def xmm_gti(filename, df=False):
'''
Read GTI fits file and return the total GTI time in ks.
'''
inp = tab(fits.getdata(filename)).to_pandas()
gti = 0.
for index, row in inp.iterrows():
gti = gti + row.STOP - row.START
return gti / 1000.
def xmm_gti(filename, df=False):
'''
Read GTI fits file and return the total GTI time in ks.
'''
inp = tab(fits.getdata(filename)).to_pandas()
gti = 0.
for index, row in inp.iterrows():
gti = gti + row.STOP-row.START
return gti/1000.
def load_SDSS_phot_dr12(ra,dec,search_radius,pandas=None,ver=None,columns=None):
'''
ra in degrees, dec in degrees, search_radius in arcmin.
'''
def gen_SDSS_sql(ra, dec, search_radius,columns=columns):
if columns is None:
query_out = ' p.*'
else:
query_out = columns+',p.ra,p.dec'
query_from = ' FROM fGetNearbyObjEq({ra},{dec},{search_radius}) n, PhotoPrimary p WHERE n.objID=p.objID'.format(ra=str(ra),dec=str(dec),search_radius=str(search_radius))
query_str='SELECT'+query_out+query_from
return query_str
def query_SDSS(sSQL_query):
sURL = 'http://skyserver.sdss.org/dr12/en/tools/search/x_sql.aspx?'
# for POST request
values = {'cmd': sSQL_query,
'format': 'csv'}
data = urllib.urlencode(values)
request = urllib2.Request(sURL, data)
response = urllib2.urlopen(request)
return response.read()
sql_str=gen_SDSS_sql(ra,dec,search_radius)
sdss_ds=query_SDSS(sql_str)
lines=sdss_ds.split('\n')
nobj=len(lines)-2
if ver:print(str(nobj)+' SDSS objects found')
if nobj >0:
#pop table name and the EOF line
lines.pop(0)
lines.pop(-1)
cols=lines[0].split(',')
#pop column
lines.pop(0)
rows=[]
for i in lines:
tt=i.split(',')
tt=map(float,tt)
rows.append(tt)
tab_out=tab(rows=rows,names=cols)
if pandas:
tab_out=pd.DataFrame.from_records(tab_out._data)
radec=coord.SkyCoord(ra,dec,unit=(u.degree,u.degree),frame='icrs')
sdss=coord.SkyCoord(tab_out.ra, tab_out.dec, unit=(u.degree,u.degree),frame='icrs')
tab_out['dist_arcsec'] = radec.separation(sdss).arcsec
#should fix objID to string
#should find out what p.type means
return tab_out
else:
return []
def READSERVS(cat=True):
#fname = '/cuc36/xxl/multiwavelength/vacc/xmm/121212/xmm-irac12-sextractor.fits.gz'
fname = '/Users/ctchen/xxl/data//servs-xmm-data-fusion-sextractor.fits.gz'
servs = tab(fits.getdata(fname, 1)).to_pandas()
servs = servs[(servs.FLUX_APER_3_1 > 1.0) & (servs.FLUX_APER_3_2 > 1.0)]
servs['ID_SERVS'] = 'IRAC1_' + servs.ID_1.astype(str).str.zfill(6)
servs['mag1'] = ab_to_jy(servs.FLUX_APER_3_1.values.copy() / 1e6,
tomag=True)
servs['mag2'] = ab_to_jy(servs.FLUX_APER_3_2.values.copy() / 1e6,
tomag=True)
servs.set_index('ID_12', inplace=True)
servs['numid'] = pd.Series(range(len(servs)), index=servs.index)
servs.rename(columns={'RA_12': 'ra', 'DEC_12': 'dec'}, inplace=True)
if cat:
catservs = makecd(servs.ra.value, servs.dec.values)
return servs, catservs #Check Data Fusion
else:
return servs
def xmm_bkgd(filename, df=False, fit=False, sig=None):
'''
The input file should be the output of the step 1 in:
http://www.cosmos.esa.int/web/xmm-newton/sas-thread-epic-filterbackground
which bins the photons in 100s time intervals
'''
if sig is None:
sig = 3
inp = fits.getdata(filename)
inp = tab(inp).to_pandas()
# Fit a gaussian model to the rate distribution
if df is True:
return inp
elif fit is True:
gmm = sklearn.mixture.GaussianMixture(n_components=1)
r = gmm.fit(inp.RATE.values[:, np.newaxis])
return r
else:
gmm = sklearn.mixture.GaussianMixture(n_components=1)
r = gmm.fit(inp.RATE.values[:, np.newaxis])
return r.means_[0, 0] + sig * np.sqrt(r.covars_[0, 0])
def xmm_bkgd(filename, df=False, fit=False, sig=None):
'''
The input file should be the output of the step 1 in:
http://www.cosmos.esa.int/web/xmm-newton/sas-thread-epic-filterbackground
which bins the photons in 100s time intervals
'''
if sig is None:
sig = 3
inp = fits.getdata(filename)
inp = tab(inp).to_pandas()
# Fit a gaussian model to the rate distribution
if df is True:
return inp
elif fit is True:
mu, std = norm.fit(inp.RATE.values)
r = [mu, std]
return r
else:
mu, std = norm.fit(inp.RATE.values)
r = [mu, std * sig]
return r
default=False,
help='savepdf if set as True.')
args = parser.parse_args()
verbose = args.verbose
vprint = verboseprint(verbose)
overwrite = args.overwrite
savepdf = args.savepdf
evt = args.evt
out = args.out
xy = args.xy
evthdu = fits.open(evt, ignore_missing_end=True)
evttab = tab(evthdu[1].data)
evttab = evttab[(evttab['PI'] >= 0) & (evttab['PI'] <= 511)]
# flattend index of the detector pixels each event
detcoor_id = evttab['RAW_X'].quantity.value * npixx + evttab[
'RAW_Y'].quantity.value
dmask = create_circular_mask(48, 48, radius=24)
img, xx, yy = np.histogram2d(evttab['RAW_X'],
evttab['RAW_Y'],
bins=[np.arange(npixx + 1),
np.arange(npixy + 1)])
if np.min(img) == 0:
ctmin = 1
else:
savepdf = args.savepdf evt = args.evt switch = args.switch arf = args.arf out = args.out psf = args.psf vig = args.vig rmf = args.rmf box = args.box bbox = args.bbox bkgout = out[:-4] + 'bkg.fits' evthdu = fits.open(evt) evttab = tab(evthdu[1].data) # kick out events with weird PI (should've been done with martfilter # already, but just in case) evttab = evttab[(evttab['PI']>=0) & (evttab['PI'] <= 511)] expvalue = evthdu[0].header['EXPOSURE'] # flattend index of the detector pixel coordinate of each event detcoor_id = evttab['RAW_X'].quantity.value * npixx + evttab['RAW_Y'].quantity.value # detector mask dmask = create_circular_mask(48,48,radius=24) img, xx, yy = np.histogram2d(evttab['RAW_X'], evttab['RAW_Y'], bins=[np.arange(npixx + 1), np.arange(npixy +1)]) if np.min(img) == 0:
for i, l in enumerate(lines):
if i == 22:
met = float(l.split()[-1])
if i >= 517:
j = l.split()
t.append(float(j[0]))
ug.append(float(j[1]))
gi.append(float(j[2]))
ih.append(float(j[3]))
ui.append(float(j[4]))
t = np.array(t)
ui = np.array(ui)
gi = np.array(gi)
ug = np.array(ug)
ih = np.array(ih)
pegase_table = tab([t, ui, gi, ug, ih],
names=("time", "u-i", "g-i", "u-g", "i-h"))
pegase_table.write("pegase_z=" + str(met) + ".fits",
format="fits",
overwrite=True)
fig = plt.scatter(ui[::skips],
ih[::skips],
c=np.log10(t * 1000000.)[::skips],
marker=markers[k],
s=100,
label=str(met),
edgecolors="none",
zorder=5,
alpha=1)
plt.plot(ui, ih, '--', color='black', alpha=.7, zorder=3)
plt.scatter(data_cat['MAG_APER_1'][:, 1] - derred[0] -
(data_cat["MAG_APER_3"][:, 1] - derred[2]),
def readfits(fname):
return tab(fits.getdata(fname)).to_pandas()
detnam = detnam_d[istr]
urdn = urdn_d[istr]
detn = detn_d[istr]
csvname = eapath + '/ARTXC_EA_M' + istr + '.csv'
df = pd.read_csv(csvname)
vigarr = np.zeros((1, 1, 31, 13))
for i in range(13):
thetac = df.loc[i, 'thetac']
sig1 = df.loc[i, 'sigma1']
sig2 = df.loc[i, 'sigma2']
a1 = df.loc[i, 'A1']
a2 = df.loc[i, 'A2']
vigarr[0,0,:,i] = func_EA(thetaarcmin, thetac, sig1, a1, sig2, a2)/\
np.max(func_EA(thetaarcmin, thetac, sig1, a1, sig2, a2))
t = tab([[en_lo], [en_hi], [thetadeg],
np.array([0.0]), vigarr],
names=('ENERG_LO', 'ENERG_HI', 'THETA', 'PHI', 'VIGNET'))
col1 = fits.Column(array=t['ENERG_LO'].data,
name='ENERG_LO',
format='13E',
unit='keV')
col2 = fits.Column(array=t['ENERG_HI'].data,
name='ENERG_HI',
format='13E',
unit='keV')
col3 = fits.Column(array=t['THETA'].data,
name='THETA',
format='31E',
unit='degree')
col4 = fits.Column(array=t['PHI'].data,
name='PHI',
for key in hdum[0].header.keys():
keylist.append(key)
if not 'HISTORY' in keylist:
vprint('No history in the primary HDU')
hdum[0].header['HISTORY'] = 'Initializing with ' + fname_m
for i in np.arange(len(evtfiles) - 1) + 1:
evta = evtfiles[i].strip()
fname_a = os.path.abspath(evta).split('/')[-2] + '/' + os.path.abspath(
evta).split('/')[-1]
for card in hdum[0].header['HISTORY']:
if fname_a in card:
print('no merging needed, ' + fname_a +
' has been merged before.')
hdua = fits.open(evta)
tabm = tab(hdum[1].data)
taba = tab(hdua[1].data)
if tabm['TIME'][-1] <= taba['TIME'][0]:
# if all events the list to be appended are later than the last event of primary
newtab = vstack([tabm, taba])
elif taba['TIME'][-1] <= tabm['TIME'][0]:
# if the first event of the primary list is later than all events in the list to be appended
newtab = vstack([taba, tabm])
elif force:
# something is wrong, sort the output
vprint('The time interval of evta is already part of evtm')
vprint('force == True, continuing now.')
newtab = vstack([tabm, taba])
newtab.sort('TIME')
else:
# something is wrong, sort the output
parser.add_argument('-overwrite', type=bool, required=False, default=True,
help='Overwrite if set as True.')
args = parser.parse_args()
verbose = args.verbose
vprint = verboseprint(verbose)
evt = args.evt
arf = args.arf
out = args.out
overwrite = args.overwrite
arfhdu = fits.open(arf)
arf1 = tab(arfhdu[1].data)
enarr = arf1['ENERG_LO'].quantity.value
enarr = np.hstack([enarr, np.array(arf1['ENERG_HI'][-1])])
arthdu = fits.open(evt)
piarr = get_pi(arthdu[1].data['ENERGY'])
evthead = arthdu[1].header
arthdu[1] = add_column(arthdu[1], piarr, 'PI', 'I', '', overwrite)
arthdu.writeto(out, overwrite=overwrite)
print('wrote PI arrays into ' + out)
help='RA in degrees')
parser.add_argument(
'-dec', type=float, required=True,
help='DEC in degrees')
args = parser.parse_args()
src_ra = args.ra
src_dec = args.dec
data = ascii.read('/home/ctchen/lib/martxc_local/artxc_survey_grid.txt')
tiles = data['tile'].quantity.value.astype(str)
for idx, tt in enumerate(tiles):
tiles[idx] = tt.zfill(6)
data['tile'] = tiles
data = tab(data).to_pandas()
raarr = data['ramin'].values
raarr = np.hstack([raarr, data['ramax'].values[-1]])
decarr = data['decmin'].values
decarr = np.hstack([decarr, data['decmax'].values[-1]])
def isintile(row, ra, dec):
if (row.ramin <= ra < row.ramax) & (row.decmin <= dec < row.decmax):
return True
else:
return False
if sum(data.apply(isintile, axis=1,args=(src_ra, src_dec))) == 1:
