lens_z = lens[:, 4]
print "randoms to lens ratio", nrands * 1.0 / len(lens)
print "assigning redshifts to randoms"
hist, bins = np.histogram(lens_z, bins=50)
bin_midpoints = bins[:-1] + np.diff(bins) / 2
cdf = np.cumsum(hist)
cdf = cdf / float(cdf[-1])
nrands = len(rname)
values = np.random.rand(nrands)
value_bins = np.searchsorted(cdf, values)
rand_z = bin_midpoints[value_bins]
R, St, Sx, W, Str, Sxr, Wr, Npairs, Sc = dsigma(lens, source)
print "done with dsigma_i"
Rc = cosmo.kpc_comoving_per_arcmin(np.median(lens_z)) * R
dsigma_file = h5py.File(
"pau_tim_deltasigma_bkg_z_" + str(zl1) + "_" + str(zl2) + "_" +
str(zpeak) + ".h5", "w")
dsigma_file.create_dataset("r", (5, ), data=Rc)
dsigma_file.create_dataset("dsigma_lens", (5, ), data=St)
dsigma_file.create_dataset("dsigma_random", (5, ), data=Str)
dsigma_file.create_dataset("npairs", (5, ), data=Npairs)
dsigma_file.create_dataset("Sc", (1, ), data=Sc)
dsigma_file.close()
print "done with writing the file for the lens bin", i
galmask = (rmag_abs < -21.) & (galZ < zmax)
galRA, galDEC, galZ, rmag, rmag_abs = galRA[galmask], galDEC[galmask], galZ[
galmask], rmag[galmask], rmag_abs[galmask]
# Calculating the number of galaxies...
Ngals = np.array([np.sum(galZ < zbins[z])
for z in range(len(zbins))]) # below each redshift bin
Ngals_high = len(galZ) - Ngals # above each redshift bin
# Calculating the volume of the cone at each redshift bin
cosmo = LambdaCDM(H0=70., Om0=0.315, Ode0=0.685)
Dcbins = (cosmo.comoving_distance(zbins).to('Mpc')
).value # Comoving distance to each bin limit
Mpc_am = (cosmo.kpc_comoving_per_arcmin(zbins).to('Mpc/arcmin')
).value # Comoving distance per arcmin at each bin limit
areabins = np.pi * (
theta * Mpc_am)**2. # Comoving area of the circle at each bin limit
#covolbins = cosmo.comoving_volume(zbins).to('kpc3').value
covolbins = 1. / 3. * areabins * Dcbins # Comoving cone volume below each bin limit
covolbins_high = covolbins[
-1] - covolbins # Comoving cone volume above each bin limit
density = Ngals / covolbins # Density below the redshift limit
density_high = Ngals_high / covolbins_high # Density above the redshift limit
densmask = (0.2 < zbins) & (zbins < 0.25)
densplus = np.sum(zbins < 0.2)
class MaNGA(object):
"""Class for a MaNGA observated galaxy"""
def __init__(self, *arg, mangaid=None):
"""use plateifu and mangaid as the keyword to define a galaxy
*arg: Only the first one is used, as the plateifu
mangaid: the mangaid of the galaxy
return MaNGA
"""
## Define the global data directories
self.COSMO = LambdaCDM(H0=70, Om0=0.3, Ode0=0.7)
self.ESP = 1e-8
self.C = 299792 # speed of light (km/s)
self.drp_version = DRP_VERSION
self.dap_version = DAP_VERSION
## Pre-read the DRP data
if arg:
self.plateifu = arg[0]
self.drp = DRP[DRP['plateifu'] == self.plateifu]
self.mangaid = self.drp['mangaid'][0]
elif mangaid:
self.mangaid = mangaid
self.drp = DRP[DRP['mangaid'] == self.mangaid]
self.plateifu = self.drp['plateifu'][0]
else:
print("No valid plateifu or mangaid detected!")
raise ValueError
self.plate, self.ifudsgn = re.split('-', self.plateifu)
self.logcube_file = "{0}/{1}/stack/manga-{1}-{2}-LOGCUBE.fits.gz".format(
DRP_DIR, self.plate, self.ifudsgn)
if DAP_VERSION < '2.3.0': # before MPL8
self.mapsfile = DAP_DIR+self.plate + '/'+self.ifudsgn+'/' \
+ 'manga-' + self.plate + '-' + self.ifudsgn \
+ '-MAPS-{}-GAU-MILESHC.fits.gz'.format(PRODOCTS)
self.datacubefile = DAP_DIR + '/'+self.plate+'/' \
+ self.ifudsgn+'/'+'manga-' + self.plate \
+ '-' + self.ifudsgn \
+ '-LOGCUBE-{}-GAU-MILESHC.fits.gz'.format(PRODOCTS)
elif DAP_VERSION >= '2.3.0': #After MPL8
self.mapsfile = '{0}/{1}/{2}/manga-{1}-{2}-MAPS-{3}-MILESHC-MILESHC.fits.gz'.format(
DAP_DIR, self.plate, self.ifudsgn, PRODOCTS)
self.datacubefile = '{0}/{1}/{2}/manga-{1}-{2}-LOGCUBE-{3}-MILESHC-MILESHC.fits.gz'.format(
DAP_DIR, self.plate, self.ifudsgn, PRODOCTS)
if IMAGE_DIR is None:
self.image_file = "{}/{}/images/{}.png".format(
DRP_DIR, self.plate, self.ifudsgn)
else:
self.image_file = "{}/{}-{}.png".format(IMAGE_DIR, self.plate,
self.ifudsgn)
self.ra = self.drp['objra'][0]
self.dec = self.drp['objdec'][0]
self.ifura = self.drp['ifura'][0]
self.ifudec = self.drp['ifudec'][0]
self.elpetro_r = self.drp['nsa_elpetro_th50_r'][0]
self.elpetro_ba = self.drp['nsa_elpetro_ba'][0]
self.elpetro_phi = self.drp['nsa_elpetro_phi'][0]
self.sersic_r = self.drp['nsa_sersic_th50'][0]
self.sersic_ba = self.drp['nsa_sersic_ba'][0]
self.sersic_phi = self.drp['nsa_sersic_phi'][0]
self.sersic_n = self.drp['nsa_sersic_n'][0]
self.psf = self.drp['rfwhm'][0]
self.z = self.drp['nsa_z'][0]
self.c = const.c.to(u.km / u.s).value
self.d = self.COSMO.luminosity_distance(self.z)
self.arcsec2kpc = self.COSMO.kpc_comoving_per_arcmin(self.z).to(
u.kpc / u.arcsec)
self.repeat, self.alter = self.find_repeat(self)
@property
def target_range(self):
# check the target type of primary and secondary
# currently we still use the 'full fill the field of view' and 'other'
# by give a resonable value, use with cautious
mngtarg1 = self.drp['mngtarg1']
if np.bitwise_and(mngtarg1, 2**10):
Rrange = 1.5 # 1.5Re Primary
elif np.bitwise_and(mngtarg1, 2**11):
Rrange = 2.5 # 2.5Re Secondary
elif np.bitwise_and(mngtarg1, 2**13):
Rrange = 1.5 # full fill the field of view
else:
Rrange = 1.5 # Other
return Rrange
def find_repeat(self, recommend=True):
# read the manga data/repeat_observation.txt to check and return all the
# repeat observations
# return the plateifu list, also return the recommend one if recommend
# is True
mangaid = self.mangaid
txt = np.loadtxt(package_path + '/data/repeat_observations.txt',
skiprows=5,
dtype='str')
target = txt[txt[:, 0] == mangaid]
repeat_list = []
if len(target) > 0:
for i in range(1, 9, 2):
plate = target[0][i]
ifu = target[0][i + 1]
if plate != '-1':
repeat_list.append(plate + '-' + ifu)
if recommend:
# pick all the ifu out and find the maximum
ifu_list = list(
map(lambda s: re.match(r"\d+-(\d+)\d", s).group(1),
repeat_list))
recommend_plateifu = np.array(repeat_list)[np.array(ifu_list)
== max(ifu_list)]
# when serveral alternative, the first one is returned
return repeat_list, recommend_plateifu[0]
return repeat_list, None
def image(self, ax=None, showImage=True):
"""return or show rgb-image
"""
try:
imagedata = mpimg.imread(self.image_file)
except:
print("{} image file doesn't exist!".format(self.plateifu))
imagedata = np.zeros((2, 2))
if ax == None:
fig = plt.figure()
ax = fig.add_subplot(111)
ax.imshow(imagedata)
ax.set_xticklabels([])
ax.set_yticklabels([])
# set the 'show=False' when use it as a figure modifier
if showImage:
plt.show()
def showdetail(self, showDRPInfo=True, showDAPInfo=True):
""" show dap and drp detail of the target
drp3qual see: https://trac.sdss.org/wiki/MANGA/TRM/TRM_MPL-5/metadata
"""
if showDRPInfo:
drp_qual_dict = dict({
0: 'GOOD',
1: 'RETIRED',
2: 'BADDEPTH',
4: 'SKYSUBBAD',
8: 'HIGHSCAT',
16: 'BADASTROM',
32: 'VARIABLELSF',
64: 'BADOMEGA',
256: 'BADFLUX',
512: 'BADPSF',
2**30: 'CRITICAL'
})
drp3qual = self.drp['drp3qual'][0]
print("****** DRP Imformation ******** ")
print('The drp3qual is: {0}'.format(drp_qual_dict[drp3qual]))
print('The image information:')
print('elpetro_r = {0}, b/a = {1}, phi = {2}'.format(
self.elpetro_r, self.elpetro_ba, self.elpetro_phi))
print('The redshift is: {0}'.format(self.z))
print('The distance is: {0}'.format(self.d))
print('Re is: {0}'.format(self.arcsec2kpc * self.elpetro_r *
u.arcsec))
# print('LOG10(LOIII) is: {0}'.format(logO3))
if showDAPInfo:
dap_qual_dict = dict({
0: 'GOOD',
1: 'FORESTAR',
2: 'BADZ',
4: 'LINELESS',
8: 'PPXFFAIL',
16: 'SINGLEBIN',
2**28: 'DRPCRIT',
2**29: 'DAPCRIT',
2**30: 'CRITICAL'
})
print("****** DAP Imformation ******** ")
print('The DAP quality is: {0}'.format(
dap_qual_dict[self.maps[0].header['DAPQUAL']]))