def sed_from_galacticus_mags(galacticus_mags, redshift, h=0.71, omega_m=0.265):
"""
galacticus_mags is a numpy array such that
galacticus_mags[i][j] is the magnitude of the jth star in the ith bandpass,
where the bandpasses are ordered in ascending order of minimum wavelength.
Will return a numpy array of SED names and a numpy array of magNorms.
"""
if not _LSST_IS_AVAILABLE:
raise RuntimeError("You cannot use sed_from_galacticus_mags\n"
"You do not have *lsst* installed and setup")
if not hasattr(sed_from_galacticus_mags, '_sed_color_tree'):
catsim_dir \
= os.path.join(getPackageDir('sims_GCRCatSimInterface'), 'data')
color_grid_file = os.path.join(catsim_dir, 'CatSimMagGrid.txt')
if not os.path.exists(color_grid_file):
msg = '\n%s does not exist\n' % color_grid_file
msg += 'Go into the directory %s ' % catsim_dir
msg += 'and run the script get_sed_mags.py'
raise RuntimeError(msg)
dtype_list = [('name', str, 200)]
for ii in range(30):
dtype_list.append(('mag%d' % ii, float))
dtype_list.append(('magNorm', float))
dtype = np.dtype(dtype_list)
sed_data = np.genfromtxt(color_grid_file, dtype=dtype)
sed_colors = np.array([sed_data['mag%d' % (ii+1)] - sed_data['mag%d' % ii]
for ii in range(29)])
sed_from_galacticus_mags._sed_colors = sed_colors.transpose()
sed_from_galacticus_mags._sed_names = sed_data['name']
sed_from_galacticus_mags._mag_norm = sed_data['magNorm']
sed_from_galacticus_mags._sed_mags = np.array([sed_data['mag%d' % ii]
for ii in range(30)]).transpose()
cosmology = CosmologyObject(H0=100.0*h, Om0=omega_m)
distance_modulus = cosmology.distanceModulus(redshift=redshift)
assert len(distance_modulus) == len(galacticus_mags[0])
galacticus_colors = np.array([galacticus_mags[ii+1]-galacticus_mags[ii]
for ii in range(29)]).transpose()
mag_dex = np.zeros(len(galacticus_colors), dtype=int)
for i_star in range(len(galacticus_colors)):
dd = np.sum((galacticus_colors[i_star]
-sed_from_galacticus_mags._sed_colors)**2, axis=1)
mag_dex[i_star] = np.argmin(dd)
output_names = sed_from_galacticus_mags._sed_names[mag_dex]
chosen_mags = sed_from_galacticus_mags._sed_mags[mag_dex]
galacticus_mags_t = galacticus_mags.transpose()
d_mag = (galacticus_mags_t - chosen_mags).sum(axis=1)/30.0
output_mag_norm = sed_from_galacticus_mags._mag_norm[mag_dex] + d_mag + distance_modulus
assert len(output_mag_norm) == len(output_names)
return output_names, output_mag_norm
def testComovingDistance(self):
"""
Test comoving distance calculation
Note: this is comoving distance defined as X in the FRW metric
ds^2 = -c^2 dt^2 + a^2 dX^2 + sin^2(X) dOmega^2
where spatial curvature is accounted for in the sin function
"""
H0 = 73.0
for Om0 in np.arange(start=0.15, stop=0.56, step=0.2):
for Ok0 in np.arange(start=-0.1, stop=0.11, step=0.2):
for w0 in np.arange(start=-1.1, stop=-0.85, step=0.2):
for wa in np.arange(start=-0.1, stop=0.115, step=0.02):
universe = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
Og0 = universe.OmegaPhotons()
Onu0 = universe.OmegaNeutrinos()
Ode0 = universe.OmegaDarkEnergy()
for zz in np.arange(start=0.1, stop=4.2, step=2.0):
comovingControl = universe.comovingDistance(redshift=zz)
comovingTest = \
self.speedOfLight*scipy.integrate.quad(comovingDistanceIntegrand, 0.0, zz,
args=(H0, Om0, Ode0,
Og0, Onu0, w0, wa))[0]
self.assertAlmostEqual(comovingControl/comovingTest, 1.0, 4)
class CosmologyMixin(object):
"""
This class is designed to operate as a mixin for InstanceCatalog classes.
It provides a member variable self.cosmology which is an instantiation
of the CosmologyObject class. self.cosmology defaults to the
Milliennium Simulation cosmology. This mixin also provides a method
self.setCosmology() which will allow the user to customize self.cosmology
and a getter for the column cosmologicalDistanceModulus that reflects the
effect of the luminosity distance on a galaxy's component magnitudes.
NOTE: one should only include this mixin in catalogs whose magNorm is
normalized to an absolute magnitude of some sort (i.e. the magnitude if
the galaxy was at redshift=0). The magNorms for galaxies stored on the
University of Washington LSSTCATSIM database do not fit this criterion.
magNorms on the University of Washington LSSTCATSIM database include the
effects of cosmological distance modulus.
"""
cosmology = CosmologyObject()
def setCosmology(self, H0=73.0, Om0=0.25, Ok0=None, w0=None, wa=None):
"""
This method customizes the member variable self.cosmology by re-instantiating
the CosmologyObject class
param [in] H0 is the Hubble parameter today in km/s/Mpc
param [in] Om0 is the density paramter (fraction of critical) associated with matter today
param [in] Ode0 is the density paratmer associated with dark energy today
param [in] w0 is the w0 parameter associated with the equation of state of dark energy
w = w0 + wa z/(1+z)
param [in] wa is the wa parameter usesd to set the equation of state of dark energy
w = w0 + wa z/(1+z)
"""
self.cosmology = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
@cached
def get_cosmologicalDistanceModulus(self):
"""
getter for cosmologicalDistanceModulus (the effect of the luminosity
distance on a galaxy's component magnitudes)
"""
redshift = self.column_by_name("redshift")
if len(redshift) == 0:
#newer versions of astropy do not appreciate being passed an
#empty numpy array of redshifts; avoid nasty exceptions by
#just returning an empty numpy array if we got an empty numpy array
return numpy.array([])
return self.cosmology.distanceModulus(redshift)
def get_m_i(abs_mag_i, redshift):
"""
Take numpy arrays of absolute i-band magnitude and
cosmological redshift. Return a numpy array of
observed i-band magnitudes
"""
z_grid, k_grid = create_k_corr_grid()
k_corr = np.interp(redshift, z_grid, k_grid)
dc2_cosmo = CosmologyObject(H0=71.0, Om0=0.265)
distance_modulus = dc2_cosmo.distanceModulus(redshift=redshift)
obs_mag_i = abs_mag_i + distance_modulus + k_corr
return obs_mag_i
def testDistanceModulusAtZero(self):
"""
Test to make sure that the distance modulus is set to zero if the distance modulus method
returns a negative number
"""
universe = CosmologyObject()
ztest = [0.0, 1.0, 2.0, 0.0, 3.0]
mm = universe.distanceModulus(redshift=ztest)
self.assertEqual(mm[0], 0.0)
self.assertEqual(mm[3], 0.0)
self.assertEqual(mm[1], 5.0*np.log10(universe.luminosityDistance(ztest[1])) + 25.0)
self.assertEqual(mm[2], 5.0*np.log10(universe.luminosityDistance(ztest[2])) + 25.0)
self.assertEqual(mm[4], 5.0*np.log10(universe.luminosityDistance(ztest[4])) + 25.0)
def testGetCurrent(self):
"""
Test to make sure that getCurrent returns the activeCosmology
"""
for Om0 in np.arange(start=0.2, stop=0.5, step=0.29):
for Ok0 in np.arange(start=-0.2, stop=0.2, step=0.39):
for w0 in np.arange(start=-1.2, stop=-0.7, step=0.49):
for wa in np.arange(start=-0.2, stop=0.2, step=0.39):
universe = CosmologyObject(Om0=Om0,
Ok0=Ok0,
w0=w0,
wa=wa)
testUniverse = universe.getCurrent()
for zz in np.arange(start=1.0, stop=2.1, step=1.0):
self.assertEqual(universe.OmegaMatter(redshift=zz),
testUniverse.Om(zz))
self.assertEqual(
universe.OmegaDarkEnergy(redshift=zz),
testUniverse.Ode(zz))
self.assertEqual(
universe.OmegaPhotons(redshift=zz),
testUniverse.Ogamma(zz))
self.assertEqual(
universe.OmegaNeutrinos(redshift=zz),
testUniverse.Onu(zz))
self.assertEqual(
universe.OmegaCurvature(redshift=zz),
testUniverse.Ok(zz))
def testLuminosityDistance(self):
"""
Test the calculation of the luminosity distance
"""
H0 = 73.0
for Om0 in numpy.arange(start=0.15, stop=0.56, step=0.2):
for Ok0 in numpy.arange(start=-0.1, stop=0.11, step=0.2):
for w0 in numpy.arange(start=-1.1, stop=-0.85, step=0.2):
for wa in numpy.arange(start=-0.1, stop=0.11, step=0.2):
universe = CosmologyObject(H0=H0,
Om0=Om0,
Ok0=Ok0,
w0=w0,
wa=wa)
sqrtkCurvature = numpy.sqrt(
numpy.abs(universe.OmegaCurvature())) * universe.H(
) / self.speedOfLight
Og0 = universe.OmegaPhotons()
Onu0 = universe.OmegaNeutrinos()
Ode0 = universe.OmegaDarkEnergy()
for zz in numpy.arange(start=0.1, stop=4.2, step=2.0):
luminosityControl = universe.luminosityDistance(
redshift=zz)
comovingDistance = self.speedOfLight * scipy.integrate.quad(
comovingDistanceIntegrand,
0.0,
zz,
args=(H0, Om0, Ode0, Og0, Onu0, w0, wa))[0]
if universe.OmegaCurvature() < 0.0:
nn = sqrtkCurvature * comovingDistance
nn = numpy.sin(nn)
luminosityTest = (1.0 +
zz) * nn / sqrtkCurvature
elif universe.OmegaCurvature() > 0.0:
nn = sqrtkCurvature * comovingDistance
nn = numpy.sinh(nn)
luminosityTest = (1.0 +
zz) * nn / sqrtkCurvature
else:
luminosityTest = (1.0 + zz) * comovingDistance
self.assertAlmostEqual(
luminosityControl / luminosityTest, 1.0, 4)
def setCosmology(self, H0=73.0, Om0=0.25, Ok0=None, w0=None, wa=None):
"""
This method customizes the member variable self.cosmology by re-instantiating
the CosmologyObject class
param [in] H0 is the Hubble parameter today in km/s/Mpc
param [in] Om0 is the density paramter (fraction of critical) associated with matter today
param [in] Ode0 is the density paratmer associated with dark energy today
param [in] w0 is the w0 parameter associated with the equation of state of dark energy
w = w0 + wa z/(1+z)
param [in] wa is the wa parameter usesd to set the equation of state of dark energy
w = w0 + wa z/(1+z)
"""
self.cosmology = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
def get_m_i(abs_mag_i, redshift):
"""
(Edited from original because of error)
Take numpy arrays of absolute i-band magnitude and
cosmological redshift.
Returns
-------
array-like
observed i-band magnitudes
"""
z_grid, k_grid = create_k_corr_grid(redshift)
k_corr = np.interp(redshift, z_grid, k_grid)
dc2_cosmo = CosmologyObject(H0=71.0, Om0=0.265)
distance_modulus = dc2_cosmo.distanceModulus(redshift=redshift)
obs_mag_i = abs_mag_i + distance_modulus + k_corr
return obs_mag_i
def testNonFlatW0Wa(self):
"""
Test the evolution of H and Omega_i as a function of redshift for non-flat
models with w = w0 + wa * z / (1+z)
"""
H0 = 60.0
for Om0 in np.arange(start=0.15, stop=0.76, step=0.3):
for Ok0 in np.arange(start=-0.1, stop=0.11, step=0.2):
for w0 in np.arange(start=-1.1, stop=-0.89, step=0.2):
for wa in np.arange(start=-0.1, stop=0.15, step=0.2):
universe = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
Og0 = universe.OmegaPhotons(redshift=0.0)
Onu0 = universe.OmegaNeutrinos(redshift=0.0)
self.assertAlmostEqual(universe.OmegaMatter(redshift=0.0), Om0, 10)
self.assertAlmostEqual(Ok0, universe.OmegaCurvature(redshift=0.0), 10)
self.assertAlmostEqual(1.0 - Om0 - Ok0 - universe.OmegaDarkEnergy(redshift=0.0),
Og0 + Onu0, 10)
self.assertAlmostEqual(universe.H(redshift=0.0), H0, 10)
Om0 = universe.OmegaMatter(redshift=0.0)
Ode0 = universe.OmegaDarkEnergy(redshift=0.0)
for zz in np.arange(start=0.0, stop=4.0, step=2.0):
wControl = w0 + wa*(1.0 - 1.0/(1.0+zz))
self.assertAlmostEqual(wControl, universe.w(redshift=zz), 6)
Hcontrol, OmControl, OdeControl, OgControl, OnuControl, \
OkControl = cosmologicalOmega(zz, H0, Om0, Og0=Og0, Onu0=Onu0,
w0=w0, wa=wa, Ode0=Ode0)
self.assertAlmostEqual(OmControl, universe.OmegaMatter(redshift=zz), 6)
self.assertAlmostEqual(OdeControl, universe.OmegaDarkEnergy(redshift=zz), 6)
self.assertAlmostEqual(OgControl, universe.OmegaPhotons(redshift=zz), 6)
self.assertAlmostEqual(OnuControl, universe.OmegaNeutrinos(redshift=zz), 6)
self.assertAlmostEqual(OkControl, universe.OmegaCurvature(redshift=zz), 6)
self.assertAlmostEqual(Hcontrol, universe.H(redshift=zz), 6)
del universe
def testCatalogDistanceModulus(self):
"""
Does cosmologicalDistanceModulus get properly applied
"""
dbObj = myTestGals(database=self.dbName)
cosmoCat = cosmologicalGalaxyCatalog(dbObj)
controlCat = absoluteGalaxyCatalog(dbObj)
cosmoIter = cosmoCat.iter_catalog(chunk_size=self.dbSize)
controlIter = controlCat.iter_catalog(chunk_size=self.dbSize)
cosmology = CosmologyObject()
for (cosmoRow, controlRow) in zip(cosmoIter, controlIter):
modulus = cosmology.distanceModulus(controlRow[25])
self.assertEqual(cosmoRow[0], controlRow[0])
self.assertEqual(cosmoRow[25], controlRow[25])
self.assertEqual(cosmoRow[26], modulus)
for i in range(1,25):
self.assertAlmostEqual(cosmoRow[i], controlRow[i] + modulus, 6)
def testCatalogDistanceModulus(self):
"""
Does cosmologicalDistanceModulus get properly applied
"""
dbObj = myTestGals(database=self.dbName)
cosmoCat = cosmologicalGalaxyCatalog(dbObj, obs_metadata=self.obs)
controlCat = absoluteGalaxyCatalog(dbObj, obs_metadata=self.obs)
cosmoIter = cosmoCat.iter_catalog(chunk_size=self.dbSize)
controlIter = controlCat.iter_catalog(chunk_size=self.dbSize)
cosmology = CosmologyObject()
for (cosmoRow, controlRow) in zip(cosmoIter, controlIter):
modulus = cosmology.distanceModulus(controlRow[25])
self.assertEqual(cosmoRow[0], controlRow[0])
self.assertEqual(cosmoRow[25], controlRow[25])
self.assertEqual(cosmoRow[26], modulus)
for i in range(1, 25):
self.assertAlmostEqual(cosmoRow[i], controlRow[i] + modulus, 6)
def testDistanceModulus(self):
"""
Test the calculation of the distance modulus out to a certain redshift
"""
H0 = 73.0
universe = CosmologyObject()
for Om0 in np.arange(start=0.15, stop=0.56, step=0.2):
for Ok0 in np.arange(start=-0.1, stop=0.11, step=0.2):
for w0 in np.arange(start=-1.1, stop=-0.85, step=0.2):
for wa in np.arange(start=-0.1, stop=0.11, step=0.2):
universe = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
sqrtkCurvature = \
np.sqrt(np.abs(universe.OmegaCurvature()))*universe.H()/self.speedOfLight
Og0 = universe.OmegaPhotons()
Onu0 = universe.OmegaNeutrinos()
Ode0 = universe.OmegaDarkEnergy()
for zz in np.arange(start=0.1, stop=4.2, step=2.0):
modulusControl = universe.distanceModulus(redshift=zz)
comovingDistance = \
self.speedOfLight*scipy.integrate.quad(comovingDistanceIntegrand, 0.0, zz,
args=(H0, Om0, Ode0, Og0,
Onu0, w0, wa))[0]
if universe.OmegaCurvature() < 0.0:
nn = sqrtkCurvature*comovingDistance
nn = np.sin(nn)
luminosityDistance = (1.0+zz)*nn/sqrtkCurvature
elif universe.OmegaCurvature() > 0.0:
nn = sqrtkCurvature*comovingDistance
nn = np.sinh(nn)
luminosityDistance = (1.0+zz)*nn/sqrtkCurvature
else:
luminosityDistance = (1.0+zz)*comovingDistance
modulusTest = 5.0*np.log10(luminosityDistance) + 25.0
self.assertAlmostEqual(modulusControl/modulusTest, 1.0, 4)
class CosmologyMixin(object):
"""
This class is designed to operate as a mixin for InstanceCatalog classes.
It provides a member variable self.cosmology which is an instantiation
of the CosmologyObject class. self.cosmology defaults to the
Milliennium Simulation cosmology. This mixin also provides a method
self.setCosmology() which will allow the user to customize self.cosmology
and a getter for the column cosmologicalDistanceModulus that reflects the
effect of the luminosity distance on a galaxy's component magnitudes.
NOTE: one should only include this mixin in catalogs whose magNorm is
normalized to an absolute magnitude of some sort (i.e. the magnitude if
the galaxy was at redshift=0). The magNorms for galaxies stored on the
University of Washington LSST database do not fit this criterion.
magNorms on the University of Washington LSST database include the
effects of cosmological distance modulus.
"""
cosmology = CosmologyObject()
def setCosmology(self, H0=73.0, Om0=0.25, Ok0=None, w0=None, wa=None):
"""
This method customizes the member variable self.cosmology by re-instantiating
the CosmologyObject class
param [in] H0 is the Hubble parameter today in km/s/Mpc
param [in] Om0 is the density paramter (fraction of critical) associated with matter today
param [in] Ode0 is the density paratmer associated with dark energy today
param [in] w0 is the w0 parameter associated with the equation of state of dark energy
w = w0 + wa z/(1+z)
param [in] wa is the wa parameter usesd to set the equation of state of dark energy
w = w0 + wa z/(1+z)
"""
self.cosmology = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
@cached
def get_cosmologicalDistanceModulus(self):
"""
getter for cosmologicalDistanceModulus (the effect of the luminosity
distance on a galaxy's component magnitudes)
"""
redshift = self.column_by_name("redshift")
if len(redshift) == 0:
#newer versions of astropy do not appreciate being passed an
#empty numpy array of redshifts; avoid nasty exceptions by
#just returning an empty numpy array if we got an empty numpy array
return numpy.array([])
return self.cosmology.distanceModulus(redshift)
def testComovingDistance(self):
"""
Test comoving distance calculation
Note: this is comoving distance defined as X in the FRW metric
ds^2 = -c^2 dt^2 + a^2 dX^2 + sin^2(X) dOmega^2
where spatial curvature is accounted for in the sin function
"""
H0 = 73.0
for Om0 in numpy.arange(start=0.15, stop=0.56, step=0.2):
for Ok0 in numpy.arange(start=-0.1, stop=0.11, step=0.2):
for w0 in numpy.arange(start=-1.1, stop=-0.85, step=0.2):
for wa in numpy.arange(start=-0.1, stop=0.115, step=0.02):
universe = CosmologyObject(H0=H0,
Om0=Om0,
Ok0=Ok0,
w0=w0,
wa=wa)
Og0 = universe.OmegaPhotons()
Onu0 = universe.OmegaNeutrinos()
Ode0 = universe.OmegaDarkEnergy()
for zz in numpy.arange(start=0.1, stop=4.2, step=2.0):
comovingControl = universe.comovingDistance(
redshift=zz)
comovingTest = \
self.speedOfLight*scipy.integrate.quad(comovingDistanceIntegrand, 0.0, zz,
args=(H0, Om0, Ode0, Og0, Onu0, w0, wa))[0]
self.assertAlmostEqual(
comovingControl / comovingTest, 1.0, 4)
def testAngularDiameterDistance(self):
"""
Test the calculation of the angular diameter distance
"""
H0 = 56.0
universe = CosmologyObject()
for Om0 in np.arange(start=0.15, stop=0.56, step=0.2):
for Ok0 in np.arange(start=-0.1, stop=0.11, step=0.2):
for w0 in np.arange(start=-1.1, stop=-0.85, step=0.2):
for wa in np.arange(start=-0.1, stop=0.11, step=0.2):
universe = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
sqrtkCurvature = \
np.sqrt(np.abs(universe.OmegaCurvature()))*universe.H()/self.speedOfLight
Og0 = universe.OmegaPhotons()
Onu0 = universe.OmegaNeutrinos()
Ode0 = universe.OmegaDarkEnergy()
for zz in np.arange(start=0.1, stop=4.2, step=2.0):
angularControl = universe.angularDiameterDistance(redshift=zz)
comovingDistance = \
self.speedOfLight*scipy.integrate.quad(comovingDistanceIntegrand, 0.0, zz,
args=(H0, Om0, Ode0, Og0, Onu0, w0, wa))[0]
if universe.OmegaCurvature() < 0.0:
nn = sqrtkCurvature*comovingDistance
nn = np.sin(nn)
angularTest = nn/sqrtkCurvature
elif universe.OmegaCurvature() > 0.0:
nn = sqrtkCurvature*comovingDistance
nn = np.sinh(nn)
angularTest = nn/sqrtkCurvature
else:
angularTest = comovingDistance
angularTest /= (1.0+zz)
self.assertAlmostEqual(angularControl/angularTest, 1.0, 4)
def sed_from_galacticus_mags(galacticus_mags,
redshift,
catalog_name='protoDC2'):
"""
galacticus_mags is a numpy array such that
galacticus_mags[i][j] is the magnitude of the jth star in the ith bandpass,
where the bandpasses are ordered in ascending order of minimum wavelength.
Will return a numpy array of SED names and a numpy array of magNorms.
"""
assert catalog_name, '`catalog_name` cannot be None or empty'
if getattr(sed_from_galacticus_mags, '_catalog_name',
None) != catalog_name:
sed_names, sed_mag_list, sed_mag_norm, cosmo = _get_sed_mags_and_cosmology(
catalog_name)
sed_colors = sed_mag_list[:, 1:] - sed_mag_list[:, :-1]
sed_from_galacticus_mags._catalog_name = catalog_name
sed_from_galacticus_mags._sed_names = sed_names # N_sed
sed_from_galacticus_mags._mag_norm = sed_mag_norm # N_sed
sed_from_galacticus_mags._sed_mags = sed_mag_list # N_sed by N_mag
sed_from_galacticus_mags._sed_colors = sed_colors # N_sed by (N_mag - 1)
sed_from_galacticus_mags._cosmo = CosmologyObject(**cosmo)
galacticus_mags_t = np.asarray(galacticus_mags).T # N_star by N_mag
assert galacticus_mags_t.shape == (
len(redshift), sed_from_galacticus_mags._sed_mags.shape[1])
def _find_closest_sed(colors_this):
return np.argmin(
np.sum((sed_from_galacticus_mags._sed_colors - colors_this)**2,
axis=1))
galacticus_colors = galacticus_mags_t[:,
1:] - galacticus_mags_t[:, :
-1] # N_star by (N_mag - 1)
sed_idx = np.fromiter(
(_find_closest_sed(colors_this) for colors_this in galacticus_colors),
np.int,
len(galacticus_colors),
) # N_star
distance_modulus = sed_from_galacticus_mags._cosmo.distanceModulus(
redshift=redshift)
output_names = sed_from_galacticus_mags._sed_names[sed_idx]
d_mag = (galacticus_mags_t -
sed_from_galacticus_mags._sed_mags[sed_idx]).mean(axis=1)
output_mag_norm = sed_from_galacticus_mags._mag_norm[
sed_idx] + d_mag + distance_modulus
return output_names, output_mag_norm
def testFlatW0(self):
"""
Test the evolution of H and Omega_i as a function of redshift for flat
models with constant w
"""
H0 = 96.0
for Om0 in numpy.arange(start=0.1, stop=0.95, step=0.4):
for w0 in numpy.arange(start=-1.5, stop=-0.49, step=1.0):
universe = CosmologyObject(H0=H0, Om0=Om0, w0=w0)
Og0 = universe.OmegaPhotons(redshift=0.0)
Onu0 = universe.OmegaNeutrinos(redshift=0.0)
self.assertAlmostEqual(universe.OmegaMatter(redshift=0.0), Om0, 10)
self.assertAlmostEqual(1.0 - Om0 - universe.OmegaDarkEnergy(redshift=0.0), Og0+Onu0, 6)
self.assertAlmostEqual(universe.H(redshift=0.0),H0,10)
self.assertEqual(universe.OmegaCurvature(),0.0)
Om0 = universe.OmegaMatter(redshift=0.0)
Ode0 = universe.OmegaDarkEnergy(redshift=0.0)
for zz in numpy.arange(start=0.0, stop=4.1, step=2.0):
self.assertAlmostEqual(w0, universe.w(redshift=zz), 6)
Hcontrol, OmControl, OdeControl, OgControl, OnuControl, \
OkControl = cosmologicalOmega(zz, H0, Om0, Og0=Og0, Onu0=Onu0,
w0=w0, wa=0.0)
self.assertAlmostEqual(OmControl, universe.OmegaMatter(redshift=zz), 6)
self.assertAlmostEqual(OdeControl, universe.OmegaDarkEnergy(redshift=zz), 6)
self.assertAlmostEqual(OgControl, universe.OmegaPhotons(redshift=zz), 6)
self.assertAlmostEqual(OnuControl, universe.OmegaNeutrinos(redshift=zz), 6)
self.assertAlmostEqual(Hcontrol, universe.H(redshift=zz), 6)
del universe
def testGetCurrent(self):
"""
Test to make sure that getCurrent returns the activeCosmology
"""
for Om0 in np.arange(start=0.2, stop=0.5, step=0.29):
for Ok0 in np.arange(start=-0.2, stop=0.2, step=0.39):
for w0 in np.arange(start=-1.2, stop=-0.7, step=0.49):
for wa in np.arange(start=-0.2, stop=0.2, step=0.39):
universe = CosmologyObject(Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
testUniverse = universe.getCurrent()
for zz in np.arange(start=1.0, stop=2.1, step=1.0):
self.assertEqual(universe.OmegaMatter(redshift=zz),
testUniverse.Om(zz))
self.assertEqual(universe.OmegaDarkEnergy(redshift=zz),
testUniverse.Ode(zz))
self.assertEqual(universe.OmegaPhotons(redshift=zz),
testUniverse.Ogamma(zz))
self.assertEqual(universe.OmegaNeutrinos(redshift=zz),
testUniverse.Onu(zz))
self.assertEqual(universe.OmegaCurvature(redshift=zz),
testUniverse.Ok(zz))
def testLuminosityDistance(self):
"""
Test the calculation of the luminosity distance
"""
H0 = 73.0
for Om0 in numpy.arange(start=0.15, stop=0.56, step=0.2):
for Ok0 in numpy.arange(start=-0.1, stop=0.11, step=0.2):
for w0 in numpy.arange(start=-1.1, stop=-0.85, step=0.2):
for wa in numpy.arange(start=-0.1, stop=0.11, step=0.2):
universe = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
sqrtkCurvature = numpy.sqrt(numpy.abs(universe.OmegaCurvature()))*universe.H()/self.speedOfLight
Og0 = universe.OmegaPhotons()
Onu0 = universe.OmegaNeutrinos()
Ode0 = universe.OmegaDarkEnergy()
for zz in numpy.arange(start=0.1, stop=4.2, step=2.0):
luminosityControl = universe.luminosityDistance(redshift=zz)
comovingDistance = self.speedOfLight*scipy.integrate.quad(comovingDistanceIntegrand, 0.0, zz,
args=(H0, Om0, Ode0, Og0, Onu0, w0, wa))[0]
if universe.OmegaCurvature()<0.0:
nn =sqrtkCurvature*comovingDistance
nn = numpy.sin(nn)
luminosityTest = (1.0+zz)*nn/sqrtkCurvature
elif universe.OmegaCurvature()>0.0:
nn = sqrtkCurvature*comovingDistance
nn = numpy.sinh(nn)
luminosityTest = (1.0+zz)*nn/sqrtkCurvature
else:
luminosityTest = (1.0+zz)*comovingDistance
self.assertAlmostEqual(luminosityControl/luminosityTest,1.0,4)
def setCosmology(self, H0=73.0, Om0=0.25, Ok0=None, w0=None, wa=None):
"""
This method customizes the member variable self.cosmology by re-instantiating
the CosmologyObject class
param [in] H0 is the Hubble parameter today in km/s/Mpc
param [in] Om0 is the density paramter (fraction of critical) associated with matter today
param [in] Ode0 is the density paratmer associated with dark energy today
param [in] w0 is the w0 parameter associated with the equation of state of dark energy
w = w0 + wa z/(1+z)
param [in] wa is the wa parameter usesd to set the equation of state of dark energy
w = w0 + wa z/(1+z)
"""
self.cosmology = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0, wa=wa)
def testDistanceModulusAtZero(self):
"""
Test to make sure that the distance modulus is set to zero if the distance modulus method
returns a negative number
"""
universe = CosmologyObject()
ztest = [0.0, 1.0, 2.0, 0.0, 3.0]
mm = universe.distanceModulus(redshift=ztest)
self.assertEqual(mm[0], 0.0)
self.assertEqual(mm[3], 0.0)
self.assertEqual(
mm[1],
5.0 * np.log10(universe.luminosityDistance(ztest[1])) + 25.0)
self.assertEqual(
mm[2],
5.0 * np.log10(universe.luminosityDistance(ztest[2])) + 25.0)
self.assertEqual(
mm[4],
5.0 * np.log10(universe.luminosityDistance(ztest[4])) + 25.0)
def testAngularDiameterDistance(self):
"""
Test the calculation of the angular diameter distance
"""
H0 = 56.0
universe = CosmologyObject()
for Om0 in np.arange(start=0.15, stop=0.56, step=0.2):
for Ok0 in np.arange(start=-0.1, stop=0.11, step=0.2):
for w0 in np.arange(start=-1.1, stop=-0.85, step=0.2):
for wa in np.arange(start=-0.1, stop=0.11, step=0.2):
universe = CosmologyObject(H0=H0,
Om0=Om0,
Ok0=Ok0,
w0=w0,
wa=wa)
sqrtkCurvature = \
np.sqrt(np.abs(universe.OmegaCurvature()))*universe.H()/self.speedOfLight
Og0 = universe.OmegaPhotons()
Onu0 = universe.OmegaNeutrinos()
Ode0 = universe.OmegaDarkEnergy()
for zz in np.arange(start=0.1, stop=4.2, step=2.0):
angularControl = universe.angularDiameterDistance(
redshift=zz)
comovingDistance = \
self.speedOfLight*scipy.integrate.quad(comovingDistanceIntegrand, 0.0, zz,
args=(H0, Om0, Ode0, Og0, Onu0, w0, wa))[0]
if universe.OmegaCurvature() < 0.0:
nn = sqrtkCurvature * comovingDistance
nn = np.sin(nn)
angularTest = nn / sqrtkCurvature
elif universe.OmegaCurvature() > 0.0:
nn = sqrtkCurvature * comovingDistance
nn = np.sinh(nn)
angularTest = nn / sqrtkCurvature
else:
angularTest = comovingDistance
angularTest /= (1.0 + zz)
self.assertAlmostEqual(
angularControl / angularTest, 1.0, 4)
#import matplotlib
#matplotlib.use('Agg')
#import matplotlib.pyplot as plt
import h5py
import sncosmo
import numpy as np
from lsst.sims.photUtils import BandpassDict
from lsst.sims.photUtils import Sed
from lsst.sims.photUtils import CosmologyObject
import time
rng = np.random.RandomState(654)
cosmo = CosmologyObject()
c0_min = -0.3
x1_min = -3.0
z_min = 0.01
c0_range = 0.6
x1_range = 6.0
z_range = 1.2
d_c0 = 0.1
d_x1 = 1.0
d_z=0.01
bp_dict = BandpassDict.loadTotalBandpassesFromFiles()
wav_grid = bp_dict['g'].wavelen
def testNonFlatLCDM(self):
"""
Test the evolution of H and Omega_i as a function of redshift for non-flat
Lambda CDM models
"""
w0 = -1.0
wa = 0.0
H0 = 77.0
for Om0 in numpy.arange(start=0.15, stop=0.96, step=0.4):
for Ok0 in numpy.arange(start=-0.1, stop=0.11, step=0.2):
universe = CosmologyObject(H0=H0,
Om0=Om0,
Ok0=Ok0,
w0=w0,
wa=wa)
Og0 = universe.OmegaPhotons(redshift=0.0)
Onu0 = universe.OmegaNeutrinos(redshift=0.0)
self.assertAlmostEqual(universe.OmegaMatter(redshift=0.0), Om0,
10)
self.assertAlmostEqual(universe.OmegaCurvature(redshift=0.0),
Ok0, 10)
self.assertAlmostEqual(
1.0 - Ok0 - Om0 - universe.OmegaDarkEnergy(redshift=0.0),
Og0 + Onu0, 6)
self.assertAlmostEqual(universe.H(redshift=0.0), H0, 10)
Om0 = universe.OmegaMatter(redshift=0.0)
Ode0 = universe.OmegaDarkEnergy(redshift=0.0)
Ok0 = universe.OmegaCurvature(redshift=0.0)
for zz in numpy.arange(start=0.0, stop=4.0, step=2.0):
Hcontrol, OmControl, OdeControl, OgControl, OnuControl, \
OkControl = cosmologicalOmega(zz, H0, Om0, Og0=Og0, Onu0=Onu0,
Ode0=Ode0)
self.assertAlmostEqual(OmControl,
universe.OmegaMatter(redshift=zz),
6)
self.assertAlmostEqual(
OdeControl, universe.OmegaDarkEnergy(redshift=zz), 6)
self.assertAlmostEqual(OgControl,
universe.OmegaPhotons(redshift=zz),
6)
self.assertAlmostEqual(
OnuControl, universe.OmegaNeutrinos(redshift=zz), 6)
self.assertAlmostEqual(
OkControl, universe.OmegaCurvature(redshift=zz), 6)
self.assertAlmostEqual(Hcontrol, universe.H(redshift=zz),
6)
del universe
ebv_list = ebv_list[first_disk]
av_list = av_list[first_disk]
true_redshift_list = catalog_qties['redshift_true'][first_disk]
full_redshift_list = catalog_qties['redshift'][first_disk]
# hack to use the redshift at the snapshot of the galaxy
true_redshift_list = []
for step in catalog_qties['step'][first_disk]:
true_redshift_list.append(step_to_z[step])
true_redshift_list = np.array(true_redshift_list)
full_redshift_list = true_redshift_list
from lsst.sims.photUtils import CosmologyObject
cosmo = CosmologyObject(H0=71.0, Om0=0.265)
dm = cosmo.distanceModulus(true_redshift_list)
fudge = 2.5*np.log10(1.0+true_redshift_list)
u_control = -2.5*np.log10(u_control) + dm - fudge
g_control = -2.5*np.log10(g_control) + dm - fudge
r_control = -2.5*np.log10(r_control) + dm - fudge
i_control = -2.5*np.log10(i_control) + dm - fudge
z_control = -2.5*np.log10(z_control) + dm - fudge
y_control = -2.5*np.log10(y_control) + dm - fudge
u_dustless = -2.5*np.log10(u_dustless) + dm - fudge
g_dustless = -2.5*np.log10(g_dustless) + dm - fudge
r_dustless = -2.5*np.log10(r_dustless) + dm - fudge
base_sed = Sed()
base_sed.readSED_flambda(sed_name)
bp_dict = BandpassDict.loadTotalBandpassesFromFiles()
bp = bp_dict['i']
z_grid = np.arange(0.0, 16.0, 0.01)
k_grid = np.zeros(len(z_grid), dtype=float)
for i_z, zz in enumerate(z_grid):
ss = Sed(flambda=base_sed.flambda, wavelen=base_sed.wavelen)
ss.redshiftSED(zz, dimming=True)
k = k_correction(ss, bp, zz)
k_grid[i_z] = k
cosmo = CosmologyObject()
db = DBObject(database='LSSTCATSIM',
host='fatboy.phys.washington.edu',
port=1433,
driver='mssql+pymssql')
query = 'SELECT magnorm_agn, redshift, varParamStr FROM '
query += 'galaxy WHERE varParamStr IS NOT NULL '
query += 'AND dec BETWEEN -2.5 AND 2.5 '
query += 'AND (ra<2.5 OR ra>357.5)'
dtype = np.dtype([('magnorm', float), ('redshift', float),
('varParamStr', str, 400)])
data_iter = db.get_arbitrary_chunk_iterator(query,
dc2_data = np.genfromtxt('data/proto_dc2_bh_params.txt', dtype=dc2_dtype)
print('max z %e' % dc2_data['redshift'].max())
valid = np.where(np.logical_and(dc2_data['bhmass']!=0.0,
dc2_data['accretion_rate']!=0.0))
dc2_data = dc2_data[valid]
mass_cut = np.where(dc2_data['bhmass']>=10.0**7)
dc2_data = dc2_data[mass_cut]
dc2_log_edd_rat = log_Eddington_ratio(dc2_data['bhmass'],
dc2_data['accretion_rate'])
dc2_abs_mag_i = M_i_from_L_Mass(dc2_log_edd_rat, np.log10(dc2_data['bhmass']))
dc2_cosmo = CosmologyObject(H0=71.0, Om0=0.265)
DM = dc2_cosmo.distanceModulus(redshift=dc2_data['redshift'])
bp_dict = BandpassDict.loadTotalBandpassesFromFiles()
bp_i = bp_dict['i']
sed_dir = os.path.join(getPackageDir('sims_sed_library'),
'agnSED')
sed_name = os.path.join(sed_dir, 'agn.spec.gz')
if not os.path.exists(sed_name):
raise RuntimeError('\n\n%s\n\nndoes not exist\n\n' % sed_name)
base_sed = Sed()
base_sed.readSED_flambda(sed_name)
z_grid = np.arange(0.0, dc2_data['redshift'].max(), 0.01)
k_grid = np.zeros(len(z_grid),dtype=float)
def testFlatLCDM(self):
"""
Test the evolution of H and Omega_i as a function of redshift for
flat Lambda CDM models
"""
H0 = 50.0
for Om0 in np.arange(start=0.1, stop=0.91, step=0.4):
universe = CosmologyObject(H0=H0, Om0=Om0)
Og0 = universe.OmegaPhotons(redshift=0.0)
Onu0 = universe.OmegaNeutrinos(redshift=0.0)
self.assertAlmostEqual(universe.OmegaMatter(redshift=0.0), Om0, 10)
self.assertAlmostEqual(
1.0 - Om0 - universe.OmegaDarkEnergy(redshift=0.0), Og0 + Onu0,
6)
self.assertAlmostEqual(universe.H(redshift=0.0), H0, 10)
self.assertEqual(universe.OmegaCurvature(), 0.0)
Om0 = universe.OmegaMatter(redshift=0.0)
for zz in np.arange(start=0.0, stop=4.1, step=2.0):
Hcontrol, OmControl, OdeControl, OgControl, OnuControl, \
OkControl, = cosmologicalOmega(zz, H0, Om0, Og0=Og0, Onu0=Onu0)
self.assertAlmostEqual(OmControl,
universe.OmegaMatter(redshift=zz), 6)
self.assertAlmostEqual(OdeControl,
universe.OmegaDarkEnergy(redshift=zz),
6)
self.assertAlmostEqual(OgControl,
universe.OmegaPhotons(redshift=zz), 6)
self.assertAlmostEqual(OnuControl,
universe.OmegaNeutrinos(redshift=zz), 6)
self.assertAlmostEqual(Hcontrol, universe.H(redshift=zz), 6)
del universe
def sed_from_galacticus_mags(galacticus_mags, redshift, redshift_true, H0, Om0,
wav_min, wav_width, obs_lsst_mags):
"""
Fit SEDs from sims_sed_library to Galacticus galaxies based on the
magnitudes in tophat filters.
Parameters
----------
galacticus_mags is a numpy array such that
galacticus_mags[i][j] is the magnitude of the jth star in the ith bandpass,
where the bandpasses are ordered in ascending order of minimum wavelength.
redshift is an array of redshifts for the galaxies being fit
(includes cosmology and proper motion)
redshift_true is an array of cosmological redshifts for the galaxies
being fit
H0 is the Hubbleparameter in units of km/s/Mpc
Om0 is the critical density parameter for matter
wav_min is a numpy array of the minimum wavelengths of the tophat
filters (in nm)
wav_grid is a numpy array of the widths of the tophat filters
(in nm)
ob_lsst_mags is a numpy array of observer frame LSST magnitudes.
obs_lsst_mags[0] will contain the u band magnitudes of every object.
Returns
-------
a numpy array of SED names and a numpy array of magNorms.
"""
if (not hasattr(sed_from_galacticus_mags, '_color_tree')
or not np.allclose(wav_min,
sed_from_galacticus_mags._wav_min,
atol=1.0e-10,
rtol=0.0)
or not np.allclose(wav_width,
sed_from_galacticus_mags._wav_width,
atol=1.0e-10,
rtol=0.0)):
(sed_names, sed_mag_list, sed_mag_norm, av_grid,
rv_grid) = _create_sed_library_mags(wav_min, wav_width)
assert rv_grid.min() > 0.0
assert len(np.where(np.logical_not(np.isfinite(rv_grid)))[0]) == 0
sed_colors = sed_mag_list[:, 1:] - sed_mag_list[:, :-1]
sed_from_galacticus_mags._sed_names = sed_names
sed_from_galacticus_mags._mag_norm = sed_mag_norm # N_sed
sed_from_galacticus_mags._av_grid = av_grid
sed_from_galacticus_mags._rv_grid = rv_grid
sed_from_galacticus_mags._sed_mags = sed_mag_list # N_sed by N_mag
sed_from_galacticus_mags._color_tree = scipy_spatial.cKDTree(
sed_colors)
sed_from_galacticus_mags._wav_min = wav_min
sed_from_galacticus_mags._wav_width = wav_width
if (not hasattr(sed_from_galacticus_mags, '_cosmo')
or np.abs(sed_from_galacticus_mags._cosmo.H() - H0) > 1.0e-6
or np.abs(sed_from_galacticus_mags._cosmo.OmegaMatter() - Om0) >
1.0e-6):
sed_from_galacticus_mags._cosmo = CosmologyObject(H0=H0, Om0=Om0)
galacticus_mags_t = np.asarray(galacticus_mags).T # N_star by N_mag
assert galacticus_mags_t.shape == (
len(redshift), sed_from_galacticus_mags._sed_mags.shape[1])
with np.errstate(invalid='ignore', divide='ignore'):
galacticus_colors = galacticus_mags_t[:,
1:] - galacticus_mags_t[:, :
-1] # N_star by (N_mag - 1)
t_start = time.time()
(sed_dist,
sed_idx) = sed_from_galacticus_mags._color_tree.query(galacticus_colors,
k=1)
# cKDTree returns an invalid index (==len(tree_data)) in cases
# where the distance is not finite
sed_idx = np.where(sed_idx < len(sed_from_galacticus_mags._sed_names),
sed_idx, 0)
distance_modulus = sed_from_galacticus_mags._cosmo.distanceModulus(
redshift=redshift_true)
output_names = sed_from_galacticus_mags._sed_names[sed_idx]
(lsst_bp_dict, dummy_bp_dict) = BandpassDict.loadBandpassesFromFiles()
output_mag_norm = np.zeros((6, len(output_names)), dtype=float)
base_norm = sed_from_galacticus_mags._mag_norm[sed_idx]
assert len(np.where(np.logical_not(np.isfinite(base_norm)))[0]) == 0
ccm_w = None
av_arr = sed_from_galacticus_mags._av_grid[sed_idx]
rv_arr = sed_from_galacticus_mags._rv_grid[sed_idx]
assert rv_arr.min() > 0.0
assert len(np.where(np.logical_not(np.isfinite(rv_arr)))[0]) == 0
for i_bp in range(6):
output_mag_norm[i_bp, :] = base_norm + distance_modulus
sed_dir = getPackageDir('sims_sed_library')
for i_obj in range(len(output_names)):
spec = Sed()
spec.readSED_flambda(os.path.join(sed_dir, output_names[i_obj]))
if ccm_w is None or not np.array_equal(spec.wavelen, ccm_w):
ccm_w = np.copy(spec.wavelen)
ax, bx = spec.setupCCM_ab()
spec.addDust(ax, bx, A_v=av_arr[i_obj], R_v=rv_arr[i_obj])
spec.redshiftSED(redshift[i_obj], dimming=True)
lsst_mags = lsst_bp_dict.magListForSed(spec)
d_mag = obs_lsst_mags[:, i_obj] - lsst_mags
output_mag_norm[:, i_obj] += d_mag
return (output_names, output_mag_norm, av_arr, rv_arr)
def testNonFlatW0(self):
"""
Test the evolution of H and Omega_i as a function of redshift for non-flat
models with constant w
"""
H0 = 60.0
for Om0 in np.arange(start=0.15, stop=0.76, step=0.3):
for Ok0 in np.arange(start=0.1, stop=0.11, step=0.2):
for w0 in np.arange(start=-1.1, stop=-0.89, step=0.2):
universe = CosmologyObject(H0=H0, Om0=Om0, Ok0=Ok0, w0=w0)
Og0 = universe.OmegaPhotons(redshift=0.0)
Onu0 = universe.OmegaNeutrinos(redshift=0.0)
self.assertAlmostEqual(universe.OmegaMatter(redshift=0.0),
Om0, 10)
self.assertAlmostEqual(
Ok0, universe.OmegaCurvature(redshift=0.0), 10)
self.assertAlmostEqual(
1.0 - Om0 - Ok0 -
universe.OmegaDarkEnergy(redshift=0.0), Og0 + Onu0, 10)
self.assertAlmostEqual(universe.H(redshift=0.0), H0, 10)
Om0 = universe.OmegaMatter(redshift=0.0)
Ode0 = universe.OmegaDarkEnergy(redshift=0.0)
for zz in np.arange(start=0.0, stop=4.0, step=2.0):
self.assertAlmostEqual(w0, universe.w(redshift=zz), 6)
Hcontrol, OmControl, OdeControl, OgControl, OnuControl, \
OkControl = cosmologicalOmega(zz, H0, Om0, Og0=Og0, Onu0=Onu0,
w0=w0, wa=0.0, Ode0=Ode0)
self.assertAlmostEqual(
OmControl, universe.OmegaMatter(redshift=zz), 6)
self.assertAlmostEqual(
OdeControl, universe.OmegaDarkEnergy(redshift=zz),
6)
self.assertAlmostEqual(
OgControl, universe.OmegaPhotons(redshift=zz), 6)
self.assertAlmostEqual(
OnuControl, universe.OmegaNeutrinos(redshift=zz),
6)
self.assertAlmostEqual(
OkControl, universe.OmegaCurvature(redshift=zz), 6)
self.assertAlmostEqual(Hcontrol,
universe.H(redshift=zz), 6)
del universe
def sed_from_galacticus_mags(galacticus_mags, redshift, H0, Om0, wav_min,
wav_width):
"""
Fit SEDs from sims_sed_library to Galacticus galaxies based on the
magnitudes in tophat filters.
Parameters
----------
galacticus_mags is a numpy array such that
galacticus_mags[i][j] is the magnitude of the jth star in the ith bandpass,
where the bandpasses are ordered in ascending order of minimum wavelength.
redshift is an array of redshifts for the galaxies being fit
H0 is the Hubbleparameter in units of km/s/Mpc
Om0 is the critical density parameter for matter
wav_min is a numpy array of the minimum wavelengths of the tophat
filters (in nm)
wav_grid is a numpy array of the widths of the tophat filters
(in nm)
Returns
-------
a numpy array of SED names and a numpy array of magNorms.
"""
if (not hasattr(sed_from_galacticus_mags, '_color_tree')
or not np.allclose(wav_min,
sed_from_galacticus_mags._wav_min,
atol=1.0e-10,
rtol=0.0)
or not np.allclose(wav_width,
sed_from_galacticus_mags._wav_width,
atol=1.0e-10,
rtol=0.0)):
(sed_names, sed_mag_list,
sed_mag_norm) = _create_sed_library_mags(wav_min, wav_width)
sed_colors = sed_mag_list[:, 1:] - sed_mag_list[:, :-1]
sed_from_galacticus_mags._sed_names = sed_names
sed_from_galacticus_mags._mag_norm = sed_mag_norm # N_sed
sed_from_galacticus_mags._sed_mags = sed_mag_list # N_sed by N_mag
sed_from_galacticus_mags._color_tree = scipy_spatial.cKDTree(
sed_colors)
sed_from_galacticus_mags._wav_min = wav_min
sed_from_galacticus_mags._wav_width = wav_width
if (not hasattr(sed_from_galacticus_mags, '_cosmo')
or np.abs(sed_from_galacticus_mags._cosmo.H() - H0) > 1.0e-6
or np.abs(sed_from_galacticus_mags._cosmo.OmegaMatter() - Om0) >
1.0e-6):
sed_from_galacticus_mags._cosmo = CosmologyObject(H0=H0, Om0=Om0)
galacticus_mags_t = np.asarray(galacticus_mags).T # N_star by N_mag
assert galacticus_mags_t.shape == (
len(redshift), sed_from_galacticus_mags._sed_mags.shape[1])
with np.errstate(invalid='ignore', divide='ignore'):
galacticus_colors = galacticus_mags_t[:,
1:] - galacticus_mags_t[:, :
-1] # N_star by (N_mag - 1)
(sed_dist,
sed_idx) = sed_from_galacticus_mags._color_tree.query(galacticus_colors,
k=1)
# cKDTree returns an invalid index (==len(tree_data)) in cases
# where the distance is not finite
sed_idx = np.where(sed_idx < len(sed_from_galacticus_mags._sed_names),
sed_idx, 0)
distance_modulus = sed_from_galacticus_mags._cosmo.distanceModulus(
redshift=redshift)
output_names = sed_from_galacticus_mags._sed_names[sed_idx]
d_mag = (galacticus_mags_t -
sed_from_galacticus_mags._sed_mags[sed_idx]).mean(axis=1)
output_mag_norm = sed_from_galacticus_mags._mag_norm[
sed_idx] + d_mag + distance_modulus
return output_names, output_mag_norm
def testFlatW0Wa(self):
"""
Test the evolution of H and Omega_i as a function of redshift for
flat models with w = w0 + wa * z / (1 + z)
"""
H0 = 96.0
for Om0 in np.arange(start=0.1, stop=0.95, step=0.4):
for w0 in np.arange(start=-1.1, stop=-0.89, step=0.2):
for wa in np.arange(start=-0.1, stop=0.11, step=0.2):
universe = CosmologyObject(H0=H0, Om0=Om0, w0=w0, wa=wa)
Og0 = universe.OmegaPhotons(redshift=0.0)
Onu0 = universe.OmegaNeutrinos(redshift=0.0)
self.assertAlmostEqual(universe.OmegaMatter(redshift=0.0),
Om0, 10)
self.assertAlmostEqual(
1.0 - Om0 - universe.OmegaDarkEnergy(redshift=0.0),
Og0 + Onu0, 6)
self.assertAlmostEqual(universe.H(redshift=0.0), H0, 10)
self.assertEqual(universe.OmegaCurvature(), 0.0)
Om0 = universe.OmegaMatter(redshift=0.0)
for zz in np.arange(start=0.0, stop=4.1, step=2.0):
wControl = w0 + wa * (1.0 - 1.0 / (1.0 + zz))
self.assertAlmostEqual(wControl,
universe.w(redshift=zz), 6)
Hcontrol, OmControl, OdeControl, OgControl, OnuControl, \
OkControl = cosmologicalOmega(zz, H0, Om0, Og0=Og0, Onu0=Onu0,
w0=w0, wa=wa)
self.assertAlmostEqual(
OmControl, universe.OmegaMatter(redshift=zz), 6)
self.assertAlmostEqual(
OdeControl, universe.OmegaDarkEnergy(redshift=zz),
6)
self.assertAlmostEqual(
OgControl, universe.OmegaPhotons(redshift=zz), 6)
self.assertAlmostEqual(
OnuControl, universe.OmegaNeutrinos(redshift=zz),
6)
self.assertAlmostEqual(Hcontrol,
universe.H(redshift=zz), 6)
del universe
duration = (time.time()-t_start)/3600.0
pred = n_samples*duration/ii
print('%d in %e hrs; predict %e' % (ii,duration,pred))
out_dict[dict_key] = (mag_interp, mag_truth)
if __name__ == "__main__":
parser = argparse.ArgumentParser()
parser.add_argument('--n_samples', type=int, default=1000000)
parser.add_argument('--n_processes', type=int, default=30)
args = parser.parse_args()
bp_dict = BandpassDict.loadTotalBandpassesFromFiles()
cosmo = CosmologyObject()
grid_name = '../data/sne_interp_models.h5'
rng = np.random.RandomState(44)
c0_range = 0.6
x1_range = 6.0
z_range = 1.2
abs_mag_mean = -19.3
abs_mag_std = 0.3
d_samples = args.n_samples//args.n_processes
with h5py.File(grid_name, 'r') as in_file:
param_mins = in_file['param_mins'].value
def test_sne(grid_name, x1_vals, c0_vals,
z_vals, abs_mag_vals, t_vals,
dict_key, out_dict):
bp_dict = BandpassDict.loadTotalBandpassesFromFiles()
cosmo = CosmologyObject()
n_samples = len(z_vals)
mag_truth = np.zeros((6,n_samples), dtype=float)
mag_interp = np.zeros((6,n_samples), dtype=float)
mag_grid_dict = {}
with h5py.File(grid_name, 'r') as in_file:
param_mins = in_file['param_mins'].value
d_params = in_file['d_params'].value
t_grid = in_file['t_grid'].value
for name in in_file.keys():
if name == 'param_mins':
continue
if name == 'd_params':
continue
if name == 't_grid':
continue
mag_grid_dict[name] = in_file[name].value
t_start = time.time()
for ii in range(n_samples):
x1 = x1_vals[ii]
c0 = c0_vals[ii]
z = z_vals[ii]
abs_mag = abs_mag_vals[ii]
t = t_vals[ii]
sn = sncosmo.Model(source='salt2-extended')
sn.set(x1=x1,c=c0,z=z)
sn.source.set_peakmag(abs_mag+cosmo.distanceModulus(z),
band='bessellb', magsys='ab')
flambda = 10.0*sn.flux(time=t, wave=10.0*bp_dict['g'].wavelen)
ss = Sed(flambda=flambda, wavelen=bp_dict['g'].wavelen)
mag_truth[:,ii] = bp_dict.magListForSed(ss)
i_x1 = np.round((x1-param_mins[0])/d_params[0]).astype(int)
i_c0 = np.round((c0-param_mins[1])/d_params[1]).astype(int)
i_z = np.round((z-param_mins[2])/d_params[2]).astype(int)
d_mag = abs_mag-param_mins[3]
tag = i_x1+i_c0*100+i_z*10000
mag_grid = mag_grid_dict['%d' % tag]
interp_mags = np.zeros(6, dtype=float)
for i_bp in range(6):
mm = np.interp(t, t_grid, mag_grid[i_bp])+d_mag
mag_interp[i_bp,ii] = mm
if ii>0 and ii%100 == 0:
duration = (time.time()-t_start)/3600.0
pred = n_samples*duration/ii
print('%d in %e hrs; predict %e' % (ii,duration,pred))
out_dict[dict_key] = (mag_interp, mag_truth)
def testDistanceModulus(self):
"""
Test the calculation of the distance modulus out to a certain redshift
"""
H0 = 73.0
universe = CosmologyObject()
for Om0 in np.arange(start=0.15, stop=0.56, step=0.2):
for Ok0 in np.arange(start=-0.1, stop=0.11, step=0.2):
for w0 in np.arange(start=-1.1, stop=-0.85, step=0.2):
for wa in np.arange(start=-0.1, stop=0.11, step=0.2):
universe = CosmologyObject(H0=H0,
Om0=Om0,
Ok0=Ok0,
w0=w0,
wa=wa)
sqrtkCurvature = \
np.sqrt(np.abs(universe.OmegaCurvature()))*universe.H()/self.speedOfLight
Og0 = universe.OmegaPhotons()
Onu0 = universe.OmegaNeutrinos()
Ode0 = universe.OmegaDarkEnergy()
for zz in np.arange(start=0.1, stop=4.2, step=2.0):
modulusControl = universe.distanceModulus(
redshift=zz)
comovingDistance = \
self.speedOfLight*scipy.integrate.quad(comovingDistanceIntegrand, 0.0, zz,
args=(H0, Om0, Ode0, Og0,
Onu0, w0, wa))[0]
if universe.OmegaCurvature() < 0.0:
nn = sqrtkCurvature * comovingDistance
nn = np.sin(nn)
luminosityDistance = (1.0 +
zz) * nn / sqrtkCurvature
elif universe.OmegaCurvature() > 0.0:
nn = sqrtkCurvature * comovingDistance
nn = np.sinh(nn)
luminosityDistance = (1.0 +
zz) * nn / sqrtkCurvature
else:
luminosityDistance = (1.0 +
zz) * comovingDistance
modulusTest = 5.0 * np.log10(
luminosityDistance) + 25.0
self.assertAlmostEqual(
modulusControl / modulusTest, 1.0, 4)
