.arf'
+    fout=f'{specfile}.grp'
+    
+    cmd=["grppha",
+         "infile={}".format(specfile), 
+         "outfile={}".format(fout),
+         f"comm=\'chkey BACKFILE {backfile} & chkey RESPFILE {respfile} & chkey ANCRFILE {ancrfile} & GROUP MIN {group_min}\'",
+         "tempc=EXIT",
+         "clobber=yes",
+         "chatter=0", # with chatter <= 5 being very  quite and chatter >= 20 very verbose.
+             ]
+    print((" ").join(cmd))
+    os.system((" ").join(cmd))
+    
+    fxcm = open(fout.replace("grp","xcm"), "w")
+    fxcm.write(f'data {fout}\n')
+    fxcm.write('ign **-2.\n')
+    fxcm.write('ign 11.-**\n')
+    fxcm.write('ign bad\n')
+    fxcm.write('cpd /xs\n')
+    fxcm.write('setpl en\n')
+    fxcm.write('@../../data/xspec/wabs_apec_cflux.xcm\n')
+    fxcm.write('pl lda delchi\n')
+    fxcm.close()

data/xspec/tbabs_apec_pow.xcm

@@ -0,0 +1,19 @@
+method leven 10 0.01
+abund wilm
+xsect vern
+cosmo 70 0 0.73
+xset delta 0.01
+systematic 0
+model  TBabs*constant(apec + gaussian + powerlaw)
+        8.43198      0.001          0          0     100000      1e+06
+              1         -1          0          0      1e+10      1e+10
+        3.02479          1      0.008      0.008         64         64
+            1.7         -1          0          0          5          5
+              0         -1     -0.999     -0.999         10         10
+     0.00132232       0.01          0          0      1e+20      1e+24
+            6.4         -1          0          0      1e+06      1e+06
+            0.1         -1          0          0         10         20
+    1.72861e-06       0.01          0          0      1e+20      1e+24
+           1.13         -1         -3         -2          9         10
+    3.35218e-05       0.01          0          0      1e+20      1e+24
+bayes off

data/xspec/wabs_apec_cflux.xcm

@@ -0,0 +1,21 @@
+method leven 10 0.01
+abund wilm
+xsect vern
+cosmo 70 0 0.73
+xset delta 0.01
+systematic 0
+model  wabs(apec + cflux*powerlaw + gaussian)
+        5.87869      0.001          0          0     100000      1e+06
+        2.95206       0.01      0.008      0.008         64         64
+            1.7         -1          0          0          5          5
+              0         -1     -0.999     -0.999         10         10
+     0.00139339       0.01          0          0      1e+20      1e+24
+              2         -1          0          0      1e+06      1e+06
+              8         -1          0          0      1e+06      1e+06
+       -12.5886       0.01       -100       -100        100        100
+           1.13         -1         -3         -2          9         10
+              1         -1          0          0      1e+20      1e+24
+            6.4         -1          0          0      1e+06      1e+06
+           0.01         -1          0          0         10         20
+    1.45246e-06       0.01          0          0      1e+20      1e+24
+bayes off

scripts/06_esas_group_spectra.py

@@ -0,0 +1,59 @@
+#!/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'
+events_oot_dir=root_path+'/data/processed-oot'
+products_dir=root_path+'/products'
+ds9reg_dir=root_path+'/data/ds9reg'
+
+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)
+    print(f"\n*** jump to {work_dir} ***\n")
+    os.chdir(work_dir)
+    
+    group_spectrum(key='mos1S001')
+    group_spectrum(key='mos2S002')
+    group_spectrum(key='pnS003')
+    group_spectrum(key='pnS003',oot=True)
+
+
+
+
+