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https://github.com/Richard-Sti/csiborgtools.git
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Add dumping to ASCII of halos (#89)
* Rename file * Add argument * Add ASCII positions paths * Add halo positions dumping * Update halo catalogues
This commit is contained in:
Richard Stiskalek
GitHub
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eccd8e3507
commit
9ae93bed14
@ -256,6 +256,10 @@ class BaseCatalogue(ABC):
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@observer_velocity.setter
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def observer_velocity(self, obs_vel):
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if obs_vel is None:
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self._observer_velocity = None
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return
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assert isinstance(obs_vel, (list, tuple, numpy.ndarray))
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obs_vel = numpy.asanyarray(obs_vel)
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assert obs_vel.shape == (3,)
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@ -449,6 +449,26 @@ class Paths:
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fname = f"parts_{str(nsim).zfill(5)}.h5"
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return join(fdir, fname)
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def ascii_positions(self, nsim, kind):
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"""
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Path to ASCII files containing the positions of particles or halos.
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Parameters
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----------
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nsim : int
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IC realisation index.
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kind : str
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Kind of data to extract. Must be one of `particles`,
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`particles_rsp`, `halos`, `halos_rsp`.
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"""
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assert kind in ["particles", "particles_rsp", "halos", "halos_rsp"]
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fdir = join(self.postdir, "ascii_positions")
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try_create_directory(fdir)
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fname = f"pos_{kind}_{str(nsim).zfill(5)}.txt"
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return join(fdir, fname)
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def structfit(self, nsnap, nsim, simname):
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"""
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Path to the halo catalogue from `fit_halos.py`.
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116
scripts/dump_to_ascii.py
Normal file
116
scripts/dump_to_ascii.py
Normal file
@ -0,0 +1,116 @@
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# Copyright (C) 2023 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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"""Convert the HDF5 CSiBORG particle file to an ASCII file."""
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from argparse import ArgumentParser
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import h5py
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import numpy
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from mpi4py import MPI
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from taskmaster import work_delegation
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from tqdm import trange
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import csiborgtools
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from utils import get_nsims
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def positions_to_ascii(positions, output_filename, boxsize=None,
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chunk_size=50_000, verbose=True):
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"""
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Convert array of positions to an ASCII file. If `boxsize` is given,
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multiples the positions by it.
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"""
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total_size = len(positions)
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if verbose:
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print(f"Number of rows to write: {total_size}")
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with open(output_filename, 'w') as out_file:
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# Write the header
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out_file.write("#px py pz\n")
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# Loop through data in chunks
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for i in trange(0, total_size, chunk_size,
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desc=f"Writing to ... `{output_filename}`",
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disable=not verbose):
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end = i + chunk_size
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if end > total_size:
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end = total_size
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data_chunk = positions[i:end]
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# Convert to positions Mpc / h
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data_chunk = data_chunk[:, :3]
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if boxsize is not None:
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data_chunk *= boxsize
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chunk_str = "\n".join([f"{x:.4f} {y:.4f} {z:.4f}"
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for x, y, z in data_chunk])
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out_file.write(chunk_str + "\n")
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def extract_positions(nsim, paths, kind):
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"""
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Extract either the particle or halo positions.
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"""
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if kind == "particles":
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fname = paths.particles(nsim, args.simname)
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return h5py.File(fname, 'r')["particles"]
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if kind == "particles_rsp":
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raise NotImplementedError("RSP of particles is not implemented yet.")
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fpath = paths.observer_peculiar_velocity("PCS", 512, nsim)
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vpec_observer = numpy.load(fpath)["observer_vp"][0, :]
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cat = csiborgtools.read.CSiBORGHaloCatalogue(
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nsim, paths, load_fitted=True, load_initial=False,
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observer_velocity=vpec_observer)
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if kind == "halos":
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return cat.position()
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if kind == "halos_rsp":
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return cat.redshift_space_position()
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raise ValueError(f"Unknown kind `{kind}`. Allowed values are: "
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"`particles`, `particles_rsp`, `halos`, `halos_rsp`.")
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def main(nsim, paths, kind):
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boxsize = 677.7 if "particles" in kind else None
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pos = extract_positions(nsim, paths, kind)
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output_filename = paths.ascii_positions(nsim, kind)
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positions_to_ascii(pos, output_filename, boxsize=boxsize)
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("--kind", type=str, required=True,
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choices=["particles", "particles_rsp", "halos", "halos_rsp"], # noqa
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help="Kind of data to extract.")
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parser.add_argument("--nsims", type=int, nargs="+", default=None,
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help="IC realisations. If `-1` processes all.")
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parser.add_argument("--simname", type=str, default="csiborg",
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choices=["csiborg"],
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help="Simulation name")
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args = parser.parse_args()
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsims = get_nsims(args, paths)
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def _main(nsim):
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main(nsim, paths, args.kind)
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work_delegation(main, nsims, MPI.COMM_WORLD)
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@ -180,6 +180,8 @@ if __name__ == "__main__":
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help="Field in RSP?")
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parser.add_argument("--nrand", type=int, required=True,
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help="Number of rand. positions to evaluate the field")
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parser.add_argument("--simname", type=str, default="csiborg",
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choices=["csiborg"], help="Simulation name")
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args = parser.parse_args()
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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@ -1,82 +0,0 @@
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# Copyright (C) 2023 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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"""Convert the HDF5 CSiBORG particle file to an ASCII file."""
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from argparse import ArgumentParser
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import csiborgtools
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import h5py
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from mpi4py import MPI
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from utils import get_nsims
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from tqdm import trange
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from taskmaster import work_delegation
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def h5_to_ascii(nsim, paths, chunk_size=50_000, verbose=True):
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"""
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Convert the HDF5 CSiBORG particle file to an ASCII file. Outputs only
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particle positions in Mpc / h. Ignores the unequal particle masses.
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"""
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fname = paths.particles(nsim, args.simname)
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boxsize = 677.7
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fname_out = fname.replace(".h5", ".txt")
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with h5py.File(fname, 'r') as f:
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dataset = f["particles"]
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total_size = dataset.shape[0]
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if verbose:
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print(f"Number of rows to write: {total_size}")
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with open(fname_out, 'w') as out_file:
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# Write the header
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out_file.write("#px py pz\n")
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# Loop through data in chunks
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for i in trange(0, total_size, chunk_size,
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desc=f"Writing to ... `{fname_out}`",
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disable=not verbose):
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end = i + chunk_size
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if end > total_size:
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end = total_size
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data_chunk = dataset[i:end]
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# Convert to positions Mpc / h
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data_chunk = data_chunk[:, :3] * boxsize
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chunk_str = "\n".join([f"{x:.4f} {y:.4f} {z:.4f}"
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for x, y, z in data_chunk])
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out_file.write(chunk_str + "\n")
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if __name__ == "__main__":
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parser = ArgumentParser()
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parser.add_argument("--nsims", type=int, nargs="+", default=None,
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help="IC realisations. If `-1` processes all.")
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parser.add_argument("--simname", type=str, default="csiborg",
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choices=["csiborg"],
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help="Simulation name")
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args = parser.parse_args()
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paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
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nsims = get_nsims(args, paths)
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def main(nsim):
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h5_to_ascii(nsim, paths, verbose=MPI.COMM_WORLD.Get_size() == 1)
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work_delegation(main, nsims, MPI.COMM_WORLD)
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