mirror of
https://github.com/Richard-Sti/csiborgtools.git
synced 2024-12-22 17:18:02 +00:00
Basic matching (#2)
* add recarray manipulations * add cart to radec * add behav so x can be a list * add import * create empty files * ignore plots file * add planck data * add read_mmain file * add cols_to_structured import * use cols_to_structured * add cols_to_structued * add read_mmain import * add reading planck * add mass conversion * add brute force separation calculation * update nb * rename & int dtype * add func to get csiborg ids * add list to nd array conversion * add utils * rename file * add 2M++ * add read 2mpp * add 2mpp shortcut * add randoms generator * Change range of RA [0, 360] * fix ang wrapping * add code for sphere 2pcf * rm wrapping * optionally load only a few borgs * update nb
This commit is contained in:
Richard Stiskalek
GitHub
parent
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commit
53a0629d90
17 changed files with 74697 additions and 37 deletions
1
.gitignore
vendored
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.gitignore
vendored
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@ -4,3 +4,4 @@ bin/
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.bashrc
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.bashrc
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*.pyc
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*.pyc
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*/.ipynb_checkpoints/
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*/.ipynb_checkpoints/
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plots/*
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72973
data/2M++_galaxy_catalog.dat
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72973
data/2M++_galaxy_catalog.dat
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File diff suppressed because it is too large
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124
data/2M++_galaxy_catalog_descr.txt
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data/2M++_galaxy_catalog_descr.txt
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@ -0,0 +1,124 @@
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J/MNRAS/416/2840 The 2M++ galaxy redshift catalogue (Lavaux+, 2011)
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================================================================================
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The 2M++ galaxy redshift catalogue.
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Lavaux G., Hudson M.J.
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<Mon. Not. R. Astron. Soc., 416, 2840-2856 (2011)>
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=2011MNRAS.416.2840L
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================================================================================
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ADC_Keywords: Galaxy catalogs ; Infrared sources ; Redshifts
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Keywords: methods: data analysis - methods: numerical - methods: observational -
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catalogues - galaxies: luminosity function, mass function -
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large-scale structure of Universe
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Abstract:
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Peculiar velocities arise from gravitational instability, and thus
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are linked to the surrounding distribution of matter. In order to
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understand the motion of the Local Group with respect to the cosmic
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microwave background, a deep all-sky map of the galaxy distribution
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is required. Here we present a new redshift compilation of 69160
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galaxies, dubbed 2M++, to map large-scale structures of the local
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Universe over nearly the whole sky, and reaching depths of K<=12.5,
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or 200h^-1^Mpc. The target catalogue is based on the Two-Micron
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All-Sky Survey Extended Source Catalog (2MASS-XSC). The primary
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sources of redshifts are the 2MASS Redshift Survey, the 6dF galaxy
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redshift survey and the Sloan Digital Sky Survey (Data Release 7).
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We assess redshift completeness in each region and compute the weights
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required to correct for redshift incompleteness and apparent magnitude
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limits, and discuss corrections for incompleteness in the zone of
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avoidance. We present the density field for this survey, and discuss
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the importance of large-scale structures such as the Shapley
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Concentration.
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File Summary:
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--------------------------------------------------------------------------------
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FileName Lrecl Records Explanations
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--------------------------------------------------------------------------------
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ReadMe 80 . This file
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catalog.dat 140 72973 *The 2M++ catalogue
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group.dat 64 4002 The 2M++ group catalogue
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--------------------------------------------------------------------------------
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Note on catalog.dat: Number of real galaxies = 69160;
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Number of fake galaxies in ZoA = 3813; Number of groups = 4002.
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--------------------------------------------------------------------------------
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See also:
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VII/233 : The 2MASS Extended sources (IPAC/UMass, 2003-2006)
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VII/249 : 6dF-DR2 Galaxy Survey (Jones+, 2005)
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II/294 : The SDSS Photometric Catalog, Release 7 (Adelman-McCarthy+, 2009)
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VII/260 : The SDSS-DR7 quasar catalog (Schneider+, 2010)
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http://www.sdss.org : SDSS Home Page
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Byte-by-byte Description of file: catalog.dat
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--------------------------------------------------------------------------------
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Bytes Format Units Label Explanations
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--------------------------------------------------------------------------------
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3- 18 A16 --- Name Name of the galaxy as given in the 2MASS-XSC
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database (Cat. VII/233), or ZOA fake galaxy
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20- 25 F6.2 deg RAdeg Right Ascension in decimal degrees (J2000)
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27- 32 F6.2 deg DEdeg Declination in decimal degrees (J2000)
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34- 39 F6.2 deg GLON [0/360] Galactic longitude
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41- 46 F6.2 deg GLAT Galactic latitude
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48- 52 F5.2 mag Ksmag Apparent magnitude in band K_S as defined in
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Section 2.2.
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55- 59 I5 km/s HV Heliocentric total apparent velocity
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62- 66 I5 km/s Vcmb Total apparent velocity in CMB rest frame (G1)
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68- 73 I6 km/s e_HV ?=0 Total apparent velocity error
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(equal to zero if not measured)
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77- 80 I4 --- GID ? Unique group identifier obtained from the
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algorithm of Section 4.
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84- 87 F4.2 --- c11.5 Redshift incompleteness at magnitude
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K2M++<=11.5
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91- 94 F4.2 --- c12.5 ? Redshift incompleteness at magnitude
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KM2++<=12.5 (2)
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99 I1 --- ZoA [0/1] Flag to indicate whether this is is a
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fake galaxy to fill the zone of avoidance
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following the algorithm of Section 3.
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104 I1 --- Cln [0/1] Flag to indicate if the redshift has
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been obtained by the cloning procedure
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of Section 2.3.
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109 I1 --- M0 [0/1] Flag to indicate whether this galaxy
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lies in the exclusive region covered by the
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2MRS target mask (2Mx6S region)
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114 I1 --- M1 [0/1] Flag to indicate whether this galaxy
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lies in the non-exclusion region covered by
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the SDSS
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119 I1 --- M2 [0/1] Flag to indicate whether this galaxy
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lies in the non-exclusion region covered
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by the 6dFGRS
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122-140 A19 --- Ref Reference bibcode ("zoa" for fake galaxies
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in the Zone of Avoidance)
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--------------------------------------------------------------------------------
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Note (2): It may be empty in that case the catalogue is limited to K2M++<=11.5
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in the portion of the sky holding the galaxy.
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--------------------------------------------------------------------------------
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Byte-by-byte Description of file: group.dat
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--------------------------------------------------------------------------------
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Bytes Format Units Label Explanations
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--------------------------------------------------------------------------------
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7- 10 I4 --- GID Group identifier in the catalogue
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12- 17 F6.2 deg GLON Galactic longitude
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19- 24 F6.2 deg GLAT Galactic latitude
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27- 31 F5.2 mag K2mag Apparent magnitude K2M++ (1)
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40- 42 I3 --- Rich Richness uncorrected for incompleteness effect
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45- 49 I5 km/s HV Heliocentric total apparent velocity
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52- 56 I5 km/s Vcmb Total apparent velocity in CMB rest frame (G1)
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62- 64 I3 km/s sigma Velocity dispersion in the group
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--------------------------------------------------------------------------------
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Note (1): We define as K2M++ (K2mag) the magnitude of a galaxy measured in
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the K_S_ band, within the circular isophote at 20mag/arcsec^2^, after
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various corrections described in Section 2.2. The magnitude is derived
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from the 2M++ galaxies. This is a magnitude uncorrected for
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incompleteness effect.
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--------------------------------------------------------------------------------
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Global notes:
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Note (G1): using relation from Kogut et al. (1993ApJ...419....1K) and
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Tully et al. (2008, Cat. J/ApJ/676/184)
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--------------------------------------------------------------------------------
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History:
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From electronic version of the journal
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================================================================================
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(End) Patricia Vannier [CDS] 17-Apr-2012
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610
data/HFI_PCCS_SZ-union_R2.08.fits
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610
data/HFI_PCCS_SZ-union_R2.08.fits
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File diff suppressed because one or more lines are too long
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@ -13,4 +13,4 @@
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# with this program; if not, write to the Free Software Foundation, Inc.,
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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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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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from galomatch import io
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from galomatch import (io, match, utils)
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@ -13,6 +13,8 @@
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# with this program; if not, write to the Free Software Foundation, Inc.,
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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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# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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from .readsim import (get_sim_path, open_particle, open_unbinding,
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from .readsim import (get_csiborg_ids, get_sim_path, open_particle,
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read_particle, read_clumpid, read_clumps,
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open_unbinding, read_particle, read_clumpid, read_clumps,
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read_mmain,
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convert_mass_cols, convert_position_cols, flip_cols)
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convert_mass_cols, convert_position_cols, flip_cols)
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from .readobs import (read_planck2015, read_2mpp)
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95
galomatch/io/readobs.py
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95
galomatch/io/readobs.py
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@ -0,0 +1,95 @@
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# Copyright (C) 2022 Richard Stiskalek
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# This program is free software; you can redistribute it and/or modify it
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# under the terms of the GNU General Public License as published by the
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# Free Software Foundation; either version 3 of the License, or (at your
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# option) any later version.
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#
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# This program is distributed in the hope that it will be useful, but
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# WITHOUT ANY WARRANTY; without even the implied warranty of
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General
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# Public License for more details.
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#
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# You should have received a copy of the GNU General Public License along
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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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import numpy
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from astropy.io import fits
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from ..utils import (add_columns, cols_to_structured)
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def read_planck2015(fpath, dist_cosmo, max_comdist=None):
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"""
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Read the Planck 2nd Sunyaev-Zeldovich source catalogue [1]. The following
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is performed:
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- removes clusters without a redshift estimate,
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- calculates the comoving distance with the provided cosmology.
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- Converts `MSZ` from units of :math:`1e14 M_\odot` to :math:`M_\odot`
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Parameters
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----------
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fpath : str
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Path to the source catalogue.
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dist_cosmo : `astropy.cosmology` object
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The cosmology to calculate cluster comoving distance from redshift.
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max_comdist : float, optional
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Maximum comoving distance threshold in units of :math:`\mathrm{MPc}`.
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By default `None` and no threshold is applied.
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References
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----------
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[1] https://heasarc.gsfc.nasa.gov/W3Browse/all/plancksz2.html
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Returns
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-------
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out : `astropy.io.fits.FITS_rec`
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The catalogue structured array.
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"""
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data = fits.open(fpath)[1].data
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# Convert FITS to a structured array
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out = numpy.full(data.size, numpy.nan, dtype=data.dtype.descr)
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for name in out.dtype.names:
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out[name] = data[name]
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# Take only clusters with redshifts
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out = out[out["REDSHIFT"] >= 0]
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# Add comoving distance
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dist = dist_cosmo.comoving_distance(out["REDSHIFT"]).value
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out = add_columns(out, dist, "COMDIST")
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# Convert masses
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for p in ("MSZ", "MSZ_ERR_UP", "MSZ_ERR_LOW"):
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out[p] *= 1e14
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# Distance threshold
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if max_comdist is not None:
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out = out[out["COMDIST"] < max_comdist]
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return out
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def read_2mpp(fpath):
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"""
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Read in the 2M++ galaxy redshift catalogue [1], with the catalogue at [2].
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Removes fake galaxies used to fill the zone of avoidance.
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Parameters
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----------
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fpath : str
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File path to the catalogue.
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Returns
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-------
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out : structured array
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The catalogue.
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"""
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# Read the catalogue and select non-fake galaxies
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cat = numpy.genfromtxt(fpath, delimiter="|", )
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cat = cat[cat[:, 12] == 0, :]
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F64 = numpy.float64
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cols = [("RA", F64), ("DEC", F64), ("Ksmag", F64)]
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out = cols_to_structured(cat.shape[0], cols)
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out["RA"] = cat[:, 1] - 180
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out["DEC"] = cat[:, 2]
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out["Ksmag"] = cat[:, 5]
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return out
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@ -19,8 +19,11 @@ import numpy
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from scipy.io import FortranFile
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from scipy.io import FortranFile
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from os import listdir
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from os import listdir
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from os.path import (join, isfile)
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from os.path import (join, isfile)
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from glob import glob
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from tqdm import tqdm
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from tqdm import tqdm
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from ..utils import cols_to_structured
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F16 = numpy.float16
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F16 = numpy.float16
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F32 = numpy.float32
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F32 = numpy.float32
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@ -32,6 +35,37 @@ BOXSIZE = 677.7 / little_h # Mpc. Otherwise positions in [0, 1].
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BOXMASS = 3.749e19 # Msun
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BOXMASS = 3.749e19 # Msun
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def get_csiborg_ids(srcdir):
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"""
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Get CSiBORG simulation IDs from the list of folders in `srcdir`.
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Assumes that the folders look like `ramses_out_X` and extract the `X`
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integer. Removes `5511` from the list of IDs.
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Parameters
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----------
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srcdir : string
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The folder where CSiBORG simulations are stored.
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Returns
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-------
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ids : 1-dimensional array
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Array of CSiBORG simulation IDs.
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"""
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files = glob(join(srcdir, "ramses_out*"))
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# Select only file names
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files = [f.split("/")[-1] for f in files]
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# Remove files with inverted ICs
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files = [f for f in files if "_inv" not in f]
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# Remove the filename with _old
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files = [f for f in files if "OLD" not in f]
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ids = [int(f.split("_")[-1]) for f in files]
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try:
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ids.remove(5511)
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except ValueError:
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pass
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return numpy.sort(ids)
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def get_sim_path(n, fname="ramses_out_{}", srcdir="/mnt/extraspace/hdesmond"):
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def get_sim_path(n, fname="ramses_out_{}", srcdir="/mnt/extraspace/hdesmond"):
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"""
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"""
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Get a path to a CSiBORG simulation.
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Get a path to a CSiBORG simulation.
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@ -309,15 +343,45 @@ def read_clumps(n, simpath):
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("peak_x", F64), ("peak_y", F64), ("peak_z", F64),
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("peak_x", F64), ("peak_y", F64), ("peak_z", F64),
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("rho-", F64), ("rho+", F64), ("rho_av", F64),
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("rho-", F64), ("rho+", F64), ("rho_av", F64),
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("mass_cl", F64), ("relevance", F64)]
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("mass_cl", F64), ("relevance", F64)]
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# Write to a structured array
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out = cols_to_structured(arr.shape[0], cols)
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dtype = {"names": [col[0] for col in cols],
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for i, name in enumerate(out.dtype.names):
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"formats": [col[1] for col in cols]}
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out = numpy.full(arr.shape[0], numpy.nan, dtype=dtype)
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for i, name in enumerate(dtype["names"]):
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out[name] = arr[:, i]
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out[name] = arr[:, i]
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return out
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return out
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def read_mmain(n, srcdir, fname="Mmain_{}.npy"):
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"""
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Read `mmain` numpy arrays of central halos whose mass contains their
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substracture contribution.
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Parameters
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|
----------
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n : int
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The index of the initial conditions (IC) realisation.
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srcdir : str
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The path to the folder containing the files.
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fname : str, optional
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|
The file name convention. By default `Mmain_{}.npy`, where the
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substituted value is `n`.
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|
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Returns
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|
-------
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out : structured array
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Array with the central halo information.
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"""
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||||||
|
fpath = join(srcdir, fname.format(n))
|
||||||
|
arr = numpy.load(fpath)
|
||||||
|
|
||||||
|
cols = [("index", I64), ("peak_x", F64), ("peak_y", F64),
|
||||||
|
("peak_z", F64), ("mass_cl", F64), ("sub_frac", F64)]
|
||||||
|
out = cols_to_structured(arr.shape[0], cols)
|
||||||
|
for i, name in enumerate(out.dtype.names):
|
||||||
|
out[name] = arr[:, i]
|
||||||
|
|
||||||
|
return out
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
def convert_mass_cols(arr, cols):
|
def convert_mass_cols(arr, cols):
|
||||||
"""
|
"""
|
||||||
Convert mass columns from box units to :math:`M_{odot}`. `arr` is passed by
|
Convert mass columns from box units to :math:`M_{odot}`. `arr` is passed by
|
||||||
|
|
|
||||||
17
galomatch/match/__init__.py
Normal file
17
galomatch/match/__init__.py
Normal file
|
|
@ -0,0 +1,17 @@
|
||||||
|
# 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.
|
||||||
|
|
||||||
|
from .match import brute_spatial_separation
|
||||||
|
from .correlation import (get_randoms_sphere, angular_tpcf)
|
||||||
131
galomatch/match/correlation.py
Normal file
131
galomatch/match/correlation.py
Normal file
|
|
@ -0,0 +1,131 @@
|
||||||
|
# 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.
|
||||||
|
|
||||||
|
import numpy
|
||||||
|
from Corrfunc.mocks import DDtheta_mocks
|
||||||
|
from Corrfunc.utils import convert_3d_counts_to_cf
|
||||||
|
from warnings import warn
|
||||||
|
|
||||||
|
|
||||||
|
def get_randoms_sphere(N, seed=42):
|
||||||
|
"""
|
||||||
|
Generate random points on a sphere.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
N : int
|
||||||
|
Number of points.
|
||||||
|
seed : int
|
||||||
|
Random seed.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
ra : 1-dimensional array
|
||||||
|
Right ascension in :math:`[0, 360)` degrees.
|
||||||
|
dec : 1-dimensional array
|
||||||
|
Declination in :math:`[-90, 90]` degrees.
|
||||||
|
"""
|
||||||
|
gen = numpy.random.default_rng(seed)
|
||||||
|
ra = gen.random(N) * 360
|
||||||
|
dec = numpy.rad2deg(numpy.arcsin(2 * (gen.random(N) - 0.5)))
|
||||||
|
return ra, dec
|
||||||
|
|
||||||
|
|
||||||
|
def wrapRA(ra, degrees=True):
|
||||||
|
"""
|
||||||
|
Wrap the right ascension from :math:`[-180, 180)` to :math`[0, 360)`
|
||||||
|
degrees or equivalently if `degrees=False` in radians.
|
||||||
|
|
||||||
|
Paramaters
|
||||||
|
----------
|
||||||
|
ra : 1-dimensional array
|
||||||
|
Right ascension values.
|
||||||
|
degrees : float, optional
|
||||||
|
Whether the right ascension is in degrees.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
ra : 1-dimensional array
|
||||||
|
Wrapped around right ascension.
|
||||||
|
"""
|
||||||
|
mask = ra < 0
|
||||||
|
if numpy.sum(mask) == 0:
|
||||||
|
warn("No negative right ascension found.")
|
||||||
|
ra[mask] += 360 if degrees else 2 * numpy.pi
|
||||||
|
return ra
|
||||||
|
|
||||||
|
|
||||||
|
def sphere_angular_tpcf(bins, RA1, DEC1, RA2=None, DEC2=None, nthreads=1,
|
||||||
|
Nmult=5, seed1=42, seed2=666):
|
||||||
|
"""
|
||||||
|
Calculate the angular two-point correlation function. The coordinates must
|
||||||
|
be provided in degrees. With the right ascension and degrees being
|
||||||
|
in range of :math:`[-180, 180]` and :math:`[-90, 90]` degrees, respectively.
|
||||||
|
If `RA2` and `DEC2` are provided cross-correlates the first data set with
|
||||||
|
the second. Creates a uniformly sampled randoms on the surface of a sphere
|
||||||
|
of size `Nmult` times the corresponding number of data points. Uses the
|
||||||
|
Landy-Szalay estimator.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
bins : 1-dimensional array
|
||||||
|
Angular bins to calculate the angular twop-point correlation function.
|
||||||
|
RA1 : 1-dimensional array
|
||||||
|
Right ascension of the 1st data set, in degrees.
|
||||||
|
DEC1 : 1-dimensional array
|
||||||
|
Declination of the 1st data set, in degrees.
|
||||||
|
RA2 : 1-dimensional array, optional
|
||||||
|
Right ascension of the 2nd data set, in degrees.
|
||||||
|
DEC2 : 1-dimensional array, optional
|
||||||
|
Declination of the 2nd data set, in degrees.
|
||||||
|
nthreads : int, optional
|
||||||
|
Number of threads, by default 1.
|
||||||
|
Nmult : int, optional
|
||||||
|
Relative randoms size with respect to the data set. By default 5.
|
||||||
|
seed1 : int, optional
|
||||||
|
Seed to generate the first set of randoms.
|
||||||
|
seed2 : int, optional
|
||||||
|
Seed to generate the second set of randoms.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
cf : 1-dimensional array
|
||||||
|
The angular 2-point correlation function.
|
||||||
|
"""
|
||||||
|
# If not provided calculate autocorrelation
|
||||||
|
if RA2 is None:
|
||||||
|
RA2 = RA1
|
||||||
|
DEC2 = DEC1
|
||||||
|
# Get the array sizes
|
||||||
|
ND1 = RA1.size
|
||||||
|
ND2 = RA2.size
|
||||||
|
NR1 = ND1 * Nmult
|
||||||
|
NR2 = ND2 * Nmult
|
||||||
|
# Generate randoms. Note that these are over the sphere!
|
||||||
|
randRA1, randDEC1 = get_randoms_sphere(NR1, seed1)
|
||||||
|
randRA2, randDEC2 = get_randoms_sphere(NR2, seed2)
|
||||||
|
# Wrap RA
|
||||||
|
RA1 = wrapRA(numpy.copy(RA1))
|
||||||
|
RA2 = wrapRA(numpy.copy(RA2))
|
||||||
|
# Calculate pairs
|
||||||
|
D1D2 = DDtheta_mocks(0, nthreads, bins, RA1, DEC1, RA2=RA2, DEC2=DEC2)
|
||||||
|
D1R2 = DDtheta_mocks(0, nthreads, bins, RA1, DEC1,
|
||||||
|
RA2=randRA2, DEC2=randDEC2)
|
||||||
|
D2R1 = DDtheta_mocks(0, nthreads, bins, RA2, DEC2,
|
||||||
|
RA2=randRA1, DEC2=randDEC1)
|
||||||
|
R1R2 = DDtheta_mocks(0, nthreads, bins, randRA1, randDEC1,
|
||||||
|
RA2=randRA2, DEC2=randDEC2)
|
||||||
|
# Convert to the CF
|
||||||
|
return convert_3d_counts_to_cf(ND1, ND2, NR1, NR2, D1D2, D1R2, D2R1, R1R2)
|
||||||
67
galomatch/match/match.py
Normal file
67
galomatch/match/match.py
Normal file
|
|
@ -0,0 +1,67 @@
|
||||||
|
# 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.
|
||||||
|
|
||||||
|
import numpy
|
||||||
|
from tqdm import tqdm
|
||||||
|
from astropy.coordinates import SkyCoord
|
||||||
|
|
||||||
|
|
||||||
|
def brute_spatial_separation(c1, c2, angular=False, N=None, verbose=False):
|
||||||
|
"""
|
||||||
|
Calculate for each point in `c1` the `N` closest points in `c2`.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
c1 : `astropy.coordinates.SkyCoord`
|
||||||
|
Coordinates of the first set of points.
|
||||||
|
c2 : `astropy.coordinates.SkyCoord`
|
||||||
|
Coordinates of the second set of points.
|
||||||
|
angular : bool, optional
|
||||||
|
Whether to calculate angular separation or 3D separation. By default
|
||||||
|
`False` and 3D separation is calculated.
|
||||||
|
N : int, optional
|
||||||
|
Number of closest points in `c2` to each object in `c1` to return.
|
||||||
|
verbose : bool, optional
|
||||||
|
Verbosity flag. By default `False`.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
sep : 1-dimensional array
|
||||||
|
Separation of each object in `c1` to `N` closest objects in `c2`. The
|
||||||
|
array shape is `(c1.size, N)`. Separation is in units of `c1`.
|
||||||
|
indxs : 1-dimensional array
|
||||||
|
Indexes of the closest objects in `c2` for each object in `c1`. The
|
||||||
|
array shape is `(c1.size, N)`.
|
||||||
|
"""
|
||||||
|
if not (isinstance(c1, SkyCoord) and isinstance(c2, SkyCoord)):
|
||||||
|
raise TypeError("`c1` & `c2` must be `astropy.coordinates.SkyCoord`.")
|
||||||
|
N1 = c1.size
|
||||||
|
N2 = c2.size if N is None else N
|
||||||
|
|
||||||
|
# Pre-allocate arrays
|
||||||
|
sep = numpy.full((N1, N2), numpy.nan)
|
||||||
|
indxs = numpy.full((N1, N2), numpy.nan, dtype=int)
|
||||||
|
iters = tqdm(range(N1)) if verbose else range(N1)
|
||||||
|
for i in iters:
|
||||||
|
if angular:
|
||||||
|
dist = c1[i].separation(c2).value
|
||||||
|
else:
|
||||||
|
dist = c1[i].separation_3d(c2).value
|
||||||
|
# Sort the distances
|
||||||
|
sort = numpy.argsort(dist)[:N2]
|
||||||
|
indxs[i, :] = sort
|
||||||
|
sep[i, :] = dist[sort]
|
||||||
|
|
||||||
|
return sep, indxs
|
||||||
18
galomatch/utils/__init__.py
Normal file
18
galomatch/utils/__init__.py
Normal file
|
|
@ -0,0 +1,18 @@
|
||||||
|
# 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.
|
||||||
|
|
||||||
|
from .recarray_manip import (cols_to_structured, add_columns, rm_columns,
|
||||||
|
list_to_ndarray)
|
||||||
|
from .transforms import cartesian_to_radec
|
||||||
155
galomatch/utils/recarray_manip.py
Normal file
155
galomatch/utils/recarray_manip.py
Normal file
|
|
@ -0,0 +1,155 @@
|
||||||
|
# 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.
|
||||||
|
|
||||||
|
"""Utilility functions for manipulation structured arrays."""
|
||||||
|
|
||||||
|
import numpy
|
||||||
|
|
||||||
|
def cols_to_structured(N, cols):
|
||||||
|
"""
|
||||||
|
Allocate a structured array from `cols`.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
N : int
|
||||||
|
Structured array size.
|
||||||
|
cols: list of tuples
|
||||||
|
Column names and dtypes. Each tuple must written as `(name, dtype)`.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
out : structured array
|
||||||
|
Initialised structured array.
|
||||||
|
"""
|
||||||
|
if not isinstance(cols, list) and all(isinstance(c, tuple) for c in cols):
|
||||||
|
raise TypeError("`cols` must be a list of tuples.")
|
||||||
|
|
||||||
|
dtype = {"names": [col[0] for col in cols],
|
||||||
|
"formats": [col[1] for col in cols]}
|
||||||
|
return numpy.full(N, numpy.nan, dtype=dtype)
|
||||||
|
|
||||||
|
|
||||||
|
def add_columns(arr, X, cols):
|
||||||
|
"""
|
||||||
|
Add new columns to a record array `arr`. Creates a new array.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
arr : record array
|
||||||
|
The record array to add columns to.
|
||||||
|
X : (list of) 1-dimensional array(s) or 2-dimensional array
|
||||||
|
Columns to be added.
|
||||||
|
cols : str or list of str
|
||||||
|
Column names to be added.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
out : record array
|
||||||
|
The new record array with added values.
|
||||||
|
"""
|
||||||
|
# Make sure cols is a list of str and X a 2D array
|
||||||
|
cols = [cols] if isinstance(cols, str) else cols
|
||||||
|
if isinstance(X, numpy.ndarray) and X.ndim == 1:
|
||||||
|
X = X.reshape(-1, 1)
|
||||||
|
if isinstance(X, list) and all(x.ndim == 1 for x in X):
|
||||||
|
X = numpy.vstack([X]).T
|
||||||
|
if len(cols) != X.shape[1]:
|
||||||
|
raise ValueError("Number of columns of `X` does not match `cols`.")
|
||||||
|
if arr.size != X.shape[0]:
|
||||||
|
raise ValueError("Number of rows of `X` does not match size of `arr`.")
|
||||||
|
|
||||||
|
# Get the new data types
|
||||||
|
dtype = arr.dtype.descr
|
||||||
|
for i, col in enumerate(cols):
|
||||||
|
dtype.append((col, X[i, :].dtype.descr[0][1]))
|
||||||
|
|
||||||
|
# Fill in the old array
|
||||||
|
out = numpy.full(arr.size, numpy.nan, dtype=dtype)
|
||||||
|
for col in arr.dtype.names:
|
||||||
|
out[col] = arr[col]
|
||||||
|
for i, col in enumerate(cols):
|
||||||
|
out[col] = X[:, i]
|
||||||
|
|
||||||
|
return out
|
||||||
|
|
||||||
|
def rm_columns(arr, cols):
|
||||||
|
"""
|
||||||
|
Remove columns `cols` from a record array `arr`. Creates a new array.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
arr : record array
|
||||||
|
The record array to remove columns from.
|
||||||
|
cols : str or list of str
|
||||||
|
Column names to be removed.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
out : record array
|
||||||
|
Record array with removed columns.
|
||||||
|
"""
|
||||||
|
# Check columns we wish to delete are in the array
|
||||||
|
cols = [cols] if isinstance(cols, str) else cols
|
||||||
|
for col in cols:
|
||||||
|
if col not in arr.dtype.names:
|
||||||
|
raise ValueError("Column `{}` not in `arr`.".format(col))
|
||||||
|
|
||||||
|
# Get a new dtype without the cols to be deleted
|
||||||
|
new_dtype = []
|
||||||
|
for dtype, name in zip(arr.dtype.descr, arr.dtype.names):
|
||||||
|
if name not in cols:
|
||||||
|
new_dtype.append(dtype)
|
||||||
|
|
||||||
|
# Allocate a new array and fill it in.
|
||||||
|
out = numpy.full(arr.size, numpy.nan, new_dtype)
|
||||||
|
for name in out.dtype.names:
|
||||||
|
out[name] = arr[name]
|
||||||
|
|
||||||
|
return out
|
||||||
|
|
||||||
|
|
||||||
|
def list_to_ndarray(arrs, cols):
|
||||||
|
"""
|
||||||
|
Convert a list of structured arrays of CSiBORG simulation catalogues to
|
||||||
|
an 3-dimensional array.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
arrs : list of structured arrays
|
||||||
|
List of CSiBORG catalogues.
|
||||||
|
cols : str or list of str
|
||||||
|
Columns to be extracted from the CSiBORG catalogues.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
out : 3-dimensional array
|
||||||
|
Catalogue array of shape `(n_realisations, n_samples, n_cols)`, where
|
||||||
|
`n_samples` is the maximum number of samples over the CSiBORG
|
||||||
|
catalogues.
|
||||||
|
"""
|
||||||
|
if not isinstance(arrs, list):
|
||||||
|
raise TypeError("`arrs` must be a list of structured arrays.")
|
||||||
|
cols = [cols] if isinstance(cols, str) else cols
|
||||||
|
|
||||||
|
Narr = len(arrs)
|
||||||
|
Nobj_max = max([arr.size for arr in arrs])
|
||||||
|
Ncol = len(cols)
|
||||||
|
# Preallocate the array and fill it
|
||||||
|
out = numpy.full((Narr, Nobj_max, Ncol), numpy.nan)
|
||||||
|
for i in range(Narr):
|
||||||
|
Nobj = arrs[i].size
|
||||||
|
for j in range(Ncol):
|
||||||
|
out[i, :Nobj, j] = arrs[i][cols[j]]
|
||||||
|
return out
|
||||||
56
galomatch/utils/transforms.py
Normal file
56
galomatch/utils/transforms.py
Normal file
|
|
@ -0,0 +1,56 @@
|
||||||
|
# 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.
|
||||||
|
|
||||||
|
import numpy
|
||||||
|
|
||||||
|
|
||||||
|
def cartesian_to_radec(arr, xpar="peak_x", ypar="peak_y", zpar="peak_z", degrees=True):
|
||||||
|
"""
|
||||||
|
Extract `x`, `y`, and `z` coordinates from a record array `arr` and
|
||||||
|
calculate their spherical coordinates representation.
|
||||||
|
|
||||||
|
Parameters
|
||||||
|
----------
|
||||||
|
arr : record array
|
||||||
|
Record array with the Cartesian coordinates.
|
||||||
|
xpar : str, optional
|
||||||
|
Name of the x coordinate in the record array.
|
||||||
|
ypar : str, optional
|
||||||
|
Name of the y coordinate in the record array.
|
||||||
|
zpar : str, optional
|
||||||
|
Name of the z coordinate in the record array.
|
||||||
|
degrees : bool, optional
|
||||||
|
Whether to return angles in degrees. By default `True`.
|
||||||
|
|
||||||
|
Returns
|
||||||
|
-------
|
||||||
|
dist : 1-dimensional array
|
||||||
|
Radial distance.
|
||||||
|
ra : 1-dimensional array
|
||||||
|
Right ascension.
|
||||||
|
dec : 1-dimensional array
|
||||||
|
Declination.
|
||||||
|
"""
|
||||||
|
x, y, z = arr[xpar], arr[ypar], arr[zpar]
|
||||||
|
|
||||||
|
dist = numpy.sqrt(x**2 + y**2 + z**2)
|
||||||
|
dec = numpy.arcsin(z / dist)
|
||||||
|
ra = numpy.arctan2(y, x)
|
||||||
|
|
||||||
|
if degrees:
|
||||||
|
dec = numpy.rad2deg(dec)
|
||||||
|
ra = numpy.rad2deg(ra)
|
||||||
|
|
||||||
|
return dist, ra, dec
|
||||||
File diff suppressed because one or more lines are too long
60
scripts/utils.py
Normal file
60
scripts/utils.py
Normal file
|
|
@ -0,0 +1,60 @@
|
||||||
|
# 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.
|
||||||
|
|
||||||
|
"""Notebook utility funnctions."""
|
||||||
|
|
||||||
|
try:
|
||||||
|
import galomatch
|
||||||
|
except ModuleNotFoundError:
|
||||||
|
import sys
|
||||||
|
sys.path.append("../")
|
||||||
|
|
||||||
|
|
||||||
|
def load_mmain_convert(n):
|
||||||
|
srcdir = "/users/hdesmond/Mmain"
|
||||||
|
arr = galomatch.io.read_mmain(n, srcdir)
|
||||||
|
|
||||||
|
galomatch.io.convert_mass_cols(arr, "mass_cl")
|
||||||
|
galomatch.io.convert_position_cols(arr, ["peak_x", "peak_y", "peak_z"])
|
||||||
|
galomatch.io.flip_cols(arr, "peak_x", "peak_z")
|
||||||
|
|
||||||
|
d, ra, dec = galomatch.utils.cartesian_to_radec(arr)
|
||||||
|
arr = galomatch.utils.add_columns(arr, [d, ra, dec], ["dist", "ra", "dec"])
|
||||||
|
return arr
|
||||||
|
|
||||||
|
|
||||||
|
def load_mmains(N=None, verbose=True):
|
||||||
|
from tqdm import tqdm
|
||||||
|
ids = galomatch.io.get_csiborg_ids("/mnt/extraspace/hdesmond")
|
||||||
|
N = ids.size if N is None else N
|
||||||
|
if N > ids.size:
|
||||||
|
raise ValueError("`N` cannot be larger than 101.")
|
||||||
|
out = [None] * N
|
||||||
|
iters = tqdm(range(N)) if verbose else range(N)
|
||||||
|
for i in iters:
|
||||||
|
out[i] = load_mmain_convert(ids[i])
|
||||||
|
return out
|
||||||
|
|
||||||
|
|
||||||
|
def load_planck2015(max_comdist=214):
|
||||||
|
from astropy.cosmology import FlatLambdaCDM
|
||||||
|
cosmo = FlatLambdaCDM(H0=70.5, Om0=0.307, Tcmb0=2.728)
|
||||||
|
fpath = ("/mnt/zfsusers/rstiskalek/galomatch/"
|
||||||
|
+ "data/HFI_PCCS_SZ-union_R2.08.fits")
|
||||||
|
return galomatch.io.read_planck2015(fpath, cosmo, max_comdist)
|
||||||
|
|
||||||
|
|
||||||
|
def load_2mpp():
|
||||||
|
return galomatch.io.read_2mpp("../data/2M++_galaxy_catalog.dat")
|
||||||
Loading…
Reference in a new issue