mirror of
https://github.com/Richard-Sti/csiborgtools.git
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eb1797e8a9
* Get rid of utils * Clean up imports * Move some utils here * Rename file * Add simname to boxsize * Add imports * Delete old files * Update README * Update imports * Add a new draft of the density calculator * Update fields * Draft of new density field calculatiosn * Add snapshot * Add boxsizes * Little updates * Bring back utils * Edit docstrings * Edits imports * Add progress on snapshots * edit improts * add basic snapshot catalogue * Add support for CSiBORG2 snapshot reader * add paths to fofcat for csiborg2 * Add more imports * Add more boxsize * Add more imports * Add field readers * Simplify field paths * Fix typo * Add observer vp * Clean up density field calculation * Add a short note * Edit args * Remove old comments * Edit docs * Remove blank line * Stop flipping RAMSES * Remove comment * Edit desc * Remove normalization * Remove old dist array * Remove non-volume weighting * Remove non-volume weight * Add ignore of flake8 notebooks * Fix path typo * Fix units * Edit paths docs * Update nb
230 lines
8.6 KiB
Python
230 lines
8.6 KiB
Python
# 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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"""
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Sample a CSiBORG field at galaxy positions and save the result to disk.
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"""
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from argparse import ArgumentParser
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from distutils.util import strtobool
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from os.path import join
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import numpy
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from astropy.cosmology import FlatLambdaCDM
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from h5py import File
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from mpi4py import MPI
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from taskmaster import work_delegation
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from tqdm import tqdm
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import csiborgtools
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from utils import get_nsims
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# TODO get rid of this.
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# MPC2BOX = 1 / 677.7
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SIM2BOXSIZE = {"csiborg1": 677.7,
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"csiborg2_main": None,
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"csiborg2_random": None,
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"csiborg2_varysmall": None,
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}
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def steps(cls, survey_name):
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"""Make a list of selection criteria to apply to a survey."""
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if survey_name == "SDSS":
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return [
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# (lambda x: cls[x], ("IN_DR7_LSS",)),
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# (lambda x: cls[x] < 17.6, ("ELPETRO_APPMAG_r", )),
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(lambda x: cls[x] < 155.5, ("DIST", ))
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]
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else:
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raise NotImplementedError(f"Survey `{survey_name}` not implemented.")
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def open_galaxy_positions(survey_name, comm):
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"""
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Load the survey galaxy positions and indices, broadcasting them to all
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ranks.
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"""
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rank, size = comm.Get_rank(), comm.Get_size()
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if rank == 0:
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if survey_name == "SDSS":
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survey = csiborgtools.SDSS()()
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pos = numpy.vstack([survey["DIST_UNCORRECTED"],
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survey["RA"],
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survey["DEC"]],
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).T
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pos = pos.astype(numpy.float32)
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indxs = survey["INDEX"]
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if survey_name == "SDSSxALFALFA":
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survey = csiborgtools.SDSSxALFALFA()()
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pos = numpy.vstack([survey["DIST_UNCORRECTED"],
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survey["RA_1"],
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survey["DEC_1"]],
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).T
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pos = pos.astype(numpy.float32)
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indxs = survey["INDEX"]
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elif survey_name == "GW170817":
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samples = File("/mnt/extraspace/rstiskalek/GWLSS/H1L1V1-EXTRACT_POSTERIOR_GW170817-1187008600-400.hdf", 'r')["samples"] # noqa
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cosmo = FlatLambdaCDM(H0=100, Om0=0.3175)
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pos = numpy.vstack([
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cosmo.comoving_distance(samples["redshift"][:]).value,
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samples["ra"][:] * 180 / numpy.pi,
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samples["dec"][:] * 180 / numpy.pi],
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).T
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indxs = numpy.arange(pos.shape[0])
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else:
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raise NotImplementedError(f"Survey `{survey_name}` not "
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"implemented.")
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else:
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pos = None
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indxs = None
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comm.Barrier()
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if size > 1:
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pos = comm.bcast(pos, root=0)
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indxs = comm.bcast(indxs, root=0)
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return pos, indxs
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def evaluate_field(field, pos, nrand, smooth_scales=None, seed=42,
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verbose=True):
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"""
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Evaluate the field at the given sky positions. Additionally, evaluate the
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field at `nrand` random positions.
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"""
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if smooth_scales is None:
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smooth_scales = [0.]
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nsample = pos.shape[0]
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nsmooth = len(smooth_scales)
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val = numpy.full((nsample, nsmooth), numpy.nan, dtype=field.dtype)
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if nrand > 0:
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rand_val = numpy.full((nsample, nsmooth, nrand), numpy.nan,
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dtype=field.dtype)
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else:
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rand_val = None
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for i, scale in enumerate(tqdm(smooth_scales, desc="Smoothing",
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disable=not verbose)):
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if scale > 0:
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field_smoothed = csiborgtools.field.smoothen_field(
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field, scale * MPC2BOX, boxsize=1, make_copy=True)
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else:
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field_smoothed = numpy.copy(field)
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val[:, i] = csiborgtools.field.evaluate_sky(
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field_smoothed, pos=pos, mpc2box=MPC2BOX)
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if nrand == 0:
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continue
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for j in range(nrand):
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gen = numpy.random.default_rng(seed + j)
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pos_rand = numpy.vstack([
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gen.permutation(pos[:, 0]),
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gen.uniform(0, 360, nsample),
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90 - numpy.rad2deg(numpy.arccos(gen.uniform(-1, 1, nsample))),
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]).T
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rand_val[:, i, j] = csiborgtools.field.evaluate_sky(
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field_smoothed, pos=pos_rand, mpc2box=MPC2BOX)
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return val, rand_val, smooth_scales
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def match_to_no_selection(val, rand_val, parser_args):
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if parser_args.survey == "SDSSxALFALFA":
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survey = csiborgtools.SDSSxALFALFA()()
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else:
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raise NotImplementedError(
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f"Survey `{parser_args.survey}` not implemented for matching to no selection.") # noqa
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if val is not None:
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val = csiborgtools.read.match_array_to_no_masking(val, survey)
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if rand_val is not None:
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rand_val = csiborgtools.read.match_array_to_no_masking(rand_val,
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survey)
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return val, rand_val
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def main(nsim, parser_args, pos, indxs, paths, verbose):
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"""Load the field, interpolate it and save it to disk."""
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fpath_field = paths.field(parser_args.kind, parser_args.MAS,
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parser_args.grid, nsim, parser_args.in_rsp)
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field = numpy.load(fpath_field)
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val, rand_val, smooth_scales = evaluate_field(
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field, pos, nrand=parser_args.nrand,
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smooth_scales=parser_args.smooth_scales, verbose=verbose)
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if parser_args.survey == "GW170817":
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kind = parser_args.kind
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kind = kind + "_rsp" if parser_args.in_rsp else kind
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fout = join(
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"/mnt/extraspace/rstiskalek/GWLSS/",
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f"{kind}_{parser_args.MAS}_{parser_args.grid}_{nsim}_H1L1V1-EXTRACT_POSTERIOR_GW170817-1187008600-400.npz") # noqa
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else:
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fout = paths.field_interpolated(parser_args.survey, parser_args.kind,
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parser_args.MAS, parser_args.grid,
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nsim, parser_args.in_rsp)
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# The survey above had some cuts, however for compatibility we want
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# the same shape as the `uncut` survey
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val, rand_val = match_to_no_selection(val, rand_val, parser_args)
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if verbose:
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print(f"Saving to ... `{fout}`.")
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numpy.savez(fout, val=val, rand_val=rand_val, indxs=indxs,
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smooth_scales=smooth_scales)
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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("--survey", type=str, required=True,
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choices=["SDSS", "SDSSxALFALFA", "GW170817"],
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help="Galaxy survey")
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parser.add_argument("--smooth_scales", type=float, nargs="+", default=None,
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help="Smoothing scales in Mpc / h.")
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parser.add_argument("--kind", type=str,
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choices=["density", "rspdensity", "velocity", "radvel",
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"potential"],
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help="What field to interpolate.")
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parser.add_argument("--MAS", type=str,
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choices=["NGP", "CIC", "TSC", "PCS"],
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help="Mass assignment scheme.")
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parser.add_argument("--grid", type=int, help="Grid resolution.")
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parser.add_argument("--in_rsp", type=lambda x: bool(strtobool(x)),
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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="csiborg1",
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choices=["csiborg1"], 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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pos, indxs = open_galaxy_positions(args.survey, MPI.COMM_WORLD)
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def _main(nsim):
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main(nsim, args, pos, indxs, paths,
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verbose=MPI.COMM_WORLD.Get_size() == 1)
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work_delegation(_main, nsims, MPI.COMM_WORLD)
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