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Add more flow modelling (#115)
* Add SN calibration model * Update imports * Scale Carrick field * Minor updates to flow validation * Update script * Update flow model * Add CSiBORG2 * Add CSiboRG2 params * Update imports * Add regular grid interpolator to LOS * Add nb * Remove old code * Update scripts * Minor updates * Minor updates * Add TF * Minor update * Update notebook * Update imports * Add scan and loss of numpyro * Add Pantheon * Update svript * Updaten b * Add model loader * Add jackknife * Add evidence * Update dr * Add BIC to the flow model * Update srcipt * Update nb * Update nb * Update scripts
This commit is contained in:
Richard Stiskalek
GitHub
parent
b503a6f003
commit
fb4abebeb6
11 changed files with 1949 additions and 342 deletions
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@ -58,7 +58,8 @@ def get_los(catalogue_name, simname, comm):
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if comm.Get_rank() == 0:
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folder = "/mnt/extraspace/rstiskalek/catalogs"
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if catalogue_name == "LOSS" or catalogue_name == "Foundation":
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if catalogue_name in ["LOSS", "Foundation", "SFI_gals", "2MTF",
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"Pantheon+"]:
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fpath = join(folder, "PV_compilation_Supranta2019.hdf5")
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with File(fpath, 'r') as f:
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grp = f[catalogue_name]
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@ -69,18 +70,6 @@ def get_los(catalogue_name, simname, comm):
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with File(fpath, 'r') as f:
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RA = f["RA"][:]
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dec = f["DEC"][:]
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elif "csiborg1" in catalogue_name:
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nsim = int(catalogue_name.split("_")[-1])
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cat = csiborgtools.read.CSiBORG1Catalogue(
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nsim, bounds={"totmass": (1e13, None)})
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seed = 42
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gen = np.random.default_rng(seed)
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mask = gen.choice(len(cat), size=100, replace=False)
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sph_pos = cat["spherical_pos"]
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RA = sph_pos[mask, 1]
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dec = sph_pos[mask, 2]
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else:
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raise ValueError(f"Unknown field name: `{catalogue_name}`.")
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@ -122,6 +111,9 @@ def get_field(simname, nsim, kind, MAS, grid):
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# Open the field reader.
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if simname == "csiborg1":
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field_reader = csiborgtools.read.CSiBORG1Field(nsim)
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elif "csiborg2" in simname:
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simkind = simname.split("_")[-1]
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field_reader = csiborgtools.read.CSiBORG2Field(nsim, simkind)
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elif simname == "Carrick2015":
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folder = "/mnt/extraspace/rstiskalek/catalogs"
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warn(f"Using local paths from `{folder}`.", RuntimeWarning)
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@ -130,7 +122,20 @@ def get_field(simname, nsim, kind, MAS, grid):
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return np.load(fpath).astype(np.float32)
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elif kind == "velocity":
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fpath = join(folder, "twompp_velocity_carrick2015.npy")
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return np.load(fpath).astype(np.float32)
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field = np.load(fpath).astype(np.float32)
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# Because the Carrick+2015 data is in the following form:
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# "The velocities are predicted peculiar velocities in the CMB
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# frame in Galactic Cartesian coordinates, generated from the
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# \(\delta_g^*\) field with \(\beta^* = 0.43\) and an external
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# dipole \(V_\mathrm{ext} = [89,-131,17]\) (Carrick et al Table 3)
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# has already been added.""
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field[0] -= 89
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field[1] -= -131
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field[2] -= 17
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field /= 0.43
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return field
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else:
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raise ValueError(f"Unknown field kind: `{kind}`.")
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else:
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@ -274,7 +279,7 @@ if __name__ == "__main__":
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rmax = 200
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dr = 0.5
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smooth_scales = [0, 2, 4, 6]
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smooth_scales = [0, 2]
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comm = MPI.COMM_WORLD
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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@ -1,14 +1,13 @@
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nthreads=11
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memory=64
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nthreads=4
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memory=32
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on_login=${1}
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queue="berg"
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env="/mnt/users/rstiskalek/csiborgtools/venv_csiborg/bin/python"
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file="field_los.py"
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catalogue="A2"
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# catalogue="csiborg1_9844"
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catalogue=${2}
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nsims="-1"
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simname="csiborg1"
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simname="csiborg2_main"
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MAS="SPH"
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grid=1024
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@ -26,11 +26,11 @@ import jax
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import numpy as np
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from h5py import File
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from mpi4py import MPI
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from numpyro.infer import MCMC, NUTS
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from numpyro.infer import MCMC, NUTS, init_to_sample
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from taskmaster import work_delegation # noqa
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def get_model(args, nsim):
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def get_model(args, nsim_iterator):
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"""
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Load the data and create the NumPyro model.
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@ -38,8 +38,8 @@ def get_model(args, nsim):
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----------
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args : argparse.Namespace
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Command line arguments.
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nsim : int
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Simulation index.
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nsim_iterator : int
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Simulation index, not the IC index. Ranges from 0, ... .
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Returns
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-------
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@ -49,7 +49,7 @@ def get_model(args, nsim):
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if args.catalogue == "A2":
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fpath = join(folder, "A2.h5")
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elif args.catalogue == "LOSS" or args.catalogue == "Foundation":
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raise NotImplementedError("To be implemented..")
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fpath = join(folder, "PV_compilation_Supranta2019.hdf5")
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else:
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raise ValueError(f"Unknown catalogue: `{args.catalogue}`.")
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@ -58,19 +58,51 @@ def get_model(args, nsim):
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Omega_m = csiborgtools.simname2Omega_m(args.simname)
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# Read in the data from the loader.
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los_overdensity = loader.los_density[:, nsim, :]
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los_velocity = loader.los_radial_velocity[:, nsim, :]
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los_overdensity = loader.los_density[:, nsim_iterator, :]
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los_velocity = loader.los_radial_velocity[:, nsim_iterator, :]
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RA = loader.cat["RA"]
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dec = loader.cat["DEC"]
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z_obs = loader.cat["z_obs"]
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if args.catalogue == "A2":
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RA = loader.cat["RA"]
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dec = loader.cat["DEC"]
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z_obs = loader.cat["z_obs"]
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r_hMpc = loader.cat["r_hMpc"]
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e_r_hMpc = loader.cat["e_rhMpc"]
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r_hMpc = loader.cat["r_hMpc"]
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e_r_hMpc = loader.cat["e_rhMpc"]
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return csiborgtools.flow.SD_PV_validation_model(
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los_overdensity, los_velocity, RA, dec, z_obs, r_hMpc, e_r_hMpc,
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loader.rdist, Omega_m)
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return csiborgtools.flow.SD_PV_validation_model(
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los_overdensity, los_velocity, RA, dec, z_obs, r_hMpc, e_r_hMpc,
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loader.rdist, Omega_m)
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elif args.catalogue == "LOSS" or args.catalogue == "Foundation":
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RA = loader.cat["RA"]
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dec = loader.cat["DEC"]
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zCMB = loader.cat["z_CMB"]
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mB = loader.cat["mB"]
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x1 = loader.cat["x1"]
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c = loader.cat["c"]
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e_mB = loader.cat["e_mB"]
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e_x1 = loader.cat["e_x1"]
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e_c = loader.cat["e_c"]
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return csiborgtools.flow.SN_PV_validation_model(
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los_overdensity, los_velocity, RA, dec, zCMB, mB, x1, c,
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e_mB, e_x1, e_c, loader.rdist, Omega_m)
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elif args.catalogue in ["SFI_gals", "2MTF"]:
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RA = loader.cat["RA"]
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dec = loader.cat["DEC"]
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zCMB = loader.cat["z_CMB"]
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mag = loader.cat["mag"]
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eta = loader.cat["eta"]
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e_mag = loader.cat["e_mag"]
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e_eta = loader.cat["e_eta"]
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return csiborgtools.flow.TF_PV_validation_model(
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los_overdensity, los_velocity, RA, dec, zCMB, mag, eta,
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e_mag, e_eta, loader.rdist, Omega_m)
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else:
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raise ValueError(f"Unknown catalogue: `{args.catalogue}`.")
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def run_model(model, nsteps, nchains, nsim, dump_folder, show_progress=True):
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@ -96,8 +128,8 @@ def run_model(model, nsteps, nchains, nsim, dump_folder, show_progress=True):
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-------
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None
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"""
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nuts_kernel = NUTS(model)
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mcmc = MCMC(nuts_kernel, num_warmup=nsteps // 2, num_samples=nsteps // 2,
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nuts_kernel = NUTS(model, init_strategy=init_to_sample)
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mcmc = MCMC(nuts_kernel, num_warmup=500, num_samples=nsteps,
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chain_method="sequential", num_chains=nchains,
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progress_bar=show_progress)
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rng_key = jax.random.PRNGKey(42)
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@ -185,8 +217,8 @@ if __name__ == "__main__":
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsims = paths.get_ics(args.simname)
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nsteps = 5000
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nchains = 1
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nsteps = 2000
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nchains = 2
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# Create the dumping folder.
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if comm.Get_rank() == 0:
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@ -198,12 +230,13 @@ if __name__ == "__main__":
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dump_folder = None
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dump_folder = comm.bcast(dump_folder, root=0)
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def main(nsim):
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model = get_model(args, nsim)
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run_model(model, nsteps, nchains, nsim, dump_folder,
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def main(i):
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model = get_model(args, i)
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run_model(model, nsteps, nchains, nsims[i], dump_folder,
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show_progress=size == 1)
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work_delegation(main, nsims, comm, master_verbose=True)
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work_delegation(main, [i for i in range(len(nsims))], comm,
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master_verbose=True)
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comm.Barrier()
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if rank == 0:
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@ -1,13 +1,14 @@
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memory=4
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on_login=${1}
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nthreads=${2}
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ksmooth=${3}
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queue="berg"
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env="/mnt/users/rstiskalek/csiborgtools/venv_csiborg/bin/python"
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file="flow_validation.py"
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catalogue="A2"
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simname="Carrick2015"
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ksmooth=2
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catalogue="Foundation"
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simname="csiborg2_random"
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pythoncm="$env $file --catalogue $catalogue --simname $simname --ksmooth $ksmooth"
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