mirror of
https://github.com/Richard-Sti/csiborgtools.git
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Matching paper plots (#91)
* Fix calculations of expected mass * Add paper plots * Edits to pltos * Add overlap summary * Add imports * Add import * Add binned stat * Add fit * Add more plots * Add basic env * Add histogram mode * Edit expected mass * Improve expected plots * Clean up plot * Improve separation plot * Update plots * Edit expected calculation * Update plotting * Update plots * Update plots * Update plots * Add conc fraction * Add halo maker sorting * Renaming * Add import * Add NaN treatment * add import * Move cosine smi * Update plots * Move similarity * Fix little bugs * Shorten documentation * Update plots
This commit is contained in:
Richard Stiskalek
GitHub
parent
136c552369
commit
5500fbd2b9
11 changed files with 2193 additions and 294 deletions
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@ -15,7 +15,9 @@
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from csiborgtools import clustering, field, match, read, summary # noqa
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from .utils import (center_of_mass, delta2ncells, number_counts, # noqa
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periodic_distance, periodic_distance_two_points) # noqa
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periodic_distance, periodic_distance_two_points, # noqa
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binned_statistic, cosine_similarity) # noqa
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# Arguments to csiborgtools.read.Paths.
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paths_glamdring = {"srcdir": "/mnt/extraspace/hdesmond/",
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@ -14,5 +14,5 @@
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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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from .match import (ParticleOverlap, RealisationsMatcher, # noqa
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calculate_overlap, calculate_overlap_indxs, pos2cell, # noqa
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cosine_similarity, find_neighbour, get_halo_cell_limits, # noqa
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find_neighbour, get_halo_cell_limits, # noqa
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matching_max) # noqa
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@ -660,19 +660,12 @@ class ParticleOverlap(BaseMatcher):
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def pos2cell(pos, ncells):
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"""
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Convert position to cell number if there are `ncells` cells along the axis.
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"""
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if pos.dtype.char in numpy.typecodes["AllInteger"]:
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return pos
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return numpy.floor(pos * ncells).astype(numpy.int32)
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def read_nshift(smooth_kwargs):
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"""
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Determine the number of cells to pad the density field if smoothing is
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applied. Defaults to the ceiling of three times the smoothing scale.
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"""
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return 0 if smooth_kwargs is None else ceil(3 * smooth_kwargs["sigma"])
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@ -774,33 +767,26 @@ def get_halo_cell_limits(pos, ncells, nshift=0):
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return mins, maxs
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@jit(nopython=True)
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@jit(nopython=True, boundscheck=False)
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def calculate_overlap(delta1, delta2, cellmins, delta_bckg, box_size,
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bckg_halfsize):
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r"""
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Overlap between two halos 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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"""
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Calculate overlap between two halos' density fields on the same grid.
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Parameters
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----------
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delta1: 3-dimensional array
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Density field of the first halo.
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delta2 : 3-dimensional array
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Density field of the second halo.
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cellmins : len-3 tuple
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Tuple of lower cell ID in the full box.
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delta_bckg : 3-dimensional array
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Summed background density field of the reference and cross simulations
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calculated with particles assigned to halos at the final snapshot.
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Calculated on a grid determined by `bckg_halfsize`.
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delta1, delta2 : 3D array
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Density fields of the first and second halos, respectively.
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cellmins : tuple (len=3)
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Lower cell ID in the full box.
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delta_bckg : 3D array
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Combined background density field of reference and cross simulations
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on `bckg_halfsize` grid.
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box_size : int
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Number of cells in the box.
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Cell count in the box.
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bckg_halfsize : int
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Background half-size for density field calculation. This is the
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grid distance from the center of the box to each side over which to
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evaluate the background density field. Must be less than or equal to
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half the box size.
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Grid distance from box center for background density.
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≤ 0.5 * box_size.
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Returns
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-------
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@ -834,39 +820,29 @@ def calculate_overlap(delta1, delta2, cellmins, delta_bckg, box_size,
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return intersect / (totmass - intersect)
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@jit(nopython=True)
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@jit(nopython=True, boundscheck=False)
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def calculate_overlap_indxs(delta1, delta2, cellmins, delta_bckg, nonzero,
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mass1, mass2, box_size, bckg_halfsize):
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r"""
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Overlap between two haloes whose density fields are evaluated on the
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same grid and `nonzero1` enumerates the non-zero cells of `delta1. This is
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a JIT implementation, hence it is outside of the main class.
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"""
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Calculate overlap of two halos' density fields on the same grid.
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Parameters
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----------
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delta1: 3-dimensional array
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Density field of the first halo.
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delta2 : 3-dimensional array
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Density field of the second halo.
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cellmins : len-3 tuple
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Tuple of lower cell ID in the full box.
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delta_bckg : 3-dimensional array
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Summed background density field of the reference and cross simulations
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calculated with particles assigned to halos at the final snapshot.
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Calculated on a grid determined by `bckg_halfsize`.
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nonzero : 2-dimensional array of shape `(n_cells, 3)`
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Indices of cells that are non-zero of the lower mass halo. Expected to
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be precomputed from `fill_delta_indxs`.
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mass1, mass2 : floats, optional
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Total masses of the two haloes, respectively. Optional. If not provided
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calculcated directly from the density field.
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delta1, delta2 : 3D array
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Density fields of the first and second halos, respectively.
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cellmins : tuple (len=3)
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Lower cell ID in the full box.
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delta_bckg : 3D array
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Combined background density from reference and cross simulations
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on `bckg_halfsize` grid.
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nonzero : 2D array (shape: (n_cells, 3))
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Non-zero cells for the lower mass halo (from `fill_delta_indxs`).
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mass1, mass2 : float, optional
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Halos' total masses. Calculated from density if not provided.
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box_size : int
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Number of cells in the box.
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Cell count in the box.
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bckg_halfsize : int
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Background half-size for density field calculation. This is the
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grid distance from the center of the box to each side over which to
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evaluate the background density field. Must be less than or equal to
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half the box size.
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Grid distance from box center for background density; ≤ 0.5 * box_size.
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Returns
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-------
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@ -1039,35 +1015,6 @@ def find_neighbour(nsim0, cats):
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return dists, cross_hindxs
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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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"""
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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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if y.ndim == 1:
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y = y.reshape(1, -1)
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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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return out[0] if out.size == 1 else out
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def matching_max(cat0, catx, mass_kind, mult, periodic, overlap=None,
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match_indxs=None, verbose=True):
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"""
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@ -16,7 +16,11 @@
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from .knn_summary import kNNCDFReader # noqa
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from .nearest_neighbour_summary import NearestNeighbourReader # noqa
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from .overlap_summary import weighted_stats # noqa
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from .overlap_summary import NPairsOverlap, PairOverlap, get_cross_sims # noqa
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from .overlap_summary import (NPairsOverlap, PairOverlap, get_cross_sims, # noqa
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max_overlap_agreement, max_overlap_agreements, # noqa
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find_peak) # noqa
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from .pk_summary import PKReader # noqa
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from .tpcf_summary import TPCFReader # noqa
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from .field_interp import read_interpolated_field # noqa
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from .field_interp import (read_interpolated_field, # noqa
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bayesian_bootstrap_correlation, # noqa
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correlate_at_fixed_smoothing) # noqa
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@ -15,6 +15,12 @@
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import numpy
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from tqdm import tqdm
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from numba import jit
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###############################################################################
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# Read in the field values at the galaxy positions #
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###############################################################################
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def read_interpolated_field(survey_name, kind, galaxy_index, paths, MAS, grid,
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@ -75,3 +81,142 @@ def read_interpolated_field(survey_name, kind, galaxy_index, paths, MAS, grid,
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ks[i] = j
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return out[:, ks, :]
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###############################################################################
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# Calculate the Bayesian bootstrapped correlation #
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###############################################################################
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@jit(nopython=True, fastmath=True, boundscheck=False)
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def dot_product(x, y):
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tot = 0.0
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for i in range(len(x)):
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tot += x[i] * y[i]
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return tot
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@jit(nopython=True, fastmath=True, boundscheck=False)
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def cov(x, y, mean_x, mean_y, weights):
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tot = 0.0
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for i in range(len(x)):
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tot += (x[i] - mean_x) * (y[i] - mean_y) * weights[i]
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return tot
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@jit(nopython=True, fastmath=True, boundscheck=False)
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def var(x, mean_x, weights):
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tot = 0.0
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for i in range(len(x)):
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tot += (x[i] - mean_x)**2 * weights[i]
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return tot
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@jit(nopython=True, fastmath=True, boundscheck=False)
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def weighted_correlation(x, y, weights):
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mean_x = dot_product(x, weights)
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mean_y = dot_product(y, weights)
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cov_xy = cov(x, y, mean_x, mean_y, weights)
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var_x = var(x, mean_x, weights)
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var_y = var(y, mean_y, weights)
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return cov_xy / numpy.sqrt(var_x * var_y)
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@jit(nopython=True, fastmath=True, boundscheck=False)
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def _bayesian_bootstrap_correlation(x, y, weights):
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nweights = len(weights)
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bootstrapped_correlations = numpy.full(nweights, numpy.nan, dtype=x.dtype)
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for i in range(nweights):
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bootstrapped_correlations[i] = weighted_correlation(x, y, weights[i])
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return bootstrapped_correlations
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@jit(nopython=True, fastmath=True, boundscheck=False)
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def rank(x):
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order = numpy.argsort(x)
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ranks = order.argsort()
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return ranks
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@jit(nopython=True, fastmath=True, boundscheck=False)
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def bayesian_bootstrap_correlation(x, y, kind="spearman", n_bootstrap=10000):
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"""
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Calculate the Bayesian bootstrapped correlation between two arrays.
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Parameters
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----------
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x, y : 1-dimensional arrays
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The two arrays to calculate the correlation between.
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kind : str, optional
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The type of correlation to calculate. Either `spearman` or `pearson`.
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n_bootstrap : int, optional
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The number of bootstrap samples to use.
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Returns
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-------
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corr : 1-dimensional array of shape `(n_bootstrap,)`
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"""
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if len(x) != len(y):
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raise ValueError("Input arrays must have the same length")
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if kind not in ["spearman", "pearson"]:
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raise ValueError("kind must be either `spearman` or `pearson`")
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if kind == "spearman":
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dtype = x.dtype
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x = rank(x).astype(dtype)
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y = rank(y).astype(dtype)
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alphas = numpy.ones(len(x), dtype=x.dtype)
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weights = numpy.random.dirichlet(alphas, size=n_bootstrap)
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return _bayesian_bootstrap_correlation(x, y, weights)
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###############################################################################
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# Distribution disagreement #
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###############################################################################
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def distribution_disagreement(x, y):
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"""
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Think about this more when stacking non-Gaussian distributions.
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"""
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delta = x - y
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return numpy.abs(delta.mean()) / delta.std()
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"""
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field will be of value (nsims, ngal, nsmooth)
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Calculate the correlation for each sim and smoothing scale (nsims, nsmooth)
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For each of the above stack the distributions?
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"""
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def correlate_at_fixed_smoothing(field_values, galaxy_property,
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kind="spearman", n_bootstrap=1000):
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galaxy_property = galaxy_property.astype(field_values.dtype)
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nsims = len(field_values)
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distributions = numpy.empty((nsims, n_bootstrap), dtype=field_values.dtype)
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from tqdm import trange
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for i in trange(nsims):
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distributions[i] = bayesian_bootstrap_correlation(
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field_values[i], galaxy_property, kind=kind, n_bootstrap=n_bootstrap)
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return distributions
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def do_something(field_values, galaxy_property):
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pass
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@ -23,6 +23,30 @@ from tqdm import tqdm, trange
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from ..utils import periodic_distance
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###############################################################################
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# Utility functions #
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###############################################################################
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def find_peak(x, weights, shrink=0.95, min_obs=5):
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"""
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Find the peak of a 1D distribution using a shrinking window.
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"""
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assert shrink <= 1.
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xmin, xmax = numpy.min(x), numpy.max(x)
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xpos = (xmax + xmin) / 2
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rad = (xmax - xmin) / 2
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while True:
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mask = numpy.abs(x - xpos) < rad
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if mask.sum() < min_obs:
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return xpos
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xpos = numpy.average(x[mask], weights=weights[mask])
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rad *= shrink
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###############################################################################
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# Overlap of two simulations #
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###############################################################################
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@ -251,42 +275,16 @@ class PairOverlap:
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----------
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from_smoothed : bool
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Whether to use the smoothed overlap or not.
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Returns
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-------
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summed_overlap : 1-dimensional array of shape `(nhalos, )`
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"""
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overlap = self.overlap(from_smoothed)
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out = numpy.full(len(overlap), numpy.nan, dtype=numpy.float32)
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out = numpy.zeros(len(overlap), dtype=numpy.float32)
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for i in range(len(overlap)):
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if len(overlap[i]) > 0:
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out[i] = numpy.sum(overlap[i])
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else:
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out[i] = 0
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return out
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def prob_nomatch(self, from_smoothed):
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"""
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Probability of no match for each halo in the reference simulation with
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the cross simulation. Defined as a product of 1 - overlap with other
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halos.
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Parameters
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----------
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from_smoothed : bool
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Whether to use the smoothed overlap or not.
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Returns
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-------
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prob_nomatch : 1-dimensional array of shape `(nhalos, )`
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"""
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overlap = self.overlap(from_smoothed)
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out = numpy.full(len(overlap), numpy.nan, dtype=numpy.float32)
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for i in range(len(overlap)):
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if len(overlap[i]) > 0:
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out[i] = numpy.product(numpy.subtract(1, overlap[i]))
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else:
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out[i] = 1
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return out
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def dist(self, in_initial, boxsize, norm_kind=None):
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@ -308,8 +306,7 @@ class PairOverlap:
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-------
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dist : array of 1-dimensional arrays of shape `(nhalos, )`
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"""
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assert (norm_kind is None
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or norm_kind in ("r200c", "ref_patch", "sum_patch"))
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assert (norm_kind is None or norm_kind in ("r200c", "ref_patch", "sum_patch")) # noqa
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# Get positions either in the initial or final snapshot
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pos0 = self.cat0().position(in_initial=in_initial)
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posx = self.catx().position(in_initial=in_initial)
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@ -400,60 +397,6 @@ class PairOverlap:
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return out
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def counterpart_mass(self, from_smoothed, overlap_threshold=0.,
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mass_kind="totpartmass"):
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"""
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Calculate the expected counterpart mass of each halo in the reference
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simulation from the crossed simulation.
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Parameters
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----------
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from_smoothed : bool
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Whether to use the smoothed overlap or not.
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overlap_threshold : float, optional
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Minimum overlap required for a halo to be considered a match. By
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default 0.0, i.e. no threshold.
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mass_kind : str, optional
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The mass kind whose ratio is to be calculated. 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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Returns
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-------
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mean, std : 1-dimensional arrays of shape `(nhalos, )`
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"""
|
||||
mean = numpy.full(len(self), numpy.nan, dtype=numpy.float32)
|
||||
std = numpy.full(len(self), numpy.nan, dtype=numpy.float32)
|
||||
|
||||
massx = self.catx(mass_kind) # Create references to speed
|
||||
overlap = self.overlap(from_smoothed) # up the loop below
|
||||
|
||||
for i, match_ind in enumerate(self["match_indxs"]):
|
||||
# Skip if no match
|
||||
if len(match_ind) == 0:
|
||||
continue
|
||||
|
||||
massx_ = massx[match_ind] # Again just create references
|
||||
overlap_ = overlap[i] # to the appropriate elements
|
||||
|
||||
# Optionally apply overlap threshold
|
||||
if overlap_threshold > 0.:
|
||||
mask = overlap_ > overlap_threshold
|
||||
if numpy.sum(mask) == 0:
|
||||
continue
|
||||
massx_ = massx_[mask]
|
||||
overlap_ = overlap_[mask]
|
||||
|
||||
massx_ = numpy.log10(massx_)
|
||||
# Weighted average and *biased* standard deviation
|
||||
mean_ = numpy.average(massx_, weights=overlap_)
|
||||
std_ = numpy.average((massx_ - mean_)**2, weights=overlap_)**0.5
|
||||
|
||||
mean[i] = mean_
|
||||
std[i] = std_
|
||||
|
||||
return mean, std
|
||||
|
||||
def copy_per_match(self, par):
|
||||
"""
|
||||
Make an array like `self.match_indxs` where each of its element is an
|
||||
|
|
@ -525,6 +468,82 @@ class PairOverlap:
|
|||
return self["match_indxs"].size
|
||||
|
||||
|
||||
###############################################################################
|
||||
# Support functions for pair overlaps #
|
||||
###############################################################################
|
||||
|
||||
|
||||
def max_overlap_agreement(cat0, catx, min_logmass, maxdist, paths):
|
||||
r"""
|
||||
Calculate whether for a halo `A` from catalogue `cat0` that has a maximum
|
||||
overlap with halo `B` from catalogue `catx` it is also `B` that has a
|
||||
maximum overlap with `A`.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
cat0 : instance of :py:class:`csiborgtools.read.BaseCatalogue`
|
||||
Halo catalogue corresponding to the reference simulation.
|
||||
catx : instance of :py:class:`csiborgtools.read.BaseCatalogue`
|
||||
Halo catalogue corresponding to the cross simulation.
|
||||
min_logmass : float
|
||||
Minimum halo mass in :math:`\log_{10} M_\odot / h` to consider.
|
||||
maxdist : float, optional
|
||||
Maximum halo distance in :math:`\mathrm{Mpc} / h` from the centre
|
||||
of the high-resolution region.
|
||||
paths : py:class`csiborgtools.read.Paths`
|
||||
CSiBORG paths object.
|
||||
|
||||
Returns
|
||||
-------
|
||||
agreement : 1-dimensional array of shape `(nhalos, )`
|
||||
"""
|
||||
kwargs = {"paths": paths, "min_logmass": min_logmass, "maxdist": maxdist}
|
||||
pair_forward = PairOverlap(cat0, catx, **kwargs)
|
||||
pair_backward = PairOverlap(catx, cat0, **kwargs)
|
||||
|
||||
nhalos = len(pair_forward.cat0())
|
||||
agreement = numpy.full(nhalos, numpy.nan, dtype=numpy.float32)
|
||||
|
||||
for i in range(nhalos):
|
||||
match_indxs_forward = pair_forward["match_indxs"][i]
|
||||
|
||||
if len(match_indxs_forward) == 0:
|
||||
continue
|
||||
|
||||
overlap_forward = pair_forward["smoothed_overlap"][i]
|
||||
|
||||
kmax = match_indxs_forward[numpy.argmax(overlap_forward)]
|
||||
match_indxs_backward = pair_backward["match_indxs"][kmax]
|
||||
overlap_backward = pair_backward["smoothed_overlap"][kmax]
|
||||
|
||||
imatch = match_indxs_backward[numpy.argmax(overlap_backward)]
|
||||
agreement[i] = imatch == i
|
||||
|
||||
return agreement
|
||||
|
||||
|
||||
def max_overlap_agreements(cat0, catxs, min_logmass, maxdist, paths,
|
||||
verbose=True):
|
||||
"""
|
||||
Repeat `max_overlap_agreement` for many cross simulations.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
...
|
||||
|
||||
Returns
|
||||
-------
|
||||
agreements : 2-dimensional array of shape `(ncatxs, nhalos)`
|
||||
"""
|
||||
agreements = [None] * len(catxs)
|
||||
desc = "Calculating maximum overlap agreement"
|
||||
for i, catx in enumerate(tqdm(catxs, desc=desc, disable=not verbose)):
|
||||
agreements[i] = max_overlap_agreement(cat0, catx, min_logmass,
|
||||
maxdist, paths)
|
||||
|
||||
return numpy.asanyarray(agreements)
|
||||
|
||||
|
||||
def weighted_stats(x, weights, min_weight=0, verbose=False):
|
||||
"""
|
||||
Calculate the weighted mean and standard deviation of `x` using `weights`
|
||||
|
|
@ -544,11 +563,10 @@ def weighted_stats(x, weights, min_weight=0, verbose=False):
|
|||
|
||||
Returns
|
||||
-------
|
||||
stat : 2-dimensional array of shape `(len(x), 2)`
|
||||
The first column is the weighted mean and the second column is the
|
||||
weighted standard deviation.
|
||||
mu, std : 1-dimensional arrays of shape `(len(x), )`
|
||||
"""
|
||||
out = numpy.full((x.size, 2), numpy.nan, dtype=numpy.float32)
|
||||
mu = numpy.full(x.size, numpy.nan, dtype=numpy.float32)
|
||||
std = numpy.full(x.size, numpy.nan, dtype=numpy.float32)
|
||||
|
||||
for i in trange(len(x), disable=not verbose):
|
||||
x_, w_ = numpy.asarray(x[i]), numpy.asarray(weights[i])
|
||||
|
|
@ -557,9 +575,9 @@ def weighted_stats(x, weights, min_weight=0, verbose=False):
|
|||
w_ = w_[mask]
|
||||
if len(w_) == 0:
|
||||
continue
|
||||
out[i, 0] = numpy.average(x_, weights=w_)
|
||||
out[i, 1] = numpy.average((x_ - out[i, 0])**2, weights=w_)**0.5
|
||||
return out
|
||||
mu[i] = numpy.average(x_, weights=w_)
|
||||
std[i] = numpy.average((x_ - mu[i])**2, weights=w_)**0.5
|
||||
return mu, std
|
||||
|
||||
|
||||
###############################################################################
|
||||
|
|
@ -684,92 +702,87 @@ class NPairsOverlap:
|
|||
out[i] = pair.summed_overlap(from_smoothed)
|
||||
return numpy.vstack(out).T
|
||||
|
||||
def prob_nomatch(self, from_smoothed, verbose=True):
|
||||
"""
|
||||
Probability of no match for each halo in the reference simulation with
|
||||
the cross simulation.
|
||||
def expected_property_single(self, k, key, from_smoothed, in_log=True):
|
||||
ys = [None] * len(self)
|
||||
overlaps = [None] * len(self)
|
||||
for i, pair in enumerate(self):
|
||||
overlap = pair.overlap(from_smoothed)
|
||||
if len(overlap[k]) == 0:
|
||||
ys[i] = numpy.nan
|
||||
overlaps[i] = numpy.nan
|
||||
continue
|
||||
match_indxs = pair["match_indxs"]
|
||||
j = numpy.argmax(overlap[k])
|
||||
|
||||
Parameters
|
||||
----------
|
||||
from_smoothed : bool
|
||||
Whether to use the smoothed overlap or not.
|
||||
verbose : bool, optional
|
||||
Verbosity flag.
|
||||
ys[i] = pair.catx(key)[match_indxs[k][j]]
|
||||
if in_log:
|
||||
ys[i] = numpy.log10(ys[i])
|
||||
overlaps[i] = overlap[k][j]
|
||||
|
||||
Returns
|
||||
-------
|
||||
prob_nomatch : 2-dimensional array of shape `(nhalos, ncatxs)`
|
||||
"""
|
||||
iterator = tqdm(self.pairs,
|
||||
desc="Calculating probability of no match",
|
||||
disable=not verbose
|
||||
)
|
||||
out = [None] * len(self)
|
||||
for i, pair in enumerate(iterator):
|
||||
out[i] = pair.prob_nomatch(from_smoothed)
|
||||
return numpy.vstack(out).T
|
||||
return ys, overlaps
|
||||
|
||||
def counterpart_mass(self, from_smoothed, overlap_threshold=0.,
|
||||
mass_kind="totpartmass", return_full=False,
|
||||
verbose=True):
|
||||
def expected_property(self, key, from_smoothed, min_logmass,
|
||||
in_log=True, mass_kind="totpartmass", verbose=True):
|
||||
"""
|
||||
Calculate the expected counterpart mass of each halo in the reference
|
||||
simulation from the crossed simulation.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
key : str
|
||||
Property key.
|
||||
from_smoothed : bool
|
||||
Whether to use the smoothed overlap or not.
|
||||
overlap_threshold : float, optional
|
||||
Minimum overlap required for a halo to be considered a match. By
|
||||
default 0.0, i.e. no threshold.
|
||||
min_logmass : float
|
||||
Minimum log mass of reference halos to consider.
|
||||
in_log : bool, optional
|
||||
Whether to calculated the expected property in log10.
|
||||
mass_kind : str, optional
|
||||
The mass kind whose ratio is to be calculated. Must be a valid
|
||||
catalogue key. By default `totpartmass`, i.e. the total particle
|
||||
mass associated with a halo.
|
||||
return_full : bool, optional
|
||||
Whether to return the full results of matching each pair or
|
||||
calculate summary statistics by Gaussian averaging.
|
||||
verbose : bool, optional
|
||||
Verbosity flag.
|
||||
|
||||
Returns
|
||||
-------
|
||||
mu, std : 1-dimensional arrays of shape `(nhalos,)`
|
||||
Summary expected mass and standard deviation from all cross
|
||||
simulations.
|
||||
mus, stds : 2-dimensional arrays of shape `(nhalos, ncatx)`, optional
|
||||
Expected mass and standard deviation from each cross simulation.
|
||||
Returned only if `return_full` is `True`.
|
||||
mean_expected : 1-dimensional array of shape `(nhalos, )`
|
||||
Expected property from all cross simulations.
|
||||
std_expected : 1-dimensional array of shape `(nhalos, )`
|
||||
Standard deviation of the expected property.
|
||||
"""
|
||||
iterator = tqdm(self.pairs,
|
||||
desc="Calculating counterpart masses",
|
||||
disable=not verbose)
|
||||
mus, stds = [None] * len(self), [None] * len(self)
|
||||
for i, pair in enumerate(iterator):
|
||||
mus[i], stds[i] = pair.counterpart_mass(
|
||||
from_smoothed=from_smoothed,
|
||||
overlap_threshold=overlap_threshold, mass_kind=mass_kind)
|
||||
mus, stds = numpy.vstack(mus).T, numpy.vstack(stds).T
|
||||
log_mass0 = numpy.log10(self.cat0(mass_kind))
|
||||
ntot = len(log_mass0)
|
||||
mean_expected = numpy.full(ntot, numpy.nan, dtype=numpy.float32)
|
||||
std_expected = numpy.full(ntot, numpy.nan, dtype=numpy.float32)
|
||||
|
||||
# Prob of > 0 matches
|
||||
probmatch = 1 - self.prob_nomatch(from_smoothed)
|
||||
# Normalise it for weighted sums etc.
|
||||
norm_probmatch = numpy.apply_along_axis(
|
||||
lambda x: x / numpy.sum(x), axis=1, arr=probmatch)
|
||||
indxs = numpy.where(log_mass0 > min_logmass)[0]
|
||||
for i in tqdm(indxs, disable=not verbose,
|
||||
desc="Calculating expectation"):
|
||||
ys = numpy.full(len(self), numpy.nan, dtype=numpy.float32)
|
||||
weights = numpy.full(len(self), numpy.nan, dtype=numpy.float32)
|
||||
for j, pair in enumerate(self):
|
||||
overlap = pair.overlap(from_smoothed)
|
||||
if len(overlap[i]) == 0:
|
||||
continue
|
||||
|
||||
# Mean and standard deviation of weighted stacked Gaussians
|
||||
mu = numpy.sum((norm_probmatch * mus), axis=1)
|
||||
std = numpy.sum((norm_probmatch * (mus**2 + stds**2)), axis=1) - mu**2
|
||||
std **= 0.5
|
||||
k = numpy.argmax(overlap[i])
|
||||
ys[j] = pair.catx(key)[pair["match_indxs"][i][k]]
|
||||
weights[j] = overlap[i][k]
|
||||
|
||||
mask = mu <= 0
|
||||
mu[mask] = numpy.nan
|
||||
std[mask] = numpy.nan
|
||||
if in_log:
|
||||
ys[j] = numpy.log10(ys[j])
|
||||
|
||||
if return_full:
|
||||
return mu, std, mus, stds
|
||||
return mu, std
|
||||
mask = numpy.isfinite(ys) & numpy.isfinite(weights)
|
||||
if numpy.sum(mask) <= 2:
|
||||
continue
|
||||
|
||||
mean_expected[i] = find_peak(ys[mask], weights=weights[mask])
|
||||
std_expected[i] = numpy.average((ys[mask] - mean_expected[i])**2,
|
||||
weights=weights[mask])**0.5
|
||||
print(log_mass0[i], mean_expected[i], std_expected[i])
|
||||
|
||||
return mean_expected, std_expected
|
||||
|
||||
@property
|
||||
def pairs(self):
|
||||
|
|
|
|||
|
|
@ -150,6 +150,35 @@ def radec_to_cartesian(X):
|
|||
]).T
|
||||
|
||||
|
||||
def cosine_similarity(x, y):
|
||||
r"""
|
||||
Calculate the cosine similarity between two Cartesian vectors. Defined
|
||||
as :math:`\Sum_{i} x_i y_{i} / (|x| * |y|)`.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
x : 1-dimensional array
|
||||
The first vector.
|
||||
y : 1- or 2-dimensional array
|
||||
The second vector. Can be 2-dimensional of shape `(n_samples, 3)`,
|
||||
in which case the calculation is broadcasted.
|
||||
|
||||
Returns
|
||||
-------
|
||||
out : float or 1-dimensional array
|
||||
"""
|
||||
if x.ndim != 1:
|
||||
raise ValueError("`x` must be a 1-dimensional array.")
|
||||
|
||||
if y.ndim == 1:
|
||||
y = y.reshape(1, -1)
|
||||
|
||||
out = numpy.sum(x * y, axis=1)
|
||||
out /= numpy.linalg.norm(x) * numpy.linalg.norm(y, axis=1)
|
||||
|
||||
return out[0] if out.size == 1 else out
|
||||
|
||||
|
||||
def real2redshift(pos, vel, observer_location, observer_velocity, box,
|
||||
periodic_wrap=True, make_copy=True):
|
||||
r"""
|
||||
|
|
@ -219,3 +248,17 @@ def number_counts(x, bin_edges):
|
|||
for i in range(bin_edges.size - 1):
|
||||
out[i] = numpy.sum((x >= bin_edges[i]) & (x < bin_edges[i + 1]))
|
||||
return out
|
||||
|
||||
|
||||
def binned_statistic(x, y, left_edges, bin_width, statistic):
|
||||
"""
|
||||
Calculate a binned statistic.
|
||||
"""
|
||||
out = numpy.full(left_edges.size, numpy.nan, dtype=x.dtype)
|
||||
|
||||
for i in range(left_edges.size):
|
||||
mask = (x >= left_edges[i]) & (x < left_edges[i] + bin_width)
|
||||
|
||||
if numpy.any(mask):
|
||||
out[i] = statistic(y[mask])
|
||||
return out
|
||||
|
|
|
|||
100
scripts/sort_halomaker.py
Normal file
100
scripts/sort_halomaker.py
Normal file
|
|
@ -0,0 +1,100 @@
|
|||
# Copyright (C) 2022 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 sort the HaloMaker's `particle_membership` file to match the ordering
|
||||
of particles in the simulation snapshot.
|
||||
"""
|
||||
from argparse import ArgumentParser
|
||||
from datetime import datetime
|
||||
from glob import iglob
|
||||
|
||||
import h5py
|
||||
import numpy
|
||||
import pynbody
|
||||
from mpi4py import MPI
|
||||
from taskmaster import work_delegation
|
||||
from tqdm import trange
|
||||
|
||||
import csiborgtools
|
||||
|
||||
|
||||
def sort_particle_membership(nsim, nsnap, method):
|
||||
"""
|
||||
Read the FoF particle halo membership and sort the halo IDs to the ordering
|
||||
of particles in the PHEW clump IDs.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
nsim : int
|
||||
IC realisation index.
|
||||
verbose : bool, optional
|
||||
Verbosity flag.
|
||||
"""
|
||||
print(f"{datetime.now()}: starting simulation {nsim}, snapshot {nsnap} and method {method}.") # noqa
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
|
||||
fpath = next(iglob(f"/mnt/extraspace/rstiskalek/CSiBORG/halo_maker/ramses_{nsim}/output_{str(nsnap).zfill(5)}/**/*particle_membership*", recursive=True), None) # noqa
|
||||
print(f"{datetime.now()}: loading particle membership `{fpath}`.")
|
||||
# Columns are halo ID, particle ID
|
||||
membership = numpy.genfromtxt(fpath, dtype=int)
|
||||
|
||||
print(f"{datetime.now()}: loading particle IDs from the snapshot.")
|
||||
sim = pynbody.load(paths.snapshot(nsnap, nsim, "csiborg"))
|
||||
pids = numpy.asanyarray(sim["iord"])
|
||||
|
||||
print(f"{datetime.now()}: mapping particle IDs to their indices.")
|
||||
pids_idx = {pid: i for i, pid in enumerate(pids)}
|
||||
|
||||
print(f"{datetime.now()}: mapping HIDs to their array indices.")
|
||||
# Unassigned particle IDs are assigned a halo ID of 0.
|
||||
hids = numpy.zeros(pids.size, dtype=numpy.int32)
|
||||
for i in trange(membership.shape[0]):
|
||||
hid, pid = membership[i]
|
||||
hids[pids_idx[pid]] = hid
|
||||
|
||||
fout = fpath + "_sorted.hdf5"
|
||||
print(f"{datetime.now()}: saving the sorted data to ... `{fout}`")
|
||||
|
||||
header = """
|
||||
This dataset represents halo indices for each particle.
|
||||
- The particles are ordered as they appear in the simulation snapshot.
|
||||
- Unassigned particles are given a halo index of 0.
|
||||
"""
|
||||
with h5py.File(fout, 'w') as hdf:
|
||||
dset = hdf.create_dataset('hids_dataset', data=hids)
|
||||
dset.attrs['header'] = header
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
parser = ArgumentParser()
|
||||
parser.add_argument("--method", type=str, required=True,
|
||||
help="HaloMaker method")
|
||||
parser.add_argument("--nsim", type=int, required=False, default=None,
|
||||
help="IC index. If not set process all.")
|
||||
args = parser.parse_args()
|
||||
paths = csiborgtools.read.Paths(**csiborgtools.paths_glamdring)
|
||||
|
||||
if args.nsim is None:
|
||||
ics = paths.get_ics("csiborg")
|
||||
else:
|
||||
ics = [args.nsim]
|
||||
|
||||
snaps = numpy.array([max(paths.get_snapshots(nsim, "csiborg"))
|
||||
for nsim in ics])
|
||||
|
||||
def main(n):
|
||||
sort_particle_membership(ics[n], snaps[n], args.method)
|
||||
|
||||
work_delegation(main, list(range(len(ics))), MPI.COMM_WORLD)
|
||||
|
|
@ -29,16 +29,9 @@ import numpy
|
|||
from mpi4py import MPI
|
||||
from taskmaster import work_delegation
|
||||
|
||||
import csiborgtools
|
||||
from utils import get_nsims
|
||||
|
||||
try:
|
||||
import csiborgtools
|
||||
except ModuleNotFoundError:
|
||||
import sys
|
||||
|
||||
sys.path.append("../")
|
||||
import csiborgtools
|
||||
|
||||
|
||||
def _main(nsim, simname, verbose):
|
||||
"""
|
||||
|
|
@ -51,9 +44,7 @@ def _main(nsim, simname, verbose):
|
|||
else:
|
||||
partreader = csiborgtools.read.QuijoteReader(paths)
|
||||
|
||||
if verbose:
|
||||
print(f"{datetime.now()}: reading and processing simulation `{nsim}`.",
|
||||
flush=True)
|
||||
print(f"{datetime.now()}: processing simulation `{nsim}`.", flush=True)
|
||||
# We first load the particle IDs in the final snapshot.
|
||||
pidf = csiborgtools.read.read_h5(paths.particles(nsim, simname))
|
||||
pidf = pidf["particle_ids"]
|
||||
1632
scripts_plots/paper_match.py
Normal file
1632
scripts_plots/paper_match.py
Normal file
File diff suppressed because it is too large
Load diff
|
|
@ -66,6 +66,12 @@ def plot_mass_vs_ncells(nsim, pdf=False):
|
|||
cat = open_csiborg(nsim)
|
||||
mpart = 4.38304044e+09
|
||||
|
||||
x = numpy.log10(cat["totpartmass"])
|
||||
y = numpy.log10(cat["lagpatch_ncells"])
|
||||
|
||||
p = numpy.polyfit(x, y, 1)
|
||||
print("Fitted parameters are: ", p)
|
||||
|
||||
with plt.style.context(plt_utils.mplstyle):
|
||||
plt.figure()
|
||||
plt.scatter(cat["totpartmass"], cat["lagpatch_ncells"], s=0.25,
|
||||
|
|
@ -105,9 +111,9 @@ def plot_hmf(pdf=False):
|
|||
csiborg_counts = numpy.full((len(csiborg_nsims), len(bins) - 1),
|
||||
numpy.nan, dtype=numpy.float32)
|
||||
csiborg_counts[i, :] = data["counts"]
|
||||
# csiborg_counts /= numpy.diff(bins).reshape(1, -1)
|
||||
csiborg_counts /= numpy.diff(bins).reshape(1, -1)
|
||||
|
||||
csiborg5511 = numpy.load(paths.halo_counts("csiborg", 5511))["counts"]
|
||||
# csiborg5511 = numpy.load(paths.halo_counts("csiborg", 5511))["counts"]
|
||||
# csiborg5511 /= numpy.diff(data["bins"])
|
||||
|
||||
print("Loading Quijote halo counts.", flush=True)
|
||||
|
|
@ -121,73 +127,89 @@ def plot_hmf(pdf=False):
|
|||
(len(quijote_nsims) * nmax, len(bins) - 1), numpy.nan,
|
||||
dtype=numpy.float32)
|
||||
quijote_counts[i * nmax:(i + 1) * nmax, :] = data["counts"]
|
||||
# quijote_counts /= numpy.diff(bins).reshape(1, -1)
|
||||
quijote_counts /= numpy.diff(bins).reshape(1, -1)
|
||||
|
||||
# vol = 155.5**3
|
||||
# csiborg_counts /= vol
|
||||
# quijote_counts /= vol
|
||||
vol = 4 * numpy.pi / 3 * 155.5**3
|
||||
csiborg_counts /= vol
|
||||
quijote_counts /= vol
|
||||
# csiborg5511 /= vol
|
||||
|
||||
x = 10**(0.5 * (bins[1:] + bins[:-1]))
|
||||
# Edit lower limits
|
||||
csiborg_counts[:, x < 1e12] = numpy.nan
|
||||
csiborg_counts[:, x < 10**13.1] = numpy.nan
|
||||
quijote_counts[:, x < 10**(13.1)] = numpy.nan
|
||||
# Edit upper limits
|
||||
csiborg_counts[:, x > 3e15] = numpy.nan
|
||||
quijote_counts[:, x > 3e15] = numpy.nan
|
||||
csiborg5511[x > 3e15] = numpy.nan
|
||||
# csiborg5511[x > 3e15] = numpy.nan
|
||||
|
||||
with plt.style.context(plt_utils.mplstyle):
|
||||
cols = plt.rcParams["axes.prop_cycle"].by_key()["color"]
|
||||
fig, ax = plt.subplots(nrows=2, sharex=True,
|
||||
figsize=(3.5, 2.625 * 1.25),
|
||||
gridspec_kw={"height_ratios": [1, 0.45]})
|
||||
fig.subplots_adjust(hspace=0, wspace=0)
|
||||
fig, ax = plt.subplots(nrows=1, sharex=True,
|
||||
figsize=(3.5, 2.625))
|
||||
ax = [ax]
|
||||
# fig, ax = plt.subplots(nrows=2, sharex=True,
|
||||
# figsize=(3.5, 2.625 * 1.25),
|
||||
# gridspec_kw={"height_ratios": [1, 0.25]})
|
||||
# fig.subplots_adjust(hspace=0, wspace=0)
|
||||
|
||||
# Upper panel data
|
||||
mean_csiborg = numpy.mean(csiborg_counts, axis=0)
|
||||
std_csiborg = numpy.std(csiborg_counts, axis=0)
|
||||
ax[0].plot(x, mean_csiborg, label="CSiBORG", c=cols[0])
|
||||
ax[0].fill_between(x, mean_csiborg - std_csiborg,
|
||||
mean_csiborg + std_csiborg,
|
||||
alpha=0.5, color=cols[0])
|
||||
|
||||
for i in range(len(csiborg_counts)):
|
||||
ax[0].plot(x, csiborg_counts[i, :], c="cornflowerblue", lw=0.5, zorder=0)
|
||||
|
||||
ax[0].plot(x, mean_csiborg, label="CSiBORG", c="mediumblue", zorder=1)
|
||||
# ax[0].fill_between(x, mean_csiborg - std_csiborg,
|
||||
# mean_csiborg + std_csiborg,
|
||||
# alpha=0.5, color=cols[0])
|
||||
|
||||
mean_quijote = numpy.mean(quijote_counts, axis=0)
|
||||
std_quijote = numpy.std(quijote_counts, axis=0)
|
||||
ax[0].plot(x, mean_quijote, label="Quijote", c=cols[1])
|
||||
ax[0].fill_between(x, mean_quijote - std_quijote,
|
||||
mean_quijote + std_quijote, alpha=0.5,
|
||||
color=cols[1])
|
||||
|
||||
ax[0].plot(x, csiborg5511, label="CSiBORG 5511", c="k", ls="--")
|
||||
std5511 = numpy.sqrt(csiborg5511)
|
||||
ax[0].fill_between(x, csiborg5511 - std_csiborg, csiborg5511 + std5511,
|
||||
alpha=0.2, color="k")
|
||||
# Lower panel data
|
||||
log_y = numpy.log10(mean_csiborg / mean_quijote)
|
||||
err = numpy.sqrt((std_csiborg / mean_csiborg / numpy.log(10))**2
|
||||
+ (std_quijote / mean_quijote / numpy.log(10))**2)
|
||||
ax[1].plot(x, 10**log_y, c=cols[0])
|
||||
ax[1].fill_between(x, 10**(log_y - err), 10**(log_y + err), alpha=0.5,
|
||||
color=cols[0])
|
||||
for i in range(len(quijote_counts)):
|
||||
ax[0].plot(x, quijote_counts[i, :], c="palegreen", lw=0.5, zorder=-1)
|
||||
|
||||
ax[1].plot(x, csiborg5511 / mean_quijote, c="k", ls="--")
|
||||
|
||||
|
||||
ax[0].plot(x, mean_quijote, label="Quijote", c="darkgreen", zorder=1)
|
||||
# ax[0].fill_between(x, mean_quijote - std_quijote,
|
||||
# mean_quijote + std_quijote, alpha=0.5,
|
||||
# color=cols[1])
|
||||
|
||||
# ax[0].plot(x, csiborg5511, label="CSiBORG 5511", c="k", ls="--")
|
||||
# std5511 = numpy.sqrt(csiborg5511)
|
||||
# ax[0].fill_between(x, csiborg5511 - std_csiborg, csiborg5511 + std5511,
|
||||
# alpha=0.2, color="k")
|
||||
|
||||
# # Lower panel data
|
||||
# log_y = numpy.log10(mean_csiborg / mean_quijote)
|
||||
# err = numpy.sqrt((std_csiborg / mean_csiborg / numpy.log(10))**2
|
||||
# + (std_quijote / mean_quijote / numpy.log(10))**2)
|
||||
# ax[1].plot(x, 10**log_y, c=cols[0])
|
||||
# ax[1].fill_between(x, 10**(log_y - err), 10**(log_y + err), alpha=0.5,
|
||||
# color="k")
|
||||
|
||||
# ax[1].plot(x, csiborg5511 / mean_quijote, c="k", ls="--")
|
||||
|
||||
# Labels and accesories
|
||||
ax[1].axhline(1, color="k", ls="--",
|
||||
lw=0.5 * plt.rcParams["lines.linewidth"], zorder=0)
|
||||
# ax[1].axhline(1, color="k", ls="--",
|
||||
# lw=0.5 * plt.rcParams["lines.linewidth"], zorder=0)
|
||||
# ax[0].set_ylabel(r"$\frac{\mathrm{d}^2 N}{\mathrm{d} V \mathrm{d}\log M_{\rm tot}}~[\mathrm{dex}^{-1} (\mathrm{Mpc} / h)^{-3}]$", # noqa
|
||||
# fontsize="small")
|
||||
ax[0].set_ylabel("Counts in bins")
|
||||
ax[1].set_xlabel(r"$M_{\rm tot}~[M_\odot / h]$", fontsize="small")
|
||||
ax[1].set_ylabel(r"$\mathrm{CSiBORG} / \mathrm{Quijote}$",
|
||||
fontsize="small")
|
||||
m = numpy.isfinite(mean_quijote)
|
||||
ax[0].set_xlim(x[m].min(), x[m].max())
|
||||
ax[0].set_ylabel(r"$\mathrm{HMF}~[\mathrm{dex}^{-1} (\mathrm{Mpc} / h)^{-3}]$")
|
||||
ax[0].set_xlabel(r"$M_{\rm tot}~[M_\odot / h]$", fontsize="small")
|
||||
# ax[1].set_ylabel(r"$\mathrm{CSiBORG} / \mathrm{Quijote}$",
|
||||
# fontsize="small")
|
||||
|
||||
ax[0].set_xscale("log")
|
||||
ax[0].set_yscale("log")
|
||||
ax[1].set_ylim(0.5, 2.0)
|
||||
# ax[1].set_ylim(0.5, 1.5)
|
||||
# ax[1].set_yscale("log")
|
||||
ax[0].legend(fontsize="small")
|
||||
ax[0].legend()
|
||||
|
||||
fig.tight_layout(h_pad=0, w_pad=0)
|
||||
for ext in ["png"] if pdf is False else ["png", "pdf"]:
|
||||
|
|
@ -556,8 +578,8 @@ if __name__ == "__main__":
|
|||
if False:
|
||||
plot_mass_vs_ncells(7444, pdf=False)
|
||||
|
||||
if False:
|
||||
plot_hmf(pdf=False)
|
||||
if True:
|
||||
plot_hmf(pdf=True)
|
||||
|
||||
if False:
|
||||
plot_hmf_quijote_full(pdf=False)
|
||||
|
|
@ -569,7 +591,7 @@ if __name__ == "__main__":
|
|||
plot_groups=False, dmin=45, dmax=60,
|
||||
plot_halos=5e13, volume_weight=True)
|
||||
|
||||
if True:
|
||||
if False:
|
||||
kind = "environment"
|
||||
grid = 512
|
||||
smooth_scale = 8.0
|
||||
|
|
|
|||
Loading…
Reference in a new issue