Fix overlap runs (#125)

* Update nb

* Update script

* Update script

* Rename

* Update script

* Update script

* Remove warning

* Ignore minors when extracting MAH

* Fix paths bug

* Move notebooks

* Move files

* Rename and delete things

* Rename file

* Move file

* Rename things

* Remove old print statement

* Add basic MAH plot

* Add random MAH path

* Output snapshot numbers

* Add MAH random extraction

* Fix redshift bug

* Edit script

* Add extracting random MAH

* Little updates

* Add CB2 redshift

* Add some caching

* Add diagnostic plots

* Add caching

* Minor updates

* Update nb

* Update notebook

* Update script

* Add Sorce randoms

* Add CB2 varysmall

* Update nb

* Update nb

* Update nb

* Use catalogue HMF

* Move definition of radec2galactic

* Update nb

* Update import

* Update import

* Add galatic coords to catalogues

* Update nb

notebooks/diagnostic/hmf.py

@@ -0,0 +1,48 @@
+# Copyright (C) 2024 Richard Stiskalek
+# This program is free software; you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation; either version 3 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General
+# Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
+"""Script to help with `hmf.py`."""
+
+import csiborgtools
+import numpy as np
+from tqdm import tqdm
+
+
+def calculate_hmf(simname, bin_edges, halofinder="FOF", max_distance=135):
+    """
+    Calculate the halo mass function for a given simulation from catalogues.
+    """
+    paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
+    nsims = paths.get_ics(simname)
+    bounds = {"dist": (0, max_distance)}
+
+    hmf = np.full((len(nsims), len(bin_edges) - 1), np.nan)
+    volume = 4 / 3 * np.pi * max_distance**3
+    for i, nsim in enumerate(tqdm(nsims)):
+        if "csiborg2_" in simname:
+            kind = simname.split("_")[-1]
+            if halofinder == "FOF":
+                cat = csiborgtools.read.CSiBORG2Catalogue(
+                    nsim, 99, kind, bounds=bounds)
+            elif halofinder == "SUBFIND":
+                cat = csiborgtools.read.CSiBORG2SUBFINDCatalogue(
+                    nsim, 99, kind, kind, bounds=bounds)
+            else:
+                raise ValueError(f"Unknown halofinder: {halofinder}")
+        else:
+            raise ValueError(f"Unknown simname: {simname}")
+
+        hmf[i] = cat.halo_mass_function(bin_edges, volume, "totmass")[1]
+
+    return hmf