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This commit is contained in:
Roman Krivonos
2025-10-23 13:20:50 +03:00
parent 2dee828098
commit 22c164cd41
20 changed files with 2240 additions and 256 deletions
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303
arches/arches/utils.py
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@@ -60,6 +60,19 @@ def remove_file(filename):
if(os.path.isfile(filename)==True):
os.remove(filename)
def move_files(pattern, destination):
for file in glob.glob(pattern):
shutil.move(file, os.path.join(destination,file))
def get_first_file(pattern):
files = glob.glob(pattern)
if not (files):
print(f"Files not found from pattern {pattern}")
sys.exit()
filename = files[0]
return filename
# Function to plot Lightcurve
def plotLC(plt,threshold,fileName):
if fileName != "NOT FOUND":
@@ -119,6 +132,9 @@ def init_work_dir(obsid,products_dir=None):
events_dir=root_path+'/data/processed'
ds9reg_dir=root_path+'/data/ds9reg'
if (products_dir==None):
print('products_dir is not defined')
sys.exit()
create_folder(products_dir)
#inargs = ['--version']
@@ -153,6 +169,10 @@ def init_work_dir(obsid,products_dir=None):
""" See also convregion task, for conversion of regions """
def get_det_coords(ra,dec,image,key):
if(os.path.isfile(image)==False):
print(f"{image} is not found")
sys.exit()
logfile=f'{key}-ecoordconv.log'
remove_file(logfile)
""" Convert sky coordinates to correct DETX/Y """
@@ -174,12 +194,39 @@ def get_det_coords(ra,dec,image,key):
dety=float(dy)
return detx,dety
def run_mosspectra(key,ccds,check=True,elow="350",ehigh="1100"):
def run_mosspectra(key,ccds,check=False,elow="350",ehigh="1100"):
eventfile = f'{key}-allevc.fits'
if(os.path.isfile(eventfile)==False):
print(f"{eventfile} is not found, run 01_init_events*.py and above")
cwd = os.getcwd()
print(f"Current directory: {cwd}")
sys.exit()
unfilt_image = eventfile.replace("allevc","ffov")
inargs = [f'table={eventfile}',
'withimageset=yes', f'imageset={unfilt_image}',
#'filtertype=expression', f'expression={expression}',
'ignorelegallimits=yes', 'imagebinning=imageSize',
'xcolumn=DETX','ycolumn=DETY','ximagesize=780','yimagesize=780',
'ximagemax=19500','yimagemax=19500', 'ximagemin=-19499', 'yimagemin=-19499',]
w('evselect', inargs).run()
if(os.path.isfile(unfilt_image)==False):
print(f"{unfilt_image} is not found")
cwd = os.getcwd()
print(f"Current directory: {cwd}")
sys.exit()
if(check):
d = pyds9.DS9()
d.set("file "+unfilt_image)
d.set('cmap bb')
d.set('scale log')
#return
(detx,dety)=get_det_coords(arches_ra,arches_dec,f'{key}-fovimt.fits',key)
#(detx,dety)=get_det_coords(arches_ra,arches_dec,f'{key}-fovimt.fits',key)
(detx,dety)=get_det_coords(arches_ra,arches_dec,unfilt_image,key)
arches_Rmax_pix=int(np.round(arches_Rmax_as/det_pix_as))
region_fn=f'{key}.txt'
remove_file(region_fn)
@@ -188,24 +235,15 @@ def run_mosspectra(key,ccds,check=True,elow="350",ehigh="1100"):
freg.write(f'&&{expression}\n')
freg.close()
# check selected region
if(check):
unfilt_image = eventfile.replace("allevc","region")
inargs = [f'table={eventfile}',
'withimageset=yes', f'imageset={unfilt_image}',
'filtertype=expression', f'expression={expression}',
'ignorelegallimits=yes', 'imagebinning=imageSize',
'xcolumn=DETX','ycolumn=DETY','ximagesize=780','yimagesize=780',
'ximagemax=19500','yimagemax=19500', 'ximagemin=-19499', 'yimagemin=-19499',]
w('evselect', inargs).run()
#d = pyds9.DS9()
#d.set("file "+unfilt_image)
#d.set('cmap bb')
#d.set('scale log')
#return
unfilt_image = eventfile.replace("allevc","region")
inargs = [f'table={eventfile}',
'withimageset=yes', f'imageset={unfilt_image}',
'filtertype=expression', f'expression={expression}',
'ignorelegallimits=yes', 'imagebinning=imageSize',
'xcolumn=DETX','ycolumn=DETY','ximagesize=780','yimagesize=780',
'ximagemax=19500','yimagemax=19500', 'ximagemin=-19499', 'yimagemin=-19499',]
w('evselect', inargs).run()
inargs = [f'eventfile={eventfile}',
'withsrcrem=yes',
f'cornerfile={key}-corevc.fits',
@@ -221,6 +259,11 @@ def run_mosspectra(key,ccds,check=True,elow="350",ehigh="1100"):
f'ccds="{ccds}"',]
w('mosspectra', inargs).run()
# check coordinate conversion
#(detx,dety)=get_det_coords(arches_ra,arches_dec,f'{key}-fovimt.fits',key) # image input in X,Y
#(detx,dety)=get_det_coords(arches_ra,arches_dec,unfilt_image,key) # image input in DETX,DETY
#sys.exit()
def run_bkgimsky(key,elow="350",ehigh="1100"):
@@ -233,10 +276,32 @@ def run_bkgimsky(key,elow="350",ehigh="1100"):
'withdetxy=false', 'withskyxy=false',]
w('rotdet2sky', inargs).run()
def run_pnspectra(key,quads,check=True,elow="350",ehigh="1100"):
def run_pnspectra(key,quads,check=True,elow="350",ehigh="1100",pattern=0):
eventfile = f'{key}-allevc.fits'
if(os.path.isfile(eventfile)==False):
print(f"{eventfile} is not found, run 01_init_events*.py and above")
sys.exit()
(detx,dety)=get_det_coords(arches_ra,arches_dec,f'{key}-fovimt.fits',key)
# write image file with full fov
unfilt_image = eventfile.replace("allevc","ffov")
inargs = [f'table={eventfile}',
'withimageset=yes', f'imageset={unfilt_image}',
#'filtertype=expression', f'expression={expression}',
'ignorelegallimits=yes', 'imagebinning=imageSize',
'xcolumn=DETX','ycolumn=DETY','ximagesize=780','yimagesize=780',
'ximagemax=19500','yimagemax=19500', 'ximagemin=-19499', 'yimagemin=-19499',]
w('evselect', inargs).run()
if(check):
d = pyds9.DS9()
d.set("file "+unfilt_image)
d.set('cmap bb')
d.set('scale log')
#return
#(detx,dety)=get_det_coords(arches_ra,arches_dec,f'{key}-fovimt.fits',key)
(detx,dety)=get_det_coords(arches_ra,arches_dec,unfilt_image,key)
arches_Rmax_pix=int(np.round(arches_Rmax_as/det_pix_as))
region_fn=f'{key}.txt'
@@ -245,23 +310,15 @@ def run_pnspectra(key,quads,check=True,elow="350",ehigh="1100"):
expression=f"((DETX,DETY) IN circle({detx},{dety},{arches_Rmax_pix}))"
freg.write(f'&&{expression}\n')
freg.close()
# check selected region
if(check):
unfilt_image = eventfile.replace("allevc","region")
inargs = [f'table={eventfile}',
'withimageset=yes', f'imageset={unfilt_image}',
'filtertype=expression', f'expression={expression}',
'ignorelegallimits=yes', 'imagebinning=imageSize',
'xcolumn=DETX','ycolumn=DETY','ximagesize=780','yimagesize=780',
'ximagemax=19500','yimagemax=19500', 'ximagemin=-19499', 'yimagemin=-19499',]
w('evselect', inargs).run()
#d = pyds9.DS9()
#d.set("file "+unfilt_image)
#d.set('cmap bb')
#d.set('scale log')
#return
unfilt_image = eventfile.replace("allevc","region")
inargs = [f'table={eventfile}',
'withimageset=yes', f'imageset={unfilt_image}',
'filtertype=expression', f'expression={expression}',
'ignorelegallimits=yes', 'imagebinning=imageSize',
'xcolumn=DETX','ycolumn=DETY','ximagesize=780','yimagesize=780',
'ximagemax=19500','yimagemax=19500', 'ximagemin=-19499', 'yimagemin=-19499',]
w('evselect', inargs).run()
inargs = [f'eventfile={key}-allevc.fits',
'withsrcrem=yes',
@@ -274,7 +331,7 @@ def run_pnspectra(key,quads,check=True,elow="350",ehigh="1100"):
'withregion=yes',
f'regionfile={region_fn}',
'keepinterfiles=yes',
'pattern=0',
f'pattern={pattern}',
f'elow={elow}',
f'ehigh={ehigh}',
f'quads="{quads}"',]
@@ -299,18 +356,77 @@ def run_pnback(key,quads):
w('pnback', inargs).run()
def group_spectrum(key=None, group_min=25, oot=False):
def run_mossave(key,elow="350",ehigh="1100"):
dd=f'ffov_{key}'
create_folder(dd)
move_files(f'{key}*-{elow}-{ehigh}*',dd)
move_files(f'{key}*-{elow}-{ehigh}*',dd)
move_files(f'{key}*.pi',dd)
move_files(f'{key}*.qdp',dd)
move_files(f'{key}*.ps',dd)
move_files(f'{key}*imt*',dd)
move_files(f'{key}*.arf',dd)
move_files(f'{key}*.rmf',dd)
move_files(f'{key}*imspdet*',dd)
move_files(f'{key}*bkgimsky*',dd)
def run_pnsave(key,elow="350",ehigh="1100",pattern=0):
dd=f'ffov_{key}_{pattern}'
create_folder(dd)
move_files(f'pn*-{elow}-{ehigh}*',dd)
move_files(f'pn*-{elow}-{ehigh}*',dd)
move_files(f'pn*.pi',dd)
move_files(f'pn*.qdp',dd)
move_files(f'pn*.ps',dd)
move_files(f'pn*imt*',dd)
move_files(f'pn*.arf',dd)
move_files(f'pn*.rmf',dd)
move_files(f'pn*imspdet*',dd)
move_files(f'pn*bkgimsky*',dd)
def group_spectrum(key=None, group_min=25, oot=False, chdir=None, cpdir=None, pattern=None):
if not (key):
print("Provide key= parameter, e.g. mos1S001")
return
prefix=''
try:
if(chdir):
prefix='../'
os.chdir(chdir)
except:
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'
if(pattern!=None):
specfile0=specfile
backfile0=backfile
respfile0=respfile
ancrfile0=ancrfile
fout0=fout
specfile=f'{key}_{pattern}-fovt.pi' if not (oot) else f'{key}_{pattern}-fovtootsub.pi'
backfile=f'{key}_{pattern}-bkg.pi'
respfile=f'{key}_{pattern}.rmf'
ancrfile=f'{key}_{pattern}.arf'
fout=f'{specfile}.grp'
shutil.copyfile(specfile0, specfile)
shutil.copyfile(backfile0, backfile)
shutil.copyfile(respfile0, respfile)
shutil.copyfile(ancrfile0, ancrfile)
shutil.copyfile(fout0, fout)
cmd=["grppha",
"infile={}".format(specfile),
"outfile={}".format(fout),
@@ -321,14 +437,107 @@ def group_spectrum(key=None, group_min=25, oot=False):
]
print((" ").join(cmd))
os.system((" ").join(cmd))
fxcm = open(fout.replace("grp","xcm"), "w")
with fits.open(specfile) as hdul:
header = hdul['SPECTRUM'].header
backscal = header['BACKSCAL']
area_arcmin2 = float(backscal)*(det_pix_as/60)**2
print(f"Value of BACKSCAL: {backscal} area: {area_arcmin2:.4f} arcmin2")
fout_xcm=fout.replace("grp","xcm")
fxcm = open(fout_xcm, "w")
fxcm.write(f'# backscal {backscal} pix2\n')
fxcm.write(f'# area {area_arcmin2:.8f} arcmin2\n')
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(f'@{prefix}../../../data/xspec/wabs_apec_cflux.xcm\n')
fxcm.write('pl lda delchi\n')
fxcm.close()
if(cpdir):
shutil.copyfile(specfile, os.path.join('../',cpdir,specfile))
shutil.copyfile(backfile, os.path.join('../',cpdir,backfile))
shutil.copyfile(respfile, os.path.join('../',cpdir,respfile))
shutil.copyfile(ancrfile, os.path.join('../',cpdir,ancrfile))
shutil.copyfile(fout, os.path.join('../',cpdir,fout))
shutil.copyfile(fout_xcm, os.path.join('../',cpdir,fout_xcm))
if(chdir):
os.chdir('../')
def get_ds9_regions(image, src_fn, bkg_fn):
# Visualize the image with ds9
d = pyds9.DS9()
d.set("file "+image)
d.set('cmap bb')
d.set('scale log')
#d.set(f"region {ds9reg_dir}/arches.reg")
if(os.path.isfile(src_fn)==True):
d.set(f"region {src_fn}")
else:
print(f'src_fn: {src_fn} is not found')
sys.exit()
if(os.path.isfile(bkg_fn)==True):
d.set(f"region {bkg_fn}")
else:
print(f'bkg_fn: {bkg_fn} is not found')
sys.exit()
#reply = input(f"{obsid}: Proceed to make spectrum/lightcurve? [y/[n]] ")
#if reply!='y':
# continue
print(d.get("regions"))
# Extract the relevant information from the ds9 regions.
region1=(re.split("circle|annulus",d.get("regions").partition("physical")[2]))[1].replace('(','').replace(')','').replace('#',',')
region2=(re.split("circle|annulus",d.get("regions").partition("physical")[2]))[2].replace('(','').replace(')','').replace('#',',')
print("Identified first region: ", region1)
print("Identified second region: ", region2)
#print("region1 "+region1.partition("color")[2].replace('=','').replace('\n',''))
#print("region2 "+region2.partition("color")[2].replace('=','').replace('\n',''))
# Identify source and background regions using the 'white' color.
c1=region1.partition("color")[2].replace('=','').replace('\n','')
print("Region1 color: "+c1)
if(c1=='white'):
regionsrc = region1
regionbkg = region2
else:
regionsrc = region2
regionbkg = region1
# Save and print selected region coordinates.
x_source = regionsrc.split(",")[0].replace('\n','')
y_source = regionsrc.split(",")[1].replace('\n','')
r_source = regionsrc.split(",")[2].replace('\n','')
print("The coordinates of the selected source region are: \n")
print(" x_source = ", x_source, "(physical)")
print(" y_source = ", y_source, "(physical)")
print(" r_source = ", r_source, "(physical) \n")
x_bkg = regionbkg.split(",")[0].replace('\n','')
y_bkg = regionbkg.split(",")[1].replace('\n','')
r_bkg = regionbkg.split(",")[2].replace('\n','')
print("The coordinates of the selected background region are: \n")
print(" x_bkg = ", x_bkg, "(physical)")
print(" y_bkg = ", y_bkg, "(physical)")
print(" r_bkg = ", r_bkg, "(physical) \n")
# If the background is an annulus, save and print R2.
r2_bkg=None
if "annulus" in str(d.get("regions")):
r2_bkg = regionbkg.split(",")[3].replace('\n','')
print(" r2_bkg = ", r2_bkg, "(physical, annulus)")
return x_source,y_source,r_source,x_bkg,y_bkg,r_bkg,r2_bkg