Add new ICs (#59)

* edit IC paths

* Remove import

* Edit path

* Change naming

* Add __main__

* Script to match everything

* Edit docs

* Remove test statement

* Move import

* Update nb

csiborgtools/__init__.py

@@ -16,5 +16,5 @@ from csiborgtools import clustering, field, fits, match, read  # noqa
 
 # Arguments to csiborgtools.read.CSiBORGPaths.
 paths_glamdring = {"srcdir": "/mnt/extraspace/hdesmond/",
-                   "postdir": "/mnt/extraspace/rstiskalek/csiborg/",
+                   "postdir": "/mnt/extraspace/rstiskalek/CSiBORG/",
                    }

csiborgtools/read/overlap_summary.py

@@ -258,22 +258,22 @@ class PairOverlap:
         in_initial : bool
             Whether to calculate separation in the initial or final snapshot.
         norm_kind : str, optional
-            The kind of normalisation to apply to the distances. Can be `r200`,
-            `ref_patch` or `sum_patch`.
+            The kind of normalisation to apply to the distances.
+            Can be `r200c`, `ref_patch` or `sum_patch`.
 
         Returns
         -------
         dist : array of 1-dimensional arrays of shape `(nhalos, )`
         """
         assert (norm_kind is None
-                or norm_kind in ("r200", "ref_patch", "sum_patch"))
+                or norm_kind in ("r200c", "ref_patch", "sum_patch"))
         # Get positions either in the initial or final snapshot
         pos0 = self.cat0().position(in_initial)
         posx = self.catx().position(in_initial)
 
         # Get the normalisation array if applicable
-        if norm_kind == "r200":
-            norm = self.cat0("r200")
+        if norm_kind == "r200c":
+            norm = self.cat0("r200c")
         if norm_kind == "ref_patch":
             norm = self.cat0("lagpatch")
         if norm_kind == "sum_patch":

csiborgtools/read/paths.py

@@ -146,34 +146,25 @@ class CSiBORGPaths:
             warn(f"Created directory `{fdir}`.", UserWarning, stacklevel=1)
         return join(fdir, f"{kind}_{str(nsim).zfill(5)}.{ftype}")
 
-    def get_ics(self, tonew):
+    def get_ics(self):
         """
         Get CSiBORG IC realisation IDs from the list of folders in
         `self.srcdir`.
 
-        Parameters
-        ----------
-        tonew : bool
-            If `True`, path to the '_new' ICs is returned.
-
         Returns
         -------
         ids : 1-dimensional array
         """
         files = glob(join(self.srcdir, "ramses_out*"))
-        files = [f.split("/")[-1] for f in files]  # Select only file names
-        if tonew:
-            files = [f for f in files if "_new" in f]
-            ids = [int(f.split("_")[2]) for f in files]  # Take the IC IDs
-        else:
-            files = [f for f in files if "_inv" not in f]  # Remove inv. ICs
-            files = [f for f in files if "_new" not in f]  # Remove _new
-            files = [f for f in files if "OLD" not in f]  # Remove _old
-            ids = [int(f.split("_")[-1]) for f in files]
-            try:
-                ids.remove(5511)
-            except ValueError:
-                pass
+        files = [f.split("/")[-1] for f in files]      # Select only file names
+        files = [f for f in files if "_inv" not in f]  # Remove inv. ICs
+        files = [f for f in files if "_new" not in f]  # Remove _new
+        files = [f for f in files if "OLD" not in f]   # Remove _old
+        ids = [int(f.split("_")[-1]) for f in files]
+        try:
+            ids.remove(5511)
+        except ValueError:
+            pass
         return numpy.sort(ids)
 
     def ic_path(self, nsim, tonew=False):
@@ -194,6 +185,8 @@ class CSiBORGPaths:
         fname = "ramses_out_{}"
         if tonew:
             fname += "_new"
+            return join(self.postdir, "output", fname.format(nsim))
+
         return join(self.srcdir, fname.format(nsim))
 
     def get_snapshots(self, nsim):

csiborgtools/read/pk_summary.py

@@ -24,7 +24,7 @@ class PKReader:
 
     Parameters
     ----------
-    get_ics : list of int
+    ics : list of int
         IC IDs to be read.
     hw : float
         Box half-width.
@@ -35,8 +35,8 @@ class PKReader:
     dtype : dtype, optional
         Output precision. By default `numpy.float32`.
     """
-    def __init__(self, get_ics, hw, fskel=None, dtype=numpy.float32):
-        self.get_ics = get_ics
+    def __init__(self, ics, hw, fskel=None, dtype=numpy.float32):
+        self.ics= ics
         self.hw = hw
         if fskel is None:
             fskel = "/mnt/extraspace/rstiskalek/csiborg/crosspk/out_{}_{}_{}.p"
@@ -69,19 +69,19 @@ class PKReader:
         -------
         ks : 1-dimensional array
             Array of wavenumbers.
-        pks : 2-dimensional array of shape `(len(self.get_ics), ks.size)`
+        pks : 2-dimensional array of shape `(len(self.ics), ks.size)`
             Autocorrelation of each simulation.
         """
         kmin, kmax = self._set_klim(kmin, kmax)
         ks, pks, sel = None, None, None
-        for i, nsim in enumerate(self.get_ics):
+        for i, nsim in enumerate(self.ics):
             pk = joblib.load(self.fskel.format(nsim, nsim, self.hw))
             # Get cuts and pre-allocate arrays
             if i == 0:
                 x = pk.k3D
                 sel = (kmin < x) & (x < kmax)
                 ks = x[sel].astype(self.dtype)
-                pks = numpy.full((len(self.get_ics), numpy.sum(sel)),
+                pks = numpy.full((len(self.ics), numpy.sum(sel)),
                                  numpy.nan, dtype=self.dtype)
             pks[i, :] = pk.Pk[sel, 0, 0]
 
@@ -144,12 +144,12 @@ class PKReader:
             Cross-correlations. The first column is the the IC and is being
             cross-correlated with the remaining ICs, in the second column.
         """
-        nics = len(self.get_ics)
+        nics = len(self.ics)
 
         ks, xpks = None, None
-        for i, ic0 in enumerate(tqdm(self.get_ics)):
+        for i, ic0 in enumerate(tqdm(self.ics)):
             k = 0
-            for ic1 in self.get_ics:
+            for ic1 in self.ics:
                 # We don't want cross-correlation
                 if ic0 == ic1:
                     continue