Include all the stupid tools required for BORG analysis and plotting
This commit is contained in:
Guilhem Lavaux
parent
81f4b642e4
commit
a56eb021c4
111
python_sample/build_2lpt_ksz.py
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111
python_sample/build_2lpt_ksz.py
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import healpy as hp
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import numpy as np
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import cosmotool as ct
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import argparse
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import h5py as h5
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from matplotlib import pyplot as plt
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Mpc=3.08e22
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rhoc = 1.8864883524081933e-26 # m^(-3)
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sigmaT = 6.6524e-29
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mp = 1.6726e-27
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lightspeed = 299792458.
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v_unit = 1e3 # Unit of 1 km/s
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T_cmb=2.725
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h = 0.71
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Y = 0.245 #The Helium abundance
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Omega_matter = 0.26
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Omega_baryon=0.0445
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G=6.67e-11
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MassSun=2e30
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frac_electron = 1.0 # Hmmmm
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frac_gas_galaxy = 0.14
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mu = 1/(1-0.5*Y)
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baryon_fraction = Omega_baryon / Omega_matter
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ksz_normalization = T_cmb*sigmaT*v_unit/(lightspeed*mu*mp) * baryon_fraction
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rho_mean_matter = Omega_matter * (3*(100e3/Mpc)**2/(8*np.pi*G))
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parser=argparse.ArgumentParser(description="Generate Skymaps from CIC maps")
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parser.add_argument('--boxsize', type=float, required=True)
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parser.add_argument('--Nside', type=int, default=128)
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parser.add_argument('--base_h5', type=str, required=True)
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parser.add_argument('--base_fig', type=str, required=True)
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parser.add_argument('--start', type=int, required=True)
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parser.add_argument('--end', type=int, required=True)
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parser.add_argument('--step', type=int, required=True)
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parser.add_argument('--minval', type=float, default=-0.5)
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parser.add_argument('--maxval', type=float, default=0.5)
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parser.add_argument('--depth_min', type=float, default=10)
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parser.add_argument('--depth_max', type=float, default=60)
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parser.add_argument('--iid', type=int, default=0)
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parser.add_argument('--ksz_map', type=str, required=True)
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args = parser.parse_args()
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L = args.boxsize
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Nside = args.Nside
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def build_sky_proj(density, dmax=60.,dmin=0,iid=0):
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N = density.shape[0]
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ix = (np.arange(N)-0.5)*L/N - 0.5 * L
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dist2 = (ix[:,None,None]**2 + ix[None,:,None]**2 + ix[None,None,:]**2)
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flux = density.transpose().astype(ct.DTYPE) # / dist2
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dmax=N*dmax/L
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dmin=N*dmin/L
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if iid == 0:
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shifter = np.array([0.5,0.5,0.5])
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else:
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shifter = np.array([0.,0.,0.])
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projsky1 = ct.spherical_projection(Nside, flux, dmin, dmax, integrator_id=iid, shifter=shifter, progress=1)
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return projsky1*L/N
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def build_unit_vectors(N):
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ii = np.arange(N)*L/N - 0.5*L
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d = np.sqrt(ii[:,None,None]**2 + ii[None,:,None]**2 + ii[None,None,:]**2)
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d[N/2,N/2,N/2] = 1
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ux = ii[:,None,None] / d
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uy = ii[None,:,None] / d
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uz = ii[None,None,:] / d
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return ux,uy,uz
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for i in xrange(args.start,args.end,args.step):
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ff=plt.figure(1)
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plt.clf()
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with h5.File(args.base_h5 % i, mode="r") as f:
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p = f['velocity'][:]
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davg = np.average(np.average(np.average(f['density'][:],axis=0),axis=0),axis=0)
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p /= davg # Now we have momentum scaled to the mean density
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# Rescale by Omega_b / Omega_m
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p = p.astype(np.float64)
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print p.max(), p.min(), ksz_normalization, rho_mean_matter
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p *= ksz_normalization*rho_mean_matter
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p *= 1e6 # Put it in uK
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p *= -1 # ksz has a minus
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ux,uy,uz = build_unit_vectors(p.shape[0])
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pr = p[:,:,:,0] * ux + p[:,:,:,1] * uy + p[:,:,:,2] * uz
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print p.max(), p.min()
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print pr.max()*Mpc, pr.min()*Mpc
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@ct.timeit_quiet
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def run_proj():
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return build_sky_proj(pr*Mpc, dmin=args.depth_min,dmax=args.depth_max,iid=args.iid)
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proj = run_proj()
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hp.write_map(args.ksz_map % i, proj)
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hp.mollview(proj, fig=1, coord='CG', cmap=plt.cm.coolwarm, title='Sample %d' % i, min=args.minval,
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max=args.maxval)
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ff.savefig(args.base_fig % i)
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68
python_sample/build_2lpt_skymap.py
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68
python_sample/build_2lpt_skymap.py
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import healpy as hp
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import numpy as np
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import cosmotool as ct
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import argparse
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import h5py as h5
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from matplotlib import pyplot as plt
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parser=argparse.ArgumentParser(description="Generate Skymaps from CIC maps")
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parser.add_argument('--boxsize', type=float, required=True)
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parser.add_argument('--Nside', type=int, default=128)
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parser.add_argument('--base_cic', type=str, required=True)
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parser.add_argument('--base_fig', type=str, required=True)
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parser.add_argument('--start', type=int, required=True)
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parser.add_argument('--end', type=int, required=True)
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parser.add_argument('--step', type=int, required=True)
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parser.add_argument('--minval', type=float, default=0)
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parser.add_argument('--maxval', type=float, default=60)
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parser.add_argument('--depth_min', type=float, default=10)
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parser.add_argument('--depth_max', type=float, default=60)
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parser.add_argument('--iid', type=int, default=0)
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args = parser.parse_args()
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INDATA="/nethome/lavaux/Copy/PlusSimulation/BORG/Input_Data/2m++.npy"
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tmpp = np.load(INDATA)
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L = args.boxsize
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Nside = args.Nside
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def build_sky_proj(density, dmax=60.,dmin=0,iid=0):
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N = density.shape[0]
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ix = (np.arange(N)-0.5)*L/N - 0.5 * L
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dist2 = (ix[:,None,None]**2 + ix[None,:,None]**2 + ix[None,None,:]**2)
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flux = density.transpose().astype(ct.DTYPE) # / dist2
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dmax=N*dmax/L
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dmin=N*dmin/L
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if iid == 0:
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shifter = np.array([0.5,0.5,0.5])
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else:
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shifter = np.array([0.,0.,0.])
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projsky1 = ct.spherical_projection(Nside, flux, dmin, dmax, integrator_id=iid, shifter=shifter)
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return projsky1*L/N
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l,b = tmpp['gal_long'],tmpp['gal_lat']
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l = np.radians(l)
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b = np.pi/2 - np.radians(b)
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dcmb = tmpp['velcmb']/100.
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idx = np.where((dcmb>args.depth_min)*(dcmb<args.depth_max))
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for i in xrange(args.start,args.end,args.step):
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ff=plt.figure(1)
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plt.clf()
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d = np.load(args.base_cic % i)
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proj = build_sky_proj(1+d, dmin=args.depth_min,dmax=args.depth_max,iid=args.iid)
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hp.mollview(proj, fig=1, coord='CG', cmap=plt.cm.coolwarm, title='Sample %d' % i, min=args.minval, max=args.maxval)
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hp.projscatter(b[idx], l[idx], lw=0, color='g', s=2.0, alpha=0.7)
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ff.savefig(args.base_fig % i)
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@ -1 +0,0 @@
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/nethome/lavaux/wuala/WualaDrive/g_lavaux/PythonCode/BORG/build_nbody_skymap.py
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58
python_sample/build_nbody_skymap.py
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python_sample/build_nbody_skymap.py
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import healpy as hp
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import numpy as np
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import cosmotool as ct
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import h5py as h5
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from matplotlib import pyplot as plt
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L=600.
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Nside=128
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INDATA="/nethome/lavaux/Copy/PlusSimulation/BORG/Input_Data/2m++.npy"
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tmpp = np.load(INDATA)
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def build_sky_proj(density, dmax=60.,dmin=0):
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N = density.shape[0]
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ix = (np.arange(N)-0.5)*L/N - 0.5 * L
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dist2 = (ix[:,None,None]**2 + ix[None,:,None]**2 + ix[None,None,:]**2)
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flux = density.transpose().astype(ct.DTYPE) # / dist2
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dmax=N*dmax/L
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dmin=N*dmin/L
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projsky1 = ct.spherical_projection(Nside, flux, dmin, dmax, integrator_id=1)
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# projsky0 = ct.spherical_projection(Nside, flux, 0, 52, integrator_id=0)
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return projsky1*L/N#,projsky0
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l,b = tmpp['gal_long'],tmpp['gal_lat']
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l = np.radians(l)
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b = np.pi/2 - np.radians(b)
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dcmb = tmpp['velcmb']/100.
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idx = np.where((dcmb>10)*(dcmb<60))
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plt.figure(1)
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plt.clf()
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if True:
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with h5.File("fields.h5", mode="r") as f:
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d = f["density"][:].transpose()
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d /= np.average(np.average(np.average(d,axis=0),axis=0),axis=0)
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proj = build_sky_proj(d, dmin=10,dmax=60.)
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proj0 = proj1 = proj
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else:
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d = np.load("icgen/dcic0.npy")
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proj0 = build_sky_proj(1+d, dmin=10,dmax=60.)
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d = np.load("icgen/dcic1.npy")
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proj1 = build_sky_proj(1+d, dmin=10,dmax=60.)
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hp.mollview(proj0, fig=1, coord='CG', max=60, cmap=plt.cm.coolwarm)
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hp.projscatter(b[idx], l[idx], lw=0, color='g', s=5.0, alpha=0.8)
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plt.figure(2)
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plt.clf()
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hp.mollview(proj1, fig=2, coord='CG', max=60, cmap=plt.cm.coolwarm)
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hp.projscatter(b[idx], l[idx], lw=0, color='g', s=5.0, alpha=0.8)
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47
python_sample/gen_2lpt_asmooth.py
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python_sample/gen_2lpt_asmooth.py
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import os
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import h5py as h5
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import numpy as np
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import cosmotool as ct
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import icgen as bic
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import icgen.cosmogrowth as cg
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import sys
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import argparse
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ADAPT_SMOOTH="/home/bergeron1NS/lavaux/Software/cosmotool/build/sample/simple3DFilter"
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cosmo={'omega_M_0':0.3175, 'h':0.6711}
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cosmo['omega_lambda_0']=1-cosmo['omega_M_0']
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cosmo['omega_k_0'] = 0
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cosmo['omega_B_0']=0.049
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cosmo['SIGMA8']=0.8344
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cosmo['ns']=0.9624
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N0=256
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doSimulation=True
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astart=1.
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parser=argparse.ArgumentParser(description="Generate CIC density from 2LPT")
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parser.add_argument('--start', type=int, required=True)
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parser.add_argument('--end', type=int, required=True)
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parser.add_argument('--step', type=int, required=True)
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parser.add_argument('--base', type=str, required=True)
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parser.add_argument('--N', type=int, default=256)
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parser.add_argument('--output', type=str, default="fields_%d.h5")
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parser.add_argument('--supersample', type=int, default=1)
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args = parser.parse_args()
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for i in xrange(args.start, args.end, args.step):
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print i
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pos,vel,density,N,L,_ = bic.run_generation("%s/initial_density_%d.dat" % (args.base,i), 0.001, astart,
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cosmo, supersample=args.supersample, do_lpt2=True)
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q = pos + vel
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with h5.File("particles.h5", mode="w") as f:
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f.create_dataset("particles", data=np.array(q).transpose())
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os.system(ADAPT_SMOOTH + " %s %lg %lg %d %lg %lg %lg" % ("particles.h5", 3000000, L, args.N, 0, 0, 0))
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os.rename("fields.h5", args.output % i)
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42
python_sample/gen_2lpt_density.py
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python_sample/gen_2lpt_density.py
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import numpy as np
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import cosmotool as ct
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import icgen as bic
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import icgen.cosmogrowth as cg
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import sys
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import argparse
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cosmo={'omega_M_0':0.3175, 'h':0.6711}
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cosmo['omega_lambda_0']=1-cosmo['omega_M_0']
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cosmo['omega_k_0'] = 0
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cosmo['omega_B_0']=0.049
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cosmo['SIGMA8']=0.8344
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cosmo['ns']=0.9624
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N0=256
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doSimulation=True
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astart=1.
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parser=argparse.ArgumentParser(description="Generate CIC density from 2LPT")
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parser.add_argument('--start', type=int, required=True)
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parser.add_argument('--end', type=int, required=True)
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parser.add_argument('--step', type=int, required=True)
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parser.add_argument('--base', type=str, required=True)
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parser.add_argument('--N', type=int, default=256)
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parser.add_argument('--output', type=str, default="dcic_%d.npy")
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parser.add_argument('--supersample', type=int, default=1)
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args = parser.parse_args()
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for i in xrange(args.start, args.end, args.step):
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print i
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# pos,_,density,N,L,_ = bic.run_generation("/nethome/lavaux/remote/borg_2m++_128/initial_density_%d.dat" % i, 0.001, astart, cosmo, supersample=2, do_lpt2=True)
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pos,_,density,N,L,_ = bic.run_generation("%s/initial_density_%d.dat" % (args.base,i), 0.001, astart,
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cosmo, supersample=args.supersample, do_lpt2=True)
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dcic = ct.cicParticles(pos, L, args.N)
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dcic /= np.average(np.average(np.average(dcic, axis=0), axis=0), axis=0)
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dcic -= 1
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np.save(args.output % i, dcic)
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41
python_sample/icgen/test_whitify.py
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41
python_sample/icgen/test_whitify.py
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import numpy as np
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import cosmotool as ct
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import borgicgen as bic
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from matplotlib import pyplot as plt
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cosmo={'omega_M_0':0.3175, 'h':0.6711}
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cosmo['omega_lambda_0']=1-cosmo['omega_M_0']
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cosmo['omega_k_0'] = 0
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cosmo['omega_B_0']=0.049
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cosmo['SIGMA8']=0.8344
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cosmo['ns']=0.9624
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zstart=50
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astart=1/(1.+zstart)
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halfPixelShift=False
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posx,vel,density,N,L,a_ic,cosmo = bic.run_generation("initial_condition_borg.dat", 0.001, astart, cosmo, supersample=1, shiftPixel=halfPixelShift, do_lpt2=False)
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w1 = bic.whitify(density, L, cosmo, supergenerate=1)
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w2 = bic.whitify(density, L, cosmo, supergenerate=2)
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N = w1.shape[0]
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Ns = w2.shape[0]
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w1_hat = np.fft.rfftn(w1)*(L/N)**3
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w2_hat = np.fft.rfftn(w2)*(L/Ns)**3
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P1, b1, dev1 = bic.bin_power(np.abs(w1_hat)**2, L, range=(0,3),bins=150,dev=True)
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P2, b2, dev2 = bic.bin_power(np.abs(w2_hat)**2, L, range=(0,3),bins=150,dev=True)
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fig = plt.figure(1)
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fig.clf()
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plt.fill_between(b1, P1*(1-dev1), P1*(1+dev1), label='Supergen=1', color='b')
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plt.fill_between(b2, P2*(1-dev2), P2*(1+dev2), label='Supergen=2', color='g', alpha=0.5)
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ax = plt.gca()
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ax.set_xscale('log')
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plt.ylim(0.5,1.5)
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plt.xlim(1e-2,4)
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plt.axhline(1.0, color='red', lw=4.0)
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plt.legend()
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plt.show()
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14
python_sample/ramsesToArray.py
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14
python_sample/ramsesToArray.py
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import numpy as np
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import sys
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import h5py as h5
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import cosmotool as ct
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s = ct.loadRamsesAll(sys.argv[1], int(sys.argv[2]), doublePrecision=True, loadVelocity=True)
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q = [p for p in s.getPositions()]
|
||||
q += [p for p in s.getVelocities()]
|
||||
q = np.array(q)
|
||||
|
||||
with h5.File("particles.h5", mode="w") as f:
|
||||
f.create_dataset("particles", data=q.transpose())
|
||||
@ -1 +0,0 @@
|
||||
/nethome/lavaux/wuala/WualaDrive/g_lavaux/PythonCode/BORG/test_spheric_proj.py
|
||||
20
python_sample/test_spheric_proj.py
Normal file
20
python_sample/test_spheric_proj.py
Normal file
@ -0,0 +1,20 @@
|
||||
import cosmotool as ct
|
||||
import numpy as np
|
||||
import healpy as hp
|
||||
|
||||
d = np.zeros((64,64,64), ct.DTYPE)
|
||||
|
||||
d[32,32,32] = 1
|
||||
|
||||
ii=np.arange(256)*64/256.-32
|
||||
xx = ii[:,None,None].repeat(256,axis=1).repeat(256,axis=2).reshape(256**3)
|
||||
yy = ii[None,:,None].repeat(256,axis=0).repeat(256,axis=2).reshape(256**3)
|
||||
zz = ii[None,None,:].repeat(256,axis=0).repeat(256,axis=1).reshape(256**3)
|
||||
|
||||
d_high = ct.interp3d(xx, yy, zz, d, 64, periodic=True)
|
||||
d_high = d_high.reshape((256,256,256))
|
||||
|
||||
proj0 = ct.spherical_projection(64, d, 0, 20, integrator_id=0, shifter=np.array([0.5,0.5,0.5]))
|
||||
proj1 = ct.spherical_projection(64, d, 0, 20, integrator_id=1)
|
||||
|
||||
proj0_high = ct.spherical_projection(256, d_high, 0, 30, integrator_id=0, shifter=np.array([0.5,0.5,0.5]))
|
||||
Loading…
Reference in New Issue
Block a user