def radial_prof(eq_coords, odf_dir):
logger.info("TASK: eradial")
images_dir = odf_dir + "/images"
image_low = glob.glob("{}/image_filtered_low*".format(images_dir))[0]
image_high = glob.glob("{}/image_filtered_high*".format(images_dir))[0]
# Find circle values on ds9:
# !!! No coger valores de radio inferiores a 400
# ------------------------------------------------------------------
r = 2.0 / 60.
circle = "{},{},{}".format(eq_coords[0], eq_coords[1], r)
logger.info("CIRCLE: {}".format(circle))
# ------------------------------------------------------------------
task = f"eradial imageset={image_low} srcexp='(RA,DEC) in CIRCLE({circle})' psfenergy=1.0 centroid='yes' binwidth=1.0"
logger.info("COMMAND: {}".format(task))
status = exec_task(task)
if (status != 0):
raise Exception
os.rename("radprof.ds", f"radprof_low.ds")
task = f"eradial imageset={image_high} srcexp='(RA,DEC) in CIRCLE({circle})' psfenergy=5.0 centroid='yes' binwidth=1.0" # binwidth = 4.0 or 6.0
logger.info("COMMAND: {}".format(task))
status = exec_task(task)
if (status != 0):
raise Exception
os.rename("radprof.ds", f"radprof_high.ds")
logger.info("Radial profiles generated correctly.")
def generate_filtered_images(odf_dir, bin_size, pi):
logger.info("TASK: evselect")
images_dir = odf_dir + "/images"
os.chdir(images_dir)
filtered = glob.glob("{}/filtered_*".format(odf_dir))[0]
expr_high = f'PI in [{pi[2]}:{pi[3]}] && FLAG==0 && PATTERN in [0:4]'
expr_low = f'PI in [{pi[0]}:{pi[1]}] && FLAG==0 && PATTERN in [0:4]'
task = f'evselect table={filtered} xcolumn=X ycolumn=Y imagebinning=binSize' + \
f' ximagebinsize={bin_size} yimagebinsize={bin_size}' + \
f' expression=\'{expr_high}\'' + \
f' withimageset=true imageset=image_filtered_high.fits'
logger.info("COMMAND: {}\n".format(task))
status = exec_task(task)
if (status != 0):
raise Exception
task = f'evselect table={filtered} xcolumn=X ycolumn=Y imagebinning=binSize' + \
f' ximagebinsize={bin_size} yimagebinsize={bin_size}' + \
f' expression=\'{expr_low}\'' + \
f' withimageset=true imageset=image_filtered_low.fits'
logger.info("COMMAND: {}".format(task))
status = exec_task(task)
if (status != 0):
raise Exception
os.chdir(odf_dir)
logger.info("Images generated correctly.")
def edetect_chain(odf_dir, pi):
logger.info("TASK: edetect_chain")
images_dir = odf_dir + "/images"
os.chdir(images_dir)
logger.info("Using:")
image_low = glob.glob("*_500_2000.fits")[0]
logger.info("{}".format(image_low))
image_high = glob.glob("*_4500_10000.fits")[0]
logger.info("{}".format(image_high))
clean_evts = glob.glob("{}/clean_*".format(odf_dir))[0]
logger.info("{}".format(clean_evts))
attitude_file = glob.glob("{}/atthk*".format(odf_dir))[0]
logger.info("{}".format(attitude_file))
ecf = 1 # Cuentas a flujo, nos da igual.
task = f"edetect_chain imagesets={image_low} eventsets={clean_evts} " + \
f"attitudeset={attitude_file} pimin={pi[0]} pimax={pi[1]} ecf={ecf} " + \
"eboxl_list='pn_eboxlist_l_low.fits' eboxm_list='pn_eboxlist_m_low.fits' " + \
"esp_nsplinenodes=16 eml_list='pn_emllist_low.fits' esen_mlmin=15 -V 5"
status = exec_task(task)
if (status != 0):
print(f"Task \"{task}\" failed")
raise Exception
task = f"edetect_chain imagesets={image_high} eventsets={clean_evts} " + \
f"attitudeset={attitude_file} pimin={pi[2]} pimax={pi[3]} ecf={ecf} " + \
"eboxl_list='pn_eboxlist_l_high.fits' eboxm_list='pn_eboxlist_m_high.fits' " + \
"esp_nsplinenodes=16 eml_list='pn_emllist_high.fits' esen_mlmin=15"
status = exec_task(task)
if (status != 0):
logger.info(
"ERROR: Task edetect_chain failed. Check {}/tmp.log for more information"
.format(odf_dir))
raise Exception
logger.info("Sources detected correctly.")
def psf_gen(coords):
images_dir = ""
image_low = glob.glob("{}/image_filtered_low*".format(images_dir))[0]
task = f"psfgen image={image_low} energy=1000 level=ELLBETA coordtype=EQPOS x={coords[0]} y={coords[1]} xsize=400 ysize=400 output=psf.fits"
status = exec_task(task)
if (status != 0):
raise Exception
def tabgtigen(odf_dir):
logger.info("TASK: tabgtigen")
gti_dir = "{}/gti".format(odf_dir)
rate = glob.glob("{}/rate_*".format(odf_dir))[0]
os.chdir(gti_dir)
if (len(rate) == 0):
logger.info("No rate file found in {}".format(odf_dir))
else:
logger.info("Found {} calibrated events list.".format(rate))
logger.info("Generating Good Time Intervals for {}...".format(rate))
expo = rate.split('rate')[1]
gti = 'gti{}'.format(expo)
logger.info("GTI: {}".format(gti))
expr = 'RATE<=0.4'
task = f'tabgtigen table="{rate}" gtiset={gti}' + \
f' expression=\'{expr}\''
logger.info("COMMAND: {}".format(task))
status = exec_task(task)
if status != 0:
logger.info(
"ERROR: Task tabgtigen failed. Check {}/tmp.log for more information"
.format(odf_dir))
raise Exception
os.chdir(odf_dir)
logger.info("{} generated correctly.".format(gti))
return gti_dir
def generate_images(odf_dir, bin_size, pi):
logger.info("TASK: evselect")
logger.info("ENERGY BAND 1: {} - {} eV".format(pi[0], pi[1]))
logger.info("ENERGY BAND 2: {} - {} eV".format(pi[2], pi[3]))
logger.info("BIN SIZE: {}".format(bin_size))
os.chdir("{}/pps".format(odf_dir))
evlist = glob.glob("*PIEVLI0000.fits")[0]
expo = evlist.split('PIEVLI0000.fits')[0]
clean_file = glob.glob("{}/clean_*".format(odf_dir))[0]
images_dir = "{}/images".format(odf_dir)
os.chdir(images_dir)
image_name = [
f'image_{expo}_{pi[0]}_{pi[1]}.fits',
f'image_{expo}_{pi[2]}_{pi[3]}.fits'
]
expr = [
f'PI in [{pi[0]}:{pi[1]}] && FLAG==0 && PATTERN in [0:4]',
f'PI in [{pi[2]}:{pi[3]}] && FLAG==0 && PATTERN in [0:4]'
]
for i in range(len(expr)):
task = f'evselect table={clean_file} xcolumn=X ycolumn=Y imagebinning=binSize' + \
f' ximagebinsize={bin_size} yimagebinsize={bin_size}' + \
f' expression=\'{expr[i]}\'' + \
f' withimageset=true imageset={image_name[i]}'
logger.info("COMMAND: {}\n".format(task))
status = exec_task(task)
if status != 0:
logger.info(
"ERROR: Task evselect failed. Check {}/tmp.log for more information"
.format(odf_dir))
raise Exception
logger.info("Image {} generated.".format(image_name[i]))
logger.info("Images generated correctly.")
def ecoordconv(obsid):
logger.info("TASK: ecoordconv")
bll_catalog = fits.open(
'/home/aaranda/tfm/bllacs_PN_NopileupNofasttiming.fits')
data = bll_catalog[1].data
RA = ""
DEC = ""
for row in data:
if row[5] == obsid:
RA = row[1]
logger.info("COORDINATES: RA: {}".format(RA))
DEC = row[2]
logger.info("COORDINATES: DEC: {}".format(DEC))
if RA == "" and DEC == "":
logger.info("Coordinates not found in catalog.")
images_dir = odf_dir + "/images"
image_low = glob.glob("{}/*_500_2000.fits".format(images_dir))[0]
coords = []
task = f'ecoordconv imageset={image_low} x="{RA}" y="{DEC}" coordtype=eqpos'
logger.info("COMMAND: {}".format(task))
status = exec_task(task)
if (status != 0):
print(f"Task \"{task}\" failed")
raise Exception
file = "tmp.log"
with open(file, "r") as f:
for line in f:
if "X: Y:" in line:
X = float(line.split(" ")[3])
Y = float(line.split(" ")[4])
coords.append([X, Y])
print("X value is {}".format(X))
print("Y value is {}".format(Y))
logger.info("COORDINATES: X: {}".format(X))
logger.info("COORDINATES: Y: {}".format(Y))
# Delete the corresponding row in bkg_region.ds file.
bkg_region = fits.open(f'bkg_region.ds', mode='update')
data = bkg_region[1].data
err = 50
count = 0
bad_row = None
for row in data:
if ((X - err) <= row[1][0] <= (X + err)) and ((Y - err) <= row[2][0] <=
(Y + err)):
bad_row = count
count += 1
if bad_row != None:
data = np.delete(data, bad_row) # !!!maybe repeated rows
bkg_region[1].data = data
bkg_region.writeto(f'bkg_region_clean.ds')
logger.info("RA, DEC obtained correctly.\n\n")
return [RA, DEC]
def detmask(odf_dir, pi):
logger.info("TASK: atthkgen")
task = "atthkgen"
status = exec_task(task)
if (status != 0):
raise Exception
logger.info("atthkegn generated correctly.")
logger.info("TASK: atthkgen")
image_low = "{}/images/image_filtered_low.fits".format(odf_dir)
image_high = "{}/images/image_filtered_high.fits".format(odf_dir)
atthk = glob.glob("atthk.dat")[0]
evlist = glob.glob("filtered_clean_*")[0]
expfile_low = "expfile_low.fits"
expfile_high = "expfile_high.fits"
task = f'eexpmap imageset={image_low} attitudeset={atthk} eventset={evlist} ' + \
f'expimageset={expfile_low} pimin={pi[0]} pimax={pi[1]}'
status = exec_task(task)
if (status != 0):
raise Exception
task = f'eexpmap imageset={image_high} attitudeset={atthk} eventset={evlist} ' + \
f'expimageset={expfile_high} pimin={pi[2]} pimax={pi[3]}'
status = exec_task(task)
if (status != 0):
raise Exception
logger.info("expfiles generated correctly.")
detfile_low = "detfile_low.fits"
detfile_high = "detfile_high.fits"
task = f"emask expimageset={expfile_low} detmaskset={detfile_low} threshold1=0.3 threshold2=0.5 withregionset=true regionset=bkg_region_clean.ds"
#task = f"emask expimageset={expfile_low} detmaskset={detfile_low} threshold1=0.3 threshold2=0.5"
status = exec_task(task)
if (status != 0):
raise Exception
task = f"emask expimageset={expfile_high} detmaskset={detfile_high} threshold1=0.0 threshold2=0.3 withregionset=true regionset=bkg_region_clean.ds"
status = exec_task(task)
if (status != 0):
raise Exception
# task = f"emask expimageset=psf.fits detmaskset={detfile_high} regionset='bkg_region_clean.ds' threshold1=0.3 threshold2=0.5"
# status = exec_task(task)
# if (status != 0):
# raise Exception
logger.info("detfiles generated correctly.")
def odfingest(odf_dir):
os.chdir(odf_dir)
SUM_SAS_file = glob.glob("*SUM.SAS")
if len(SUM_SAS_file) != 0:
for sum_sas in SUM_SAS_file:
os.remove(sum_sas)
status = exec_task("odfingest")
if (status != 0):
print(f"Task odfingest failed")
raise Exception
SUM_SAS_file = glob.glob("*SUM.SAS")[0]
os.environ['SAS_ODF'] = SUM_SAS_file
print("SAS_ODF={}".format(SUM_SAS_file))
def filtered_region():
logger.info("TASK: region")
clean_evts = glob.glob("clean_*")[0]
filtered_set = "filtered_{}".format(clean_evts)
expr = f"region(bkg_region_clean.ds)"
task = f'evselect table={clean_evts} filteredset={filtered_set} '+ \
f'expression="{expr}"'
logger.info("COMMAND: {}".format(task))
status = exec_task(task)
if (status != 0):
print(f"Task \"{task}\" failed")
raise Exception
logger.info("Image filtered with bkg_region_clean.ds generated correctly.")
def cifbuild(odf_dir):
os.chdir(odf_dir)
cif_file = "{}/ccf.cif".format(odf_dir)
if not os.path.isfile(cif_file):
status = exec_task("cifbuild")
if (status != 0):
raise Exception
print("{} generated correctly.".format(cif_file))
os.environ['SAS_CCF'] = cif_file
print("SAS_CCF={}".format(cif_file))
else:
print("cif.ccf already exists.")
os.environ['SAS_CCF'] = cif_file
print("SAS_CCF={}".format(cif_file))
def evselect(odf_dir):
logger.info("TASK: evselect")
os.chdir("{}/pps".format(odf_dir))
evlist = glob.glob("*PIEVLI0000.fits")[0]
logger.info("EVENTS LIST: {}".format(evlist))
expo = evlist.split('PIEVLI0000.fits')[0]
rate = "{}/rate_{}.fits".format(odf_dir, expo)
logger.info("RATE: {}".format(rate))
expr = '#XMMEA_EP && (PI>10000&&PI<12000) && (PATTERN==0)'
task = f'evselect table={evlist} withrateset=Y rateset={rate}' + \
' maketimecolumn=Y timebinsize=100 makeratecolumn=Y' + \
f' expression=\'{expr}\''
logger.info("COMMAND: {}".format(task))
status = exec_task(task)
if status != 0:
logger.info(
"ERROR: Task evselect failed. Check {}/tmp.log for more information"
.format(odf_dir))
raise Exception
logger.info("rate file generated correctly.")
def evselect_clean(odf_dir, gti_dir):
logger.info("TASK: evselect")
os.chdir("{}/pps".format(odf_dir))
evlist = glob.glob("*PIEVLI0000.fits")[0]
gti = glob.glob("{}/gti_*".format(gti_dir))[0]
expo = evlist.split('PIEVLI0000.fits')[0]
logger.info("Using PI>150 for evselect.".format(gti))
expr = f"#XMMEA_EP && gti({gti},TIME) && (PI>150)"
task = f'evselect table={evlist} withfilteredset=Y ' + \
f'filteredset={odf_dir}/clean_{expo}.fits ' + \
f'destruct=Y keepfilteroutput=T expression=\'{expr}\''
logger.info("Filtering {} with GTI...".format(expo))
logger.info("COMMAND: {}".format(task))
status = exec_task(task)
if status != 0:
logger.info(
"ERROR: Task evselect failed. Check {}/tmp.log for more information"
.format(odf_dir))
raise Exception
logger.info("clean file generated correctly.")
os.chdir(odf_dir)
def radial_prof_psf(eq_coords, logfile):
log = open(logfile, "a")
log.write("TASK: eradial\n")
image = glob.glob("psf.fits")[0]
# Find circle values on ds9:
# !!! No coger valores de radio inferiores a 400
# ------------------------------------------------------------------
r = 2.0 / 60.
circle = "{},{},{}".format(eq_coords[0], eq_coords[1], r)
log.write("CIRCLE: {}\n".format(circle))
# ------------------------------------------------------------------
task = f"eradial imageset={image} srcexp='(RA,DEC) in CIRCLE({circle})' psfenergy=1.0 centroid='yes' binwidth=6.0"
log.write("COMMAND: {}\n".format(task))
status = exec_task(task)
if (status != 0):
raise Exception
os.rename("radprof.ds", f"radprof_psf.ds")
log.write("Theorical PSF radial profile generated correctly.\n\n")
log.close()
def region(odf_dir):
logger.info("TASK: region")
os.chdir(odf_dir)
bkg_file = glob.glob("bkg_*")
if len(bkg_file) != 0:
for bkg in bkg_file:
os.remove(bkg)
clean_evts = glob.glob("clean_*")[0]
# Region for OBSMLI downloaded from te pipeline
src_file = glob.glob("pps/*OBSMLI0000.fits")[0]
task = f"region eventset={clean_evts} tempset=tempset.ds " + \
f"srclisttab={src_file} operationstyle='global'"# radiusstyle='contour' outunit='xy' -V 5"
# ## Region for the srclist from edetect_chain
# src_file = glob.glob("{}/pn_emllist*".format(images_dir))[0]
# task = f"region eventset={clean_evts} tempset=tempset.ds " + \
# f"srclisttab={src_file} operationstyle='global'"# radiusstyle='contour' outunit='xy' -V 5"
logger.info("COMMAND: {}".format(task))
status = exec_task(task)
if (status != 0):
print(f"Task \"{task}\" failed")
raise Exception
logger.info("bkg file generated correctly.")
def cal_view():
task = "calview"
status = exec_task(task)
if (status != 0):
raise Exception
def psf_gen(center, energy, box, psf_out):
psfgen = f'psfgen image={fits_image} withimage=yes instrument=PN level=ELLBETA energy={energy} ' + \
f'x={center.ra.value} y={center.dec.value} coordtype=EQPOS xsize={box} ysize={box} output={psf_out}'
status = exec_task(psfgen)
if (status != 0):
raise RuntimeError