mirror of
https://github.com/Richard-Sti/csiborgtools.git
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Overlap calculation (#18)
* Move cosine similarity out * Basic overlap calculation * add overlap import * Add clump0 dict path * Update README * fix path bug * Save as dict instead * Change format to array of arrays * Update paths * Take fewer ICs for now * Change to structured array * Add overlap calculation * Start saving IDs * Add a blank space * Update TODO
This commit is contained in:
Richard Stiskalek
GitHub
parent
13a9d11afe
commit
18f09767f4
@ -7,14 +7,11 @@
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## Short-term TODO
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- [x] Add code to calculate the cross-correlation for resolved region only.
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- [ ] Calculate the spectra for all 101 boxes and visualise them.
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- [ ] See about the $z=70$ particles.
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- [ ] Implement the CIC binning.
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- [ ] Write a script to perform the matching on a node.
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## Long-term TODO
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- [ ] Calculate the cross-correlation in CSiBORG. Should see the scale of the constraints?
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- [ ] Find the distribution of particles in the first snapshot
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- [ ] Implement a custom model for matchin galaxies to halos.
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@ -13,6 +13,6 @@
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# with this program; if not, write to the Free Software Foundation, Inc.,
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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from .match import (brute_spatial_separation, RealisationsMatcher) # noqa
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from .match import (brute_spatial_separation, RealisationsMatcher, cosine_similarity, ParticleOverlap) # noqa
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from .num_density import (binned_counts, number_density) # noqa
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# from .correlation import (get_randoms_sphere, sphere_angular_tpcf) # noqa
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@ -79,6 +79,9 @@ class RealisationsMatcher:
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----------
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cats : :py:class`csiborgtools.read.CombinedHaloCatalogue`
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Combined halo catalogue to search.
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# NOTE add later
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# dtype : dtype, optional
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# Output precision. By default `numpy.float32`.
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"""
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_cats = None
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@ -122,42 +125,42 @@ class RealisationsMatcher:
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"""
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return [i for i in range(self.cats.N) if i != n_sim]
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def cosine_similarity(self, x, y):
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r"""
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Calculate the cosine similarity between two Cartesian vectors. Defined
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as :math:`\Sum_{i} x_i y_{i} / (|x| * |y|)`.
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def _check_masskind(self, mass_kind):
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"""Check that `mass_kind` is a valid key."""
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if mass_kind not in self.cats[0].keys:
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raise ValueError("Invalid mass kind `{}`.".format(mass_kind))
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@staticmethod
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def _cat2clump_mapping(cat_indxs, clump_indxs):
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"""
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Create a mapping from a catalogue array index to a clump array index.
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Parameters
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----------
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x : 1-dimensional array
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The first vector.
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y : 1- or 2-dimensional array
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The second vector. Can be 2-dimensional of shape `(n_samples, 3)`,
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in which case the calculation is broadcasted.
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cat_indxs : 1-dimensional array
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Clump indices in the catalogue array.
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clump_indxs : 1-dimensional array
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Clump indices in the clump array.
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Returns
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-------
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out : float or 1-dimensional array
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The cosine similarity. If y is 1-dimensinal returns only a float.
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mapping : 1-dimensional array
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Mapping. The array indices match catalogue array and values are
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array positions in the clump array.
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"""
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# Quick check of dimensions
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if x.ndim != 1:
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raise ValueError("`x` must be a 1-dimensional array.")
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y = y.reshape(-1, 3) if y.ndim == 1 else y
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out = numpy.sum(x * y, axis=1)
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out /= numpy.linalg.norm(x) * numpy.linalg.norm(y, axis=1)
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if out.size == 1:
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return out[0]
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return out
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mapping = numpy.full(cat_indxs.size, numpy.nan, dtype=int)
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__, ind1, ind2 = numpy.intersect1d(clump_indxs, cat_indxs,
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return_indices=True)
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mapping[ind2] = ind1
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return mapping
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def cross_knn_position_single(self, n_sim, nmult=5, dlogmass=None,
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init_dist=False, verbose=True):
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mass_kind="totpartmass", init_dist=False,
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overlap=False, verbose=True):
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r"""
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Find all neighbours within :math:`n_{\rm mult} R_{200c}` of halos in
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the `nsim`th simulation. Also enforces that the neighbours'
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:math:`\log M_{200c}` be within `dlogmass` dex.
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:math:`\log M / M_\odot` be within `dlogmass` dex.
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Parameters
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----------
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@ -169,43 +172,71 @@ class RealisationsMatcher:
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default 5.
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dlogmass : float, optional
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Tolerance on mass logarithmic mass difference. By default `None`.
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mass_kind : str, optional
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The mass kind whose similarity is to be checked. Must be a valid
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catalogue key. By default `totpartmass`, i.e. the total particle
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mass associated with a halo.
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init_dist : bool, optional
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Whether to calculate separation of the initial CMs. By default
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`False`.
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overlap : bool, optional
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Whether to calculate overlap between clumps in the initial
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snapshot. By default `False`. Note that this operation is
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substantially slower.
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verbose : bool, optional
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Iterator verbosity flag. By default `True`.
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Returns
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-------
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matches : composite array
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Array, indices are `(n_sims - 1, 3, n_halos, n_matches)`. The
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Array, indices are `(n_sims - 1, 4, n_halos, n_matches)`. The
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2nd axis is `index` of the neighbouring halo in its catalogue,
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`dist`, which is the 3D distance to the halo whose neighbours are
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searched, and `dist0` which is the separation of the initial CMs.
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The latter is calculated only if `init_dist` is `True`.
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`dist` is the 3D distance to the halo whose neighbours are
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searched, `dist0` is the separation of the initial CMs and
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`overlap` is the overlap over the initial clumps, all respectively.
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The latter two are calculated only if `init_dist` or `overlap` is
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`True`.
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TODO:
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- [ ] Precalculate the mapping from halo index to clump array position
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"""
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# Radius, M200c and positions of halos in `n_sim` IC realisation
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logm200 = numpy.log10(self.cats[n_sim]["m200"])
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self._check_masskind(mass_kind)
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# Radius, mass and positions of halos in `n_sim` IC realisation
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logmass = numpy.log10(self.cats[n_sim][mass_kind])
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R = self.cats[n_sim]["r200"]
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pos = self.cats[n_sim].positions
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if init_dist:
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pos0 = self.cats[n_sim].positions0 # These are CM positions
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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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# 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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clumps0 = numpy.load(f, allow_pickle=True)
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overlapper = ParticleOverlap()
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cat2clumps0 = self._cat2clump_mapping(self.cats[n_sim]["index"],
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clumps0["ID"])
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matches = [None] * (self.cats.N - 1)
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# Verbose iterator
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if verbose:
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iters = enumerate(tqdm(self.search_sim_indices(n_sim)))
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else:
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iters = enumerate(self.search_sim_indices(n_sim))
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iters = enumerate(self.search_sim_indices(n_sim))
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# Search for neighbours in the other simulations
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for count, i in iters:
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dist, indxs = self.cats[i].radius_neigbours(pos, R * nmult)
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# Get rid of neighbors whose mass is too off
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if dlogmass is not None:
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for j, indx in enumerate(indxs):
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match_logm200 = numpy.log10(self.cats[i]["m200"][indx])
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mask = numpy.abs(match_logm200 - logm200[j]) < dlogmass
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match_logmass = numpy.log10(self.cats[i][mass_kind][indx])
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mask = numpy.abs(match_logmass - logmass[j]) < dlogmass
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dist[j] = dist[j][mask]
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indxs[j] = indx[mask]
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# Find distance to the between the initial CM
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dist0 = [numpy.asanyarray([], dtype=numpy.float64)] * dist.size
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if init_dist:
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@ -215,13 +246,47 @@ class RealisationsMatcher:
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dist0[k] = numpy.linalg.norm(
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pos0[k] - self.cats[i].positions0[indxs[k]], axis=1)
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# Calculate the initial snapshot overlap
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cross = [numpy.asanyarray([], dtype=numpy.float64)] * dist.size
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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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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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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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with_neigbours = numpy.where([ii.size > 0 for ii in indxs])[0]
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for k in tqdm(with_neigbours) if verbose else with_neigbours:
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# Find which clump matches index of this halo from cat
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match0 = cat2clumps0[k]
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# Get the clump and pre-calculate its cell assignment
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cl0 = clumps0["clump"][match0]
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cl0_cells = overlapper.assign_to_cell(
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*(cl0[p] for p in ('x', 'y', 'z')))
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dint = numpy.full(indxs[k].size, numpy.nan, numpy.float64)
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# Loop over the ones we cross-correlate with
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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.mass_overlap(
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cl0, clumpsx["clump"][matchx], cl0_cells)
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cross[k] = dint
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# Append as a composite array
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matches[count] = numpy.asarray([indxs, dist, dist0], dtype=object)
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matches[count] = numpy.asarray(
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[indxs, dist, dist0, cross], dtype=object)
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return numpy.asarray(matches, dtype=object)
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def cross_knn_position_all(self, nmult=5, dlogmass=None,
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init_dist=False, verbose=True):
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mass_kind="totpartmass", init_dist=False,
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overlap=False, verbose=True):
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r"""
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Find all neighbours within :math:`n_{\rm mult} R_{200c}` of halos in
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all simulations listed in `self.cats`. Also enforces that the
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@ -234,9 +299,17 @@ class RealisationsMatcher:
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default 5.
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dlogmass : float, optional
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Tolerance on mass logarithmic mass difference. By default `None`.
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mass_kind : str, optional
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The mass kind whose similarity is to be checked. Must be a valid
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catalogue key. By default `totpartmass`, i.e. the total particle
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mass associated with a halo.
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init_dist : bool, optional
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Whether to calculate separation of the initial CMs. By default
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`False`.
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overlap : bool, optional
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Whether to calculate overlap between clumps in the initial
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snapshot. By default `False`. Note that this operation is
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substantially slower.
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verbose : bool, optional
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Iterator verbosity flag. By default `True`.
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@ -251,5 +324,136 @@ class RealisationsMatcher:
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# Loop over each catalogue
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for i in trange(N) if verbose else range(N):
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matches[i] = self.cross_knn_position_single(
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i, nmult, dlogmass, init_dist)
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i, nmult, dlogmass, mass_kind=mass_kind, init_dist=init_dist,
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overlap=overlap, verbose=verbose)
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return matches
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###############################################################################
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# Matching statistics #
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###############################################################################
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def cosine_similarity(x, y):
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r"""
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Calculate the cosine similarity between two Cartesian vectors. Defined
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as :math:`\Sum_{i} x_i y_{i} / (|x| * |y|)`.
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Parameters
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----------
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x : 1-dimensional array
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The first vector.
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y : 1- or 2-dimensional array
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The second vector. Can be 2-dimensional of shape `(n_samples, 3)`,
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in which case the calculation is broadcasted.
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Returns
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-------
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out : float or 1-dimensional array
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The cosine similarity. If y is 1-dimensinal returns only a float.
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"""
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# Quick check of dimensions
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if x.ndim != 1:
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raise ValueError("`x` must be a 1-dimensional array.")
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y = y.reshape(-1, 3) if y.ndim == 1 else y
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out = numpy.sum(x * y, axis=1)
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out /= numpy.linalg.norm(x) * numpy.linalg.norm(y, axis=1)
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if out.size == 1:
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return out[0]
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return out
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class ParticleOverlap:
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"""
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TODO:
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- [ ] Class documentation
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"""
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_bins = None
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def __init__(self, bins=None):
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if bins is None:
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dx = 1 / 2**11
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bins = numpy.arange(0, 1 + dx, dx)
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self.bins = bins
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@property
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def bins(self):
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"""
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The grid spacing. Assumed to be equal for all three dimensions. Units
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ought to match the requested coordinates.
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Returns
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-------
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bins : 1-dimensional array
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"""
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return self._bins
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@bins.setter
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def bins(self, bins):
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"""Sets `bins`."""
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bins = numpy.asarray(bins) if isinstance(bins, list) else bins
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assert bins.ndim == 1, "`bins` must be a 1-dimensional array."
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self._bins = bins
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def assign_to_cell(self, x, y, z):
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"""
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Assign particles specified by coordinates `x`, `y`, and `z` to grid
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cells.
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Parameters
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----------
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x, y, z : 1-dimensional arrays
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Positions of particles in the box.
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Returns
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-------
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cells : 1-dimensional array
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Cell ID of each particle.
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"""
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assert x.ndim == 1 and x.size == y.size == z.size
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xbin = numpy.digitize(x, self.bins)
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ybin = numpy.digitize(y, self.bins)
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zbin = numpy.digitize(z, self.bins)
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N = self.bins.size
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return xbin + ybin * N + zbin * N**2
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def mass_overlap(self, clump1, clump2, cells1=None):
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r"""
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Calculate the particle, mass-weighted overlap between two halos.
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Defined as
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..math::
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(M_{u,1} + M_{u,2}) / (M_1 + M_2),
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where :math:`M_{u, 1}` is the mass of particles of the first halo in
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cells that are also present in the second halo and :math:`M_1` is the
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total particle mass of the first halo.
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Parameters
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----------
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clump1, clump2 : structured arrays
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Structured arrays corresponding to the two clumps. Should contain
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keys `x`, `y`, `z` and `M`.
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cells1 : 1-dimensional array, optional
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Optionlaly precomputed cells of `clump1`. Be careful when using
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this to ensure it matches `clump1`.
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Returns
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-------
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overlap : float
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"""
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# 1-dimensional cell ID of each particle in clump1 and clump2
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if cells1 is None:
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cells1 = self.assign_to_cell(*[clump1[p] for p in ('x', 'y', 'z')])
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cells2 = self.assign_to_cell(*[clump2[p] for p in ('x', 'y', 'z')])
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# Elementwise cells1 in cells2 and vice versa
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m1 = numpy.isin(cells1, cells2)
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m2 = numpy.isin(cells2, cells1)
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# Summed shared mass and the total
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interp = numpy.sum(clump1["M"][m1]) + numpy.sum(clump2["M"][m2])
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mtot = numpy.sum(clump1["M"]) + numpy.sum(clump2["M"])
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return interp / mtot
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@ -378,7 +378,8 @@ class CombinedHaloCatalogue:
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def __init__(self, paths, min_m500=None, max_dist=None, verbose=True):
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# Read simulations and their maximum snapshots
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# NOTE later change this back to all simulations
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self._n_sims = [7468, 7588, 8020, 8452, 8836]
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# self._n_sims = [7468, 7588, 8020, 8452, 8836]
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self._n_sims = [7468, 7588]
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# self._n_sims = paths.ic_ids
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n_snaps = [paths.get_maximum_snapshot(i) for i in self._n_sims]
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self._n_snaps = numpy.asanyarray(n_snaps)
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@ -72,7 +72,6 @@ class CSiBORGPaths:
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_initmatch_path = None
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_to_new = None
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# NOTE deuglify this stuff
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def __init__(self, n_sim=None, n_snap=None, srcdir=None, dumpdir=None,
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mmain_path=None, initmatch_path=None, to_new=False):
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if srcdir is None:
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@ -425,6 +424,24 @@ class CSiBORGPaths:
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n_sim = self.get_n_sim(n_sim)
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return min(self.get_snapshots(n_sim))
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def clump0_path(self, nsim):
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"""
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Path to a single dumped clump's particles. This is expected to point
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to a dictonary whose keys are the clump indices and items structured
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arrays with the clump's particles in the initial snapshot.
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Parameters
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----------
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nsim : int
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Index of the initial conditions (IC) realisation.
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Returns
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-------
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path : str
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"""
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cdir = join(self.dumpdir, "initmatch")
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return join(cdir, "clump_{}_{}.npy".format(nsim, "particles"))
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def snapshot_path(self, n_snap=None, n_sim=None):
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"""
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Path to a CSiBORG IC realisation snapshot.
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@ -839,7 +856,7 @@ def read_mmain(n, srcdir, fname="Mmain_{}.npy"):
|
||||
return out
|
||||
|
||||
|
||||
def read_initcm(n, srcdir, fname="clump_cm_{}.npy"):
|
||||
def read_initcm(n, srcdir, fname="clump_{}_cm.npy"):
|
||||
"""
|
||||
Read `clump_cm`, i.e. the center of mass of a clump at redshift z = 70.
|
||||
If the file does not exist returns `None`.
|
||||
|
||||
@ -24,8 +24,7 @@ import numpy
|
||||
from datetime import datetime
|
||||
from mpi4py import MPI
|
||||
from distutils.util import strtobool
|
||||
from os.path import join, isdir
|
||||
from os import mkdir
|
||||
from os.path import join
|
||||
from os import remove
|
||||
from sys import stdout
|
||||
from gc import collect
|
||||
@ -51,21 +50,15 @@ fin_paths = csiborgtools.read.CSiBORGPaths(to_new=False)
|
||||
nsims = init_paths.ic_ids
|
||||
|
||||
# Output files
|
||||
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/initmatch"
|
||||
ftemp = join(dumpdir, "temp", "temp_{}_{}.npy")
|
||||
fperm = join(dumpdir, "clump_cm_{}.npy")
|
||||
dumpdir = "/mnt/extraspace/rstiskalek/csiborg/"
|
||||
ftemp = join(dumpdir, "temp_initmatch", "temp_{}_{}_{}.npy")
|
||||
fpermcm = join(dumpdir, "initmatch", "clump_{}_cm.npy")
|
||||
fpermpart = join(dumpdir, "initmatch", "clump_{}_particles.npy")
|
||||
|
||||
for nsim in nsims:
|
||||
if rank == 0:
|
||||
print("{}: reading simulation {}.".format(datetime.now(), nsim))
|
||||
stdout.flush()
|
||||
# Check that the output folder for this sim exists
|
||||
clumpdumpdir = join(dumpdir, "out_{}".format(nsim))
|
||||
if args.dump_clumps and rank == 0 and not isdir(clumpdumpdir):
|
||||
mkdir(clumpdumpdir)
|
||||
|
||||
# Barrier to make sure we created the directory with the rank 0
|
||||
comm.Barrier()
|
||||
|
||||
# Set the snapshot numbers
|
||||
init_paths.set_info(nsim, init_paths.get_minimum_snapshot(nsim))
|
||||
@ -111,15 +104,16 @@ for nsim in nsims:
|
||||
cm = numpy.asanyarray(
|
||||
[numpy.average(x0[p], weights=x0["M"]) for p in ('x', 'y', 'z')])
|
||||
# Dump the center of mass
|
||||
with open(ftemp.format(nsim, n), 'wb') as f:
|
||||
with open(ftemp.format(nsim, n, "cm"), 'wb') as f:
|
||||
numpy.save(f, cm)
|
||||
# Optionally dump the entire clump
|
||||
if args.dump_clumps:
|
||||
fout = join(clumpdumpdir, "clump_{}.npy".format(n))
|
||||
stdout.flush()
|
||||
with open(fout, "wb") as f:
|
||||
with open(ftemp.format(nsim, n, "clump"), "wb") as f:
|
||||
numpy.save(f, x0)
|
||||
|
||||
del part0, clump_ids
|
||||
collect()
|
||||
|
||||
comm.Barrier()
|
||||
if rank == 0:
|
||||
print("Collecting CM files...")
|
||||
@ -130,14 +124,33 @@ for nsim in nsims:
|
||||
out = numpy.full(njobs, numpy.nan, dtype=dtype)
|
||||
|
||||
for i, n in enumerate(unique_clumpids):
|
||||
with open(ftemp.format(nsim, n), 'rb') as f:
|
||||
fpath = ftemp.format(nsim, n, "cm")
|
||||
with open(fpath, 'rb') as f:
|
||||
fin = numpy.load(f)
|
||||
out['x'][i] = fin[0]
|
||||
out['y'][i] = fin[1]
|
||||
out['z'][i] = fin[2]
|
||||
out["ID"][i] = n
|
||||
remove(ftemp.format(nsim, n))
|
||||
|
||||
print("Dumping CM files to .. `{}`.".format(fperm.format(nsim)))
|
||||
with open(fperm.format(nsim), 'wb') as f:
|
||||
remove(fpath)
|
||||
print("Dumping CM files to .. `{}`.".format(fpermcm.format(nsim)))
|
||||
with open(fpermcm.format(nsim), 'wb') as f:
|
||||
numpy.save(f, out)
|
||||
|
||||
print("Collecting clump files...")
|
||||
stdout.flush()
|
||||
out = [None] * unique_clumpids.size
|
||||
dtype = {"names": ["clump", "ID"], "formats": [object, numpy.int32]}
|
||||
out = numpy.full(unique_clumpids.size, numpy.nan, dtype=dtype)
|
||||
for i, n in enumerate(unique_clumpids):
|
||||
fpath = ftemp.format(nsim, n, "clump")
|
||||
with open(fpath, 'rb') as f:
|
||||
fin = numpy.load(f)
|
||||
out["clump"][i] = fin
|
||||
out["ID"][i] = n
|
||||
remove(fpath)
|
||||
print("Dumping clump files to .. `{}`.".format(fpermpart.format(nsim)))
|
||||
with open(fpermpart.format(nsim), "wb") as f:
|
||||
numpy.save(f, out)
|
||||
|
||||
del out
|
||||
collect()
|
||||
|
||||
Loading…
Reference in New Issue
Block a user