Correct fitting script for both clumps and halos (#46)

* Minor typos

* fix minor bugs

* pep8

* formatting

* pep8

* Fix minor bugs

* New path & pep8

* add splitt

* Updates

* Improve calculation within radius

* pep8

* pep8

* get the script working

* Add matter overdensity

* Add m200m to the script

* Fix looping bug

* add parents support

* add import

* Optionally concatenate velocities

* Make optional masking

* Ignore the error message

* Start reading in raw data

* Fix cat reading

* Additional units conversions

* Add clump reading

* Fix indexing

* Remove old comment

* Remove old comment

* set npart to 0 instead of overflow from NaN

* fix docs

* rm boring stuff

* Remove old stuff

* Remove old stuff

* Remove old comment

* Update nb

scripts/cluster_knn_cross.py

@@ -16,7 +16,6 @@
 from argparse import ArgumentParser
 from datetime import datetime
 from itertools import combinations
-from os.path import join
 from warnings import warn
 
 import joblib
@@ -30,6 +29,7 @@ try:
     import csiborgtools
 except ModuleNotFoundError:
     import sys
+
     sys.path.append("../")
     import csiborgtools
 
@@ -44,24 +44,12 @@ nproc = comm.Get_size()
 parser = ArgumentParser()
 parser.add_argument("--runs", type=str, nargs="+")
 args = parser.parse_args()
-with open('../scripts/knn_cross.yml', 'r') as file:
+with open("../scripts/knn_cross.yml", "r") as file:
     config = yaml.safe_load(file)
 
 Rmax = 155 / 0.705  # Mpc (h = 0.705) high resolution region radius
-minmass = 1e12
-ics = [7444, 7468, 7492, 7516, 7540, 7564, 7588, 7612, 7636, 7660, 7684,
-       7708, 7732, 7756, 7780, 7804, 7828, 7852, 7876, 7900, 7924, 7948,
-       7972, 7996, 8020, 8044, 8068, 8092, 8116, 8140, 8164, 8188, 8212,
-       8236, 8260, 8284, 8308, 8332, 8356, 8380, 8404, 8428, 8452, 8476,
-       8500, 8524, 8548, 8572, 8596, 8620, 8644, 8668, 8692, 8716, 8740,
-       8764, 8788, 8812, 8836, 8860, 8884, 8908, 8932, 8956, 8980, 9004,
-       9028, 9052, 9076, 9100, 9124, 9148, 9172, 9196, 9220, 9244, 9268,
-       9292, 9316, 9340, 9364, 9388, 9412, 9436, 9460, 9484, 9508, 9532,
-       9556, 9580, 9604, 9628, 9652, 9676, 9700, 9724, 9748, 9772, 9796,
-       9820, 9844]
 paths = csiborgtools.read.CSiBORGPaths(**csiborgtools.paths_glamdring)
-dumpdir = "/mnt/extraspace/rstiskalek/csiborg/knn"
-fout = join(dumpdir, "cross", "knncdf_{}_{}_{}.p")
+ics = paths.get_ics(False)
 knncdf = csiborgtools.clustering.kNN_CDF()
 
 ###############################################################################
@@ -76,9 +64,9 @@ def read_single(selection, cat):
     psel = selection["primary"]
     pmin, pmax = psel.get("min", None), psel.get("max", None)
     if pmin is not None:
-        mmask &= (cat[psel["name"]] >= pmin)
+        mmask &= cat[psel["name"]] >= pmin
     if pmax is not None:
-        mmask &= (cat[psel["name"]] < pmax)
+        mmask &= cat[psel["name"]] < pmax
     return pos[mmask, ...]
 
 
@@ -99,10 +87,17 @@ def do_cross(run, ics):
     knn2.fit(pos2)
 
     rs, cdf0, cdf1, joint_cdf = knncdf.joint(
-        knn1, knn2, rvs_gen=rvs_gen, nneighbours=int(config["nneighbours"]),
-        rmin=config["rmin"], rmax=config["rmax"],
-        nsamples=int(config["nsamples"]), neval=int(config["neval"]),
-        batch_size=int(config["batch_size"]), random_state=config["seed"])
+        knn1,
+        knn2,
+        rvs_gen=rvs_gen,
+        nneighbours=int(config["nneighbours"]),
+        rmin=config["rmin"],
+        rmax=config["rmax"],
+        nsamples=int(config["nsamples"]),
+        neval=int(config["neval"]),
+        batch_size=int(config["batch_size"]),
+        random_state=config["seed"],
+    )
 
     corr = knncdf.joint_to_corr(cdf0, cdf1, joint_cdf)
     joblib.dump({"rs": rs, "corr": corr}, paths.knncross_path(run, ics))
@@ -135,4 +130,4 @@ comm.Barrier()
 
 if rank == 0:
     print("{}: all finished.".format(datetime.now()))
-quit()  # Force quit the script
+quit()  # Force quit the script