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Improve paths and documentation (#38)

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* pep8

* style issue

* Documentation edits

* Remove old files

* Remove more old files

* Doc & stop setting snap and nsim in paths

* add nsnap, nsim support

* Remove blank space

* docs

* Docs edits

* Reduce redudant code

* docs

* Documentation

* Docs

* Simplify

* add nsnap nsim arguments

* Remove redundant docs

* Fix typos

* Shorten catalogue

* Remove import

* Remove blank line

* Docs only edits

* Rearrange imports

* Remove blank space

* Rearrange imports

* Rearrange imports

* Remove blank space

* Update submission scritp

* Edit docs

* Remove blank line

* new paths

* Update submission scripts

* Update file handling

* Remove blank line

* Move things around

* Ne paths

* Edit submission script

* edit paths

* Fix typo

* Fix bug

* Remove import

* Update nb
This commit is contained in:
Richard Stiskalek 2023-04-04 15:22:00 +01:00 • committed by GitHub
parent 035d7e0071
commit 8d34b832af
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32 changed files with 954 additions and 5358 deletions
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13
scripts/run_knn.py
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@ -62,6 +62,7 @@ ics = [7444, 7468, 7492, 7516, 7540, 7564, 7588, 7612, 7636, 7660, 7684,
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/knn"
fout_auto = join(dumpdir, "auto", "knncdf_{}.p")
fout_cross = join(dumpdir, "cross", "knncdf_{}_{}.p")
paths = csiborgtools.read.CSiBORGPaths()
###############################################################################
@ -72,11 +73,11 @@ knncdf = csiborgtools.match.kNN_CDF()
def do_auto(ic):
out = {}
cat = csiborgtools.read.HaloCatalogue(ic, max_dist=Rmax)
cat = csiborgtools.read.HaloCatalogue(ic, paths, max_dist=Rmax)
for i, mmin in enumerate(mass_threshold):
knn = NearestNeighbors()
knn.fit(cat.positions[cat["totpartmass"] > mmin, ...])
knn.fit(cat.positions(False)[cat["totpartmass"] > mmin, ...])
rs, cdf = knncdf(knn, nneighbours=args.nneighbours, Rmax=Rmax,
rmin=args.rmin, rmax=args.rmax, nsamples=args.nsamples,
@ -90,15 +91,15 @@ def do_auto(ic):
def do_cross(ics):
out = {}
cat1 = csiborgtools.read.HaloCatalogue(ics[0], max_dist=Rmax)
cat2 = csiborgtools.read.HaloCatalogue(ics[1], max_dist=Rmax)
cat1 = csiborgtools.read.HaloCatalogue(ics[0], paths, max_dist=Rmax)
cat2 = csiborgtools.read.HaloCatalogue(ics[1], paths, max_dist=Rmax)
for i, mmin in enumerate(mass_threshold):
knn1 = NearestNeighbors()
knn1.fit(cat1.positions[cat1["totpartmass"] > mmin, ...])
knn1.fit(cat1.positions()[cat1["totpartmass"] > mmin, ...])
knn2 = NearestNeighbors()
knn2.fit(cat2.positions[cat2["totpartmass"] > mmin, ...])
knn2.fit(cat2.positions()[cat2["totpartmass"] > mmin, ...])
rs, cdf0, cdf1, joint_cdf = knncdf.joint(
knn1, knn2, nneighbours=args.nneighbours, Rmax=Rmax,