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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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34
scripts/fit_halos.py
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@ -20,6 +20,7 @@ from argparse import ArgumentParser
from datetime import datetime
from os.path import join
import h5py
import numpy
from mpi4py import MPI
from tqdm import tqdm
@ -94,19 +95,18 @@ def fit_clump(particles, clump_info, box):
return out
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.
"""
@ -115,14 +115,13 @@ def load_parent_particles(clumpid, particle_archive, clumps_cat):
# 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, None])
clumps.append(parts)
if len(clumps) == 0:
return None
return csiborgtools.match.concatenate_parts(clumps,
include_velocities=True)
return numpy.concatenate(clumps)
# We now start looping over all simulations
@ -133,10 +132,10 @@ for i, nsim in enumerate(paths.get_ics(tonew=False)):
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))
clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, maxdist=None,
minmass=None, rawdata=True,
# Particle archive
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, rawdata=True,
load_fitted=False)
# We check whether we fit halos or clumps, will be indexing over different
# iterators.
@ -159,9 +158,10 @@ for i, nsim in enumerate(paths.get_ics(tonew=False)):
continue
if args.kind == "halos":
part = load_parent_particles(clumpid, particle_archive, clumps_cat)
part = load_parent_particles(clumpid, particles, clump_map,
clumps_cat)
else:
part = load_clump_particles(clumpid, particle_archive)
part = load_clump_particles(clumpid, particles, clump_map)
# We fit the particles if there are any. If not we assign the index,
# otherwise it would be NaN converted to integers (-2147483648) and