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Switch to h5py format (#52)

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* Edit the particle paths

* Remove script

* Add h5py to dumping

* Minor adjustments

* add h5py support

* remove split path

* h5py support

* Type

* Edit initmatch paths

* Shorten func

* dist_centmass to work with 2D arrays

* Forgot to return the centre of mass

* Fixed code

* Fix halo bug

* Start MPI broadcasting

* Mini bug

* Remove commenting

* Remove test statement

* Fix index

* Printing from rank 0 only

* Move where clump index stored

* Add dtype options

* Add dtype options
This commit is contained in:
Richard Stiskalek 2023-05-02 13:57:13 +01:00 • committed by GitHub
parent 553eec8228
commit 1a9e6177d7
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8 changed files with 236 additions and 323 deletions
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33
scripts/fit_profiles.py
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@ -20,6 +20,7 @@ from argparse import ArgumentParser
from datetime import datetime
from gc import collect
import h5py
import numpy
from mpi4py import MPI
from tqdm import trange
@ -46,7 +47,6 @@ if nproc > 1:
raise NotImplementedError("MPI is not implemented implemented yet.")
paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
partreader = csiborgtools.read.ParticleReader(paths)
cols_collect = [("r", numpy.float32), ("M", numpy.float32)]
if args.ics is None or args.ics == -1:
nsims = paths.get_ics(tonew=False)
@ -54,37 +54,36 @@ else:
nsims = args.ics
def load_clump_particles(clumpid, particle_archive):
def load_clump_particles(clumpid, particles, clump_map):
"""
Load a clump's particles from the particle archive. If it is not there, i.e
clump has no associated particles, return `None`.
Load a clump's particles. If it is not there, i.e clump has no associated
particles, return `None`.
"""
try:
part = particle_archive[str(clumpid)]
return particles[clump_map[clumpid], :]
except KeyError:
part = None
return part
return None
def load_parent_particles(clumpid, particle_archive, clumps_cat):
def load_parent_particles(clumpid, particles, clump_map, clumps_cat):
"""
Load a parent halo's particles.
"""
indxs = clumps_cat["index"][clumps_cat["parent"] == clumpid]
# We first load the particles of each clump belonging to this
# parent and then concatenate them for further analysis.
# We first load the particles of each clump belonging to this parent
# and then concatenate them for further analysis.
clumps = []
for ind in indxs:
parts = load_clump_particles(ind, particle_archive)
parts = load_clump_particles(ind, particles, clump_map)
if parts is not None:
clumps.append(parts)
if len(clumps) == 0:
return None
return csiborgtools.match.concatenate_parts(clumps)
return numpy.concatenate(clumps)
# We loop over simulations. Here later optionlaly add MPI.
# We loop over simulations. Here later optionally add MPI.
for i, nsim in enumerate(nsims):
if rank == 0:
now = datetime.now()
@ -92,8 +91,8 @@ for i, nsim in enumerate(nsims):
nsnap = max(paths.get_snapshots(nsim))
box = csiborgtools.read.BoxUnits(nsnap, nsim, paths)
# Archive of clumps, keywords are their clump IDs
particle_archive = numpy.load(paths.split_path(nsnap, nsim))
particles = h5py.File(paths.particle_h5py_path(nsim), 'r')["particles"]
clump_map = h5py.File(paths.particle_h5py_path(nsim, "clumpmap"), 'r')
clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, maxdist=None,
minmass=None, rawdata=True,
load_fitted=False)
@ -109,8 +108,8 @@ for i, nsim in enumerate(nsims):
continue
clumpid = clumps_cat["index"][j]
parts = load_parent_particles(clumpid, particle_archive, clumps_cat)
parts = load_parent_particles(clumpid, particles, clump_map,
clumps_cat)
# If we have no particles, then do not save anything.
if parts is None:
continue