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https://github.com/Richard-Sti/csiborgtools.git
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Fix weights definition (#24)
* Fix running script * Increase outside boundary size * Add new weight scheme * Edit docs
This commit is contained in:
Richard Stiskalek
GitHub
parent
279580e041
commit
830b1b8daf
2 changed files with 68 additions and 37 deletions
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@ -18,7 +18,7 @@ from scipy.ndimage import gaussian_filter
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from tqdm import (tqdm, trange)
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from astropy.coordinates import SkyCoord
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from numba import jit
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from ..read import CombinedHaloCatalogue
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from ..read import (CombinedHaloCatalogue, concatenate_clumps)
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def brute_spatial_separation(c1, c2, angular=False, N=None, verbose=False):
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@ -209,7 +209,7 @@ class RealisationsMatcher:
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if overlap:
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if verbose:
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print("Loading initial clump particles for `n_sim = {}`."
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.format(n_sim))
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.format(n_sim), flush=True)
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# Grab a paths object. What it is set to is unimportant
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paths = self.cats[0].paths
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with open(paths.clump0_path(self.cats.n_sims[n_sim]), "rb") as f:
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@ -250,10 +250,19 @@ class RealisationsMatcher:
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if overlap:
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if verbose:
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print("Loading initial clump particles for `n_sim = {}` "
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"to compare against `n_sim = {}`.".format(i, n_sim))
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"to compare against `n_sim = {}`.".format(i, n_sim),
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flush=True)
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with open(paths.clump0_path(self.cats.n_sims[i]), 'rb') as f:
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clumpsx = numpy.load(f, allow_pickle=True)
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# Calculate the particle field
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if verbose:
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print("Loading and smoothing the crossed total field.",
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flush=True)
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particles = concatenate_clumps(clumpsx)
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delta = overlapper.make_delta(particles, to_smooth=False)
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delta = overlapper.smooth_highres(delta)
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cat2clumpsx = self._cat2clump_mapping(self.cats[i]["index"],
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clumpsx["ID"])
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# Loop only over halos that have neighbours
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@ -270,7 +279,8 @@ class RealisationsMatcher:
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for ii, ind in enumerate(indxs[k]):
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# Again which cross clump to this index
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matchx = cat2clumpsx[ind]
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dint[ii] = overlapper(cl0, clumpsx["clump"][matchx])
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dint[ii] = overlapper(cl0, clumpsx["clump"][matchx],
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delta)
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cross[k] = dint
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@ -376,6 +386,9 @@ class ParticleOverlap:
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inv_clength : float, optional
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Inverse cell length in box units. By default :math:`2^11`, which
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matches the initial RAMSES grid resolution.
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nshift : int, optional
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Number of cells by which to shift the subbox from the outside-most
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cell containing a particle. By default 5.
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smooth_scale : float or integer, optional
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Optional Gaussian smoothing scale to by applied to the fields. By
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default no smoothing is applied. Otherwise the scale is to be
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@ -384,10 +397,12 @@ class ParticleOverlap:
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_inv_clength = None
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_smooth_scale = None
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_clength = None
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_nshift = None
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def __init__(self, inv_clength=2**11, smooth_scale=None):
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def __init__(self, inv_clength=2**11, smooth_scale=None, nshift=5):
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self.inv_clength = inv_clength
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self.smooth_scale = smooth_scale
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self.nshift = nshift
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@property
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def inv_clength(self):
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@ -423,7 +438,9 @@ class ParticleOverlap:
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@smooth_scale.setter
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def smooth_scale(self, smooth_scale):
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"""Sets `smooth_scale`."""
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if smooth_scale is not None:
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if smooth_scale is None:
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self._smooth_scale = None
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else:
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assert smooth_scale > 0
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self._smooth_scale = smooth_scale
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@ -443,7 +460,8 @@ class ParticleOverlap:
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def smooth_highres(self, delta):
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"""
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Smooth the central region of a full box density field.
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Smooth the central region of a full box density field. Note that if
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`self.smooth_scale` is `None` then quietly exits the function.
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Parameters
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----------
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@ -454,7 +472,7 @@ class ParticleOverlap:
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smooth_delta : 3-dimensional arrray
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"""
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if self.smooth_scale is None:
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raise ValueError("`smooth_scale` is not set!")
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return delta
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msg = "Shape of `delta` must match the entire box."
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assert delta.shape == (self._inv_clength,)*3, msg
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@ -490,10 +508,14 @@ class ParticleOverlap:
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xcell, ycell, zcell = (self.pos2cell(clump[p]) for p in coords)
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if subbox:
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# Shift the box so that each non-zero grid cell is 0th
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xcell -= numpy.min(xcell)
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ycell -= numpy.min(ycell)
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zcell -= numpy.min(zcell)
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ncells = max(*(numpy.max(p) for p in (xcell, ycell, zcell))) + 1
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xcell -= max(numpy.min(xcell) - self.nshift, 0)
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ycell -= max(numpy.min(ycell) - self.nshift, 0)
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zcell -= max(numpy.min(zcell) - self.nshift, 0)
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ncells = max(*(numpy.max(p) + self.nshift
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for p in (xcell, ycell, zcell)))
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ncells += 1 # Bump up by one to get NUMBER of cells
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ncells = min(ncells, self.inv_clength)
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else:
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ncells = self.inv_clength
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@ -528,9 +550,10 @@ class ParticleOverlap:
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xcell2, ycell2, zcell2 = (self.pos2cell(clump2[p]) for p in coords)
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# Minimum cell number of the two halos along each dimension
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xmin = min(numpy.min(xcell1), numpy.min(xcell2))
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ymin = min(numpy.min(ycell1), numpy.min(ycell2))
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zmin = min(numpy.min(zcell1), numpy.min(zcell2))
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xmin = min(numpy.min(xcell1), numpy.min(xcell2)) - self.nshift
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ymin = min(numpy.min(ycell1), numpy.min(ycell2)) - self.nshift
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zmin = min(numpy.min(zcell1), numpy.min(zcell2)) - self.nshift
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xmin, ymin, zmin = max(xmin, 0), max(ymin, 0), max(zmin, 0)
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cellmins = (xmin, ymin, zmin)
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# Maximum cell number of the two halos along each dimension
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xmax = max(numpy.max(xcell1), numpy.max(xcell2))
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@ -538,7 +561,9 @@ class ParticleOverlap:
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zmax = max(numpy.max(zcell1), numpy.max(zcell2))
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# Number of cells is the maximum + 1
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ncells = max(xmax - xmin, ymax - ymin, zmax - zmin) + 1
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ncells = max(xmax - xmin, ymax - ymin, zmax - zmin) + self.nshift
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ncells += 1
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ncells = min(ncells, self.inv_clength)
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# Shift the box so that the first non-zero grid cell is 0th
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xcell1 -= xmin
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@ -579,10 +604,7 @@ class ParticleOverlap:
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-------
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overlap : float
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"""
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mass1 = numpy.sum(delta1)
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mass2 = numpy.sum(delta2)
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intersect = calc_intersect(delta1, delta2, cellmins, delta2_full)
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return intersect / (mass1 + mass2 - intersect)
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return _calculate_overlap(delta1, delta2, cellmins, delta2_full)
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def __call__(self, clump1, clump2, delta2_full):
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"""
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@ -606,7 +628,7 @@ class ParticleOverlap:
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overlap : float
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"""
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delta1, delta2, cellmins = self.make_deltas(clump1, clump2)
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return self.overlap(delta1, delta2, cellmins, delta2_full)
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return _calculate_overlap(delta1, delta2, cellmins, delta2_full)
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@jit(nopython=True)
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@ -633,40 +655,49 @@ def fill_delta(delta, xcell, ycell, zcell, weights):
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@jit(nopython=True)
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def calc_intersect(delta1, delta2, cellmins, delta2_full):
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"""
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Calculate weighted intersect between two density fields.
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def _calculate_overlap(delta1, delta2, cellmins, delta2_full):
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r"""
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Overlap between two clumps whose density fields are evaluated on the
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same grid. This is a JIT implementation, hence it is outside of the main
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class.
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Parameters
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----------
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delta1, delta2 : 3-dimensional arrays
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Density fields of `clump1` and `clump2`, respectively.
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Clumps density fields.
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cellmins : len-3 tuple
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Tuple of left-most cell ID in the full box.
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delta2_full : 3-dimensional array
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Density field of the whole box calculated with particles assigned to
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halos at zero redshift.
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Density field of the whole box calculated with particles assigned
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to halos at zero redshift.
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Returns
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-------
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intersect : float
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overlap : float
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"""
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imax, jmax, kmax = delta1.shape
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intersect = 0.
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totmass = 0. # Total mass of clump 1 and clump 2
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intersect = 0. # Mass of pixels that are non-zero in both clumps
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weight = 0. # Weight to account for other halos
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count = 0 # Total number of pixels that are both non-zero
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for i in range(imax):
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ii = cellmins[0] + i
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for j in range(jmax):
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jj = cellmins[1] + j
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for k in range(kmax):
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kk = cellmins[2] + k
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# Unpack the densities of the clumps
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cell1, cell2 = delta1[i, j, k], delta2[i, j, k]
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totmass += cell1 + cell2
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# If both are zero then skip
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if not (cell1 > 0 and cell2 > 0):
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continue
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if cell1 > 0 and cell2 > 0:
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intersect += cell1 + cell2
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weight += cell2 / delta2_full[ii, jj, kk]
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count += 1
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weight = cell2 / delta2_full[ii, jj, kk]
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intersect += 0.5 * weight * (cell1 + cell2)
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return intersect
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# Normalise the intersect and weights
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intersect *= 0.5
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weight = weight / count if count > 0 else 0.
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return weight * intersect / (totmass - intersect)
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@ -448,7 +448,7 @@ class CombinedHaloCatalogue:
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def concatenate_clumps(clumps):
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"""
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Concatenate a list of clumps to a single array containing all particles.
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Concatenate an array of clumps to a single array containing all particles.
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Parameters
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----------
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