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Plots of VF (#134)
* Add VF plots * Update nb * Add CMB velocity note * rm nb * Add option to return alllikelihood * Add simulation weights * Update nb * Add bulkflow * Update nb * Add values of beta * Update imports * Update imports * Add paths to Carrick and Lilow fiels * Add Carrick and Lilow fields * Add support for more fields * Update bulkflow comp * Update nb * Update script
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Richard Stiskalek
GitHub
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13 changed files with 1208 additions and 2680 deletions
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notebooks/flow/reconstruction_comparison.py
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notebooks/flow/reconstruction_comparison.py
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# Copyright (C) 2024 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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"""Script to help with plots in `flow_calibration.ipynb`."""
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from copy import copy
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from os.path import join
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import numpy as np
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from jax import numpy as jnp
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from getdist import MCSamples
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from h5py import File
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import csiborgtools
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###############################################################################
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# Convert between coordinate systems #
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###############################################################################
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def cartesian_to_radec(x, y, z):
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d = (x**2 + y**2 + z**2)**0.5
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dec = np.arcsin(z / d)
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ra = np.arctan2(y, x)
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ra[ra < 0] += 2 * np.pi
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ra *= 180 / np.pi
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dec *= 180 / np.pi
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return d, ra, dec
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###############################################################################
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# Get the filename of the samples #
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###############################################################################
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def get_fname(simname, catalogue, ksmooth=0, nsim=None, sample_beta=True):
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"""Get the filename of the HDF5 file containing the posterior samples."""
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FDIR = "/mnt/extraspace/rstiskalek/csiborg_postprocessing/peculiar_velocity/" # noqa
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fname = join(FDIR, f"samples_{simname}_{catalogue}_ksmooth{ksmooth}.hdf5")
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if nsim is not None:
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fname = fname.replace(".hdf5", f"_nsim{nsim}.hdf5")
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if sample_beta:
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fname = fname.replace(".hdf5", "_sample_beta.hdf5")
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return fname
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###############################################################################
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# Convert names to LaTeX #
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###############################################################################
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def names_to_latex(names, for_corner=False):
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"""Convert the names of the parameters to LaTeX."""
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ltx = {"alpha": "\\alpha",
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"beta": "\\beta",
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"Vmag": "V_{\\rm ext}",
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"sigma_v": "\\sigma_v",
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"alpha_cal": "\\mathcal{A}",
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"beta_cal": "\\mathcal{B}",
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"mag_cal": "\\mathcal{M}",
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"e_mu": "\\sigma_\\mu",
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"aTF": "a_{\\rm TF}",
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"bTF": "b_{\\rm TF}",
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}
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ltx_corner = {"alpha": r"$\alpha$",
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"beta": r"$\beta$",
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"Vmag": r"$V_{\rm ext}$",
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"l": r"$\ell_{V_{\rm ext}}$",
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"b": r"$b_{V_{\rm ext}}$",
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"sigma_v": r"$\sigma_v$",
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"alpha_cal": r"$\mathcal{A}$",
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"beta_cal": r"$\mathcal{B}$",
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"mag_cal": r"$\mathcal{M}$",
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"e_mu": r"$\sigma_\mu$",
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"aTF": r"$a_{\rm TF}$",
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"bTF": r"$b_{\rm TF}$",
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}
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labels = copy(names)
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for i, label in enumerate(names):
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if for_corner:
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labels[i] = ltx_corner[label] if label in ltx_corner else label
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else:
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labels[i] = ltx[label] if label in ltx else label
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return labels
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def simname_to_pretty(simname):
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ltx = {"Carrick2015": "Carrick+15",
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"Lilow2024": "Lilow+24",
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"csiborg1": "CB1",
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"csiborg2_main": "CB2",
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"csiborg2X": "Manticore",
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}
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if isinstance(simname, list):
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return [ltx[s] if s in ltx else s for s in simname]
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return ltx[simname] if simname in ltx else simname
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###############################################################################
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# Read in goodness-of-fit #
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###############################################################################
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def get_gof(kind, simname, catalogue, ksmooth=0, nsim=None, sample_beta=True):
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"""Read in the goodness-of-fit statistics `kind`."""
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if kind not in ["BIC", "AIC", "lnZ"]:
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raise ValueError("`kind` must be one of 'BIC', 'AIC', 'lnZ'")
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fname = get_fname(simname, catalogue, ksmooth, nsim, sample_beta)
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with File(fname, 'r') as f:
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return f[f"gof/{kind}"][()]
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###############################################################################
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# Read in samples #
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###############################################################################
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def get_samples(simname, catalogue, ksmooth=0, nsim=None, sample_beta=True,
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convert_Vext_to_galactic=True):
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"""Read in the samples from the HDF5 file."""
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fname = get_fname(simname, catalogue, ksmooth, nsim, sample_beta)
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samples = {}
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with File(fname, 'r') as f:
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grp = f["samples"]
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for key in grp.keys():
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samples[key] = grp[key][...]
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# Rename TF parameters
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if "a" in samples:
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samples["aTF"] = samples.pop("a")
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if "b" in samples:
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samples["bTF"] = samples.pop("b")
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if convert_Vext_to_galactic:
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Vext = samples.pop("Vext")
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samples["Vmag"] = np.linalg.norm(Vext, axis=1)
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Vext = csiborgtools.cartesian_to_radec(Vext)
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samples["l"], samples["b"] = csiborgtools.radec_to_galactic(
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Vext[:, 1], Vext[:, 2])
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return samples
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###############################################################################
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def get_bulkflow(simname, catalogue, ksmooth=0, nsim=None, sample_beta=True,
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convert_to_galactic=True, simulation_only=False):
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# Read in the samples
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fname_samples = get_fname(simname, catalogue, ksmooth, nsim, sample_beta)
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with File(fname_samples, 'r') as f:
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simulation_weights = jnp.exp(f["simulation_weights"][...])
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Vext = f["samples/Vext"][...]
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try:
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beta = f["samples/beta"][...]
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except KeyError:
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beta = jnp.ones_like(simulation_weights)
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# Read in the bulk flow
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f = np.load(f"/mnt/extraspace/rstiskalek/csiborg_postprocessing/field_shells/enclosed_mass_{simname}.npz") # noqa
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r, Bsim = f["distances"], f["cumulative_velocity"]
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# Mask out the unconstrained large scales
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Rmax = 150 # Mpc/h
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mask = r < Rmax
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r = r[mask]
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Bsim = Bsim[:, mask, :]
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# Add the external flow to the bulk flow and weight it
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B = Bsim[:, :, None, :] * beta[None, None, :, None] # noqa
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if not simulation_only:
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B += Vext[None, None, :, :]
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B = jnp.sum(B * simulation_weights.T[:, None, :, None], axis=0)
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if convert_to_galactic:
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Bmag, Bl, Bb = cartesian_to_radec(B[..., 0], B[..., 1], B[..., 2])
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Bl, Bb = csiborgtools.radec_to_galactic(Bl, Bb)
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return r, np.stack([Bmag, Bl, Bb], axis=-1)
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return r, B
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###############################################################################
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# Prepare samples for plotting #
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###############################################################################
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def samples_for_corner(samples):
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if any(x.ndim > 1 for x in samples.values()):
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raise ValueError("All samples must be 1D arrays.")
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data = np.vstack([x for x in samples.values()]).T
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labels = names_to_latex(list(samples.keys()), for_corner=True)
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return data, labels
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def samples_to_getdist(samples, simname, catalogue=None):
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data, __ = samples_for_corner(samples)
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names = list(samples.keys())
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if catalogue is None:
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label = simname_to_pretty(simname)
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else:
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label = catalogue
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return MCSamples(
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samples=data, names=names,
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labels=names_to_latex(names, for_corner=False),
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label=label)
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