def mk_mock_coords(radeczfile, outfile, simul_cosmo):
if simul_cosmo == "Planck":
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif simul_cosmo == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
rad = np.arange(1.0, 67.0, 5.0)
radecz = h5_arr(radeczfile, "radecz")
cart = np.zeros(radecz.shape)
for i, rdz in enumerate(radecz):
ra = Angle(rdz[0], u.deg)
dec = Angle(rdz[1], u.deg)
losd = cosmo.comoving_distance(rdz[2])
dis = Distance(losd)
coord = ICRSCoordinates(ra, dec, distance=dis)
cart[i, :] = np.array([coord.x.value, coord.y.value, coord.z.value])
np.savetxt(outfile, cart)
def mk_mock_coords(radeczfile, outfile, simul_cosmo):
if simul_cosmo == "Planck":
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif simul_cosmo == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
rad = np.arange(1.0, 67.0, 5.0)
radecz = h5_arr(radeczfile, "radecz")
cart = np.zeros(radecz.shape)
for i, rdz in enumerate(radecz):
ra = Angle(rdz[0], u.deg)
dec = Angle(rdz[1], u.deg)
losd = cosmo.comoving_distance(rdz[2])
dis = Distance(losd, u.Mpc)
coord = ICRSCoordinates(ra, dec, distance=dis)
cart[i, :] = np.array([coord.x, coord.y, coord.z])
arr2h5(cart, outfile, "coords", mode='w')
def LumFunc(mr, name=None, mr_bin=None):
''' luminosity function
:param mr:
array of r-band luminosities
:param name:
string specifying data set, which is used to get comoving volume in
units of (Mpc/h)^3
:return mr_bin_mid:
middle values of M_r bins
:return phi:
luminosity function (Mpc/h)^-3
'''
assert name is not None, "specify name for comoving volume"
if mr_bin is None:
mr_bin = np.linspace(-25., -20., 11)
dmr = mr_bin[1:] - mr_bin[:-1]
if name == 'sdss': # volume of SDSS
from astropy.cosmology import Planck13 as cosmo
vol = (cosmo.comoving_volume(0.033390).value -
cosmo.comoving_volume(0.01069).value) * \
(7966./41253.) * cosmo.h**3 # (Mpc/h)^3
else:
vol = {'simba': 100.**3, 'tng': 75.**3}[name]
Ngal, _ = np.histogram(mr, bins=mr_bin)
phi = Ngal.astype(float) / vol / dmr
return 0.5 * (mr_bin[1:] + mr_bin[:-1]), phi
def __init__(self, CE):
self._base_dir = '/virgo/simulations/Hydrangea/10r200/CE-{:.0f}/'\
'HYDRO/highlev/'.format(CE)
self._propfile = path.join(self._base_dir, 'FullGalaxyTables.hdf5')
self._posfile = path.join(self._base_dir, 'GalaxyPositionsSnap.hdf5')
self._snepfile = path.join(self._base_dir, 'GalaxyPaths.hdf5')
self._interp_file = path.join(self._base_dir,
'GalaxyCoordinates10Myr.hdf5')
with h5py.File(self._snepfile, 'r') as f:
self.snep_redshifts = np.array([
f['Snepshot_{:04d}'.format(sn_i)].attrs['Redshift'][0]
for sn_i in f['RootIndex/Basic']
])
self.snap_redshifts = np.array([
f['Snepshot_{:04d}'.format(sn_i)].attrs['Redshift'][0]
for sn_i in f['SnapshotIndex']
])
self.snip_redshifts = np.array([
f['Snepshot_{:04d}'.format(sn_i)].attrs['Redshift'][0]
for sn_i in f['SnipshotIndex']
])
self.snap_scales = 1 / (1 + self.snap_redshifts)
self.snap_times = cosmo.age(self.snap_redshifts)
self.snip_scales = 1 / (1 + self.snip_redshifts)
self.snip_times = cosmo.age(self.snip_redshifts)
self.snep_scales = 1 / (1 + self.snep_redshifts)
self.snep_times = cosmo.age(self.snep_redshifts)
self._data = dict()
return
def __init__(self):
"""
Container class to compute window functions due to resolution and volume effects. See for example https://arxiv.org/pdf/1907.10067.pdf
"""
# Set constants
self.fromHztoeV = 6.58e-16
self.gramstoeV = 1 / (1.78 * 1e-33)
self.mtoev = 1 / (1.97 * 1e-7)
self.H0 = cosmo.H(0).value * 1e3 / (1e3 * const.kpc.value
) #expressed in 1/s
self.rhocritical = cosmo.critical_density(0).value * self.gramstoeV / (
1e-2)**3 # eV/m**3
self.Om0 = cosmo.Om0 #total matter
self.OLambda0 = cosmo.Ode0 # cosmological constant
self.DM0 = self.Om0 - cosmo.Ob0 # dark matter
self.evtonJoule = 1.60218 * 1e-10 # from eV to nJ
self.evtoJoule = 1.60218 * 1e-19 # from eV to J
self.h = 0.6766
self.Mpc = 1e3 * const.kpc.value
self.zmin = 0.001
self.zmax = 30.001
self.zbins = 301
self.h = cosmo.h
def main():
fil = pysysp.StarSpectrum()
fil.setwavelength(np.arange(1000, 30000, 0.4))
fil.setflux( 1e-15 * (fil.wavelength/10000.0)**(-1.5))
i = pysysp.BandPass('/Users/jselsing/github/pysysp/pysysp/filters/ugriz/i.dat')
dl = (cosmo.luminosity_distance(1.2)) * 1e5
Mz0 = -5 * np.log10(dl.value) + fil.apmag(band=i, mag='AB')
print('Mz0 = '+str(Mz0))
i.wavelength /= (1 + 2)
# fil.flux = fil.flux * (1 + 2)
i.update_bandpass()
dl = (cosmo.luminosity_distance(1.2)) * 1e5
Mz2 = -5 * np.log10(dl.value) + fil.apmag(band=i, mag='AB') #- 2.5 * np.log10(1 + 2)
print('Mz2 = '+str(Mz2))
# i.wavelength *= (1 + 2)
# i.update_bandpass()
# fil.wavelength = fil.wavelength * (1 + 2)
# fil.flux = fil.flux / (1 + 2)
# dl = (cosmo.luminosity_distance(1.2)) * 1e5
# Mz2 = -5 * np.log10(dl.value) + fil.apmag(band=i, mag='AB')
# print('Mz2 = '+str(Mz2))
print('Mz0 - Mz2 = '+str(Mz0 - Mz2))
def parse_input(self, ConfigFile):
"""
Parse the geom. parameters from the configuration file to the object
Parameters
----------
ConfigFile : string
path to the configuration file (filename)
Self consistent calculations of the cosmological luminosity distance}
and the angular diameter distance are also performed and added as
attributes of the object
"""
run_config = configparser.SafeConfigParser({}, allow_no_value=True)
run_config.read(ConfigFile)
self.incl = run_config.getfloat('geometry','incl')
self.pa = run_config.getfloat('geometry','pa')
self.x0 = run_config.getfloat('geometry','x0')
self.y0 = run_config.getfloat('geometry','y0')
self.vsys = run_config.getfloat('geometry','Vsys')
self.z = run_config.getfloat('geometry','z')
self.dl = cosmo.luminosity_distance(self.z).to('Mpc').value
# note that the following could have been computed from the angular
# diameter distance as well, it is equivalent
self.dtheta = cosmo.kpc_proper_per_arcmin(self.z).to('kpc / arcsec').value
def mk_coords(radecfile, outfile, cosmology):
# Set the cosmology with h free
if cosmology == "Planck":
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif cosmology == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
f_in = h5.File(radecfile)
radecz = f_in["radecz"]
f_out = h5.File(outfile)
cart = f_out.create_dataset("cart_pts", shape=(radecz.shape[0], 3),
dtype='float64')
for i in range(radecz.shape[0]):
ra = Angle(radecz[i, 0], u.deg)
dec = Angle(radecz[i, 1], u.deg)
losd = cosmo.comoving_distance(radecz[i, 2])
dis = Distance(losd)
coord = ICRSCoordinates(ra, dec, distance=dis)
cart[i, :] = np.array([coord.x, coord.y, coord.z])
f_in.close()
f_out.close()
def getPhysical(z, radio_data):
DAkpc = float(cosmo.angular_diameter_distance(z) /
u.kpc) #angular diameter distance in kpc
DLm = float(cosmo.luminosity_distance(z) / u.m) #luminosity distance in m
maxPhysicalExtentKpc = DAkpc * radio_data['radio'][
'max_angular_extent'] * np.pi / 180 / 3600 #arcseconds to radians
totalCrossSectionKpc2 = np.square(
DAkpc) * radio_data['radio']['total_solid_angle'] * np.square(
np.pi / 180 / 3600) #arcseconds^2 to radians^2
totalLuminosityWHz = radio_data['radio'][
'total_flux'] * 1e-29 * 4 * np.pi * np.square(
DLm) #mJy to W/(m^2 Hz), kpc to m
totalLuminosityErrWHz = radio_data['radio'][
'total_flux_err'] * 1e-29 * 4 * np.pi * np.square(DLm)
peakLuminosityErrWHz = radio_data['radio'][
'peak_flux_err'] * 1e-29 * 4 * np.pi * np.square(DLm)
for component in radio_data['radio']['components']:
component['physical_extent'] = DAkpc * component[
'angular_extent'] * np.pi / 180 / 3600
component['cross_section'] = np.square(
DAkpc) * component['solid_angle'] * np.square(np.pi / 180 / 3600)
component['luminosity'] = component[
'flux'] * 1e-29 * 4 * np.pi * np.square(DLm)
component['luminosity_err'] = component[
'flux_err'] * 1e-29 * 4 * np.pi * np.square(DLm)
for peak in radio_data['radio']['peaks']:
peak['luminosity'] = peak['flux'] * 1e-29 * 4 * np.pi * np.square(DLm)
physical = {'max_physical_extent':maxPhysicalExtentKpc, 'total_cross_section':totalCrossSectionKpc2, \
'total_luminosity':totalLuminosityWHz, 'total_luminosity_err':totalLuminosityErrWHz, \
'peak_luminosity_err':peakLuminosityErrWHz}
return physical
def mk_coords(radecfile, outfile, cosmology):
# Set the cosmology with h free
if cosmology == "Planck":
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif cosmology == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
f_in = h5.File(radecfile)
radecz = f_in["radecz"]
f_out = h5.File(outfile)
cart = f_out.create_dataset("cart_pts",
shape=(radecz.shape[0], 3),
dtype='float64')
for i in range(radecz.shape[0]):
ra = Angle(radecz[i, 0], u.deg)
dec = Angle(radecz[i, 1], u.deg)
losd = cosmo.comoving_distance(radecz[i, 2])
dis = Distance(losd)
coord = ICRSCoordinates(ra, dec, distance=dis)
cart[i, :] = np.array([coord.x, coord.y, coord.z])
f_in.close()
f_out.close()
def __init__(self):
"""
Container class to compute the Cl due to high-z contributions; we first define the window functions
"""
# Set constants
self.fromHztoeV = 6.58e-16
self.gramstoeV = 1 / (1.78 * 1e-33)
self.mtoev = 1 / (1.97 * 1e-7)
self.H0 = cosmo.H(0).value * 1e3 / (1e3 * const.kpc.value
) #expressed in 1/s
self.rhocritical = cosmo.critical_density(0).value * self.gramstoeV / (
1e-2)**3 # eV/m**3
self.Om0 = cosmo.Om0 #total matter
self.OLambda0 = cosmo.Ode0 # cosmological constant
self.DM0 = self.Om0 - cosmo.Ob0 # dark matter
self.evtonJoule = 1.60218 * 1e-10 # from eV to nJ
self.evtoJoule = 1.60218 * 1e-19 # from eV to J
self.h = 0.6766
PS1h = np.loadtxt(
"/Users/andreacaputo/Desktop/Phd/AxionDecayCrossCorr/Codes/NIRB_PS/PS_DM_1h.dat"
)
PS2h = np.loadtxt(
"/Users/andreacaputo/Desktop/Phd/AxionDecayCrossCorr/Codes/NIRB_PS/PS_DM_2h.dat"
)
self.Mpctometer = 3.086e+22 # from Mpc to meters
self.Mpc = 1e3 * const.kpc.value
self.zmin = 0.001
self.zmax = 30.001
self.zbins = 301
self.h = cosmo.h
self.TotPower = PS1h + PS2h
self.z_vect = np.linspace(self.zmin, self.zmax, self.zbins)
self.k_vect = PS1h[:, 0] * self.h
self.Power = self.TotPower[:, 1:] / self.h**3
self.Praw_prova = interp2d(self.k_vect, self.z_vect,
np.transpose(self.Power))
self.Msun = const.M_sun.value #Kg
self.Lsun = const.L_sun.value # in W
self.Sb = const.sigma_sb.value # Stefan-Boltzmann constant in W/m**2/K**4
self.Rsun = const.R_sun.value # in meters
self.hplanck = const.h.value # Js
self.cc = const.c.value #m/s
self.kb = const.k_B.value # kb constant J/K
self.mp = const.m_p.value # proton mass in Kg
self.Hseconds = cosmo.H(0).value / (1e6 * u.parsec.to(u.km)) # in 1/s
self.nHnebula = 1e4 / (
1e-2)**3 # in m**-3, is also equal to the electron number density
self.eVtoK = 1.16e4 # from eV to K
self.year = 3.154e+7 # from year to seconds
self.Ry = 1.1e7 #1/m Rydberg constant
self.ergtoJoule = 1e-7 # from erg to Joule
self.fromJouletoeV = 6.242e+18 # from Joule to eV
self.Mpc = 1e3 * const.kpc.value
self.RyK = 13.6057 * self.eVtoK
self.Tgas = 3e4 # Kelvin, below Eq.9 in the paper, said to be used to calculate alphaB
self.nuly = 2.4663495e15 # Lyman alpha frequency in Hz, which corresponds to a photon energy of
def get_inv_efunc(cosmology):
if cosmology == "Planck":
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif cosmology == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
return cosmo.inv_efunc
def get_comv(cosmology):
if cosmology == "Planck":
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif cosmology == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
return cosmo.comoving_distance
def slice_z_cosmo(slice, z, radius):
"""Slices in redshift considering a distance to cut"""
zmax = z_at_value(cosmo.comoving_distance, cosmo.comoving_distance(z) + radius)
zmin = z_at_value(cosmo.comoving_distance, cosmo.comoving_distance(z) - radius)
print zmin - zmax
slice = slice[np.where(slice["zb_1"] < zmax)]
slice = slice[np.where(slice["zb_1"] > zmin)]
return slice
def r200(z,M_200): ## unit: arcsec critical_density = Planck13.critical_density(z).si.value # unit: kg/m^3 m2arcs = np.degrees(1.0/Planck13.angular_diameter_distance(z).si.value)*3600. critical_density = critical_density*Planck13.H0/100./m2arcs**3/2e30 # unit: Msun/arcsec^3/h r200_cube = 200*critical_density/M_200/(4./3.*np.pi) r200 = r200_cube**(1./3.) return r200
def r200(z, M_200): ## unit: arcsec
critical_density = Planck13.critical_density(z).si.value # unit: kg/m^3
m2arcs = np.degrees(
1.0 / Planck13.angular_diameter_distance(z).si.value) * 3600.
critical_density = critical_density * Planck13.H0 / 100. / m2arcs**3 / 2e30 # unit: Msun/arcsec^3/h
r200_cube = 200 * critical_density / M_200 / (4. / 3. * np.pi)
r200 = r200_cube**(1. / 3.)
return r200.value
def mk_mock_srch(radecfile, nzdictfile, Nsph, simul_cosmo):
if simul_cosmo == "Planck":
# First make h free
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif simul_cosmo == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
comv = cosmo.comoving_distance
radecarr = h5_arr(radecfile, "good_pts")
nzdict = json.load(open(nzdictfile))
Nrands = radecarr.shape[0]
Narrs = Nsph / Nrands
remain = Nsph % Nrands
radecz = np.zeros((Nsph, 3))
for i in range(Narrs):
start = Nrands * i
stop = Nrands * (i + 1)
radecz[start:stop, :2] = radecarr[:, :]
endchunk = Nrands * (Narrs)
radecz[endchunk:, :2] = radecarr[:remain, :]
rad = np.arange(1.0, 67.0, 5.0)
zlo = nzdict["zlo"]
zhi = nzdict["zhi"]
radeczlist = len(rad) * [radecz]
for r_i, r in enumerate(rad):
dis_near = Distance(comv(zlo).value + r, u.Mpc)
dis_far = Distance(comv(zhi).value - r, u.Mpc)
z_a = dis_near.compute_z(cosmology=cosmo)
z_b = dis_far.compute_z(cosmology=cosmo)
randz = (z_a ** 3 + \
(z_b ** 3 - z_a ** 3) * np.random.rand(Nsph)) ** (1. / 3.)
radeczlist[r_i][:, 2] = randz[:]
arr2h5(
radeczlist[r_i], "{0}/{1}/mocks/mock_srch_pts.hdf5".format(
os.path.dirname(radecfile), simul_cosmo),
"radecz_{0}".format(str(r_i * 5 + 1)))
def calc_ages(z, a_born):
# Convert scale factor into redshift
z_born = 1 / a_born - 1
# Convert to time in Gyrs
t = cosmo.age(z)
t_born = cosmo.age(z_born)
# Calculate the VR
ages = (t - t_born).to(u.Myr)
return ages.value
def M_to_sigma(M, z=0, mode='3D'):
if mode == '3D':
ndim_scale = np.sqrt(3)
elif mode == '1D':
ndim_scale = 1.
# return prefac * .00989 * U.km / U.s \
# * np.power(M.to(U.Msun).value, 1 / 3)
# Note: Delta_vir returns the overdensity in units of background,
# which is Delta_c * Om in B&N98 notation.
return 0.016742 * U.km * U.s**-1 * np.power(
np.power(M.to(U.Msun).value, 2) * Delta_vir(z) / Delta_vir(0) *
cosmo.Om(z) / cosmo.Om0 * np.power(cosmo.H(z) / cosmo.H0, 2),
1 / 6) / ndim_scale
def mk_mock_srch(radecfile, nzdictfile, Nsph, simul_cosmo):
if simul_cosmo == "Planck":
# First make h free
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif simul_cosmo == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
comv = cosmo.comoving_distance
radecarr = h5_arr(radecfile, "good_pts")
nzdict = json.load(open(nzdictfile))
Nrands = radecarr.shape[0]
Narrs = Nsph / Nrands
remain = Nsph % Nrands
radecz = np.zeros((Nsph, 3))
for i in range(Narrs):
start = Nrands * i
stop = Nrands * (i + 1)
radecz[start:stop, :2] = radecarr[:, :]
endchunk = Nrands * (Narrs)
radecz[endchunk:, :2] = radecarr[:remain, :]
rad = np.arange(1.0, 67.0, 5.0)
zlo = nzdict["zlo"]
zhi = nzdict["zhi"]
radeczlist = len(rad) * [radecz]
for r_i, r in enumerate(rad):
dis_near = Distance(comv(zlo) + r, u.Mpc)
dis_far = Distance(comv(zhi) - r, u.Mpc)
z_a = dis_near.compute_z(cosmology=cosmo)
z_b = dis_far.compute_z(cosmology=cosmo)
randz = (z_a ** 3 + \
(z_b ** 3 - z_a ** 3) * np.random.rand(Nsph)) ** (1. / 3.)
radeczlist[r_i][:, 2] = randz[:]
arr2h5(radeczlist[r_i], "{0}/{1}/mocks/mock_srch_pts.hdf5".format(os.path.dirname(radecfile), simul_cosmo), "radecz_{0}".format(str(r_i * 5 + 1)))
def __init__(self):
"""
Container class to compute various quantities for low-z Galaxy as studied here --> https://arxiv.org/pdf/1201.4398.pdf
"""
# Set constants
self.fromHztoeV = 6.58e-16
self.gramstoeV = 1 / (1.78 * 1e-33)
self.mtoev = 1 / (1.97 * 1e-7)
self.H0 = cosmo.H(0).value * 1e3 / (1e3 * const.kpc.value
) #expressed in 1/s
self.rhocritical = cosmo.critical_density(0).value * self.gramstoeV / (
1e-2)**3 # eV/m**3
self.Om0 = cosmo.Om0 #total matter
self.OLambda0 = cosmo.Ode0 # cosmological constant
self.DM0 = self.Om0 - cosmo.Ob0 # dark matter
self.evtonJoule = 1.60218 * 1e-10 # from eV to nJ
self.evtoJoule = 1.60218 * 1e-19 # from eV to J
self.h = 0.6766
self.Mpc = 1e3 * const.kpc.value
self.zmin = 0.001
self.zmax = 30.001
self.zbins = 301
self.h = cosmo.h
self.lambda_eff = np.array([
0.15, 0.36, 0.45, 0.55, 0.65, 0.79, 0.91, 1.27, 1.63, 2.20, 3.60,
4.50
])
self.Mstar0_vect = np.array([
-19.62, -20.20, -21.35, -22.13, -22.40, -22.80, -22.86, -23.04,
-23.41, -22.97, -22.40, -21.84
])
self.q_vect = np.array(
[1.1, 1.0, 0.6, 0.5, 0.5, 0.4, 0.4, 0.4, 0.5, 0.4, 0.2, 0.3])
self.phistar0_vect = np.array([
2.43, 5.46, 3.41, 2.42, 2.25, 2.05, 2.55, 2.21, 1.91, 2.74, 3.29,
3.29
])
self.p_vect = np.array(
[0.2, 0.5, 0.4, 0.5, 0.5, 0.4, 0.4, 0.6, 0.8, 0.8, 0.8, 0.8])
self.alpha0_vect = np.array(
[-1., -1., -1., -1., -1., -1., -1., -1., -1., -1., -1., -1.])
self.r_vect = np.array([
0.086, 0.076, 0.055, 0.060, 0.070, 0.070, 0.060, 0.035, 0.035,
0.035, 0.035, 0.035
])
self.zmax_vect = np.array(
[8.0, 4.5, 4.5, 3.6, 3.0, 3.0, 2.9, 3.2, 3.2, 3.8, 0.7, 0.7])
def mock_vpf(mock_cart_coords, spheresfile, simul_cosmo, rad):
gals = h5_arr(mock_cart_coords, "coords")
print gals
name = mock_cart_coords.split("/")[-1].split(".")[0]
if simul_cosmo == "Planck":
# First make h free
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif simul_cosmo == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
comv = cosmo.comoving_distance
gal_baum = cKDTree(gals)
spheres = h5_arr(spheresfile, "radecz_{0}".format(str(int(rad))))
print spheres
for i, sphere in enumerate(spheres):
rang = Angle(sphere[0], u.deg)
decang = Angle(sphere[1], u.deg)
dis = Distance(comv(sphere[2]), u.Mpc)
coord = ICRSCoordinates(rang, decang, distance=dis)
sph_cen = np.array([coord.x, coord.y, coord.z])
nn = gal_baum.query(sph_cen)
print "rad: ", rad, ", sphere: ", i
f = open(
"{0}/vpf_out/ascii/{1}_{2}.dat".format(
os.path.dirname(spheresfile), name, str(int(rad))), 'a')
if not nn[0] < rad:
f.write("1\n")
else:
f.write("0\n")
f.close()
def read_data(fnm, desi=None, template=None, desi_dir=None): if desi_dir: wave_obs, flux_obs_in, flux_obs_err_in = spec_desi.parse_1D_spectra(desi_dir + fnm) redshift = spec_desi.get_redshift(desi_dir+fnm) flux_obs_in = flux_obs_in*1e-17*1e-7*1e4 #from 10-17 ergs/s/cm2/AA to W/AA/m^2 flux_obs_err_in = flux_obs_err_in*1e-17*1e-7*1e4 #from 10-17 ergs/s/cm2/AA to W/AA/m^2 if template: hdu = fits.open(spectradir + fnm) redshift = hdu[0].header['redshift'] data = hdu[1].data wave_obs = np.array(data['wave']) flux_obs_in = np.array(data['flux_nodust_noise']) flux_obs_err_in = np.array(data['flux_nodust_noise_err']) #flux in W/AA/m^2 wave_obs = wave_obs[flux_obs_in > 0] flux_obs_err_in = flux_obs_err_in[flux_obs_in > 0] flux_obs_in = flux_obs_in[flux_obs_in > 0] #shift to rest-frame wave_gal = wave_obs / (1.0 + redshift) dL = cosmo.luminosity_distance(redshift) #luminosity distance in meters dL = dL.to(u.m) #interpolate to models wavelength resolution - DO BETTER flux_obs = np.interp(wave, wave_gal, flux_obs_in) * (4*np.pi*dL.value**2*(1+redshift)) #convert to luminosity in W/AA flux_obs_err = np.interp(wave, wave_gal, flux_obs_err_in) * (4*np.pi*dL.value**2*(1+redshift)) return wave, flux_obs, flux_obs_err
def ClHighCooray(self, nuobs, l, T, fesc): #zmin,zmax,N
arrayz = np.logspace(np.log10(6), np.log10(30), 60)
arraytoint = np.array([self.to_integrateCooray(nuobs,l/cosmo.comoving_distance(z).value,z, T,fesc)[0] \
for z in arrayz])
return np.trapz(arraytoint, arrayz) # (nW/m^2/sr)**2
def get_catalog(df, weights=None, shear=False, lens=False, z_lens=None):
"""Return TreeCorr Catalog in Mpc."""
if z_lens is None:
raise ValueError('must enter a value for z_lens')
else:
dA_lens = cosmo.angular_diameter_distance(z_lens)
if type(df) != pd.core.frame.DataFrame:
raise TypeError('df must be a dataframe')
if lens is True:
cdf_zslice = df[np.isclose(df.z, z_lens)]
x_lens_mpc = pix2rad(cdf_zslice['x[0]']) * dA_lens
y_lens_mpc = pix2rad(cdf_zslice['x[1]']) * dA_lens
cat = treecorr.Catalog(x=x_lens_mpc, y=y_lens_mpc)
elif shear is True:
# insert function to select on zphot & P(z) conditions
# sdf_z = df[df.zphot > z_lens && 90% P(z) above z_lens]
x_shear_mpc = pix2rad(df['x[0]']) * dA_lens # tbr
y_shear_mpc = pix2rad(df['x[1]']) * dA_lens # tbr
cat = treecorr.Catalog(x=x_shear_mpc, y=y_shear_mpc,
g1=df['e[0]'], g2=df['e[1]'])
else:
x_mpc = pix2rad(df['x[0]']) * dA_lens
y_mpc = pix2rad(df['x[1]']) * dA_lens
cat = treecorr.Catalog(x=x_mpc, y=y_mpc)
if weights is not None:
cat.k = np.ones(df.shape[0])
for w in weights:
cat.k *= df[w].values
return cat
def get_redmapper(objID, ir, z, z_err, transverse, dz):
'''
Find the corresponding galaxy cluster in the redMaPPer catalog
First check against member catalog, then check radially
If multiple clusters match, choose the one with least angular separation
'''
# If the galaxy is too close, physical separations become too great on the sky
# Restrict redshifts to at least 0.01
if z < 0.01:
return None
member = rm_m.find_one({'ObjID':objID})
if member is not None:
return rm_c.find_one({'ID':member['ID']})
# Maximum separation
max_sep = float(transverse * u.Mpc / cosmo.angular_diameter_distance(z) * u.rad / u.deg)
best_sep = np.inf
cluster = None
for temp_c in rm_c.find({'RAdeg':{'$gt':ir.ra.deg-max_sep, '$lt':ir.ra.deg+max_sep}, 'DEdeg':{'$gt':ir.dec.deg-max_sep, '$lt':ir.dec.deg+max_sep}, \
'$or':[{'zspec':{'$gt':z-dz, '$lt':z+dz}}, {'zlambda':{'$gt':z-dz, '$lt':z+dz}}]}):
current_sep = ir.separation( coord.SkyCoord(temp_c['RAdeg'], temp_c['DEdeg'], unit=(u.deg,u.deg), frame='icrs') )
if (current_sep < best_sep) and (current_sep < max_sep*u.deg):
best_sep = current_sep
cluster = temp_c
return cluster
def tab_L(X):
m, a, m1, m2, m3, m4, m5, m6, m7, m8, m9, m10, z, d, lm = X
sp.params['dust2'] = d
sp.params['dust1'] = d
sp.params['logzsol'] = np.log10(m)
time, sfr, tmax = convert_sfh(agebins,
[m1, m2, m3, m4, m5, m6, m7, m8, m9, m10])
sp.set_tabular_sfh(time, sfr)
wave, flux = sp.get_spectrum(tage=a, peraa=True)
D_l = cosmo.luminosity_distance(z).value # in Mpc
mass_transform = (10**lm /
sp.stellar_mass) * lsol_to_fsol / (4 * np.pi *
(D_l * conv)**2)
Gmfl, Pmfl = Full_forward_model(sim2, wave, flux * mass_transform, z)
Gchi, Pchi = Full_fit(sim2, Gmfl, Pmfl)
return -0.5 * (Gchi + Pchi)
def producing_lensed_images(xi1, xi2, source_cat, lens_cat):
xlc1 = lens_cat[0]
xlc2 = lens_cat[1]
ql = lens_cat[2]
rlc = 0.0
rle = re_sv(lens_cat[3], lens_cat[5],
source_cat[7]) #Einstein radius of lens Arc Seconds.
phl = lens_cat[4]
#----------------------------------------------------------------------
ai1, ai2, mua = lens_equation_sie(xi1, xi2, xlc1, xlc2, ql, rlc, rle, phl)
yi1 = xi1 - ai1 * 0.0
yi2 = xi2 - ai2 * 0.0
ysc1 = source_cat[0]
ysc2 = source_cat[1]
mag_tot = source_cat[2]
Reff_arc = np.sqrt(source_cat[3] * source_cat[4])
qs = np.sqrt(source_cat[3] / source_cat[4])
phs = source_cat[5]
ndex = source_cat[6]
zs = source_cat[7]
#g_limage = sersic_SB_2D_tot(yi1,yi2,ysc1,ysc2,mag_tot,Reff_arc,qs,phs,zs)
Da_s = p13.angular_diameter_distance(2.0).value
Reff = Reff_arc * Da_s / apr * 1e6 # pc
Ieff = sersic_mag_tot_to_Ieff(mag_tot, Reff, ndex, zs)
g_limage = sersic_2d(yi1, yi2, ysc1, ysc2, Ieff, Reff_arc, qs, phs, ndex)
return g_limage
def tuple_to_sfh_stand_alone(sfh_tuple, zval):
mass_quantiles = np.array([0., 0., 0.25, 0.5, 0.75, 1., 1., 1., 1., 1.])
time_quantiles = np.array([
0, 0.01, sfh_tuple[3], sfh_tuple[4], sfh_tuple[5], 0.96, 0.97, 0.98,
0.99, 1
])
time_arr_interp, mass_arr_interp = gp_interpolator(time_quantiles,
mass_quantiles,
Nparam=3)
sfh_scale = 10**(sfh_tuple[0]) / (cosmo.age(zval).value * 1e9 / 1000)
sfh = np.diff(mass_arr_interp) * sfh_scale
sfh[sfh < 0] = 0
sfh = np.insert(sfh, 0, [0])
return sfh, time_arr_interp * cosmo.age(zval).value
def find_rvirial(dd, ds, center, start_rad = 0, delta_rad_coarse = 20, delta_rad_fine = 1, rad_units = 'kpc'):
vir_check = 0
r0 = ds.arr(start_rad, rad_units)
critical_density = cosmo.critical_density(ds.current_redshift).value #is in g/cm^3
max_ndens_arr=center
while True:
r0_prev = r0
r0 = r0_prev + ds.arr(delta_rad_coarse, rad_units)
v_sphere = ds.sphere(max_ndens_arr, r0)
dark_mass = v_sphere[('DarkMatter', 'Mass')].in_units('Msun').sum()
rho_internal = dark_mass.in_units('g')/((r0.in_units('cm'))**3.*(pi*4/3.))
print rho_internal, r0, dark_mass
if rho_internal < 200*ds.arr(critical_density,'g')/ds.arr(1.,'cm')**3.:
#now run fine test
print('\tNow running fine search on the virial radius')
r0 = r0_prev
while True:
r0 += ds.arr(delta_rad_fine, rad_units)
v_sphere = ds.sphere(max_ndens_arr, r0)
dark_mass = v_sphere[('DarkMatter', 'Mass')].in_units('Msun').sum()
rho_internal = dark_mass.in_units('g')/((r0.in_units('cm'))**3.*(pi*4/3.))
print rho_internal, r0
if rho_internal < 200*ds.arr(critical_density,'g')/ds.arr(1.,'cm')**3.:
rvir = r0
print dark_mass.in_units('Msun'), rvir.in_units('kpc')
return rvir
def producing_lensed_images(xi1,xi2,source_cat,lens_cat):
xlc1 = lens_cat[0]
xlc2 = lens_cat[1]
ql = lens_cat[2]
rlc = 0.0
rle = re_sv(lens_cat[3],lens_cat[5],source_cat[7]) #Einstein radius of lens Arc Seconds.
phl = lens_cat[4]
#----------------------------------------------------------------------
ai1,ai2,mua = lens_equation_sie(xi1,xi2,xlc1,xlc2,ql,rlc,rle,phl)
yi1 = xi1-ai1*0.0
yi2 = xi2-ai2*0.0
ysc1 = source_cat[0]
ysc2 = source_cat[1]
mag_tot = source_cat[2]
Reff_arc = np.sqrt(source_cat[3]*source_cat[4])
qs = np.sqrt(source_cat[3]/source_cat[4])
phs = source_cat[5]
ndex = source_cat[6]
zs = source_cat[7]
#g_limage = sersic_SB_2D_tot(yi1,yi2,ysc1,ysc2,mag_tot,Reff_arc,qs,phs,zs)
Da_s = p13.angular_diameter_distance(2.0).value
Reff = Reff_arc*Da_s/apr*1e6 # pc
Ieff = sersic_mag_tot_to_Ieff(mag_tot,Reff,ndex,zs)
g_limage = sersic_2d(yi1,yi2,ysc1,ysc2,Ieff,Reff_arc,qs,phs,ndex)
return g_limage
def luminosity(z, flux):
from astropy.cosmology import Planck13 as cosmo
#cosmo = {'omega_M_0':0.3, 'omega_lambda_0':0.7, 'omega_k_0':0.0, 'h':0.72}
#d_lum= cd.luminosity_distance(z, **cosmo)*(3.08*10**24)
d_lum = cosmo.luminosity_distance(z) * (3.08 * 10**24)
L = 4 * pi * (d_lum**2) * flux
return np.array(L.value, dtype=float)
def lensed_sersic(xi1,xi2,source_cat,lens_cat):
xlc1 = lens_cat[0] # x position of the lens, arcseconds
xlc2 = lens_cat[1] # y position of the lens, arcseconds
rlc = 0.0 # core size of Non-singular Isothermal Ellipsoid
rle = re_sv(lens_cat[2],lens_cat[5],source_cat[7]) #Einstein radius of lens, arcseconds.
ql = lens_cat[3] # axis ratio b/a
phl = lens_cat[4] # orientation, degree
#----------------------------------------------------------------------
ai1,ai2,mua = lens_equation_sie(xi1,xi2,xlc1,xlc2,ql,rlc,rle,phl)
yi1 = xi1-ai1
yi2 = xi2-ai2
ysc1 = source_cat[0] # x position of the source, arcseconds
ysc2 = source_cat[1] # y position of the source, arcseconds
mag_tot = source_cat[2] # total magnitude of the source
Reff_arc = source_cat[3] # Effective Radius of the source, arcseconds
qs = source_cat[4] # axis ratio of the source, b/a
phs = source_cat[5] # orientation of the source, degree
ndex = source_cat[6] # index of the source
zs = source_cat[7] # redshift of the source
Da_s = p13.angular_diameter_distance(zs).value
Reff = Reff_arc*Da_s/apr*1e6 # pc
Ieff = sersic_mag_tot_to_Ieff(mag_tot,Reff,ndex,zs) #L_sun/kpc^2
g_limage = sersic_2d(yi1,yi2,ysc1,ysc2,Ieff,Reff_arc,qs,phs,ndex)
g_source = sersic_2d(xi1,xi2,ysc1,ysc2,Ieff,Reff_arc,qs,phs,ndex)
mag_lensed = mag_tot - np.log(np.sum(g_limage)/np.sum(g_source))
return mag_lensed, g_limage
def vmax_profile(ds, DDname, center, start_rad=5, end_rad=220., delta_rad=5):
rs = np.arange(start_rad, end_rad, delta_rad)
r_arr = zeros(len(rs))
m_arr = zeros(len(r_arr))
for rr, r in enumerate(rs):
print(rr, r)
r0 = ds.arr(r, 'kpc')
r_arr[rr] = r0
critical_density = cosmo.critical_density(ds.current_redshift).value
r0 = ds.arr(delta_rad, 'kpc')
v_sphere = ds.sphere(center, r0)
cell_mass, particle_mass = v_sphere.quantities.total_quantity(
["cell_mass", "particle_mass"])
m_arr[rr] = cell_mass.in_units('Msun') + particle_mass.in_units('Msun')
m_arr = yt.YTArray(m_arr, 'Msun')
r_arr = yt.YTArray(r_arr, 'kpc')
to_save = {}
to_save['m'] = m_arr
to_save['r'] = r_arr
G = yt.YTArray([c.G.value], 'm**3/kg/s**2')
to_save['v'] = sqrt(2 * G * m_arr / r_arr).to('km/s')
np.save(
'/nobackupp2/rcsimons/foggie_momentum/catalogs/vescape/%s_%s_vescape.npy'
% (DDname, simname), to_save)
def test_redshift_temperature():
"""Test :func:`astropy.cosmology.units.redshift_temperature`."""
cosmo = Planck13.clone(Tcmb0=3 * u.K)
default_cosmo = default_cosmology.get()
z = 15 * cu.redshift
Tcmb = cosmo.Tcmb(z)
# 1) Default (without specifying the cosmology)
with default_cosmology.set(cosmo):
equivalency = cu.redshift_temperature()
assert_quantity_allclose(z.to(u.K, equivalency), Tcmb)
assert_quantity_allclose(Tcmb.to(cu.redshift, equivalency), z)
# showing the answer changes if the cosmology changes
# this test uses the default cosmology
equivalency = cu.redshift_temperature()
assert_quantity_allclose(z.to(u.K, equivalency), default_cosmo.Tcmb(z))
assert default_cosmo.Tcmb(z) != Tcmb
# 2) Specifying the cosmology
equivalency = cu.redshift_temperature(cosmo)
assert_quantity_allclose(z.to(u.K, equivalency), Tcmb)
assert_quantity_allclose(Tcmb.to(cu.redshift, equivalency), z)
# Test `atzkw`
equivalency = cu.redshift_temperature(cosmo, ztol=1e-10)
assert_quantity_allclose(Tcmb.to(cu.redshift, equivalency), z)
def myFirefly_lgal_sourceSpec(galid, dust=False, lib='bc03', model='m11', model_lib='MILES', imf='kr'):
''' run firefly on simulated source spectra from testGalIDs LGal
'''
# read in source spectra
specin = lgal_sourceSpectra(galid, lib=lib)
redshift = specin['meta']['REDSHIFT']
print('z = %f' % redshift)
wave = specin['wave']
wave_rest = wave / (1.+redshift)
if not dust:
flux = specin['flux_nodust_nonoise']
# output firefly file
f_specin = f_Source(galid, lib=lib)
if not dust:
f_firefly = ''.join([UT.dat_dir(), 'spectral_challenge/bgs/',
'myFirefly.', model, '.', model_lib, '.imf_', imf, '.nodust__',
f_specin.rsplit('/', 1)[1].rsplit('.fits', 1)[0], '.nodust.hdf5'])
ffly = Fitters.myFirefly(
Planck13, # comsology
model=model,
model_lib=model_lib,
imf=imf,
dust_corr=False, # no dust correction
age_lim=[0., Planck13.age(redshift).value], # can't have older populations
logZ_lim=[-2.,1.])
mask = ffly.emissionlineMask(wave_rest)
ff_fit, ff_prop = ffly.Fit(wave, flux, flux*0.001, redshift, mask=mask, flux_unit=1e-17, f_output=f_firefly, silent=False)
print ff_prop['logM_total']
return None
def sersic_mag_tot_to_Ieff(mag_tot,Reff,ndex,z,Rcut=100): # g band
bn = 2.0*ndex-1/3.0+0.009876/ndex
xtmp = bn*(Rcut)**(1.0/ndex)
ktmp = 2.0*np.pi*ndex*(np.e**bn/(bn**(2.0*ndex)))*spf.gammainc(2.0*ndex,xtmp)*spf.gamma(2.0*ndex)
Dl_s = p13.luminosity_distance(z).value*1e6
Ieff = 10.0**((5.12-2.5*np.log10(ktmp)-5.0*np.log10(Reff)+5.0*np.log10(Dl_s/10)-mag_tot)*0.4) # L_sun/pc^2
return Ieff
def test_fast_comoving_distance(self):
z_params = {'z_start': 1.8, 'z_end': 3.7, 'z_step': 0.001}
cd = comoving_distance.ComovingDistance(**z_params)
ar_z = np.arange(1.952, 3.6, 0.132)
ar_dist = cd.fast_comoving_distance(ar_z)
ar_dist_reference = Planck13.comoving_transverse_distance(ar_z) / u.Mpc
print(ar_dist - ar_dist_reference)
self.assertTrue(np.allclose(ar_dist, ar_dist_reference))
def mock_vpf(mock_cart_coords, spheresfile, simul_cosmo, rad):
gals = h5_arr(mock_cart_coords, "coords")
print gals
name = mock_cart_coords.split("/")[-1].split(".")[0]
if simul_cosmo == "Planck":
# First make h free
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif simul_cosmo == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
comv = cosmo.comoving_distance
gal_baum = cKDTree(gals)
spheres = h5_arr(spheresfile, "radecz_{0}".format(str(int(rad))))
print spheres
for i, sphere in enumerate(spheres):
rang = Angle(sphere[0], u.deg)
decang = Angle(sphere[1], u.deg)
dis = Distance(comv(sphere[2]), u.Mpc)
coord = ICRSCoordinates(rang, decang, distance=dis)
sph_cen = np.array([coord.x, coord.y, coord.z])
nn = gal_baum.query(sph_cen)
print "rad: ", rad, ", sphere: ", i
f = open("{0}/vpf_out/ascii/{1}_{2}.dat".format(os.path.dirname(spheresfile), name, str(int(rad))), 'a')
if not nn[0] < rad:
f.write("1\n")
else:
f.write("0\n")
f.close()
def __init__(self, redshifts, cosmology='Planck13', cm='DuttonMaccio'):
if type(redshifts) != np.ndarray:
redshifts = np.array(redshifts)
if redshifts.ndim != 1:
raise ValueError("Input redshift array must have 1 dimension.")
if np.sum(redshifts < 0.) > 0:
raise ValueError("Redshifts cannot be negative.")
if cosmology == 'Planck13':
from astropy.cosmology import Planck13 as cosmo
elif cosmology == 'WMAP9':
from astropy.cosmology import WMAP9 as cosmo
elif cosmology == 'WMAP7':
from astropy.cosmology import WMAP7 as cosmo
elif cosmology == 'WMAP5':
from astropy.cosmology import WMAP5 as cosmo
else:
raise ValueError('Input cosmology must be one of: \
Planck13, WMAP9, WMAP7, WMAP5.')
self._cosmo = cosmo
if cm == 'DuttonMaccio':
self._cm = 'DuttonMaccio'
elif cm == 'Prada':
self._cm = 'Prada'
elif cm == 'Duffy':
self._cm = 'Duffy'
else:
raise ValueError('Input concentration-mass relation must be \
one of: DuttonMaccio, Prada, Duffy.')
self.describe = "Ensemble of galaxy clusters and their properties."
self.number = redshifts.shape[0]
self._z = redshifts
self._rho_crit = cosmo.critical_density(self._z)
self._massrich_norm = 2.7 * (10**13) * units.Msun
self._massrich_slope = 1.4
self._df = pd.DataFrame(self._z, columns=['z'])
self._Dang_l = cosmo.angular_diameter_distance(self._z)
self._m200 = None
self._n200 = None
self._r200 = None
self._rs = None
self._c200 = None
self._deltac = None
def mock_vpf(mock_cart_coords, spheresfile, simul_cosmo):
gals = h5_arr(mock_cart_coords, "coords")
name = mock_cart_coords.split("/")[-1].split(".")[0]
if simul_cosmo == "Planck":
# First make h free
Planck13.__init__(100.0, Planck13.Om0)
cosmo = Planck13
elif simul_cosmo == "WMAP":
WMAP5.__init__(100.0, WMAP5.Om0)
cosmo = WMAP5
comv = cosmo.comoving_distance
gal_baum = cKDTree(gals)
rad = np.arange(1.0, 67.0, 5.0)
for r_i, r in enumerate(rad):
spheres = h5_arr(spheresfile, "radecz_{0}".format(str(r_i * 5 + 1)))
voids = np.zeros(spheres.shape[0])
for i, sphere in enumerate(spheres):
rang = Angle(sphere[0], u.deg)
decang = Angle(sphere[1], u.deg)
dis = Distance(comv(sphere[2]), u.Mpc)
coord = ICRSCoordinates(rang, decang, distance=dis)
sph_cen = np.array([coord.x.value, coord.y.value, coord.z.value])
nn = gal_baum.query(sph_cen)
print "rad: ", r, ", sphere: ", i
if not nn[0] < r:
voids[i] = 1
arr2h5(voids,
"{0}/vpf_out/{1}.hdf5".format(os.path.dirname(spheresfile), name),
"voids_{0}".format(str(r_i * 5 + 1)))
def bolometric(model, luminosity=True):
phase = model.source._phase
flux = np.sum(model.source.flux(phase, model.source._wave) * dwave, axis=1)
if luminosity:
z = model.get('z')
dl = Planck13.luminosity_distance(z).to('cm').value
L = 4 * np.pi * flux * dl * dl
return L
return flux
def JeansLength(self,z):
"""
Computes Jeans length in unitless Delta z
lambda_J=2.3 Mpc (1+z)^-3/2 Pshirkov 2016
"""
dist=Planck13.lookback_distance(z).value # in Mpc
jeanslength=2.3*(1+z)**(-1.5) # in Mpc
z1=z_at_value(Planck13.lookback_distance,(dist+jeanslength)*u.Mpc)
return z1-z
def luminosity_X(z, flux, gamma):
#cosmo = {'omega_M_0':0.3, 'omega_lambda_0':0.7, 'omega_k_0':0.0, 'h':0.72}
#d_lum= cd.luminosity_distance(z, **cosmo)*(3.08*10**24)
d_lum = (cosmo.luminosity_distance(z) * (3.08 * 10**24)).value
d_lum = np.array(d_lum)
L = 4 * pi * (d_lum**2) * flux * (1 + z)**(gamma - 2)
return L
def z_to_time(z,cosmology=None):
"""
gives the time, in years, since the big bang given an astropy cosmology
and a redshift. if no cosmology passed in, assumes Planck13
"""
if cosmology is None:
from astropy.cosmology import Planck13 as cosmology
from yt import YTArray
t = cosmology.age(z)
return YTArray(t*t.unit.in_units('yr'),'yr')
def sersic_SB_2D_tot(xi1,xi2,xc1,xc2,mag_tot,Reff_arc,ql,pha,z,ndex=4.0):
#Dl_s = p13.luminosity_distance(z).value
Da_s = p13.angular_diameter_distance(z).value
Reff = Reff_arc*Da_s/apr*1e6
mueff=sersic_mag_tot_to_mueff(mag_tot,Reff,ndex,z)
bn = 2.0*ndex-1/3.0+0.009876/ndex
(xi1new,xi2new) = xy_rotate(xi1, xi2, xc1, xc2, pha)
R_arc = np.sqrt((xi1new**2)*ql+(xi2new**2)/ql)/Reff_arc
res = mueff + (2.5*bn)/np.log(10.0)*((R_arc/Reff_arc)**(1.0/ndex)-1.0)
return res
def bolometric(model, luminosity=True, dl=None):
phase = model.source._phase
dwave = np.gradient(model.source._wave)
flux = np.sum(model.source.flux(phase, model.source._wave) * dwave, axis=1)
if luminosity:
z = model.get('z')
if dl is None:
dl = Planck13.luminosity_distance(z).to('cm').value
else:
dl = (dl * u.Mpc).to('cm').value
L = 4 * np.pi * flux * dl * dl
return L
return flux
def get_densities(slice, large_slice):
"""Measures the density for each galaxy in the slice
using a larger slice, because of borders effects from z
(RA Dec not taken in accounts) and also to include all masses
and not only the current mass bin"""
radius = .5*u.Mpc
densities = np.array([])
meanmasses = np.array([])
medianmasses = np.array([])
print datetime.datetime.now()
for galaxy in slice:
z = galaxy["zb_1"]
RA = galaxy["RA"]
Dec = galaxy["Dec"]
Mpc_per_deg = cosmo.kpc_comoving_per_arcmin(z).to(u.Mpc/u.deg)
dRA = radius / Mpc_per_deg
dDec = dRA
slicetmp = large_slice
slicetmp = slice_RA(slicetmp, RA, dRA)
slicetmp = slice_Dec(slicetmp, Dec, dDec)
#slicetmp = slice_z_cosmo(slicetmp, z, radius)
velocity_limit = 500 #km/s
#print zobs(-(velocity_limit), z) - zobs(velocity_limit, z)
slicetmp = slice_z_minmax(slicetmp, zobs(-(velocity_limit), z), zobs(velocity_limit, z))
meanmass_comp = np.mean(slicetmp["Stell_Mass_1"][np.where(slicetmp["ID"] != galaxy["ID"])])
medianmass_comp = np.median(slicetmp["Stell_Mass_1"][np.where(slicetmp["ID"] != galaxy["ID"])])
densities = np.append(densities, len(slicetmp)-1)
meanmasses = np.append(meanmasses, meanmass_comp)
medianmasses = np.append(medianmasses, medianmass_comp)
#print len(slicetmp)-1
slice.add_column(Column(data=densities, name="densities"))
slice.add_column(Column(data=meanmasses, name="meanmasses"))
slice.add_column(Column(data=medianmasses, name="medianmasses"))
print datetime.datetime.now()
return slice
def lens_img_cat(lens_cat):
xlc1 = lens_cat[0]
xlc2 = lens_cat[1]
ql = lens_cat[2]
sigmav = lens_cat[3]
phl = lens_cat[4]
zl = lens_cat[5]
ndex = 4
zl_array, sv_array, re_array, le_array=np.loadtxt("./apj512628t1_ascii.txt",comments='#', usecols=(0,1,2,3),unpack=True)
Reff_r,Iebar_r = vd_matching(sigmav,sv_array, re_array, le_array)
Ieff_r = sersic.sersic_Iebar_to_Ieff(Iebar_r,Reff_r,ndex)
mag_tot = sersic.sersic_mag_in_Rcut(Ieff_r,Reff_r*1e3,ndex,zl)
Da_l = p13.angular_diameter_distance(zl).value
Reff_arc = Reff_r*0.001/Da_l*apr
return [xlc1, xlc2, mag_tot, Reff_arc/np.sqrt(ql), Reff_arc*np.sqrt(ql), phl, ndex, zl, lens_cat[6]]
def lens_img_cat(lens_cat):
xlc1 = lens_cat[0]
xlc2 = lens_cat[1]
ql = lens_cat[2]
sigmav = lens_cat[3]
phl = lens_cat[4]
zl = lens_cat[5]
zl_array, sv_array, re_array, le_array=np.loadtxt("./apj512628t1_ascii.txt",comments='#', usecols=(0,1,2,3),unpack=True)
Reff_r,log10_Ieff_r = return_re_le(sigmav,sv_array, re_array, le_array)
#Dl_l = p13.luminosity_distance(zl)
Da_l = p13.angular_diameter_distance(zl).value
Reff_arc = Reff_r/Da_l*apr*0.001 # arcsec
Ieff_r = 10.0**(log10_Ieff_r) #/3.61 # http://www.astro.spbu.ru/staff/resh/Lectures/lec2.pdf
ndex = 4
mag_tot = sersic.sersic_mag_in_Rcut(Ieff_r,Reff_r,ndex)
return [xlc1, xlc2, mag_tot, Reff_arc/np.sqrt(ql), Reff_arc*np.sqrt(ql), phl, ndex, zl]
def get_amf(ir, z, z_err, transverse, dz):
'''
Find the corresponding galaxy cluster in the WHL15 catalog
If multiple clusters match, choose the one with least angular separation
'''
# If the galaxy is too close, physical separations become too great on the sky
# Restrict redshifts to at least 0.01
if z < 0.01:
return None
# Maximum separation
max_sep = float(transverse * u.Mpc / cosmo.angular_diameter_distance(z) * u.rad / u.deg)
best_sep = np.inf
cluster = None
for temp_c in amf.find({'ra':{'$gt':ir.ra.deg-max_sep, '$lt':ir.ra.deg+max_sep}, 'dec':{'$gt':ir.dec.deg-max_sep, '$lt':ir.dec.deg+max_sep}, \
'z':{'$gt':z-dz, '$lt':z+dz}}):
current_sep = ir.separation( coord.SkyCoord(temp_c['ra'], temp_c['dec'], unit=(u.deg,u.deg), frame='icrs') )
if (current_sep < best_sep) and (current_sep < max_sep*u.deg):
best_sep = current_sep
cluster = temp_c
return cluster
def single_run_test(ind,ysc1,ysc2,q,vd,pha,zl,zs):
dsx_sdss = 0.396 # pixel size of SDSS detector.
R = 3.0000 #
nnn = 300 #Image dimension
bsz = 9.0 # arcsecs
dsx = bsz/nnn # pixel size of SDSS detector.
nstd = 59 #^2
xx01 = np.linspace(-bsz/2.0,bsz/2.0,nnn)+0.5*dsx
xx02 = np.linspace(-bsz/2.0,bsz/2.0,nnn)+0.5*dsx
xi2,xi1 = np.meshgrid(xx01,xx02)
#----------------------------------------------------------------------
dsi = 0.03
g_source = pyfits.getdata("./439.0_149.482739_1.889989_processed.fits")
g_source = np.array(g_source,dtype="<d")*10.0
g_source[g_source<=0.0001] = 1e-6
#----------------------------------------------------------------------
xc1 = 0.0 #x coordinate of the center of lens (in units of Einstein radius).
xc2 = 0.0 #y coordinate of the center of lens (in units of Einstein radius).
#q = 0.7 #Ellipticity of lens.
rc = 0.0 #Core size of lens (in units of Einstein radius).
re = re_sv(vd,zl,zs) #Einstein radius of lens.
#pha = 45.0 #Orintation of lens.
lpar = np.asarray([xc1,xc2,q,rc,re,pha])
#----------------------------------------------------------------------
ai1,ai2,mua = lens_equation_sie(xi1,xi2,lpar)
yi1 = xi1-ai1
yi2 = xi2-ai2
g_limage = lv4.call_ray_tracing(g_source,xi1,xi2,ysc1,ysc2,dsi)
g_limage[g_limage<=0.0001] = 1e-6
g_limage = p2p.cosccd2mag(g_limage)
g_limage = p2p.mag2sdssccd(g_limage)
#-------------------------------------------------------------
# Need to be Caliborate the mags
dA = Planck13.comoving_distance(zl).value*1000./(1+zl)
Re = dA*np.sin(R*np.pi/180./3600.)
counts =Brightness(Re,vd)
vpar = np.asarray([counts,R,xc1,xc2,q,pha])
#g_lens = deVaucouleurs(xi1,xi2,xc1,xc2,counts,R,1.0-q,pha)
g_lens = de_vaucouleurs_2d(xi1,xi2,vpar)
#pl.figure()
#pl.contourf(g_lens)
#pl.colorbar()
g_clean_ccd1 = g_lens*0.0+g_limage
g_clean_ccd2 = g_lens*1.0+g_limage
from scipy.ndimage.filters import gaussian_filter
pl.figure()
pl.contourf(g_clean_ccd1)
pl.colorbar()
pl.savefig("/Users/uranus/GitHub/data_arc_finding_cnn/unlensed_output_pngs/"+str(i)+"_lensed_imgs_only.png")
#-------------------------------------------------------------
g_images_psf1 = gaussian_filter(g_clean_ccd1, 2.0)
g_images_psf2 = gaussian_filter(g_clean_ccd2, 2.0)
#g_images_psf = ss.convolve(g_clean_ccd,g_psf,mode="same")
#g_images_psf = g_clean_ccd
#-------------------------------------------------------------
# Need to be Caliborate the mags
g_noise = noise_map(nnn,nnn,np.sqrt(nstd),"Gaussian")
#output_filename = "./output_fits/noise_map.fits"
#pyfits.writeto(output_filename,g_noise,clobber=True)
#-------------------------------------------------------------
g_final1 = g_images_psf1+g_noise
output_filename = "/Users/uranus/GitHub/data_arc_finding_cnn/unlensed_output_fits/"+str(i)+"_lensed_imgs_only.fits"
pyfits.writeto(output_filename,g_final1,clobber=True)
#-------------------------------------------------------------
g_final2 = g_images_psf2+g_noise
output_filename = "/Users/uranus/GitHub/data_arc_finding_cnn/unlensed_output_fits/"+str(i)+"_all_imgs.fits"
pyfits.writeto(output_filename,g_final2,clobber=True)
return 0
def single_run_test(ind, ysc1, ysc2, q, vd, pha, zl, zs, lens_tag=1):
# dsx_sdss = 0.396 # pixel size of SDSS detector.
R = 3.0
nnn = 400 # Image dimension
bsz = 9.0 # arcsecs
dsx = bsz / nnn # pixel size of SDSS detector.
nstd = 59 # ^2
xi1, xi2 = make_r_coor(nnn, dsx)
# ----------------------------------------------------------------------
dsi = 0.03
g_source = pyfits.getdata(
"./gals_sources/439.0_149.482739_1.889989_processed.fits")
g_source = np.array(g_source, dtype="<d") * 10.0
g_source[g_source <= 0.0001] = 1e-6
# ----------------------------------------------------------------------
# x coordinate of the center of lens (in units of Einstein radius).
xc1 = 0.0
# y coordinate of the center of lens (in units of Einstein radius).
xc2 = 0.0
rc = 0.0 # Core size of lens (in units of Einstein radius).
re = re_sv(vd, zl, zs) # Einstein radius of lens.
print "re = ", re
re_sub = 0.0 * re
a_sub = a_b_bh(re_sub, re)
ext_shears = 0.06
ext_angle = -0.39
ext_kappa = 0.08
# ext_shears = 0.0
# ext_angle = 0.0
# ext_kappa = 0.0
# ----------------------------------------------------------------------
#lpar = np.asarray([xc1, xc2, q, rc, re, pha])
#ai1, ai2, kappa_out, shr1, shr2, mua = lensing_signals_sie(xi1, xi2, lpar)
#ar = np.sqrt(ai1 * ai1 + ai2 * ai2)
# psi_nie = psk.potential_nie(xc1, xc2, pha, q, re, rc, ext_shears, ext_angle,
# ext_kappa, xi1, xi2)
#ai1, ai2 = np.gradient(psi_nie, dsx)
ai1, ai2 = psk.deflection_nie(xc1, xc2, pha, q, re, rc, ext_shears, ext_angle,
ext_kappa, xi1, xi2)
as1, as2 = psk.deflection_sub_pJaffe(0.0, -2.169, re_sub, 0.0, a_sub, xi1, xi2)
yi1 = xi1 - ai1 - as1
yi2 = xi2 - ai2 - as2
g_limage = lv4.call_ray_tracing(g_source, yi1, yi2, ysc1, ysc2, dsi)
g_limage[g_limage <= 0.25] = 1e-6
# pl.figure()
# pl.contourf(g_limage)
# pl.colorbar()
g_limage = cosccd2mag(g_limage)
g_limage = mag2sdssccd(g_limage)
# pl.figure()
# pl.contourf(g_limage)
# pl.colorbar()
# -------------------------------------------------------------
dA = Planck13.comoving_distance(zl).value * 1000. / (1.0 + zl)
Re = dA * np.sin(R * np.pi / 180. / 3600.)
counts = Brightness(Re, vd)
vpar = np.asarray([counts, R, xc1, xc2, q, pha])
g_lens = de_vaucouleurs_2d(xi1, xi2, vpar)
g_clean_ccd = g_lens * lens_tag + g_limage
output_filename = "./fits_outputs/clean_lensed_imgs.fits"
pyfits.writeto(output_filename, g_clean_ccd, overwrite=True)
# -------------------------------------------------------------
from scipy.ndimage.filters import gaussian_filter
g_images_psf = gaussian_filter(g_clean_ccd, 2.0)
# -------------------------------------------------------------
g_noise = noise_map(nnn, nnn, np.sqrt(nstd), "Gaussian")
output_filename = "./fits_outputs/noise_map.fits"
pyfits.writeto(output_filename, g_noise, overwrite=True)
g_final = g_images_psf + g_noise
# -------------------------------------------------------------
g_clean_ccd = g_limage
g_images_psf = gaussian_filter(g_clean_ccd, 2.0)
g_final = g_images_psf + g_noise
output_filename = "./fits_outputs/lensed_imgs_only.fits"
pyfits.writeto(output_filename, g_final, overwrite=True)
# -------------------------------------------------------------
output_filename = "./fits_outputs/full_lensed_imgs.fits"
pyfits.writeto(output_filename, g_final + g_lens, overwrite=True)
# pl.figure()
# pl.contourf(g_final)
# pl.colorbar()
return 0
def single_run_test(ind,ysc1,ysc2,q,vd,pha,zl,zs):
dsx_sdss = 0.396 # pixel size of SDSS detector.
R = 3.0000 #
#zl = 0.2 #zl is the redshift of the lens galaxy.
#zs = 1.0
#vd = 520 #Velocity Dispersion.
nnn = 128 #Image dimension
bsz = dsx_sdss*nnn # arcsecs
dsx = bsz/nnn # pixel size of SDSS detector.
nstd = 59 #^2
xx01 = np.linspace(-bsz/2.0,bsz/2.0,nnn)+0.5*dsx
xx02 = np.linspace(-bsz/2.0,bsz/2.0,nnn)+0.5*dsx
xi2,xi1 = np.meshgrid(xx01,xx02)
#----------------------------------------------------------------------
#ysc1 = 0.2
#ysc2 = 0.5
dsi = 0.03
g_source = pyfits.getdata("./439.0_149.482739_1.889989_processed.fits")
g_source = np.array(g_source,dtype="<d")*10.0
g_source[g_source<=0.0001] = 1e-6
#print np.sum(g_source)
#print np.max(g_source)
#pl.figure()
#pl.contourf(g_source)
#pl.colorbar()
#g_source = p2p.cosccd2mag(g_source)
##g_source = p2p.mag2sdssccd(g_source)
##print np.max(g_source*13*13*52.0)
#pl.figure()
#pl.contourf(g_source)
#pl.colorbar()
#----------------------------------------------------------------------
xc1 = 0.0 #x coordinate of the center of lens (in units of Einstein radius).
xc2 = 0.0 #y coordinate of the center of lens (in units of Einstein radius).
#q = 0.7 #Ellipticity of lens.
rc = 0.0 #Core size of lens (in units of Einstein radius).
re = re_sv(vd,zl,zs) #Einstein radius of lens.
#pha = 45.0 #Orintation of lens.
lpar = np.asarray([xc1,xc2,q,rc,re,pha])
#----------------------------------------------------------------------
ai1,ai2,mua = lens_equation_sie(xi1,xi2,lpar)
yi1 = xi1-ai1
yi2 = xi2-ai2
g_limage = lv4.call_ray_tracing(g_source,yi1,yi2,ysc1,ysc2,dsi)
g_limage[g_limage<=0.0001] = 1e-6
g_limage = p2p.cosccd2mag(g_limage)
g_limage = p2p.mag2sdssccd(g_limage)
#pl.figure()
#pl.imshow((g_limage),interpolation='lanczos',cmap=cm.gray)
#pl.colorbar()
#-------------------------------------------------------------
# Need to be Caliborate the mags
dA = Planck13.comoving_distance(zl).value*1000./(1+zl)
Re = dA*np.sin(R*np.pi/180./3600.)
counts =Brightness(Re,vd)
vpar = np.asarray([counts,R,xc1,xc2,q,pha])
#g_lens = deVaucouleurs(xi1,xi2,xc1,xc2,counts,R,1.0-q,pha)
g_lens = de_vaucouleurs_2d(xi1,xi2,vpar)
#pl.figure()
#pl.imshow((g_lens),interpolation='nearest',cmap=cm.gray)
#pl.colorbar()
g_clean_ccd = g_lens+g_limage
#pl.figure()
#pl.imshow((g_clean_ccd),interpolation='nearest',cmap=cm.gray)
#pl.colorbar()
g_clean_ccd = congrid.congrid(g_clean_ccd,[128,128])
#-------------------------------------------------------------
file_psf = "../PSF_and_noise/sdsspsf.fits"
g_psf = pyfits.getdata(file_psf)-1000.0
g_psf = g_psf/np.sum(g_psf)
#new_shape=[0,0]
#new_shape[0]=np.shape(g_psf)[0]*dsx_sdss/dsx
#new_shape[1]=np.shape(g_psf)[1]*dsx_sdss/dsx
#g_psf = rebin_psf(g_psf,new_shape)
g_images_psf = ss.fftconvolve(g_clean_ccd,g_psf,mode="same")
#g_images_psf = ss.convolve(g_clean_ccd,g_psf,mode="same")
#g_images_psf = g_clean_ccd
#pl.figure()
#pl.imshow((g_psf),interpolation='nearest',cmap=cm.gray)
#pl.colorbar()
#-------------------------------------------------------------
# Need to be Caliborate the mags
#g_noise = noise_map(nnn,nnn,np.sqrt(nstd),"Gaussian")
g_noise = noise_map(128,128,np.sqrt(nstd),"Gaussian")
g_final = g_images_psf+g_noise
#pl.figure()
#pl.imshow((g_final.T),interpolation='nearest',cmap=cm.gray)
#pl.colorbar()
g_final_rebin = congrid.congrid(g_final,[128,128])
#pl.figure()
#pl.imshow((g_final_rebin.T),interpolation='nearest',cmap=cm.gray)
#pl.colorbar()
#-------------------------------------------------------------
output_filename = "../output_fits/"+str(ind)+".fits"
pyfits.writeto(output_filename,g_final_rebin,clobber=True)
pl.show()
return 0
from astropy.constants import c as speed_of_light
# prefix, target = 'M2FS16', 'A04'
# outfile = os.path.abspath(os.path.join(os.curdir,'..','..', 'OneDrive - umich.edu','Research','M2FSReductions','catalogs','merged_target_lists', 'mtlz_{}_{}_full.fits'.format(prefix,target)))
prefix, target = 'M2FS17', 'B09'
outfile = os.path.abspath(os.path.join(os.curdir,'..','data','catalogs','merged_target_lists', 'mtlz_{}_{}_full.fits'.format(prefix,target)))
complete_table = Table.read(outfile,format='fits')
ra_clust = float(complete_table.meta['RA_TARG'])
dec_clust= float(complete_table.meta['DEC_TARG'])
z_clust = float(complete_table.meta['Z_TARG'])
kpc_p_amin = Planck13.kpc_comoving_per_arcmin(z_clust)
cluster = SkyCoord(ra=ra_clust*u.deg,dec=dec_clust*u.deg)
scalar_c = consts.c.to(u.km/u.s).value
measured_table = complete_table[np.bitwise_not(complete_table['SDSS_only'])]
corcut = 0.3
spec_overlap = measured_table[np.logical_not(measured_table['sdss_zsp'].mask)]
spec_overlap = spec_overlap[((spec_overlap['cor']>corcut))]
if len(spec_overlap)==0:
raise(TypeError,"There were no overlapping spectra and SDSS")
blue_cam = np.array([fib[0]=='b' for fib in spec_overlap['FIBNAME']])
red_cam = np.bitwise_not(blue_cam)
plt.figure()
#Find the RA, DEC, Z #galra=galdat.RA[:100] #galdec=galdat.DEC[:100] #galz=galdat.Z[:100] cutra=cutdat.RA cutdec=cutdat.DEC cutz=cutdat.Z randra=randat.RA randdec=randat.DEC randz=randat.Z #Convert redshift to Mpc (Using Planck Results stored in astropy.cosmology) #comoving=Planck13.comoving_distance(galz) cutX=Planck13.comoving_distance(cutz) randX=Planck13.comoving_distance(randz) end2=time.time() print end2-start, 'Comoving distances calculated' ''' #From working cosmology code def Horizon(x, t, Om, Og, Ol, Ok): F=(x**-2)*(Om/x**3+Og/x**4+Ol+Ok/x**2)**-0.5 return F Om=0.307 Og=0 Ol=0.693 Ok=1-(Om+Og+Ol) t=linspace(0,1,100000) DA=[]