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Fix paths (#95)

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* Fix args

* Fix paths

* Get rid of quijote backup
This commit is contained in:
Richard Stiskalek 2023-12-13 18:03:27 +00:00 committed by GitHub
parent 963a382362
commit 506d7a7c70
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3 changed files with 72 additions and 112 deletions
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173
csiborgtools/read/paths.py
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@ -17,8 +17,9 @@ CSiBORG paths manager.
"""
from glob import glob
from os import makedirs
from os.path import basename, isdir, join
from os.path import isdir, join
from warnings import warn
from re import search
import numpy
@ -66,7 +67,7 @@ class Paths:
self.postdir = postdir
def get_ics(self, simname, from_quijote_backup=False):
def get_ics(self, simname):
"""
Get available IC realisation IDs for a given simulation.
@ -74,97 +75,33 @@ class Paths:
----------
simname : str
Simulation name.
from_quijote_backup : bool, optional
Whether to return the ICs from the Quijote backup.
Returns
-------
ids : 1-dimensional array
"""
if simname == "csiborg":
if simname == "csiborg1":
files = glob(join(self.csiborg1_srcdir, "chain_*"))
files = [int(basename(f).replace("chain_", "") for f in files)]
files = [int(search(r'chain_(\d+)', f).group(1)) for f in files]
elif simname == "csiborg2_main":
files = glob(join(self.csiborg2_main_srcdir, "chain_*"))
files = [int(basename(f).replace("chain_", "") for f in files)]
files = [int(search(r'chain_(\d+)', f).group(1)) for f in files]
elif simname == "csiborg2_random":
raise NotImplementedError("TODO")
files = glob(join(self.csiborg2_random_srcdir, "chain_*"))
files = [int(search(r'chain_(\d+)', f).group(1)) for f in files]
elif simname == "csiborg2_varysmall":
raise NotImplementedError("TODO")
elif simname == "quijote" or simname == "quijote_full":
if from_quijote_backup:
files = glob(join(self.quijote_dir, "halos_backup", "*"))
else:
warn(("Taking only the snapshots that also have "
"a FoF catalogue!"))
files = glob(join(self.quijote_dir, "Snapshots_fiducial", "*"))
files = [int(f.split("/")[-1]) for f in files]
files = [f for f in files if f < 100]
files = glob(join(self.csiborg2_varysmall_srcdir, "chain_*"))
files = [int(search(r'chain_16417(\d+)', f).group(1))
for f in files]
elif simname == "quijote":
files = glob(join(self.quijote_dir, "fiducial_processed",
"chain_*"))
files = [int(search(r'chain_(\d+)', f).group(1)) for f in files]
else:
raise ValueError(f"Unknown simulation name `{simname}`.")
return numpy.sort(files)
def snapshots(self, nsim, simname):
if simname == "csiborg":
fname = "ramses_out_{}"
if tonew:
fname += "_new"
return join(self.postdir, "output", fname.format(nsim))
return join(self.csiborg1_srcdir, fname.format(nsim))
elif simname == "csiborg2_main":
return join(self.csiborg2_main_srcdir, f"chain_{nsim}", "output")
elif simname == "csiborg2_random":
raise NotImplementedError("TODO")
elif simname == "csiborg2_varysmall":
raise NotImplementedError("TODO")
elif simname == "quijote":
return join(self.quijote_dir, "Snapshots_fiducial", str(nsim))
else:
raise ValueError(f"Unknown simulation name `{simname}`.")
def snapshot(self, nsnap, nsim, simname):
"""
Path to an IC realisation snapshot.
Parameters
----------
nsnap : int
Snapshot index. For Quijote, `-1` indicates the IC snapshot.
nsim : inlot
IC realisation index.
simname : str
Simulation name.
Returns
-------
str
"""
if simname == "csiborg":
return join(self.csiborg1_srcdir, f"chain_{nsim}",
f"snapshot_{str(nsnap).zfill(5)}")
elif simname == "csiborg2_main":
return join(self.csiborg1_srcdir, f"chain_{nsim}",
f"snapshot_{str(nsnap).zfill(5)}")
elif simname == "csiborg2_random":
raise NotImplementedError("TODO")
elif simname == "csiborg2_varysmall":
raise NotImplementedError("TODO")
elif simname == "quijote":
raise NotImplementedError("TODO")
else:
raise ValueError(f"Unknown simulation name `{simname}`.")
# simpath = self.snapshots(nsim, simname, tonew=nsnap == 1)
# if simname == "csiborg":
# return join(simpath, f"output_{str(nsnap).zfill(5)}")
# else:
# if nsnap == -1:
# return join(simpath, "ICs", "ics")
# nsnap = str(nsnap).zfill(3)
# return join(simpath, f"snapdir_{nsnap}", f"snap_{nsnap}")
def get_snapshots(self, nsim, simname):
"""
List of available snapshots of simulation.
@ -180,51 +117,79 @@ class Paths:
-------
snapshots : 1-dimensional array
"""
simpath = self.snapshots(nsim, simname, tonew=False)
# simpath = self.snapshots(nsim, simname, tonew=False)
if simname == "csiborg":
# Get all files in simpath that start with output_
snaps = glob(join(simpath, "output_*"))
# Take just the last _00XXXX from each file and strip zeros
snaps = [int(snap.split("_")[-1].lstrip("0")) for snap in snaps]
if simname == "csiborg1":
snaps = glob(join(self.csiborg1_srcdir, f"chain_{nsim}",
"snapshot_*"))
snaps = [int(search(r'snapshot_(\d+)', f).group(1)) for f in snaps]
snaps = sorted(snaps)
elif simname == "csiborg2_main":
snaps = glob(join(simpath, "snapshot_*"))
snaps = [basename(snap) for snap in snaps]
snaps = [int(snap.split("_")[1]) for snap in snaps]
snaps = glob(join(self.csiborg2_main_srcdir, f"chain_{nsim}",
"output", "snapshot_*"))
snaps = [int(search(r'snapshot_(\d+)', f).group(1))
for f in snaps]
snaps = sorted(snaps)
elif simname == "csiborg2_random":
raise NotImplementedError("TODO")
snaps = glob(join(self.csiborg2_random_srcdir, f"chain_{nsim}",
"output", "snapshot_*"))
snaps = [int(search(r'snapshot_(\d+)', f).group(1))
for f in snaps]
snaps = sorted(snaps)
elif simname == "csiborg2_varysmall":
raise NotImplementedError("TODO")
snaps = glob(join(self.csiborg2_random_srcdir, f"chain_{nsim}",
"snapshot_*"))
snaps = [int(search(r'snapshot_16417_(\d+)', f).group(1))
for f in snaps]
snaps = sorted(snaps)
elif simname == "quijote":
snaps = glob(join(simpath, "snapdir_*"))
snaps = [int(snap.split("/")[-1].split("snapdir_")[-1])
for snap in snaps]
snaps = glob(join(self.quijote_dir, "fiducial_processed",
f"chain_{nsim}", "snapshot_*"))
has_ics = any("snapshot_ICs" in f for f in snaps)
snaps = [int(match.group(1))
for f in snaps if (match := search(r'snapshot_(\d+)', f))]
snaps = sorted(snaps)
if has_ics:
snaps.insert(0, "ICs")
else:
raise ValueError(f"Unknown simulation name `{simname}`.")
return numpy.sort(snaps)
return snaps
@staticmethod
def quijote_fiducial_nsim(nsim, nobs=None):
def snapshot(self, nsnap, nsim, simname):
"""
Fiducial Quijote simulation ID. Combines the IC realisation and
observer placement.
Path to a simulation snapshot.
Parameters
----------
nsnap : int
Snapshot index. For Quijote, `ICs` indicates the IC snapshot.
nsim : int
IC realisation index.
nobs : int, optional
Fiducial observer index.
simname : str
Simulation name.
Returns
-------
str
"""
if nobs is None:
assert isinstance(nsim, str)
assert len(nsim) == 5
return nsim
return f"{str(nobs).zfill(2)}{str(nsim).zfill(3)}"
if simname == "csiborg1":
return join(self.csiborg1_srcdir, f"chain_{nsim}",
f"snapshot_{str(nsnap).zfill(5)}.hdf5")
elif simname == "csiborg2_main":
return join(self.csiborg2_main_srcdir, f"chain_{nsim}",
f"snapshot_{str(nsnap).zfill(3)}.hdf5")
elif simname == "csiborg2_random":
return join(self.csiborg2_random_srcdir, f"chain_{nsim}",
f"snapshot_{str(nsnap).zfill(3)}.hdf5")
elif simname == "csiborg2_varysmall":
return join(self.csiborg2_varysmall_srcdir, f"chain_{nsim}",
f"snapshot_{str(nsnap).zfill(3)}.hdf5")
elif simname == "quijote":
return join(self.quijote_dir, "fiducial_processed",
f"chain_{nsim}",
f"snapshot_{str(nsnap).zfill(3)}.hdf5")
else:
raise ValueError(f"Unknown simulation name `{simname}`.")
def overlap(self, simname, nsim0, nsimx, min_logmass, smoothed):
"""

4
scripts/field_sample.py
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@ -188,8 +188,8 @@ if __name__ == "__main__":
help="Field in RSP?")
parser.add_argument("--nrand", type=int, required=True,
help="Number of rand. positions to evaluate the field")
parser.add_argument("--simname", type=str, default="csiborg",
choices=["csiborg"], help="Simulation name")
parser.add_argument("--simname", type=str, default="csiborg1",
choices=["csiborg1"], help="Simulation name")
args = parser.parse_args()
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)

7
scripts/utils.py
View File

@ -38,13 +38,8 @@ def get_nsims(args, paths):
"""
Get simulation indices from the command line arguments.
"""
try:
from_quijote_backup = args.from_quijote_backup
except AttributeError:
from_quijote_backup = False
if args.nsims is None or args.nsims[0] == -1:
nsims = paths.get_ics(args.simname, from_quijote_backup)
nsims = paths.get_ics(args.simname)
else:
nsims = args.nsims
return list(nsims)