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Overlapper improvements (#53)

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* Store indices as f32

* Fix init sorting

* Organise imports

* Rename pathing

* Add particle loading

* Improve particle reading

* Add h5py reader

* edit particle path

* Update particles loading

* update particles loading

* Fix particle dumping

* Add init fitting

* Fix bug due to insufficient precision

* Add commnet

* Add comment

* Add clumps catalogue to halo cat

* Add comment

* Make sure PIDS never forced to float32

* fix pid reading

* fix pid reading

* Update matching to work with new arrays

* Stop using cubical sub boxes, turn off nshift if no smoothing

* Improve caching

* Move function definitions

* Simplify calculation

* Add import

* Small updates to the halo

* Simplify calculation

* Simplify looping calculation

* fix tonew

* Add initial data

* Add skip condition

* Add unit conversion

* Add loading background in batches

* Rename mmain index

* Switch overlaps to h5

* Add finite lagpatch check

* fix column name

* Add verbosity flags

* Save halo IDs instead.

* Switch back to npz

* Delte nbs

* Reduce size of the box

* Load correct bckg of halos being matched

* Remove verbosity

* verbosity edits

* Change lower thresholds
This commit is contained in:
Richard Stiskalek 2023-05-06 16:52:48 +01:00 • committed by GitHub
parent 1c9dacfde5
commit 56e39a8b1d
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GPG key ID: 4AEE18F83AFDEB23
20 changed files with 864 additions and 3816 deletions
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45
scripts/fit_profiles.py
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@ -54,35 +54,6 @@ else:
nsims = args.ics
def load_clump_particles(clumpid, particles, clump_map):
"""
Load a clump's particles. If it is not there, i.e clump has no associated
particles, return `None`.
"""
try:
return particles[clump_map[clumpid], :]
except KeyError:
return None
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.
clumps = []
for ind in indxs:
parts = load_clump_particles(ind, particles, clump_map)
if parts is not None:
clumps.append(parts)
if len(clumps) == 0:
return None
return numpy.concatenate(clumps)
# We loop over simulations. Here later optionally add MPI.
for i, nsim in enumerate(nsims):
if rank == 0:
@ -91,10 +62,11 @@ for i, nsim in enumerate(nsims):
nsnap = max(paths.get_snapshots(nsim))
box = csiborgtools.read.BoxUnits(nsnap, nsim, paths)
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,
f = csiborgtools.read.read_h5(paths.particles_path(nsim))
particles = f["particles"]
clump_map = f["clumpmap"]
clid2map = {clid: i for i, clid in enumerate(clump_map[:, 0])}
clumps_cat = csiborgtools.read.ClumpsCatalogue(nsim, paths, rawdata=True,
load_fitted=False)
ismain = clumps_cat.ismain
ntasks = len(clumps_cat)
@ -108,8 +80,8 @@ for i, nsim in enumerate(nsims):
continue
clumpid = clumps_cat["index"][j]
parts = load_parent_particles(clumpid, particles, clump_map,
clumps_cat)
parts = csiborgtools.read.load_parent_particles(
clumpid, particles, clump_map, clid2map, clumps_cat)
# If we have no particles, then do not save anything.
if parts is None:
continue
@ -124,8 +96,7 @@ for i, nsim in enumerate(nsims):
_out["r"] = r[mask]
_out["M"] = obj["M"][mask]
out[str(clumps_cat["index"][j])] = _out
out[str(clumpid)] = _out
# Finished, so we save everything.
fout = paths.radpos_path(nsnap, nsim)